Type	Description
+	a supported DataJoint attribute type to use; e.g. "longblob", "blob@store"

Name	Type	Description	Default
`value`	+	value from the database	+ required +

Type	Description
+	object of the adapted type

Name	Type	Description	Default
`obj`	+	an object of the adapted type	+ required +

Type	Description
+	value to store in the database

Name	Type	Description	Default
`migration_schema`	+	string of target schema to be migrated	+ required +
`store`	+	string of target dj.config['store'] to be migrated	+ required +

Name	Type	Description	Default
`args`	+	addition arguments	+ required +

Type	Description
+	a new exception of the same type with the additional arguments

Name	Type	Description	Default
`restriction`	+	restriction to be applied to processlist	+ `None` +
`connection`	+	a datajoint.Connection object. Default calls datajoint.conn()	+ `None` +
`order_by`	+	order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE "%compute%"') lists only connections from hosts containing "compute". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes	+ `None` +

Name	Type	Description	Default
`schema_name`	+	the database schema to associate. schema_name=None is used to assert that the schema has already been activated.	+ `None` +
`connection`	+	Connection object. Defaults to datajoint.conn().	+ `None` +
`create_schema`	+	If False, do not create the schema and raise an error if missing.	+ `None` +
`create_tables`	+	If False, do not create tables and raise errors when attempting to access missing tables.	+ `None` +
`add_objects`	+	a mapping with additional objects to make available to the context in which table classes are declared.	+ `None` +

Type	Description
+	size of the entire schema in bytes

Name	Type	Description	Default
`context`	+	alternative context to place the missing classes into, e.g. locals()	+ `None` +

Type	Description
+	true if the associated schema exists on the server

Type	Description
+	jobs table

Type	Description
+	a string containing the body of a complete Python module defining this schema.

Type	Description
+	A list of table names from the database schema.

Name	Type	Description	Default
`context`	+	the context for foreign key resolution. If None, foreign keys are not allowed.	+ `None` +

Type	Description
+	the FROM clause of SQL SELECT statements.

Type	Description
+	the selected attributes from the SQL SELECT statement.

Name	Type	Description	Default
`primary`	+	if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute.	+ `None` +
`as_objects`	+	if False, return table names. If True, return table objects.	+ `False` +
`foreign_key_info`	+	if True, each element in result also includes foreign key info.	+ `False` +

Type	Description
+	list of parents as table names or table objects with (optional) foreign key information.

Name	Type	Description	Default
`primary`	+	if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute.	+ `None` +
`as_objects`	+	if False, return table names. If True, return table objects.	+ `False` +
`foreign_key_info`	+	if True, each element in result also includes foreign key info.	+ `False` +

Type	Description
+	list of children as table names or table objects with (optional) foreign key information.

/* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute whether the header is hidden\n *\n * If the user scrolls past a certain threshold, the header can be hidden when\n * scrolling down, and shown when scrolling up.\n *\n * @param options - Options\n *\n * @returns Toggle observable\n */\nfunction isHidden({ viewport$ }: WatchOptions): Observable {\n if (!feature(\"header.autohide\"))\n return of(false)\n\n /* Compute direction and turning point */\n const direction$ = viewport$\n .pipe(\n map(({ offset: { y } }) => y),\n bufferCount(2, 1),\n map(([a, b]) => [a < b, b] as const),\n distinctUntilKeyChanged(0)\n )\n\n /* Compute whether header should be hidden */\n const hidden$ = combineLatest([viewport$, direction$])\n .pipe(\n filter(([{ offset }, [, y]]) => Math.abs(y - offset.y) > 100),\n map(([, [direction]]) => direction),\n distinctUntilChanged()\n )\n\n /* Compute threshold for hiding */\n const search$ = watchToggle(\"search\")\n return combineLatest([viewport$, search$])\n .pipe(\n map(([{ offset }, search]) => offset.y > 400 && !search),\n distinctUntilChanged(),\n switchMap(active => active ? hidden$ : of(false)),\n startWith(false)\n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header\n *\n * @param el - Header element\n * @param options - Options\n *\n * @returns Header observable\n */\nexport function watchHeader(\n el: HTMLElement, options: WatchOptions\n): Observable

{\n return defer(() => combineLatest([\n watchElementSize(el),\n isHidden(options)\n ]))\n .pipe(\n map(([{ height }, hidden]) => ({\n height,\n hidden\n })),\n distinctUntilChanged((a, b) => (\n a.height === b.height &&\n a.hidden === b.hidden\n )),\n shareReplay(1)\n )\n}\n\n/**\n * Mount header\n *\n * This function manages the different states of the header, i.e. whether it's\n * hidden or rendered with a shadow. This depends heavily on the main area.\n *\n * @param el - Header element\n * @param options - Options\n *\n * @returns Header component observable\n */\nexport function mountHeader(\n el: HTMLElement, { header$, main$ }: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject

()\n const done$ = push$.pipe(takeLast(1))\n push$\n .pipe(\n distinctUntilKeyChanged(\"active\"),\n combineLatestWith(header$)\n )\n .subscribe(([{ active }, { hidden }]) => {\n el.classList.toggle(\"md-header--shadow\", active && !hidden)\n el.hidden = hidden\n })\n\n /* Link to main area */\n main$.subscribe(push$)\n\n /* Create and return component */\n return header$\n .pipe(\n takeUntil(done$),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n distinctUntilKeyChanged,\n finalize,\n map,\n tap\n} from \"rxjs\"\n\nimport {\n Viewport,\n getElementSize,\n getOptionalElement,\n watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Header } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface HeaderTitle {\n active: boolean /* Header title is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header title\n *\n * @param el - Heading element\n * @param options - Options\n *\n * @returns Header title observable\n */\nexport function watchHeaderTitle(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n return watchViewportAt(el, { viewport$, header$ })\n .pipe(\n map(({ offset: { y } }) => {\n const { height } = getElementSize(el)\n return {\n active: y >= height\n }\n }),\n distinctUntilKeyChanged(\"active\")\n )\n}\n\n/**\n * Mount header title\n *\n * This function swaps the header title from the site title to the title of the\n * current page when the user scrolls past the first headline.\n *\n * @param el - Header title element\n * @param options - Options\n *\n * @returns Header title component observable\n */\nexport function mountHeaderTitle(\n el: HTMLElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ active }) => {\n el.classList.toggle(\"md-header__title--active\", active)\n })\n\n /* Obtain headline, if any */\n const heading = getOptionalElement(\"article h1\")\n if (typeof heading === \"undefined\")\n return EMPTY\n\n /* Create and return component */\n return watchHeaderTitle(heading, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n map,\n switchMap\n} from \"rxjs\"\n\nimport {\n Viewport,\n watchElementSize\n} from \"~/browser\"\n\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Main area\n */\nexport interface Main {\n offset: number /* Main area top offset */\n height: number /* Main area visible height */\n active: boolean /* Main area is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

{\n\n /* Compute necessary adjustment for header */\n const adjust$ = header$\n .pipe(\n map(({ height }) => height),\n distinctUntilChanged()\n )\n\n /* Compute the main area's top and bottom borders */\n const border$ = adjust$\n .pipe(\n switchMap(() => watchElementSize(el)\n .pipe(\n map(({ height }) => ({\n top: el.offsetTop,\n bottom: el.offsetTop + height\n })),\n distinctUntilKeyChanged(\"bottom\")\n )\n )\n )\n\n /* Compute the main area's offset, visible height and if we scrolled past */\n return combineLatest([adjust$, border$, viewport$])\n .pipe(\n map(([header, { top, bottom }, { offset: { y }, size: { height } }]) => {\n height = Math.max(0, height\n - Math.max(0, top - y, header)\n - Math.max(0, height + y - bottom)\n )\n return {\n offset: top - header,\n height,\n active: top - header <= y\n }\n }),\n distinctUntilChanged((a, b) => (\n a.offset === b.offset &&\n a.height === b.height &&\n a.active === b.active\n ))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n asyncScheduler,\n defer,\n finalize,\n fromEvent,\n map,\n mergeMap,\n observeOn,\n of,\n shareReplay,\n startWith,\n tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Palette colors\n */\nexport interface PaletteColor {\n scheme?: string /* Color scheme */\n primary?: string /* Primary color */\n accent?: string /* Accent color */\n}\n\n/**\n * Palette\n */\nexport interface Palette {\n index: number /* Palette index */\n color: PaletteColor /* Palette colors */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch color palette\n *\n * @param inputs - Color palette element\n *\n * @returns Color palette observable\n */\nexport function watchPalette(\n inputs: HTMLInputElement[]\n): Observable {\n const current = __md_get(\"__palette\") || {\n index: inputs.findIndex(input => matchMedia(\n input.getAttribute(\"data-md-color-media\")!\n ).matches)\n }\n\n /* Emit changes in color palette */\n return of(...inputs)\n .pipe(\n mergeMap(input => fromEvent(input, \"change\")\n .pipe(\n map(() => input)\n )\n ),\n startWith(inputs[Math.max(0, current.index)]),\n map(input => ({\n index: inputs.indexOf(input),\n color: {\n scheme: input.getAttribute(\"data-md-color-scheme\"),\n primary: input.getAttribute(\"data-md-color-primary\"),\n accent: input.getAttribute(\"data-md-color-accent\")\n }\n } as Palette)),\n shareReplay(1)\n )\n}\n\n/**\n * Mount color palette\n *\n * @param el - Color palette element\n *\n * @returns Color palette component observable\n */\nexport function mountPalette(\n el: HTMLElement\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(palette => {\n document.body.setAttribute(\"data-md-color-switching\", \"\")\n\n /* Set color palette */\n for (const [key, value] of Object.entries(palette.color))\n document.body.setAttribute(`data-md-color-${key}`, value)\n\n /* Toggle visibility */\n for (let index = 0; index < inputs.length; index++) {\n const label = inputs[index].nextElementSibling\n if (label instanceof HTMLElement)\n label.hidden = palette.index !== index\n }\n\n /* Persist preference in local storage */\n __md_set(\"__palette\", palette)\n })\n\n /* Revert transition durations after color switch */\n push$.pipe(observeOn(asyncScheduler))\n .subscribe(() => {\n document.body.removeAttribute(\"data-md-color-switching\")\n })\n\n /* Create and return component */\n const inputs = getElements(\"input\", el)\n return watchPalette(inputs)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n Observable,\n Subject,\n map,\n tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n alert$: Subject /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Extract text to copy\n *\n * @param el - HTML element\n *\n * @returns Extracted text\n */\nfunction extract(el: HTMLElement): string {\n el.setAttribute(\"data-md-copying\", \"\")\n const text = el.innerText\n el.removeAttribute(\"data-md-copying\")\n return text\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up Clipboard.js integration\n *\n * @param options - Options\n */\nexport function setupClipboardJS(\n { alert$ }: SetupOptions\n): void {\n if (ClipboardJS.isSupported()) {\n new Observable(subscriber => {\n new ClipboardJS(\"[data-clipboard-target], [data-clipboard-text]\", {\n text: el => (\n el.getAttribute(\"data-clipboard-text\")! ||\n extract(getElement(\n el.getAttribute(\"data-clipboard-target\")!\n ))\n )\n })\n .on(\"success\", ev => subscriber.next(ev))\n })\n .pipe(\n tap(ev => {\n const trigger = ev.trigger as HTMLElement\n trigger.focus()\n }),\n map(() => translation(\"clipboard.copied\"))\n )\n .subscribe(alert$)\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map,\n of,\n tap\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport { getElements, requestXML } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sitemap, i.e. a list of URLs\n */\nexport type Sitemap = string[]\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Preprocess a list of URLs\n *\n * This function replaces the `site_url` in the sitemap with the actual base\n * URL, to allow instant loading to work in occasions like Netlify previews.\n *\n * @param urls - URLs\n *\n * @returns URL path parts\n */\nfunction preprocess(urls: Sitemap): Sitemap {\n if (urls.length < 2)\n return [\"\"]\n\n /* Take the first two URLs and remove everything after the last slash */\n const [root, next] = [...urls]\n .sort((a, b) => a.length - b.length)\n .map(url => url.replace(/[^/]+$/, \"\"))\n\n /* Compute common prefix */\n let index = 0\n if (root === next)\n index = root.length\n else\n while (root.charCodeAt(index) === next.charCodeAt(index))\n index++\n\n /* Remove common prefix and return in original order */\n return urls.map(url => url.replace(root.slice(0, index), \"\"))\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the sitemap for the given base URL\n *\n * @param base - Base URL\n *\n * @returns Sitemap observable\n */\nexport function fetchSitemap(base?: URL): Observable {\n const cached = __md_get(\"__sitemap\", sessionStorage, base)\n if (cached) {\n return of(cached)\n } else {\n const config = configuration()\n return requestXML(new URL(\"sitemap.xml\", base || config.base))\n .pipe(\n map(sitemap => preprocess(getElements(\"loc\", sitemap)\n .map(node => node.textContent!)\n )),\n catchError(() => EMPTY), // @todo refactor instant loading\n defaultIfEmpty([]),\n tap(sitemap => __md_set(\"__sitemap\", sitemap, sessionStorage, base))\n )\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n NEVER,\n Observable,\n Subject,\n bufferCount,\n catchError,\n concatMap,\n debounceTime,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n fromEvent,\n map,\n merge,\n of,\n sample,\n share,\n skip,\n skipUntil,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"~/_\"\nimport {\n Viewport,\n ViewportOffset,\n getElements,\n getOptionalElement,\n request,\n setLocation,\n setLocationHash\n} from \"~/browser\"\nimport { getComponentElement } from \"~/components\"\nimport { h } from \"~/utilities\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * History state\n */\nexport interface HistoryState {\n url: URL /* State URL */\n offset?: ViewportOffset /* State viewport offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n document$: Subject /* Document subject */\n location$: Subject /* Location subject */\n viewport$: Observable /* Viewport observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up instant loading\n *\n * When fetching, theoretically, we could use `responseType: \"document\"`, but\n * since all MkDocs links are relative, we need to make sure that the current\n * location matches the document we just loaded. Otherwise any relative links\n * in the document could use the old location.\n *\n * This is the reason why we need to synchronize history events and the process\n * of fetching the document for navigation changes (except `popstate` events):\n *\n * 1. Fetch document via `XMLHTTPRequest`\n * 2. Set new location via `history.pushState`\n * 3. Parse and emit fetched document\n *\n * For `popstate` events, we must not use `history.pushState`, or the forward\n * history will be irreversibly overwritten. In case the request fails, the\n * location change is dispatched regularly.\n *\n * @param options - Options\n */\nexport function setupInstantLoading(\n { document$, location$, viewport$ }: SetupOptions\n): void {\n const config = configuration()\n if (location.protocol === \"file:\")\n return\n\n /* Disable automatic scroll restoration */\n if (\"scrollRestoration\" in history) {\n history.scrollRestoration = \"manual\"\n\n /* Hack: ensure that reloads restore viewport offset */\n fromEvent(window, \"beforeunload\")\n .subscribe(() => {\n history.scrollRestoration = \"auto\"\n })\n }\n\n /* Hack: ensure absolute favicon link to omit 404s when switching */\n const favicon = getOptionalElement(\"link[rel=icon]\")\n if (typeof favicon !== \"undefined\")\n favicon.href = favicon.href\n\n /* Intercept internal navigation */\n const push$ = fetchSitemap()\n .pipe(\n map(paths => paths.map(path => `${new URL(path, config.base)}`)),\n switchMap(urls => fromEvent(document.body, \"click\")\n .pipe(\n filter(ev => !ev.metaKey && !ev.ctrlKey),\n switchMap(ev => {\n if (ev.target instanceof Element) {\n const el = ev.target.closest(\"a\")\n if (el && !el.target) {\n const url = new URL(el.href)\n\n /* Canonicalize URL */\n url.search = \"\"\n url.hash = \"\"\n\n /* Check if URL should be intercepted */\n if (\n url.pathname !== location.pathname &&\n urls.includes(url.toString())\n ) {\n ev.preventDefault()\n return of({\n url: new URL(el.href)\n })\n }\n }\n }\n return NEVER\n })\n )\n ),\n share()\n )\n\n /* Intercept history back and forward */\n const pop$ = fromEvent(window, \"popstate\")\n .pipe(\n filter(ev => ev.state !== null),\n map(ev => ({\n url: new URL(location.href),\n offset: ev.state\n })),\n share()\n )\n\n /* Emit location change */\n merge(push$, pop$)\n .pipe(\n distinctUntilChanged((a, b) => a.url.href === b.url.href),\n map(({ url }) => url)\n )\n .subscribe(location$)\n\n /* Fetch document via `XMLHTTPRequest` */\n const response$ = location$\n .pipe(\n distinctUntilKeyChanged(\"pathname\"),\n switchMap(url => request(url.href)\n .pipe(\n catchError(() => {\n setLocation(url)\n return NEVER\n })\n )\n ),\n share()\n )\n\n /* Set new location via `history.pushState` */\n push$\n .pipe(\n sample(response$)\n )\n .subscribe(({ url }) => {\n history.pushState({}, \"\", `${url}`)\n })\n\n /* Parse and emit fetched document */\n const dom = new DOMParser()\n response$\n .pipe(\n switchMap(res => res.text()),\n map(res => dom.parseFromString(res, \"text/html\"))\n )\n .subscribe(document$)\n\n /* Replace meta tags and components */\n document$\n .pipe(\n skip(1)\n )\n .subscribe(replacement => {\n for (const selector of [\n\n /* Meta tags */\n \"title\",\n \"link[rel=canonical]\",\n \"meta[name=author]\",\n \"meta[name=description]\",\n\n /* Components */\n \"[data-md-component=announce]\",\n \"[data-md-component=container]\",\n \"[data-md-component=header-topic]\",\n \"[data-md-component=outdated]\",\n \"[data-md-component=logo]\",\n \"[data-md-component=skip]\",\n ...feature(\"navigation.tabs.sticky\")\n ? [\"[data-md-component=tabs]\"]\n : []\n ]) {\n const source = getOptionalElement(selector)\n const target = getOptionalElement(selector, replacement)\n if (\n typeof source !== \"undefined\" &&\n typeof target !== \"undefined\"\n ) {\n source.replaceWith(target)\n }\n }\n })\n\n /* Re-evaluate scripts */\n document$\n .pipe(\n skip(1),\n map(() => getComponentElement(\"container\")),\n switchMap(el => getElements(\"script\", el)),\n concatMap(el => {\n const script = h(\"script\")\n if (el.src) {\n for (const name of el.getAttributeNames())\n script.setAttribute(name, el.getAttribute(name)!)\n el.replaceWith(script)\n\n /* Complete when script is loaded */\n return new Observable(observer => {\n script.onload = () => observer.complete()\n })\n\n /* Complete immediately */\n } else {\n script.textContent = el.textContent\n el.replaceWith(script)\n return EMPTY\n }\n })\n )\n .subscribe()\n\n /* Emit history state change */\n merge(push$, pop$)\n .pipe(\n sample(document$)\n )\n .subscribe(({ url, offset }) => {\n if (url.hash && !offset) {\n setLocationHash(url.hash)\n } else {\n window.scrollTo(0, offset?.y || 0)\n }\n })\n\n /* Debounce update of viewport offset */\n viewport$\n .pipe(\n skipUntil(push$),\n debounceTime(250),\n distinctUntilKeyChanged(\"offset\")\n )\n .subscribe(({ offset }) => {\n history.replaceState(offset, \"\")\n })\n\n /* Set viewport offset from history */\n merge(push$, pop$)\n .pipe(\n bufferCount(2, 1),\n filter(([a, b]) => a.url.pathname === b.url.pathname),\n map(([, state]) => state)\n )\n .subscribe(({ offset }) => {\n window.scrollTo(0, offset?.y || 0)\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexDocument } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search document\n */\nexport interface SearchDocument extends SearchIndexDocument {\n parent?: SearchIndexDocument /* Parent article */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search document mapping\n */\nexport type SearchDocumentMap = Map\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document mapping\n *\n * @param docs - Search index documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n docs: SearchIndexDocument[]\n): SearchDocumentMap {\n const documents = new Map()\n const parents = new Set()\n for (const doc of docs) {\n const [path, hash] = doc.location.split(\"#\")\n\n /* Extract location, title and tags */\n const location = doc.location\n const title = doc.title\n const tags = doc.tags\n\n /* Escape and cleanup text */\n const text = escapeHTML(doc.text)\n .replace(/\\s+(?=[,.:;!?])/g, \"\")\n .replace(/\\s+/g, \" \")\n\n /* Handle section */\n if (hash) {\n const parent = documents.get(path)!\n\n /* Ignore first section, override article */\n if (!parents.has(parent)) {\n parent.title = doc.title\n parent.text = text\n\n /* Remember that we processed the article */\n parents.add(parent)\n\n /* Add subsequent section */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n parent\n })\n }\n\n /* Add article */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n ...tags && { tags }\n })\n }\n }\n return documents\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexConfig } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search index configuration\n * @param escape - Whether to escape HTML\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n config: SearchIndexConfig, escape: boolean\n): SearchHighlightFactoryFn {\n const separator = new RegExp(config.separator, \"img\")\n const highlight = (_: unknown, data: string, term: string) => {\n return `${data}${term}`\n }\n\n /* Return factory function */\n return (query: string) => {\n query = query\n .replace(/[\\s*+\\-:~^]+/g, \" \")\n .trim()\n\n /* Create search term match expression */\n const match = new RegExp(`(^|${config.separator})(${\n query\n .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n .replace(separator, \"|\")\n })`, \"img\")\n\n /* Highlight string value */\n return value => (\n escape\n ? escapeHTML(value)\n : value\n )\n .replace(match, highlight)\n .replace(/<\\/mark>(\\s+)]*>/img, \"$1\")\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search transformation function\n *\n * @param value - Query value\n *\n * @returns Transformed query value\n */\nexport type SearchTransformFn = (value: string) => string\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Default transformation function\n *\n * 1. Search for terms in quotation marks and prepend a `+` modifier to denote\n * that the resulting document must contain all terms, converting the query\n * to an `AND` query (as opposed to the default `OR` behavior). While users\n * may expect terms enclosed in quotation marks to map to span queries, i.e.\n * for which order is important, Lunr.js doesn't support them, so the best\n * we can do is to convert the terms to an `AND` query.\n *\n * 2. Replace control characters which are not located at the beginning of the\n * query or preceded by white space, or are not followed by a non-whitespace\n * character or are at the end of the query string. Furthermore, filter\n * unmatched quotation marks.\n *\n * 3. Trim excess whitespace from left and right.\n *\n * @param query - Query value\n *\n * @returns Transformed query value\n */\nexport function defaultTransform(query: string): string {\n return query\n .split(/\"([^\"]+)\"/g) /* => 1 */\n .map((terms, index) => index & 1\n ? terms.replace(/^\\b|^(?![^\\x00-\\x7F]|$)|\\s+/g, \" +\")\n : terms\n )\n .join(\"\")\n .replace(/\"|(?:^|\\s+)[*+\\-:^~]+(?=\\s+|$)/g, \"\") /* => 2 */\n .trim() /* => 3 */\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SearchIndex, SearchResult } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search message type\n */\nexport const enum SearchMessageType {\n SETUP, /* Search index setup */\n READY, /* Search index ready */\n QUERY, /* Search query */\n RESULT /* Search results */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message containing the data necessary to setup the search index\n */\nexport interface SearchSetupMessage {\n type: SearchMessageType.SETUP /* Message type */\n data: SearchIndex /* Message data */\n}\n\n/**\n * Message indicating the search index is ready\n */\nexport interface SearchReadyMessage {\n type: SearchMessageType.READY /* Message type */\n}\n\n/**\n * Message containing a search query\n */\nexport interface SearchQueryMessage {\n type: SearchMessageType.QUERY /* Message type */\n data: string /* Message data */\n}\n\n/**\n * Message containing results for a search query\n */\nexport interface SearchResultMessage {\n type: SearchMessageType.RESULT /* Message type */\n data: SearchResult /* Message data */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message exchanged with the search worker\n */\nexport type SearchMessage =\n | SearchSetupMessage\n | SearchReadyMessage\n | SearchQueryMessage\n | SearchResultMessage\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Type guard for search setup messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchSetupMessage(\n message: SearchMessage\n): message is SearchSetupMessage {\n return message.type === SearchMessageType.SETUP\n}\n\n/**\n * Type guard for search ready messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchReadyMessage(\n message: SearchMessage\n): message is SearchReadyMessage {\n return message.type === SearchMessageType.READY\n}\n\n/**\n * Type guard for search query messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchQueryMessage(\n message: SearchMessage\n): message is SearchQueryMessage {\n return message.type === SearchMessageType.QUERY\n}\n\n/**\n * Type guard for search result messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchResultMessage(\n message: SearchMessage\n): message is SearchResultMessage {\n return message.type === SearchMessageType.RESULT\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n ObservableInput,\n Subject,\n from,\n map,\n share\n} from \"rxjs\"\n\nimport { configuration, feature, translation } from \"~/_\"\nimport { WorkerHandler, watchWorker } from \"~/browser\"\n\nimport { SearchIndex } from \"../../_\"\nimport {\n SearchOptions,\n SearchPipeline\n} from \"../../options\"\nimport {\n SearchMessage,\n SearchMessageType,\n SearchSetupMessage,\n isSearchResultMessage\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search worker\n */\nexport type SearchWorker = WorkerHandler\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search index\n *\n * @param data - Search index\n *\n * @returns Search index\n */\nfunction setupSearchIndex({ config, docs }: SearchIndex): SearchIndex {\n\n /* Override default language with value from translation */\n if (config.lang.length === 1 && config.lang[0] === \"en\")\n config.lang = [\n translation(\"search.config.lang\")\n ]\n\n /* Override default separator with value from translation */\n if (config.separator === \"[\\\\s\\\\-]+\")\n config.separator = translation(\"search.config.separator\")\n\n /* Set pipeline from translation */\n const pipeline = translation(\"search.config.pipeline\")\n .split(/\\s*,\\s*/)\n .filter(Boolean) as SearchPipeline\n\n /* Determine search options */\n const options: SearchOptions = {\n pipeline,\n suggestions: feature(\"search.suggest\")\n }\n\n /* Return search index after defaulting */\n return { config, docs, options }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search worker\n *\n * This function creates a web worker to set up and query the search index,\n * which is done using Lunr.js. The index must be passed as an observable to\n * enable hacks like _localsearch_ via search index embedding as JSON.\n *\n * @param url - Worker URL\n * @param index - Search index observable input\n *\n * @returns Search worker\n */\nexport function setupSearchWorker(\n url: string, index: ObservableInput\n): SearchWorker {\n const config = configuration()\n const worker = new Worker(url)\n\n /* Create communication channels and resolve relative links */\n const tx$ = new Subject()\n const rx$ = watchWorker(worker, { tx$ })\n .pipe(\n map(message => {\n if (isSearchResultMessage(message)) {\n for (const result of message.data.items)\n for (const document of result)\n document.location = `${new URL(document.location, config.base)}`\n }\n return message\n }),\n share()\n )\n\n /* Set up search index */\n from(index)\n .pipe(\n map(data => ({\n type: SearchMessageType.SETUP,\n data: setupSearchIndex(data)\n } as SearchSetupMessage))\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Return search worker */\n return { tx$, rx$ }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Subject,\n catchError,\n combineLatest,\n filter,\n fromEvent,\n map,\n of,\n switchMap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n getElement,\n getLocation,\n requestJSON,\n setLocation\n} from \"~/browser\"\nimport { getComponentElements } from \"~/components\"\nimport {\n Version,\n renderVersionSelector\n} from \"~/templates\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n document$: Subject /* Document subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up version selector\n *\n * @param options - Options\n */\nexport function setupVersionSelector(\n { document$ }: SetupOptions\n): void {\n const config = configuration()\n const versions$ = requestJSON(\n new URL(\"../versions.json\", config.base)\n )\n .pipe(\n catchError(() => EMPTY) // @todo refactor instant loading\n )\n\n /* Determine current version */\n const current$ = versions$\n .pipe(\n map(versions => {\n const [, current] = config.base.match(/([^/]+)\\/?$/)!\n return versions.find(({ version, aliases }) => (\n version === current || aliases.includes(current)\n )) || versions[0]\n })\n )\n\n /* Intercept inter-version navigation */\n versions$\n .pipe(\n map(versions => new Map(versions.map(version => [\n `${new URL(`../${version.version}/`, config.base)}`,\n version\n ]))),\n switchMap(urls => fromEvent(document.body, \"click\")\n .pipe(\n filter(ev => !ev.metaKey && !ev.ctrlKey),\n withLatestFrom(current$),\n switchMap(([ev, current]) => {\n if (ev.target instanceof Element) {\n const el = ev.target.closest(\"a\")\n if (el && !el.target && urls.has(el.href)) {\n const url = el.href\n // This is a temporary hack to detect if a version inside the\n // version selector or on another part of the site was clicked.\n // If we're inside the version selector, we definitely want to\n // find the same page, as we might have different deployments\n // due to aliases. However, if we're outside the version\n // selector, we must abort here, because we might otherwise\n // interfere with instant loading. We need to refactor this\n // at some point together with instant loading.\n //\n // See https://github.com/squidfunk/mkdocs-material/issues/4012\n if (!ev.target.closest(\".md-version\")) {\n const version = urls.get(url)!\n if (version === current)\n return EMPTY\n }\n ev.preventDefault()\n return of(url)\n }\n }\n return EMPTY\n }),\n switchMap(url => {\n const { version } = urls.get(url)!\n return fetchSitemap(new URL(url))\n .pipe(\n map(sitemap => {\n const location = getLocation()\n const path = location.href.replace(config.base, \"\")\n return sitemap.includes(path.split(\"#\")[0])\n ? new URL(`../${version}/${path}`, config.base)\n : new URL(url)\n })\n )\n })\n )\n )\n )\n .subscribe(url => setLocation(url))\n\n /* Render version selector and warning */\n combineLatest([versions$, current$])\n .subscribe(([versions, current]) => {\n const topic = getElement(\".md-header__topic\")\n topic.appendChild(renderVersionSelector(versions, current))\n })\n\n /* Integrate outdated version banner with instant loading */\n document$.pipe(switchMap(() => current$))\n .subscribe(current => {\n\n /* Check if version state was already determined */\n let outdated = __md_get(\"__outdated\", sessionStorage)\n if (outdated === null) {\n const latest = config.version?.default || \"latest\"\n outdated = !current.aliases.includes(latest)\n\n /* Persist version state in session storage */\n __md_set(\"__outdated\", outdated, sessionStorage)\n }\n\n /* Unhide outdated version banner */\n if (outdated)\n for (const warning of getComponentElements(\"outdated\"))\n warning.hidden = false\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n combineLatest,\n delay,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n finalize,\n fromEvent,\n map,\n merge,\n share,\n shareReplay,\n startWith,\n take,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n getLocation,\n setToggle,\n watchElementFocus,\n watchToggle\n} from \"~/browser\"\nimport {\n SearchMessageType,\n SearchQueryMessage,\n SearchWorker,\n defaultTransform,\n isSearchReadyMessage\n} from \"~/integrations\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query\n */\nexport interface SearchQuery {\n value: string /* Query value */\n focus: boolean /* Query focus */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch search query\n *\n * Note that the focus event which triggers re-reading the current query value\n * is delayed by `1ms` so the input's empty state is allowed to propagate.\n *\n * @param el - Search query element\n * @param worker - Search worker\n *\n * @returns Search query observable\n */\nexport function watchSearchQuery(\n el: HTMLInputElement, { rx$ }: SearchWorker\n): Observable {\n const fn = __search?.transform || defaultTransform\n\n /* Immediately show search dialog */\n const { searchParams } = getLocation()\n if (searchParams.has(\"q\"))\n setToggle(\"search\", true)\n\n /* Intercept query parameter (deep link) */\n const param$ = rx$\n .pipe(\n filter(isSearchReadyMessage),\n take(1),\n map(() => searchParams.get(\"q\") || \"\")\n )\n\n /* Remove query parameter when search is closed */\n watchToggle(\"search\")\n .pipe(\n filter(active => !active),\n take(1)\n )\n .subscribe(() => {\n const url = new URL(location.href)\n url.searchParams.delete(\"q\")\n history.replaceState({}, \"\", `${url}`)\n })\n\n /* Set query from parameter */\n param$.subscribe(value => { // TODO: not ideal - find a better way\n if (value) {\n el.value = value\n el.focus()\n }\n })\n\n /* Intercept focus and input events */\n const focus$ = watchElementFocus(el)\n const value$ = merge(\n fromEvent(el, \"keyup\"),\n fromEvent(el, \"focus\").pipe(delay(1)),\n param$\n )\n .pipe(\n map(() => fn(el.value)),\n startWith(\"\"),\n distinctUntilChanged(),\n )\n\n /* Combine into single observable */\n return combineLatest([value$, focus$])\n .pipe(\n map(([value, focus]) => ({ value, focus })),\n shareReplay(1)\n )\n}\n\n/**\n * Mount search query\n *\n * @param el - Search query element\n * @param worker - Search worker\n *\n * @returns Search query component observable\n */\nexport function mountSearchQuery(\n el: HTMLInputElement, { tx$, rx$ }: SearchWorker\n): Observable> {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n\n /* Handle value changes */\n push$\n .pipe(\n distinctUntilKeyChanged(\"value\"),\n map(({ value }): SearchQueryMessage => ({\n type: SearchMessageType.QUERY,\n data: value\n }))\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Handle focus changes */\n push$\n .pipe(\n distinctUntilKeyChanged(\"focus\")\n )\n .subscribe(({ focus }) => {\n if (focus) {\n setToggle(\"search\", focus)\n el.placeholder = \"\"\n } else {\n el.placeholder = translation(\"search.placeholder\")\n }\n })\n\n /* Handle reset */\n fromEvent(el.form!, \"reset\")\n .pipe(\n takeUntil(done$)\n )\n .subscribe(() => el.focus())\n\n /* Create and return component */\n return watchSearchQuery(el, { tx$, rx$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state })),\n share()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n filter,\n finalize,\n map,\n merge,\n of,\n skipUntil,\n switchMap,\n take,\n tap,\n withLatestFrom,\n zipWith\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n getElement,\n watchElementBoundary\n} from \"~/browser\"\nimport {\n SearchResult,\n SearchWorker,\n isSearchReadyMessage,\n isSearchResultMessage\n} from \"~/integrations\"\nimport { renderSearchResultItem } from \"~/templates\"\nimport { round } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n query$: Observable /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search result list\n *\n * This function performs a lazy rendering of the search results, depending on\n * the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param worker - Search worker\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchResult(\n el: HTMLElement, { rx$ }: SearchWorker, { query$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n const boundary$ = watchElementBoundary(el.parentElement!)\n .pipe(\n filter(Boolean)\n )\n\n /* Retrieve nested components */\n const meta = getElement(\":scope > :first-child\", el)\n const list = getElement(\":scope > :last-child\", el)\n\n /* Wait until search is ready */\n const ready$ = rx$\n .pipe(\n filter(isSearchReadyMessage),\n take(1)\n )\n\n /* Update search result metadata */\n push$\n .pipe(\n withLatestFrom(query$),\n skipUntil(ready$)\n )\n .subscribe(([{ items }, { value }]) => {\n if (value) {\n switch (items.length) {\n\n /* No results */\n case 0:\n meta.textContent = translation(\"search.result.none\")\n break\n\n /* One result */\n case 1:\n meta.textContent = translation(\"search.result.one\")\n break\n\n /* Multiple result */\n default:\n meta.textContent = translation(\n \"search.result.other\",\n round(items.length)\n )\n }\n } else {\n meta.textContent = translation(\"search.result.placeholder\")\n }\n })\n\n /* Update search result list */\n push$\n .pipe(\n tap(() => list.innerHTML = \"\"),\n switchMap(({ items }) => merge(\n of(...items.slice(0, 10)),\n of(...items.slice(10))\n .pipe(\n bufferCount(4),\n zipWith(boundary$),\n switchMap(([chunk]) => chunk)\n )\n ))\n )\n .subscribe(result => list.appendChild(\n renderSearchResultItem(result)\n ))\n\n /* Filter search result message */\n const result$ = rx$\n .pipe(\n filter(isSearchResultMessage),\n map(({ data }) => data)\n )\n\n /* Create and return component */\n return result$\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n finalize,\n fromEvent,\n map,\n tap\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search sharing\n */\nexport interface SearchShare {\n url: URL /* Deep link for sharing */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n query$: Observable /* Search query observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n query$: Observable /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search sharing\n *\n * @param _el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing observable\n */\nexport function watchSearchShare(\n _el: HTMLElement, { query$ }: WatchOptions\n): Observable {\n return query$\n .pipe(\n map(({ value }) => {\n const url = getLocation()\n url.hash = \"\"\n url.searchParams.delete(\"h\")\n url.searchParams.set(\"q\", value)\n return { url }\n })\n )\n}\n\n/**\n * Mount search sharing\n *\n * @param el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing component observable\n */\nexport function mountSearchShare(\n el: HTMLAnchorElement, options: MountOptions\n): Observable> {\n const push$ = new Subject()\n push$.subscribe(({ url }) => {\n el.setAttribute(\"data-clipboard-text\", el.href)\n el.href = `${url}`\n })\n\n /* Prevent following of link */\n fromEvent(el, \"click\")\n .subscribe(ev => ev.preventDefault())\n\n /* Create and return component */\n return watchSearchShare(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n asyncScheduler,\n combineLatestWith,\n distinctUntilChanged,\n filter,\n finalize,\n fromEvent,\n map,\n merge,\n observeOn,\n tap\n} from \"rxjs\"\n\nimport { Keyboard } from \"~/browser\"\nimport {\n SearchResult,\n SearchWorker,\n isSearchResultMessage\n} from \"~/integrations\"\n\nimport { Component, getComponentElement } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search suggestions\n */\nexport interface SearchSuggest {}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n keyboard$: Observable /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search suggestions\n *\n * This function will perform a lazy rendering of the search results, depending\n * on the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param worker - Search worker\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchSuggest(\n el: HTMLElement, { rx$ }: SearchWorker, { keyboard$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n\n /* Retrieve query component and track all changes */\n const query = getComponentElement(\"search-query\")\n const query$ = merge(\n fromEvent(query, \"keydown\"),\n fromEvent(query, \"focus\")\n )\n .pipe(\n observeOn(asyncScheduler),\n map(() => query.value),\n distinctUntilChanged(),\n )\n\n /* Update search suggestions */\n push$\n .pipe(\n combineLatestWith(query$),\n map(([{ suggestions }, value]) => {\n const words = value.split(/([\\s-]+)/)\n if (suggestions?.length && words[words.length - 1]) {\n const last = suggestions[suggestions.length - 1]\n if (last.startsWith(words[words.length - 1]))\n words[words.length - 1] = last\n } else {\n words.length = 0\n }\n return words\n })\n )\n .subscribe(words => el.innerHTML = words\n .join(\"\")\n .replace(/\\s/g, \" \")\n )\n\n /* Set up search keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"search\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Right arrow: accept current suggestion */\n case \"ArrowRight\":\n if (\n el.innerText.length &&\n query.selectionStart === query.value.length\n )\n query.value = el.innerText\n break\n }\n })\n\n /* Filter search result message */\n const result$ = rx$\n .pipe(\n filter(isSearchResultMessage),\n map(({ data }) => data)\n )\n\n /* Create and return component */\n return result$\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(() => ({ ref: el }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n NEVER,\n Observable,\n ObservableInput,\n filter,\n merge,\n mergeWith,\n sample,\n take\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n Keyboard,\n getActiveElement,\n getElements,\n setToggle\n} from \"~/browser\"\nimport {\n SearchIndex,\n SearchResult,\n isSearchQueryMessage,\n isSearchReadyMessage,\n setupSearchWorker\n} from \"~/integrations\"\n\nimport {\n Component,\n getComponentElement,\n getComponentElements\n} from \"../../_\"\nimport {\n SearchQuery,\n mountSearchQuery\n} from \"../query\"\nimport { mountSearchResult } from \"../result\"\nimport {\n SearchShare,\n mountSearchShare\n} from \"../share\"\nimport {\n SearchSuggest,\n mountSearchSuggest\n} from \"../suggest\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search\n */\nexport type Search =\n | SearchQuery\n | SearchResult\n | SearchShare\n | SearchSuggest\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n index$: ObservableInput /* Search index observable */\n keyboard$: Observable /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search\n *\n * This function sets up the search functionality, including the underlying\n * web worker and all keyboard bindings.\n *\n * @param el - Search element\n * @param options - Options\n *\n * @returns Search component observable\n */\nexport function mountSearch(\n el: HTMLElement, { index$, keyboard$ }: MountOptions\n): Observable> {\n const config = configuration()\n try {\n const url = __search?.worker || config.search\n const worker = setupSearchWorker(url, index$)\n\n /* Retrieve query and result components */\n const query = getComponentElement(\"search-query\", el)\n const result = getComponentElement(\"search-result\", el)\n\n /* Re-emit query when search is ready */\n const { tx$, rx$ } = worker\n tx$\n .pipe(\n filter(isSearchQueryMessage),\n sample(rx$.pipe(filter(isSearchReadyMessage))),\n take(1)\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Set up search keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"search\")\n )\n .subscribe(key => {\n const active = getActiveElement()\n switch (key.type) {\n\n /* Enter: go to first (best) result */\n case \"Enter\":\n if (active === query) {\n const anchors = new Map()\n for (const anchor of getElements(\n \":first-child [href]\", result\n )) {\n const article = anchor.firstElementChild!\n anchors.set(anchor, parseFloat(\n article.getAttribute(\"data-md-score\")!\n ))\n }\n\n /* Go to result with highest score, if any */\n if (anchors.size) {\n const [[best]] = [...anchors].sort(([, a], [, b]) => b - a)\n best.click()\n }\n\n /* Otherwise omit form submission */\n key.claim()\n }\n break\n\n /* Escape or Tab: close search */\n case \"Escape\":\n case \"Tab\":\n setToggle(\"search\", false)\n query.blur()\n break\n\n /* Vertical arrows: select previous or next search result */\n case \"ArrowUp\":\n case \"ArrowDown\":\n if (typeof active === \"undefined\") {\n query.focus()\n } else {\n const els = [query, ...getElements(\n \":not(details) > [href], summary, details[open] [href]\",\n result\n )]\n const i = Math.max(0, (\n Math.max(0, els.indexOf(active)) + els.length + (\n key.type === \"ArrowUp\" ? -1 : +1\n )\n ) % els.length)\n els[i].focus()\n }\n\n /* Prevent scrolling of page */\n key.claim()\n break\n\n /* All other keys: hand to search query */\n default:\n if (query !== getActiveElement())\n query.focus()\n }\n })\n\n /* Set up global keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\"),\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Open search and select query */\n case \"f\":\n case \"s\":\n case \"/\":\n query.focus()\n query.select()\n\n /* Prevent scrolling of page */\n key.claim()\n break\n }\n })\n\n /* Create and return component */\n const query$ = mountSearchQuery(query, worker)\n const result$ = mountSearchResult(result, worker, { query$ })\n return merge(query$, result$)\n .pipe(\n mergeWith(\n\n /* Search sharing */\n ...getComponentElements(\"search-share\", el)\n .map(child => mountSearchShare(child, { query$ })),\n\n /* Search suggestions */\n ...getComponentElements(\"search-suggest\", el)\n .map(child => mountSearchSuggest(child, worker, { keyboard$ }))\n )\n )\n\n /* Gracefully handle broken search */\n } catch (err) {\n el.hidden = true\n return NEVER\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n ObservableInput,\n combineLatest,\n filter,\n map,\n startWith\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\nimport {\n SearchIndex,\n setupSearchHighlighter\n} from \"~/integrations\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlighting\n */\nexport interface SearchHighlight {\n nodes: Map /* Map of replacements */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n index$: ObservableInput /* Search index observable */\n location$: Observable /* Location observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search highlighting\n *\n * @param el - Content element\n * @param options - Options\n *\n * @returns Search highlighting component observable\n */\nexport function mountSearchHiglight(\n el: HTMLElement, { index$, location$ }: MountOptions\n): Observable> {\n return combineLatest([\n index$,\n location$\n .pipe(\n startWith(getLocation()),\n filter(url => !!url.searchParams.get(\"h\"))\n )\n ])\n .pipe(\n map(([index, url]) => setupSearchHighlighter(index.config, true)(\n url.searchParams.get(\"h\")!\n )),\n map(fn => {\n const nodes = new Map()\n\n /* Traverse text nodes and collect matches */\n const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n for (let node = it.nextNode(); node; node = it.nextNode()) {\n if (node.parentElement?.offsetHeight) {\n const original = node.textContent!\n const replaced = fn(original)\n if (replaced.length > original.length)\n nodes.set(node as ChildNode, replaced)\n }\n }\n\n /* Replace original nodes with matches */\n for (const [node, text] of nodes) {\n const { childNodes } = h(\"span\", null, text)\n node.replaceWith(...Array.from(childNodes))\n }\n\n /* Return component */\n return { ref: el, nodes }\n })\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n animationFrameScheduler,\n auditTime,\n combineLatest,\n defer,\n distinctUntilChanged,\n finalize,\n map,\n observeOn,\n take,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport {\n Viewport,\n getElement,\n getElementContainer,\n getElementOffset,\n getElementSize,\n getElements\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sidebar\n */\nexport interface Sidebar {\n height: number /* Sidebar height */\n locked: boolean /* Sidebar is locked */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n main$: Observable

/* Main area observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n main$: Observable

/* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch sidebar\n *\n * This function returns an observable that computes the visual parameters of\n * the sidebar which depends on the vertical viewport offset, as well as the\n * height of the main area. When the page is scrolled beyond the header, the\n * sidebar is locked and fills the remaining space.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar observable\n */\nexport function watchSidebar(\n el: HTMLElement, { viewport$, main$ }: WatchOptions\n): Observable {\n const parent = el.parentElement!\n const adjust =\n parent.offsetTop -\n parent.parentElement!.offsetTop\n\n /* Compute the sidebar's available height and if it should be locked */\n return combineLatest([main$, viewport$])\n .pipe(\n map(([{ offset, height }, { offset: { y } }]) => {\n height = height\n + Math.min(adjust, Math.max(0, y - offset))\n - adjust\n return {\n height,\n locked: y >= offset + adjust\n }\n }),\n distinctUntilChanged((a, b) => (\n a.height === b.height &&\n a.locked === b.locked\n ))\n )\n}\n\n/**\n * Mount sidebar\n *\n * This function doesn't set the height of the actual sidebar, but of its first\n * child \u2013 the `.md-sidebar__scrollwrap` element in order to mitigiate jittery\n * sidebars when the footer is scrolled into view. At some point we switched\n * from `absolute` / `fixed` positioning to `sticky` positioning, significantly\n * reducing jitter in some browsers (respectively Firefox and Safari) when\n * scrolling from the top. However, top-aligned sticky positioning means that\n * the sidebar snaps to the bottom when the end of the container is reached.\n * This is what leads to the mentioned jitter, as the sidebar's height may be\n * updated too slowly.\n *\n * This behaviour can be mitigiated by setting the height of the sidebar to `0`\n * while preserving the padding, and the height on its first element.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar component observable\n */\nexport function mountSidebar(\n el: HTMLElement, { header$, ...options }: MountOptions\n): Observable> {\n const inner = getElement(\".md-sidebar__scrollwrap\", el)\n const { y } = getElementOffset(inner)\n return defer(() => {\n const push$ = new Subject()\n push$\n .pipe(\n auditTime(0, animationFrameScheduler),\n withLatestFrom(header$)\n )\n .subscribe({\n\n /* Handle emission */\n next([{ height }, { height: offset }]) {\n inner.style.height = `${height - 2 * y}px`\n el.style.top = `${offset}px`\n },\n\n /* Handle complete */\n complete() {\n inner.style.height = \"\"\n el.style.top = \"\"\n }\n })\n\n /* Bring active item into view on initial load */\n push$\n .pipe(\n observeOn(animationFrameScheduler),\n take(1)\n )\n .subscribe(() => {\n for (const item of getElements(\".md-nav__link--active[href]\", el)) {\n const container = getElementContainer(item)\n if (typeof container !== \"undefined\") {\n const offset = item.offsetTop - container.offsetTop\n const { height } = getElementSize(container)\n container.scrollTo({\n top: offset - height / 2\n })\n }\n }\n })\n\n /* Create and return component */\n return watchSidebar(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Repo, User } from \"github-types\"\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map,\n zip\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * GitHub release (partial)\n */\ninterface Release {\n tag_name: string /* Tag name */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitHub repository facts\n *\n * @param user - GitHub user or organization\n * @param repo - GitHub repository\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitHub(\n user: string, repo?: string\n): Observable {\n if (typeof repo !== \"undefined\") {\n const url = `https://api.github.com/repos/${user}/${repo}`\n return zip(\n\n /* Fetch version */\n requestJSON(`${url}/releases/latest`)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(release => ({\n version: release.tag_name\n })),\n defaultIfEmpty({})\n ),\n\n /* Fetch stars and forks */\n requestJSON(url)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(info => ({\n stars: info.stargazers_count,\n forks: info.forks_count\n })),\n defaultIfEmpty({})\n )\n )\n .pipe(\n map(([release, info]) => ({ ...release, ...info }))\n )\n\n /* User or organization */\n } else {\n const url = `https://api.github.com/users/${user}`\n return requestJSON(url)\n .pipe(\n map(info => ({\n repositories: info.public_repos\n })),\n defaultIfEmpty({})\n )\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ProjectSchema } from \"gitlab\"\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitLab repository facts\n *\n * @param base - GitLab base\n * @param project - GitLab project\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitLab(\n base: string, project: string\n): Observable {\n const url = `https://${base}/api/v4/projects/${encodeURIComponent(project)}`\n return requestJSON(url)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(({ star_count, forks_count }) => ({\n stars: star_count,\n forks: forks_count\n })),\n defaultIfEmpty({})\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { EMPTY, Observable } from \"rxjs\"\n\nimport { fetchSourceFactsFromGitHub } from \"../github\"\nimport { fetchSourceFactsFromGitLab } from \"../gitlab\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository facts for repositories\n */\nexport interface RepositoryFacts {\n stars?: number /* Number of stars */\n forks?: number /* Number of forks */\n version?: string /* Latest version */\n}\n\n/**\n * Repository facts for organizations\n */\nexport interface OrganizationFacts {\n repositories?: number /* Number of repositories */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Repository facts\n */\nexport type SourceFacts =\n | RepositoryFacts\n | OrganizationFacts\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch repository facts\n *\n * @param url - Repository URL\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFacts(\n url: string\n): Observable {\n\n /* Try to match GitHub repository */\n let match = url.match(/^.+github\\.com\\/([^/]+)\\/?([^/]+)?/i)\n if (match) {\n const [, user, repo] = match\n return fetchSourceFactsFromGitHub(user, repo)\n }\n\n /* Try to match GitLab repository */\n match = url.match(/^.+?([^/]*gitlab[^/]+)\\/(.+?)\\/?$/i)\n if (match) {\n const [, base, slug] = match\n return fetchSourceFactsFromGitLab(base, slug)\n }\n\n /* Fallback */\n return EMPTY\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n catchError,\n defer,\n filter,\n finalize,\n map,\n of,\n shareReplay,\n tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\nimport { ConsentDefaults } from \"~/components/consent\"\nimport { renderSourceFacts } from \"~/templates\"\n\nimport {\n Component,\n getComponentElements\n} from \"../../_\"\nimport {\n SourceFacts,\n fetchSourceFacts\n} from \"../facts\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information\n */\nexport interface Source {\n facts: SourceFacts /* Repository facts */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information observable\n */\nlet fetch$: Observable\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch repository information\n *\n * This function tries to read the repository facts from session storage, and\n * if unsuccessful, fetches them from the underlying provider.\n *\n * @param el - Repository information element\n *\n * @returns Repository information observable\n */\nexport function watchSource(\n el: HTMLAnchorElement\n): Observable {\n return fetch$ ||= defer(() => {\n const cached = __md_get(\"__source\", sessionStorage)\n if (cached) {\n return of(cached)\n } else {\n\n /* Check if consent is configured and was given */\n const els = getComponentElements(\"consent\")\n if (els.length) {\n const consent = __md_get(\"__consent\")\n if (!(consent && consent.github))\n return EMPTY\n }\n\n /* Fetch repository facts */\n return fetchSourceFacts(el.href)\n .pipe(\n tap(facts => __md_set(\"__source\", facts, sessionStorage))\n )\n }\n })\n .pipe(\n catchError(() => EMPTY),\n filter(facts => Object.keys(facts).length > 0),\n map(facts => ({ facts })),\n shareReplay(1)\n )\n}\n\n/**\n * Mount repository information\n *\n * @param el - Repository information element\n *\n * @returns Repository information component observable\n */\nexport function mountSource(\n el: HTMLAnchorElement\n): Observable> {\n const inner = getElement(\":scope > :last-child\", el)\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ facts }) => {\n inner.appendChild(renderSourceFacts(facts))\n inner.classList.add(\"md-source__repository--active\")\n })\n\n /* Create and return component */\n return watchSource(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n defer,\n distinctUntilKeyChanged,\n finalize,\n map,\n of,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n watchElementSize,\n watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Navigation tabs\n */\nexport interface Tabs {\n hidden: boolean /* Navigation tabs are hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch navigation tabs\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs observable\n */\nexport function watchTabs(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n return watchElementSize(document.body)\n .pipe(\n switchMap(() => watchViewportAt(el, { header$, viewport$ })),\n map(({ offset: { y } }) => {\n return {\n hidden: y >= 10\n }\n }),\n distinctUntilKeyChanged(\"hidden\")\n )\n}\n\n/**\n * Mount navigation tabs\n *\n * This function hides the navigation tabs when scrolling past the threshold\n * and makes them reappear in a nice CSS animation when scrolling back up.\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs component observable\n */\nexport function mountTabs(\n el: HTMLElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe({\n\n /* Handle emission */\n next({ hidden }) {\n el.hidden = hidden\n },\n\n /* Handle complete */\n complete() {\n el.hidden = false\n }\n })\n\n /* Create and return component */\n return (\n feature(\"navigation.tabs.sticky\")\n ? of({ hidden: false })\n : watchTabs(el, options)\n )\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatestWith,\n debounceTime,\n defer,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n finalize,\n map,\n merge,\n of,\n repeat,\n scan,\n share,\n skip,\n startWith,\n switchMap,\n takeLast,\n takeUntil,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n getElement,\n getElementContainer,\n getElementSize,\n getElements,\n getLocation,\n getOptionalElement,\n watchElementSize\n} from \"~/browser\"\n\nimport {\n Component,\n getComponentElement\n} from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Table of contents\n */\nexport interface TableOfContents {\n prev: HTMLAnchorElement[][] /* Anchors (previous) */\n next: HTMLAnchorElement[][] /* Anchors (next) */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n target$: Observable /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch table of contents\n *\n * This is effectively a scroll spy implementation which will account for the\n * fixed header and automatically re-calculate anchor offsets when the viewport\n * is resized. The returned observable will only emit if the table of contents\n * needs to be repainted.\n *\n * This implementation tracks an anchor element's entire path starting from its\n * level up to the top-most anchor element, e.g. `[h3, h2, h1]`. Although the\n * Material theme currently doesn't make use of this information, it enables\n * the styling of the entire hierarchy through customization.\n *\n * Note that the current anchor is the last item of the `prev` anchor list.\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents observable\n */\nexport function watchTableOfContents(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n const table = new Map()\n\n /* Compute anchor-to-target mapping */\n const anchors = getElements(\"[href^=\\\\#]\", el)\n for (const anchor of anchors) {\n const id = decodeURIComponent(anchor.hash.substring(1))\n const target = getOptionalElement(`[id=\"${id}\"]`)\n if (typeof target !== \"undefined\")\n table.set(anchor, target)\n }\n\n /* Compute necessary adjustment for header */\n const adjust$ = header$\n .pipe(\n distinctUntilKeyChanged(\"height\"),\n map(({ height }) => {\n const main = getComponentElement(\"main\")\n const grid = getElement(\":scope > :first-child\", main)\n return height + 0.8 * (\n grid.offsetTop -\n main.offsetTop\n )\n }),\n share()\n )\n\n /* Compute partition of previous and next anchors */\n const partition$ = watchElementSize(document.body)\n .pipe(\n distinctUntilKeyChanged(\"height\"),\n\n /* Build index to map anchor paths to vertical offsets */\n switchMap(body => defer(() => {\n let path: HTMLAnchorElement[] = []\n return of([...table].reduce((index, [anchor, target]) => {\n while (path.length) {\n const last = table.get(path[path.length - 1])!\n if (last.tagName >= target.tagName) {\n path.pop()\n } else {\n break\n }\n }\n\n /* If the current anchor is hidden, continue with its parent */\n let offset = target.offsetTop\n while (!offset && target.parentElement) {\n target = target.parentElement\n offset = target.offsetTop\n }\n\n /* Map reversed anchor path to vertical offset */\n return index.set(\n [...path = [...path, anchor]].reverse(),\n offset\n )\n }, new Map()))\n })\n .pipe(\n\n /* Sort index by vertical offset (see https://bit.ly/30z6QSO) */\n map(index => new Map([...index].sort(([, a], [, b]) => a - b))),\n combineLatestWith(adjust$),\n\n /* Re-compute partition when viewport offset changes */\n switchMap(([index, adjust]) => viewport$\n .pipe(\n scan(([prev, next], { offset: { y }, size }) => {\n const last = y + size.height >= Math.floor(body.height)\n\n /* Look forward */\n while (next.length) {\n const [, offset] = next[0]\n if (offset - adjust < y || last) {\n prev = [...prev, next.shift()!]\n } else {\n break\n }\n }\n\n /* Look backward */\n while (prev.length) {\n const [, offset] = prev[prev.length - 1]\n if (offset - adjust >= y && !last) {\n next = [prev.pop()!, ...next]\n } else {\n break\n }\n }\n\n /* Return partition */\n return [prev, next]\n }, [[], [...index]]),\n distinctUntilChanged((a, b) => (\n a[0] === b[0] &&\n a[1] === b[1]\n ))\n )\n )\n )\n )\n )\n\n /* Compute and return anchor list migrations */\n return partition$\n .pipe(\n map(([prev, next]) => ({\n prev: prev.map(([path]) => path),\n next: next.map(([path]) => path)\n })),\n\n /* Extract anchor list migrations */\n startWith({ prev: [], next: [] }),\n bufferCount(2, 1),\n map(([a, b]) => {\n\n /* Moving down */\n if (a.prev.length < b.prev.length) {\n return {\n prev: b.prev.slice(Math.max(0, a.prev.length - 1), b.prev.length),\n next: []\n }\n\n /* Moving up */\n } else {\n return {\n prev: b.prev.slice(-1),\n next: b.next.slice(0, b.next.length - a.next.length)\n }\n }\n })\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount table of contents\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents component observable\n */\nexport function mountTableOfContents(\n el: HTMLElement, { viewport$, header$, target$ }: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n push$.subscribe(({ prev, next }) => {\n\n /* Look forward */\n for (const [anchor] of next) {\n anchor.classList.remove(\"md-nav__link--passed\")\n anchor.classList.remove(\"md-nav__link--active\")\n }\n\n /* Look backward */\n for (const [index, [anchor]] of prev.entries()) {\n anchor.classList.add(\"md-nav__link--passed\")\n anchor.classList.toggle(\n \"md-nav__link--active\",\n index === prev.length - 1\n )\n }\n })\n\n /* Set up following, if enabled */\n if (feature(\"toc.follow\")) {\n\n /* Toggle smooth scrolling only for anchor clicks */\n const smooth$ = merge(\n viewport$.pipe(debounceTime(1), map(() => undefined)),\n viewport$.pipe(debounceTime(250), map(() => \"smooth\" as const))\n )\n\n /* Bring active anchor into view */\n push$\n .pipe(\n filter(({ prev }) => prev.length > 0),\n withLatestFrom(smooth$)\n )\n .subscribe(([{ prev }, behavior]) => {\n const [anchor] = prev[prev.length - 1]\n if (anchor.offsetHeight) {\n\n /* Retrieve overflowing container and scroll */\n const container = getElementContainer(anchor)\n if (typeof container !== \"undefined\") {\n const offset = anchor.offsetTop - container.offsetTop\n const { height } = getElementSize(container)\n container.scrollTo({\n top: offset - height / 2,\n behavior\n })\n }\n }\n })\n }\n\n /* Set up anchor tracking, if enabled */\n if (feature(\"navigation.tracking\"))\n viewport$\n .pipe(\n takeUntil(done$),\n distinctUntilKeyChanged(\"offset\"),\n debounceTime(250),\n skip(1),\n takeUntil(target$.pipe(skip(1))),\n repeat({ delay: 250 }),\n withLatestFrom(push$)\n )\n .subscribe(([, { prev }]) => {\n const url = getLocation()\n\n /* Set hash fragment to active anchor */\n const anchor = prev[prev.length - 1]\n if (anchor && anchor.length) {\n const [active] = anchor\n const { hash } = new URL(active.href)\n if (url.hash !== hash) {\n url.hash = hash\n history.replaceState({}, \"\", `${url}`)\n }\n\n /* Reset anchor when at the top */\n } else {\n url.hash = \"\"\n history.replaceState({}, \"\", `${url}`)\n }\n })\n\n /* Create and return component */\n return watchTableOfContents(el, { viewport$, header$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatest,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n endWith,\n finalize,\n map,\n repeat,\n skip,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { Viewport } from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Back-to-top button\n */\nexport interface BackToTop {\n hidden: boolean /* Back-to-top button is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n main$: Observable

/* Main area observable */\n target$: Observable /* Location target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable

/* Header observable */\n main$: Observable

/* Main area observable */\n target$: Observable /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch back-to-top\n *\n * @param _el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top observable\n */\nexport function watchBackToTop(\n _el: HTMLElement, { viewport$, main$, target$ }: WatchOptions\n): Observable {\n\n /* Compute direction */\n const direction$ = viewport$\n .pipe(\n map(({ offset: { y } }) => y),\n bufferCount(2, 1),\n map(([a, b]) => a > b && b > 0),\n distinctUntilChanged()\n )\n\n /* Compute whether main area is active */\n const active$ = main$\n .pipe(\n map(({ active }) => active)\n )\n\n /* Compute threshold for hiding */\n return combineLatest([active$, direction$])\n .pipe(\n map(([active, direction]) => !(active && direction)),\n distinctUntilChanged(),\n takeUntil(target$.pipe(skip(1))),\n endWith(true),\n repeat({ delay: 250 }),\n map(hidden => ({ hidden }))\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount back-to-top\n *\n * @param el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top component observable\n */\nexport function mountBackToTop(\n el: HTMLElement, { viewport$, header$, main$, target$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n push$.subscribe({\n\n /* Handle emission */\n next({ hidden }) {\n el.hidden = hidden\n if (hidden) {\n el.setAttribute(\"tabindex\", \"-1\")\n el.blur()\n } else {\n el.removeAttribute(\"tabindex\")\n }\n },\n\n /* Handle complete */\n complete() {\n el.style.top = \"\"\n el.hidden = true\n el.removeAttribute(\"tabindex\")\n }\n })\n\n /* Watch header height */\n header$\n .pipe(\n takeUntil(done$),\n distinctUntilKeyChanged(\"height\")\n )\n .subscribe(({ height }) => {\n el.style.top = `${height + 16}px`\n })\n\n /* Create and return component */\n return watchBackToTop(el, { viewport$, main$, target$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n mergeMap,\n switchMap,\n takeWhile,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n document$: Observable /* Document observable */\n tablet$: Observable /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch indeterminate checkboxes\n *\n * This function replaces the indeterminate \"pseudo state\" with the actual\n * indeterminate state, which is used to keep navigation always expanded.\n *\n * @param options - Options\n */\nexport function patchIndeterminate(\n { document$, tablet$ }: PatchOptions\n): void {\n document$\n .pipe(\n switchMap(() => getElements(\n // @todo `data-md-state` is deprecated and removed in v9\n \".md-toggle--indeterminate, [data-md-state=indeterminate]\"\n )),\n tap(el => {\n el.indeterminate = true\n el.checked = false\n }),\n mergeMap(el => fromEvent(el, \"change\")\n .pipe(\n takeWhile(() => el.classList.contains(\"md-toggle--indeterminate\")),\n map(() => el)\n )\n ),\n withLatestFrom(tablet$)\n )\n .subscribe(([el, tablet]) => {\n el.classList.remove(\"md-toggle--indeterminate\")\n if (tablet)\n el.checked = false\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n filter,\n fromEvent,\n map,\n mergeMap,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n document$: Observable /* Document observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether the given device is an Apple device\n *\n * @returns Test result\n */\nfunction isAppleDevice(): boolean {\n return /(iPad|iPhone|iPod)/.test(navigator.userAgent)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch all elements with `data-md-scrollfix` attributes\n *\n * This is a year-old patch which ensures that overflow scrolling works at the\n * top and bottom of containers on iOS by ensuring a `1px` scroll offset upon\n * the start of a touch event.\n *\n * @see https://bit.ly/2SCtAOO - Original source\n *\n * @param options - Options\n */\nexport function patchScrollfix(\n { document$ }: PatchOptions\n): void {\n document$\n .pipe(\n switchMap(() => getElements(\"[data-md-scrollfix]\")),\n tap(el => el.removeAttribute(\"data-md-scrollfix\")),\n filter(isAppleDevice),\n mergeMap(el => fromEvent(el, \"touchstart\")\n .pipe(\n map(() => el)\n )\n )\n )\n .subscribe(el => {\n const top = el.scrollTop\n\n /* We're at the top of the container */\n if (top === 0) {\n el.scrollTop = 1\n\n /* We're at the bottom of the container */\n } else if (top + el.offsetHeight === el.scrollHeight) {\n el.scrollTop = top - 1\n }\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n delay,\n map,\n of,\n switchMap,\n withLatestFrom\n} from \"rxjs\"\n\nimport {\n Viewport,\n watchToggle\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n viewport$: Observable /* Viewport observable */\n tablet$: Observable /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch the document body to lock when search is open\n *\n * For mobile and tablet viewports, the search is rendered full screen, which\n * leads to scroll leaking when at the top or bottom of the search result. This\n * function locks the body when the search is in full screen mode, and restores\n * the scroll position when leaving.\n *\n * @param options - Options\n */\nexport function patchScrolllock(\n { viewport$, tablet$ }: PatchOptions\n): void {\n combineLatest([watchToggle(\"search\"), tablet$])\n .pipe(\n map(([active, tablet]) => active && !tablet),\n switchMap(active => of(active)\n .pipe(\n delay(active ? 400 : 100)\n )\n ),\n withLatestFrom(viewport$)\n )\n .subscribe(([active, { offset: { y }}]) => {\n if (active) {\n document.body.setAttribute(\"data-md-scrolllock\", \"\")\n document.body.style.top = `-${y}px`\n } else {\n const value = -1 * parseInt(document.body.style.top, 10)\n document.body.removeAttribute(\"data-md-scrolllock\")\n document.body.style.top = \"\"\n if (value)\n window.scrollTo(0, value)\n }\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n Object.entries = function (obj: object) {\n const data: [string, string][] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push([key, obj[key]])\n\n /* Return entries */\n return data\n }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n Object.values = function (obj: object) {\n const data: string[] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push(obj[key])\n\n /* Return values */\n return data\n }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n /* Polyfill `Element.scrollTo` */\n if (!Element.prototype.scrollTo)\n Element.prototype.scrollTo = function (\n x?: ScrollToOptions | number, y?: number\n ): void {\n if (typeof x === \"object\") {\n this.scrollLeft = x.left!\n this.scrollTop = x.top!\n } else {\n this.scrollLeft = x!\n this.scrollTop = y!\n }\n }\n\n /* Polyfill `Element.replaceWith` */\n if (!Element.prototype.replaceWith)\n Element.prototype.replaceWith = function (\n ...nodes: Array\n ): void {\n const parent = this.parentNode\n if (parent) {\n if (nodes.length === 0)\n parent.removeChild(this)\n\n /* Replace children and create text nodes */\n for (let i = nodes.length - 1; i >= 0; i--) {\n let node = nodes[i]\n if (typeof node === \"string\")\n node = document.createTextNode(node)\n else if (node.parentNode)\n node.parentNode.removeChild(node)\n\n /* Replace child or insert before previous sibling */\n if (!i)\n parent.replaceChild(node, this)\n else\n parent.insertBefore(this.previousSibling!, node)\n }\n }\n }\n}\n"], + "mappings": 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nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}}); \ No newline at end of file diff --git a/0.13/assets/javascripts/lunr/min/lunr.de.min.js b/0.13/assets/javascripts/lunr/min/lunr.de.min.js new file mode 100644 index 000000000..f3b5c108c --- /dev/null +++ b/0.13/assets/javascripts/lunr/min/lunr.de.min.js @@ -0,0 +1,18 @@ +/*! + * Lunr languages, `German` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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andere anderem anderen anderer anderes anderm andern anderr anders auch auf aus bei bin bis bist da damit dann das dasselbe dazu daß dein deine deinem deinen deiner deines dem demselben den denn denselben der derer derselbe derselben des desselben dessen dich die dies diese dieselbe dieselben diesem diesen dieser dieses dir doch dort du durch ein eine einem einen einer eines einig einige einigem einigen einiger einiges einmal er es etwas euch euer eure eurem euren eurer eures für gegen gewesen hab habe haben hat hatte hatten hier hin hinter ich ihm ihn ihnen ihr ihre ihrem ihren ihrer ihres im in indem ins ist jede jedem jeden jeder jedes jene jenem jenen jener jenes jetzt kann kein keine keinem keinen keiner keines können könnte machen man manche manchem manchen mancher manches mein meine meinem meinen meiner meines mich mir mit muss musste nach nicht nichts noch nun nur ob oder ohne sehr sein seine seinem seinen seiner seines selbst sich sie sind so solche solchem solchen solcher solches soll sollte sondern sonst um und uns unse unsem unsen unser unses unter viel vom von vor war waren warst was weg weil weiter welche welchem welchen welcher welches wenn werde werden wie wieder will wir wird wirst wo wollen wollte während würde würden zu zum zur zwar zwischen über".split(" ")),e.Pipeline.registerFunction(e.de.stopWordFilter,"stopWordFilter-de")}}); \ No newline at end of file diff --git a/0.13/assets/javascripts/lunr/min/lunr.du.min.js b/0.13/assets/javascripts/lunr/min/lunr.du.min.js new file mode 100644 index 000000000..49a0f3f0a --- /dev/null +++ b/0.13/assets/javascripts/lunr/min/lunr.du.min.js @@ -0,0 +1,18 @@ +/*! + * Lunr languages, `Dutch` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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+1,18 @@ +/*! + * Lunr languages, `Italian` language + * https://github.com/MihaiValentin/lunr-languages + * + * Copyright 2014, Mihai Valentin + * http://www.mozilla.org/MPL/ + */ +/*! + * based on + * Snowball JavaScript Library v0.3 + * http://code.google.com/p/urim/ + * http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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avevo avrai avranno avrebbe avrebbero avrei avremmo avremo avreste avresti avrete avrà avrò avuta avute avuti avuto c che chi ci coi col come con contro cui da dagl dagli dai dal dall dalla dalle dallo degl degli dei del dell della delle dello di dov dove e ebbe ebbero ebbi ed era erano eravamo eravate eri ero essendo faccia facciamo facciano facciate faccio facemmo facendo facesse facessero facessi facessimo faceste facesti faceva facevamo facevano facevate facevi facevo fai fanno farai faranno farebbe farebbero farei faremmo faremo fareste faresti farete farà farò fece fecero feci fosse fossero fossi fossimo foste fosti fu fui fummo furono gli ha hai hanno ho i il in io l la le lei li lo loro lui ma mi mia mie miei mio ne negl negli nei nel nell nella nelle nello noi non nostra nostre nostri nostro o per perché più quale quanta quante quanti quanto quella quelle quelli quello questa queste questi questo sarai saranno sarebbe sarebbero sarei saremmo saremo sareste saresti sarete sarà sarò se sei si sia siamo siano siate siete sono sta stai stando stanno starai staranno starebbe starebbero starei staremmo staremo stareste staresti starete starà starò stava stavamo stavano stavate stavi stavo stemmo stesse stessero stessi stessimo steste stesti stette stettero stetti stia stiamo stiano stiate sto su sua sue sugl sugli sui sul sull sulla sulle sullo suo suoi ti tra tu tua tue tuo tuoi tutti tutto un una uno vi voi vostra vostre vostri vostro è".split(" ")),e.Pipeline.registerFunction(e.it.stopWordFilter,"stopWordFilter-it")}}); \ No newline at end of file diff --git a/0.13/assets/javascripts/lunr/min/lunr.ja.min.js b/0.13/assets/javascripts/lunr/min/lunr.ja.min.js new file mode 100644 index 000000000..5f254ebe9 --- /dev/null +++ b/0.13/assets/javascripts/lunr/min/lunr.ja.min.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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* http://snowball.tartarus.org/ + * + * Copyright 2010, Oleg Mazko + * http://www.mozilla.org/MPL/ + */ + +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,!p()&&(Dr.cursor=Dr.limit-e,!f()&&(Dr.cursor=Dr.limit-e,!_())))return!1;if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,r=Dr.limit-Dr.cursor,a())Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()||(Dr.cursor=Dr.limit-i);else if(Dr.cursor=Dr.limit-r,!W())return!0;return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,K(),!0}function R(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,W())return Dr.bra=Dr.cursor,Dr.slice_del(),void K();if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,q())if(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-r,!m())){if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!W())return;if(Dr.bra=Dr.cursor,Dr.slice_del(),!K())return}Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}else 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e;this.setCurrent=function(r){Dr.setCurrent(r)},this.getCurrent=function(){return Dr.getCurrent()},this.stem=function(){return!!($()&&(Dr.limit_backward=Dr.cursor,Dr.cursor=Dr.limit,J(),Dr.cursor=Dr.limit,nr&&(R(),Dr.cursor=Dr.limit_backward,er())))}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.tr.stemmer,"stemmer-tr"),r.tr.stopWordFilter=r.generateStopWordFilter("acaba altmış altı ama ancak arada aslında ayrıca bana bazı belki ben benden beni benim beri beş bile bin bir biri birkaç birkez birçok birşey birşeyi biz bizden bize bizi bizim bu buna bunda bundan bunlar bunları bunların bunu bunun burada böyle böylece da daha dahi de defa değil diye diğer doksan dokuz dolayı dolayısıyla dört edecek eden ederek edilecek ediliyor edilmesi ediyor elli en etmesi etti ettiği ettiğini eğer gibi göre halen hangi hatta hem henüz hep hepsi her herhangi herkesin hiç hiçbir iki ile ilgili ise itibaren itibariyle için işte kadar karşın katrilyon kendi kendilerine kendini kendisi kendisine kendisini kez ki kim kimden kime kimi kimse kırk milyar milyon mu mü mı nasıl ne neden nedenle nerde nerede nereye niye niçin o olan olarak oldu olduklarını olduğu olduğunu olmadı olmadığı olmak olması olmayan olmaz olsa olsun olup olur olursa oluyor on ona ondan onlar onlardan onları onların onu onun otuz oysa pek rağmen sadece sanki sekiz seksen sen senden seni senin siz sizden sizi sizin tarafından trilyon tüm var vardı ve veya ya yani yapacak yapmak yaptı yaptıkları yaptığı yaptığını yapılan yapılması yapıyor yedi yerine yetmiş yine yirmi yoksa yüz zaten çok çünkü öyle üzere üç şey şeyden şeyi şeyler şu şuna şunda şundan şunları şunu şöyle".split(" ")),r.Pipeline.registerFunction(r.tr.stopWordFilter,"stopWordFilter-tr")}}); \ No newline at end of file diff --git a/0.13/assets/javascripts/lunr/min/lunr.vi.min.js b/0.13/assets/javascripts/lunr/min/lunr.vi.min.js new file mode 100644 index 000000000..22aed28c4 --- /dev/null +++ b/0.13/assets/javascripts/lunr/min/lunr.vi.min.js @@ -0,0 +1 @@ +!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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Register as an anonymous module. + define(factory) + } else if (typeof exports === 'object') { + /** + * Node. 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+ + return this; + } + TinySegmenter.prototype.ctype_ = function(str) { + for (var i in this.chartype_) { + if (str.match(this.chartype_[i][0])) { + return this.chartype_[i][1]; + } + } + return "O"; + } + + TinySegmenter.prototype.ts_ = function(v) { + if (v) { return v; } + return 0; + } + + TinySegmenter.prototype.segment = function(input) { + if (input == null || input == undefined || input == "") { + return []; + } + var result = []; + var seg = ["B3","B2","B1"]; + var ctype = ["O","O","O"]; + var o = input.split(""); + for (i = 0; i < o.length; ++i) { + seg.push(o[i]); + ctype.push(this.ctype_(o[i])) + } + seg.push("E1"); + seg.push("E2"); + seg.push("E3"); + ctype.push("O"); + ctype.push("O"); + ctype.push("O"); + var word = seg[3]; + var p1 = "U"; + var p2 = "U"; + var p3 = "U"; + for (var i = 4; i < seg.length - 3; ++i) { + var score = this.BIAS__; + var w1 = seg[i-3]; + var w2 = seg[i-2]; + var w3 = seg[i-1]; + var w4 = seg[i]; + var w5 = seg[i+1]; + var w6 = seg[i+2]; + var c1 = ctype[i-3]; + var c2 = ctype[i-2]; + var c3 = ctype[i-1]; + var c4 = ctype[i]; + var c5 = ctype[i+1]; + var c6 = ctype[i+2]; + score += this.ts_(this.UP1__[p1]); + score += this.ts_(this.UP2__[p2]); + score += this.ts_(this.UP3__[p3]); + score += this.ts_(this.BP1__[p1 + p2]); + score += this.ts_(this.BP2__[p2 + p3]); + score += this.ts_(this.UW1__[w1]); + score += this.ts_(this.UW2__[w2]); + score += this.ts_(this.UW3__[w3]); + score += this.ts_(this.UW4__[w4]); + score += this.ts_(this.UW5__[w5]); + score += this.ts_(this.UW6__[w6]); + score += this.ts_(this.BW1__[w2 + w3]); + score += this.ts_(this.BW2__[w3 + w4]); + score += this.ts_(this.BW3__[w4 + w5]); + score += this.ts_(this.TW1__[w1 + w2 + w3]); + score += this.ts_(this.TW2__[w2 + w3 + w4]); + score += this.ts_(this.TW3__[w3 + w4 + w5]); + score += this.ts_(this.TW4__[w4 + w5 + w6]); + score += this.ts_(this.UC1__[c1]); + score += this.ts_(this.UC2__[c2]); + score += this.ts_(this.UC3__[c3]); + score += this.ts_(this.UC4__[c4]); + score += this.ts_(this.UC5__[c5]); + score += this.ts_(this.UC6__[c6]); + score += this.ts_(this.BC1__[c2 + c3]); + score += this.ts_(this.BC2__[c3 + c4]); + score += this.ts_(this.BC3__[c4 + c5]); + score += this.ts_(this.TC1__[c1 + c2 + c3]); + score += this.ts_(this.TC2__[c2 + c3 + c4]); + score += this.ts_(this.TC3__[c3 + c4 + c5]); + score += this.ts_(this.TC4__[c4 + c5 + c6]); + // score += this.ts_(this.TC5__[c4 + c5 + c6]); + score += this.ts_(this.UQ1__[p1 + c1]); + score += this.ts_(this.UQ2__[p2 + c2]); + score += this.ts_(this.UQ3__[p3 + c3]); + score += this.ts_(this.BQ1__[p2 + c2 + c3]); + score += this.ts_(this.BQ2__[p2 + c3 + c4]); + score += this.ts_(this.BQ3__[p3 + c2 + c3]); + score += this.ts_(this.BQ4__[p3 + c3 + c4]); + score += this.ts_(this.TQ1__[p2 + c1 + c2 + c3]); + score += this.ts_(this.TQ2__[p2 + c2 + c3 + c4]); + score += this.ts_(this.TQ3__[p3 + c1 + c2 + c3]); + score += this.ts_(this.TQ4__[p3 + c2 + c3 + c4]); + var p = "O"; + if (score > 0) { + result.push(word); + word = ""; + p = "B"; + } + p1 = p2; + p2 = p3; + p3 = p; + word += seg[i]; + } + result.push(word); + + return result; + } + + lunr.TinySegmenter = TinySegmenter; + }; + +})); \ No newline at end of file diff --git a/0.13/assets/javascripts/lunr/wordcut.js b/0.13/assets/javascripts/lunr/wordcut.js new file mode 100644 index 000000000..146f4b44b --- /dev/null +++ b/0.13/assets/javascripts/lunr/wordcut.js @@ -0,0 +1,6708 @@ +(function(f){if(typeof exports==="object"&&typeof module!=="undefined"){module.exports=f()}else if(typeof define==="function"&&define.amd){define([],f)}else{var g;if(typeof window!=="undefined"){g=window}else if(typeof global!=="undefined"){g=global}else if(typeof self!=="undefined"){g=self}else{g=this}(g.lunr || (g.lunr = {})).wordcut = f()}})(function(){var define,module,exports;return (function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o 1; + }) + this.addWords(words, false) + } + if(finalize){ + this.finalizeDict(); + } + }, + + dictSeek: function (l, r, ch, strOffset, pos) { + var ans = null; + while (l <= r) { + var m = Math.floor((l + r) / 2), + dict_item = this.dict[m], + len = dict_item.length; + if (len <= strOffset) { + l = m + 1; + } else { + var ch_ = dict_item[strOffset]; + if (ch_ < ch) { + l = m + 1; + } else if (ch_ > ch) { + r = m - 1; + } else { + ans = m; + if (pos == LEFT) { + r = m - 1; + } else { + l = m + 1; + } + } + } + } + return ans; + }, + + isFinal: function (acceptor) { + return this.dict[acceptor.l].length == acceptor.strOffset; + }, + + createAcceptor: function () { + return { + l: 0, + r: this.dict.length - 1, + strOffset: 0, + isFinal: false, + dict: this, + transit: function (ch) { + return this.dict.transit(this, ch); + }, + isError: false, + tag: "DICT", + w: 1, + type: "DICT" + }; + }, + + transit: function (acceptor, ch) { + var l = this.dictSeek(acceptor.l, + acceptor.r, + ch, + acceptor.strOffset, + LEFT); + if (l !== null) { + var r = this.dictSeek(l, + acceptor.r, + ch, + acceptor.strOffset, + RIGHT); + acceptor.l = l; + acceptor.r = r; + acceptor.strOffset++; + acceptor.isFinal = this.isFinal(acceptor); + } else { + acceptor.isError = true; + } + return acceptor; + }, + + sortuniq: function(a){ + return a.sort().filter(function(item, pos, arr){ + return !pos || item != arr[pos - 1]; + }) + }, + + flatten: function(a){ + //[[1,2],[3]] -> [1,2,3] + return [].concat.apply([], a); + } +}; +module.exports = WordcutDict; + +}).call(this,"/dist/tmp") +},{"glob":16,"path":22}],3:[function(require,module,exports){ +var WordRule = { + createAcceptor: function(tag) { + if (tag["WORD_RULE"]) + return null; + + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + var lch = ch.toLowerCase(); + if (lch >= "a" && lch <= "z") { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "WORD_RULE", + type: "WORD_RULE", + w: 1}; + } +}; + +var NumberRule = { + createAcceptor: function(tag) { + if (tag["NUMBER_RULE"]) + return null; + + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (ch >= "0" && ch <= "9") { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "NUMBER_RULE", + type: "NUMBER_RULE", + w: 1}; + } +}; + +var SpaceRule = { + tag: "SPACE_RULE", + createAcceptor: function(tag) { + + if (tag["SPACE_RULE"]) + return null; + + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (ch == " " || ch == "\t" || ch == "\r" || ch == "\n" || + ch == "\u00A0" || ch=="\u2003"//nbsp and emsp + ) { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: SpaceRule.tag, + w: 1, + type: "SPACE_RULE"}; + } +} + +var SingleSymbolRule = { + tag: "SINSYM", + createAcceptor: function(tag) { + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (this.strOffset == 0 && ch.match(/^[\@\/\,\-\."`]$/)) { + this.isFinal = true; + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "SINSYM", + w: 1, + type: "SINSYM"}; + } +} + + +var LatinRules = [WordRule, SpaceRule, SingleSymbolRule, NumberRule]; + +module.exports = LatinRules; + +},{}],4:[function(require,module,exports){ +var _ = require("underscore") + , WordcutCore = require("./wordcut_core"); +var PathInfoBuilder = { + + /* + buildByPartAcceptors: function(path, acceptors, i) { + var + var genInfos = partAcceptors.reduce(function(genInfos, acceptor) { + + }, []); + + return genInfos; + } + */ + + buildByAcceptors: function(path, finalAcceptors, i) { + var self = this; + var infos = finalAcceptors.map(function(acceptor) { + var p = i - acceptor.strOffset + 1 + , _info = path[p]; + + var info = {p: p, + mw: _info.mw + (acceptor.mw === undefined ? 0 : acceptor.mw), + w: acceptor.w + _info.w, + unk: (acceptor.unk ? acceptor.unk : 0) + _info.unk, + type: acceptor.type}; + + if (acceptor.type == "PART") { + for(var j = p + 1; j <= i; j++) { + path[j].merge = p; + } + info.merge = p; + } + + return info; + }); + return infos.filter(function(info) { return info; }); + }, + + fallback: function(path, leftBoundary, text, i) { + var _info = path[leftBoundary]; + if (text[i].match(/[\u0E48-\u0E4E]/)) { + if (leftBoundary != 0) + leftBoundary = path[leftBoundary].p; + return {p: leftBoundary, + mw: 0, + w: 1 + _info.w, + unk: 1 + _info.unk, + type: "UNK"}; +/* } else if(leftBoundary > 0 && path[leftBoundary].type !== "UNK") { + leftBoundary = path[leftBoundary].p; + return {p: leftBoundary, + w: 1 + _info.w, + unk: 1 + _info.unk, + type: "UNK"}; */ + } else { + return {p: leftBoundary, + mw: _info.mw, + w: 1 + _info.w, + unk: 1 + _info.unk, + type: "UNK"}; + } + }, + + build: function(path, finalAcceptors, i, leftBoundary, text) { + var basicPathInfos = this.buildByAcceptors(path, finalAcceptors, i); + if (basicPathInfos.length > 0) { + return basicPathInfos; + } else { + return [this.fallback(path, leftBoundary, text, i)]; + } + } +}; + +module.exports = function() { + return _.clone(PathInfoBuilder); +} + +},{"./wordcut_core":8,"underscore":25}],5:[function(require,module,exports){ +var _ = require("underscore"); + + +var PathSelector = { + selectPath: function(paths) { + var path = paths.reduce(function(selectedPath, path) { + if (selectedPath == null) { + return path; + } else { + if (path.unk < selectedPath.unk) + return path; + if (path.unk == selectedPath.unk) { + if (path.mw < selectedPath.mw) + return path + if (path.mw == selectedPath.mw) { + if (path.w < selectedPath.w) + return path; + } + } + return selectedPath; + } + }, null); + return path; + }, + + createPath: function() { + return [{p:null, w:0, unk:0, type: "INIT", mw:0}]; + } +}; + +module.exports = function() { + return _.clone(PathSelector); +}; + +},{"underscore":25}],6:[function(require,module,exports){ +function isMatch(pat, offset, ch) { + if (pat.length <= offset) + return false; + var _ch = pat[offset]; + return _ch == ch || + (_ch.match(/[กข]/) && ch.match(/[ก-ฮ]/)) || + (_ch.match(/[มบ]/) && ch.match(/[ก-ฮ]/)) || + (_ch.match(/\u0E49/) && ch.match(/[\u0E48-\u0E4B]/)); +} + +var Rule0 = { + pat: "เหก็ม", + createAcceptor: function(tag) { + return {strOffset: 0, + isFinal: false, + transit: function(ch) { + if (isMatch(Rule0.pat, this.strOffset,ch)) { + this.isFinal = (this.strOffset + 1 == Rule0.pat.length); + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "THAI_RULE", + type: "THAI_RULE", + w: 1}; + } +}; + +var PartRule = { + createAcceptor: function(tag) { + return {strOffset: 0, + patterns: [ + "แก", "เก", "ก้", "กก์", "กา", "กี", "กิ", "กืก" + ], + isFinal: false, + transit: function(ch) { + var offset = this.strOffset; + this.patterns = this.patterns.filter(function(pat) { + return isMatch(pat, offset, ch); + }); + + if (this.patterns.length > 0) { + var len = 1 + offset; + this.isFinal = this.patterns.some(function(pat) { + return pat.length == len; + }); + this.strOffset++; + } else { + this.isError = true; + } + return this; + }, + isError: false, + tag: "PART", + type: "PART", + unk: 1, + w: 1}; + } +}; + +var ThaiRules = [Rule0, PartRule]; + +module.exports = ThaiRules; + +},{}],7:[function(require,module,exports){ +var sys = require("sys") + , WordcutDict = require("./dict") + , WordcutCore = require("./wordcut_core") + , PathInfoBuilder = require("./path_info_builder") + , PathSelector = require("./path_selector") + , Acceptors = require("./acceptors") + , latinRules = require("./latin_rules") + , thaiRules = require("./thai_rules") + , _ = require("underscore"); + + +var Wordcut = Object.create(WordcutCore); +Wordcut.defaultPathInfoBuilder = PathInfoBuilder; +Wordcut.defaultPathSelector = PathSelector; +Wordcut.defaultAcceptors = Acceptors; +Wordcut.defaultLatinRules = latinRules; +Wordcut.defaultThaiRules = thaiRules; +Wordcut.defaultDict = WordcutDict; + + +Wordcut.initNoDict = function(dict_path) { + var self = this; + self.pathInfoBuilder = new self.defaultPathInfoBuilder; + self.pathSelector = new self.defaultPathSelector; + self.acceptors = new self.defaultAcceptors; + self.defaultLatinRules.forEach(function(rule) { + self.acceptors.creators.push(rule); + }); + self.defaultThaiRules.forEach(function(rule) { + self.acceptors.creators.push(rule); + }); +}; + +Wordcut.init = function(dict_path, withDefault, additionalWords) { + withDefault = withDefault || false; + this.initNoDict(); + var dict = _.clone(this.defaultDict); + dict.init(dict_path, withDefault, additionalWords); + this.acceptors.creators.push(dict); +}; + +module.exports = Wordcut; + +},{"./acceptors":1,"./dict":2,"./latin_rules":3,"./path_info_builder":4,"./path_selector":5,"./thai_rules":6,"./wordcut_core":8,"sys":28,"underscore":25}],8:[function(require,module,exports){ +var WordcutCore = { + + buildPath: function(text) { + var self = this + , path = self.pathSelector.createPath() + , leftBoundary = 0; + self.acceptors.reset(); + for (var i = 0; i < text.length; i++) { + var ch = text[i]; + self.acceptors.transit(ch); + + var possiblePathInfos = self + .pathInfoBuilder + .build(path, + self.acceptors.getFinalAcceptors(), + i, + leftBoundary, + text); + var selectedPath = self.pathSelector.selectPath(possiblePathInfos) + + path.push(selectedPath); + if (selectedPath.type !== "UNK") { + leftBoundary = i; + } + } + return path; + }, + + pathToRanges: function(path) { + var e = path.length - 1 + , ranges = []; + + while (e > 0) { + var info = path[e] + , s = info.p; + + if (info.merge !== undefined && ranges.length > 0) { + var r = ranges[ranges.length - 1]; + r.s = info.merge; + s = r.s; + } else { + ranges.push({s:s, e:e}); + } + e = s; + } + return ranges.reverse(); + }, + + rangesToText: function(text, ranges, delimiter) { + return ranges.map(function(r) { + return text.substring(r.s, r.e); + }).join(delimiter); + }, + + cut: function(text, delimiter) { + var path = this.buildPath(text) + , ranges = this.pathToRanges(path); + return this + .rangesToText(text, ranges, + (delimiter === undefined ? "|" : delimiter)); + }, + + cutIntoRanges: function(text, noText) { + var path = this.buildPath(text) + , ranges = this.pathToRanges(path); + + if (!noText) { + ranges.forEach(function(r) { + r.text = text.substring(r.s, r.e); + }); + } + return ranges; + }, + + cutIntoArray: function(text) { + var path = this.buildPath(text) + , ranges = this.pathToRanges(path); + + return ranges.map(function(r) { + return text.substring(r.s, r.e) + }); + } +}; + +module.exports = WordcutCore; + +},{}],9:[function(require,module,exports){ +// http://wiki.commonjs.org/wiki/Unit_Testing/1.0 +// +// THIS IS NOT TESTED NOR LIKELY TO WORK OUTSIDE V8! +// +// Originally from narwhal.js (http://narwhaljs.org) +// Copyright (c) 2009 Thomas Robinson <280north.com> +// +// Permission is hereby granted, free of charge, to any person obtaining a copy +// of this software and associated documentation files (the 'Software'), to +// deal in the Software without restriction, including without limitation the +// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or +// sell copies of the Software, and to permit persons to whom the Software is +// furnished to do so, subject to the following conditions: +// +// The above copyright notice and this permission notice shall be included in +// all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +// AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN +// ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +// when used in node, this will actually load the util module we depend on +// versus loading the builtin util module as happens otherwise +// this is a bug in node module loading as far as I am concerned +var util = require('util/'); + +var pSlice = Array.prototype.slice; +var hasOwn = Object.prototype.hasOwnProperty; + +// 1. The assert module provides functions that throw +// AssertionError's when particular conditions are not met. The +// assert module must conform to the following interface. + +var assert = module.exports = ok; + +// 2. The AssertionError is defined in assert. +// new assert.AssertionError({ message: message, +// actual: actual, +// expected: expected }) + +assert.AssertionError = function AssertionError(options) { + this.name = 'AssertionError'; + this.actual = options.actual; + this.expected = options.expected; + this.operator = options.operator; + if (options.message) { + this.message = options.message; + this.generatedMessage = false; + } else { + this.message = getMessage(this); + this.generatedMessage = true; + } + var stackStartFunction = options.stackStartFunction || fail; + + if (Error.captureStackTrace) { + Error.captureStackTrace(this, stackStartFunction); + } + else { + // non v8 browsers so we can have a stacktrace + var err = new Error(); + if (err.stack) { + var out = err.stack; + + // try to strip useless frames + var fn_name = stackStartFunction.name; + var idx = out.indexOf('\n' + fn_name); + if (idx >= 0) { + // once we have located the function frame + // we need to strip out everything before it (and its line) + var next_line = out.indexOf('\n', idx + 1); + out = out.substring(next_line + 1); + } + + this.stack = out; + } + } +}; + +// assert.AssertionError instanceof Error +util.inherits(assert.AssertionError, Error); + +function replacer(key, value) { + if (util.isUndefined(value)) { + return '' + value; + } + if (util.isNumber(value) && !isFinite(value)) { + return value.toString(); + } + if (util.isFunction(value) || util.isRegExp(value)) { + return value.toString(); + } + return value; +} + +function truncate(s, n) { + if (util.isString(s)) { + return s.length < n ? s : s.slice(0, n); + } else { + return s; + } +} + +function getMessage(self) { + return truncate(JSON.stringify(self.actual, replacer), 128) + ' ' + + self.operator + ' ' + + truncate(JSON.stringify(self.expected, replacer), 128); +} + +// At present only the three keys mentioned above are used and +// understood by the spec. Implementations or sub modules can pass +// other keys to the AssertionError's constructor - they will be +// ignored. + +// 3. All of the following functions must throw an AssertionError +// when a corresponding condition is not met, with a message that +// may be undefined if not provided. All assertion methods provide +// both the actual and expected values to the assertion error for +// display purposes. + +function fail(actual, expected, message, operator, stackStartFunction) { + throw new assert.AssertionError({ + message: message, + actual: actual, + expected: expected, + operator: operator, + stackStartFunction: stackStartFunction + }); +} + +// EXTENSION! allows for well behaved errors defined elsewhere. +assert.fail = fail; + +// 4. Pure assertion tests whether a value is truthy, as determined +// by !!guard. +// assert.ok(guard, message_opt); +// This statement is equivalent to assert.equal(true, !!guard, +// message_opt);. To test strictly for the value true, use +// assert.strictEqual(true, guard, message_opt);. + +function ok(value, message) { + if (!value) fail(value, true, message, '==', assert.ok); +} +assert.ok = ok; + +// 5. The equality assertion tests shallow, coercive equality with +// ==. +// assert.equal(actual, expected, message_opt); + +assert.equal = function equal(actual, expected, message) { + if (actual != expected) fail(actual, expected, message, '==', assert.equal); +}; + +// 6. The non-equality assertion tests for whether two objects are not equal +// with != assert.notEqual(actual, expected, message_opt); + +assert.notEqual = function notEqual(actual, expected, message) { + if (actual == expected) { + fail(actual, expected, message, '!=', assert.notEqual); + } +}; + +// 7. The equivalence assertion tests a deep equality relation. +// assert.deepEqual(actual, expected, message_opt); + +assert.deepEqual = function deepEqual(actual, expected, message) { + if (!_deepEqual(actual, expected)) { + fail(actual, expected, message, 'deepEqual', assert.deepEqual); + } +}; + +function _deepEqual(actual, expected) { + // 7.1. All identical values are equivalent, as determined by ===. + if (actual === expected) { + return true; + + } else if (util.isBuffer(actual) && util.isBuffer(expected)) { + if (actual.length != expected.length) return false; + + for (var i = 0; i < actual.length; i++) { + if (actual[i] !== expected[i]) return false; + } + + return true; + + // 7.2. If the expected value is a Date object, the actual value is + // equivalent if it is also a Date object that refers to the same time. + } else if (util.isDate(actual) && util.isDate(expected)) { + return actual.getTime() === expected.getTime(); + + // 7.3 If the expected value is a RegExp object, the actual value is + // equivalent if it is also a RegExp object with the same source and + // properties (`global`, `multiline`, `lastIndex`, `ignoreCase`). + } else if (util.isRegExp(actual) && util.isRegExp(expected)) { + return actual.source === expected.source && + actual.global === expected.global && + actual.multiline === expected.multiline && + actual.lastIndex === expected.lastIndex && + actual.ignoreCase === expected.ignoreCase; + + // 7.4. Other pairs that do not both pass typeof value == 'object', + // equivalence is determined by ==. + } else if (!util.isObject(actual) && !util.isObject(expected)) { + return actual == expected; + + // 7.5 For all other Object pairs, including Array objects, equivalence is + // determined by having the same number of owned properties (as verified + // with Object.prototype.hasOwnProperty.call), the same set of keys + // (although not necessarily the same order), equivalent values for every + // corresponding key, and an identical 'prototype' property. Note: this + // accounts for both named and indexed properties on Arrays. + } else { + return objEquiv(actual, expected); + } +} + +function isArguments(object) { + return Object.prototype.toString.call(object) == '[object Arguments]'; +} + +function objEquiv(a, b) { + if (util.isNullOrUndefined(a) || util.isNullOrUndefined(b)) + return false; + // an identical 'prototype' property. + if (a.prototype !== b.prototype) return false; + // if one is a primitive, the other must be same + if (util.isPrimitive(a) || util.isPrimitive(b)) { + return a === b; + } + var aIsArgs = isArguments(a), + bIsArgs = isArguments(b); + if ((aIsArgs && !bIsArgs) || (!aIsArgs && bIsArgs)) + return false; + if (aIsArgs) { + a = pSlice.call(a); + b = pSlice.call(b); + return _deepEqual(a, b); + } + var ka = objectKeys(a), + kb = objectKeys(b), + key, i; + // having the same number of owned properties (keys incorporates + // hasOwnProperty) + if (ka.length != kb.length) + return false; + //the same set of keys (although not necessarily the same order), + ka.sort(); + kb.sort(); + //~~~cheap key test + for (i = ka.length - 1; i >= 0; i--) { + if (ka[i] != kb[i]) + return false; + } + //equivalent values for every corresponding key, and + //~~~possibly expensive deep test + for (i = ka.length - 1; i >= 0; i--) { + key = ka[i]; + if (!_deepEqual(a[key], b[key])) return false; + } + return true; +} + +// 8. The non-equivalence assertion tests for any deep inequality. +// assert.notDeepEqual(actual, expected, message_opt); + +assert.notDeepEqual = function notDeepEqual(actual, expected, message) { + if (_deepEqual(actual, expected)) { + fail(actual, expected, message, 'notDeepEqual', assert.notDeepEqual); + } +}; + +// 9. The strict equality assertion tests strict equality, as determined by ===. +// assert.strictEqual(actual, expected, message_opt); + +assert.strictEqual = function strictEqual(actual, expected, message) { + if (actual !== expected) { + fail(actual, expected, message, '===', assert.strictEqual); + } +}; + +// 10. The strict non-equality assertion tests for strict inequality, as +// determined by !==. assert.notStrictEqual(actual, expected, message_opt); + +assert.notStrictEqual = function notStrictEqual(actual, expected, message) { + if (actual === expected) { + fail(actual, expected, message, '!==', assert.notStrictEqual); + } +}; + +function expectedException(actual, expected) { + if (!actual || !expected) { + return false; + } + + if (Object.prototype.toString.call(expected) == '[object RegExp]') { + return expected.test(actual); + } else if (actual instanceof expected) { + return true; + } else if (expected.call({}, actual) === true) { + return true; + } + + return false; +} + +function _throws(shouldThrow, block, expected, message) { + var actual; + + if (util.isString(expected)) { + message = expected; + expected = null; + } + + try { + block(); + } catch (e) { + actual = e; + } + + message = (expected && expected.name ? ' (' + expected.name + ').' : '.') + + (message ? ' ' + message : '.'); + + if (shouldThrow && !actual) { + fail(actual, expected, 'Missing expected exception' + message); + } + + if (!shouldThrow && expectedException(actual, expected)) { + fail(actual, expected, 'Got unwanted exception' + message); + } + + if ((shouldThrow && actual && expected && + !expectedException(actual, expected)) || (!shouldThrow && actual)) { + throw actual; + } +} + +// 11. Expected to throw an error: +// assert.throws(block, Error_opt, message_opt); + +assert.throws = function(block, /*optional*/error, /*optional*/message) { + _throws.apply(this, [true].concat(pSlice.call(arguments))); +}; + +// EXTENSION! This is annoying to write outside this module. +assert.doesNotThrow = function(block, /*optional*/message) { + _throws.apply(this, [false].concat(pSlice.call(arguments))); +}; + +assert.ifError = function(err) { if (err) {throw err;}}; + +var objectKeys = Object.keys || function (obj) { + var keys = []; + for (var key in obj) { + if (hasOwn.call(obj, key)) keys.push(key); + } + return keys; +}; + +},{"util/":28}],10:[function(require,module,exports){ +'use strict'; +module.exports = balanced; +function balanced(a, b, str) { + if (a instanceof RegExp) a = maybeMatch(a, str); + if (b instanceof RegExp) b = maybeMatch(b, str); + + var r = range(a, b, str); + + return r && { + start: r[0], + end: r[1], + pre: str.slice(0, r[0]), + body: str.slice(r[0] + a.length, r[1]), + post: str.slice(r[1] + b.length) + }; +} + +function maybeMatch(reg, str) { + var m = str.match(reg); + return m ? m[0] : null; +} + +balanced.range = range; +function range(a, b, str) { + var begs, beg, left, right, result; + var ai = str.indexOf(a); + var bi = str.indexOf(b, ai + 1); + var i = ai; + + if (ai >= 0 && bi > 0) { + begs = []; + left = str.length; + + while (i >= 0 && !result) { + if (i == ai) { + begs.push(i); + ai = str.indexOf(a, i + 1); + } else if (begs.length == 1) { + result = [ begs.pop(), bi ]; + } else { + beg = begs.pop(); + if (beg < left) { + left = beg; + right = bi; + } + + bi = str.indexOf(b, i + 1); + } + + i = ai < bi && ai >= 0 ? ai : bi; + } + + if (begs.length) { + result = [ left, right ]; + } + } + + return result; +} + +},{}],11:[function(require,module,exports){ +var concatMap = require('concat-map'); +var balanced = require('balanced-match'); + +module.exports = expandTop; + +var escSlash = '\0SLASH'+Math.random()+'\0'; +var escOpen = '\0OPEN'+Math.random()+'\0'; +var escClose = '\0CLOSE'+Math.random()+'\0'; +var escComma = '\0COMMA'+Math.random()+'\0'; +var escPeriod = '\0PERIOD'+Math.random()+'\0'; + +function numeric(str) { + return parseInt(str, 10) == str + ? parseInt(str, 10) + : str.charCodeAt(0); +} + +function escapeBraces(str) { + return str.split('\\\\').join(escSlash) + .split('\\{').join(escOpen) + .split('\\}').join(escClose) + .split('\\,').join(escComma) + .split('\\.').join(escPeriod); +} + +function unescapeBraces(str) { + return str.split(escSlash).join('\\') + .split(escOpen).join('{') + .split(escClose).join('}') + .split(escComma).join(',') + .split(escPeriod).join('.'); +} + + +// Basically just str.split(","), but handling cases +// where we have nested braced sections, which should be +// treated as individual members, like {a,{b,c},d} +function parseCommaParts(str) { + if (!str) + return ['']; + + var parts = []; + var m = balanced('{', '}', str); + + if (!m) + return str.split(','); + + var pre = m.pre; + var body = m.body; + var post = m.post; + var p = pre.split(','); + + p[p.length-1] += '{' + body + '}'; + var postParts = parseCommaParts(post); + if (post.length) { + p[p.length-1] += postParts.shift(); + p.push.apply(p, postParts); + } + + parts.push.apply(parts, p); + + return parts; +} + +function expandTop(str) { + if (!str) + return []; + + // I don't know why Bash 4.3 does this, but it does. + // Anything starting with {} will have the first two bytes preserved + // but *only* at the top level, so {},a}b will not expand to anything, + // but a{},b}c will be expanded to [a}c,abc]. + // One could argue that this is a bug in Bash, but since the goal of + // this module is to match Bash's rules, we escape a leading {} + if (str.substr(0, 2) === '{}') { + str = '\\{\\}' + str.substr(2); + } + + return expand(escapeBraces(str), true).map(unescapeBraces); +} + +function identity(e) { + return e; +} + +function embrace(str) { + return '{' + str + '}'; +} +function isPadded(el) { + return /^-?0\d/.test(el); +} + +function lte(i, y) { + return i <= y; +} +function gte(i, y) { + return i >= y; +} + +function expand(str, isTop) { + var expansions = []; + + var m = balanced('{', '}', str); + if (!m || /\$$/.test(m.pre)) return [str]; + + var isNumericSequence = /^-?\d+\.\.-?\d+(?:\.\.-?\d+)?$/.test(m.body); + var isAlphaSequence = /^[a-zA-Z]\.\.[a-zA-Z](?:\.\.-?\d+)?$/.test(m.body); + var isSequence = isNumericSequence || isAlphaSequence; + var isOptions = m.body.indexOf(',') >= 0; + if (!isSequence && !isOptions) { + // {a},b} + if (m.post.match(/,.*\}/)) { + str = m.pre + '{' + m.body + escClose + m.post; + return expand(str); + } + return [str]; + } + + var n; + if (isSequence) { + n = m.body.split(/\.\./); + } else { + n = parseCommaParts(m.body); + if (n.length === 1) { + // x{{a,b}}y ==> x{a}y x{b}y + n = expand(n[0], false).map(embrace); + if (n.length === 1) { + var post = m.post.length + ? expand(m.post, false) + : ['']; + return post.map(function(p) { + return m.pre + n[0] + p; + }); + } + } + } + + // at this point, n is the parts, and we know it's not a comma set + // with a single entry. + + // no need to expand pre, since it is guaranteed to be free of brace-sets + var pre = m.pre; + var post = m.post.length + ? expand(m.post, false) + : ['']; + + var N; + + if (isSequence) { + var x = numeric(n[0]); + var y = numeric(n[1]); + var width = Math.max(n[0].length, n[1].length) + var incr = n.length == 3 + ? Math.abs(numeric(n[2])) + : 1; + var test = lte; + var reverse = y < x; + if (reverse) { + incr *= -1; + test = gte; + } + var pad = n.some(isPadded); + + N = []; + + for (var i = x; test(i, y); i += incr) { + var c; + if (isAlphaSequence) { + c = String.fromCharCode(i); + if (c === '\\') + c = ''; + } else { + c = String(i); + if (pad) { + var need = width - c.length; + if (need > 0) { + var z = new Array(need + 1).join('0'); + if (i < 0) + c = '-' + z + c.slice(1); + else + c = z + c; + } + } + } + N.push(c); + } + } else { + N = concatMap(n, function(el) { return expand(el, false) }); + } + + for (var j = 0; j < N.length; j++) { + for (var k = 0; k < post.length; k++) { + var expansion = pre + N[j] + post[k]; + if (!isTop || isSequence || expansion) + expansions.push(expansion); + } + } + + return expansions; +} + + +},{"balanced-match":10,"concat-map":13}],12:[function(require,module,exports){ + +},{}],13:[function(require,module,exports){ +module.exports = function (xs, fn) { + var res = []; + for (var i = 0; i < xs.length; i++) { + var x = fn(xs[i], i); + if (isArray(x)) res.push.apply(res, x); + else res.push(x); + } + return res; +}; + +var isArray = Array.isArray || function (xs) { + return Object.prototype.toString.call(xs) === '[object Array]'; +}; + +},{}],14:[function(require,module,exports){ +// Copyright Joyent, Inc. and other Node contributors. +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the +// "Software"), to deal in the Software without restriction, including +// without limitation the rights to use, copy, modify, merge, publish, +// distribute, sublicense, and/or sell copies of the Software, and to permit +// persons to whom the Software is furnished to do so, subject to the +// following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN +// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +// USE OR OTHER DEALINGS IN THE SOFTWARE. + +function EventEmitter() { + this._events = this._events || {}; + this._maxListeners = this._maxListeners || undefined; +} +module.exports = EventEmitter; + +// Backwards-compat with node 0.10.x +EventEmitter.EventEmitter = EventEmitter; + +EventEmitter.prototype._events = undefined; +EventEmitter.prototype._maxListeners = undefined; + +// By default EventEmitters will print a warning if more than 10 listeners are +// added to it. This is a useful default which helps finding memory leaks. +EventEmitter.defaultMaxListeners = 10; + +// Obviously not all Emitters should be limited to 10. This function allows +// that to be increased. Set to zero for unlimited. +EventEmitter.prototype.setMaxListeners = function(n) { + if (!isNumber(n) || n < 0 || isNaN(n)) + throw TypeError('n must be a positive number'); + this._maxListeners = n; + return this; +}; + +EventEmitter.prototype.emit = function(type) { + var er, handler, len, args, i, listeners; + + if (!this._events) + this._events = {}; + + // If there is no 'error' event listener then throw. + if (type === 'error') { + if (!this._events.error || + (isObject(this._events.error) && !this._events.error.length)) { + er = arguments[1]; + if (er instanceof Error) { + throw er; // Unhandled 'error' event + } + throw TypeError('Uncaught, unspecified "error" event.'); + } + } + + handler = this._events[type]; + + if (isUndefined(handler)) + return false; + + if (isFunction(handler)) { + switch (arguments.length) { + // fast cases + case 1: + handler.call(this); + break; + case 2: + handler.call(this, arguments[1]); + break; + case 3: + handler.call(this, arguments[1], arguments[2]); + break; + // slower + default: + len = arguments.length; + args = new Array(len - 1); + for (i = 1; i < len; i++) + args[i - 1] = arguments[i]; + handler.apply(this, args); + } + } else if (isObject(handler)) { + len = arguments.length; + args = new Array(len - 1); + for (i = 1; i < len; i++) + args[i - 1] = arguments[i]; + + listeners = handler.slice(); + len = listeners.length; + for (i = 0; i < len; i++) + listeners[i].apply(this, args); + } + + return true; +}; + +EventEmitter.prototype.addListener = function(type, listener) { + var m; + + if (!isFunction(listener)) + throw TypeError('listener must be a function'); + + if (!this._events) + this._events = {}; + + // To avoid recursion in the case that type === "newListener"! Before + // adding it to the listeners, first emit "newListener". + if (this._events.newListener) + this.emit('newListener', type, + isFunction(listener.listener) ? + listener.listener : listener); + + if (!this._events[type]) + // Optimize the case of one listener. Don't need the extra array object. + this._events[type] = listener; + else if (isObject(this._events[type])) + // If we've already got an array, just append. + this._events[type].push(listener); + else + // Adding the second element, need to change to array. + this._events[type] = [this._events[type], listener]; + + // Check for listener leak + if (isObject(this._events[type]) && !this._events[type].warned) { + var m; + if (!isUndefined(this._maxListeners)) { + m = this._maxListeners; + } else { + m = EventEmitter.defaultMaxListeners; + } + + if (m && m > 0 && this._events[type].length > m) { + this._events[type].warned = true; + console.error('(node) warning: possible EventEmitter memory ' + + 'leak detected. %d listeners added. ' + + 'Use emitter.setMaxListeners() to increase limit.', + this._events[type].length); + if (typeof console.trace === 'function') { + // not supported in IE 10 + console.trace(); + } + } + } + + return this; +}; + +EventEmitter.prototype.on = EventEmitter.prototype.addListener; + +EventEmitter.prototype.once = function(type, listener) { + if (!isFunction(listener)) + throw TypeError('listener must be a function'); + + var fired = false; + + function g() { + this.removeListener(type, g); + + if (!fired) { + fired = true; + listener.apply(this, arguments); + } + } + + g.listener = listener; + this.on(type, g); + + return this; +}; + +// emits a 'removeListener' event iff the listener was removed +EventEmitter.prototype.removeListener = function(type, listener) { + var list, position, length, i; + + if (!isFunction(listener)) + throw TypeError('listener must be a function'); + + if (!this._events || !this._events[type]) + return this; + + list = this._events[type]; + length = list.length; + position = -1; + + if (list === listener || + (isFunction(list.listener) && list.listener === listener)) { + delete this._events[type]; + if (this._events.removeListener) + this.emit('removeListener', type, listener); + + } else if (isObject(list)) { + for (i = length; i-- > 0;) { + if (list[i] === listener || + (list[i].listener && list[i].listener === listener)) { + position = i; + break; + } + } + + if (position < 0) + return this; + + if (list.length === 1) { + list.length = 0; + delete this._events[type]; + } else { + list.splice(position, 1); + } + + if (this._events.removeListener) + this.emit('removeListener', type, listener); + } + + return this; +}; + +EventEmitter.prototype.removeAllListeners = function(type) { + var key, listeners; + + if (!this._events) + return this; + + // not listening for removeListener, no need to emit + if (!this._events.removeListener) { + if (arguments.length === 0) + this._events = {}; + else if (this._events[type]) + delete this._events[type]; + return this; + } + + // emit removeListener for all listeners on all events + if (arguments.length === 0) { + for (key in this._events) { + if (key === 'removeListener') continue; + this.removeAllListeners(key); + } + this.removeAllListeners('removeListener'); + this._events = {}; + return this; + } + + listeners = this._events[type]; + + if (isFunction(listeners)) { + this.removeListener(type, listeners); + } else { + // LIFO order + while (listeners.length) + this.removeListener(type, listeners[listeners.length - 1]); + } + delete this._events[type]; + + return this; +}; + +EventEmitter.prototype.listeners = function(type) { + var ret; + if (!this._events || !this._events[type]) + ret = []; + else if (isFunction(this._events[type])) + ret = [this._events[type]]; + else + ret = this._events[type].slice(); + return ret; +}; + +EventEmitter.listenerCount = function(emitter, type) { + var ret; + if (!emitter._events || !emitter._events[type]) + ret = 0; + else if (isFunction(emitter._events[type])) + ret = 1; + else + ret = emitter._events[type].length; + return ret; +}; + +function isFunction(arg) { + return typeof arg === 'function'; +} + +function isNumber(arg) { + return typeof arg === 'number'; +} + +function isObject(arg) { + return typeof arg === 'object' && arg !== null; +} + +function isUndefined(arg) { + return arg === void 0; +} + +},{}],15:[function(require,module,exports){ +(function (process){ +exports.alphasort = alphasort +exports.alphasorti = alphasorti +exports.setopts = setopts +exports.ownProp = ownProp +exports.makeAbs = makeAbs +exports.finish = finish +exports.mark = mark +exports.isIgnored = isIgnored +exports.childrenIgnored = childrenIgnored + +function ownProp (obj, field) { + return Object.prototype.hasOwnProperty.call(obj, field) +} + +var path = require("path") +var minimatch = require("minimatch") +var isAbsolute = require("path-is-absolute") +var Minimatch = minimatch.Minimatch + +function alphasorti (a, b) { + return a.toLowerCase().localeCompare(b.toLowerCase()) +} + +function alphasort (a, b) { + return a.localeCompare(b) +} + +function setupIgnores (self, options) { + self.ignore = options.ignore || [] + + if (!Array.isArray(self.ignore)) + self.ignore = [self.ignore] + + if (self.ignore.length) { + self.ignore = self.ignore.map(ignoreMap) + } +} + +function ignoreMap (pattern) { + var gmatcher = null + if (pattern.slice(-3) === '/**') { + var gpattern = pattern.replace(/(\/\*\*)+$/, '') + gmatcher = new Minimatch(gpattern) + } + + return { + matcher: new Minimatch(pattern), + gmatcher: gmatcher + } +} + +function setopts (self, pattern, options) { + if (!options) + options = {} + + // base-matching: just use globstar for that. + if (options.matchBase && -1 === pattern.indexOf("/")) { + if (options.noglobstar) { + throw new Error("base matching requires globstar") + } + pattern = "**/" + pattern + } + + self.silent = !!options.silent + self.pattern = pattern + self.strict = options.strict !== false + self.realpath = !!options.realpath + self.realpathCache = options.realpathCache || Object.create(null) + self.follow = !!options.follow + self.dot = !!options.dot + self.mark = !!options.mark + self.nodir = !!options.nodir + if (self.nodir) + self.mark = true + self.sync = !!options.sync + self.nounique = !!options.nounique + self.nonull = !!options.nonull + self.nosort = !!options.nosort + self.nocase = !!options.nocase + self.stat = !!options.stat + self.noprocess = !!options.noprocess + + self.maxLength = options.maxLength || Infinity + self.cache = options.cache || Object.create(null) + self.statCache = options.statCache || Object.create(null) + self.symlinks = options.symlinks || Object.create(null) + + setupIgnores(self, options) + + self.changedCwd = false + var cwd = process.cwd() + if (!ownProp(options, "cwd")) + self.cwd = cwd + else { + self.cwd = options.cwd + self.changedCwd = path.resolve(options.cwd) !== cwd + } + + self.root = options.root || path.resolve(self.cwd, "/") + self.root = path.resolve(self.root) + if (process.platform === "win32") + self.root = self.root.replace(/\\/g, "/") + + self.nomount = !!options.nomount + + // disable comments and negation unless the user explicitly + // passes in false as the option. + options.nonegate = options.nonegate === false ? false : true + options.nocomment = options.nocomment === false ? false : true + deprecationWarning(options) + + self.minimatch = new Minimatch(pattern, options) + self.options = self.minimatch.options +} + +// TODO(isaacs): remove entirely in v6 +// exported to reset in tests +exports.deprecationWarned +function deprecationWarning(options) { + if (!options.nonegate || !options.nocomment) { + if (process.noDeprecation !== true && !exports.deprecationWarned) { + var msg = 'glob WARNING: comments and negation will be disabled in v6' + if (process.throwDeprecation) + throw new Error(msg) + else if (process.traceDeprecation) + console.trace(msg) + else + console.error(msg) + + exports.deprecationWarned = true + } + } +} + +function finish (self) { + var nou = self.nounique + var all = nou ? [] : Object.create(null) + + for (var i = 0, l = self.matches.length; i < l; i ++) { + var matches = self.matches[i] + if (!matches || Object.keys(matches).length === 0) { + if (self.nonull) { + // do like the shell, and spit out the literal glob + var literal = self.minimatch.globSet[i] + if (nou) + all.push(literal) + else + all[literal] = true + } + } else { + // had matches + var m = Object.keys(matches) + if (nou) + all.push.apply(all, m) + else + m.forEach(function (m) { + all[m] = true + }) + } + } + + if (!nou) + all = Object.keys(all) + + if (!self.nosort) + all = all.sort(self.nocase ? alphasorti : alphasort) + + // at *some* point we statted all of these + if (self.mark) { + for (var i = 0; i < all.length; i++) { + all[i] = self._mark(all[i]) + } + if (self.nodir) { + all = all.filter(function (e) { + return !(/\/$/.test(e)) + }) + } + } + + if (self.ignore.length) + all = all.filter(function(m) { + return !isIgnored(self, m) + }) + + self.found = all +} + +function mark (self, p) { + var abs = makeAbs(self, p) + var c = self.cache[abs] + var m = p + if (c) { + var isDir = c === 'DIR' || Array.isArray(c) + var slash = p.slice(-1) === '/' + + if (isDir && !slash) + m += '/' + else if (!isDir && slash) + m = m.slice(0, -1) + + if (m !== p) { + var mabs = makeAbs(self, m) + self.statCache[mabs] = self.statCache[abs] + self.cache[mabs] = self.cache[abs] + } + } + + return m +} + +// lotta situps... +function makeAbs (self, f) { + var abs = f + if (f.charAt(0) === '/') { + abs = path.join(self.root, f) + } else if (isAbsolute(f) || f === '') { + abs = f + } else if (self.changedCwd) { + abs = path.resolve(self.cwd, f) + } else { + abs = path.resolve(f) + } + return abs +} + + +// Return true, if pattern ends with globstar '**', for the accompanying parent directory. +// Ex:- If node_modules/** is the pattern, add 'node_modules' to ignore list along with it's contents +function isIgnored (self, path) { + if (!self.ignore.length) + return false + + return self.ignore.some(function(item) { + return item.matcher.match(path) || !!(item.gmatcher && item.gmatcher.match(path)) + }) +} + +function childrenIgnored (self, path) { + if (!self.ignore.length) + return false + + return self.ignore.some(function(item) { + return !!(item.gmatcher && item.gmatcher.match(path)) + }) +} + +}).call(this,require('_process')) +},{"_process":24,"minimatch":20,"path":22,"path-is-absolute":23}],16:[function(require,module,exports){ +(function (process){ +// Approach: +// +// 1. Get the minimatch set +// 2. For each pattern in the set, PROCESS(pattern, false) +// 3. Store matches per-set, then uniq them +// +// PROCESS(pattern, inGlobStar) +// Get the first [n] items from pattern that are all strings +// Join these together. This is PREFIX. +// If there is no more remaining, then stat(PREFIX) and +// add to matches if it succeeds. END. +// +// If inGlobStar and PREFIX is symlink and points to dir +// set ENTRIES = [] +// else readdir(PREFIX) as ENTRIES +// If fail, END +// +// with ENTRIES +// If pattern[n] is GLOBSTAR +// // handle the case where the globstar match is empty +// // by pruning it out, and testing the resulting pattern +// PROCESS(pattern[0..n] + pattern[n+1 .. $], false) +// // handle other cases. +// for ENTRY in ENTRIES (not dotfiles) +// // attach globstar + tail onto the entry +// // Mark that this entry is a globstar match +// PROCESS(pattern[0..n] + ENTRY + pattern[n .. $], true) +// +// else // not globstar +// for ENTRY in ENTRIES (not dotfiles, unless pattern[n] is dot) +// Test ENTRY against pattern[n] +// If fails, continue +// If passes, PROCESS(pattern[0..n] + item + pattern[n+1 .. $]) +// +// Caveat: +// Cache all stats and readdirs results to minimize syscall. Since all +// we ever care about is existence and directory-ness, we can just keep +// `true` for files, and [children,...] for directories, or `false` for +// things that don't exist. + +module.exports = glob + +var fs = require('fs') +var minimatch = require('minimatch') +var Minimatch = minimatch.Minimatch +var inherits = require('inherits') +var EE = require('events').EventEmitter +var path = require('path') +var assert = require('assert') +var isAbsolute = require('path-is-absolute') +var globSync = require('./sync.js') +var common = require('./common.js') +var alphasort = common.alphasort +var alphasorti = common.alphasorti +var setopts = common.setopts +var ownProp = common.ownProp +var inflight = require('inflight') +var util = require('util') +var childrenIgnored = common.childrenIgnored +var isIgnored = common.isIgnored + +var once = require('once') + +function glob (pattern, options, cb) { + if (typeof options === 'function') cb = options, options = {} + if (!options) options = {} + + if (options.sync) { + if (cb) + throw new TypeError('callback provided to sync glob') + return globSync(pattern, options) + } + + return new Glob(pattern, options, cb) +} + +glob.sync = globSync +var GlobSync = glob.GlobSync = globSync.GlobSync + +// old api surface +glob.glob = glob + +glob.hasMagic = function (pattern, options_) { + var options = util._extend({}, options_) + options.noprocess = true + + var g = new Glob(pattern, options) + var set = g.minimatch.set + if (set.length > 1) + return true + + for (var j = 0; j < set[0].length; j++) { + if (typeof set[0][j] !== 'string') + return true + } + + return false +} + +glob.Glob = Glob +inherits(Glob, EE) +function Glob (pattern, options, cb) { + if (typeof options === 'function') { + cb = options + options = null + } + + if (options && options.sync) { + if (cb) + throw new TypeError('callback provided to sync glob') + return new GlobSync(pattern, options) + } + + if (!(this instanceof Glob)) + return new Glob(pattern, options, cb) + + setopts(this, pattern, options) + this._didRealPath = false + + // process each pattern in the minimatch set + var n = this.minimatch.set.length + + // The matches are stored as {: true,...} so that + // duplicates are automagically pruned. + // Later, we do an Object.keys() on these. + // Keep them as a list so we can fill in when nonull is set. + this.matches = new Array(n) + + if (typeof cb === 'function') { + cb = once(cb) + this.on('error', cb) + this.on('end', function (matches) { + cb(null, matches) + }) + } + + var self = this + var n = this.minimatch.set.length + this._processing = 0 + this.matches = new Array(n) + + this._emitQueue = [] + this._processQueue = [] + this.paused = false + + if (this.noprocess) + return this + + if (n === 0) + return done() + + for (var i = 0; i < n; i ++) { + this._process(this.minimatch.set[i], i, false, done) + } + + function done () { + --self._processing + if (self._processing <= 0) + self._finish() + } +} + +Glob.prototype._finish = function () { + assert(this instanceof Glob) + if (this.aborted) + return + + if (this.realpath && !this._didRealpath) + return this._realpath() + + common.finish(this) + this.emit('end', this.found) +} + +Glob.prototype._realpath = function () { + if (this._didRealpath) + return + + this._didRealpath = true + + var n = this.matches.length + if (n === 0) + return this._finish() + + var self = this + for (var i = 0; i < this.matches.length; i++) + this._realpathSet(i, next) + + function next () { + if (--n === 0) + self._finish() + } +} + +Glob.prototype._realpathSet = function (index, cb) { + var matchset = this.matches[index] + if (!matchset) + return cb() + + var found = Object.keys(matchset) + var self = this + var n = found.length + + if (n === 0) + return cb() + + var set = this.matches[index] = Object.create(null) + found.forEach(function (p, i) { + // If there's a problem with the stat, then it means that + // one or more of the links in the realpath couldn't be + // resolved. just return the abs value in that case. + p = self._makeAbs(p) + fs.realpath(p, self.realpathCache, function (er, real) { + if (!er) + set[real] = true + else if (er.syscall === 'stat') + set[p] = true + else + self.emit('error', er) // srsly wtf right here + + if (--n === 0) { + self.matches[index] = set + cb() + } + }) + }) +} + +Glob.prototype._mark = function (p) { + return common.mark(this, p) +} + +Glob.prototype._makeAbs = function (f) { + return common.makeAbs(this, f) +} + +Glob.prototype.abort = function () { + this.aborted = true + this.emit('abort') +} + +Glob.prototype.pause = function () { + if (!this.paused) { + this.paused = true + this.emit('pause') + } +} + +Glob.prototype.resume = function () { + if (this.paused) { + this.emit('resume') + this.paused = false + if (this._emitQueue.length) { + var eq = this._emitQueue.slice(0) + this._emitQueue.length = 0 + for (var i = 0; i < eq.length; i ++) { + var e = eq[i] + this._emitMatch(e[0], e[1]) + } + } + if (this._processQueue.length) { + var pq = this._processQueue.slice(0) + this._processQueue.length = 0 + for (var i = 0; i < pq.length; i ++) { + var p = pq[i] + this._processing-- + this._process(p[0], p[1], p[2], p[3]) + } + } + } +} + +Glob.prototype._process = function (pattern, index, inGlobStar, cb) { + assert(this instanceof Glob) + assert(typeof cb === 'function') + + if (this.aborted) + return + + this._processing++ + if (this.paused) { + this._processQueue.push([pattern, index, inGlobStar, cb]) + return + } + + //console.error('PROCESS %d', this._processing, pattern) + + // Get the first [n] parts of pattern that are all strings. + var n = 0 + while (typeof pattern[n] === 'string') { + n ++ + } + // now n is the index of the first one that is *not* a string. + + // see if there's anything else + var prefix + switch (n) { + // if not, then this is rather simple + case pattern.length: + this._processSimple(pattern.join('/'), index, cb) + return + + case 0: + // pattern *starts* with some non-trivial item. + // going to readdir(cwd), but not include the prefix in matches. + prefix = null + break + + default: + // pattern has some string bits in the front. + // whatever it starts with, whether that's 'absolute' like /foo/bar, + // or 'relative' like '../baz' + prefix = pattern.slice(0, n).join('/') + break + } + + var remain = pattern.slice(n) + + // get the list of entries. + var read + if (prefix === null) + read = '.' + else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) { + if (!prefix || !isAbsolute(prefix)) + prefix = '/' + prefix + read = prefix + } else + read = prefix + + var abs = this._makeAbs(read) + + //if ignored, skip _processing + if (childrenIgnored(this, read)) + return cb() + + var isGlobStar = remain[0] === minimatch.GLOBSTAR + if (isGlobStar) + this._processGlobStar(prefix, read, abs, remain, index, inGlobStar, cb) + else + this._processReaddir(prefix, read, abs, remain, index, inGlobStar, cb) +} + +Glob.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar, cb) { + var self = this + this._readdir(abs, inGlobStar, function (er, entries) { + return self._processReaddir2(prefix, read, abs, remain, index, inGlobStar, entries, cb) + }) +} + +Glob.prototype._processReaddir2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) { + + // if the abs isn't a dir, then nothing can match! + if (!entries) + return cb() + + // It will only match dot entries if it starts with a dot, or if + // dot is set. Stuff like @(.foo|.bar) isn't allowed. + var pn = remain[0] + var negate = !!this.minimatch.negate + var rawGlob = pn._glob + var dotOk = this.dot || rawGlob.charAt(0) === '.' + + var matchedEntries = [] + for (var i = 0; i < entries.length; i++) { + var e = entries[i] + if (e.charAt(0) !== '.' || dotOk) { + var m + if (negate && !prefix) { + m = !e.match(pn) + } else { + m = e.match(pn) + } + if (m) + matchedEntries.push(e) + } + } + + //console.error('prd2', prefix, entries, remain[0]._glob, matchedEntries) + + var len = matchedEntries.length + // If there are no matched entries, then nothing matches. + if (len === 0) + return cb() + + // if this is the last remaining pattern bit, then no need for + // an additional stat *unless* the user has specified mark or + // stat explicitly. We know they exist, since readdir returned + // them. + + if (remain.length === 1 && !this.mark && !this.stat) { + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + if (prefix) { + if (prefix !== '/') + e = prefix + '/' + e + else + e = prefix + e + } + + if (e.charAt(0) === '/' && !this.nomount) { + e = path.join(this.root, e) + } + this._emitMatch(index, e) + } + // This was the last one, and no stats were needed + return cb() + } + + // now test all matched entries as stand-ins for that part + // of the pattern. + remain.shift() + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + var newPattern + if (prefix) { + if (prefix !== '/') + e = prefix + '/' + e + else + e = prefix + e + } + this._process([e].concat(remain), index, inGlobStar, cb) + } + cb() +} + +Glob.prototype._emitMatch = function (index, e) { + if (this.aborted) + return + + if (this.matches[index][e]) + return + + if (isIgnored(this, e)) + return + + if (this.paused) { + this._emitQueue.push([index, e]) + return + } + + var abs = this._makeAbs(e) + + if (this.nodir) { + var c = this.cache[abs] + if (c === 'DIR' || Array.isArray(c)) + return + } + + if (this.mark) + e = this._mark(e) + + this.matches[index][e] = true + + var st = this.statCache[abs] + if (st) + this.emit('stat', e, st) + + this.emit('match', e) +} + +Glob.prototype._readdirInGlobStar = function (abs, cb) { + if (this.aborted) + return + + // follow all symlinked directories forever + // just proceed as if this is a non-globstar situation + if (this.follow) + return this._readdir(abs, false, cb) + + var lstatkey = 'lstat\0' + abs + var self = this + var lstatcb = inflight(lstatkey, lstatcb_) + + if (lstatcb) + fs.lstat(abs, lstatcb) + + function lstatcb_ (er, lstat) { + if (er) + return cb() + + var isSym = lstat.isSymbolicLink() + self.symlinks[abs] = isSym + + // If it's not a symlink or a dir, then it's definitely a regular file. + // don't bother doing a readdir in that case. + if (!isSym && !lstat.isDirectory()) { + self.cache[abs] = 'FILE' + cb() + } else + self._readdir(abs, false, cb) + } +} + +Glob.prototype._readdir = function (abs, inGlobStar, cb) { + if (this.aborted) + return + + cb = inflight('readdir\0'+abs+'\0'+inGlobStar, cb) + if (!cb) + return + + //console.error('RD %j %j', +inGlobStar, abs) + if (inGlobStar && !ownProp(this.symlinks, abs)) + return this._readdirInGlobStar(abs, cb) + + if (ownProp(this.cache, abs)) { + var c = this.cache[abs] + if (!c || c === 'FILE') + return cb() + + if (Array.isArray(c)) + return cb(null, c) + } + + var self = this + fs.readdir(abs, readdirCb(this, abs, cb)) +} + +function readdirCb (self, abs, cb) { + return function (er, entries) { + if (er) + self._readdirError(abs, er, cb) + else + self._readdirEntries(abs, entries, cb) + } +} + +Glob.prototype._readdirEntries = function (abs, entries, cb) { + if (this.aborted) + return + + // if we haven't asked to stat everything, then just + // assume that everything in there exists, so we can avoid + // having to stat it a second time. + if (!this.mark && !this.stat) { + for (var i = 0; i < entries.length; i ++) { + var e = entries[i] + if (abs === '/') + e = abs + e + else + e = abs + '/' + e + this.cache[e] = true + } + } + + this.cache[abs] = entries + return cb(null, entries) +} + +Glob.prototype._readdirError = function (f, er, cb) { + if (this.aborted) + return + + // handle errors, and cache the information + switch (er.code) { + case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205 + case 'ENOTDIR': // totally normal. means it *does* exist. + this.cache[this._makeAbs(f)] = 'FILE' + break + + case 'ENOENT': // not terribly unusual + case 'ELOOP': + case 'ENAMETOOLONG': + case 'UNKNOWN': + this.cache[this._makeAbs(f)] = false + break + + default: // some unusual error. Treat as failure. + this.cache[this._makeAbs(f)] = false + if (this.strict) { + this.emit('error', er) + // If the error is handled, then we abort + // if not, we threw out of here + this.abort() + } + if (!this.silent) + console.error('glob error', er) + break + } + + return cb() +} + +Glob.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar, cb) { + var self = this + this._readdir(abs, inGlobStar, function (er, entries) { + self._processGlobStar2(prefix, read, abs, remain, index, inGlobStar, entries, cb) + }) +} + + +Glob.prototype._processGlobStar2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) { + //console.error('pgs2', prefix, remain[0], entries) + + // no entries means not a dir, so it can never have matches + // foo.txt/** doesn't match foo.txt + if (!entries) + return cb() + + // test without the globstar, and with every child both below + // and replacing the globstar. + var remainWithoutGlobStar = remain.slice(1) + var gspref = prefix ? [ prefix ] : [] + var noGlobStar = gspref.concat(remainWithoutGlobStar) + + // the noGlobStar pattern exits the inGlobStar state + this._process(noGlobStar, index, false, cb) + + var isSym = this.symlinks[abs] + var len = entries.length + + // If it's a symlink, and we're in a globstar, then stop + if (isSym && inGlobStar) + return cb() + + for (var i = 0; i < len; i++) { + var e = entries[i] + if (e.charAt(0) === '.' && !this.dot) + continue + + // these two cases enter the inGlobStar state + var instead = gspref.concat(entries[i], remainWithoutGlobStar) + this._process(instead, index, true, cb) + + var below = gspref.concat(entries[i], remain) + this._process(below, index, true, cb) + } + + cb() +} + +Glob.prototype._processSimple = function (prefix, index, cb) { + // XXX review this. Shouldn't it be doing the mounting etc + // before doing stat? kinda weird? + var self = this + this._stat(prefix, function (er, exists) { + self._processSimple2(prefix, index, er, exists, cb) + }) +} +Glob.prototype._processSimple2 = function (prefix, index, er, exists, cb) { + + //console.error('ps2', prefix, exists) + + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + // If it doesn't exist, then just mark the lack of results + if (!exists) + return cb() + + if (prefix && isAbsolute(prefix) && !this.nomount) { + var trail = /[\/\\]$/.test(prefix) + if (prefix.charAt(0) === '/') { + prefix = path.join(this.root, prefix) + } else { + prefix = path.resolve(this.root, prefix) + if (trail) + prefix += '/' + } + } + + if (process.platform === 'win32') + prefix = prefix.replace(/\\/g, '/') + + // Mark this as a match + this._emitMatch(index, prefix) + cb() +} + +// Returns either 'DIR', 'FILE', or false +Glob.prototype._stat = function (f, cb) { + var abs = this._makeAbs(f) + var needDir = f.slice(-1) === '/' + + if (f.length > this.maxLength) + return cb() + + if (!this.stat && ownProp(this.cache, abs)) { + var c = this.cache[abs] + + if (Array.isArray(c)) + c = 'DIR' + + // It exists, but maybe not how we need it + if (!needDir || c === 'DIR') + return cb(null, c) + + if (needDir && c === 'FILE') + return cb() + + // otherwise we have to stat, because maybe c=true + // if we know it exists, but not what it is. + } + + var exists + var stat = this.statCache[abs] + if (stat !== undefined) { + if (stat === false) + return cb(null, stat) + else { + var type = stat.isDirectory() ? 'DIR' : 'FILE' + if (needDir && type === 'FILE') + return cb() + else + return cb(null, type, stat) + } + } + + var self = this + var statcb = inflight('stat\0' + abs, lstatcb_) + if (statcb) + fs.lstat(abs, statcb) + + function lstatcb_ (er, lstat) { + if (lstat && lstat.isSymbolicLink()) { + // If it's a symlink, then treat it as the target, unless + // the target does not exist, then treat it as a file. + return fs.stat(abs, function (er, stat) { + if (er) + self._stat2(f, abs, null, lstat, cb) + else + self._stat2(f, abs, er, stat, cb) + }) + } else { + self._stat2(f, abs, er, lstat, cb) + } + } +} + +Glob.prototype._stat2 = function (f, abs, er, stat, cb) { + if (er) { + this.statCache[abs] = false + return cb() + } + + var needDir = f.slice(-1) === '/' + this.statCache[abs] = stat + + if (abs.slice(-1) === '/' && !stat.isDirectory()) + return cb(null, false, stat) + + var c = stat.isDirectory() ? 'DIR' : 'FILE' + this.cache[abs] = this.cache[abs] || c + + if (needDir && c !== 'DIR') + return cb() + + return cb(null, c, stat) +} + +}).call(this,require('_process')) +},{"./common.js":15,"./sync.js":17,"_process":24,"assert":9,"events":14,"fs":12,"inflight":18,"inherits":19,"minimatch":20,"once":21,"path":22,"path-is-absolute":23,"util":28}],17:[function(require,module,exports){ +(function (process){ +module.exports = globSync +globSync.GlobSync = GlobSync + +var fs = require('fs') +var minimatch = require('minimatch') +var Minimatch = minimatch.Minimatch +var Glob = require('./glob.js').Glob +var util = require('util') +var path = require('path') +var assert = require('assert') +var isAbsolute = require('path-is-absolute') +var common = require('./common.js') +var alphasort = common.alphasort +var alphasorti = common.alphasorti +var setopts = common.setopts +var ownProp = common.ownProp +var childrenIgnored = common.childrenIgnored + +function globSync (pattern, options) { + if (typeof options === 'function' || arguments.length === 3) + throw new TypeError('callback provided to sync glob\n'+ + 'See: https://github.com/isaacs/node-glob/issues/167') + + return new GlobSync(pattern, options).found +} + +function GlobSync (pattern, options) { + if (!pattern) + throw new Error('must provide pattern') + + if (typeof options === 'function' || arguments.length === 3) + throw new TypeError('callback provided to sync glob\n'+ + 'See: https://github.com/isaacs/node-glob/issues/167') + + if (!(this instanceof GlobSync)) + return new GlobSync(pattern, options) + + setopts(this, pattern, options) + + if (this.noprocess) + return this + + var n = this.minimatch.set.length + this.matches = new Array(n) + for (var i = 0; i < n; i ++) { + this._process(this.minimatch.set[i], i, false) + } + this._finish() +} + +GlobSync.prototype._finish = function () { + assert(this instanceof GlobSync) + if (this.realpath) { + var self = this + this.matches.forEach(function (matchset, index) { + var set = self.matches[index] = Object.create(null) + for (var p in matchset) { + try { + p = self._makeAbs(p) + var real = fs.realpathSync(p, self.realpathCache) + set[real] = true + } catch (er) { + if (er.syscall === 'stat') + set[self._makeAbs(p)] = true + else + throw er + } + } + }) + } + common.finish(this) +} + + +GlobSync.prototype._process = function (pattern, index, inGlobStar) { + assert(this instanceof GlobSync) + + // Get the first [n] parts of pattern that are all strings. + var n = 0 + while (typeof pattern[n] === 'string') { + n ++ + } + // now n is the index of the first one that is *not* a string. + + // See if there's anything else + var prefix + switch (n) { + // if not, then this is rather simple + case pattern.length: + this._processSimple(pattern.join('/'), index) + return + + case 0: + // pattern *starts* with some non-trivial item. + // going to readdir(cwd), but not include the prefix in matches. + prefix = null + break + + default: + // pattern has some string bits in the front. + // whatever it starts with, whether that's 'absolute' like /foo/bar, + // or 'relative' like '../baz' + prefix = pattern.slice(0, n).join('/') + break + } + + var remain = pattern.slice(n) + + // get the list of entries. + var read + if (prefix === null) + read = '.' + else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) { + if (!prefix || !isAbsolute(prefix)) + prefix = '/' + prefix + read = prefix + } else + read = prefix + + var abs = this._makeAbs(read) + + //if ignored, skip processing + if (childrenIgnored(this, read)) + return + + var isGlobStar = remain[0] === minimatch.GLOBSTAR + if (isGlobStar) + this._processGlobStar(prefix, read, abs, remain, index, inGlobStar) + else + this._processReaddir(prefix, read, abs, remain, index, inGlobStar) +} + + +GlobSync.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar) { + var entries = this._readdir(abs, inGlobStar) + + // if the abs isn't a dir, then nothing can match! + if (!entries) + return + + // It will only match dot entries if it starts with a dot, or if + // dot is set. Stuff like @(.foo|.bar) isn't allowed. + var pn = remain[0] + var negate = !!this.minimatch.negate + var rawGlob = pn._glob + var dotOk = this.dot || rawGlob.charAt(0) === '.' + + var matchedEntries = [] + for (var i = 0; i < entries.length; i++) { + var e = entries[i] + if (e.charAt(0) !== '.' || dotOk) { + var m + if (negate && !prefix) { + m = !e.match(pn) + } else { + m = e.match(pn) + } + if (m) + matchedEntries.push(e) + } + } + + var len = matchedEntries.length + // If there are no matched entries, then nothing matches. + if (len === 0) + return + + // if this is the last remaining pattern bit, then no need for + // an additional stat *unless* the user has specified mark or + // stat explicitly. We know they exist, since readdir returned + // them. + + if (remain.length === 1 && !this.mark && !this.stat) { + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + if (prefix) { + if (prefix.slice(-1) !== '/') + e = prefix + '/' + e + else + e = prefix + e + } + + if (e.charAt(0) === '/' && !this.nomount) { + e = path.join(this.root, e) + } + this.matches[index][e] = true + } + // This was the last one, and no stats were needed + return + } + + // now test all matched entries as stand-ins for that part + // of the pattern. + remain.shift() + for (var i = 0; i < len; i ++) { + var e = matchedEntries[i] + var newPattern + if (prefix) + newPattern = [prefix, e] + else + newPattern = [e] + this._process(newPattern.concat(remain), index, inGlobStar) + } +} + + +GlobSync.prototype._emitMatch = function (index, e) { + var abs = this._makeAbs(e) + if (this.mark) + e = this._mark(e) + + if (this.matches[index][e]) + return + + if (this.nodir) { + var c = this.cache[this._makeAbs(e)] + if (c === 'DIR' || Array.isArray(c)) + return + } + + this.matches[index][e] = true + if (this.stat) + this._stat(e) +} + + +GlobSync.prototype._readdirInGlobStar = function (abs) { + // follow all symlinked directories forever + // just proceed as if this is a non-globstar situation + if (this.follow) + return this._readdir(abs, false) + + var entries + var lstat + var stat + try { + lstat = fs.lstatSync(abs) + } catch (er) { + // lstat failed, doesn't exist + return null + } + + var isSym = lstat.isSymbolicLink() + this.symlinks[abs] = isSym + + // If it's not a symlink or a dir, then it's definitely a regular file. + // don't bother doing a readdir in that case. + if (!isSym && !lstat.isDirectory()) + this.cache[abs] = 'FILE' + else + entries = this._readdir(abs, false) + + return entries +} + +GlobSync.prototype._readdir = function (abs, inGlobStar) { + var entries + + if (inGlobStar && !ownProp(this.symlinks, abs)) + return this._readdirInGlobStar(abs) + + if (ownProp(this.cache, abs)) { + var c = this.cache[abs] + if (!c || c === 'FILE') + return null + + if (Array.isArray(c)) + return c + } + + try { + return this._readdirEntries(abs, fs.readdirSync(abs)) + } catch (er) { + this._readdirError(abs, er) + return null + } +} + +GlobSync.prototype._readdirEntries = function (abs, entries) { + // if we haven't asked to stat everything, then just + // assume that everything in there exists, so we can avoid + // having to stat it a second time. + if (!this.mark && !this.stat) { + for (var i = 0; i < entries.length; i ++) { + var e = entries[i] + if (abs === '/') + e = abs + e + else + e = abs + '/' + e + this.cache[e] = true + } + } + + this.cache[abs] = entries + + // mark and cache dir-ness + return entries +} + +GlobSync.prototype._readdirError = function (f, er) { + // handle errors, and cache the information + switch (er.code) { + case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205 + case 'ENOTDIR': // totally normal. means it *does* exist. + this.cache[this._makeAbs(f)] = 'FILE' + break + + case 'ENOENT': // not terribly unusual + case 'ELOOP': + case 'ENAMETOOLONG': + case 'UNKNOWN': + this.cache[this._makeAbs(f)] = false + break + + default: // some unusual error. Treat as failure. + this.cache[this._makeAbs(f)] = false + if (this.strict) + throw er + if (!this.silent) + console.error('glob error', er) + break + } +} + +GlobSync.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar) { + + var entries = this._readdir(abs, inGlobStar) + + // no entries means not a dir, so it can never have matches + // foo.txt/** doesn't match foo.txt + if (!entries) + return + + // test without the globstar, and with every child both below + // and replacing the globstar. + var remainWithoutGlobStar = remain.slice(1) + var gspref = prefix ? [ prefix ] : [] + var noGlobStar = gspref.concat(remainWithoutGlobStar) + + // the noGlobStar pattern exits the inGlobStar state + this._process(noGlobStar, index, false) + + var len = entries.length + var isSym = this.symlinks[abs] + + // If it's a symlink, and we're in a globstar, then stop + if (isSym && inGlobStar) + return + + for (var i = 0; i < len; i++) { + var e = entries[i] + if (e.charAt(0) === '.' && !this.dot) + continue + + // these two cases enter the inGlobStar state + var instead = gspref.concat(entries[i], remainWithoutGlobStar) + this._process(instead, index, true) + + var below = gspref.concat(entries[i], remain) + this._process(below, index, true) + } +} + +GlobSync.prototype._processSimple = function (prefix, index) { + // XXX review this. Shouldn't it be doing the mounting etc + // before doing stat? kinda weird? + var exists = this._stat(prefix) + + if (!this.matches[index]) + this.matches[index] = Object.create(null) + + // If it doesn't exist, then just mark the lack of results + if (!exists) + return + + if (prefix && isAbsolute(prefix) && !this.nomount) { + var trail = /[\/\\]$/.test(prefix) + if (prefix.charAt(0) === '/') { + prefix = path.join(this.root, prefix) + } else { + prefix = path.resolve(this.root, prefix) + if (trail) + prefix += '/' + } + } + + if (process.platform === 'win32') + prefix = prefix.replace(/\\/g, '/') + + // Mark this as a match + this.matches[index][prefix] = true +} + +// Returns either 'DIR', 'FILE', or false +GlobSync.prototype._stat = function (f) { + var abs = this._makeAbs(f) + var needDir = f.slice(-1) === '/' + + if (f.length > this.maxLength) + return false + + if (!this.stat && ownProp(this.cache, abs)) { + var c = this.cache[abs] + + if (Array.isArray(c)) + c = 'DIR' + + // It exists, but maybe not how we need it + if (!needDir || c === 'DIR') + return c + + if (needDir && c === 'FILE') + return false + + // otherwise we have to stat, because maybe c=true + // if we know it exists, but not what it is. + } + + var exists + var stat = this.statCache[abs] + if (!stat) { + var lstat + try { + lstat = fs.lstatSync(abs) + } catch (er) { + return false + } + + if (lstat.isSymbolicLink()) { + try { + stat = fs.statSync(abs) + } catch (er) { + stat = lstat + } + } else { + stat = lstat + } + } + + this.statCache[abs] = stat + + var c = stat.isDirectory() ? 'DIR' : 'FILE' + this.cache[abs] = this.cache[abs] || c + + if (needDir && c !== 'DIR') + return false + + return c +} + +GlobSync.prototype._mark = function (p) { + return common.mark(this, p) +} + +GlobSync.prototype._makeAbs = function (f) { + return common.makeAbs(this, f) +} + +}).call(this,require('_process')) +},{"./common.js":15,"./glob.js":16,"_process":24,"assert":9,"fs":12,"minimatch":20,"path":22,"path-is-absolute":23,"util":28}],18:[function(require,module,exports){ +(function (process){ +var wrappy = require('wrappy') +var reqs = Object.create(null) +var once = require('once') + +module.exports = wrappy(inflight) + +function inflight (key, cb) { + if (reqs[key]) { + reqs[key].push(cb) + return null + } else { + reqs[key] = [cb] + return makeres(key) + } +} + +function makeres (key) { + return once(function RES () { + var cbs = reqs[key] + var len = cbs.length + var args = slice(arguments) + + // XXX It's somewhat ambiguous whether a new callback added in this + // pass should be queued for later execution if something in the + // list of callbacks throws, or if it should just be discarded. + // However, it's such an edge case that it hardly matters, and either + // choice is likely as surprising as the other. + // As it happens, we do go ahead and schedule it for later execution. + try { + for (var i = 0; i < len; i++) { + cbs[i].apply(null, args) + } + } finally { + if (cbs.length > len) { + // added more in the interim. + // de-zalgo, just in case, but don't call again. + cbs.splice(0, len) + process.nextTick(function () { + RES.apply(null, args) + }) + } else { + delete reqs[key] + } + } + }) +} + +function slice (args) { + var length = args.length + var array = [] + + for (var i = 0; i < length; i++) array[i] = args[i] + return array +} + +}).call(this,require('_process')) +},{"_process":24,"once":21,"wrappy":29}],19:[function(require,module,exports){ +if (typeof Object.create === 'function') { + // implementation from standard node.js 'util' module + module.exports = function inherits(ctor, superCtor) { + ctor.super_ = superCtor + ctor.prototype = Object.create(superCtor.prototype, { + constructor: { + value: ctor, + enumerable: false, + writable: true, + configurable: true + } + }); + }; +} else { + // old school shim for old browsers + module.exports = function inherits(ctor, superCtor) { + ctor.super_ = superCtor + var TempCtor = function () {} + TempCtor.prototype = superCtor.prototype + ctor.prototype = new TempCtor() + ctor.prototype.constructor = ctor + } +} + +},{}],20:[function(require,module,exports){ +module.exports = minimatch +minimatch.Minimatch = Minimatch + +var path = { sep: '/' } +try { + path = require('path') +} catch (er) {} + +var GLOBSTAR = minimatch.GLOBSTAR = Minimatch.GLOBSTAR = {} +var expand = require('brace-expansion') + +var plTypes = { + '!': { open: '(?:(?!(?:', close: '))[^/]*?)'}, + '?': { open: '(?:', close: ')?' }, + '+': { open: '(?:', close: ')+' }, + '*': { open: '(?:', close: ')*' }, + '@': { open: '(?:', close: ')' } +} + +// any single thing other than / +// don't need to escape / when using new RegExp() +var qmark = '[^/]' + +// * => any number of characters +var star = qmark + '*?' + +// ** when dots are allowed. Anything goes, except .. and . +// not (^ or / followed by one or two dots followed by $ or /), +// followed by anything, any number of times. +var twoStarDot = '(?:(?!(?:\\\/|^)(?:\\.{1,2})($|\\\/)).)*?' + +// not a ^ or / followed by a dot, +// followed by anything, any number of times. +var twoStarNoDot = '(?:(?!(?:\\\/|^)\\.).)*?' + +// characters that need to be escaped in RegExp. +var reSpecials = charSet('().*{}+?[]^$\\!') + +// "abc" -> { a:true, b:true, c:true } +function charSet (s) { + return s.split('').reduce(function (set, c) { + set[c] = true + return set + }, {}) +} + +// normalizes slashes. +var slashSplit = /\/+/ + +minimatch.filter = filter +function filter (pattern, options) { + options = options || {} + return function (p, i, list) { + return minimatch(p, pattern, options) + } +} + +function ext (a, b) { + a = a || {} + b = b || {} + var t = {} + Object.keys(b).forEach(function (k) { + t[k] = b[k] + }) + Object.keys(a).forEach(function (k) { + t[k] = a[k] + }) + return t +} + +minimatch.defaults = function (def) { + if (!def || !Object.keys(def).length) return minimatch + + var orig = minimatch + + var m = function minimatch (p, pattern, options) { + return orig.minimatch(p, pattern, ext(def, options)) + } + + m.Minimatch = function Minimatch (pattern, options) { + return new orig.Minimatch(pattern, ext(def, options)) + } + + return m +} + +Minimatch.defaults = function (def) { + if (!def || !Object.keys(def).length) return Minimatch + return minimatch.defaults(def).Minimatch +} + +function minimatch (p, pattern, options) { + if (typeof pattern !== 'string') { + throw new TypeError('glob pattern string required') + } + + if (!options) options = {} + + // shortcut: comments match nothing. + if (!options.nocomment && pattern.charAt(0) === '#') { + return false + } + + // "" only matches "" + if (pattern.trim() === '') return p === '' + + return new Minimatch(pattern, options).match(p) +} + +function Minimatch (pattern, options) { + if (!(this instanceof Minimatch)) { + return new Minimatch(pattern, options) + } + + if (typeof pattern !== 'string') { + throw new TypeError('glob pattern string required') + } + + if (!options) options = {} + pattern = pattern.trim() + + // windows support: need to use /, not \ + if (path.sep !== '/') { + pattern = pattern.split(path.sep).join('/') + } + + this.options = options + this.set = [] + this.pattern = pattern + this.regexp = null + this.negate = false + this.comment = false + this.empty = false + + // make the set of regexps etc. + this.make() +} + +Minimatch.prototype.debug = function () {} + +Minimatch.prototype.make = make +function make () { + // don't do it more than once. + if (this._made) return + + var pattern = this.pattern + var options = this.options + + // empty patterns and comments match nothing. + if (!options.nocomment && pattern.charAt(0) === '#') { + this.comment = true + return + } + if (!pattern) { + this.empty = true + return + } + + // step 1: figure out negation, etc. + this.parseNegate() + + // step 2: expand braces + var set = this.globSet = this.braceExpand() + + if (options.debug) this.debug = console.error + + this.debug(this.pattern, set) + + // step 3: now we have a set, so turn each one into a series of path-portion + // matching patterns. + // These will be regexps, except in the case of "**", which is + // set to the GLOBSTAR object for globstar behavior, + // and will not contain any / characters + set = this.globParts = set.map(function (s) { + return s.split(slashSplit) + }) + + this.debug(this.pattern, set) + + // glob --> regexps + set = set.map(function (s, si, set) { + return s.map(this.parse, this) + }, this) + + this.debug(this.pattern, set) + + // filter out everything that didn't compile properly. + set = set.filter(function (s) { + return s.indexOf(false) === -1 + }) + + this.debug(this.pattern, set) + + this.set = set +} + +Minimatch.prototype.parseNegate = parseNegate +function parseNegate () { + var pattern = this.pattern + var negate = false + var options = this.options + var negateOffset = 0 + + if (options.nonegate) return + + for (var i = 0, l = pattern.length + ; i < l && pattern.charAt(i) === '!' + ; i++) { + negate = !negate + negateOffset++ + } + + if (negateOffset) this.pattern = pattern.substr(negateOffset) + this.negate = negate +} + +// Brace expansion: +// a{b,c}d -> abd acd +// a{b,}c -> abc ac +// a{0..3}d -> a0d a1d a2d a3d +// a{b,c{d,e}f}g -> abg acdfg acefg +// a{b,c}d{e,f}g -> abdeg acdeg abdeg abdfg +// +// Invalid sets are not expanded. +// a{2..}b -> a{2..}b +// a{b}c -> a{b}c +minimatch.braceExpand = function (pattern, options) { + return braceExpand(pattern, options) +} + +Minimatch.prototype.braceExpand = braceExpand + +function braceExpand (pattern, options) { + if (!options) { + if (this instanceof Minimatch) { + options = this.options + } else { + options = {} + } + } + + pattern = typeof pattern === 'undefined' + ? this.pattern : pattern + + if (typeof pattern === 'undefined') { + throw new TypeError('undefined pattern') + } + + if (options.nobrace || + !pattern.match(/\{.*\}/)) { + // shortcut. no need to expand. + return [pattern] + } + + return expand(pattern) +} + +// parse a component of the expanded set. +// At this point, no pattern may contain "/" in it +// so we're going to return a 2d array, where each entry is the full +// pattern, split on '/', and then turned into a regular expression. +// A regexp is made at the end which joins each array with an +// escaped /, and another full one which joins each regexp with |. +// +// Following the lead of Bash 4.1, note that "**" only has special meaning +// when it is the *only* thing in a path portion. Otherwise, any series +// of * is equivalent to a single *. Globstar behavior is enabled by +// default, and can be disabled by setting options.noglobstar. +Minimatch.prototype.parse = parse +var SUBPARSE = {} +function parse (pattern, isSub) { + if (pattern.length > 1024 * 64) { + throw new TypeError('pattern is too long') + } + + var options = this.options + + // shortcuts + if (!options.noglobstar && pattern === '**') return GLOBSTAR + if (pattern === '') return '' + + var re = '' + var hasMagic = !!options.nocase + var escaping = false + // ? => one single character + var patternListStack = [] + var negativeLists = [] + var stateChar + var inClass = false + var reClassStart = -1 + var classStart = -1 + // . and .. never match anything that doesn't start with ., + // even when options.dot is set. + var patternStart = pattern.charAt(0) === '.' ? '' // anything + // not (start or / followed by . or .. followed by / or end) + : options.dot ? '(?!(?:^|\\\/)\\.{1,2}(?:$|\\\/))' + : '(?!\\.)' + var self = this + + function clearStateChar () { + if (stateChar) { + // we had some state-tracking character + // that wasn't consumed by this pass. + switch (stateChar) { + case '*': + re += star + hasMagic = true + break + case '?': + re += qmark + hasMagic = true + break + default: + re += '\\' + stateChar + break + } + self.debug('clearStateChar %j %j', stateChar, re) + stateChar = false + } + } + + for (var i = 0, len = pattern.length, c + ; (i < len) && (c = pattern.charAt(i)) + ; i++) { + this.debug('%s\t%s %s %j', pattern, i, re, c) + + // skip over any that are escaped. + if (escaping && reSpecials[c]) { + re += '\\' + c + escaping = false + continue + } + + switch (c) { + case '/': + // completely not allowed, even escaped. + // Should already be path-split by now. + return false + + case '\\': + clearStateChar() + escaping = true + continue + + // the various stateChar values + // for the "extglob" stuff. + case '?': + case '*': + case '+': + case '@': + case '!': + this.debug('%s\t%s %s %j <-- stateChar', pattern, i, re, c) + + // all of those are literals inside a class, except that + // the glob [!a] means [^a] in regexp + if (inClass) { + this.debug(' in class') + if (c === '!' && i === classStart + 1) c = '^' + re += c + continue + } + + // if we already have a stateChar, then it means + // that there was something like ** or +? in there. + // Handle the stateChar, then proceed with this one. + self.debug('call clearStateChar %j', stateChar) + clearStateChar() + stateChar = c + // if extglob is disabled, then +(asdf|foo) isn't a thing. + // just clear the statechar *now*, rather than even diving into + // the patternList stuff. + if (options.noext) clearStateChar() + continue + + case '(': + if (inClass) { + re += '(' + continue + } + + if (!stateChar) { + re += '\$' + continue + } + + patternListStack.push({ + type: stateChar, + start: i - 1, + reStart: re.length, + open: plTypes[stateChar].open, + close: plTypes[stateChar].close + }) + // negation is (?:(?!js)[^/]*) + re += stateChar === '!' ? '(?:(?!(?:' : '(?:' + this.debug('plType %j %j', stateChar, re) + stateChar = false + continue + + case ')': + if (inClass || !patternListStack.length) { + re += '\$' + continue + } + + clearStateChar() + hasMagic = true + var pl = patternListStack.pop() + // negation is (?:(?!js)[^/]*) + // The others are (?:) + re += pl.close + if (pl.type === '!') { + negativeLists.push(pl) + } + pl.reEnd = re.length + continue + + case '|': + if (inClass || !patternListStack.length || escaping) { + re += '\\|' + escaping = false + continue + } + + clearStateChar() + re += '|' + continue + + // these are mostly the same in regexp and glob + case '[': + // swallow any state-tracking char before the [ + clearStateChar() + + if (inClass) { + re += '\\' + c + continue + } + + inClass = true + classStart = i + reClassStart = re.length + re += c + continue + + case ']': + // a right bracket shall lose its special + // meaning and represent itself in + // a bracket expression if it occurs + // first in the list. -- POSIX.2 2.8.3.2 + if (i === classStart + 1 || !inClass) { + re += '\\' + c + escaping = false + continue + } + + // handle the case where we left a class open. + // "[z-a]" is valid, equivalent to "\[z-a\]" + if (inClass) { + // split where the last [ was, make sure we don't have + // an invalid re. if so, re-walk the contents of the + // would-be class to re-translate any characters that + // were passed through as-is + // TODO: It would probably be faster to determine this + // without a try/catch and a new RegExp, but it's tricky + // to do safely. For now, this is safe and works. + var cs = pattern.substring(classStart + 1, i) + try { + RegExp('[' + cs + ']') + } catch (er) { + // not a valid class! + var sp = this.parse(cs, SUBPARSE) + re = re.substr(0, reClassStart) + '\\[' + sp[0] + '\\]' + hasMagic = hasMagic || sp[1] + inClass = false + continue + } + } + + // finish up the class. + hasMagic = true + inClass = false + re += c + continue + + default: + // swallow any state char that wasn't consumed + clearStateChar() + + if (escaping) { + // no need + escaping = false + } else if (reSpecials[c] + && !(c === '^' && inClass)) { + re += '\\' + } + + re += c + + } // switch + } // for + + // handle the case where we left a class open. + // "[abc" is valid, equivalent to "\[abc" + if (inClass) { + // split where the last [ was, and escape it + // this is a huge pita. We now have to re-walk + // the contents of the would-be class to re-translate + // any characters that were passed through as-is + cs = pattern.substr(classStart + 1) + sp = this.parse(cs, SUBPARSE) + re = re.substr(0, reClassStart) + '\\[' + sp[0] + hasMagic = hasMagic || sp[1] + } + + // handle the case where we had a +( thing at the *end* + // of the pattern. + // each pattern list stack adds 3 chars, and we need to go through + // and escape any | chars that were passed through as-is for the regexp. + // Go through and escape them, taking care not to double-escape any + // | chars that were already escaped. + for (pl = patternListStack.pop(); pl; pl = patternListStack.pop()) { + var tail = re.slice(pl.reStart + pl.open.length) + this.debug('setting tail', re, pl) + // maybe some even number of \, then maybe 1 \, followed by a | + tail = tail.replace(/((?:\\{2}){0,64})(\\?)\|/g, function (_, $1, $2) { + if (!$2) { + // the | isn't already escaped, so escape it. + $2 = '\\' + } + + // need to escape all those slashes *again*, without escaping the + // one that we need for escaping the | character. As it works out, + // escaping an even number of slashes can be done by simply repeating + // it exactly after itself. That's why this trick works. + // + // I am sorry that you have to see this. + return $1 + $1 + $2 + '|' + }) + + this.debug('tail=%j\n %s', tail, tail, pl, re) + var t = pl.type === '*' ? star + : pl.type === '?' ? qmark + : '\\' + pl.type + + hasMagic = true + re = re.slice(0, pl.reStart) + t + '\\(' + tail + } + + // handle trailing things that only matter at the very end. + clearStateChar() + if (escaping) { + // trailing \\ + re += '\\\\' + } + + // only need to apply the nodot start if the re starts with + // something that could conceivably capture a dot + var addPatternStart = false + switch (re.charAt(0)) { + case '.': + case '[': + case '(': addPatternStart = true + } + + // Hack to work around lack of negative lookbehind in JS + // A pattern like: *.!(x).!(y|z) needs to ensure that a name + // like 'a.xyz.yz' doesn't match. So, the first negative + // lookahead, has to look ALL the way ahead, to the end of + // the pattern. + for (var n = negativeLists.length - 1; n > -1; n--) { + var nl = negativeLists[n] + + var nlBefore = re.slice(0, nl.reStart) + var nlFirst = re.slice(nl.reStart, nl.reEnd - 8) + var nlLast = re.slice(nl.reEnd - 8, nl.reEnd) + var nlAfter = re.slice(nl.reEnd) + + nlLast += nlAfter + + // Handle nested stuff like *(*.js|!(*.json)), where open parens + // mean that we should *not* include the ) in the bit that is considered + // "after" the negated section. + var openParensBefore = nlBefore.split('(').length - 1 + var cleanAfter = nlAfter + for (i = 0; i < openParensBefore; i++) { + cleanAfter = cleanAfter.replace(/\)[+*?]?/, '') + } + nlAfter = cleanAfter + + var dollar = '' + if (nlAfter === '' && isSub !== SUBPARSE) { + dollar = '$' + } + var newRe = nlBefore + nlFirst + nlAfter + dollar + nlLast + re = newRe + } + + // if the re is not "" at this point, then we need to make sure + // it doesn't match against an empty path part. + // Otherwise a/* will match a/, which it should not. + if (re !== '' && hasMagic) { + re = '(?=.)' + re + } + + if (addPatternStart) { + re = patternStart + re + } + + // parsing just a piece of a larger pattern. + if (isSub === SUBPARSE) { + return [re, hasMagic] + } + + // skip the regexp for non-magical patterns + // unescape anything in it, though, so that it'll be + // an exact match against a file etc. + if (!hasMagic) { + return globUnescape(pattern) + } + + var flags = options.nocase ? 'i' : '' + try { + var regExp = new RegExp('^' + re + '$', flags) + } catch (er) { + // If it was an invalid regular expression, then it can't match + // anything. This trick looks for a character after the end of + // the string, which is of course impossible, except in multi-line + // mode, but it's not a /m regex. + return new RegExp('$.') + } + + regExp._glob = pattern + regExp._src = re + + return regExp +} + +minimatch.makeRe = function (pattern, options) { + return new Minimatch(pattern, options || {}).makeRe() +} + +Minimatch.prototype.makeRe = makeRe +function makeRe () { + if (this.regexp || this.regexp === false) return this.regexp + + // at this point, this.set is a 2d array of partial + // pattern strings, or "**". + // + // It's better to use .match(). This function shouldn't + // be used, really, but it's pretty convenient sometimes, + // when you just want to work with a regex. + var set = this.set + + if (!set.length) { + this.regexp = false + return this.regexp + } + var options = this.options + + var twoStar = options.noglobstar ? star + : options.dot ? twoStarDot + : twoStarNoDot + var flags = options.nocase ? 'i' : '' + + var re = set.map(function (pattern) { + return pattern.map(function (p) { + return (p === GLOBSTAR) ? twoStar + : (typeof p === 'string') ? regExpEscape(p) + : p._src + }).join('\\\/') + }).join('|') + + // must match entire pattern + // ending in a * or ** will make it less strict. + re = '^(?:' + re + ')$' + + // can match anything, as long as it's not this. + if (this.negate) re = '^(?!' + re + ').*$' + + try { + this.regexp = new RegExp(re, flags) + } catch (ex) { + this.regexp = false + } + return this.regexp +} + +minimatch.match = function (list, pattern, options) { + options = options || {} + var mm = new Minimatch(pattern, options) + list = list.filter(function (f) { + return mm.match(f) + }) + if (mm.options.nonull && !list.length) { + list.push(pattern) + } + return list +} + +Minimatch.prototype.match = match +function match (f, partial) { + this.debug('match', f, this.pattern) + // short-circuit in the case of busted things. + // comments, etc. + if (this.comment) return false + if (this.empty) return f === '' + + if (f === '/' && partial) return true + + var options = this.options + + // windows: need to use /, not \ + if (path.sep !== '/') { + f = f.split(path.sep).join('/') + } + + // treat the test path as a set of pathparts. + f = f.split(slashSplit) + this.debug(this.pattern, 'split', f) + + // just ONE of the pattern sets in this.set needs to match + // in order for it to be valid. If negating, then just one + // match means that we have failed. + // Either way, return on the first hit. + + var set = this.set + this.debug(this.pattern, 'set', set) + + // Find the basename of the path by looking for the last non-empty segment + var filename + var i + for (i = f.length - 1; i >= 0; i--) { + filename = f[i] + if (filename) break + } + + for (i = 0; i < set.length; i++) { + var pattern = set[i] + var file = f + if (options.matchBase && pattern.length === 1) { + file = [filename] + } + var hit = this.matchOne(file, pattern, partial) + if (hit) { + if (options.flipNegate) return true + return !this.negate + } + } + + // didn't get any hits. this is success if it's a negative + // pattern, failure otherwise. + if (options.flipNegate) return false + return this.negate +} + +// set partial to true to test if, for example, +// "/a/b" matches the start of "/*/b/*/d" +// Partial means, if you run out of file before you run +// out of pattern, then that's fine, as long as all +// the parts match. +Minimatch.prototype.matchOne = function (file, pattern, partial) { + var options = this.options + + this.debug('matchOne', + { 'this': this, file: file, pattern: pattern }) + + this.debug('matchOne', file.length, pattern.length) + + for (var fi = 0, + pi = 0, + fl = file.length, + pl = pattern.length + ; (fi < fl) && (pi < pl) + ; fi++, pi++) { + this.debug('matchOne loop') + var p = pattern[pi] + var f = file[fi] + + this.debug(pattern, p, f) + + // should be impossible. + // some invalid regexp stuff in the set. + if (p === false) return false + + if (p === GLOBSTAR) { + this.debug('GLOBSTAR', [pattern, p, f]) + + // "**" + // a/**/b/**/c would match the following: + // a/b/x/y/z/c + // a/x/y/z/b/c + // a/b/x/b/x/c + // a/b/c + // To do this, take the rest of the pattern after + // the **, and see if it would match the file remainder. + // If so, return success. + // If not, the ** "swallows" a segment, and try again. + // This is recursively awful. + // + // a/**/b/**/c matching a/b/x/y/z/c + // - a matches a + // - doublestar + // - matchOne(b/x/y/z/c, b/**/c) + // - b matches b + // - doublestar + // - matchOne(x/y/z/c, c) -> no + // - matchOne(y/z/c, c) -> no + // - matchOne(z/c, c) -> no + // - matchOne(c, c) yes, hit + var fr = fi + var pr = pi + 1 + if (pr === pl) { + this.debug('** at the end') + // a ** at the end will just swallow the rest. + // We have found a match. + // however, it will not swallow /.x, unless + // options.dot is set. + // . and .. are *never* matched by **, for explosively + // exponential reasons. + for (; fi < fl; fi++) { + if (file[fi] === '.' || file[fi] === '..' || + (!options.dot && file[fi].charAt(0) === '.')) return false + } + return true + } + + // ok, let's see if we can swallow whatever we can. + while (fr < fl) { + var swallowee = file[fr] + + this.debug('\nglobstar while', file, fr, pattern, pr, swallowee) + + // XXX remove this slice. Just pass the start index. + if (this.matchOne(file.slice(fr), pattern.slice(pr), partial)) { + this.debug('globstar found match!', fr, fl, swallowee) + // found a match. + return true + } else { + // can't swallow "." or ".." ever. + // can only swallow ".foo" when explicitly asked. + if (swallowee === '.' || swallowee === '..' || + (!options.dot && swallowee.charAt(0) === '.')) { + this.debug('dot detected!', file, fr, pattern, pr) + break + } + + // ** swallows a segment, and continue. + this.debug('globstar swallow a segment, and continue') + fr++ + } + } + + // no match was found. + // However, in partial mode, we can't say this is necessarily over. + // If there's more *pattern* left, then + if (partial) { + // ran out of file + this.debug('\n>>> no match, partial?', file, fr, pattern, pr) + if (fr === fl) return true + } + return false + } + + // something other than ** + // non-magic patterns just have to match exactly + // patterns with magic have been turned into regexps. + var hit + if (typeof p === 'string') { + if (options.nocase) { + hit = f.toLowerCase() === p.toLowerCase() + } else { + hit = f === p + } + this.debug('string match', p, f, hit) + } else { + hit = f.match(p) + this.debug('pattern match', p, f, hit) + } + + if (!hit) return false + } + + // Note: ending in / means that we'll get a final "" + // at the end of the pattern. This can only match a + // corresponding "" at the end of the file. + // If the file ends in /, then it can only match a + // a pattern that ends in /, unless the pattern just + // doesn't have any more for it. But, a/b/ should *not* + // match "a/b/*", even though "" matches against the + // [^/]*? pattern, except in partial mode, where it might + // simply not be reached yet. + // However, a/b/ should still satisfy a/* + + // now either we fell off the end of the pattern, or we're done. + if (fi === fl && pi === pl) { + // ran out of pattern and filename at the same time. + // an exact hit! + return true + } else if (fi === fl) { + // ran out of file, but still had pattern left. + // this is ok if we're doing the match as part of + // a glob fs traversal. + return partial + } else if (pi === pl) { + // ran out of pattern, still have file left. + // this is only acceptable if we're on the very last + // empty segment of a file with a trailing slash. + // a/* should match a/b/ + var emptyFileEnd = (fi === fl - 1) && (file[fi] === '') + return emptyFileEnd + } + + // should be unreachable. + throw new Error('wtf?') +} + +// replace stuff like \* with * +function globUnescape (s) { + return s.replace(/\\(.)/g, '$1') +} + +function regExpEscape (s) { + return s.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&') +} + +},{"brace-expansion":11,"path":22}],21:[function(require,module,exports){ +var wrappy = require('wrappy') +module.exports = wrappy(once) +module.exports.strict = wrappy(onceStrict) + +once.proto = once(function () { + Object.defineProperty(Function.prototype, 'once', { + value: function () { + return once(this) + }, + configurable: true + }) + + Object.defineProperty(Function.prototype, 'onceStrict', { + value: function () { + return onceStrict(this) + }, + configurable: true + }) +}) + +function once (fn) { + var f = function () { + if (f.called) return f.value + f.called = true + return f.value = fn.apply(this, arguments) + } + f.called = false + return f +} + +function onceStrict (fn) { + var f = function () { + if (f.called) + throw new Error(f.onceError) + f.called = true + return f.value = fn.apply(this, arguments) + } + var name = fn.name || 'Function wrapped with `once`' + f.onceError = name + " shouldn't be called more than once" + f.called = false + return f +} + +},{"wrappy":29}],22:[function(require,module,exports){ +(function (process){ +// Copyright Joyent, Inc. and other Node contributors. +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the +// "Software"), to deal in the Software without restriction, including +// without limitation the rights to use, copy, modify, merge, publish, +// distribute, sublicense, and/or sell copies of the Software, and to permit +// persons to whom the Software is furnished to do so, subject to the +// following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN +// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +// USE OR OTHER DEALINGS IN THE SOFTWARE. + +// resolves . and .. elements in a path array with directory names there +// must be no slashes, empty elements, or device names (c:\) in the array +// (so also no leading and trailing slashes - it does not distinguish +// relative and absolute paths) +function normalizeArray(parts, allowAboveRoot) { + // if the path tries to go above the root, `up` ends up > 0 + var up = 0; + for (var i = parts.length - 1; i >= 0; i--) { + var last = parts[i]; + if (last === '.') { + parts.splice(i, 1); + } else if (last === '..') { + parts.splice(i, 1); + up++; + } else if (up) { + parts.splice(i, 1); + up--; + } + } + + // if the path is allowed to go above the root, restore leading ..s + if (allowAboveRoot) { + for (; up--; up) { + parts.unshift('..'); + } + } + + return parts; +} + +// Split a filename into [root, dir, basename, ext], unix version +// 'root' is just a slash, or nothing. +var splitPathRe = + /^(\/?|)([\s\S]*?)((?:\.{1,2}|[^\/]+?|)(\.[^.\/]*|))(?:[\/]*)$/; +var splitPath = function(filename) { + return splitPathRe.exec(filename).slice(1); +}; + +// path.resolve([from ...], to) +// posix version +exports.resolve = function() { + var resolvedPath = '', + resolvedAbsolute = false; + + for (var i = arguments.length - 1; i >= -1 && !resolvedAbsolute; i--) { + var path = (i >= 0) ? arguments[i] : process.cwd(); + + // Skip empty and invalid entries + if (typeof path !== 'string') { + throw new TypeError('Arguments to path.resolve must be strings'); + } else if (!path) { + continue; + } + + resolvedPath = path + '/' + resolvedPath; + resolvedAbsolute = path.charAt(0) === '/'; + } + + // At this point the path should be resolved to a full absolute path, but + // handle relative paths to be safe (might happen when process.cwd() fails) + + // Normalize the path + resolvedPath = normalizeArray(filter(resolvedPath.split('/'), function(p) { + return !!p; + }), !resolvedAbsolute).join('/'); + + return ((resolvedAbsolute ? '/' : '') + resolvedPath) || '.'; +}; + +// path.normalize(path) +// posix version +exports.normalize = function(path) { + var isAbsolute = exports.isAbsolute(path), + trailingSlash = substr(path, -1) === '/'; + + // Normalize the path + path = normalizeArray(filter(path.split('/'), function(p) { + return !!p; + }), !isAbsolute).join('/'); + + if (!path && !isAbsolute) { + path = '.'; + } + if (path && trailingSlash) { + path += '/'; + } + + return (isAbsolute ? '/' : '') + path; +}; + +// posix version +exports.isAbsolute = function(path) { + return path.charAt(0) === '/'; +}; + +// posix version +exports.join = function() { + var paths = Array.prototype.slice.call(arguments, 0); + return exports.normalize(filter(paths, function(p, index) { + if (typeof p !== 'string') { + throw new TypeError('Arguments to path.join must be strings'); + } + return p; + }).join('/')); +}; + + +// path.relative(from, to) +// posix version +exports.relative = function(from, to) { + from = exports.resolve(from).substr(1); + to = exports.resolve(to).substr(1); + + function trim(arr) { + var start = 0; + for (; start < arr.length; start++) { + if (arr[start] !== '') break; + } + + var end = arr.length - 1; + for (; end >= 0; end--) { + if (arr[end] !== '') break; + } + + if (start > end) return []; + return arr.slice(start, end - start + 1); + } + + var fromParts = trim(from.split('/')); + var toParts = trim(to.split('/')); + + var length = Math.min(fromParts.length, toParts.length); + var samePartsLength = length; + for (var i = 0; i < length; i++) { + if (fromParts[i] !== toParts[i]) { + samePartsLength = i; + break; + } + } + + var outputParts = []; + for (var i = samePartsLength; i < fromParts.length; i++) { + outputParts.push('..'); + } + + outputParts = outputParts.concat(toParts.slice(samePartsLength)); + + return outputParts.join('/'); +}; + +exports.sep = '/'; +exports.delimiter = ':'; + +exports.dirname = function(path) { + var result = splitPath(path), + root = result[0], + dir = result[1]; + + if (!root && !dir) { + // No dirname whatsoever + return '.'; + } + + if (dir) { + // It has a dirname, strip trailing slash + dir = dir.substr(0, dir.length - 1); + } + + return root + dir; +}; + + +exports.basename = function(path, ext) { + var f = splitPath(path)[2]; + // TODO: make this comparison case-insensitive on windows? + if (ext && f.substr(-1 * ext.length) === ext) { + f = f.substr(0, f.length - ext.length); + } + return f; +}; + + +exports.extname = function(path) { + return splitPath(path)[3]; +}; + +function filter (xs, f) { + if (xs.filter) return xs.filter(f); + var res = []; + for (var i = 0; i < xs.length; i++) { + if (f(xs[i], i, xs)) res.push(xs[i]); + } + return res; +} + +// String.prototype.substr - negative index don't work in IE8 +var substr = 'ab'.substr(-1) === 'b' + ? function (str, start, len) { return str.substr(start, len) } + : function (str, start, len) { + if (start < 0) start = str.length + start; + return str.substr(start, len); + } +; + +}).call(this,require('_process')) +},{"_process":24}],23:[function(require,module,exports){ +(function (process){ +'use strict'; + +function posix(path) { + return path.charAt(0) === '/'; +} + +function win32(path) { + // https://github.com/nodejs/node/blob/b3fcc245fb25539909ef1d5eaa01dbf92e168633/lib/path.js#L56 + var splitDeviceRe = /^([a-zA-Z]:|[\\\/]{2}[^\\\/]+[\\\/]+[^\\\/]+)?([\\\/])?([\s\S]*?)$/; + var result = splitDeviceRe.exec(path); + var device = result[1] || ''; + var isUnc = Boolean(device && device.charAt(1) !== ':'); + + // UNC paths are always absolute + return Boolean(result[2] || isUnc); +} + +module.exports = process.platform === 'win32' ? win32 : posix; +module.exports.posix = posix; +module.exports.win32 = win32; + +}).call(this,require('_process')) +},{"_process":24}],24:[function(require,module,exports){ +// shim for using process in browser +var process = module.exports = {}; + +// cached from whatever global is present so that test runners that stub it +// don't break things. But we need to wrap it in a try catch in case it is +// wrapped in strict mode code which doesn't define any globals. It's inside a +// function because try/catches deoptimize in certain engines. + +var cachedSetTimeout; +var cachedClearTimeout; + +function defaultSetTimout() { + throw new Error('setTimeout has not been defined'); +} +function defaultClearTimeout () { + throw new Error('clearTimeout has not been defined'); +} +(function () { + try { + if (typeof setTimeout === 'function') { + cachedSetTimeout = setTimeout; + } else { + cachedSetTimeout = defaultSetTimout; + } + } catch (e) { + cachedSetTimeout = defaultSetTimout; + } + try { + if (typeof clearTimeout === 'function') { + cachedClearTimeout = clearTimeout; + } else { + cachedClearTimeout = defaultClearTimeout; + } + } catch (e) { + cachedClearTimeout = defaultClearTimeout; + } +} ()) +function runTimeout(fun) { + if (cachedSetTimeout === setTimeout) { + //normal enviroments in sane situations + return setTimeout(fun, 0); + } + // if setTimeout wasn't available but was latter defined + if ((cachedSetTimeout === defaultSetTimout || !cachedSetTimeout) && setTimeout) { + cachedSetTimeout = setTimeout; + return setTimeout(fun, 0); + } + try { + // when when somebody has screwed with setTimeout but no I.E. maddness + return cachedSetTimeout(fun, 0); + } catch(e){ + try { + // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally + return cachedSetTimeout.call(null, fun, 0); + } catch(e){ + // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error + return cachedSetTimeout.call(this, fun, 0); + } + } + + +} +function runClearTimeout(marker) { + if (cachedClearTimeout === clearTimeout) { + //normal enviroments in sane situations + return clearTimeout(marker); + } + // if clearTimeout wasn't available but was latter defined + if ((cachedClearTimeout === defaultClearTimeout || !cachedClearTimeout) && clearTimeout) { + cachedClearTimeout = clearTimeout; + return clearTimeout(marker); + } + try { + // when when somebody has screwed with setTimeout but no I.E. maddness + return cachedClearTimeout(marker); + } catch (e){ + try { + // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally + return cachedClearTimeout.call(null, marker); + } catch (e){ + // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error. + // Some versions of I.E. have different rules for clearTimeout vs setTimeout + return cachedClearTimeout.call(this, marker); + } + } + + + +} +var queue = []; +var draining = false; +var currentQueue; +var queueIndex = -1; + +function cleanUpNextTick() { + if (!draining || !currentQueue) { + return; + } + draining = false; + if (currentQueue.length) { + queue = currentQueue.concat(queue); + } else { + queueIndex = -1; + } + if (queue.length) { + drainQueue(); + } +} + +function drainQueue() { + if (draining) { + return; + } + var timeout = runTimeout(cleanUpNextTick); + draining = true; + + var len = queue.length; + while(len) { + currentQueue = queue; + queue = []; + while (++queueIndex < len) { + if (currentQueue) { + currentQueue[queueIndex].run(); + } + } + queueIndex = -1; + len = queue.length; + } + currentQueue = null; + draining = false; + runClearTimeout(timeout); +} + +process.nextTick = function (fun) { + var args = new Array(arguments.length - 1); + if (arguments.length > 1) { + for (var i = 1; i < arguments.length; i++) { + args[i - 1] = arguments[i]; + } + } + queue.push(new Item(fun, args)); + if (queue.length === 1 && !draining) { + runTimeout(drainQueue); + } +}; + +// v8 likes predictible objects +function Item(fun, array) { + this.fun = fun; + this.array = array; +} +Item.prototype.run = function () { + this.fun.apply(null, this.array); +}; +process.title = 'browser'; +process.browser = true; +process.env = {}; +process.argv = []; +process.version = ''; // empty string to avoid regexp issues +process.versions = {}; + +function noop() {} + +process.on = noop; +process.addListener = noop; +process.once = noop; +process.off = noop; +process.removeListener = noop; +process.removeAllListeners = noop; +process.emit = noop; +process.prependListener = noop; +process.prependOnceListener = noop; + +process.listeners = function (name) { return [] } + +process.binding = function (name) { + throw new Error('process.binding is not supported'); +}; + +process.cwd = function () { return '/' }; +process.chdir = function (dir) { + throw new Error('process.chdir is not supported'); +}; +process.umask = function() { return 0; }; + +},{}],25:[function(require,module,exports){ +// Underscore.js 1.8.3 +// http://underscorejs.org +// (c) 2009-2015 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors +// Underscore may be freely distributed under the MIT license. + +(function() { + + // Baseline setup + // -------------- + + // Establish the root object, `window` in the browser, or `exports` on the server. + var root = this; + + // Save the previous value of the `_` variable. + var previousUnderscore = root._; + + // Save bytes in the minified (but not gzipped) version: + var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; + + // Create quick reference variables for speed access to core prototypes. + var + push = ArrayProto.push, + slice = ArrayProto.slice, + toString = ObjProto.toString, + hasOwnProperty = ObjProto.hasOwnProperty; + + // All **ECMAScript 5** native function implementations that we hope to use + // are declared here. + var + nativeIsArray = Array.isArray, + nativeKeys = Object.keys, + nativeBind = FuncProto.bind, + nativeCreate = Object.create; + + // Naked function reference for surrogate-prototype-swapping. + var Ctor = function(){}; + + // Create a safe reference to the Underscore object for use below. + var _ = function(obj) { + if (obj instanceof _) return obj; + if (!(this instanceof _)) return new _(obj); + this._wrapped = obj; + }; + + // Export the Underscore object for **Node.js**, with + // backwards-compatibility for the old `require()` API. If we're in + // the browser, add `_` as a global object. + if (typeof exports !== 'undefined') { + if (typeof module !== 'undefined' && module.exports) { + exports = module.exports = _; + } + exports._ = _; + } else { + root._ = _; + } + + // Current version. + _.VERSION = '1.8.3'; + + // Internal function that returns an efficient (for current engines) version + // of the passed-in callback, to be repeatedly applied in other Underscore + // functions. + var optimizeCb = function(func, context, argCount) { + if (context === void 0) return func; + switch (argCount == null ? 3 : argCount) { + case 1: return function(value) { + return func.call(context, value); + }; + case 2: return function(value, other) { + return func.call(context, value, other); + }; + case 3: return function(value, index, collection) { + return func.call(context, value, index, collection); + }; + case 4: return function(accumulator, value, index, collection) { + return func.call(context, accumulator, value, index, collection); + }; + } + return function() { + return func.apply(context, arguments); + }; + }; + + // A mostly-internal function to generate callbacks that can be applied + // to each element in a collection, returning the desired result — either + // identity, an arbitrary callback, a property matcher, or a property accessor. + var cb = function(value, context, argCount) { + if (value == null) return _.identity; + if (_.isFunction(value)) return optimizeCb(value, context, argCount); + if (_.isObject(value)) return _.matcher(value); + return _.property(value); + }; + _.iteratee = function(value, context) { + return cb(value, context, Infinity); + }; + + // An internal function for creating assigner functions. + var createAssigner = function(keysFunc, undefinedOnly) { + return function(obj) { + var length = arguments.length; + if (length < 2 || obj == null) return obj; + for (var index = 1; index < length; index++) { + var source = arguments[index], + keys = keysFunc(source), + l = keys.length; + for (var i = 0; i < l; i++) { + var key = keys[i]; + if (!undefinedOnly || obj[key] === void 0) obj[key] = source[key]; + } + } + return obj; + }; + }; + + // An internal function for creating a new object that inherits from another. + var baseCreate = function(prototype) { + if (!_.isObject(prototype)) return {}; + if (nativeCreate) return nativeCreate(prototype); + Ctor.prototype = prototype; + var result = new Ctor; + Ctor.prototype = null; + return result; + }; + + var property = function(key) { + return function(obj) { + return obj == null ? void 0 : obj[key]; + }; + }; + + // Helper for collection methods to determine whether a collection + // should be iterated as an array or as an object + // Related: http://people.mozilla.org/~jorendorff/es6-draft.html#sec-tolength + // Avoids a very nasty iOS 8 JIT bug on ARM-64. #2094 + var MAX_ARRAY_INDEX = Math.pow(2, 53) - 1; + var getLength = property('length'); + var isArrayLike = function(collection) { + var length = getLength(collection); + return typeof length == 'number' && length >= 0 && length <= MAX_ARRAY_INDEX; + }; + + // Collection Functions + // -------------------- + + // The cornerstone, an `each` implementation, aka `forEach`. + // Handles raw objects in addition to array-likes. Treats all + // sparse array-likes as if they were dense. + _.each = _.forEach = function(obj, iteratee, context) { + iteratee = optimizeCb(iteratee, context); + var i, length; + if (isArrayLike(obj)) { + for (i = 0, length = obj.length; i < length; i++) { + iteratee(obj[i], i, obj); + } + } else { + var keys = _.keys(obj); + for (i = 0, length = keys.length; i < length; i++) { + iteratee(obj[keys[i]], keys[i], obj); + } + } + return obj; + }; + + // Return the results of applying the iteratee to each element. + _.map = _.collect = function(obj, iteratee, context) { + iteratee = cb(iteratee, context); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length, + results = Array(length); + for (var index = 0; index < length; index++) { + var currentKey = keys ? keys[index] : index; + results[index] = iteratee(obj[currentKey], currentKey, obj); + } + return results; + }; + + // Create a reducing function iterating left or right. + function createReduce(dir) { + // Optimized iterator function as using arguments.length + // in the main function will deoptimize the, see #1991. + function iterator(obj, iteratee, memo, keys, index, length) { + for (; index >= 0 && index < length; index += dir) { + var currentKey = keys ? keys[index] : index; + memo = iteratee(memo, obj[currentKey], currentKey, obj); + } + return memo; + } + + return function(obj, iteratee, memo, context) { + iteratee = optimizeCb(iteratee, context, 4); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length, + index = dir > 0 ? 0 : length - 1; + // Determine the initial value if none is provided. + if (arguments.length < 3) { + memo = obj[keys ? keys[index] : index]; + index += dir; + } + return iterator(obj, iteratee, memo, keys, index, length); + }; + } + + // **Reduce** builds up a single result from a list of values, aka `inject`, + // or `foldl`. + _.reduce = _.foldl = _.inject = createReduce(1); + + // The right-associative version of reduce, also known as `foldr`. + _.reduceRight = _.foldr = createReduce(-1); + + // Return the first value which passes a truth test. Aliased as `detect`. + _.find = _.detect = function(obj, predicate, context) { + var key; + if (isArrayLike(obj)) { + key = _.findIndex(obj, predicate, context); + } else { + key = _.findKey(obj, predicate, context); + } + if (key !== void 0 && key !== -1) return obj[key]; + }; + + // Return all the elements that pass a truth test. + // Aliased as `select`. + _.filter = _.select = function(obj, predicate, context) { + var results = []; + predicate = cb(predicate, context); + _.each(obj, function(value, index, list) { + if (predicate(value, index, list)) results.push(value); + }); + return results; + }; + + // Return all the elements for which a truth test fails. + _.reject = function(obj, predicate, context) { + return _.filter(obj, _.negate(cb(predicate)), context); + }; + + // Determine whether all of the elements match a truth test. + // Aliased as `all`. + _.every = _.all = function(obj, predicate, context) { + predicate = cb(predicate, context); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length; + for (var index = 0; index < length; index++) { + var currentKey = keys ? keys[index] : index; + if (!predicate(obj[currentKey], currentKey, obj)) return false; + } + return true; + }; + + // Determine if at least one element in the object matches a truth test. + // Aliased as `any`. + _.some = _.any = function(obj, predicate, context) { + predicate = cb(predicate, context); + var keys = !isArrayLike(obj) && _.keys(obj), + length = (keys || obj).length; + for (var index = 0; index < length; index++) { + var currentKey = keys ? keys[index] : index; + if (predicate(obj[currentKey], currentKey, obj)) return true; + } + return false; + }; + + // Determine if the array or object contains a given item (using `===`). + // Aliased as `includes` and `include`. + _.contains = _.includes = _.include = function(obj, item, fromIndex, guard) { + if (!isArrayLike(obj)) obj = _.values(obj); + if (typeof fromIndex != 'number' || guard) fromIndex = 0; + return _.indexOf(obj, item, fromIndex) >= 0; + }; + + // Invoke a method (with arguments) on every item in a collection. + _.invoke = function(obj, method) { + var args = slice.call(arguments, 2); + var isFunc = _.isFunction(method); + return _.map(obj, function(value) { + var func = isFunc ? method : value[method]; + return func == null ? func : func.apply(value, args); + }); + }; + + // Convenience version of a common use case of `map`: fetching a property. + _.pluck = function(obj, key) { + return _.map(obj, _.property(key)); + }; + + // Convenience version of a common use case of `filter`: selecting only objects + // containing specific `key:value` pairs. + _.where = function(obj, attrs) { + return _.filter(obj, _.matcher(attrs)); + }; + + // Convenience version of a common use case of `find`: getting the first object + // containing specific `key:value` pairs. + _.findWhere = function(obj, attrs) { + return _.find(obj, _.matcher(attrs)); + }; + + // Return the maximum element (or element-based computation). + _.max = function(obj, iteratee, context) { + var result = -Infinity, lastComputed = -Infinity, + value, computed; + if (iteratee == null && obj != null) { + obj = isArrayLike(obj) ? obj : _.values(obj); + for (var i = 0, length = obj.length; i < length; i++) { + value = obj[i]; + if (value > result) { + result = value; + } + } + } else { + iteratee = cb(iteratee, context); + _.each(obj, function(value, index, list) { + computed = iteratee(value, index, list); + if (computed > lastComputed || computed === -Infinity && result === -Infinity) { + result = value; + lastComputed = computed; + } + }); + } + return result; + }; + + // Return the minimum element (or element-based computation). + _.min = function(obj, iteratee, context) { + var result = Infinity, lastComputed = Infinity, + value, computed; + if (iteratee == null && obj != null) { + obj = isArrayLike(obj) ? obj : _.values(obj); + for (var i = 0, length = obj.length; i < length; i++) { + value = obj[i]; + if (value < result) { + result = value; + } + } + } else { + iteratee = cb(iteratee, context); + _.each(obj, function(value, index, list) { + computed = iteratee(value, index, list); + if (computed < lastComputed || computed === Infinity && result === Infinity) { + result = value; + lastComputed = computed; + } + }); + } + return result; + }; + + // Shuffle a collection, using the modern version of the + // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle). + _.shuffle = function(obj) { + var set = isArrayLike(obj) ? obj : _.values(obj); + var length = set.length; + var shuffled = Array(length); + for (var index = 0, rand; index < length; index++) { + rand = _.random(0, index); + if (rand !== index) shuffled[index] = shuffled[rand]; + shuffled[rand] = set[index]; + } + return shuffled; + }; + + // Sample **n** random values from a collection. + // If **n** is not specified, returns a single random element. + // The internal `guard` argument allows it to work with `map`. + _.sample = function(obj, n, guard) { + if (n == null || guard) { + if (!isArrayLike(obj)) obj = _.values(obj); + return obj[_.random(obj.length - 1)]; + } + return _.shuffle(obj).slice(0, Math.max(0, n)); + }; + + // Sort the object's values by a criterion produced by an iteratee. + _.sortBy = function(obj, iteratee, context) { + iteratee = cb(iteratee, context); + return _.pluck(_.map(obj, function(value, index, list) { + return { + value: value, + index: index, + criteria: iteratee(value, index, list) + }; + }).sort(function(left, right) { + var a = left.criteria; + var b = right.criteria; + if (a !== b) { + if (a > b || a === void 0) return 1; + if (a < b || b === void 0) return -1; + } + return left.index - right.index; + }), 'value'); + }; + + // An internal function used for aggregate "group by" operations. + var group = function(behavior) { + return function(obj, iteratee, context) { + var result = {}; + iteratee = cb(iteratee, context); + _.each(obj, function(value, index) { + var key = iteratee(value, index, obj); + behavior(result, value, key); + }); + return result; + }; + }; + + // Groups the object's values by a criterion. Pass either a string attribute + // to group by, or a function that returns the criterion. + _.groupBy = group(function(result, value, key) { + if (_.has(result, key)) result[key].push(value); else result[key] = [value]; + }); + + // Indexes the object's values by a criterion, similar to `groupBy`, but for + // when you know that your index values will be unique. + _.indexBy = group(function(result, value, key) { + result[key] = value; + }); + + // Counts instances of an object that group by a certain criterion. Pass + // either a string attribute to count by, or a function that returns the + // criterion. + _.countBy = group(function(result, value, key) { + if (_.has(result, key)) result[key]++; else result[key] = 1; + }); + + // Safely create a real, live array from anything iterable. + _.toArray = function(obj) { + if (!obj) return []; + if (_.isArray(obj)) return slice.call(obj); + if (isArrayLike(obj)) return _.map(obj, _.identity); + return _.values(obj); + }; + + // Return the number of elements in an object. + _.size = function(obj) { + if (obj == null) return 0; + return isArrayLike(obj) ? obj.length : _.keys(obj).length; + }; + + // Split a collection into two arrays: one whose elements all satisfy the given + // predicate, and one whose elements all do not satisfy the predicate. + _.partition = function(obj, predicate, context) { + predicate = cb(predicate, context); + var pass = [], fail = []; + _.each(obj, function(value, key, obj) { + (predicate(value, key, obj) ? pass : fail).push(value); + }); + return [pass, fail]; + }; + + // Array Functions + // --------------- + + // Get the first element of an array. Passing **n** will return the first N + // values in the array. Aliased as `head` and `take`. The **guard** check + // allows it to work with `_.map`. + _.first = _.head = _.take = function(array, n, guard) { + if (array == null) return void 0; + if (n == null || guard) return array[0]; + return _.initial(array, array.length - n); + }; + + // Returns everything but the last entry of the array. Especially useful on + // the arguments object. Passing **n** will return all the values in + // the array, excluding the last N. + _.initial = function(array, n, guard) { + return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n))); + }; + + // Get the last element of an array. Passing **n** will return the last N + // values in the array. + _.last = function(array, n, guard) { + if (array == null) return void 0; + if (n == null || guard) return array[array.length - 1]; + return _.rest(array, Math.max(0, array.length - n)); + }; + + // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. + // Especially useful on the arguments object. Passing an **n** will return + // the rest N values in the array. + _.rest = _.tail = _.drop = function(array, n, guard) { + return slice.call(array, n == null || guard ? 1 : n); + }; + + // Trim out all falsy values from an array. + _.compact = function(array) { + return _.filter(array, _.identity); + }; + + // Internal implementation of a recursive `flatten` function. + var flatten = function(input, shallow, strict, startIndex) { + var output = [], idx = 0; + for (var i = startIndex || 0, length = getLength(input); i < length; i++) { + var value = input[i]; + if (isArrayLike(value) && (_.isArray(value) || _.isArguments(value))) { + //flatten current level of array or arguments object + if (!shallow) value = flatten(value, shallow, strict); + var j = 0, len = value.length; + output.length += len; + while (j < len) { + output[idx++] = value[j++]; + } + } else if (!strict) { + output[idx++] = value; + } + } + return output; + }; + + // Flatten out an array, either recursively (by default), or just one level. + _.flatten = function(array, shallow) { + return flatten(array, shallow, false); + }; + + // Return a version of the array that does not contain the specified value(s). + _.without = function(array) { + return _.difference(array, slice.call(arguments, 1)); + }; + + // Produce a duplicate-free version of the array. If the array has already + // been sorted, you have the option of using a faster algorithm. + // Aliased as `unique`. + _.uniq = _.unique = function(array, isSorted, iteratee, context) { + if (!_.isBoolean(isSorted)) { + context = iteratee; + iteratee = isSorted; + isSorted = false; + } + if (iteratee != null) iteratee = cb(iteratee, context); + var result = []; + var seen = []; + for (var i = 0, length = getLength(array); i < length; i++) { + var value = array[i], + computed = iteratee ? iteratee(value, i, array) : value; + if (isSorted) { + if (!i || seen !== computed) result.push(value); + seen = computed; + } else if (iteratee) { + if (!_.contains(seen, computed)) { + seen.push(computed); + result.push(value); + } + } else if (!_.contains(result, value)) { + result.push(value); + } + } + return result; + }; + + // Produce an array that contains the union: each distinct element from all of + // the passed-in arrays. + _.union = function() { + return _.uniq(flatten(arguments, true, true)); + }; + + // Produce an array that contains every item shared between all the + // passed-in arrays. + _.intersection = function(array) { + var result = []; + var argsLength = arguments.length; + for (var i = 0, length = getLength(array); i < length; i++) { + var item = array[i]; + if (_.contains(result, item)) continue; + for (var j = 1; j < argsLength; j++) { + if (!_.contains(arguments[j], item)) break; + } + if (j === argsLength) result.push(item); + } + return result; + }; + + // Take the difference between one array and a number of other arrays. + // Only the elements present in just the first array will remain. + _.difference = function(array) { + var rest = flatten(arguments, true, true, 1); + return _.filter(array, function(value){ + return !_.contains(rest, value); + }); + }; + + // Zip together multiple lists into a single array -- elements that share + // an index go together. + _.zip = function() { + return _.unzip(arguments); + }; + + // Complement of _.zip. Unzip accepts an array of arrays and groups + // each array's elements on shared indices + _.unzip = function(array) { + var length = array && _.max(array, getLength).length || 0; + var result = Array(length); + + for (var index = 0; index < length; index++) { + result[index] = _.pluck(array, index); + } + return result; + }; + + // Converts lists into objects. Pass either a single array of `[key, value]` + // pairs, or two parallel arrays of the same length -- one of keys, and one of + // the corresponding values. + _.object = function(list, values) { + var result = {}; + for (var i = 0, length = getLength(list); i < length; i++) { + if (values) { + result[list[i]] = values[i]; + } else { + result[list[i][0]] = list[i][1]; + } + } + return result; + }; + + // Generator function to create the findIndex and findLastIndex functions + function createPredicateIndexFinder(dir) { + return function(array, predicate, context) { + predicate = cb(predicate, context); + var length = getLength(array); + var index = dir > 0 ? 0 : length - 1; + for (; index >= 0 && index < length; index += dir) { + if (predicate(array[index], index, array)) return index; + } + return -1; + }; + } + + // Returns the first index on an array-like that passes a predicate test + _.findIndex = createPredicateIndexFinder(1); + _.findLastIndex = createPredicateIndexFinder(-1); + + // Use a comparator function to figure out the smallest index at which + // an object should be inserted so as to maintain order. Uses binary search. + _.sortedIndex = function(array, obj, iteratee, context) { + iteratee = cb(iteratee, context, 1); + var value = iteratee(obj); + var low = 0, high = getLength(array); + while (low < high) { + var mid = Math.floor((low + high) / 2); + if (iteratee(array[mid]) < value) low = mid + 1; else high = mid; + } + return low; + }; + + // Generator function to create the indexOf and lastIndexOf functions + function createIndexFinder(dir, predicateFind, sortedIndex) { + return function(array, item, idx) { + var i = 0, length = getLength(array); + if (typeof idx == 'number') { + if (dir > 0) { + i = idx >= 0 ? idx : Math.max(idx + length, i); + } else { + length = idx >= 0 ? Math.min(idx + 1, length) : idx + length + 1; + } + } else if (sortedIndex && idx && length) { + idx = sortedIndex(array, item); + return array[idx] === item ? idx : -1; + } + if (item !== item) { + idx = predicateFind(slice.call(array, i, length), _.isNaN); + return idx >= 0 ? idx + i : -1; + } + for (idx = dir > 0 ? i : length - 1; idx >= 0 && idx < length; idx += dir) { + if (array[idx] === item) return idx; + } + return -1; + }; + } + + // Return the position of the first occurrence of an item in an array, + // or -1 if the item is not included in the array. + // If the array is large and already in sort order, pass `true` + // for **isSorted** to use binary search. + _.indexOf = createIndexFinder(1, _.findIndex, _.sortedIndex); + _.lastIndexOf = createIndexFinder(-1, _.findLastIndex); + + // Generate an integer Array containing an arithmetic progression. A port of + // the native Python `range()` function. See + // [the Python documentation](http://docs.python.org/library/functions.html#range). + _.range = function(start, stop, step) { + if (stop == null) { + stop = start || 0; + start = 0; + } + step = step || 1; + + var length = Math.max(Math.ceil((stop - start) / step), 0); + var range = Array(length); + + for (var idx = 0; idx < length; idx++, start += step) { + range[idx] = start; + } + + return range; + }; + + // Function (ahem) Functions + // ------------------ + + // Determines whether to execute a function as a constructor + // or a normal function with the provided arguments + var executeBound = function(sourceFunc, boundFunc, context, callingContext, args) { + if (!(callingContext instanceof boundFunc)) return sourceFunc.apply(context, args); + var self = baseCreate(sourceFunc.prototype); + var result = sourceFunc.apply(self, args); + if (_.isObject(result)) return result; + return self; + }; + + // Create a function bound to a given object (assigning `this`, and arguments, + // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if + // available. + _.bind = function(func, context) { + if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1)); + if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function'); + var args = slice.call(arguments, 2); + var bound = function() { + return executeBound(func, bound, context, this, args.concat(slice.call(arguments))); + }; + return bound; + }; + + // Partially apply a function by creating a version that has had some of its + // arguments pre-filled, without changing its dynamic `this` context. _ acts + // as a placeholder, allowing any combination of arguments to be pre-filled. + _.partial = function(func) { + var boundArgs = slice.call(arguments, 1); + var bound = function() { + var position = 0, length = boundArgs.length; + var args = Array(length); + for (var i = 0; i < length; i++) { + args[i] = boundArgs[i] === _ ? arguments[position++] : boundArgs[i]; + } + while (position < arguments.length) args.push(arguments[position++]); + return executeBound(func, bound, this, this, args); + }; + return bound; + }; + + // Bind a number of an object's methods to that object. Remaining arguments + // are the method names to be bound. Useful for ensuring that all callbacks + // defined on an object belong to it. + _.bindAll = function(obj) { + var i, length = arguments.length, key; + if (length <= 1) throw new Error('bindAll must be passed function names'); + for (i = 1; i < length; i++) { + key = arguments[i]; + obj[key] = _.bind(obj[key], obj); + } + return obj; + }; + + // Memoize an expensive function by storing its results. + _.memoize = function(func, hasher) { + var memoize = function(key) { + var cache = memoize.cache; + var address = '' + (hasher ? hasher.apply(this, arguments) : key); + if (!_.has(cache, address)) cache[address] = func.apply(this, arguments); + return cache[address]; + }; + memoize.cache = {}; + return memoize; + }; + + // Delays a function for the given number of milliseconds, and then calls + // it with the arguments supplied. + _.delay = function(func, wait) { + var args = slice.call(arguments, 2); + return setTimeout(function(){ + return func.apply(null, args); + }, wait); + }; + + // Defers a function, scheduling it to run after the current call stack has + // cleared. + _.defer = _.partial(_.delay, _, 1); + + // Returns a function, that, when invoked, will only be triggered at most once + // during a given window of time. Normally, the throttled function will run + // as much as it can, without ever going more than once per `wait` duration; + // but if you'd like to disable the execution on the leading edge, pass + // `{leading: false}`. To disable execution on the trailing edge, ditto. + _.throttle = function(func, wait, options) { + var context, args, result; + var timeout = null; + var previous = 0; + if (!options) options = {}; + var later = function() { + previous = options.leading === false ? 0 : _.now(); + timeout = null; + result = func.apply(context, args); + if (!timeout) context = args = null; + }; + return function() { + var now = _.now(); + if (!previous && options.leading === false) previous = now; + var remaining = wait - (now - previous); + context = this; + args = arguments; + if (remaining <= 0 || remaining > wait) { + if (timeout) { + clearTimeout(timeout); + timeout = null; + } + previous = now; + result = func.apply(context, args); + if (!timeout) context = args = null; + } else if (!timeout && options.trailing !== false) { + timeout = setTimeout(later, remaining); + } + return result; + }; + }; + + // Returns a function, that, as long as it continues to be invoked, will not + // be triggered. The function will be called after it stops being called for + // N milliseconds. If `immediate` is passed, trigger the function on the + // leading edge, instead of the trailing. + _.debounce = function(func, wait, immediate) { + var timeout, args, context, timestamp, result; + + var later = function() { + var last = _.now() - timestamp; + + if (last < wait && last >= 0) { + timeout = setTimeout(later, wait - last); + } else { + timeout = null; + if (!immediate) { + result = func.apply(context, args); + if (!timeout) context = args = null; + } + } + }; + + return function() { + context = this; + args = arguments; + timestamp = _.now(); + var callNow = immediate && !timeout; + if (!timeout) timeout = setTimeout(later, wait); + if (callNow) { + result = func.apply(context, args); + context = args = null; + } + + return result; + }; + }; + + // Returns the first function passed as an argument to the second, + // allowing you to adjust arguments, run code before and after, and + // conditionally execute the original function. + _.wrap = function(func, wrapper) { + return _.partial(wrapper, func); + }; + + // Returns a negated version of the passed-in predicate. + _.negate = function(predicate) { + return function() { + return !predicate.apply(this, arguments); + }; + }; + + // Returns a function that is the composition of a list of functions, each + // consuming the return value of the function that follows. + _.compose = function() { + var args = arguments; + var start = args.length - 1; + return function() { + var i = start; + var result = args[start].apply(this, arguments); + while (i--) result = args[i].call(this, result); + return result; + }; + }; + + // Returns a function that will only be executed on and after the Nth call. + _.after = function(times, func) { + return function() { + if (--times < 1) { + return func.apply(this, arguments); + } + }; + }; + + // Returns a function that will only be executed up to (but not including) the Nth call. + _.before = function(times, func) { + var memo; + return function() { + if (--times > 0) { + memo = func.apply(this, arguments); + } + if (times <= 1) func = null; + return memo; + }; + }; + + // Returns a function that will be executed at most one time, no matter how + // often you call it. Useful for lazy initialization. + _.once = _.partial(_.before, 2); + + // Object Functions + // ---------------- + + // Keys in IE < 9 that won't be iterated by `for key in ...` and thus missed. + var hasEnumBug = !{toString: null}.propertyIsEnumerable('toString'); + var nonEnumerableProps = ['valueOf', 'isPrototypeOf', 'toString', + 'propertyIsEnumerable', 'hasOwnProperty', 'toLocaleString']; + + function collectNonEnumProps(obj, keys) { + var nonEnumIdx = nonEnumerableProps.length; + var constructor = obj.constructor; + var proto = (_.isFunction(constructor) && constructor.prototype) || ObjProto; + + // Constructor is a special case. + var prop = 'constructor'; + if (_.has(obj, prop) && !_.contains(keys, prop)) keys.push(prop); + + while (nonEnumIdx--) { + prop = nonEnumerableProps[nonEnumIdx]; + if (prop in obj && obj[prop] !== proto[prop] && !_.contains(keys, prop)) { + keys.push(prop); + } + } + } + + // Retrieve the names of an object's own properties. + // Delegates to **ECMAScript 5**'s native `Object.keys` + _.keys = function(obj) { + if (!_.isObject(obj)) return []; + if (nativeKeys) return nativeKeys(obj); + var keys = []; + for (var key in obj) if (_.has(obj, key)) keys.push(key); + // Ahem, IE < 9. + if (hasEnumBug) collectNonEnumProps(obj, keys); + return keys; + }; + + // Retrieve all the property names of an object. + _.allKeys = function(obj) { + if (!_.isObject(obj)) return []; + var keys = []; + for (var key in obj) keys.push(key); + // Ahem, IE < 9. + if (hasEnumBug) collectNonEnumProps(obj, keys); + return keys; + }; + + // Retrieve the values of an object's properties. + _.values = function(obj) { + var keys = _.keys(obj); + var length = keys.length; + var values = Array(length); + for (var i = 0; i < length; i++) { + values[i] = obj[keys[i]]; + } + return values; + }; + + // Returns the results of applying the iteratee to each element of the object + // In contrast to _.map it returns an object + _.mapObject = function(obj, iteratee, context) { + iteratee = cb(iteratee, context); + var keys = _.keys(obj), + length = keys.length, + results = {}, + currentKey; + for (var index = 0; index < length; index++) { + currentKey = keys[index]; + results[currentKey] = iteratee(obj[currentKey], currentKey, obj); + } + return results; + }; + + // Convert an object into a list of `[key, value]` pairs. + _.pairs = function(obj) { + var keys = _.keys(obj); + var length = keys.length; + var pairs = Array(length); + for (var i = 0; i < length; i++) { + pairs[i] = [keys[i], obj[keys[i]]]; + } + return pairs; + }; + + // Invert the keys and values of an object. The values must be serializable. + _.invert = function(obj) { + var result = {}; + var keys = _.keys(obj); + for (var i = 0, length = keys.length; i < length; i++) { + result[obj[keys[i]]] = keys[i]; + } + return result; + }; + + // Return a sorted list of the function names available on the object. + // Aliased as `methods` + _.functions = _.methods = function(obj) { + var names = []; + for (var key in obj) { + if (_.isFunction(obj[key])) names.push(key); + } + return names.sort(); + }; + + // Extend a given object with all the properties in passed-in object(s). + _.extend = createAssigner(_.allKeys); + + // Assigns a given object with all the own properties in the passed-in object(s) + // (https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object/assign) + _.extendOwn = _.assign = createAssigner(_.keys); + + // Returns the first key on an object that passes a predicate test + _.findKey = function(obj, predicate, context) { + predicate = cb(predicate, context); + var keys = _.keys(obj), key; + for (var i = 0, length = keys.length; i < length; i++) { + key = keys[i]; + if (predicate(obj[key], key, obj)) return key; + } + }; + + // Return a copy of the object only containing the whitelisted properties. + _.pick = function(object, oiteratee, context) { + var result = {}, obj = object, iteratee, keys; + if (obj == null) return result; + if (_.isFunction(oiteratee)) { + keys = _.allKeys(obj); + iteratee = optimizeCb(oiteratee, context); + } else { + keys = flatten(arguments, false, false, 1); + iteratee = function(value, key, obj) { return key in obj; }; + obj = Object(obj); + } + for (var i = 0, length = keys.length; i < length; i++) { + var key = keys[i]; + var value = obj[key]; + if (iteratee(value, key, obj)) result[key] = value; + } + return result; + }; + + // Return a copy of the object without the blacklisted properties. + _.omit = function(obj, iteratee, context) { + if (_.isFunction(iteratee)) { + iteratee = _.negate(iteratee); + } else { + var keys = _.map(flatten(arguments, false, false, 1), String); + iteratee = function(value, key) { + return !_.contains(keys, key); + }; + } + return _.pick(obj, iteratee, context); + }; + + // Fill in a given object with default properties. + _.defaults = createAssigner(_.allKeys, true); + + // Creates an object that inherits from the given prototype object. + // If additional properties are provided then they will be added to the + // created object. + _.create = function(prototype, props) { + var result = baseCreate(prototype); + if (props) _.extendOwn(result, props); + return result; + }; + + // Create a (shallow-cloned) duplicate of an object. + _.clone = function(obj) { + if (!_.isObject(obj)) return obj; + return _.isArray(obj) ? obj.slice() : _.extend({}, obj); + }; + + // Invokes interceptor with the obj, and then returns obj. + // The primary purpose of this method is to "tap into" a method chain, in + // order to perform operations on intermediate results within the chain. + _.tap = function(obj, interceptor) { + interceptor(obj); + return obj; + }; + + // Returns whether an object has a given set of `key:value` pairs. + _.isMatch = function(object, attrs) { + var keys = _.keys(attrs), length = keys.length; + if (object == null) return !length; + var obj = Object(object); + for (var i = 0; i < length; i++) { + var key = keys[i]; + if (attrs[key] !== obj[key] || !(key in obj)) return false; + } + return true; + }; + + + // Internal recursive comparison function for `isEqual`. + var eq = function(a, b, aStack, bStack) { + // Identical objects are equal. `0 === -0`, but they aren't identical. + // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal). + if (a === b) return a !== 0 || 1 / a === 1 / b; + // A strict comparison is necessary because `null == undefined`. + if (a == null || b == null) return a === b; + // Unwrap any wrapped objects. + if (a instanceof _) a = a._wrapped; + if (b instanceof _) b = b._wrapped; + // Compare `[[Class]]` names. + var className = toString.call(a); + if (className !== toString.call(b)) return false; + switch (className) { + // Strings, numbers, regular expressions, dates, and booleans are compared by value. + case '[object RegExp]': + // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i') + case '[object String]': + // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is + // equivalent to `new String("5")`. + return '' + a === '' + b; + case '[object Number]': + // `NaN`s are equivalent, but non-reflexive. + // Object(NaN) is equivalent to NaN + if (+a !== +a) return +b !== +b; + // An `egal` comparison is performed for other numeric values. + return +a === 0 ? 1 / +a === 1 / b : +a === +b; + case '[object Date]': + case '[object Boolean]': + // Coerce dates and booleans to numeric primitive values. Dates are compared by their + // millisecond representations. Note that invalid dates with millisecond representations + // of `NaN` are not equivalent. + return +a === +b; + } + + var areArrays = className === '[object Array]'; + if (!areArrays) { + if (typeof a != 'object' || typeof b != 'object') return false; + + // Objects with different constructors are not equivalent, but `Object`s or `Array`s + // from different frames are. + var aCtor = a.constructor, bCtor = b.constructor; + if (aCtor !== bCtor && !(_.isFunction(aCtor) && aCtor instanceof aCtor && + _.isFunction(bCtor) && bCtor instanceof bCtor) + && ('constructor' in a && 'constructor' in b)) { + return false; + } + } + // Assume equality for cyclic structures. The algorithm for detecting cyclic + // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. + + // Initializing stack of traversed objects. + // It's done here since we only need them for objects and arrays comparison. + aStack = aStack || []; + bStack = bStack || []; + var length = aStack.length; + while (length--) { + // Linear search. Performance is inversely proportional to the number of + // unique nested structures. + if (aStack[length] === a) return bStack[length] === b; + } + + // Add the first object to the stack of traversed objects. + aStack.push(a); + bStack.push(b); + + // Recursively compare objects and arrays. + if (areArrays) { + // Compare array lengths to determine if a deep comparison is necessary. + length = a.length; + if (length !== b.length) return false; + // Deep compare the contents, ignoring non-numeric properties. + while (length--) { + if (!eq(a[length], b[length], aStack, bStack)) return false; + } + } else { + // Deep compare objects. + var keys = _.keys(a), key; + length = keys.length; + // Ensure that both objects contain the same number of properties before comparing deep equality. + if (_.keys(b).length !== length) return false; + while (length--) { + // Deep compare each member + key = keys[length]; + if (!(_.has(b, key) && eq(a[key], b[key], aStack, bStack))) return false; + } + } + // Remove the first object from the stack of traversed objects. + aStack.pop(); + bStack.pop(); + return true; + }; + + // Perform a deep comparison to check if two objects are equal. + _.isEqual = function(a, b) { + return eq(a, b); + }; + + // Is a given array, string, or object empty? + // An "empty" object has no enumerable own-properties. + _.isEmpty = function(obj) { + if (obj == null) return true; + if (isArrayLike(obj) && (_.isArray(obj) || _.isString(obj) || _.isArguments(obj))) return obj.length === 0; + return _.keys(obj).length === 0; + }; + + // Is a given value a DOM element? + _.isElement = function(obj) { + return !!(obj && obj.nodeType === 1); + }; + + // Is a given value an array? + // Delegates to ECMA5's native Array.isArray + _.isArray = nativeIsArray || function(obj) { + return toString.call(obj) === '[object Array]'; + }; + + // Is a given variable an object? + _.isObject = function(obj) { + var type = typeof obj; + return type === 'function' || type === 'object' && !!obj; + }; + + // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp, isError. + _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp', 'Error'], function(name) { + _['is' + name] = function(obj) { + return toString.call(obj) === '[object ' + name + ']'; + }; + }); + + // Define a fallback version of the method in browsers (ahem, IE < 9), where + // there isn't any inspectable "Arguments" type. + if (!_.isArguments(arguments)) { + _.isArguments = function(obj) { + return _.has(obj, 'callee'); + }; + } + + // Optimize `isFunction` if appropriate. Work around some typeof bugs in old v8, + // IE 11 (#1621), and in Safari 8 (#1929). + if (typeof /./ != 'function' && typeof Int8Array != 'object') { + _.isFunction = function(obj) { + return typeof obj == 'function' || false; + }; + } + + // Is a given object a finite number? + _.isFinite = function(obj) { + return isFinite(obj) && !isNaN(parseFloat(obj)); + }; + + // Is the given value `NaN`? (NaN is the only number which does not equal itself). + _.isNaN = function(obj) { + return _.isNumber(obj) && obj !== +obj; + }; + + // Is a given value a boolean? + _.isBoolean = function(obj) { + return obj === true || obj === false || toString.call(obj) === '[object Boolean]'; + }; + + // Is a given value equal to null? + _.isNull = function(obj) { + return obj === null; + }; + + // Is a given variable undefined? + _.isUndefined = function(obj) { + return obj === void 0; + }; + + // Shortcut function for checking if an object has a given property directly + // on itself (in other words, not on a prototype). + _.has = function(obj, key) { + return obj != null && hasOwnProperty.call(obj, key); + }; + + // Utility Functions + // ----------------- + + // Run Underscore.js in *noConflict* mode, returning the `_` variable to its + // previous owner. Returns a reference to the Underscore object. + _.noConflict = function() { + root._ = previousUnderscore; + return this; + }; + + // Keep the identity function around for default iteratees. + _.identity = function(value) { + return value; + }; + + // Predicate-generating functions. Often useful outside of Underscore. + _.constant = function(value) { + return function() { + return value; + }; + }; + + _.noop = function(){}; + + _.property = property; + + // Generates a function for a given object that returns a given property. + _.propertyOf = function(obj) { + return obj == null ? function(){} : function(key) { + return obj[key]; + }; + }; + + // Returns a predicate for checking whether an object has a given set of + // `key:value` pairs. + _.matcher = _.matches = function(attrs) { + attrs = _.extendOwn({}, attrs); + return function(obj) { + return _.isMatch(obj, attrs); + }; + }; + + // Run a function **n** times. + _.times = function(n, iteratee, context) { + var accum = Array(Math.max(0, n)); + iteratee = optimizeCb(iteratee, context, 1); + for (var i = 0; i < n; i++) accum[i] = iteratee(i); + return accum; + }; + + // Return a random integer between min and max (inclusive). + _.random = function(min, max) { + if (max == null) { + max = min; + min = 0; + } + return min + Math.floor(Math.random() * (max - min + 1)); + }; + + // A (possibly faster) way to get the current timestamp as an integer. + _.now = Date.now || function() { + return new Date().getTime(); + }; + + // List of HTML entities for escaping. + var escapeMap = { + '&': '&', + '<': '<', + '>': '>', + '"': '"', + "'": ''', + '`': '`' + }; + var unescapeMap = _.invert(escapeMap); + + // Functions for escaping and unescaping strings to/from HTML interpolation. + var createEscaper = function(map) { + var escaper = function(match) { + return map[match]; + }; + // Regexes for identifying a key that needs to be escaped + var source = '(?:' + _.keys(map).join('|') + ')'; + var testRegexp = RegExp(source); + var replaceRegexp = RegExp(source, 'g'); + return function(string) { + string = string == null ? '' : '' + string; + return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string; + }; + }; + _.escape = createEscaper(escapeMap); + _.unescape = createEscaper(unescapeMap); + + // If the value of the named `property` is a function then invoke it with the + // `object` as context; otherwise, return it. + _.result = function(object, property, fallback) { + var value = object == null ? void 0 : object[property]; + if (value === void 0) { + value = fallback; + } + return _.isFunction(value) ? value.call(object) : value; + }; + + // Generate a unique integer id (unique within the entire client session). + // Useful for temporary DOM ids. + var idCounter = 0; + _.uniqueId = function(prefix) { + var id = ++idCounter + ''; + return prefix ? prefix + id : id; + }; + + // By default, Underscore uses ERB-style template delimiters, change the + // following template settings to use alternative delimiters. + _.templateSettings = { + evaluate : /<%([\s\S]+?)%>/g, + interpolate : /<%=([\s\S]+?)%>/g, + escape : /<%-([\s\S]+?)%>/g + }; + + // When customizing `templateSettings`, if you don't want to define an + // interpolation, evaluation or escaping regex, we need one that is + // guaranteed not to match. + var noMatch = /(.)^/; + + // Certain characters need to be escaped so that they can be put into a + // string literal. + var escapes = { + "'": "'", + '\\': '\\', + '\r': 'r', + '\n': 'n', + '\u2028': 'u2028', + '\u2029': 'u2029' + }; + + var escaper = /\\|'|\r|\n|\u2028|\u2029/g; + + var escapeChar = function(match) { + return '\\' + escapes[match]; + }; + + // JavaScript micro-templating, similar to John Resig's implementation. + // Underscore templating handles arbitrary delimiters, preserves whitespace, + // and correctly escapes quotes within interpolated code. + // NB: `oldSettings` only exists for backwards compatibility. + _.template = function(text, settings, oldSettings) { + if (!settings && oldSettings) settings = oldSettings; + settings = _.defaults({}, settings, _.templateSettings); + + // Combine delimiters into one regular expression via alternation. + var matcher = RegExp([ + (settings.escape || noMatch).source, + (settings.interpolate || noMatch).source, + (settings.evaluate || noMatch).source + ].join('|') + '|$', 'g'); + + // Compile the template source, escaping string literals appropriately. + var index = 0; + var source = "__p+='"; + text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { + source += text.slice(index, offset).replace(escaper, escapeChar); + index = offset + match.length; + + if (escape) { + source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'"; + } else if (interpolate) { + source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'"; + } else if (evaluate) { + source += "';\n" + evaluate + "\n__p+='"; + } + + // Adobe VMs need the match returned to produce the correct offest. + return match; + }); + source += "';\n"; + + // If a variable is not specified, place data values in local scope. + if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; + + source = "var __t,__p='',__j=Array.prototype.join," + + "print=function(){__p+=__j.call(arguments,'');};\n" + + source + 'return __p;\n'; + + try { + var render = new Function(settings.variable || 'obj', '_', source); + } catch (e) { + e.source = source; + throw e; + } + + var template = function(data) { + return render.call(this, data, _); + }; + + // Provide the compiled source as a convenience for precompilation. + var argument = settings.variable || 'obj'; + template.source = 'function(' + argument + '){\n' + source + '}'; + + return template; + }; + + // Add a "chain" function. Start chaining a wrapped Underscore object. + _.chain = function(obj) { + var instance = _(obj); + instance._chain = true; + return instance; + }; + + // OOP + // --------------- + // If Underscore is called as a function, it returns a wrapped object that + // can be used OO-style. This wrapper holds altered versions of all the + // underscore functions. Wrapped objects may be chained. + + // Helper function to continue chaining intermediate results. + var result = function(instance, obj) { + return instance._chain ? _(obj).chain() : obj; + }; + + // Add your own custom functions to the Underscore object. + _.mixin = function(obj) { + _.each(_.functions(obj), function(name) { + var func = _[name] = obj[name]; + _.prototype[name] = function() { + var args = [this._wrapped]; + push.apply(args, arguments); + return result(this, func.apply(_, args)); + }; + }); + }; + + // Add all of the Underscore functions to the wrapper object. + _.mixin(_); + + // Add all mutator Array functions to the wrapper. + _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { + var method = ArrayProto[name]; + _.prototype[name] = function() { + var obj = this._wrapped; + method.apply(obj, arguments); + if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0]; + return result(this, obj); + }; + }); + + // Add all accessor Array functions to the wrapper. + _.each(['concat', 'join', 'slice'], function(name) { + var method = ArrayProto[name]; + _.prototype[name] = function() { + return result(this, method.apply(this._wrapped, arguments)); + }; + }); + + // Extracts the result from a wrapped and chained object. + _.prototype.value = function() { + return this._wrapped; + }; + + // Provide unwrapping proxy for some methods used in engine operations + // such as arithmetic and JSON stringification. + _.prototype.valueOf = _.prototype.toJSON = _.prototype.value; + + _.prototype.toString = function() { + return '' + this._wrapped; + }; + + // AMD registration happens at the end for compatibility with AMD loaders + // that may not enforce next-turn semantics on modules. Even though general + // practice for AMD registration is to be anonymous, underscore registers + // as a named module because, like jQuery, it is a base library that is + // popular enough to be bundled in a third party lib, but not be part of + // an AMD load request. Those cases could generate an error when an + // anonymous define() is called outside of a loader request. + if (typeof define === 'function' && define.amd) { + define('underscore', [], function() { + return _; + }); + } +}.call(this)); + +},{}],26:[function(require,module,exports){ +arguments[4][19][0].apply(exports,arguments) +},{"dup":19}],27:[function(require,module,exports){ +module.exports = function isBuffer(arg) { + return arg && typeof arg === 'object' + && typeof arg.copy === 'function' + && typeof arg.fill === 'function' + && typeof arg.readUInt8 === 'function'; +} +},{}],28:[function(require,module,exports){ +(function (process,global){ +// Copyright Joyent, Inc. and other Node contributors. +// +// Permission is hereby granted, free of charge, to any person obtaining a +// copy of this software and associated documentation files (the +// "Software"), to deal in the Software without restriction, including +// without limitation the rights to use, copy, modify, merge, publish, +// distribute, sublicense, and/or sell copies of the Software, and to permit +// persons to whom the Software is furnished to do so, subject to the +// following conditions: +// +// The above copyright notice and this permission notice shall be included +// in all copies or substantial portions of the Software. +// +// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN +// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, +// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR +// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +// USE OR OTHER DEALINGS IN THE SOFTWARE. + +var formatRegExp = /%[sdj%]/g; +exports.format = function(f) { + if (!isString(f)) { + var objects = []; + for (var i = 0; i < arguments.length; i++) { + objects.push(inspect(arguments[i])); + } + return objects.join(' '); + } + + var i = 1; + var args = arguments; + var len = args.length; + var str = String(f).replace(formatRegExp, function(x) { + if (x === '%%') return '%'; + if (i >= len) return x; + switch (x) { + case '%s': return String(args[i++]); + case '%d': return Number(args[i++]); + case '%j': + try { + return JSON.stringify(args[i++]); + } catch (_) { + return '[Circular]'; + } + default: + return x; + } + }); + for (var x = args[i]; i < len; x = args[++i]) { + if (isNull(x) || !isObject(x)) { + str += ' ' + x; + } else { + str += ' ' + inspect(x); + } + } + return str; +}; + + +// Mark that a method should not be used. +// Returns a modified function which warns once by default. +// If --no-deprecation is set, then it is a no-op. +exports.deprecate = function(fn, msg) { + // Allow for deprecating things in the process of starting up. + if (isUndefined(global.process)) { + return function() { + return exports.deprecate(fn, msg).apply(this, arguments); + }; + } + + if (process.noDeprecation === true) { + return fn; + } + + var warned = false; + function deprecated() { + if (!warned) { + if (process.throwDeprecation) { + throw new Error(msg); + } else if (process.traceDeprecation) { + console.trace(msg); + } else { + console.error(msg); + } + warned = true; + } + return fn.apply(this, arguments); + } + + return deprecated; +}; + + +var debugs = {}; +var debugEnviron; +exports.debuglog = function(set) { + if (isUndefined(debugEnviron)) + debugEnviron = process.env.NODE_DEBUG || ''; + set = set.toUpperCase(); + if (!debugs[set]) { + if (new RegExp('\\b' + set + '\\b', 'i').test(debugEnviron)) { + var pid = process.pid; + debugs[set] = function() { + var msg = exports.format.apply(exports, arguments); + console.error('%s %d: %s', set, pid, msg); + }; + } else { + debugs[set] = function() {}; + } + } + return debugs[set]; +}; + + +/** + * Echos the value of a value. Trys to print the value out + * in the best way possible given the different types. + * + * @param {Object} obj The object to print out. + * @param {Object} opts Optional options object that alters the output. + */ +/* legacy: obj, showHidden, depth, colors*/ +function inspect(obj, opts) { + // default options + var ctx = { + seen: [], + stylize: stylizeNoColor + }; + // legacy... + if (arguments.length >= 3) ctx.depth = arguments[2]; + if (arguments.length >= 4) ctx.colors = arguments[3]; + if (isBoolean(opts)) { + // legacy... + ctx.showHidden = opts; + } else if (opts) { + // got an "options" object + exports._extend(ctx, opts); + } + // set default options + if (isUndefined(ctx.showHidden)) ctx.showHidden = false; + if (isUndefined(ctx.depth)) ctx.depth = 2; + if (isUndefined(ctx.colors)) ctx.colors = false; + if (isUndefined(ctx.customInspect)) ctx.customInspect = true; + if (ctx.colors) ctx.stylize = stylizeWithColor; + return formatValue(ctx, obj, ctx.depth); +} +exports.inspect = inspect; + + +// http://en.wikipedia.org/wiki/ANSI_escape_code#graphics +inspect.colors = { + 'bold' : [1, 22], + 'italic' : [3, 23], + 'underline' : [4, 24], + 'inverse' : [7, 27], + 'white' : [37, 39], + 'grey' : [90, 39], + 'black' : [30, 39], + 'blue' : [34, 39], + 'cyan' : [36, 39], + 'green' : [32, 39], + 'magenta' : [35, 39], + 'red' : [31, 39], + 'yellow' : [33, 39] +}; + +// Don't use 'blue' not visible on cmd.exe +inspect.styles = { + 'special': 'cyan', + 'number': 'yellow', + 'boolean': 'yellow', + 'undefined': 'grey', + 'null': 'bold', + 'string': 'green', + 'date': 'magenta', + // "name": intentionally not styling + 'regexp': 'red' +}; + + +function stylizeWithColor(str, styleType) { + var style = inspect.styles[styleType]; + + if (style) { + return '\u001b[' + inspect.colors[style][0] + 'm' + str + + '\u001b[' + inspect.colors[style][1] + 'm'; + } else { + return str; + } +} + + +function stylizeNoColor(str, styleType) { + return str; +} + + +function arrayToHash(array) { + var hash = {}; + + array.forEach(function(val, idx) { + hash[val] = true; + }); + + return hash; +} + + +function formatValue(ctx, value, recurseTimes) { + // Provide a hook for user-specified inspect functions. + // Check that value is an object with an inspect function on it + if (ctx.customInspect && + value && + isFunction(value.inspect) && + // Filter out the util module, it's inspect function is special + value.inspect !== exports.inspect && + // Also filter out any prototype objects using the circular check. + !(value.constructor && value.constructor.prototype === value)) { + var ret = value.inspect(recurseTimes, ctx); + if (!isString(ret)) { + ret = formatValue(ctx, ret, recurseTimes); + } + return ret; + } + + // Primitive types cannot have properties + var primitive = formatPrimitive(ctx, value); + if (primitive) { + return primitive; + } + + // Look up the keys of the object. + var keys = Object.keys(value); + var visibleKeys = arrayToHash(keys); + + if (ctx.showHidden) { + keys = Object.getOwnPropertyNames(value); + } + + // IE doesn't make error fields non-enumerable + // http://msdn.microsoft.com/en-us/library/ie/dww52sbt(v=vs.94).aspx + if (isError(value) + && (keys.indexOf('message') >= 0 || keys.indexOf('description') >= 0)) { + return formatError(value); + } + + // Some type of object without properties can be shortcutted. + if (keys.length === 0) { + if (isFunction(value)) { + var name = value.name ? ': ' + value.name : ''; + return ctx.stylize('[Function' + name + ']', 'special'); + } + if (isRegExp(value)) { + return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp'); + } + if (isDate(value)) { + return ctx.stylize(Date.prototype.toString.call(value), 'date'); + } + if (isError(value)) { + return formatError(value); + } + } + + var base = '', array = false, braces = ['{', '}']; + + // Make Array say that they are Array + if (isArray(value)) { + array = true; + braces = ['[', ']']; + } + + // Make functions say that they are functions + if (isFunction(value)) { + var n = value.name ? ': ' + value.name : ''; + base = ' [Function' + n + ']'; + } + + // Make RegExps say that they are RegExps + if (isRegExp(value)) { + base = ' ' + RegExp.prototype.toString.call(value); + } + + // Make dates with properties first say the date + if (isDate(value)) { + base = ' ' + Date.prototype.toUTCString.call(value); + } + + // Make error with message first say the error + if (isError(value)) { + base = ' ' + formatError(value); + } + + if (keys.length === 0 && (!array || value.length == 0)) { + return braces[0] + base + braces[1]; + } + + if (recurseTimes < 0) { + if (isRegExp(value)) { + return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp'); + } else { + return ctx.stylize('[Object]', 'special'); + } + } + + ctx.seen.push(value); + + var output; + if (array) { + output = formatArray(ctx, value, recurseTimes, visibleKeys, keys); + } else { + output = keys.map(function(key) { + return formatProperty(ctx, value, recurseTimes, visibleKeys, key, array); + }); + } + + ctx.seen.pop(); + + return reduceToSingleString(output, base, braces); +} + + +function formatPrimitive(ctx, value) { + if (isUndefined(value)) + return ctx.stylize('undefined', 'undefined'); + if (isString(value)) { + var simple = '\'' + JSON.stringify(value).replace(/^"|"$/g, '') + .replace(/'/g, "\\'") + .replace(/\\"/g, '"') + '\''; + return ctx.stylize(simple, 'string'); + } + if (isNumber(value)) + return ctx.stylize('' + value, 'number'); + if (isBoolean(value)) + return ctx.stylize('' + value, 'boolean'); + // For some reason typeof null is "object", so special case here. + if (isNull(value)) + return ctx.stylize('null', 'null'); +} + + +function formatError(value) { + return '[' + Error.prototype.toString.call(value) + ']'; +} + + +function formatArray(ctx, value, recurseTimes, visibleKeys, keys) { + var output = []; + for (var i = 0, l = value.length; i < l; ++i) { + if (hasOwnProperty(value, String(i))) { + output.push(formatProperty(ctx, value, recurseTimes, visibleKeys, + String(i), true)); + } else { + output.push(''); + } + } + keys.forEach(function(key) { + if (!key.match(/^\d+$/)) { + output.push(formatProperty(ctx, value, recurseTimes, visibleKeys, + key, true)); + } + }); + return output; +} + + +function formatProperty(ctx, value, recurseTimes, visibleKeys, key, array) { + var name, str, desc; + desc = Object.getOwnPropertyDescriptor(value, key) || { value: value[key] }; + if (desc.get) { + if (desc.set) { + str = ctx.stylize('[Getter/Setter]', 'special'); + } else { + str = ctx.stylize('[Getter]', 'special'); + } + } else { + if (desc.set) { + str = ctx.stylize('[Setter]', 'special'); + } + } + if (!hasOwnProperty(visibleKeys, key)) { + name = '[' + key + ']'; + } + if (!str) { + if (ctx.seen.indexOf(desc.value) < 0) { + if (isNull(recurseTimes)) { + str = formatValue(ctx, desc.value, null); + } else { + str = formatValue(ctx, desc.value, recurseTimes - 1); + } + if (str.indexOf('\n') > -1) { + if (array) { + str = str.split('\n').map(function(line) { + return ' ' + line; + }).join('\n').substr(2); + } else { + str = '\n' + str.split('\n').map(function(line) { + return ' ' + line; + }).join('\n'); + } + } + } else { + str = ctx.stylize('[Circular]', 'special'); + } + } + if (isUndefined(name)) { + if (array && key.match(/^\d+$/)) { + return str; + } + name = JSON.stringify('' + key); + if (name.match(/^"([a-zA-Z_][a-zA-Z_0-9]*)"$/)) { + name = name.substr(1, name.length - 2); + name = ctx.stylize(name, 'name'); + } else { + name = name.replace(/'/g, "\\'") + .replace(/\\"/g, '"') + .replace(/(^"|"$)/g, "'"); + name = ctx.stylize(name, 'string'); + } + } + + return name + ': ' + str; +} + + +function reduceToSingleString(output, base, braces) { + var numLinesEst = 0; + var length = output.reduce(function(prev, cur) { + numLinesEst++; + if (cur.indexOf('\n') >= 0) numLinesEst++; + return prev + cur.replace(/\u001b\[\d\d?m/g, '').length + 1; + }, 0); + + if (length > 60) { + return braces[0] + + (base === '' ? '' : base + '\n ') + + ' ' + + output.join(',\n ') + + ' ' + + braces[1]; + } + + return braces[0] + base + ' ' + output.join(', ') + ' ' + braces[1]; +} + + +// NOTE: These type checking functions intentionally don't use `instanceof` +// because it is fragile and can be easily faked with `Object.create()`. +function isArray(ar) { + return Array.isArray(ar); +} +exports.isArray = isArray; + +function isBoolean(arg) { + return typeof arg === 'boolean'; +} +exports.isBoolean = isBoolean; + +function isNull(arg) { + return arg === null; +} +exports.isNull = isNull; + +function isNullOrUndefined(arg) { + return arg == null; +} +exports.isNullOrUndefined = isNullOrUndefined; + +function isNumber(arg) { + return typeof arg === 'number'; +} +exports.isNumber = isNumber; + +function isString(arg) { + return typeof arg === 'string'; +} +exports.isString = isString; + +function isSymbol(arg) { + return typeof arg === 'symbol'; +} +exports.isSymbol = isSymbol; + +function isUndefined(arg) { + return arg === void 0; +} +exports.isUndefined = isUndefined; + +function isRegExp(re) { + return isObject(re) && objectToString(re) === '[object RegExp]'; +} +exports.isRegExp = isRegExp; + +function isObject(arg) { + return typeof arg === 'object' && arg !== null; +} +exports.isObject = isObject; + +function isDate(d) { + return isObject(d) && objectToString(d) === '[object Date]'; +} +exports.isDate = isDate; + +function isError(e) { + return isObject(e) && + (objectToString(e) === '[object Error]' || e instanceof Error); +} +exports.isError = isError; + +function isFunction(arg) { + return typeof arg === 'function'; +} +exports.isFunction = isFunction; + +function isPrimitive(arg) { + return arg === null || + typeof arg === 'boolean' || + typeof arg === 'number' || + typeof arg === 'string' || + typeof arg === 'symbol' || // ES6 symbol + typeof arg === 'undefined'; +} +exports.isPrimitive = isPrimitive; + +exports.isBuffer = require('./support/isBuffer'); + +function objectToString(o) { + return Object.prototype.toString.call(o); +} + + +function pad(n) { + return n < 10 ? '0' + n.toString(10) : n.toString(10); +} + + +var months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', + 'Oct', 'Nov', 'Dec']; + +// 26 Feb 16:19:34 +function timestamp() { + var d = new Date(); + var time = [pad(d.getHours()), + pad(d.getMinutes()), + pad(d.getSeconds())].join(':'); + return [d.getDate(), months[d.getMonth()], time].join(' '); +} + + +// log is just a thin wrapper to console.log that prepends a timestamp +exports.log = function() { + console.log('%s - %s', timestamp(), exports.format.apply(exports, arguments)); +}; + + +/** + * Inherit the prototype methods from one constructor into another. + * + * The Function.prototype.inherits from lang.js rewritten as a standalone + * function (not on Function.prototype). NOTE: If this file is to be loaded + * during bootstrapping this function needs to be rewritten using some native + * functions as prototype setup using normal JavaScript does not work as + * expected during bootstrapping (see mirror.js in r114903). + * + * @param {function} ctor Constructor function which needs to inherit the + * prototype. + * @param {function} superCtor Constructor function to inherit prototype from. + */ +exports.inherits = require('inherits'); + +exports._extend = function(origin, add) { + // Don't do anything if add isn't an object + if (!add || !isObject(add)) return origin; + + var keys = Object.keys(add); + var i = keys.length; + while (i--) { + origin[keys[i]] = add[keys[i]]; + } + return origin; +}; + +function hasOwnProperty(obj, prop) { + return Object.prototype.hasOwnProperty.call(obj, prop); +} + +}).call(this,require('_process'),typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) +},{"./support/isBuffer":27,"_process":24,"inherits":26}],29:[function(require,module,exports){ +// Returns a wrapper function that returns a wrapped callback +// The wrapper function should do some stuff, and return a +// presumably different callback function. +// This makes sure that own properties are retained, so that +// decorations and such are not lost along the way. +module.exports = wrappy +function wrappy (fn, cb) { + if (fn && cb) return wrappy(fn)(cb) + + if (typeof fn !== 'function') + throw new TypeError('need wrapper function') + + Object.keys(fn).forEach(function (k) { + wrapper[k] = fn[k] + }) + + return wrapper + + function wrapper() { + var args = new Array(arguments.length) + for (var i = 0; i < args.length; i++) { + args[i] = arguments[i] + } + var ret = fn.apply(this, args) + var cb = args[args.length-1] + if (typeof ret === 'function' && ret !== cb) { + Object.keys(cb).forEach(function (k) { + ret[k] = cb[k] + }) + } + return ret + } +} + +},{}]},{},[7])(7) +}); \ No newline at end of file diff --git a/0.13/assets/javascripts/workers/search.16e2a7d4.min.js b/0.13/assets/javascripts/workers/search.16e2a7d4.min.js new file mode 100644 index 000000000..e0dc159e8 --- /dev/null +++ b/0.13/assets/javascripts/workers/search.16e2a7d4.min.js @@ -0,0 +1,48 @@ +"use strict";(()=>{var ge=Object.create;var W=Object.defineProperty,ye=Object.defineProperties,me=Object.getOwnPropertyDescriptor,ve=Object.getOwnPropertyDescriptors,xe=Object.getOwnPropertyNames,G=Object.getOwnPropertySymbols,Se=Object.getPrototypeOf,X=Object.prototype.hasOwnProperty,Qe=Object.prototype.propertyIsEnumerable;var J=(t,e,r)=>e in t?W(t,e,{enumerable:!0,configurable:!0,writable:!0,value:r}):t[e]=r,M=(t,e)=>{for(var r in e||(e={}))X.call(e,r)&&J(t,r,e[r]);if(G)for(var r of G(e))Qe.call(e,r)&&J(t,r,e[r]);return t},Z=(t,e)=>ye(t,ve(e));var K=(t,e)=>()=>(e||t((e={exports:{}}).exports,e),e.exports);var be=(t,e,r,n)=>{if(e&&typeof e=="object"||typeof e=="function")for(let i of xe(e))!X.call(t,i)&&i!==r&&W(t,i,{get:()=>e[i],enumerable:!(n=me(e,i))||n.enumerable});return t};var H=(t,e,r)=>(r=t!=null?ge(Se(t)):{},be(e||!t||!t.__esModule?W(r,"default",{value:t,enumerable:!0}):r,t));var z=(t,e,r)=>new Promise((n,i)=>{var s=u=>{try{a(r.next(u))}catch(c){i(c)}},o=u=>{try{a(r.throw(u))}catch(c){i(c)}},a=u=>u.done?n(u.value):Promise.resolve(u.value).then(s,o);a((r=r.apply(t,e)).next())});var re=K((ee,te)=>{/** + * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9 + * Copyright (C) 2020 Oliver Nightingale + * @license MIT + */(function(){var t=function(e){var r=new t.Builder;return r.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),r.searchPipeline.add(t.stemmer),e.call(r,r),r.build()};t.version="2.3.9";/*! + * lunr.utils + * Copyright (C) 2020 Oliver Nightingale + */t.utils={},t.utils.warn=function(e){return function(r){e.console&&console.warn&&console.warn(r)}}(this),t.utils.asString=function(e){return e==null?"":e.toString()},t.utils.clone=function(e){if(e==null)return e;for(var r=Object.create(null),n=Object.keys(e),i=0;i0){var h=t.utils.clone(r)||{};h.position=[a,c],h.index=s.length,s.push(new t.Token(n.slice(a,o),h))}a=o+1}}return s},t.tokenizer.separator=/[\s\-]+/;/*! + * lunr.Pipeline + * Copyright (C) 2020 Oliver Nightingale + */t.Pipeline=function(){this._stack=[]},t.Pipeline.registeredFunctions=Object.create(null),t.Pipeline.registerFunction=function(e,r){r in this.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+r),e.label=r,t.Pipeline.registeredFunctions[e.label]=e},t.Pipeline.warnIfFunctionNotRegistered=function(e){var r=e.label&&e.label in this.registeredFunctions;r||t.utils.warn(`Function is not registered with pipeline. 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this.pos1&&(e.backup(),e.emit(t.QueryLexer.TERM)),e.ignore(),e.more())return t.QueryLexer.lexText},t.QueryLexer.lexEditDistance=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.EDIT_DISTANCE),t.QueryLexer.lexText},t.QueryLexer.lexBoost=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.BOOST),t.QueryLexer.lexText},t.QueryLexer.lexEOS=function(e){e.width()>0&&e.emit(t.QueryLexer.TERM)},t.QueryLexer.termSeparator=t.tokenizer.separator,t.QueryLexer.lexText=function(e){for(;;){var r=e.next();if(r==t.QueryLexer.EOS)return t.QueryLexer.lexEOS;if(r.charCodeAt(0)==92){e.escapeCharacter();continue}if(r==":")return t.QueryLexer.lexField;if(r=="~")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexEditDistance;if(r=="^")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexBoost;if(r=="+"&&e.width()===1||r=="-"&&e.width()===1)return e.emit(t.QueryLexer.PRESENCE),t.QueryLexer.lexText;if(r.match(t.QueryLexer.termSeparator))return t.QueryLexer.lexTerm}},t.QueryParser=function(e,r){this.lexer=new t.QueryLexer(e),this.query=r,this.currentClause={},this.lexemeIdx=0},t.QueryParser.prototype.parse=function(){this.lexer.run(),this.lexemes=this.lexer.lexemes;for(var e=t.QueryParser.parseClause;e;)e=e(this);return this.query},t.QueryParser.prototype.peekLexeme=function(){return this.lexemes[this.lexemeIdx]},t.QueryParser.prototype.consumeLexeme=function(){var e=this.peekLexeme();return this.lexemeIdx+=1,e},t.QueryParser.prototype.nextClause=function(){var e=this.currentClause;this.query.clause(e),this.currentClause={}},t.QueryParser.parseClause=function(e){var r=e.peekLexeme();if(r!=null)switch(r.type){case t.QueryLexer.PRESENCE:return t.QueryParser.parsePresence;case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expected either a field or a term, found "+r.type;throw r.str.length>=1&&(n+=" with value '"+r.str+"'"),new t.QueryParseError(n,r.start,r.end)}},t.QueryParser.parsePresence=function(e){var r=e.consumeLexeme();if(r!=null){switch(r.str){case"-":e.currentClause.presence=t.Query.presence.PROHIBITED;break;case"+":e.currentClause.presence=t.Query.presence.REQUIRED;break;default:var n="unrecognised presence operator'"+r.str+"'";throw new t.QueryParseError(n,r.start,r.end)}var i=e.peekLexeme();if(i==null){var n="expecting term or field, found nothing";throw new t.QueryParseError(n,r.start,r.end)}switch(i.type){case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expecting term or field, found '"+i.type+"'";throw new t.QueryParseError(n,i.start,i.end)}}},t.QueryParser.parseField=function(e){var r=e.consumeLexeme();if(r!=null){if(e.query.allFields.indexOf(r.str)==-1){var n=e.query.allFields.map(function(o){return"'"+o+"'"}).join(", "),i="unrecognised field '"+r.str+"', possible fields: "+n;throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.fields=[r.str];var s=e.peekLexeme();if(s==null){var i="expecting term, found nothing";throw new t.QueryParseError(i,r.start,r.end)}switch(s.type){case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var i="expecting term, found '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseTerm=function(e){var r=e.consumeLexeme();if(r!=null){e.currentClause.term=r.str.toLowerCase(),r.str.indexOf("*")!=-1&&(e.currentClause.usePipeline=!1);var n=e.peekLexeme();if(n==null){e.nextClause();return}switch(n.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+n.type+"'";throw new t.QueryParseError(i,n.start,n.end)}}},t.QueryParser.parseEditDistance=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="edit distance must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.editDistance=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseBoost=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="boost must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.boost=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},function(e,r){typeof define=="function"&&define.amd?define(r):typeof ee=="object"?te.exports=r():e.lunr=r()}(this,function(){return t})})()});var q=K((Re,ne)=>{"use strict";/*! + * escape-html + * Copyright(c) 2012-2013 TJ Holowaychuk + * Copyright(c) 2015 Andreas Lubbe + * Copyright(c) 2015 Tiancheng "Timothy" Gu + * MIT Licensed + */var Le=/["'&<>]/;ne.exports=we;function we(t){var e=""+t,r=Le.exec(e);if(!r)return e;var n,i="",s=0,o=0;for(s=r.index;s=0;r--){let n=t[r];typeof n=="string"?n=document.createTextNode(n):n.parentNode&&n.parentNode.removeChild(n),r?e.insertBefore(this.previousSibling,n):e.replaceChild(n,this)}}}));var ie=H(q());function se(t){let e=new Map,r=new Set;for(let n of t){let[i,s]=n.location.split("#"),o=n.location,a=n.title,u=n.tags,c=(0,ie.default)(n.text).replace(/\s+(?=[,.:;!?])/g,"").replace(/\s+/g," ");if(s){let h=e.get(i);r.has(h)?e.set(o,{location:o,title:a,text:c,parent:h}):(h.title=n.title,h.text=c,r.add(h))}else e.set(o,M({location:o,title:a,text:c},u&&{tags:u}))}return e}var oe=H(q());function ae(t,e){let r=new RegExp(t.separator,"img"),n=(i,s,o)=>`${s}${o}`;return i=>{i=i.replace(/[\s*+\-:~^]+/g," ").trim();let s=new RegExp(`(^|${t.separator})(${i.replace(/[|\\{}()[\]^$+*?.-]/g,"\\$&").replace(r,"|")})`,"img");return o=>(e?(0,oe.default)(o):o).replace(s,n).replace(/<\/mark>(\s+)]*>/img,"$1")}}function ue(t){let e=new lunr.Query(["title","text"]);return new lunr.QueryParser(t,e).parse(),e.clauses}function ce(t,e){var i;let r=new Set(t),n={};for(let s=0;s!n.has(i)))]}var U=class{constructor({config:e,docs:r,options:n}){this.options=n,this.documents=se(r),this.highlight=ae(e,!1),lunr.tokenizer.separator=new RegExp(e.separator),this.index=lunr(function(){e.lang.length===1&&e.lang[0]!=="en"?this.use(lunr[e.lang[0]]):e.lang.length>1&&this.use(lunr.multiLanguage(...e.lang));let i=Ee(["trimmer","stopWordFilter","stemmer"],n.pipeline);for(let s of e.lang.map(o=>o==="en"?lunr:lunr[o]))for(let o of i)this.pipeline.remove(s[o]),this.searchPipeline.remove(s[o]);this.ref("location"),this.field("title",{boost:1e3}),this.field("text"),this.field("tags",{boost:1e6,extractor:s=>{let{tags:o=[]}=s;return o.reduce((a,u)=>[...a,...lunr.tokenizer(u)],[])}});for(let s of r)this.add(s,{boost:s.boost})})}search(e){if(e)try{let r=this.highlight(e),n=ue(e).filter(o=>o.presence!==lunr.Query.presence.PROHIBITED),i=this.index.search(`${e}*`).reduce((o,{ref:a,score:u,matchData:c})=>{let h=this.documents.get(a);if(typeof h!="undefined"){let{location:y,title:g,text:b,tags:m,parent:Q}=h,p=ce(n,Object.keys(c.metadata)),d=+!Q+ +Object.values(p).every(w=>w);o.push(Z(M({location:y,title:r(g),text:r(b)},m&&{tags:m.map(r)}),{score:u*(1+d),terms:p}))}return o},[]).sort((o,a)=>a.score-o.score).reduce((o,a)=>{let u=this.documents.get(a.location);if(typeof u!="undefined"){let c="parent"in u?u.parent.location:u.location;o.set(c,[...o.get(c)||[],a])}return o},new Map),s;if(this.options.suggestions){let o=this.index.query(a=>{for(let u of n)a.term(u.term,{fields:["title"],presence:lunr.Query.presence.REQUIRED,wildcard:lunr.Query.wildcard.TRAILING})});s=o.length?Object.keys(o[0].matchData.metadata):[]}return M({items:[...i.values()]},typeof s!="undefined"&&{suggestions:s})}catch(r){console.warn(`Invalid query: ${e} \u2013 see https://bit.ly/2s3ChXG`)}return{items:[]}}};var Y;function ke(t){return z(this,null,function*(){let e="../lunr";if(typeof parent!="undefined"&&"IFrameWorker"in parent){let n=document.querySelector("script[src]"),[i]=n.src.split("/worker");e=e.replace("..",i)}let r=[];for(let n of t.lang){switch(n){case"ja":r.push(`${e}/tinyseg.js`);break;case"hi":case"th":r.push(`${e}/wordcut.js`);break}n!=="en"&&r.push(`${e}/min/lunr.${n}.min.js`)}t.lang.length>1&&r.push(`${e}/min/lunr.multi.min.js`),r.length&&(yield importScripts(`${e}/min/lunr.stemmer.support.min.js`,...r))})}function Te(t){return z(this,null,function*(){switch(t.type){case 0:return yield ke(t.data.config),Y=new U(t.data),{type:1};case 2:return{type:3,data:Y?Y.search(t.data):{items:[]}};default:throw new TypeError("Invalid message type")}})}self.lunr=le.default;addEventListener("message",t=>z(void 0,null,function*(){postMessage(yield Te(t.data))}));})(); +//# sourceMappingURL=search.16e2a7d4.min.js.map + diff --git a/0.13/assets/javascripts/workers/search.16e2a7d4.min.js.map b/0.13/assets/javascripts/workers/search.16e2a7d4.min.js.map new file mode 100644 index 000000000..fa01f3742 --- /dev/null +++ b/0.13/assets/javascripts/workers/search.16e2a7d4.min.js.map @@ -0,0 +1,8 @@ +{ + "version": 3, + "sources": ["node_modules/lunr/lunr.js", "node_modules/escape-html/index.js", "src/assets/javascripts/integrations/search/worker/main/index.ts", "src/assets/javascripts/polyfills/index.ts", "src/assets/javascripts/integrations/search/document/index.ts", "src/assets/javascripts/integrations/search/highlighter/index.ts", "src/assets/javascripts/integrations/search/query/_/index.ts", "src/assets/javascripts/integrations/search/_/index.ts"], + "sourceRoot": "../../../..", + "sourcesContent": ["/**\n * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9\n * Copyright (C) 2020 Oliver Nightingale\n * @license MIT\n */\n\n;(function(){\n\n/**\n * A convenience function for configuring and constructing\n * a new lunr Index.\n *\n * A lunr.Builder instance is created and the pipeline setup\n * with a trimmer, stop word filter and stemmer.\n *\n * This builder object is yielded to the configuration function\n * that is passed as a parameter, allowing the list of fields\n * and other builder parameters to be customised.\n *\n * All documents _must_ be added within the passed config function.\n *\n * @example\n * var idx = lunr(function () {\n * this.field('title')\n * this.field('body')\n * this.ref('id')\n *\n * documents.forEach(function (doc) {\n * this.add(doc)\n * }, this)\n * })\n *\n * @see {@link lunr.Builder}\n * @see {@link lunr.Pipeline}\n * @see {@link lunr.trimmer}\n * @see {@link lunr.stopWordFilter}\n * @see {@link lunr.stemmer}\n * @namespace {function} lunr\n */\nvar lunr = function (config) {\n var builder = new lunr.Builder\n\n builder.pipeline.add(\n lunr.trimmer,\n lunr.stopWordFilter,\n lunr.stemmer\n )\n\n builder.searchPipeline.add(\n lunr.stemmer\n )\n\n config.call(builder, builder)\n return builder.build()\n}\n\nlunr.version = \"2.3.9\"\n/*!\n * lunr.utils\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A namespace containing utils for the rest of the lunr library\n * @namespace lunr.utils\n */\nlunr.utils = {}\n\n/**\n * Print a warning message to the console.\n *\n * @param {String} message The message to be printed.\n * @memberOf lunr.utils\n * @function\n */\nlunr.utils.warn = (function (global) {\n /* eslint-disable no-console */\n return function (message) {\n if (global.console && console.warn) {\n console.warn(message)\n }\n }\n /* eslint-enable no-console */\n})(this)\n\n/**\n * Convert an object to a string.\n *\n * In the case of `null` and `undefined` the function returns\n * the empty string, in all other cases the result of calling\n * `toString` on the passed object is returned.\n *\n * @param {Any} obj The object to convert to a string.\n * @return {String} string representation of the passed object.\n * @memberOf lunr.utils\n */\nlunr.utils.asString = function (obj) {\n if (obj === void 0 || obj === null) {\n return \"\"\n } else {\n return obj.toString()\n }\n}\n\n/**\n * Clones an object.\n *\n * Will create a copy of an existing object such that any mutations\n * on the copy cannot affect the original.\n *\n * Only shallow objects are supported, passing a nested object to this\n * function will cause a TypeError.\n *\n * Objects with primitives, and arrays of primitives are supported.\n *\n * @param {Object} obj The object to clone.\n * @return {Object} a clone of the passed object.\n * @throws {TypeError} when a nested object is passed.\n * @memberOf Utils\n */\nlunr.utils.clone = function (obj) {\n if (obj === null || obj === undefined) {\n return obj\n }\n\n var clone = Object.create(null),\n keys = Object.keys(obj)\n\n for (var i = 0; i < keys.length; i++) {\n var key = keys[i],\n val = obj[key]\n\n if (Array.isArray(val)) {\n clone[key] = val.slice()\n continue\n }\n\n if (typeof val === 'string' ||\n typeof val === 'number' ||\n typeof val === 'boolean') {\n clone[key] = val\n continue\n }\n\n throw new TypeError(\"clone is not deep and does not support nested objects\")\n }\n\n return clone\n}\nlunr.FieldRef = function (docRef, fieldName, stringValue) {\n this.docRef = docRef\n this.fieldName = fieldName\n this._stringValue = stringValue\n}\n\nlunr.FieldRef.joiner = \"/\"\n\nlunr.FieldRef.fromString = function (s) {\n var n = s.indexOf(lunr.FieldRef.joiner)\n\n if (n === -1) {\n throw \"malformed field ref string\"\n }\n\n var fieldRef = s.slice(0, n),\n docRef = s.slice(n + 1)\n\n return new lunr.FieldRef (docRef, fieldRef, s)\n}\n\nlunr.FieldRef.prototype.toString = function () {\n if (this._stringValue == undefined) {\n this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef\n }\n\n return this._stringValue\n}\n/*!\n * lunr.Set\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A lunr set.\n *\n * @constructor\n */\nlunr.Set = function (elements) {\n this.elements = Object.create(null)\n\n if (elements) {\n this.length = elements.length\n\n for (var i = 0; i < this.length; i++) {\n this.elements[elements[i]] = true\n }\n } else {\n this.length = 0\n }\n}\n\n/**\n * A complete set that contains all elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.complete = {\n intersect: function (other) {\n return other\n },\n\n union: function () {\n return this\n },\n\n contains: function () {\n return true\n }\n}\n\n/**\n * An empty set that contains no elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.empty = {\n intersect: function () {\n return this\n },\n\n union: function (other) {\n return other\n },\n\n contains: function () {\n return false\n }\n}\n\n/**\n * Returns true if this set contains the specified object.\n *\n * @param {object} object - Object whose presence in this set is to be tested.\n * @returns {boolean} - True if this set contains the specified object.\n */\nlunr.Set.prototype.contains = function (object) {\n return !!this.elements[object]\n}\n\n/**\n * Returns a new set containing only the elements that are present in both\n * this set and the specified set.\n *\n * @param {lunr.Set} other - set to intersect with this set.\n * @returns {lunr.Set} a new set that is the intersection of this and the specified set.\n */\n\nlunr.Set.prototype.intersect = function (other) {\n var a, b, elements, intersection = []\n\n if (other === lunr.Set.complete) {\n return this\n }\n\n if (other === lunr.Set.empty) {\n return other\n }\n\n if (this.length < other.length) {\n a = this\n b = other\n } else {\n a = other\n b = this\n }\n\n elements = Object.keys(a.elements)\n\n for (var i = 0; i < elements.length; i++) {\n var element = elements[i]\n if (element in b.elements) {\n intersection.push(element)\n }\n }\n\n return new lunr.Set (intersection)\n}\n\n/**\n * Returns a new set combining the elements of this and the specified set.\n *\n * @param {lunr.Set} other - set to union with this set.\n * @return {lunr.Set} a new set that is the union of this and the specified set.\n */\n\nlunr.Set.prototype.union = function (other) {\n if (other === lunr.Set.complete) {\n return lunr.Set.complete\n }\n\n if (other === lunr.Set.empty) {\n return this\n }\n\n return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))\n}\n/**\n * A function to calculate the inverse document frequency for\n * a posting. This is shared between the builder and the index\n *\n * @private\n * @param {object} posting - The posting for a given term\n * @param {number} documentCount - The total number of documents.\n */\nlunr.idf = function (posting, documentCount) {\n var documentsWithTerm = 0\n\n for (var fieldName in posting) {\n if (fieldName == '_index') continue // Ignore the term index, its not a field\n documentsWithTerm += Object.keys(posting[fieldName]).length\n }\n\n var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)\n\n return Math.log(1 + Math.abs(x))\n}\n\n/**\n * A token wraps a string representation of a token\n * as it is passed through the text processing pipeline.\n *\n * @constructor\n * @param {string} [str=''] - The string token being wrapped.\n * @param {object} [metadata={}] - Metadata associated with this token.\n */\nlunr.Token = function (str, metadata) {\n this.str = str || \"\"\n this.metadata = metadata || {}\n}\n\n/**\n * Returns the token string that is being wrapped by this object.\n *\n * @returns {string}\n */\nlunr.Token.prototype.toString = function () {\n return this.str\n}\n\n/**\n * A token update function is used when updating or optionally\n * when cloning a token.\n *\n * @callback lunr.Token~updateFunction\n * @param {string} str - The string representation of the token.\n * @param {Object} metadata - All metadata associated with this token.\n */\n\n/**\n * Applies the given function to the wrapped string token.\n *\n * @example\n * token.update(function (str, metadata) {\n * return str.toUpperCase()\n * })\n *\n * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.update = function (fn) {\n this.str = fn(this.str, this.metadata)\n return this\n}\n\n/**\n * Creates a clone of this token. Optionally a function can be\n * applied to the cloned token.\n *\n * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.clone = function (fn) {\n fn = fn || function (s) { return s }\n return new lunr.Token (fn(this.str, this.metadata), this.metadata)\n}\n/*!\n * lunr.tokenizer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A function for splitting a string into tokens ready to be inserted into\n * the search index. Uses `lunr.tokenizer.separator` to split strings, change\n * the value of this property to change how strings are split into tokens.\n *\n * This tokenizer will convert its parameter to a string by calling `toString` and\n * then will split this string on the character in `lunr.tokenizer.separator`.\n * Arrays will have their elements converted to strings and wrapped in a lunr.Token.\n *\n * Optional metadata can be passed to the tokenizer, this metadata will be cloned and\n * added as metadata to every token that is created from the object to be tokenized.\n *\n * @static\n * @param {?(string|object|object[])} obj - The object to convert into tokens\n * @param {?object} metadata - Optional metadata to associate with every token\n * @returns {lunr.Token[]}\n * @see {@link lunr.Pipeline}\n */\nlunr.tokenizer = function (obj, metadata) {\n if (obj == null || obj == undefined) {\n return []\n }\n\n if (Array.isArray(obj)) {\n return obj.map(function (t) {\n return new lunr.Token(\n lunr.utils.asString(t).toLowerCase(),\n lunr.utils.clone(metadata)\n )\n })\n }\n\n var str = obj.toString().toLowerCase(),\n len = str.length,\n tokens = []\n\n for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {\n var char = str.charAt(sliceEnd),\n sliceLength = sliceEnd - sliceStart\n\n if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {\n\n if (sliceLength > 0) {\n var tokenMetadata = lunr.utils.clone(metadata) || {}\n tokenMetadata[\"position\"] = [sliceStart, sliceLength]\n tokenMetadata[\"index\"] = tokens.length\n\n tokens.push(\n new lunr.Token (\n str.slice(sliceStart, sliceEnd),\n tokenMetadata\n )\n )\n }\n\n sliceStart = sliceEnd + 1\n }\n\n }\n\n return tokens\n}\n\n/**\n * The separator used to split a string into tokens. Override this property to change the behaviour of\n * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.\n *\n * @static\n * @see lunr.tokenizer\n */\nlunr.tokenizer.separator = /[\\s\\-]+/\n/*!\n * lunr.Pipeline\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Pipelines maintain an ordered list of functions to be applied to all\n * tokens in documents entering the search index and queries being ran against\n * the index.\n *\n * An instance of lunr.Index created with the lunr shortcut will contain a\n * pipeline with a stop word filter and an English language stemmer. Extra\n * functions can be added before or after either of these functions or these\n * default functions can be removed.\n *\n * When run the pipeline will call each function in turn, passing a token, the\n * index of that token in the original list of all tokens and finally a list of\n * all the original tokens.\n *\n * The output of functions in the pipeline will be passed to the next function\n * in the pipeline. To exclude a token from entering the index the function\n * should return undefined, the rest of the pipeline will not be called with\n * this token.\n *\n * For serialisation of pipelines to work, all functions used in an instance of\n * a pipeline should be registered with lunr.Pipeline. Registered functions can\n * then be loaded. If trying to load a serialised pipeline that uses functions\n * that are not registered an error will be thrown.\n *\n * If not planning on serialising the pipeline then registering pipeline functions\n * is not necessary.\n *\n * @constructor\n */\nlunr.Pipeline = function () {\n this._stack = []\n}\n\nlunr.Pipeline.registeredFunctions = Object.create(null)\n\n/**\n * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token\n * string as well as all known metadata. A pipeline function can mutate the token string\n * or mutate (or add) metadata for a given token.\n *\n * A pipeline function can indicate that the passed token should be discarded by returning\n * null, undefined or an empty string. This token will not be passed to any downstream pipeline\n * functions and will not be added to the index.\n *\n * Multiple tokens can be returned by returning an array of tokens. Each token will be passed\n * to any downstream pipeline functions and all will returned tokens will be added to the index.\n *\n * Any number of pipeline functions may be chained together using a lunr.Pipeline.\n *\n * @interface lunr.PipelineFunction\n * @param {lunr.Token} token - A token from the document being processed.\n * @param {number} i - The index of this token in the complete list of tokens for this document/field.\n * @param {lunr.Token[]} tokens - All tokens for this document/field.\n * @returns {(?lunr.Token|lunr.Token[])}\n */\n\n/**\n * Register a function with the pipeline.\n *\n * Functions that are used in the pipeline should be registered if the pipeline\n * needs to be serialised, or a serialised pipeline needs to be loaded.\n *\n * Registering a function does not add it to a pipeline, functions must still be\n * added to instances of the pipeline for them to be used when running a pipeline.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @param {String} label - The label to register this function with\n */\nlunr.Pipeline.registerFunction = function (fn, label) {\n if (label in this.registeredFunctions) {\n lunr.utils.warn('Overwriting existing registered function: ' + label)\n }\n\n fn.label = label\n lunr.Pipeline.registeredFunctions[fn.label] = fn\n}\n\n/**\n * Warns if the function is not registered as a Pipeline function.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @private\n */\nlunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {\n var isRegistered = fn.label && (fn.label in this.registeredFunctions)\n\n if (!isRegistered) {\n lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\\n', fn)\n }\n}\n\n/**\n * Loads a previously serialised pipeline.\n *\n * All functions to be loaded must already be registered with lunr.Pipeline.\n * If any function from the serialised data has not been registered then an\n * error will be thrown.\n *\n * @param {Object} serialised - The serialised pipeline to load.\n * @returns {lunr.Pipeline}\n */\nlunr.Pipeline.load = function (serialised) {\n var pipeline = new lunr.Pipeline\n\n serialised.forEach(function (fnName) {\n var fn = lunr.Pipeline.registeredFunctions[fnName]\n\n if (fn) {\n pipeline.add(fn)\n } else {\n throw new Error('Cannot load unregistered function: ' + fnName)\n }\n })\n\n return pipeline\n}\n\n/**\n * Adds new functions to the end of the pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.\n */\nlunr.Pipeline.prototype.add = function () {\n var fns = Array.prototype.slice.call(arguments)\n\n fns.forEach(function (fn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n this._stack.push(fn)\n }, this)\n}\n\n/**\n * Adds a single function after a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.after = function (existingFn, newFn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n var pos = this._stack.indexOf(existingFn)\n if (pos == -1) {\n throw new Error('Cannot find existingFn')\n }\n\n pos = pos + 1\n this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Adds a single function before a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.before = function (existingFn, newFn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n var pos = this._stack.indexOf(existingFn)\n if (pos == -1) {\n throw new Error('Cannot find existingFn')\n }\n\n this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Removes a function from the pipeline.\n *\n * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.\n */\nlunr.Pipeline.prototype.remove = function (fn) {\n var pos = this._stack.indexOf(fn)\n if (pos == -1) {\n return\n }\n\n this._stack.splice(pos, 1)\n}\n\n/**\n * Runs the current list of functions that make up the pipeline against the\n * passed tokens.\n *\n * @param {Array} tokens The tokens to run through the pipeline.\n * @returns {Array}\n */\nlunr.Pipeline.prototype.run = function (tokens) {\n var stackLength = this._stack.length\n\n for (var i = 0; i < stackLength; i++) {\n var fn = this._stack[i]\n var memo = []\n\n for (var j = 0; j < tokens.length; j++) {\n var result = fn(tokens[j], j, tokens)\n\n if (result === null || result === void 0 || result === '') continue\n\n if (Array.isArray(result)) {\n for (var k = 0; k < result.length; k++) {\n memo.push(result[k])\n }\n } else {\n memo.push(result)\n }\n }\n\n tokens = memo\n }\n\n return tokens\n}\n\n/**\n * Convenience method for passing a string through a pipeline and getting\n * strings out. This method takes care of wrapping the passed string in a\n * token and mapping the resulting tokens back to strings.\n *\n * @param {string} str - The string to pass through the pipeline.\n * @param {?object} metadata - Optional metadata to associate with the token\n * passed to the pipeline.\n * @returns {string[]}\n */\nlunr.Pipeline.prototype.runString = function (str, metadata) {\n var token = new lunr.Token (str, metadata)\n\n return this.run([token]).map(function (t) {\n return t.toString()\n })\n}\n\n/**\n * Resets the pipeline by removing any existing processors.\n *\n */\nlunr.Pipeline.prototype.reset = function () {\n this._stack = []\n}\n\n/**\n * Returns a representation of the pipeline ready for serialisation.\n *\n * Logs a warning if the function has not been registered.\n *\n * @returns {Array}\n */\nlunr.Pipeline.prototype.toJSON = function () {\n return this._stack.map(function (fn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n\n return fn.label\n })\n}\n/*!\n * lunr.Vector\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A vector is used to construct the vector space of documents and queries. These\n * vectors support operations to determine the similarity between two documents or\n * a document and a query.\n *\n * Normally no parameters are required for initializing a vector, but in the case of\n * loading a previously dumped vector the raw elements can be provided to the constructor.\n *\n * For performance reasons vectors are implemented with a flat array, where an elements\n * index is immediately followed by its value. E.g. [index, value, index, value]. This\n * allows the underlying array to be as sparse as possible and still offer decent\n * performance when being used for vector calculations.\n *\n * @constructor\n * @param {Number[]} [elements] - The flat list of element index and element value pairs.\n */\nlunr.Vector = function (elements) {\n this._magnitude = 0\n this.elements = elements || []\n}\n\n\n/**\n * Calculates the position within the vector to insert a given index.\n *\n * This is used internally by insert and upsert. If there are duplicate indexes then\n * the position is returned as if the value for that index were to be updated, but it\n * is the callers responsibility to check whether there is a duplicate at that index\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @returns {Number}\n */\nlunr.Vector.prototype.positionForIndex = function (index) {\n // For an empty vector the tuple can be inserted at the beginning\n if (this.elements.length == 0) {\n return 0\n }\n\n var start = 0,\n end = this.elements.length / 2,\n sliceLength = end - start,\n pivotPoint = Math.floor(sliceLength / 2),\n pivotIndex = this.elements[pivotPoint * 2]\n\n while (sliceLength > 1) {\n if (pivotIndex < index) {\n start = pivotPoint\n }\n\n if (pivotIndex > index) {\n end = pivotPoint\n }\n\n if (pivotIndex == index) {\n break\n }\n\n sliceLength = end - start\n pivotPoint = start + Math.floor(sliceLength / 2)\n pivotIndex = this.elements[pivotPoint * 2]\n }\n\n if (pivotIndex == index) {\n return pivotPoint * 2\n }\n\n if (pivotIndex > index) {\n return pivotPoint * 2\n }\n\n if (pivotIndex < index) {\n return (pivotPoint + 1) * 2\n }\n}\n\n/**\n * Inserts an element at an index within the vector.\n *\n * Does not allow duplicates, will throw an error if there is already an entry\n * for this index.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n */\nlunr.Vector.prototype.insert = function (insertIdx, val) {\n this.upsert(insertIdx, val, function () {\n throw \"duplicate index\"\n })\n}\n\n/**\n * Inserts or updates an existing index within the vector.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n * @param {function} fn - A function that is called for updates, the existing value and the\n * requested value are passed as arguments\n */\nlunr.Vector.prototype.upsert = function (insertIdx, val, fn) {\n this._magnitude = 0\n var position = this.positionForIndex(insertIdx)\n\n if (this.elements[position] == insertIdx) {\n this.elements[position + 1] = fn(this.elements[position + 1], val)\n } else {\n this.elements.splice(position, 0, insertIdx, val)\n }\n}\n\n/**\n * Calculates the magnitude of this vector.\n *\n * @returns {Number}\n */\nlunr.Vector.prototype.magnitude = function () {\n if (this._magnitude) return this._magnitude\n\n var sumOfSquares = 0,\n elementsLength = this.elements.length\n\n for (var i = 1; i < elementsLength; i += 2) {\n var val = this.elements[i]\n sumOfSquares += val * val\n }\n\n return this._magnitude = Math.sqrt(sumOfSquares)\n}\n\n/**\n * Calculates the dot product of this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The vector to compute the dot product with.\n * @returns {Number}\n */\nlunr.Vector.prototype.dot = function (otherVector) {\n var dotProduct = 0,\n a = this.elements, b = otherVector.elements,\n aLen = a.length, bLen = b.length,\n aVal = 0, bVal = 0,\n i = 0, j = 0\n\n while (i < aLen && j < bLen) {\n aVal = a[i], bVal = b[j]\n if (aVal < bVal) {\n i += 2\n } else if (aVal > bVal) {\n j += 2\n } else if (aVal == bVal) {\n dotProduct += a[i + 1] * b[j + 1]\n i += 2\n j += 2\n }\n }\n\n return dotProduct\n}\n\n/**\n * Calculates the similarity between this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The other vector to calculate the\n * similarity with.\n * @returns {Number}\n */\nlunr.Vector.prototype.similarity = function (otherVector) {\n return this.dot(otherVector) / this.magnitude() || 0\n}\n\n/**\n * Converts the vector to an array of the elements within the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toArray = function () {\n var output = new Array (this.elements.length / 2)\n\n for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {\n output[j] = this.elements[i]\n }\n\n return output\n}\n\n/**\n * A JSON serializable representation of the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toJSON = function () {\n return this.elements\n}\n/* eslint-disable */\n/*!\n * lunr.stemmer\n * Copyright (C) 2020 Oliver Nightingale\n * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt\n */\n\n/**\n * lunr.stemmer is an english language stemmer, this is a JavaScript\n * implementation of the PorterStemmer taken from http://tartarus.org/~martin\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token - The string to stem\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n * @function\n */\nlunr.stemmer = (function(){\n var step2list = {\n \"ational\" : \"ate\",\n \"tional\" : \"tion\",\n \"enci\" : \"ence\",\n \"anci\" : \"ance\",\n \"izer\" : \"ize\",\n \"bli\" : \"ble\",\n \"alli\" : \"al\",\n \"entli\" : \"ent\",\n \"eli\" : \"e\",\n \"ousli\" : \"ous\",\n \"ization\" : \"ize\",\n \"ation\" : \"ate\",\n \"ator\" : \"ate\",\n \"alism\" : \"al\",\n \"iveness\" : \"ive\",\n \"fulness\" : \"ful\",\n \"ousness\" : \"ous\",\n \"aliti\" : \"al\",\n \"iviti\" : \"ive\",\n \"biliti\" : \"ble\",\n \"logi\" : \"log\"\n },\n\n step3list = {\n \"icate\" : \"ic\",\n \"ative\" : \"\",\n \"alize\" : \"al\",\n \"iciti\" : \"ic\",\n \"ical\" : \"ic\",\n \"ful\" : \"\",\n \"ness\" : \"\"\n },\n\n c = \"[^aeiou]\", // consonant\n v = \"[aeiouy]\", // vowel\n C = c + \"[^aeiouy]*\", // consonant sequence\n V = v + \"[aeiou]*\", // vowel sequence\n\n mgr0 = \"^(\" + C + \")?\" + V + C, // [C]VC... is m>0\n meq1 = \"^(\" + C + \")?\" + V + C + \"(\" + V + \")?$\", // [C]VC[V] is m=1\n mgr1 = \"^(\" + C + \")?\" + V + C + V + C, // [C]VCVC... is m>1\n s_v = \"^(\" + C + \")?\" + v; // vowel in stem\n\n var re_mgr0 = new RegExp(mgr0);\n var re_mgr1 = new RegExp(mgr1);\n var re_meq1 = new RegExp(meq1);\n var re_s_v = new RegExp(s_v);\n\n var re_1a = /^(.+?)(ss|i)es$/;\n var re2_1a = /^(.+?)([^s])s$/;\n var re_1b = /^(.+?)eed$/;\n var re2_1b = /^(.+?)(ed|ing)$/;\n var re_1b_2 = /.$/;\n var re2_1b_2 = /(at|bl|iz)$/;\n var re3_1b_2 = new RegExp(\"([^aeiouylsz])\\\\1$\");\n var re4_1b_2 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n var re_1c = /^(.+?[^aeiou])y$/;\n var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;\n\n var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;\n\n var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;\n var re2_4 = /^(.+?)(s|t)(ion)$/;\n\n var re_5 = /^(.+?)e$/;\n var re_5_1 = /ll$/;\n var re3_5 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n var porterStemmer = function porterStemmer(w) {\n var stem,\n suffix,\n firstch,\n re,\n re2,\n re3,\n re4;\n\n if (w.length < 3) { return w; }\n\n firstch = w.substr(0,1);\n if (firstch == \"y\") {\n w = firstch.toUpperCase() + w.substr(1);\n }\n\n // Step 1a\n re = re_1a\n re2 = re2_1a;\n\n if (re.test(w)) { w = w.replace(re,\"$1$2\"); }\n else if (re2.test(w)) { w = w.replace(re2,\"$1$2\"); }\n\n // Step 1b\n re = re_1b;\n re2 = re2_1b;\n if (re.test(w)) {\n var fp = re.exec(w);\n re = re_mgr0;\n if (re.test(fp[1])) {\n re = re_1b_2;\n w = w.replace(re,\"\");\n }\n } else if (re2.test(w)) {\n var fp = re2.exec(w);\n stem = fp[1];\n re2 = re_s_v;\n if (re2.test(stem)) {\n w = stem;\n re2 = re2_1b_2;\n re3 = re3_1b_2;\n re4 = re4_1b_2;\n if (re2.test(w)) { w = w + \"e\"; }\n else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,\"\"); }\n else if (re4.test(w)) { w = w + \"e\"; }\n }\n }\n\n // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)\n re = re_1c;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n w = stem + \"i\";\n }\n\n // Step 2\n re = re_2;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n suffix = fp[2];\n re = re_mgr0;\n if (re.test(stem)) {\n w = stem + step2list[suffix];\n }\n }\n\n // Step 3\n re = re_3;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n suffix = fp[2];\n re = re_mgr0;\n if (re.test(stem)) {\n w = stem + step3list[suffix];\n }\n }\n\n // Step 4\n re = re_4;\n re2 = re2_4;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n re = re_mgr1;\n if (re.test(stem)) {\n w = stem;\n }\n } else if (re2.test(w)) {\n var fp = re2.exec(w);\n stem = fp[1] + fp[2];\n re2 = re_mgr1;\n if (re2.test(stem)) {\n w = stem;\n }\n }\n\n // Step 5\n re = re_5;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n re = re_mgr1;\n re2 = re_meq1;\n re3 = re3_5;\n if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {\n w = stem;\n }\n }\n\n re = re_5_1;\n re2 = re_mgr1;\n if (re.test(w) && re2.test(w)) {\n re = re_1b_2;\n w = w.replace(re,\"\");\n }\n\n // and turn initial Y back to y\n\n if (firstch == \"y\") {\n w = firstch.toLowerCase() + w.substr(1);\n }\n\n return w;\n };\n\n return function (token) {\n return token.update(porterStemmer);\n }\n})();\n\nlunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')\n/*!\n * lunr.stopWordFilter\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.generateStopWordFilter builds a stopWordFilter function from the provided\n * list of stop words.\n *\n * The built in lunr.stopWordFilter is built using this generator and can be used\n * to generate custom stopWordFilters for applications or non English languages.\n *\n * @function\n * @param {Array} token The token to pass through the filter\n * @returns {lunr.PipelineFunction}\n * @see lunr.Pipeline\n * @see lunr.stopWordFilter\n */\nlunr.generateStopWordFilter = function (stopWords) {\n var words = stopWords.reduce(function (memo, stopWord) {\n memo[stopWord] = stopWord\n return memo\n }, {})\n\n return function (token) {\n if (token && words[token.toString()] !== token.toString()) return token\n }\n}\n\n/**\n * lunr.stopWordFilter is an English language stop word list filter, any words\n * contained in the list will not be passed through the filter.\n *\n * This is intended to be used in the Pipeline. If the token does not pass the\n * filter then undefined will be returned.\n *\n * @function\n * @implements {lunr.PipelineFunction}\n * @params {lunr.Token} token - A token to check for being a stop word.\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n */\nlunr.stopWordFilter = lunr.generateStopWordFilter([\n 'a',\n 'able',\n 'about',\n 'across',\n 'after',\n 'all',\n 'almost',\n 'also',\n 'am',\n 'among',\n 'an',\n 'and',\n 'any',\n 'are',\n 'as',\n 'at',\n 'be',\n 'because',\n 'been',\n 'but',\n 'by',\n 'can',\n 'cannot',\n 'could',\n 'dear',\n 'did',\n 'do',\n 'does',\n 'either',\n 'else',\n 'ever',\n 'every',\n 'for',\n 'from',\n 'get',\n 'got',\n 'had',\n 'has',\n 'have',\n 'he',\n 'her',\n 'hers',\n 'him',\n 'his',\n 'how',\n 'however',\n 'i',\n 'if',\n 'in',\n 'into',\n 'is',\n 'it',\n 'its',\n 'just',\n 'least',\n 'let',\n 'like',\n 'likely',\n 'may',\n 'me',\n 'might',\n 'most',\n 'must',\n 'my',\n 'neither',\n 'no',\n 'nor',\n 'not',\n 'of',\n 'off',\n 'often',\n 'on',\n 'only',\n 'or',\n 'other',\n 'our',\n 'own',\n 'rather',\n 'said',\n 'say',\n 'says',\n 'she',\n 'should',\n 'since',\n 'so',\n 'some',\n 'than',\n 'that',\n 'the',\n 'their',\n 'them',\n 'then',\n 'there',\n 'these',\n 'they',\n 'this',\n 'tis',\n 'to',\n 'too',\n 'twas',\n 'us',\n 'wants',\n 'was',\n 'we',\n 'were',\n 'what',\n 'when',\n 'where',\n 'which',\n 'while',\n 'who',\n 'whom',\n 'why',\n 'will',\n 'with',\n 'would',\n 'yet',\n 'you',\n 'your'\n])\n\nlunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')\n/*!\n * lunr.trimmer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.trimmer is a pipeline function for trimming non word\n * characters from the beginning and end of tokens before they\n * enter the index.\n *\n * This implementation may not work correctly for non latin\n * characters and should either be removed or adapted for use\n * with languages with non-latin characters.\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token The token to pass through the filter\n * @returns {lunr.Token}\n * @see lunr.Pipeline\n */\nlunr.trimmer = function (token) {\n return token.update(function (s) {\n return s.replace(/^\\W+/, '').replace(/\\W+$/, '')\n })\n}\n\nlunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')\n/*!\n * lunr.TokenSet\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A token set is used to store the unique list of all tokens\n * within an index. Token sets are also used to represent an\n * incoming query to the index, this query token set and index\n * token set are then intersected to find which tokens to look\n * up in the inverted index.\n *\n * A token set can hold multiple tokens, as in the case of the\n * index token set, or it can hold a single token as in the\n * case of a simple query token set.\n *\n * Additionally token sets are used to perform wildcard matching.\n * Leading, contained and trailing wildcards are supported, and\n * from this edit distance matching can also be provided.\n *\n * Token sets are implemented as a minimal finite state automata,\n * where both common prefixes and suffixes are shared between tokens.\n * This helps to reduce the space used for storing the token set.\n *\n * @constructor\n */\nlunr.TokenSet = function () {\n this.final = false\n this.edges = {}\n this.id = lunr.TokenSet._nextId\n lunr.TokenSet._nextId += 1\n}\n\n/**\n * Keeps track of the next, auto increment, identifier to assign\n * to a new tokenSet.\n *\n * TokenSets require a unique identifier to be correctly minimised.\n *\n * @private\n */\nlunr.TokenSet._nextId = 1\n\n/**\n * Creates a TokenSet instance from the given sorted array of words.\n *\n * @param {String[]} arr - A sorted array of strings to create the set from.\n * @returns {lunr.TokenSet}\n * @throws Will throw an error if the input array is not sorted.\n */\nlunr.TokenSet.fromArray = function (arr) {\n var builder = new lunr.TokenSet.Builder\n\n for (var i = 0, len = arr.length; i < len; i++) {\n builder.insert(arr[i])\n }\n\n builder.finish()\n return builder.root\n}\n\n/**\n * Creates a token set from a query clause.\n *\n * @private\n * @param {Object} clause - A single clause from lunr.Query.\n * @param {string} clause.term - The query clause term.\n * @param {number} [clause.editDistance] - The optional edit distance for the term.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromClause = function (clause) {\n if ('editDistance' in clause) {\n return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)\n } else {\n return lunr.TokenSet.fromString(clause.term)\n }\n}\n\n/**\n * Creates a token set representing a single string with a specified\n * edit distance.\n *\n * Insertions, deletions, substitutions and transpositions are each\n * treated as an edit distance of 1.\n *\n * Increasing the allowed edit distance will have a dramatic impact\n * on the performance of both creating and intersecting these TokenSets.\n * It is advised to keep the edit distance less than 3.\n *\n * @param {string} str - The string to create the token set from.\n * @param {number} editDistance - The allowed edit distance to match.\n * @returns {lunr.Vector}\n */\nlunr.TokenSet.fromFuzzyString = function (str, editDistance) {\n var root = new lunr.TokenSet\n\n var stack = [{\n node: root,\n editsRemaining: editDistance,\n str: str\n }]\n\n while (stack.length) {\n var frame = stack.pop()\n\n // no edit\n if (frame.str.length > 0) {\n var char = frame.str.charAt(0),\n noEditNode\n\n if (char in frame.node.edges) {\n noEditNode = frame.node.edges[char]\n } else {\n noEditNode = new lunr.TokenSet\n frame.node.edges[char] = noEditNode\n }\n\n if (frame.str.length == 1) {\n noEditNode.final = true\n }\n\n stack.push({\n node: noEditNode,\n editsRemaining: frame.editsRemaining,\n str: frame.str.slice(1)\n })\n }\n\n if (frame.editsRemaining == 0) {\n continue\n }\n\n // insertion\n if (\"*\" in frame.node.edges) {\n var insertionNode = frame.node.edges[\"*\"]\n } else {\n var insertionNode = new lunr.TokenSet\n frame.node.edges[\"*\"] = insertionNode\n }\n\n if (frame.str.length == 0) {\n insertionNode.final = true\n }\n\n stack.push({\n node: insertionNode,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str\n })\n\n // deletion\n // can only do a deletion if we have enough edits remaining\n // and if there are characters left to delete in the string\n if (frame.str.length > 1) {\n stack.push({\n node: frame.node,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str.slice(1)\n })\n }\n\n // deletion\n // just removing the last character from the str\n if (frame.str.length == 1) {\n frame.node.final = true\n }\n\n // substitution\n // can only do a substitution if we have enough edits remaining\n // and if there are characters left to substitute\n if (frame.str.length >= 1) {\n if (\"*\" in frame.node.edges) {\n var substitutionNode = frame.node.edges[\"*\"]\n } else {\n var substitutionNode = new lunr.TokenSet\n frame.node.edges[\"*\"] = substitutionNode\n }\n\n if (frame.str.length == 1) {\n substitutionNode.final = true\n }\n\n stack.push({\n node: substitutionNode,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str.slice(1)\n })\n }\n\n // transposition\n // can only do a transposition if there are edits remaining\n // and there are enough characters to transpose\n if (frame.str.length > 1) {\n var charA = frame.str.charAt(0),\n charB = frame.str.charAt(1),\n transposeNode\n\n if (charB in frame.node.edges) {\n transposeNode = frame.node.edges[charB]\n } else {\n transposeNode = new lunr.TokenSet\n frame.node.edges[charB] = transposeNode\n }\n\n if (frame.str.length == 1) {\n transposeNode.final = true\n }\n\n stack.push({\n node: transposeNode,\n editsRemaining: frame.editsRemaining - 1,\n str: charA + frame.str.slice(2)\n })\n }\n }\n\n return root\n}\n\n/**\n * Creates a TokenSet from a string.\n *\n * The string may contain one or more wildcard characters (*)\n * that will allow wildcard matching when intersecting with\n * another TokenSet.\n *\n * @param {string} str - The string to create a TokenSet from.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromString = function (str) {\n var node = new lunr.TokenSet,\n root = node\n\n /*\n * Iterates through all characters within the passed string\n * appending a node for each character.\n *\n * When a wildcard character is found then a self\n * referencing edge is introduced to continually match\n * any number of any characters.\n */\n for (var i = 0, len = str.length; i < len; i++) {\n var char = str[i],\n final = (i == len - 1)\n\n if (char == \"*\") {\n node.edges[char] = node\n node.final = final\n\n } else {\n var next = new lunr.TokenSet\n next.final = final\n\n node.edges[char] = next\n node = next\n }\n }\n\n return root\n}\n\n/**\n * Converts this TokenSet into an array of strings\n * contained within the TokenSet.\n *\n * This is not intended to be used on a TokenSet that\n * contains wildcards, in these cases the results are\n * undefined and are likely to cause an infinite loop.\n *\n * @returns {string[]}\n */\nlunr.TokenSet.prototype.toArray = function () {\n var words = []\n\n var stack = [{\n prefix: \"\",\n node: this\n }]\n\n while (stack.length) {\n var frame = stack.pop(),\n edges = Object.keys(frame.node.edges),\n len = edges.length\n\n if (frame.node.final) {\n /* In Safari, at this point the prefix is sometimes corrupted, see:\n * https://github.com/olivernn/lunr.js/issues/279 Calling any\n * String.prototype method forces Safari to \"cast\" this string to what\n * it's supposed to be, fixing the bug. */\n frame.prefix.charAt(0)\n words.push(frame.prefix)\n }\n\n for (var i = 0; i < len; i++) {\n var edge = edges[i]\n\n stack.push({\n prefix: frame.prefix.concat(edge),\n node: frame.node.edges[edge]\n })\n }\n }\n\n return words\n}\n\n/**\n * Generates a string representation of a TokenSet.\n *\n * This is intended to allow TokenSets to be used as keys\n * in objects, largely to aid the construction and minimisation\n * of a TokenSet. As such it is not designed to be a human\n * friendly representation of the TokenSet.\n *\n * @returns {string}\n */\nlunr.TokenSet.prototype.toString = function () {\n // NOTE: Using Object.keys here as this.edges is very likely\n // to enter 'hash-mode' with many keys being added\n //\n // avoiding a for-in loop here as it leads to the function\n // being de-optimised (at least in V8). From some simple\n // benchmarks the performance is comparable, but allowing\n // V8 to optimize may mean easy performance wins in the future.\n\n if (this._str) {\n return this._str\n }\n\n var str = this.final ? '1' : '0',\n labels = Object.keys(this.edges).sort(),\n len = labels.length\n\n for (var i = 0; i < len; i++) {\n var label = labels[i],\n node = this.edges[label]\n\n str = str + label + node.id\n }\n\n return str\n}\n\n/**\n * Returns a new TokenSet that is the intersection of\n * this TokenSet and the passed TokenSet.\n *\n * This intersection will take into account any wildcards\n * contained within the TokenSet.\n *\n * @param {lunr.TokenSet} b - An other TokenSet to intersect with.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.prototype.intersect = function (b) {\n var output = new lunr.TokenSet,\n frame = undefined\n\n var stack = [{\n qNode: b,\n output: output,\n node: this\n }]\n\n while (stack.length) {\n frame = stack.pop()\n\n // NOTE: As with the #toString method, we are using\n // Object.keys and a for loop instead of a for-in loop\n // as both of these objects enter 'hash' mode, causing\n // the function to be de-optimised in V8\n var qEdges = Object.keys(frame.qNode.edges),\n qLen = qEdges.length,\n nEdges = Object.keys(frame.node.edges),\n nLen = nEdges.length\n\n for (var q = 0; q < qLen; q++) {\n var qEdge = qEdges[q]\n\n for (var n = 0; n < nLen; n++) {\n var nEdge = nEdges[n]\n\n if (nEdge == qEdge || qEdge == '*') {\n var node = frame.node.edges[nEdge],\n qNode = frame.qNode.edges[qEdge],\n final = node.final && qNode.final,\n next = undefined\n\n if (nEdge in frame.output.edges) {\n // an edge already exists for this character\n // no need to create a new node, just set the finality\n // bit unless this node is already final\n next = frame.output.edges[nEdge]\n next.final = next.final || final\n\n } else {\n // no edge exists yet, must create one\n // set the finality bit and insert it\n // into the output\n next = new lunr.TokenSet\n next.final = final\n frame.output.edges[nEdge] = next\n }\n\n stack.push({\n qNode: qNode,\n output: next,\n node: node\n })\n }\n }\n }\n }\n\n return output\n}\nlunr.TokenSet.Builder = function () {\n this.previousWord = \"\"\n this.root = new lunr.TokenSet\n this.uncheckedNodes = []\n this.minimizedNodes = {}\n}\n\nlunr.TokenSet.Builder.prototype.insert = function (word) {\n var node,\n commonPrefix = 0\n\n if (word < this.previousWord) {\n throw new Error (\"Out of order word insertion\")\n }\n\n for (var i = 0; i < word.length && i < this.previousWord.length; i++) {\n if (word[i] != this.previousWord[i]) break\n commonPrefix++\n }\n\n this.minimize(commonPrefix)\n\n if (this.uncheckedNodes.length == 0) {\n node = this.root\n } else {\n node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child\n }\n\n for (var i = commonPrefix; i < word.length; i++) {\n var nextNode = new lunr.TokenSet,\n char = word[i]\n\n node.edges[char] = nextNode\n\n this.uncheckedNodes.push({\n parent: node,\n char: char,\n child: nextNode\n })\n\n node = nextNode\n }\n\n node.final = true\n this.previousWord = word\n}\n\nlunr.TokenSet.Builder.prototype.finish = function () {\n this.minimize(0)\n}\n\nlunr.TokenSet.Builder.prototype.minimize = function (downTo) {\n for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {\n var node = this.uncheckedNodes[i],\n childKey = node.child.toString()\n\n if (childKey in this.minimizedNodes) {\n node.parent.edges[node.char] = this.minimizedNodes[childKey]\n } else {\n // Cache the key for this node since\n // we know it can't change anymore\n node.child._str = childKey\n\n this.minimizedNodes[childKey] = node.child\n }\n\n this.uncheckedNodes.pop()\n }\n}\n/*!\n * lunr.Index\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * An index contains the built index of all documents and provides a query interface\n * to the index.\n *\n * Usually instances of lunr.Index will not be created using this constructor, instead\n * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be\n * used to load previously built and serialized indexes.\n *\n * @constructor\n * @param {Object} attrs - The attributes of the built search index.\n * @param {Object} attrs.invertedIndex - An index of term/field to document reference.\n * @param {Object} attrs.fieldVectors - Field vectors\n * @param {lunr.TokenSet} attrs.tokenSet - An set of all corpus tokens.\n * @param {string[]} attrs.fields - The names of indexed document fields.\n * @param {lunr.Pipeline} attrs.pipeline - The pipeline to use for search terms.\n */\nlunr.Index = function (attrs) {\n this.invertedIndex = attrs.invertedIndex\n this.fieldVectors = attrs.fieldVectors\n this.tokenSet = attrs.tokenSet\n this.fields = attrs.fields\n this.pipeline = attrs.pipeline\n}\n\n/**\n * A result contains details of a document matching a search query.\n * @typedef {Object} lunr.Index~Result\n * @property {string} ref - The reference of the document this result represents.\n * @property {number} score - A number between 0 and 1 representing how similar this document is to the query.\n * @property {lunr.MatchData} matchData - Contains metadata about this match including which term(s) caused the match.\n */\n\n/**\n * Although lunr provides the ability to create queries using lunr.Query, it also provides a simple\n * query language which itself is parsed into an instance of lunr.Query.\n *\n * For programmatically building queries it is advised to directly use lunr.Query, the query language\n * is best used for human entered text rather than program generated text.\n *\n * At its simplest queries can just be a single term, e.g. `hello`, multiple terms are also supported\n * and will be combined with OR, e.g `hello world` will match documents that contain either 'hello'\n * or 'world', though those that contain both will rank higher in the results.\n *\n * Wildcards can be included in terms to match one or more unspecified characters, these wildcards can\n * be inserted anywhere within the term, and more than one wildcard can exist in a single term. Adding\n * wildcards will increase the number of documents that will be found but can also have a negative\n * impact on query performance, especially with wildcards at the beginning of a term.\n *\n * Terms can be restricted to specific fields, e.g. `title:hello`, only documents with the term\n * hello in the title field will match this query. Using a field not present in the index will lead\n * to an error being thrown.\n *\n * Modifiers can also be added to terms, lunr supports edit distance and boost modifiers on terms. A term\n * boost will make documents matching that term score higher, e.g. `foo^5`. Edit distance is also supported\n * to provide fuzzy matching, e.g. 'hello~2' will match documents with hello with an edit distance of 2.\n * Avoid large values for edit distance to improve query performance.\n *\n * Each term also supports a presence modifier. By default a term's presence in document is optional, however\n * this can be changed to either required or prohibited. For a term's presence to be required in a document the\n * term should be prefixed with a '+', e.g. `+foo bar` is a search for documents that must contain 'foo' and\n * optionally contain 'bar'. Conversely a leading '-' sets the terms presence to prohibited, i.e. it must not\n * appear in a document, e.g. `-foo bar` is a search for documents that do not contain 'foo' but may contain 'bar'.\n *\n * To escape special characters the backslash character '\\' can be used, this allows searches to include\n * characters that would normally be considered modifiers, e.g. `foo\\~2` will search for a term \"foo~2\" instead\n * of attempting to apply a boost of 2 to the search term \"foo\".\n *\n * @typedef {string} lunr.Index~QueryString\n * @example Simple single term query\n * hello\n * @example Multiple term query\n * hello world\n * @example term scoped to a field\n * title:hello\n * @example term with a boost of 10\n * hello^10\n * @example term with an edit distance of 2\n * hello~2\n * @example terms with presence modifiers\n * -foo +bar baz\n */\n\n/**\n * Performs a search against the index using lunr query syntax.\n *\n * Results will be returned sorted by their score, the most relevant results\n * will be returned first. For details on how the score is calculated, please see\n * the {@link https://lunrjs.com/guides/searching.html#scoring|guide}.\n *\n * For more programmatic querying use lunr.Index#query.\n *\n * @param {lunr.Index~QueryString} queryString - A string containing a lunr query.\n * @throws {lunr.QueryParseError} If the passed query string cannot be parsed.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.search = function (queryString) {\n return this.query(function (query) {\n var parser = new lunr.QueryParser(queryString, query)\n parser.parse()\n })\n}\n\n/**\n * A query builder callback provides a query object to be used to express\n * the query to perform on the index.\n *\n * @callback lunr.Index~queryBuilder\n * @param {lunr.Query} query - The query object to build up.\n * @this lunr.Query\n */\n\n/**\n * Performs a query against the index using the yielded lunr.Query object.\n *\n * If performing programmatic queries against the index, this method is preferred\n * over lunr.Index#search so as to avoid the additional query parsing overhead.\n *\n * A query object is yielded to the supplied function which should be used to\n * express the query to be run against the index.\n *\n * Note that although this function takes a callback parameter it is _not_ an\n * asynchronous operation, the callback is just yielded a query object to be\n * customized.\n *\n * @param {lunr.Index~queryBuilder} fn - A function that is used to build the query.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.query = function (fn) {\n // for each query clause\n // * process terms\n // * expand terms from token set\n // * find matching documents and metadata\n // * get document vectors\n // * score documents\n\n var query = new lunr.Query(this.fields),\n matchingFields = Object.create(null),\n queryVectors = Object.create(null),\n termFieldCache = Object.create(null),\n requiredMatches = Object.create(null),\n prohibitedMatches = Object.create(null)\n\n /*\n * To support field level boosts a query vector is created per\n * field. An empty vector is eagerly created to support negated\n * queries.\n */\n for (var i = 0; i < this.fields.length; i++) {\n queryVectors[this.fields[i]] = new lunr.Vector\n }\n\n fn.call(query, query)\n\n for (var i = 0; i < query.clauses.length; i++) {\n /*\n * Unless the pipeline has been disabled for this term, which is\n * the case for terms with wildcards, we need to pass the clause\n * term through the search pipeline. A pipeline returns an array\n * of processed terms. Pipeline functions may expand the passed\n * term, which means we may end up performing multiple index lookups\n * for a single query term.\n */\n var clause = query.clauses[i],\n terms = null,\n clauseMatches = lunr.Set.empty\n\n if (clause.usePipeline) {\n terms = this.pipeline.runString(clause.term, {\n fields: clause.fields\n })\n } else {\n terms = [clause.term]\n }\n\n for (var m = 0; m < terms.length; m++) {\n var term = terms[m]\n\n /*\n * Each term returned from the pipeline needs to use the same query\n * clause object, e.g. the same boost and or edit distance. The\n * simplest way to do this is to re-use the clause object but mutate\n * its term property.\n */\n clause.term = term\n\n /*\n * From the term in the clause we create a token set which will then\n * be used to intersect the indexes token set to get a list of terms\n * to lookup in the inverted index\n */\n var termTokenSet = lunr.TokenSet.fromClause(clause),\n expandedTerms = this.tokenSet.intersect(termTokenSet).toArray()\n\n /*\n * If a term marked as required does not exist in the tokenSet it is\n * impossible for the search to return any matches. We set all the field\n * scoped required matches set to empty and stop examining any further\n * clauses.\n */\n if (expandedTerms.length === 0 && clause.presence === lunr.Query.presence.REQUIRED) {\n for (var k = 0; k < clause.fields.length; k++) {\n var field = clause.fields[k]\n requiredMatches[field] = lunr.Set.empty\n }\n\n break\n }\n\n for (var j = 0; j < expandedTerms.length; j++) {\n /*\n * For each term get the posting and termIndex, this is required for\n * building the query vector.\n */\n var expandedTerm = expandedTerms[j],\n posting = this.invertedIndex[expandedTerm],\n termIndex = posting._index\n\n for (var k = 0; k < clause.fields.length; k++) {\n /*\n * For each field that this query term is scoped by (by default\n * all fields are in scope) we need to get all the document refs\n * that have this term in that field.\n *\n * The posting is the entry in the invertedIndex for the matching\n * term from above.\n */\n var field = clause.fields[k],\n fieldPosting = posting[field],\n matchingDocumentRefs = Object.keys(fieldPosting),\n termField = expandedTerm + \"/\" + field,\n matchingDocumentsSet = new lunr.Set(matchingDocumentRefs)\n\n /*\n * if the presence of this term is required ensure that the matching\n * documents are added to the set of required matches for this clause.\n *\n */\n if (clause.presence == lunr.Query.presence.REQUIRED) {\n clauseMatches = clauseMatches.union(matchingDocumentsSet)\n\n if (requiredMatches[field] === undefined) {\n requiredMatches[field] = lunr.Set.complete\n }\n }\n\n /*\n * if the presence of this term is prohibited ensure that the matching\n * documents are added to the set of prohibited matches for this field,\n * creating that set if it does not yet exist.\n */\n if (clause.presence == lunr.Query.presence.PROHIBITED) {\n if (prohibitedMatches[field] === undefined) {\n prohibitedMatches[field] = lunr.Set.empty\n }\n\n prohibitedMatches[field] = prohibitedMatches[field].union(matchingDocumentsSet)\n\n /*\n * Prohibited matches should not be part of the query vector used for\n * similarity scoring and no metadata should be extracted so we continue\n * to the next field\n */\n continue\n }\n\n /*\n * The query field vector is populated using the termIndex found for\n * the term and a unit value with the appropriate boost applied.\n * Using upsert because there could already be an entry in the vector\n * for the term we are working with. In that case we just add the scores\n * together.\n */\n queryVectors[field].upsert(termIndex, clause.boost, function (a, b) { return a + b })\n\n /**\n * If we've already seen this term, field combo then we've already collected\n * the matching documents and metadata, no need to go through all that again\n */\n if (termFieldCache[termField]) {\n continue\n }\n\n for (var l = 0; l < matchingDocumentRefs.length; l++) {\n /*\n * All metadata for this term/field/document triple\n * are then extracted and collected into an instance\n * of lunr.MatchData ready to be returned in the query\n * results\n */\n var matchingDocumentRef = matchingDocumentRefs[l],\n matchingFieldRef = new lunr.FieldRef (matchingDocumentRef, field),\n metadata = fieldPosting[matchingDocumentRef],\n fieldMatch\n\n if ((fieldMatch = matchingFields[matchingFieldRef]) === undefined) {\n matchingFields[matchingFieldRef] = new lunr.MatchData (expandedTerm, field, metadata)\n } else {\n fieldMatch.add(expandedTerm, field, metadata)\n }\n\n }\n\n termFieldCache[termField] = true\n }\n }\n }\n\n /**\n * If the presence was required we need to update the requiredMatches field sets.\n * We do this after all fields for the term have collected their matches because\n * the clause terms presence is required in _any_ of the fields not _all_ of the\n * fields.\n */\n if (clause.presence === lunr.Query.presence.REQUIRED) {\n for (var k = 0; k < clause.fields.length; k++) {\n var field = clause.fields[k]\n requiredMatches[field] = requiredMatches[field].intersect(clauseMatches)\n }\n }\n }\n\n /**\n * Need to combine the field scoped required and prohibited\n * matching documents into a global set of required and prohibited\n * matches\n */\n var allRequiredMatches = lunr.Set.complete,\n allProhibitedMatches = lunr.Set.empty\n\n for (var i = 0; i < this.fields.length; i++) {\n var field = this.fields[i]\n\n if (requiredMatches[field]) {\n allRequiredMatches = allRequiredMatches.intersect(requiredMatches[field])\n }\n\n if (prohibitedMatches[field]) {\n allProhibitedMatches = allProhibitedMatches.union(prohibitedMatches[field])\n }\n }\n\n var matchingFieldRefs = Object.keys(matchingFields),\n results = [],\n matches = Object.create(null)\n\n /*\n * If the query is negated (contains only prohibited terms)\n * we need to get _all_ fieldRefs currently existing in the\n * index. This is only done when we know that the query is\n * entirely prohibited terms to avoid any cost of getting all\n * fieldRefs unnecessarily.\n *\n * Additionally, blank MatchData must be created to correctly\n * populate the results.\n */\n if (query.isNegated()) {\n matchingFieldRefs = Object.keys(this.fieldVectors)\n\n for (var i = 0; i < matchingFieldRefs.length; i++) {\n var matchingFieldRef = matchingFieldRefs[i]\n var fieldRef = lunr.FieldRef.fromString(matchingFieldRef)\n matchingFields[matchingFieldRef] = new lunr.MatchData\n }\n }\n\n for (var i = 0; i < matchingFieldRefs.length; i++) {\n /*\n * Currently we have document fields that match the query, but we\n * need to return documents. The matchData and scores are combined\n * from multiple fields belonging to the same document.\n *\n * Scores are calculated by field, using the query vectors created\n * above, and combined into a final document score using addition.\n */\n var fieldRef = lunr.FieldRef.fromString(matchingFieldRefs[i]),\n docRef = fieldRef.docRef\n\n if (!allRequiredMatches.contains(docRef)) {\n continue\n }\n\n if (allProhibitedMatches.contains(docRef)) {\n continue\n }\n\n var fieldVector = this.fieldVectors[fieldRef],\n score = queryVectors[fieldRef.fieldName].similarity(fieldVector),\n docMatch\n\n if ((docMatch = matches[docRef]) !== undefined) {\n docMatch.score += score\n docMatch.matchData.combine(matchingFields[fieldRef])\n } else {\n var match = {\n ref: docRef,\n score: score,\n matchData: matchingFields[fieldRef]\n }\n matches[docRef] = match\n results.push(match)\n }\n }\n\n /*\n * Sort the results objects by score, highest first.\n */\n return results.sort(function (a, b) {\n return b.score - a.score\n })\n}\n\n/**\n * Prepares the index for JSON serialization.\n *\n * The schema for this JSON blob will be described in a\n * separate JSON schema file.\n *\n * @returns {Object}\n */\nlunr.Index.prototype.toJSON = function () {\n var invertedIndex = Object.keys(this.invertedIndex)\n .sort()\n .map(function (term) {\n return [term, this.invertedIndex[term]]\n }, this)\n\n var fieldVectors = Object.keys(this.fieldVectors)\n .map(function (ref) {\n return [ref, this.fieldVectors[ref].toJSON()]\n }, this)\n\n return {\n version: lunr.version,\n fields: this.fields,\n fieldVectors: fieldVectors,\n invertedIndex: invertedIndex,\n pipeline: this.pipeline.toJSON()\n }\n}\n\n/**\n * Loads a previously serialized lunr.Index\n *\n * @param {Object} serializedIndex - A previously serialized lunr.Index\n * @returns {lunr.Index}\n */\nlunr.Index.load = function (serializedIndex) {\n var attrs = {},\n fieldVectors = {},\n serializedVectors = serializedIndex.fieldVectors,\n invertedIndex = Object.create(null),\n serializedInvertedIndex = serializedIndex.invertedIndex,\n tokenSetBuilder = new lunr.TokenSet.Builder,\n pipeline = lunr.Pipeline.load(serializedIndex.pipeline)\n\n if (serializedIndex.version != lunr.version) {\n lunr.utils.warn(\"Version mismatch when loading serialised index. Current version of lunr '\" + lunr.version + \"' does not match serialized index '\" + serializedIndex.version + \"'\")\n }\n\n for (var i = 0; i < serializedVectors.length; i++) {\n var tuple = serializedVectors[i],\n ref = tuple[0],\n elements = tuple[1]\n\n fieldVectors[ref] = new lunr.Vector(elements)\n }\n\n for (var i = 0; i < serializedInvertedIndex.length; i++) {\n var tuple = serializedInvertedIndex[i],\n term = tuple[0],\n posting = tuple[1]\n\n tokenSetBuilder.insert(term)\n invertedIndex[term] = posting\n }\n\n tokenSetBuilder.finish()\n\n attrs.fields = serializedIndex.fields\n\n attrs.fieldVectors = fieldVectors\n attrs.invertedIndex = invertedIndex\n attrs.tokenSet = tokenSetBuilder.root\n attrs.pipeline = pipeline\n\n return new lunr.Index(attrs)\n}\n/*!\n * lunr.Builder\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Builder performs indexing on a set of documents and\n * returns instances of lunr.Index ready for querying.\n *\n * All configuration of the index is done via the builder, the\n * fields to index, the document reference, the text processing\n * pipeline and document scoring parameters are all set on the\n * builder before indexing.\n *\n * @constructor\n * @property {string} _ref - Internal reference to the document reference field.\n * @property {string[]} _fields - Internal reference to the document fields to index.\n * @property {object} invertedIndex - The inverted index maps terms to document fields.\n * @property {object} documentTermFrequencies - Keeps track of document term frequencies.\n * @property {object} documentLengths - Keeps track of the length of documents added to the index.\n * @property {lunr.tokenizer} tokenizer - Function for splitting strings into tokens for indexing.\n * @property {lunr.Pipeline} pipeline - The pipeline performs text processing on tokens before indexing.\n * @property {lunr.Pipeline} searchPipeline - A pipeline for processing search terms before querying the index.\n * @property {number} documentCount - Keeps track of the total number of documents indexed.\n * @property {number} _b - A parameter to control field length normalization, setting this to 0 disabled normalization, 1 fully normalizes field lengths, the default value is 0.75.\n * @property {number} _k1 - A parameter to control how quickly an increase in term frequency results in term frequency saturation, the default value is 1.2.\n * @property {number} termIndex - A counter incremented for each unique term, used to identify a terms position in the vector space.\n * @property {array} metadataWhitelist - A list of metadata keys that have been whitelisted for entry in the index.\n */\nlunr.Builder = function () {\n this._ref = \"id\"\n this._fields = Object.create(null)\n this._documents = Object.create(null)\n this.invertedIndex = Object.create(null)\n this.fieldTermFrequencies = {}\n this.fieldLengths = {}\n this.tokenizer = lunr.tokenizer\n this.pipeline = new lunr.Pipeline\n this.searchPipeline = new lunr.Pipeline\n this.documentCount = 0\n this._b = 0.75\n this._k1 = 1.2\n this.termIndex = 0\n this.metadataWhitelist = []\n}\n\n/**\n * Sets the document field used as the document reference. Every document must have this field.\n * The type of this field in the document should be a string, if it is not a string it will be\n * coerced into a string by calling toString.\n *\n * The default ref is 'id'.\n *\n * The ref should _not_ be changed during indexing, it should be set before any documents are\n * added to the index. Changing it during indexing can lead to inconsistent results.\n *\n * @param {string} ref - The name of the reference field in the document.\n */\nlunr.Builder.prototype.ref = function (ref) {\n this._ref = ref\n}\n\n/**\n * A function that is used to extract a field from a document.\n *\n * Lunr expects a field to be at the top level of a document, if however the field\n * is deeply nested within a document an extractor function can be used to extract\n * the right field for indexing.\n *\n * @callback fieldExtractor\n * @param {object} doc - The document being added to the index.\n * @returns {?(string|object|object[])} obj - The object that will be indexed for this field.\n * @example Extracting a nested field\n * function (doc) { return doc.nested.field }\n */\n\n/**\n * Adds a field to the list of document fields that will be indexed. Every document being\n * indexed should have this field. Null values for this field in indexed documents will\n * not cause errors but will limit the chance of that document being retrieved by searches.\n *\n * All fields should be added before adding documents to the index. Adding fields after\n * a document has been indexed will have no effect on already indexed documents.\n *\n * Fields can be boosted at build time. This allows terms within that field to have more\n * importance when ranking search results. Use a field boost to specify that matches within\n * one field are more important than other fields.\n *\n * @param {string} fieldName - The name of a field to index in all documents.\n * @param {object} attributes - Optional attributes associated with this field.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this field.\n * @param {fieldExtractor} [attributes.extractor] - Function to extract a field from a document.\n * @throws {RangeError} fieldName cannot contain unsupported characters '/'\n */\nlunr.Builder.prototype.field = function (fieldName, attributes) {\n if (/\\//.test(fieldName)) {\n throw new RangeError (\"Field '\" + fieldName + \"' contains illegal character '/'\")\n }\n\n this._fields[fieldName] = attributes || {}\n}\n\n/**\n * A parameter to tune the amount of field length normalisation that is applied when\n * calculating relevance scores. A value of 0 will completely disable any normalisation\n * and a value of 1 will fully normalise field lengths. The default is 0.75. Values of b\n * will be clamped to the range 0 - 1.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.b = function (number) {\n if (number < 0) {\n this._b = 0\n } else if (number > 1) {\n this._b = 1\n } else {\n this._b = number\n }\n}\n\n/**\n * A parameter that controls the speed at which a rise in term frequency results in term\n * frequency saturation. The default value is 1.2. Setting this to a higher value will give\n * slower saturation levels, a lower value will result in quicker saturation.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.k1 = function (number) {\n this._k1 = number\n}\n\n/**\n * Adds a document to the index.\n *\n * Before adding fields to the index the index should have been fully setup, with the document\n * ref and all fields to index already having been specified.\n *\n * The document must have a field name as specified by the ref (by default this is 'id') and\n * it should have all fields defined for indexing, though null or undefined values will not\n * cause errors.\n *\n * Entire documents can be boosted at build time. Applying a boost to a document indicates that\n * this document should rank higher in search results than other documents.\n *\n * @param {object} doc - The document to add to the index.\n * @param {object} attributes - Optional attributes associated with this document.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this document.\n */\nlunr.Builder.prototype.add = function (doc, attributes) {\n var docRef = doc[this._ref],\n fields = Object.keys(this._fields)\n\n this._documents[docRef] = attributes || {}\n this.documentCount += 1\n\n for (var i = 0; i < fields.length; i++) {\n var fieldName = fields[i],\n extractor = this._fields[fieldName].extractor,\n field = extractor ? extractor(doc) : doc[fieldName],\n tokens = this.tokenizer(field, {\n fields: [fieldName]\n }),\n terms = this.pipeline.run(tokens),\n fieldRef = new lunr.FieldRef (docRef, fieldName),\n fieldTerms = Object.create(null)\n\n this.fieldTermFrequencies[fieldRef] = fieldTerms\n this.fieldLengths[fieldRef] = 0\n\n // store the length of this field for this document\n this.fieldLengths[fieldRef] += terms.length\n\n // calculate term frequencies for this field\n for (var j = 0; j < terms.length; j++) {\n var term = terms[j]\n\n if (fieldTerms[term] == undefined) {\n fieldTerms[term] = 0\n }\n\n fieldTerms[term] += 1\n\n // add to inverted index\n // create an initial posting if one doesn't exist\n if (this.invertedIndex[term] == undefined) {\n var posting = Object.create(null)\n posting[\"_index\"] = this.termIndex\n this.termIndex += 1\n\n for (var k = 0; k < fields.length; k++) {\n posting[fields[k]] = Object.create(null)\n }\n\n this.invertedIndex[term] = posting\n }\n\n // add an entry for this term/fieldName/docRef to the invertedIndex\n if (this.invertedIndex[term][fieldName][docRef] == undefined) {\n this.invertedIndex[term][fieldName][docRef] = Object.create(null)\n }\n\n // store all whitelisted metadata about this token in the\n // inverted index\n for (var l = 0; l < this.metadataWhitelist.length; l++) {\n var metadataKey = this.metadataWhitelist[l],\n metadata = term.metadata[metadataKey]\n\n if (this.invertedIndex[term][fieldName][docRef][metadataKey] == undefined) {\n this.invertedIndex[term][fieldName][docRef][metadataKey] = []\n }\n\n this.invertedIndex[term][fieldName][docRef][metadataKey].push(metadata)\n }\n }\n\n }\n}\n\n/**\n * Calculates the average document length for this index\n *\n * @private\n */\nlunr.Builder.prototype.calculateAverageFieldLengths = function () {\n\n var fieldRefs = Object.keys(this.fieldLengths),\n numberOfFields = fieldRefs.length,\n accumulator = {},\n documentsWithField = {}\n\n for (var i = 0; i < numberOfFields; i++) {\n var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n field = fieldRef.fieldName\n\n documentsWithField[field] || (documentsWithField[field] = 0)\n documentsWithField[field] += 1\n\n accumulator[field] || (accumulator[field] = 0)\n accumulator[field] += this.fieldLengths[fieldRef]\n }\n\n var fields = Object.keys(this._fields)\n\n for (var i = 0; i < fields.length; i++) {\n var fieldName = fields[i]\n accumulator[fieldName] = accumulator[fieldName] / documentsWithField[fieldName]\n }\n\n this.averageFieldLength = accumulator\n}\n\n/**\n * Builds a vector space model of every document using lunr.Vector\n *\n * @private\n */\nlunr.Builder.prototype.createFieldVectors = function () {\n var fieldVectors = {},\n fieldRefs = Object.keys(this.fieldTermFrequencies),\n fieldRefsLength = fieldRefs.length,\n termIdfCache = Object.create(null)\n\n for (var i = 0; i < fieldRefsLength; i++) {\n var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n fieldName = fieldRef.fieldName,\n fieldLength = this.fieldLengths[fieldRef],\n fieldVector = new lunr.Vector,\n termFrequencies = this.fieldTermFrequencies[fieldRef],\n terms = Object.keys(termFrequencies),\n termsLength = terms.length\n\n\n var fieldBoost = this._fields[fieldName].boost || 1,\n docBoost = this._documents[fieldRef.docRef].boost || 1\n\n for (var j = 0; j < termsLength; j++) {\n var term = terms[j],\n tf = termFrequencies[term],\n termIndex = this.invertedIndex[term]._index,\n idf, score, scoreWithPrecision\n\n if (termIdfCache[term] === undefined) {\n idf = lunr.idf(this.invertedIndex[term], this.documentCount)\n termIdfCache[term] = idf\n } else {\n idf = termIdfCache[term]\n }\n\n score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[fieldName])) + tf)\n score *= fieldBoost\n score *= docBoost\n scoreWithPrecision = Math.round(score * 1000) / 1000\n // Converts 1.23456789 to 1.234.\n // Reducing the precision so that the vectors take up less\n // space when serialised. Doing it now so that they behave\n // the same before and after serialisation. Also, this is\n // the fastest approach to reducing a number's precision in\n // JavaScript.\n\n fieldVector.insert(termIndex, scoreWithPrecision)\n }\n\n fieldVectors[fieldRef] = fieldVector\n }\n\n this.fieldVectors = fieldVectors\n}\n\n/**\n * Creates a token set of all tokens in the index using lunr.TokenSet\n *\n * @private\n */\nlunr.Builder.prototype.createTokenSet = function () {\n this.tokenSet = lunr.TokenSet.fromArray(\n Object.keys(this.invertedIndex).sort()\n )\n}\n\n/**\n * Builds the index, creating an instance of lunr.Index.\n *\n * This completes the indexing process and should only be called\n * once all documents have been added to the index.\n *\n * @returns {lunr.Index}\n */\nlunr.Builder.prototype.build = function () {\n this.calculateAverageFieldLengths()\n this.createFieldVectors()\n this.createTokenSet()\n\n return new lunr.Index({\n invertedIndex: this.invertedIndex,\n fieldVectors: this.fieldVectors,\n tokenSet: this.tokenSet,\n fields: Object.keys(this._fields),\n pipeline: this.searchPipeline\n })\n}\n\n/**\n * Applies a plugin to the index builder.\n *\n * A plugin is a function that is called with the index builder as its context.\n * Plugins can be used to customise or extend the behaviour of the index\n * in some way. A plugin is just a function, that encapsulated the custom\n * behaviour that should be applied when building the index.\n *\n * The plugin function will be called with the index builder as its argument, additional\n * arguments can also be passed when calling use. The function will be called\n * with the index builder as its context.\n *\n * @param {Function} plugin The plugin to apply.\n */\nlunr.Builder.prototype.use = function (fn) {\n var args = Array.prototype.slice.call(arguments, 1)\n args.unshift(this)\n fn.apply(this, args)\n}\n/**\n * Contains and collects metadata about a matching document.\n * A single instance of lunr.MatchData is returned as part of every\n * lunr.Index~Result.\n *\n * @constructor\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n * @property {object} metadata - A cloned collection of metadata associated with this document.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData = function (term, field, metadata) {\n var clonedMetadata = Object.create(null),\n metadataKeys = Object.keys(metadata || {})\n\n // Cloning the metadata to prevent the original\n // being mutated during match data combination.\n // Metadata is kept in an array within the inverted\n // index so cloning the data can be done with\n // Array#slice\n for (var i = 0; i < metadataKeys.length; i++) {\n var key = metadataKeys[i]\n clonedMetadata[key] = metadata[key].slice()\n }\n\n this.metadata = Object.create(null)\n\n if (term !== undefined) {\n this.metadata[term] = Object.create(null)\n this.metadata[term][field] = clonedMetadata\n }\n}\n\n/**\n * An instance of lunr.MatchData will be created for every term that matches a\n * document. However only one instance is required in a lunr.Index~Result. This\n * method combines metadata from another instance of lunr.MatchData with this\n * objects metadata.\n *\n * @param {lunr.MatchData} otherMatchData - Another instance of match data to merge with this one.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData.prototype.combine = function (otherMatchData) {\n var terms = Object.keys(otherMatchData.metadata)\n\n for (var i = 0; i < terms.length; i++) {\n var term = terms[i],\n fields = Object.keys(otherMatchData.metadata[term])\n\n if (this.metadata[term] == undefined) {\n this.metadata[term] = Object.create(null)\n }\n\n for (var j = 0; j < fields.length; j++) {\n var field = fields[j],\n keys = Object.keys(otherMatchData.metadata[term][field])\n\n if (this.metadata[term][field] == undefined) {\n this.metadata[term][field] = Object.create(null)\n }\n\n for (var k = 0; k < keys.length; k++) {\n var key = keys[k]\n\n if (this.metadata[term][field][key] == undefined) {\n this.metadata[term][field][key] = otherMatchData.metadata[term][field][key]\n } else {\n this.metadata[term][field][key] = this.metadata[term][field][key].concat(otherMatchData.metadata[term][field][key])\n }\n\n }\n }\n }\n}\n\n/**\n * Add metadata for a term/field pair to this instance of match data.\n *\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n */\nlunr.MatchData.prototype.add = function (term, field, metadata) {\n if (!(term in this.metadata)) {\n this.metadata[term] = Object.create(null)\n this.metadata[term][field] = metadata\n return\n }\n\n if (!(field in this.metadata[term])) {\n this.metadata[term][field] = metadata\n return\n }\n\n var metadataKeys = Object.keys(metadata)\n\n for (var i = 0; i < metadataKeys.length; i++) {\n var key = metadataKeys[i]\n\n if (key in this.metadata[term][field]) {\n this.metadata[term][field][key] = this.metadata[term][field][key].concat(metadata[key])\n } else {\n this.metadata[term][field][key] = metadata[key]\n }\n }\n}\n/**\n * A lunr.Query provides a programmatic way of defining queries to be performed\n * against a {@link lunr.Index}.\n *\n * Prefer constructing a lunr.Query using the {@link lunr.Index#query} method\n * so the query object is pre-initialized with the right index fields.\n *\n * @constructor\n * @property {lunr.Query~Clause[]} clauses - An array of query clauses.\n * @property {string[]} allFields - An array of all available fields in a lunr.Index.\n */\nlunr.Query = function (allFields) {\n this.clauses = []\n this.allFields = allFields\n}\n\n/**\n * Constants for indicating what kind of automatic wildcard insertion will be used when constructing a query clause.\n *\n * This allows wildcards to be added to the beginning and end of a term without having to manually do any string\n * concatenation.\n *\n * The wildcard constants can be bitwise combined to select both leading and trailing wildcards.\n *\n * @constant\n * @default\n * @property {number} wildcard.NONE - The term will have no wildcards inserted, this is the default behaviour\n * @property {number} wildcard.LEADING - Prepend the term with a wildcard, unless a leading wildcard already exists\n * @property {number} wildcard.TRAILING - Append a wildcard to the term, unless a trailing wildcard already exists\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example query term with trailing wildcard\n * query.term('foo', { wildcard: lunr.Query.wildcard.TRAILING })\n * @example query term with leading and trailing wildcard\n * query.term('foo', {\n * wildcard: lunr.Query.wildcard.LEADING | lunr.Query.wildcard.TRAILING\n * })\n */\n\nlunr.Query.wildcard = new String (\"*\")\nlunr.Query.wildcard.NONE = 0\nlunr.Query.wildcard.LEADING = 1\nlunr.Query.wildcard.TRAILING = 2\n\n/**\n * Constants for indicating what kind of presence a term must have in matching documents.\n *\n * @constant\n * @enum {number}\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example query term with required presence\n * query.term('foo', { presence: lunr.Query.presence.REQUIRED })\n */\nlunr.Query.presence = {\n /**\n * Term's presence in a document is optional, this is the default value.\n */\n OPTIONAL: 1,\n\n /**\n * Term's presence in a document is required, documents that do not contain\n * this term will not be returned.\n */\n REQUIRED: 2,\n\n /**\n * Term's presence in a document is prohibited, documents that do contain\n * this term will not be returned.\n */\n PROHIBITED: 3\n}\n\n/**\n * A single clause in a {@link lunr.Query} contains a term and details on how to\n * match that term against a {@link lunr.Index}.\n *\n * @typedef {Object} lunr.Query~Clause\n * @property {string[]} fields - The fields in an index this clause should be matched against.\n * @property {number} [boost=1] - Any boost that should be applied when matching this clause.\n * @property {number} [editDistance] - Whether the term should have fuzzy matching applied, and how fuzzy the match should be.\n * @property {boolean} [usePipeline] - Whether the term should be passed through the search pipeline.\n * @property {number} [wildcard=lunr.Query.wildcard.NONE] - Whether the term should have wildcards appended or prepended.\n * @property {number} [presence=lunr.Query.presence.OPTIONAL] - The terms presence in any matching documents.\n */\n\n/**\n * Adds a {@link lunr.Query~Clause} to this query.\n *\n * Unless the clause contains the fields to be matched all fields will be matched. In addition\n * a default boost of 1 is applied to the clause.\n *\n * @param {lunr.Query~Clause} clause - The clause to add to this query.\n * @see lunr.Query~Clause\n * @returns {lunr.Query}\n */\nlunr.Query.prototype.clause = function (clause) {\n if (!('fields' in clause)) {\n clause.fields = this.allFields\n }\n\n if (!('boost' in clause)) {\n clause.boost = 1\n }\n\n if (!('usePipeline' in clause)) {\n clause.usePipeline = true\n }\n\n if (!('wildcard' in clause)) {\n clause.wildcard = lunr.Query.wildcard.NONE\n }\n\n if ((clause.wildcard & lunr.Query.wildcard.LEADING) && (clause.term.charAt(0) != lunr.Query.wildcard)) {\n clause.term = \"*\" + clause.term\n }\n\n if ((clause.wildcard & lunr.Query.wildcard.TRAILING) && (clause.term.slice(-1) != lunr.Query.wildcard)) {\n clause.term = \"\" + clause.term + \"*\"\n }\n\n if (!('presence' in clause)) {\n clause.presence = lunr.Query.presence.OPTIONAL\n }\n\n this.clauses.push(clause)\n\n return this\n}\n\n/**\n * A negated query is one in which every clause has a presence of\n * prohibited. These queries require some special processing to return\n * the expected results.\n *\n * @returns boolean\n */\nlunr.Query.prototype.isNegated = function () {\n for (var i = 0; i < this.clauses.length; i++) {\n if (this.clauses[i].presence != lunr.Query.presence.PROHIBITED) {\n return false\n }\n }\n\n return true\n}\n\n/**\n * Adds a term to the current query, under the covers this will create a {@link lunr.Query~Clause}\n * to the list of clauses that make up this query.\n *\n * The term is used as is, i.e. no tokenization will be performed by this method. Instead conversion\n * to a token or token-like string should be done before calling this method.\n *\n * The term will be converted to a string by calling `toString`. Multiple terms can be passed as an\n * array, each term in the array will share the same options.\n *\n * @param {object|object[]} term - The term(s) to add to the query.\n * @param {object} [options] - Any additional properties to add to the query clause.\n * @returns {lunr.Query}\n * @see lunr.Query#clause\n * @see lunr.Query~Clause\n * @example adding a single term to a query\n * query.term(\"foo\")\n * @example adding a single term to a query and specifying search fields, term boost and automatic trailing wildcard\n * query.term(\"foo\", {\n * fields: [\"title\"],\n * boost: 10,\n * wildcard: lunr.Query.wildcard.TRAILING\n * })\n * @example using lunr.tokenizer to convert a string to tokens before using them as terms\n * query.term(lunr.tokenizer(\"foo bar\"))\n */\nlunr.Query.prototype.term = function (term, options) {\n if (Array.isArray(term)) {\n term.forEach(function (t) { this.term(t, lunr.utils.clone(options)) }, this)\n return this\n }\n\n var clause = options || {}\n clause.term = term.toString()\n\n this.clause(clause)\n\n return this\n}\nlunr.QueryParseError = function (message, start, end) {\n this.name = \"QueryParseError\"\n this.message = message\n this.start = start\n this.end = end\n}\n\nlunr.QueryParseError.prototype = new Error\nlunr.QueryLexer = function (str) {\n this.lexemes = []\n this.str = str\n this.length = str.length\n this.pos = 0\n this.start = 0\n this.escapeCharPositions = []\n}\n\nlunr.QueryLexer.prototype.run = function () {\n var state = lunr.QueryLexer.lexText\n\n while (state) {\n state = state(this)\n }\n}\n\nlunr.QueryLexer.prototype.sliceString = function () {\n var subSlices = [],\n sliceStart = this.start,\n sliceEnd = this.pos\n\n for (var i = 0; i < this.escapeCharPositions.length; i++) {\n sliceEnd = this.escapeCharPositions[i]\n subSlices.push(this.str.slice(sliceStart, sliceEnd))\n sliceStart = sliceEnd + 1\n }\n\n subSlices.push(this.str.slice(sliceStart, this.pos))\n this.escapeCharPositions.length = 0\n\n return subSlices.join('')\n}\n\nlunr.QueryLexer.prototype.emit = function (type) {\n this.lexemes.push({\n type: type,\n str: this.sliceString(),\n start: this.start,\n end: this.pos\n })\n\n this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.escapeCharacter = function () {\n this.escapeCharPositions.push(this.pos - 1)\n this.pos += 1\n}\n\nlunr.QueryLexer.prototype.next = function () {\n if (this.pos >= this.length) {\n return lunr.QueryLexer.EOS\n }\n\n var char = this.str.charAt(this.pos)\n this.pos += 1\n return char\n}\n\nlunr.QueryLexer.prototype.width = function () {\n return this.pos - this.start\n}\n\nlunr.QueryLexer.prototype.ignore = function () {\n if (this.start == this.pos) {\n this.pos += 1\n }\n\n this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.backup = function () {\n this.pos -= 1\n}\n\nlunr.QueryLexer.prototype.acceptDigitRun = function () {\n var char, charCode\n\n do {\n char = this.next()\n charCode = char.charCodeAt(0)\n } while (charCode > 47 && charCode < 58)\n\n if (char != lunr.QueryLexer.EOS) {\n this.backup()\n }\n}\n\nlunr.QueryLexer.prototype.more = function () {\n return this.pos < this.length\n}\n\nlunr.QueryLexer.EOS = 'EOS'\nlunr.QueryLexer.FIELD = 'FIELD'\nlunr.QueryLexer.TERM = 'TERM'\nlunr.QueryLexer.EDIT_DISTANCE = 'EDIT_DISTANCE'\nlunr.QueryLexer.BOOST = 'BOOST'\nlunr.QueryLexer.PRESENCE = 'PRESENCE'\n\nlunr.QueryLexer.lexField = function (lexer) {\n lexer.backup()\n lexer.emit(lunr.QueryLexer.FIELD)\n lexer.ignore()\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexTerm = function (lexer) {\n if (lexer.width() > 1) {\n lexer.backup()\n lexer.emit(lunr.QueryLexer.TERM)\n }\n\n lexer.ignore()\n\n if (lexer.more()) {\n return lunr.QueryLexer.lexText\n }\n}\n\nlunr.QueryLexer.lexEditDistance = function (lexer) {\n lexer.ignore()\n lexer.acceptDigitRun()\n lexer.emit(lunr.QueryLexer.EDIT_DISTANCE)\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexBoost = function (lexer) {\n lexer.ignore()\n lexer.acceptDigitRun()\n lexer.emit(lunr.QueryLexer.BOOST)\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexEOS = function (lexer) {\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n}\n\n// This matches the separator used when tokenising fields\n// within a document. These should match otherwise it is\n// not possible to search for some tokens within a document.\n//\n// It is possible for the user to change the separator on the\n// tokenizer so it _might_ clash with any other of the special\n// characters already used within the search string, e.g. :.\n//\n// This means that it is possible to change the separator in\n// such a way that makes some words unsearchable using a search\n// string.\nlunr.QueryLexer.termSeparator = lunr.tokenizer.separator\n\nlunr.QueryLexer.lexText = function (lexer) {\n while (true) {\n var char = lexer.next()\n\n if (char == lunr.QueryLexer.EOS) {\n return lunr.QueryLexer.lexEOS\n }\n\n // Escape character is '\\'\n if (char.charCodeAt(0) == 92) {\n lexer.escapeCharacter()\n continue\n }\n\n if (char == \":\") {\n return lunr.QueryLexer.lexField\n }\n\n if (char == \"~\") {\n lexer.backup()\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n return lunr.QueryLexer.lexEditDistance\n }\n\n if (char == \"^\") {\n lexer.backup()\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n return lunr.QueryLexer.lexBoost\n }\n\n // \"+\" indicates term presence is required\n // checking for length to ensure that only\n // leading \"+\" are considered\n if (char == \"+\" && lexer.width() === 1) {\n lexer.emit(lunr.QueryLexer.PRESENCE)\n return lunr.QueryLexer.lexText\n }\n\n // \"-\" indicates term presence is prohibited\n // checking for length to ensure that only\n // leading \"-\" are considered\n if (char == \"-\" && lexer.width() === 1) {\n lexer.emit(lunr.QueryLexer.PRESENCE)\n return lunr.QueryLexer.lexText\n }\n\n if (char.match(lunr.QueryLexer.termSeparator)) {\n return lunr.QueryLexer.lexTerm\n }\n }\n}\n\nlunr.QueryParser = function (str, query) {\n this.lexer = new lunr.QueryLexer (str)\n this.query = query\n this.currentClause = {}\n this.lexemeIdx = 0\n}\n\nlunr.QueryParser.prototype.parse = function () {\n this.lexer.run()\n this.lexemes = this.lexer.lexemes\n\n var state = lunr.QueryParser.parseClause\n\n while (state) {\n state = state(this)\n }\n\n return this.query\n}\n\nlunr.QueryParser.prototype.peekLexeme = function () {\n return this.lexemes[this.lexemeIdx]\n}\n\nlunr.QueryParser.prototype.consumeLexeme = function () {\n var lexeme = this.peekLexeme()\n this.lexemeIdx += 1\n return lexeme\n}\n\nlunr.QueryParser.prototype.nextClause = function () {\n var completedClause = this.currentClause\n this.query.clause(completedClause)\n this.currentClause = {}\n}\n\nlunr.QueryParser.parseClause = function (parser) {\n var lexeme = parser.peekLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n switch (lexeme.type) {\n case lunr.QueryLexer.PRESENCE:\n return lunr.QueryParser.parsePresence\n case lunr.QueryLexer.FIELD:\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expected either a field or a term, found \" + lexeme.type\n\n if (lexeme.str.length >= 1) {\n errorMessage += \" with value '\" + lexeme.str + \"'\"\n }\n\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n}\n\nlunr.QueryParser.parsePresence = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n switch (lexeme.str) {\n case \"-\":\n parser.currentClause.presence = lunr.Query.presence.PROHIBITED\n break\n case \"+\":\n parser.currentClause.presence = lunr.Query.presence.REQUIRED\n break\n default:\n var errorMessage = \"unrecognised presence operator'\" + lexeme.str + \"'\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n var errorMessage = \"expecting term or field, found nothing\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.FIELD:\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expecting term or field, found '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseField = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n if (parser.query.allFields.indexOf(lexeme.str) == -1) {\n var possibleFields = parser.query.allFields.map(function (f) { return \"'\" + f + \"'\" }).join(', '),\n errorMessage = \"unrecognised field '\" + lexeme.str + \"', possible fields: \" + possibleFields\n\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.fields = [lexeme.str]\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n var errorMessage = \"expecting term, found nothing\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expecting term, found '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseTerm = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n parser.currentClause.term = lexeme.str.toLowerCase()\n\n if (lexeme.str.indexOf(\"*\") != -1) {\n parser.currentClause.usePipeline = false\n }\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseEditDistance = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n var editDistance = parseInt(lexeme.str, 10)\n\n if (isNaN(editDistance)) {\n var errorMessage = \"edit distance must be numeric\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.editDistance = editDistance\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseBoost = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n var boost = parseInt(lexeme.str, 10)\n\n if (isNaN(boost)) {\n var errorMessage = \"boost must be numeric\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.boost = boost\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\n /**\n * export the module via AMD, CommonJS or as a browser global\n * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js\n */\n ;(function (root, factory) {\n if (typeof define === 'function' && define.amd) {\n // AMD. Register as an anonymous module.\n define(factory)\n } else if (typeof exports === 'object') {\n /**\n * Node. Does not work with strict CommonJS, but\n * only CommonJS-like enviroments that support module.exports,\n * like Node.\n */\n module.exports = factory()\n } else {\n // Browser globals (root is window)\n root.lunr = factory()\n }\n }(this, function () {\n /**\n * Just return a value to define the module export.\n * This example returns an object, but the module\n * can return a function as the exported value.\n */\n return lunr\n }))\n})();\n", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport lunr from \"lunr\"\n\nimport \"~/polyfills\"\n\nimport { Search, SearchIndexConfig } from \"../../_\"\nimport {\n SearchMessage,\n SearchMessageType\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Add support for usage with `iframe-worker` polyfill\n *\n * While `importScripts` is synchronous when executed inside of a web worker,\n * it's not possible to provide a synchronous polyfilled implementation. The\n * cool thing is that awaiting a non-Promise is a noop, so extending the type\n * definition to return a `Promise` shouldn't break anything.\n *\n * @see https://bit.ly/2PjDnXi - GitHub comment\n */\ndeclare global {\n function importScripts(...urls: string[]): Promise | void\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nlet index: Search\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch (= import) multi-language support through `lunr-languages`\n *\n * This function automatically imports the stemmers necessary to process the\n * languages, which are defined through the search index configuration.\n *\n * If the worker runs inside of an `iframe` (when using `iframe-worker` as\n * a shim), the base URL for the stemmers to be loaded must be determined by\n * searching for the first `script` element with a `src` attribute, which will\n * contain the contents of this script.\n *\n * @param config - Search index configuration\n *\n * @returns Promise resolving with no result\n */\nasync function setupSearchLanguages(\n config: SearchIndexConfig\n): Promise {\n let base = \"../lunr\"\n\n /* Detect `iframe-worker` and fix base URL */\n if (typeof parent !== \"undefined\" && \"IFrameWorker\" in parent) {\n const worker = document.querySelector(\"script[src]\")!\n const [path] = worker.src.split(\"/worker\")\n\n /* Prefix base with path */\n base = base.replace(\"..\", path)\n }\n\n /* Add scripts for languages */\n const scripts = []\n for (const lang of config.lang) {\n switch (lang) {\n\n /* Add segmenter for Japanese */\n case \"ja\":\n scripts.push(`${base}/tinyseg.js`)\n break\n\n /* Add segmenter for Hindi and Thai */\n case \"hi\":\n case \"th\":\n scripts.push(`${base}/wordcut.js`)\n break\n }\n\n /* Add language support */\n if (lang !== \"en\")\n scripts.push(`${base}/min/lunr.${lang}.min.js`)\n }\n\n /* Add multi-language support */\n if (config.lang.length > 1)\n scripts.push(`${base}/min/lunr.multi.min.js`)\n\n /* Load scripts synchronously */\n if (scripts.length)\n await importScripts(\n `${base}/min/lunr.stemmer.support.min.js`,\n ...scripts\n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Message handler\n *\n * @param message - Source message\n *\n * @returns Target message\n */\nexport async function handler(\n message: SearchMessage\n): Promise {\n switch (message.type) {\n\n /* Search setup message */\n case SearchMessageType.SETUP:\n await setupSearchLanguages(message.data.config)\n index = new Search(message.data)\n return {\n type: SearchMessageType.READY\n }\n\n /* Search query message */\n case SearchMessageType.QUERY:\n return {\n type: SearchMessageType.RESULT,\n data: index ? index.search(message.data) : { items: [] }\n }\n\n /* All other messages */\n default:\n throw new TypeError(\"Invalid message type\")\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Worker\n * ------------------------------------------------------------------------- */\n\n/* @ts-expect-error - expose Lunr.js in global scope, or stemmers won't work */\nself.lunr = lunr\n\n/* Handle messages */\naddEventListener(\"message\", async ev => {\n postMessage(await handler(ev.data))\n})\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n Object.entries = function (obj: object) {\n const data: [string, string][] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push([key, obj[key]])\n\n /* Return entries */\n return data\n }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n Object.values = function (obj: object) {\n const data: string[] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push(obj[key])\n\n /* Return values */\n return data\n }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n /* Polyfill `Element.scrollTo` */\n if (!Element.prototype.scrollTo)\n Element.prototype.scrollTo = function (\n x?: ScrollToOptions | number, y?: number\n ): void {\n if (typeof x === \"object\") {\n this.scrollLeft = x.left!\n this.scrollTop = x.top!\n } else {\n this.scrollLeft = x!\n this.scrollTop = y!\n }\n }\n\n /* Polyfill `Element.replaceWith` */\n if (!Element.prototype.replaceWith)\n Element.prototype.replaceWith = function (\n ...nodes: Array\n ): void {\n const parent = this.parentNode\n if (parent) {\n if (nodes.length === 0)\n parent.removeChild(this)\n\n /* Replace children and create text nodes */\n for (let i = nodes.length - 1; i >= 0; i--) {\n let node = nodes[i]\n if (typeof node === \"string\")\n node = document.createTextNode(node)\n else if (node.parentNode)\n node.parentNode.removeChild(node)\n\n /* Replace child or insert before previous sibling */\n if (!i)\n parent.replaceChild(node, this)\n else\n parent.insertBefore(this.previousSibling!, node)\n }\n }\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexDocument } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search document\n */\nexport interface SearchDocument extends SearchIndexDocument {\n parent?: SearchIndexDocument /* Parent article */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search document mapping\n */\nexport type SearchDocumentMap = Map\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document mapping\n *\n * @param docs - Search index documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n docs: SearchIndexDocument[]\n): SearchDocumentMap {\n const documents = new Map()\n const parents = new Set()\n for (const doc of docs) {\n const [path, hash] = doc.location.split(\"#\")\n\n /* Extract location, title and tags */\n const location = doc.location\n const title = doc.title\n const tags = doc.tags\n\n /* Escape and cleanup text */\n const text = escapeHTML(doc.text)\n .replace(/\\s+(?=[,.:;!?])/g, \"\")\n .replace(/\\s+/g, \" \")\n\n /* Handle section */\n if (hash) {\n const parent = documents.get(path)!\n\n /* Ignore first section, override article */\n if (!parents.has(parent)) {\n parent.title = doc.title\n parent.text = text\n\n /* Remember that we processed the article */\n parents.add(parent)\n\n /* Add subsequent section */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n parent\n })\n }\n\n /* Add article */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n ...tags && { tags }\n })\n }\n }\n return documents\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexConfig } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search index configuration\n * @param escape - Whether to escape HTML\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n config: SearchIndexConfig, escape: boolean\n): SearchHighlightFactoryFn {\n const separator = new RegExp(config.separator, \"img\")\n const highlight = (_: unknown, data: string, term: string) => {\n return `${data}${term}`\n }\n\n /* Return factory function */\n return (query: string) => {\n query = query\n .replace(/[\\s*+\\-:~^]+/g, \" \")\n .trim()\n\n /* Create search term match expression */\n const match = new RegExp(`(^|${config.separator})(${\n query\n .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n .replace(separator, \"|\")\n })`, \"img\")\n\n /* Highlight string value */\n return value => (\n escape\n ? escapeHTML(value)\n : value\n )\n .replace(match, highlight)\n .replace(/<\\/mark>(\\s+)]*>/img, \"$1\")\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query clause\n */\nexport interface SearchQueryClause {\n presence: lunr.Query.presence /* Clause presence */\n term: string /* Clause term */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search query terms\n */\nexport type SearchQueryTerms = Record\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Parse a search query for analysis\n *\n * @param value - Query value\n *\n * @returns Search query clauses\n */\nexport function parseSearchQuery(\n value: string\n): SearchQueryClause[] {\n const query = new (lunr as any).Query([\"title\", \"text\"])\n const parser = new (lunr as any).QueryParser(value, query)\n\n /* Parse and return query clauses */\n parser.parse()\n return query.clauses\n}\n\n/**\n * Analyze the search query clauses in regard to the search terms found\n *\n * @param query - Search query clauses\n * @param terms - Search terms\n *\n * @returns Search query terms\n */\nexport function getSearchQueryTerms(\n query: SearchQueryClause[], terms: string[]\n): SearchQueryTerms {\n const clauses = new Set(query)\n\n /* Match query clauses against terms */\n const result: SearchQueryTerms = {}\n for (let t = 0; t < terms.length; t++)\n for (const clause of clauses)\n if (terms[t].startsWith(clause.term)) {\n result[clause.term] = true\n clauses.delete(clause)\n }\n\n /* Annotate unmatched non-stopword query clauses */\n for (const clause of clauses)\n if (lunr.stopWordFilter?.(clause.term as any))\n result[clause.term] = false\n\n /* Return query terms */\n return result\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n SearchDocument,\n SearchDocumentMap,\n setupSearchDocumentMap\n} from \"../document\"\nimport {\n SearchHighlightFactoryFn,\n setupSearchHighlighter\n} from \"../highlighter\"\nimport { SearchOptions } from \"../options\"\nimport {\n SearchQueryTerms,\n getSearchQueryTerms,\n parseSearchQuery\n} from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index configuration\n */\nexport interface SearchIndexConfig {\n lang: string[] /* Search languages */\n separator: string /* Search separator */\n}\n\n/**\n * Search index document\n */\nexport interface SearchIndexDocument {\n location: string /* Document location */\n title: string /* Document title */\n text: string /* Document text */\n tags?: string[] /* Document tags */\n boost?: number /* Document boost */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search index\n *\n * This interfaces describes the format of the `search_index.json` file which\n * is automatically built by the MkDocs search plugin.\n */\nexport interface SearchIndex {\n config: SearchIndexConfig /* Search index configuration */\n docs: SearchIndexDocument[] /* Search index documents */\n options: SearchOptions /* Search options */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search metadata\n */\nexport interface SearchMetadata {\n score: number /* Score (relevance) */\n terms: SearchQueryTerms /* Search query terms */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search result document\n */\nexport type SearchResultDocument = SearchDocument & SearchMetadata\n\n/**\n * Search result item\n */\nexport type SearchResultItem = SearchResultDocument[]\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search result\n */\nexport interface SearchResult {\n items: SearchResultItem[] /* Search result items */\n suggestions?: string[] /* Search suggestions */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute the difference of two lists of strings\n *\n * @param a - 1st list of strings\n * @param b - 2nd list of strings\n *\n * @returns Difference\n */\nfunction difference(a: string[], b: string[]): string[] {\n const [x, y] = [new Set(a), new Set(b)]\n return [\n ...new Set([...x].filter(value => !y.has(value)))\n ]\n}\n\n/* ----------------------------------------------------------------------------\n * Class\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nexport class Search {\n\n /**\n * Search document mapping\n *\n * A mapping of URLs (including hash fragments) to the actual articles and\n * sections of the documentation. The search document mapping must be created\n * regardless of whether the index was prebuilt or not, as Lunr.js itself\n * only stores the actual index.\n */\n protected documents: SearchDocumentMap\n\n /**\n * Search highlight factory function\n */\n protected highlight: SearchHighlightFactoryFn\n\n /**\n * The underlying Lunr.js search index\n */\n protected index: lunr.Index\n\n /**\n * Search options\n */\n protected options: SearchOptions\n\n /**\n * Create the search integration\n *\n * @param data - Search index\n */\n public constructor({ config, docs, options }: SearchIndex) {\n this.options = options\n\n /* Set up document map and highlighter factory */\n this.documents = setupSearchDocumentMap(docs)\n this.highlight = setupSearchHighlighter(config, false)\n\n /* Set separator for tokenizer */\n lunr.tokenizer.separator = new RegExp(config.separator)\n\n /* Create search index */\n this.index = lunr(function () {\n\n /* Set up multi-language support */\n if (config.lang.length === 1 && config.lang[0] !== \"en\") {\n this.use((lunr as any)[config.lang[0]])\n } else if (config.lang.length > 1) {\n this.use((lunr as any).multiLanguage(...config.lang))\n }\n\n /* Compute functions to be removed from the pipeline */\n const fns = difference([\n \"trimmer\", \"stopWordFilter\", \"stemmer\"\n ], options.pipeline)\n\n /* Remove functions from the pipeline for registered languages */\n for (const lang of config.lang.map(language => (\n language === \"en\" ? lunr : (lunr as any)[language]\n ))) {\n for (const fn of fns) {\n this.pipeline.remove(lang[fn])\n this.searchPipeline.remove(lang[fn])\n }\n }\n\n /* Set up reference */\n this.ref(\"location\")\n\n /* Set up fields */\n this.field(\"title\", { boost: 1e3 })\n this.field(\"text\")\n this.field(\"tags\", { boost: 1e6, extractor: doc => {\n const { tags = [] } = doc as SearchDocument\n return tags.reduce((list, tag) => [\n ...list,\n ...lunr.tokenizer(tag)\n ], [] as lunr.Token[])\n } })\n\n /* Index documents */\n for (const doc of docs)\n this.add(doc, { boost: doc.boost })\n })\n }\n\n /**\n * Search for matching documents\n *\n * The search index which MkDocs provides is divided up into articles, which\n * contain the whole content of the individual pages, and sections, which only\n * contain the contents of the subsections obtained by breaking the individual\n * pages up at `h1` ... `h6`. As there may be many sections on different pages\n * with identical titles (for example within this very project, e.g. \"Usage\"\n * or \"Installation\"), they need to be put into the context of the containing\n * page. For this reason, section results are grouped within their respective\n * articles which are the top-level results that are returned.\n *\n * @param query - Query value\n *\n * @returns Search results\n */\n public search(query: string): SearchResult {\n if (query) {\n try {\n const highlight = this.highlight(query)\n\n /* Parse query to extract clauses for analysis */\n const clauses = parseSearchQuery(query)\n .filter(clause => (\n clause.presence !== lunr.Query.presence.PROHIBITED\n ))\n\n /* Perform search and post-process results */\n const groups = this.index.search(`${query}*`)\n\n /* Apply post-query boosts based on title and search query terms */\n .reduce((item, { ref, score, matchData }) => {\n const document = this.documents.get(ref)\n if (typeof document !== \"undefined\") {\n const { location, title, text, tags, parent } = document\n\n /* Compute and analyze search query terms */\n const terms = getSearchQueryTerms(\n clauses,\n Object.keys(matchData.metadata)\n )\n\n /* Highlight title and text and apply post-query boosts */\n const boost = +!parent + +Object.values(terms).every(t => t)\n item.push({\n location,\n title: highlight(title),\n text: highlight(text),\n ...tags && { tags: tags.map(highlight) },\n score: score * (1 + boost),\n terms\n })\n }\n return item\n }, [])\n\n /* Sort search results again after applying boosts */\n .sort((a, b) => b.score - a.score)\n\n /* Group search results by page */\n .reduce((items, result) => {\n const document = this.documents.get(result.location)\n if (typeof document !== \"undefined\") {\n const ref = \"parent\" in document\n ? document.parent!.location\n : document.location\n items.set(ref, [...items.get(ref) || [], result])\n }\n return items\n }, new Map())\n\n /* Generate search suggestions, if desired */\n let suggestions: string[] | undefined\n if (this.options.suggestions) {\n const titles = this.index.query(builder => {\n for (const clause of clauses)\n builder.term(clause.term, {\n fields: [\"title\"],\n presence: lunr.Query.presence.REQUIRED,\n wildcard: lunr.Query.wildcard.TRAILING\n })\n })\n\n /* Retrieve suggestions for best match */\n suggestions = titles.length\n ? Object.keys(titles[0].matchData.metadata)\n : []\n }\n\n /* Return items and suggestions */\n return {\n items: [...groups.values()],\n ...typeof suggestions !== \"undefined\" && { suggestions }\n }\n\n /* Log errors to console (for now) */\n } catch {\n console.warn(`Invalid query: ${query} \u2013 see https://bit.ly/2s3ChXG`)\n }\n }\n\n /* Return nothing in case of error or empty query */\n return { items: [] }\n }\n}\n"], + "mappings": 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\ No newline at end of file diff --git a/0.13/concepts/existing-pipelines/index.html b/0.13/concepts/existing-pipelines/index.html new file mode 100644 index 000000000..939d6a231 --- /dev/null +++ b/0.13/concepts/existing-pipelines/index.html @@ -0,0 +1,1277 @@ + + + + + + + + + + + + + + + + Existing Pipelines - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

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+ + DataJoint Python + +

+ + + Existing Pipelines + + +

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+ +

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+ +

+ + + + + + +

+ + + +

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+ + + + + + + + + + + ⬅ Home + + + +

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+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + + + + + + + + Existing Pipelines + + + + + Existing Pipelines + + + + +
+ + + + + + + + + Table of contents + +
- + + Loading Classes + + +
- + + Spawning Missing Classes + + +
- + + Virtual Modules + + +
+ +
+ +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + Operators + +
- + + Iteration + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Existing Pipelines¶

This section describes how to work with database schemas without access to the original +code that generated the schema. These situations often arise when the database is +created by another user who has not shared the generating code yet or when the database +schema is created from a programming language other than Python.

Loading Classes¶

Typically, a DataJoint schema is created as a dedicated Python module. This module +defines a schema object that is used to link classes declared in the module to tables +in the database schema. With the module installed, you can simply import it to interact +with its tables:

import datajoint as dj
+from element_calcium_imaging import scan # (1)
+

This and other DataJoint Elements are +installable via pip or downloadable via their respective GitHub repositories.

To visualize an unfamiliar schema, see commands for generating diagrams.

Spawning Missing Classes¶

Now, imagine we do not have access to the +Python definition of Scan, +or we're unsure if the version on our server matches the definition available. We can +use the dj.list_schemas function to list the available database schemas.

import datajoint as dj
+dj.conn() # (1)
+dj.list_schemas() # (2)
+dj.Schema('schema_name').list_tables() # (3)
+

Establish a connection to the server.
List the available schemas on the server.
List the tables for a given schema from the previous step. These will appear in their +raw database form, with underscores instead of camelcase and special characters for Part +tables.

Just as with a new schema, we can create a schema object to connect to the chosen +database schema. If the schema already exists, dj.Schema is initialized as usual.

If a diagram will shows a mixture of class names and database table names, the +spawn_missing_classes method will spawn classes into the local namespace for any +tables missing their classes. This will allow us to interact with all tables as if +they were declared in the current namespace.

schema.spawn_missing_classes()
+

Virtual Modules¶

While spawn_missing_classes creates the new classes in the local namespace, it is +often more convenient to import a schema with its Python module, equivalent to the +Python command. We can mimmick this import without having access to the schema using +the VirtualModule class object:

import datajoint as dj
+subject = dj.create_virtual_module(module_name='subject', schema_name='db_subject')
+

Now, subject behaves as an imported module complete with the schema object and all the +table classes.

The class object VirtualModule of the dj.Schema class provides access to virtual +modules. It creates a python module with the given name from the name of a schema on +the server, automatically adds classes to it corresponding to the tables in the +schema.

The function can take several parameters:

module_name: displayed module name.

schema_name: name of the database in MySQL.

create_schema: if True, create the schema on the database server if it does not + already exist; if False (default), raise an error when the schema is not found.

create_tables: if True, module.schema can be used as the decorator for declaring + new classes; if False, such use will raise an error stating that the module is + intend only to work with existing tables.

The function returns the Python module containing classes from the schema object with +all the table classes already declared inside it.

create_schema=False may be useful if we want to make sure that the schema already +exists. If none exists, create_schema=True will create an empty schema.

dj.VirtualModule('what', 'nonexistent')
+

Returns

DataJointError: Database named `nonexistent` was not defined. Set argument create_schema=True to create it.
+

create_tables=False prevents the use of the schema object of the virtual module for +creating new tables in the existing schema. This is a precautionary measure since +virtual modules are often used for completed schemas. create_tables=True will new +tables to the existing schema. A more common approach in this scenario would be to +create a new schema object and to use the spawn_missing_classes function to make the +classes available.

However, you if do decide to create new tables in an existing tables using the virtual +module, you may do so by using the schema object from the module as the decorator for +declaring new tables:

uni = dj.VirtualModule('university.py', 'dimitri_university', create_tables=True)
+

@uni.schema
+class Example(dj.Manual):
+    definition = """
+    -> uni.Student
+    ---
+    example : varchar(255)
+    """
+

dj.Diagram(uni)
+

+ + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/concepts/index.html b/0.13/concepts/index.html new file mode 100644 index 000000000..04b7f8ced --- /dev/null +++ b/0.13/concepts/index.html @@ -0,0 +1,1083 @@ + + + + + + + + + + + + + + + + Concepts - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ +

+ + + + + + +

+ + + + + + + + + + + + +

+ + DataJoint Python + +

+ + + Concepts + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + Operators + +
- + + Iteration + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Concepts

+ + + + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/getting-started/index.html b/0.13/getting-started/index.html new file mode 100644 index 000000000..7724cc732 --- /dev/null +++ b/0.13/getting-started/index.html @@ -0,0 +1,1507 @@ + + + + + + + + + + + + + + + + Getting Started - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + +

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+ + + Getting Started + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + + + + + + + + Getting Started + + + + + Getting Started + + + + +
+ + + + + + + + + Table of contents + +
- + + Installation + + +
- + + Connection + + +
- + + Data Pipeline Definition + + +
- + + Diagram + + +
  +
  - + + Display + + +
  - + + Customize + + +
  - + + Save + + +
  +
  + +
- + + Add data + + +
- + + Run computation + + +
- + + Query + + +
+ +
+ +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + Operators + +
- + + Iteration + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Getting Started¶

Installation¶

First, please install Python version +3.7 or later. We recommend 3.8.

Next, please install DataJoint via one of the following:

condapip + pip + pip +

Pre-Requisites

Ensure you have conda +installed.

To add the conda-forge channel:

conda config --add channels conda-forge
+

To install:

conda install -c conda-forge datajoint
+

Pre-Requisites

Ensure you have pip installed.
Install graphviz pre-requisite for + diagram visualization.

To install:

pip install datajoint
+

Pre-Requisites

Ensure you have pip installed.
Install graphviz pre-requisite for + diagram visualization.

To install:

pip install datajoint
+

Pre-Requisites

Ensure you have pip installed.
Install graphviz pre-requisite for + diagram visualization.

To install:

pip install datajoint
+

Connection¶

Note

Although you may connect to any MySQL server of your choice, the DataJoint company +offers an online tutorial environment. Simply sign up for a free +DataJoint account. +You will be granted privileges to create schemas +that are prefixed as {user}_.

environment variablesmemoryfile

Before using datajoint, set the following environment variables like so:

DJ_HOST=tutorial-db.datajoint.io
+DJ_USER={user}
+DJ_PASS={password}
+

To set connection settings within Python, perform:

1
+2
+3
+4
+5
import datajoint as dj
+
+dj.config["database.host"] = "tutorial-db.datajoint.io"
+dj.config["database.user"] = "{user}"
+dj.config["database.password"] = "{password}"
+

These configuration settings can be saved either locally or system-wide using one +of the following commands: +

dj.config.save_local()
+dj.config.save_global()
+

Before using datajoint, create a file named dj_local_conf.json in the current +directory like so:

1
+2
+3
+4
+5
{
+    "database.host": "tutorial-db.datajoint.io",
+    "database.user": "{user}",
+    "database.password": "{password}"
+}
+

These settings will be loaded whenever a Python instance is launched from this +directory. To configure settings globally, save a similar file as +.datajoint_config.json in your home directory. A local config, if present, will +take precedent over global settings.

Data Pipeline Definition¶

Let's definite a simple data pipeline.

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+ 3
+ 4
+ 5
+ 6
+ 7
+ 8
+ 9
+10
+11
+12
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+14
+15
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import datajoint as dj
+schema = dj.Schema(f"{dj.config['database.user']}_shapes") # (1)
+
+@schema # (2)
+class Rectangle(dj.Manual):
+    definition = """ # (3)
+    shape_id: int
+    ---
+    shape_height: float
+    shape_width: float
+    """
+
+
+@schema
+class Area(dj.Computed):
+    definition = """
+    -> Rectangle
+    ---
+    shape_area: float
+    """
+    def make(self, key):
+        rectangle = (Rectangle & key).fetch1()
+        Area.insert1(
+            dict(
+                shape_id=rectangle["shape_id"],
+                shape_area=rectangle["shape_height"] * rectangle["shape_width"],
+            )
+        )
+

+
This statement creates the database schema {username}_shapes on the server.
+
+
The @schema decorator for DataJoint classes creates the table on the server.
+
+
The table is defined by the the definition property.
+

It is a common practice to have a separate Python module for each schema. Therefore, +each such module has only one dj.Schema object defined and is usually named +schema.

The dj.Schema constructor can take a number of optional parameters +after the schema name.

context - Dictionary for looking up foreign key references. + Defaults to None to use local context.
connection - Specifies the DataJoint connection object. Defaults + to dj.conn().
create_schema - When False, the schema object will not create a + schema on the database and will raise an error if one does not + already exist. Defaults to True.
create_tables - When False, the schema object will not create + tables on the database and will raise errors when accessing missing + tables. Defaults to True.

The @schema decorator uses the class name and the data tier to check whether an +appropriate table exists on the database. If a table does not already exist, the +decorator creates one on the database using the definition property. The decorator +attaches the information about the table to the class, and then returns the class.

Diagram¶

Display¶

The diagram displays the relationship of the data model in the data pipeline.

This can be done for an entire schema:

dj.Diagram(schema)
+

pipeline

Or for individual or sets of tables: +

dj.Diagram(schema.Rectangle)
+dj.Diagram(schema.Rectangle) + dj.Diagram(schema.Area)
+

What if I don't see the diagram?

Some Python interfaces may require additional draw method.

dj.Diagram(schema).draw()
+

Calling the .draw() method is not necessary when working in a Jupyter notebook by +entering dj.Diagram(schema) in a notebook cell. The Diagram will automatically +render in the notebook by calling its _repr_html_ method. A Diagram displayed +without .draw() will be rendered as an SVG, and hovering the mouse over a table +will reveal a compact version of the output of the .describe() method.

Customize¶

Adding or substracting a number to a diagram object adds nodes downstream or upstream, +respectively, in the pipeline.

(dj.Diagram(schema.Rectangle)+1).draw() # (1)
+

Plot all the tables directly downstream from schema.Rectangle

(dj.Diagram('my_schema')-1+1).draw() # (1)
+

Plot all tables directly downstream of those directly upstream of this schema.

Save¶

The diagram can be saved as either png or svg.

dj.Diagram(schema).save(filename='my-diagram', format='png')
+

Add data¶

Let's add data for a rectangle:

Rectangle.insert1(dict(shape_id=1, shape_height=2, shape_width=4))
+

Run computation¶

Let's start the computations on our entity: Area.

Area.populate(display_progress=True)
+

Query¶

Let's inspect the results.

Area & "shape_area >= 8"
+

+ + + + + + + + + + + + + +

shaped_id	shape_area
1	8.0

+ + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/images/shapes_pipeline.svg b/0.13/images/shapes_pipeline.svg new file mode 100644 index 000000000..203b7b47c --- /dev/null +++ b/0.13/images/shapes_pipeline.svg @@ -0,0 +1,36 @@ + \ No newline at end of file diff --git a/0.13/index.html b/0.13/index.html new file mode 100644 index 000000000..0060d0b48 --- /dev/null +++ b/0.13/index.html @@ -0,0 +1,15 @@ + + + + + + Redirecting... + + + + + + +Redirecting... + + diff --git a/0.13/objects.inv b/0.13/objects.inv new file mode 100644 index 000000000..61ecda095 Binary files /dev/null and b/0.13/objects.inv differ diff --git a/0.13/query-lang/common-commands/index.html b/0.13/query-lang/common-commands/index.html new file mode 100644 index 000000000..4da2f85cb --- /dev/null +++ b/0.13/query-lang/common-commands/index.html @@ -0,0 +1,1294 @@ + + + + + + + + + + + + + + + + Common Commands - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + +

+ + + + + + + + + + + + +

+ + DataJoint Python + +

+ + + Common Commands + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + + + + + + Common Commands + + + + + Common Commands + + + + +
  + + + + + + + Table of contents + +
  - + + Make + + +
  - + + Fetch + + +
    +
    + +
    + + Entire table + + +
    + +
    + + Separate variables + + +
    + +
    + + Primary key values + + +
    + +
    + + Sorting results + + +
    + +
    + + Limiting results + + +
    + +
    + + Usage with Pandas + + +
    + +
    +
    + +
  + +
  + +
- + + Operators + +
- + + Iteration + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Common Commands

+ + + +

Make¶

See the article on make methods

Fetch¶

Entire table¶

A fetch command can either retrieve table data as a NumPy +recarray +or a as a list of dict

data = query.fetch() # (1)
+data = query.fetch(as_dict=True) # (2)
+

NumPy recarray
List of dict:

For very large tables...

In some cases, the amount of data returned by fetch can be quite large; it can be +useful to use the size_on_disk attribute to determine if running a bare fetch +would be wise. Please note that it is only currently possible to query the size of +entire tables stored directly in the database at this time.

Separate variables¶

name, img = query.fetch1('name', 'image')  # when query has exactly one entity
+name, img = query.fetch('name', 'image')   # [name, ...] [image, ...]
+

Primary key values¶

keydict = tab.fetch1("KEY")  # single key dict when tab has exactly one entity
+keylist = tab.fetch("KEY")   # list of key dictionaries [{}, ...]
+

KEY can also used when returning attribute values as separate +variables, such that one of the returned variables contains the entire +primary keys.

Sorting results¶

To sort the result, use the order_by keyword argument.

data = query.fetch(order_by='name')                 # ascending order
+data = query.fetch(order_by='name desc')            # descending order
+data = query.fetch(order_by=('name desc', 'year'))  # by name first, year second
+data = query.fetch(order_by='KEY')                  # sort by the primary key
+data = query.fetch(order_by=('name', 'KEY desc'))   # sort by name but for same names order by primary key
+

The order_by argument can be a string specifying the attribute to sort by. By default +the sort is in ascending order. Use 'attr desc' to sort in descending order by +attribute attr. The value can also be a sequence of strings, in which case, the sort +performed on all the attributes jointly in the order specified.

The special attribute name 'KEY' represents the primary key attributes in order that +they appear in the index. Otherwise, this name can be used as any other argument.

If an attribute happens to be a SQL reserved word, it needs to be enclosed in +backquotes. For example:

data = query.fetch(order_by='`select` desc')
+

The order_by value is eventually passed to the ORDER BY +clause.

Limiting results¶

Similar to sorting, the limit and offset arguments can be used to limit the result +to a subset of entities.

data = query.fetch(order_by='name', limit=10, offset=5)
+

Note that an offset cannot be used without specifying a limit as +well.

Usage with Pandas¶

The pandas library is a popular library for data analysis +in Python which can easily be used with DataJoint query results. Since the records +returned by fetch() are contained within a numpy.recarray, they can be easily +converted to pandas.DataFrame objects by passing them into the pandas.DataFrame +constructor. For example:

import pandas as pd
+frame = pd.DataFrame(tab.fetch())
+

Calling fetch() with the argument format="frame" returns results as +pandas.DataFrame objects indexed by the table's primary key attributes.

frame = tab.fetch(format="frame")
+

Returning results as a DataFrame is not possible when fetching a particular subset of +attributes or when as_dict is set to True.

+ + + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/query-lang/iteration/index.html b/0.13/query-lang/iteration/index.html new file mode 100644 index 000000000..4bd0799df --- /dev/null +++ b/0.13/query-lang/iteration/index.html @@ -0,0 +1,1160 @@ + + + + + + + + + + + + + + + + Iteration - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + +

+ + + + + + + + + + + + +

+ + DataJoint Python + +

+ + + Iteration + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + Operators + +
- + + + + + + + + + Iteration + + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Iteration¶

The DataJoint model primarily handles data as sets, in the form of tables. However, it +can sometimes be useful to access or to perform actions such as visualization upon +individual entities sequentially. In DataJoint this is accomplished through iteration.

In the simple example below, iteration is used to display the names and values of the +attributes of each entity in the simple table or table expression.

for entity in table:
+    print(entity)
+

This example illustrates the function of the iterator: DataJoint iterates through the +whole table expression, returning the entire entity during each step. In this case, +each entity will be returned as a dict containing all attributes.

At the start of the above loop, DataJoint internally fetches only the primary keys of +the entities. Since only the primary keys are needed to distinguish between entities, +DataJoint can then iterate over the list of primary keys to execute the loop. At each +step of the loop, DataJoint uses a single primary key to fetch an entire entity for use +in the iteration, such that print(entity) will print all attributes of each entity. +By first fetching only the primary keys and then fetching each entity individually, +DataJoint saves memory at the cost of network overhead. This can be particularly useful +for tables containing large amounts of data in secondary attributes.

The memory savings of the above syntax may not be worth the additional network overhead +in all cases, such as for tables with little data stored as secondary attributes. In +the example below, DataJoint fetches all of the attributes of each entity in a single +call and then iterates over the list of entities stored in memory.

for entity in table.fetch(as_dict=True):
+    print(entity)
+

+ + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/query-lang/operators/index.html b/0.13/query-lang/operators/index.html new file mode 100644 index 000000000..dc11a36ec --- /dev/null +++ b/0.13/query-lang/operators/index.html @@ -0,0 +1,1339 @@ + + + + + + + + + + + + + + + + Operators - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + +

+ + + + + + + + + + + + +

+ + DataJoint Python + +

+ + + Operators + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + + + + + + + + Operators + + + + + Operators + + + + +
  + + + + + + + + + Table of contents + +
  - + + Restriction + + +
    +
    + +
    + + By a mapping + + +
    + +
    + + By a string + + +
    + +
    + + By a collection + + +
    + +
    + + By a Not object + + +
    + +
    + + By a query + + +
    + +
    +
    + +
  - + + Proj + + +
  - + + Aggr + + +
  - + + Universal set + + +
  + +
  + +
- + + Iteration + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Operators¶

The examples below will use the table definitions in table tiers.

+ + +

Restriction¶

& and - operators permit restriction.

By a mapping¶

For a Session table, that has the attribute +session_date, we can restrict to sessions from January 1st, 2022:

Session & {'session_date': "2022-01-01"}
+

If there were any typos (e.g., using sess_date instead of session_date), our query +will return all of the entities of Session.

By a string¶

Conditions may include arithmetic operations, functions, range tests, etc. Restriction +of table A by a string containing an attribute not found in table A produces an +error.

Session & 'user = "Alice"' # (1)
+Session & 'session_date >= "2022-01-01"' # (2)
+

All the sessions performed by Alice
All of the sessions on or after January 1st, 2022

By a collection¶

When cond is a collection of conditions, the conditions are applied by logical +disjunction (logical OR). Restricting a table by a collection will return all entities +that meet any of the conditions in the collection.

For example, if we restrict the Session table by a collection containing two +conditions, one for user and one for date, the query will return any sessions with a +matching user or date.

A collection can be a list, a tuple, or a Pandas DataFrame.

cond_list = ['user = "Alice"', 'session_date = "2022-01-01"'] # (1)
+cond_tuple = ('user = "Alice"', 'session_date = "2022-01-01"') # (2)
+import pandas as pd
+cond_frame = pd.DataFrame(data={'user': ['Alice'], 'session_date': ['2022-01-01']}) # (3)
+
+Session() & ['user = "Alice"', 'session_date = "2022-01-01"']
+

A list
A tuple
A data frame

dj.AndList represents logical conjunction(logical AND). Restricting a table by an +AndList will return all entities that meet all of the conditions in the list. A & +dj.AndList([c1, c2, c3]) is equivalent to A & c1 & c2 & c3.

Student() & dj.AndList(['user = "Alice"', 'session_date = "2022-01-01"'])
+

The above will show all the sessions that Alice conducted on the given day.

By a `Not` object¶

The special function dj.Not represents logical negation, such that A & dj.Not +(cond) is equivalent to A - cond.

By a query¶

Restriction by a query object is a generalization of restriction by a table. The example +below creates a query object corresponding to all the users named Alice. The Session +table is then restricted by the query object, returning all the sessions performed by +Alice.

query = User & 'user = "Alice"'
+Session & query
+

Proj¶

Renaming an attribute in python can be done via keyword arguments:

table.proj(new_attr='old_attr')
+

This can be done in the context of a table definition:

@schema
+class Session(dj.Manual):
+    definition = """
+    # Experiment Session
+    -> Animal
+    session             : smallint  # session number for the animal
+    ---
+    session_datetime    : datetime  # YYYY-MM-DD HH:MM:SS
+    session_start_time  : float     # seconds relative to session_datetime
+    session_end_time    : float     # seconds relative to session_datetime
+    -> User.proj(experimenter='username')
+    -> User.proj(supervisor='username')
+    """
+

Or to rename multiple values in a table with the following syntax: +Table.proj(*existing_attributes,*renamed_attributes)

Session.proj('session','session_date',start='session_start_time',end='session_end_time')
+

Projection can also be used to to compute new attributes from existing ones.

Session.proj(duration='session_end_time-session_start_time') & 'duration > 10'
+

Aggr¶

For more complicated calculations, we can use aggregation.

Subject.aggr(Session,n="count(*)") # (1)
+Subject.aggr(Session,average_start="avg(session_start_time)") # (2)
+

Number of sessions per subject.
Average session_start_time for each subject

+ + +

Universal set¶

Universal sets offer the complete list of combinations of attributes.

# All home cities of students
+dj.U('laser_wavelength', 'laser_power') & Scan # (1)
+dj.U('laser_wavelength', 'laser_power').aggr(Scan, n="count(*)") # (2)
+dj.U().aggr(Session, n="max(session)") # (3)
+

All combinations of wavelength and power.
Total number of scans for each combination.
Largest session number.

dj.U(), as shown in the last example above, is often useful for integer IDs. +For an example of this process, see the source code for +Element Array Electrophysiology's insert_new_params.

+ + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/query-lang/query-caching/index.html b/0.13/query-lang/query-caching/index.html new file mode 100644 index 000000000..66f56a702 --- /dev/null +++ b/0.13/query-lang/query-caching/index.html @@ -0,0 +1,1165 @@ + + + + + + + + + + + + + + + + Query Caching - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + +

+ + + + + + + + + + + + +

+ + DataJoint Python + +

+ + + Query Caching + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + Operators + +
- + + Iteration + +
- + + + + + + + + + Query Caching + + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Query Caching¶

Query caching allows avoiding repeated queries to the database by caching the results +locally for faster retrieval.

To enable queries, set the query cache local path in dj.config, create the directory, +and activate the query caching.

dj.config['query_cache'] = os.path.expanduser('~/dj_query_cache') # (1)
+# (2)
+conn = dj.conn()                # if queries co-located with tables
+conn = module.schema.connection # if schema co-located with tables
+conn = module.table.connection  # most flexible
+
+conn.set_query_cache(query_cache='main') # (3)
+

Set the query cache path
Access the active connection object for the tables
Activate query caching for a namespace called 'main'

The query_cache argument is an arbitrary string serving to differentiate cache states; +setting a new value will effectively start a new cache, triggering retrieval of new +values once.

To turn off query caching, use the following:

conn.set_query_cache(query_cache=None)
+## OR
+conn.set_query_cache()
+

While query caching is enabled, any insert or delete calls and any transactions are +disabled and will raise an error. This ensures that stale data are not used for +updating the database in violation of data integrity.

To clear and remove the query cache, use the following:

conn.purge_query_cache() # Purge the cached queries
+

+ + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/reproduce/make-method/index.html b/0.13/reproduce/make-method/index.html new file mode 100644 index 000000000..267bcea49 --- /dev/null +++ b/0.13/reproduce/make-method/index.html @@ -0,0 +1,1263 @@ + + + + + + + + + + + + + + + + Make Method - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + +

+ + + + + + + + + + + + +

+ + DataJoint Python + +

+ + + Make Method + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + Operators + +
- + + Iteration + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + Table Tiers + +
- + + + + + + + + + Make Method + + + + + Make Method + + + + +
  + + + + + + + + + Table of contents + +
  - + + Optional Arguments + + +
  - + + Progress + + +
  + +
  + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Make Method¶

Consider the following table definition from the article on +table tiers:

@schema
+class FilteredImage(dj.Computed):
+    definition = """ # Filtered image
+    -> Image
+    ---
+    filtered_image : longblob
+    """
+
+    def make(self, key):
+        img = (test.Image & key).fetch1('image')
+        key['filtered_image'] = my_filter(img)
+        self.insert1(key)
+

The FilteredImage table can be populated as

FilteredImage.populate()
+

The make method receives one argument: the dict key containing the primary key value +of an element of key source to be worked on.

Optional Arguments¶

The make method also accepts a number of optional arguments that provide more features +and allow greater control over the method's behavior.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Argument	Default	Description
`restrictions`		A list of restrictions, restricting as `(tab.key_source & AndList (restrictions)) - tab.proj()`. Here `target` is the table to be populated, usually `tab` itself.
`suppress_errors`	`False`	If `True`, encountering an error will cancel the current `make` call, log the error, and continue to the next `make` call. Error messages will be logged in the job reservation table (if `reserve_jobs` is `True`) and returned as a list. See also `return_exception_objects` and `reserve_jobs`.
`return_exception_objects`	`False`	If `True`, error objects are returned instead of error messages. This applies only when `suppress_errors` is `True`.
`reserve_jobs`	`False`	If `True`, reserves job to indicate to other distributed processes. The job reservation table may be access as `schema.jobs`. Errors are logged in the jobs table.
`order`	`original`	The order of execution, either `"original"`, `"reverse"`, or `"random"`.
`limit`	`None`	If not `None`, checks at most this number of keys.
`max_calls`	`None`	If not `None`, populates at most this many keys. Defaults to no limit.
`display_progress`	`False`	If `True`, displays a progress bar.
`processes`	`1`	Number of processes to use. Set to `None` to use all cores
`make_kwargs`	`None`	Keyword arguments which do not affect the result of computation to be passed down to each `make()` call. Computation arguments should be specified within the pipeline e.g. using a `dj.Lookup` table.

Progress¶

The method table.progress reports how many key_source entries have been populated +and how many remain. Two optional parameters allow more advanced use of the method. A +parameter of restriction conditions can be provided, specifying which entities to +consider. A Boolean parameter display (default is True) allows disabling the +output, such that the numbers of remaining and total entities are returned but not +printed.

+ + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/reproduce/table-tiers/index.html b/0.13/reproduce/table-tiers/index.html new file mode 100644 index 000000000..54ad20ccd --- /dev/null +++ b/0.13/reproduce/table-tiers/index.html @@ -0,0 +1,1319 @@ + + + + + + + + + + + + + + + + Table Tiers - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + +

+ + + + + + + + + + + + +

+ + DataJoint Python + +

+ + + Table Tiers + + +

+ + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ + + + + +

+ + + + + + + + + + + ⬅ Home + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + DataJoint Python + +
+ + Getting Started + +
+ + Existing Pipelines + +
+ + + + + + + + + Query Language + + + +
+ + + Query Language + +
- + + Common Commands + +
- + + Operators + +
- + + Iteration + +
- + + Query Caching + +
+
+
+ + + + + + + + + Reproducibility + + + +
+ + + Reproducibility + +
- + + + + + + + + + Table Tiers + + + + + Table Tiers + + + + +
  + + + + + + + + + Table of contents + +
  - + + Manual Tables + + +
  - + + Lookup Tables + + +
  - + + Imported and Computed Tables + + +
  - + + Part Tables + + +
  + +
  + +
- + + Make Method + +
+
+
+ + Tutorials + +
+ + Changelog + +
+ + + + + + + + + API + + + +
+ + + API + +
- + + + + + + + + + datajoint + + + +
  + + + datajoint + +
  - + + __init__.py + +
  - + + admin.py + +
  - + + attribute_adapter.py + +
  - + + autopopulate.py + +
  - + + blob.py + +
  - + + condition.py + +
  - + + connection.py + +
  - + + declare.py + +
  - + + dependencies.py + +
  - + + diagram.py + +
  - + + errors.py + +
  - + + expression.py + +
  - + + external.py + +
  - + + fetch.py + +
  - + + hash.py + +
  - + + heading.py + +
  - + + jobs.py + +
  - + + logging.py + +
  - + + migrate.py + +
  - + + plugin.py + +
  - + + preview.py + +
  - + + s3.py + +
  - + + schemas.py + +
  - + + settings.py + +
  - + + table.py + +
  - + + user_tables.py + +
  - + + utils.py + +
  - + + version.py + +
  +
  +
+
+

+ + + + +

+ + + + + + + + + +

Table Tiers¶

To define a DataJoint table in Python:

Define a class inheriting from the appropriate DataJoint class: + dj.Lookup, dj.Manual, dj.Imported or dj.Computed.
Decorate the class with the schema object (see schema)
Define the class property definition to define the table heading.

DataJoint for Python is implemented through the use of classes providing access to the +actual tables stored on the database. Since only a single table exists on the database +for any class, interactions with all instances of the class are equivalent. As such, +most methods can be called on the classes themselves rather than on an object, for +convenience. Whether calling a DataJoint method on a class or on an instance, the +result will only depend on or apply to the corresponding table. All of the basic +functionality of DataJoint is built to operate on the classes themselves, even when +called on an instance. For example, calling Person.insert(...) (on the class) and +Person.insert(...) (on an instance) both have the identical effect of inserting data +into the table on the database server. DataJoint does not prevent a user from working +with instances, but the workflow is complete without the need for instantiation. It is +up to the user whether to implement additional functionality as class methods or +methods called on instances.

Manual Tables¶

The following code defines two manual tables, Animal and Session:

@schema
+class Animal(dj.Manual):
+    definition = """
+    # information about animal
+    animal_id          : int                # animal id assigned by the lab
+    ---
+    -> Species
+    date_of_birth=null : date               # YYYY-MM-DD optional
+    sex=''             : enum('M', 'F', '') # leave empty if unspecified 
+    """
+
+@schema
+class Session(dj.Manual):
+    definition = """
+    # Experiment Session
+    -> Animal
+    session             : smallint  # session number for the animal
+    ---
+    session_datetime    : datetime  # YYYY-MM-DD HH:MM:SS
+    session_start_time  : float     # seconds relative to session_datetime
+    session_end_time    : float     # seconds relative to session_datetime
+    -> [nullable] User
+    """
+

Note that the notation to permit null entries differs for attributes versus foreign +key references.

Lookup Tables¶

Lookup tables are commonly populated from their contents property.

The table below is declared as a lookup table with its contents property +provided to generate entities.

@schema
+class User(dj.Lookup):
+    definition = """
+    # users in the lab
+    username : varchar(20)   # user in the lab
+    ---
+    first_name  : varchar(20)   # user first name
+    last_name   : varchar(20)   # user last name
+    """
+    contents = [
+        ['cajal', 'Santiago', 'Cajal'],
+        ['hubel', 'David', 'Hubel'],
+        ['wiesel', 'Torsten', 'Wiesel']
+]
+
+@schema
+class ProcessingParamSet(dj.Lookup):
+    definition = """  #  Parameter set used for processing of calcium imaging data
+    paramset_idx:  smallint
+    ---
+    -> ProcessingMethod
+    paramset_desc: varchar(128)
+    param_set_hash: uuid
+    unique index (param_set_hash) (1)
+    params: longblob  # dictionary of all applicable parameters
+    """
+

This syntax enforces uniqueness of a secondary attribute.

Imported and Computed Tables¶

Imported and Computed tables provide make methods to determine how +they are populated, either from files or other tables.

Imagine that there is a table test.Image that contains 2D grayscale images in its +image attribute. We can define the Computed table, test.FilteredImage that filters +the image in some way and saves the result in its filtered_image attribute.

@schema
+class FilteredImage(dj.Computed):
+    definition = """ # Filtered image
+    -> Image
+    ---
+    filtered_image : longblob
+    """
+
+    def make(self, key):
+        img = (test.Image & key).fetch1('image')
+        key['filtered_image'] = my_filter(img)
+        self.insert1(key)
+

Part Tables¶

The following code defines a Imported table with an associated part table. In Python, +the master-part relationship is expressed by making the part a nested class of the +master. The part is subclassed from dj.Part and does not need the @schema +decorator.

@schema
+class Scan(dj.Imported):
+    definition = """
+    # Two-photon imaging scan
+    -> Session
+    scan : smallint  # scan number within the session
+    ---
+    -> Lens
+    laser_wavelength : decimal(5,1)  # um
+    laser_power      : decimal(4,1)  # mW
+    """
+
+    class ScanField(dj.Part):
+        definition = """
+        -> master
+        ROI: longblob  # Region of interest
+        """
+
+    def make(self, key):
+        ... # (1)
+        self.insert1(key)
+        self.ScanField.insert1(ROI_information)
+

This make method is truncated for the sake of brevity. For more detailed examples, +please visit Element Calcium Imaging table definitions

+ + + + + + + + +

+ + +

+ +

+ + + +

+ + + + + + + + + \ No newline at end of file diff --git a/0.13/search/search_index.json b/0.13/search/search_index.json new file mode 100644 index 000000000..7c20b32a4 --- /dev/null +++ b/0.13/search/search_index.json @@ -0,0 +1 @@ +{"config": {"indexing": "full", "lang": ["en"], "min_search_length": 3, "prebuild_index": false, "separator": "[\\s\\-]+"}, "docs": [{"location": "concepts/", "text": "", "title": "Concepts"}, {"location": "tutorials/", "text": "Tutorials \u00b6 Coming soon!", "title": "Tutorials"}, {"location": "tutorials/#tutorials", "text": "Coming soon!", "title": "Tutorials"}, {"location": "about/changelog/", "text": "Release notes \u00b6 0.13.8 -- Sep 21, 2022 \u00b6 Add - New documentation structure based on markdown PR #1052 Bugfix - Fix queries with backslashes ( #999 ) PR #1052 0.13.7 -- Jul 13, 2022 \u00b6 Bugfix - Fix networkx incompatable change by version pinning to 2.6.3 (#1035) PR #1036 Add - Support for serializing numpy datetime64 types (#1022) PR #1036 Update - Add traceback to default logging PR #1036 0.13.6 -- Jun 13, 2022 \u00b6 Add - Config option to set threshold for when to stop using checksums for filepath stores. PR #1025 Add - Unified package level logger for package (#667) PR #1031 Update - Swap various datajoint messages, warnings, etc. to use the new logger. (#667) PR #1031 Bugfix - Fix query caching deleting non-datajoint files PR #1027 Update - Minimum Python version for Datajoint-Python is now 3.7 PR #1027 0.13.5 -- May 19, 2022 \u00b6 Update - Import ABC from collections.abc for Python 3.10 compatibility Bugfix - Fix multiprocessing value error (#1013) PR #1026 0.13.4 -- Mar, 28 2022 \u00b6 Add - Allow reading blobs produced by legacy 32-bit compiled mYm library for matlab. PR #995 Bugfix - Add missing jobs argument for multiprocessing PR #997 Add - Test for multiprocessing PR #1008 Bugfix - Fix external store key name doesn't allow '-' (#1005) PR #1006 Add - Adopted black formatting into code base PR #998 0.13.3 -- Feb 9, 2022 \u00b6 Bugfix - Fix error in listing ancestors, descendants with part tables. Bugfix - Fix Python 3.10 compatibility (#983) PR #972 Bugfix - Allow renaming non-conforming attributes in proj (#982) PR #972 Add - Expose proxy feature for S3 external stores (#961) PR #962 Add - implement multiprocessing in populate (#695) PR #704, #969 Bugfix - Dependencies not properly loaded on populate. (#902) PR #919 Bugfix - Replace use of numpy aliases of built-in types with built-in type. (#938) PR #939 Bugfix - Deletes and drops must include the master of each part. (#151, #374) PR #957 Bugfix - ExternalTable.delete should not remove row on error (#953) PR #956 Bugfix - Fix error handling of remove_object function in s3.py (#952) PR #955 Bugfix - Fix regression issue with DISTINCT clause and GROUP_BY (#914) PR #963 Bugfix - Fix sql code generation to comply with sql mode ONLY_FULL_GROUP_BY (#916) PR #965 Bugfix - Fix count for left-joined QueryExpressions (#951) PR #966 Bugfix - Fix assertion error when performing a union into a join (#930) PR #967 Update ~jobs.error_stack from blob to mediumblob to allow error stacks >64kB in jobs (#984) PR #986 Bugfix - Fix error when performing a union on multiple tables (#926) PR #964 Add - Allow optional keyword arguments for make() in populate() PR #971 0.13.2 -- May 7, 2021 \u00b6 Update setuptools_certificate dependency to new name otumat Bugfix - Explicit calls to dj.Connection throw error due to missing host_input (#895) PR #907 Bugfix - Correct count of deleted items. (#897) PR #912 0.13.1 -- Apr 16, 2021 \u00b6 Add None as an alias for IS NULL comparison in dict restrictions (#824) PR #893 Drop support for MySQL 5.6 since it has reached EOL PR #893 Bugfix - schema.list_tables() is not topologically sorted (#838) PR #893 Bugfix - Diagram part tables do not show proper class name (#882) PR #893 Bugfix - Error in complex restrictions (#892) PR #893 Bugfix - WHERE and GROUP BY clases are dropped on joins with aggregation (#898, #899) PR #893 0.13.0 -- Mar 24, 2021 \u00b6 Re-implement query transpilation into SQL, fixing issues (#386, #449, #450, #484, #558). PR #754 Re-implement cascading deletes for better performance. PR #839 Add support for deferred schema activation to allow for greater modularity. (#834) PR #839 Add query caching mechanism for offline development (#550) PR #839 Add table method .update1 to update a row in the table with new values (#867) PR #763, #889 Python datatypes are now enabled by default in blobs (#761). PR #859 Added permissive join and restriction operators @ and ^ (#785) PR #754 Support DataJoint datatype and connection plugins (#715, #729) PR 730, #735 Add dj.key_hash alias to dj.hash.key_hash (#804) PR #862 Default enable_python_native_blobs to True Bugfix - Regression error on joins with same attribute name (#857) PR #878 Bugfix - Error when fetch1('KEY') when dj.config['fetch_format']='frame' set (#876) PR #880, #878 Bugfix - Error when cascading deletes in tables with many, complex keys (#883, #886) PR #839 Add deprecation warning for _update . PR #889 Add purge_query_cache utility. PR #889 Add tests for query caching and permissive join and restriction. PR #889 Drop support for Python 3.5 (#829) PR #861 0.12.9 -- Mar 12, 2021 \u00b6 Fix bug with fetch1 with dj.config['fetch_format']=\"frame\" . (#876) PR #880 0.12.8 -- Jan 12, 2021 \u00b6 table.children, .parents, .descendents, and ancestors can return queryable objects. PR #833 Load dependencies before querying dependencies. (#179) PR #833 Fix display of part tables in schema.save . (#821) PR #833 Add schema.list_tables . (#838) PR #844 Fix minio new version regression. PR #847 Add more S3 logging for debugging. (#831) PR #832 Convert testing framework from TravisCI to GitHub Actions (#841) PR #840 0.12.7 -- Oct 27, 2020 \u00b6 Fix case sensitivity issues to adapt to MySQL 8+. PR #819 Fix pymysql regression bug (#814) PR #816 Adapted attribute types now have dtype=object in all recarray results. PR #811 0.12.6 -- May 15, 2020 \u00b6 Add order_by to dj.kill (#668, #779) PR #775, #783 Add explicit S3 bucket and file storage location existence checks (#748) PR #781 Modify _update to allow nullable updates for strings/date (#664) PR #760 Avoid logging events on auxiliary tables (#737) PR #753 Add kill_quick and expand display to include host (#740) PR #741 Bugfix - pandas insert fails due to additional index field (#666) PR #776 Bugfix - delete_external_files=True does not remove from S3 (#686) PR #781 Bugfix - pandas fetch throws error when fetch_format='frame' PR #774 0.12.5 -- Feb 24, 2020 \u00b6 Rename module dj.schema into dj.schemas . dj.schema remains an alias for class dj.Schema . (#731) PR #732 dj.create_virtual_module is now called dj.VirtualModule (#731) PR #732 Bugfix - SSL KeyError on failed connection (#716) PR #725 Bugfix - Unable to run unit tests using nosetests (#723) PR #724 Bugfix - suppress_errors does not suppress loss of connection error (#720) PR #721 0.12.4 -- Jan 14, 2020 \u00b6 Support for simple scalar datatypes in blobs (#690) PR #709 Add support for the serial data type in declarations: alias for bigint unsigned auto_increment PR #713 Improve the log table to avoid primary key collisions PR #713 Improve documentation in README PR #713 0.12.3 -- Nov 22, 2019 \u00b6 Bugfix - networkx 2.4 causes error in diagrams (#675) PR #705 Bugfix - include table definition in doc string and help (#698, #699) PR #706 Bugfix - job reservation fails when native python datatype support is disabled (#701) PR #702 0.12.2 -- Nov 11, 2019 \u00b6 Bugfix - Convoluted error thrown if there is a reference to a non-existent table attribute (#691) PR #696 Bugfix - Insert into external does not trim leading slash if defined in dj.config['stores']['']['location'] (#692) PR #693 0.12.1 -- Nov 2, 2019 \u00b6 Bugfix - AttributeAdapter converts into a string (#684) PR #688 0.12.0 -- Oct 31, 2019 \u00b6 Dropped support for Python 3.4 Support secure connections with TLS (aka SSL) PR #620 Convert numpy array from python object to appropriate data type if all elements are of the same type (#587) PR #608 Remove expression requirement to have additional attributes (#604) PR #604 Support for filepath datatype (#481) PR #603, #659 Support file attachment datatype (#480, #592, #637) PR #659 Fetch return a dict array when specifying as_dict=True for specified attributes. (#595) PR #593 Support of ellipsis in proj : query_expression.proj(.., '-movie') (#499) PR #578 Expand support of blob serialization (#572, #520, #427, #392, #244, #594) PR #577 Support for alter (#110) PR #573 Support for conda install datajoint via conda-forge channel (#293) dj.conn() accepts a port keyword argument (#563) PR #571 Support for UUID datatype (#562) PR #567 query_expr.fetch(\"KEY\", as_dict=False) returns results as np.recarray (#414) PR #574 dj.ERD is now called dj.Diagram (#255, #546) PR #565 dj.Diagram underlines \"distinguished\" classes (#378) PR #557 Accept alias for supported MySQL datatypes (#544) PR #545 Support for pandas in fetch (#459, #537) PR #534 Support for ordering by \"KEY\" in fetch (#541) PR #534 Add config to enable python native blobs PR #672, #676 Add secure option for external storage (#663) PR #674, #676 Add blob migration utility from DJ011 to DJ012 PR #673 Improved external storage - a migration script needed from version 0.11 (#467, #475, #480, #497) PR #532 Increase default display rows (#523) PR #526 Bugfixes (#521, #205, #279, #477, #570, #581, #597, #596, #618, #633, #643, #644, #647, #648, #650, #656) Minor improvements (#538) 0.11.3 -- Jul 26, 2019 \u00b6 Fix incompatibility with pyparsing 2.4.1 (#629) PR #631 0.11.2 -- Jul 25, 2019 \u00b6 Fix #628 - incompatibility with pyparsing 2.4.1 0.11.1 -- Nov 15, 2018 \u00b6 Fix ordering of attributes in proj (#483, #516) Prohibit direct insert into auto-populated tables (#511) 0.11.0 -- Oct 25, 2018 \u00b6 Full support of dependencies with renamed attributes using projection syntax (#300, #345, #436, #506, #507) Rename internal class and module names to comply with terminology in documentation (#494, #500) Full support of secondary indexes (#498, 500) ERD no longer shows numbers in nodes corresponding to derived dependencies (#478, #500) Full support of unique and nullable dependencies (#254, #301, #493, #495, #500) Improve memory management in populate (#461, #486) Fix query errors and redundancies (#456, #463, #482) 0.10.1 -- Aug 28, 2018 \u00b6 Fix ERD Tooltip message (#431) Networkx 2.0 support (#443) Fix insert from query with skip_duplicates=True (#451) Sped up queries (#458) Bugfix in restriction of the form (A & B) * B (#463) Improved error messages (#466) 0.10.0 -- Jan 10, 2018 \u00b6 Deletes are more efficient (#424) ERD shows table definition on tooltip hover in Jupyter (#422) S3 external storage Garbage collection for external sorage Most operators and methods of tables can be invoked as class methods rather than instance methods (#407) The schema decorator object no longer requires locals() to specify the context Compatibility with pymysql 0.8.0+ More efficient loading of dependencies (#403) 0.9.0 -- Nov 17, 2017 \u00b6 Made graphviz installation optional Implement file-based external storage Implement union operator + Implement file-based external storage 0.8.0 -- Jul 26, 2017 \u00b6 Documentation and tutorials available at https://docs.datajoint.io and https://tutorials.datajoint.io * improved the ERD graphics and features using the graphviz libraries (#207, #333) * improved password handling logic (#322, #321) * the use of the contents property to populate tables now only works in dj.Lookup classes (#310). * allow suppressing the display of size of query results through the show_tuple_count configuration option (#309) * implemented renamed foreign keys to spec (#333) * added the limit keyword argument to populate (#329) * reduced the number of displayed messages (#308) * added size_on_disk property for dj.Schema() objects (#323) * job keys are entered in the jobs table (#316, #243) * simplified the fetch and fetch1 syntax, deprecating the fetch[...] syntax (#319) * the jobs tables now store the connection ids to allow identifying abandoned jobs (#288, #317) 0.5.0 (#298) -- Mar 8, 2017 \u00b6 All fetched integers are now 64-bit long and all fetched floats are double precision. Added dj.create_virtual_module 0.4.10 (#286) -- Feb 6, 2017 \u00b6 Removed Vagrant and Readthedocs support Explicit saving of configuration (issue #284) 0.4.9 (#285) -- Feb 2, 2017 \u00b6 Fixed setup.py for pip install 0.4.7 (#281) -- Jan 24, 2017 \u00b6 Fixed issues related to order of attributes in projection. 0.4.6 (#277) -- Dec 22, 2016 \u00b6 Proper handling of interruptions during populate 0.4.5 (#274) -- Dec 20, 2016 \u00b6 Populate reports how many keys remain to be populated at the start. 0.4.3 (#271) -- Dec 6, 2016 \u00b6 Fixed aggregation issues (#270) datajoint no longer attempts to connect to server at import time dropped support of view (reversed #257) more elegant handling of insufficient privileges (#268) 0.4.2 (#267) -- Dec 6, 2016 \u00b6 improved table appearance in Jupyter 0.4.1 (#266) -- Oct 28, 2016 \u00b6 bugfix for very long error messages 0.3.9 -- Sep 27, 2016 \u00b6 Added support for datatype YEAR Fixed issues with dj.U and the aggr operator (#246, #247) 0.3.8 -- Aug 2, 2016 \u00b6 added the _update method in base_relation . It allows updating values in existing tuples. bugfix in reading values of type double. Previously it was cast as float32. 0.3.7 -- Jul 31, 2016 \u00b6 added parameter ignore_extra_fields in insert insert(..., skip_duplicates=True) now relies on SELECT IGNORE . Previously it explicitly checked if tuple already exists. table previews now include blob attributes displaying the string 0.3.6 -- Jul 30, 2016 \u00b6 bugfix in schema.spawn_missing_classes . Previously, spawned part classes would not show in ERDs. dj.key now causes fetch to return as a list of dicts. Previously it was a recarray. 0.3.5 \u00b6 dj.set_password() now asks for user confirmation before changing the password. fixed issue #228 0.3.4 \u00b6 Added method the ERD.add_parts method, which adds the part tables of all tables currently in the ERD. ERD() + arg and ERD() - arg can now accept table classes as arg. 0.3.3 \u00b6 Suppressed warnings (redirected them to logging). Previoiusly, scipy would throw warnings in ERD, for example. Added ERD.from_sequence as a shortcut to combining the ERDs of multiple sources ERD() no longer text the context argument. ERD.draw() now takes an optional context argument. By default uses the caller's locals. 0.3.2. \u00b6 Fixed issue #223: insert can insert relations without fetching. ERD() now takes the context argument, which specifies in which context to look for classes. The default is taken from the argument (schema or table). ERD.draw() no longer has the prefix argument: class names are shown as found in the context.", "title": "Changelog"}, {"location": "about/changelog/#release-notes", "text": "", "title": "Release notes"}, {"location": "about/changelog/#0138-sep-21-2022", "text": "Add - New documentation structure based on markdown PR #1052 Bugfix - Fix queries with backslashes ( #999 ) PR #1052", "title": "0.13.8 -- Sep 21, 2022"}, {"location": "about/changelog/#0137-jul-13-2022", "text": "Bugfix - Fix networkx incompatable change by version pinning to 2.6.3 (#1035) PR #1036 Add - Support for serializing numpy datetime64 types (#1022) PR #1036 Update - Add traceback to default logging PR #1036", "title": "0.13.7 -- Jul 13, 2022"}, {"location": "about/changelog/#0136-jun-13-2022", "text": "Add - Config option to set threshold for when to stop using checksums for filepath stores. PR #1025 Add - Unified package level logger for package (#667) PR #1031 Update - Swap various datajoint messages, warnings, etc. to use the new logger. (#667) PR #1031 Bugfix - Fix query caching deleting non-datajoint files PR #1027 Update - Minimum Python version for Datajoint-Python is now 3.7 PR #1027", "title": "0.13.6 -- Jun 13, 2022"}, {"location": "about/changelog/#0135-may-19-2022", "text": "Update - Import ABC from collections.abc for Python 3.10 compatibility Bugfix - Fix multiprocessing value error (#1013) PR #1026", "title": "0.13.5 -- May 19, 2022"}, {"location": "about/changelog/#0134-mar-28-2022", "text": "Add - Allow reading blobs produced by legacy 32-bit compiled mYm library for matlab. PR #995 Bugfix - Add missing jobs argument for multiprocessing PR #997 Add - Test for multiprocessing PR #1008 Bugfix - Fix external store key name doesn't allow '-' (#1005) PR #1006 Add - Adopted black formatting into code base PR #998", "title": "0.13.4 -- Mar, 28 2022"}, {"location": "about/changelog/#0133-feb-9-2022", "text": "Bugfix - Fix error in listing ancestors, descendants with part tables. Bugfix - Fix Python 3.10 compatibility (#983) PR #972 Bugfix - Allow renaming non-conforming attributes in proj (#982) PR #972 Add - Expose proxy feature for S3 external stores (#961) PR #962 Add - implement multiprocessing in populate (#695) PR #704, #969 Bugfix - Dependencies not properly loaded on populate. (#902) PR #919 Bugfix - Replace use of numpy aliases of built-in types with built-in type. (#938) PR #939 Bugfix - Deletes and drops must include the master of each part. (#151, #374) PR #957 Bugfix - ExternalTable.delete should not remove row on error (#953) PR #956 Bugfix - Fix error handling of remove_object function in s3.py (#952) PR #955 Bugfix - Fix regression issue with DISTINCT clause and GROUP_BY (#914) PR #963 Bugfix - Fix sql code generation to comply with sql mode ONLY_FULL_GROUP_BY (#916) PR #965 Bugfix - Fix count for left-joined QueryExpressions (#951) PR #966 Bugfix - Fix assertion error when performing a union into a join (#930) PR #967 Update ~jobs.error_stack from blob to mediumblob to allow error stacks >64kB in jobs (#984) PR #986 Bugfix - Fix error when performing a union on multiple tables (#926) PR #964 Add - Allow optional keyword arguments for make() in populate() PR #971", "title": "0.13.3 -- Feb 9, 2022"}, {"location": "about/changelog/#0132-may-7-2021", "text": "Update setuptools_certificate dependency to new name otumat Bugfix - Explicit calls to dj.Connection throw error due to missing host_input (#895) PR #907 Bugfix - Correct count of deleted items. (#897) PR #912", "title": "0.13.2 -- May 7, 2021"}, {"location": "about/changelog/#0131-apr-16-2021", "text": "Add None as an alias for IS NULL comparison in dict restrictions (#824) PR #893 Drop support for MySQL 5.6 since it has reached EOL PR #893 Bugfix - schema.list_tables() is not topologically sorted (#838) PR #893 Bugfix - Diagram part tables do not show proper class name (#882) PR #893 Bugfix - Error in complex restrictions (#892) PR #893 Bugfix - WHERE and GROUP BY clases are dropped on joins with aggregation (#898, #899) PR #893", "title": "0.13.1 -- Apr 16, 2021"}, {"location": "about/changelog/#0130-mar-24-2021", "text": "Re-implement query transpilation into SQL, fixing issues (#386, #449, #450, #484, #558). PR #754 Re-implement cascading deletes for better performance. PR #839 Add support for deferred schema activation to allow for greater modularity. (#834) PR #839 Add query caching mechanism for offline development (#550) PR #839 Add table method .update1 to update a row in the table with new values (#867) PR #763, #889 Python datatypes are now enabled by default in blobs (#761). PR #859 Added permissive join and restriction operators @ and ^ (#785) PR #754 Support DataJoint datatype and connection plugins (#715, #729) PR 730, #735 Add dj.key_hash alias to dj.hash.key_hash (#804) PR #862 Default enable_python_native_blobs to True Bugfix - Regression error on joins with same attribute name (#857) PR #878 Bugfix - Error when fetch1('KEY') when dj.config['fetch_format']='frame' set (#876) PR #880, #878 Bugfix - Error when cascading deletes in tables with many, complex keys (#883, #886) PR #839 Add deprecation warning for _update . PR #889 Add purge_query_cache utility. PR #889 Add tests for query caching and permissive join and restriction. PR #889 Drop support for Python 3.5 (#829) PR #861", "title": "0.13.0 -- Mar 24, 2021"}, {"location": "about/changelog/#0129-mar-12-2021", "text": "Fix bug with fetch1 with dj.config['fetch_format']=\"frame\" . (#876) PR #880", "title": "0.12.9 -- Mar 12, 2021"}, {"location": "about/changelog/#0128-jan-12-2021", "text": "table.children, .parents, .descendents, and ancestors can return queryable objects. PR #833 Load dependencies before querying dependencies. (#179) PR #833 Fix display of part tables in schema.save . (#821) PR #833 Add schema.list_tables . (#838) PR #844 Fix minio new version regression. PR #847 Add more S3 logging for debugging. (#831) PR #832 Convert testing framework from TravisCI to GitHub Actions (#841) PR #840", "title": "0.12.8 -- Jan 12, 2021"}, {"location": "about/changelog/#0127-oct-27-2020", "text": "Fix case sensitivity issues to adapt to MySQL 8+. PR #819 Fix pymysql regression bug (#814) PR #816 Adapted attribute types now have dtype=object in all recarray results. PR #811", "title": "0.12.7 -- Oct 27, 2020"}, {"location": "about/changelog/#0126-may-15-2020", "text": "Add order_by to dj.kill (#668, #779) PR #775, #783 Add explicit S3 bucket and file storage location existence checks (#748) PR #781 Modify _update to allow nullable updates for strings/date (#664) PR #760 Avoid logging events on auxiliary tables (#737) PR #753 Add kill_quick and expand display to include host (#740) PR #741 Bugfix - pandas insert fails due to additional index field (#666) PR #776 Bugfix - delete_external_files=True does not remove from S3 (#686) PR #781 Bugfix - pandas fetch throws error when fetch_format='frame' PR #774", "title": "0.12.6 -- May 15, 2020"}, {"location": "about/changelog/#0125-feb-24-2020", "text": "Rename module dj.schema into dj.schemas . dj.schema remains an alias for class dj.Schema . (#731) PR #732 dj.create_virtual_module is now called dj.VirtualModule (#731) PR #732 Bugfix - SSL KeyError on failed connection (#716) PR #725 Bugfix - Unable to run unit tests using nosetests (#723) PR #724 Bugfix - suppress_errors does not suppress loss of connection error (#720) PR #721", "title": "0.12.5 -- Feb 24, 2020"}, {"location": "about/changelog/#0124-jan-14-2020", "text": "Support for simple scalar datatypes in blobs (#690) PR #709 Add support for the serial data type in declarations: alias for bigint unsigned auto_increment PR #713 Improve the log table to avoid primary key collisions PR #713 Improve documentation in README PR #713", "title": "0.12.4 -- Jan 14, 2020"}, {"location": "about/changelog/#0123-nov-22-2019", "text": "Bugfix - networkx 2.4 causes error in diagrams (#675) PR #705 Bugfix - include table definition in doc string and help (#698, #699) PR #706 Bugfix - job reservation fails when native python datatype support is disabled (#701) PR #702", "title": "0.12.3 -- Nov 22, 2019"}, {"location": "about/changelog/#0122-nov-11-2019", "text": "Bugfix - Convoluted error thrown if there is a reference to a non-existent table attribute (#691) PR #696 Bugfix - Insert into external does not trim leading slash if defined in dj.config['stores']['']['location'] (#692) PR #693", "title": "0.12.2 -- Nov 11, 2019"}, {"location": "about/changelog/#0121-nov-2-2019", "text": "Bugfix - AttributeAdapter converts into a string (#684) PR #688", "title": "0.12.1 -- Nov 2, 2019"}, {"location": "about/changelog/#0120-oct-31-2019", "text": "Dropped support for Python 3.4 Support secure connections with TLS (aka SSL) PR #620 Convert numpy array from python object to appropriate data type if all elements are of the same type (#587) PR #608 Remove expression requirement to have additional attributes (#604) PR #604 Support for filepath datatype (#481) PR #603, #659 Support file attachment datatype (#480, #592, #637) PR #659 Fetch return a dict array when specifying as_dict=True for specified attributes. (#595) PR #593 Support of ellipsis in proj : query_expression.proj(.., '-movie') (#499) PR #578 Expand support of blob serialization (#572, #520, #427, #392, #244, #594) PR #577 Support for alter (#110) PR #573 Support for conda install datajoint via conda-forge channel (#293) dj.conn() accepts a port keyword argument (#563) PR #571 Support for UUID datatype (#562) PR #567 query_expr.fetch(\"KEY\", as_dict=False) returns results as np.recarray (#414) PR #574 dj.ERD is now called dj.Diagram (#255, #546) PR #565 dj.Diagram underlines \"distinguished\" classes (#378) PR #557 Accept alias for supported MySQL datatypes (#544) PR #545 Support for pandas in fetch (#459, #537) PR #534 Support for ordering by \"KEY\" in fetch (#541) PR #534 Add config to enable python native blobs PR #672, #676 Add secure option for external storage (#663) PR #674, #676 Add blob migration utility from DJ011 to DJ012 PR #673 Improved external storage - a migration script needed from version 0.11 (#467, #475, #480, #497) PR #532 Increase default display rows (#523) PR #526 Bugfixes (#521, #205, #279, #477, #570, #581, #597, #596, #618, #633, #643, #644, #647, #648, #650, #656) Minor improvements (#538)", "title": "0.12.0 -- Oct 31, 2019"}, {"location": "about/changelog/#0113-jul-26-2019", "text": "Fix incompatibility with pyparsing 2.4.1 (#629) PR #631", "title": "0.11.3 -- Jul 26, 2019"}, {"location": "about/changelog/#0112-jul-25-2019", "text": "Fix #628 - incompatibility with pyparsing 2.4.1", "title": "0.11.2 -- Jul 25, 2019"}, {"location": "about/changelog/#0111-nov-15-2018", "text": "Fix ordering of attributes in proj (#483, #516) Prohibit direct insert into auto-populated tables (#511)", "title": "0.11.1 -- Nov 15, 2018"}, {"location": "about/changelog/#0110-oct-25-2018", "text": "Full support of dependencies with renamed attributes using projection syntax (#300, #345, #436, #506, #507) Rename internal class and module names to comply with terminology in documentation (#494, #500) Full support of secondary indexes (#498, 500) ERD no longer shows numbers in nodes corresponding to derived dependencies (#478, #500) Full support of unique and nullable dependencies (#254, #301, #493, #495, #500) Improve memory management in populate (#461, #486) Fix query errors and redundancies (#456, #463, #482)", "title": "0.11.0 -- Oct 25, 2018"}, {"location": "about/changelog/#0101-aug-28-2018", "text": "Fix ERD Tooltip message (#431) Networkx 2.0 support (#443) Fix insert from query with skip_duplicates=True (#451) Sped up queries (#458) Bugfix in restriction of the form (A & B) * B (#463) Improved error messages (#466)", "title": "0.10.1 -- Aug 28, 2018"}, {"location": "about/changelog/#0100-jan-10-2018", "text": "Deletes are more efficient (#424) ERD shows table definition on tooltip hover in Jupyter (#422) S3 external storage Garbage collection for external sorage Most operators and methods of tables can be invoked as class methods rather than instance methods (#407) The schema decorator object no longer requires locals() to specify the context Compatibility with pymysql 0.8.0+ More efficient loading of dependencies (#403)", "title": "0.10.0 -- Jan 10, 2018"}, {"location": "about/changelog/#090-nov-17-2017", "text": "Made graphviz installation optional Implement file-based external storage Implement union operator + Implement file-based external storage", "title": "0.9.0 -- Nov 17, 2017"}, {"location": "about/changelog/#080-jul-26-2017", "text": "Documentation and tutorials available at https://docs.datajoint.io and https://tutorials.datajoint.io * improved the ERD graphics and features using the graphviz libraries (#207, #333) * improved password handling logic (#322, #321) * the use of the contents property to populate tables now only works in dj.Lookup classes (#310). * allow suppressing the display of size of query results through the show_tuple_count configuration option (#309) * implemented renamed foreign keys to spec (#333) * added the limit keyword argument to populate (#329) * reduced the number of displayed messages (#308) * added size_on_disk property for dj.Schema() objects (#323) * job keys are entered in the jobs table (#316, #243) * simplified the fetch and fetch1 syntax, deprecating the fetch[...] syntax (#319) * the jobs tables now store the connection ids to allow identifying abandoned jobs (#288, #317)", "title": "0.8.0 -- Jul 26, 2017"}, {"location": "about/changelog/#050-298-mar-8-2017", "text": "All fetched integers are now 64-bit long and all fetched floats are double precision. Added dj.create_virtual_module", "title": "0.5.0 (#298) -- Mar 8, 2017"}, {"location": "about/changelog/#0410-286-feb-6-2017", "text": "Removed Vagrant and Readthedocs support Explicit saving of configuration (issue #284)", "title": "0.4.10 (#286) -- Feb 6, 2017"}, {"location": "about/changelog/#049-285-feb-2-2017", "text": "Fixed setup.py for pip install", "title": "0.4.9 (#285) -- Feb 2, 2017"}, {"location": "about/changelog/#047-281-jan-24-2017", "text": "Fixed issues related to order of attributes in projection.", "title": "0.4.7 (#281) -- Jan 24, 2017"}, {"location": "about/changelog/#046-277-dec-22-2016", "text": "Proper handling of interruptions during populate", "title": "0.4.6 (#277) -- Dec 22, 2016"}, {"location": "about/changelog/#045-274-dec-20-2016", "text": "Populate reports how many keys remain to be populated at the start.", "title": "0.4.5 (#274) -- Dec 20, 2016"}, {"location": "about/changelog/#043-271-dec-6-2016", "text": "Fixed aggregation issues (#270) datajoint no longer attempts to connect to server at import time dropped support of view (reversed #257) more elegant handling of insufficient privileges (#268)", "title": "0.4.3 (#271) -- Dec 6, 2016"}, {"location": "about/changelog/#042-267-dec-6-2016", "text": "improved table appearance in Jupyter", "title": "0.4.2 (#267) -- Dec 6, 2016"}, {"location": "about/changelog/#041-266-oct-28-2016", "text": "bugfix for very long error messages", "title": "0.4.1 (#266) -- Oct 28, 2016"}, {"location": "about/changelog/#039-sep-27-2016", "text": "Added support for datatype YEAR Fixed issues with dj.U and the aggr operator (#246, #247)", "title": "0.3.9 -- Sep 27, 2016"}, {"location": "about/changelog/#038-aug-2-2016", "text": "added the _update method in base_relation . It allows updating values in existing tuples. bugfix in reading values of type double. Previously it was cast as float32.", "title": "0.3.8 -- Aug 2, 2016"}, {"location": "about/changelog/#037-jul-31-2016", "text": "added parameter ignore_extra_fields in insert insert(..., skip_duplicates=True) now relies on SELECT IGNORE . Previously it explicitly checked if tuple already exists. table previews now include blob attributes displaying the string", "title": "0.3.7 -- Jul 31, 2016"}, {"location": "about/changelog/#036-jul-30-2016", "text": "bugfix in schema.spawn_missing_classes . Previously, spawned part classes would not show in ERDs. dj.key now causes fetch to return as a list of dicts. Previously it was a recarray.", "title": "0.3.6 -- Jul 30, 2016"}, {"location": "about/changelog/#035", "text": "dj.set_password() now asks for user confirmation before changing the password. fixed issue #228", "title": "0.3.5"}, {"location": "about/changelog/#034", "text": "Added method the ERD.add_parts method, which adds the part tables of all tables currently in the ERD. ERD() + arg and ERD() - arg can now accept table classes as arg.", "title": "0.3.4"}, {"location": "about/changelog/#033", "text": "Suppressed warnings (redirected them to logging). Previoiusly, scipy would throw warnings in ERD, for example. Added ERD.from_sequence as a shortcut to combining the ERDs of multiple sources ERD() no longer text the context argument. ERD.draw() now takes an optional context argument. By default uses the caller's locals.", "title": "0.3.3"}, {"location": "about/changelog/#032", "text": "Fixed issue #223: insert can insert relations without fetching. ERD() now takes the context argument, which specifies in which context to look for classes. The default is taken from the argument (schema or table). ERD.draw() no longer has the prefix argument: class names are shown as found in the context.", "title": "0.3.2."}, {"location": "api/datajoint/__init__/", "text": "DataJoint for Python is a framework for building data piplines using MySQL databases to represent pipeline structure and bulk storage systems for large objects. DataJoint is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, and querying data. The DataJoint data model is described in https://arxiv.org/abs/1807.11104 DataJoint is free software under the LGPL License. In addition, we request that any use of DataJoint leading to a publication be acknowledged in the publication. Please cite: - http://biorxiv.org/content/early/2015/11/14/031658 - http://dx.doi.org/10.1101/031658 AttributeAdapter \u00b6 Base class for adapter objects for user-defined attribute types. Source code in datajoint/attribute_adapter.py 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 class AttributeAdapter : \"\"\" Base class for adapter objects for user-defined attribute types. \"\"\" @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) attribute_type () property \u00b6 Returns: Type Description a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" Source code in datajoint/attribute_adapter.py 11 12 13 14 15 16 @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) get ( value ) \u00b6 convert value retrieved from the the attribute in a table into the adapted type Parameters: Name Type Description Default value value from the database required Returns: Type Description object of the adapted type Source code in datajoint/attribute_adapter.py 18 19 20 21 22 23 24 25 26 def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) put ( obj ) \u00b6 convert an object of the adapted type into a value that DataJoint can store in a table attribute Parameters: Name Type Description Default obj an object of the adapted type required Returns: Type Description value to store in the database Source code in datajoint/attribute_adapter.py 28 29 30 31 32 33 34 35 def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) key_hash ( mapping ) \u00b6 32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. Source code in datajoint/hash.py 7 8 9 10 11 12 13 14 15 16 def key_hash ( mapping ): \"\"\" 32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. \"\"\" hashed = hashlib . md5 () for k , v in sorted ( mapping . items ()): hashed . update ( str ( v ) . encode ()) return hashed . hexdigest () migrate_dj011_external_blob_storage_to_dj012 ( migration_schema , store ) \u00b6 Utility function to migrate external blob data from 0.11 to 0.12. Parameters: Name Type Description Default migration_schema string of target schema to be migrated required store string of target dj.config['store'] to be migrated required Source code in datajoint/migrate.py 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 def migrate_dj011_external_blob_storage_to_dj012 ( migration_schema , store ): \"\"\" Utility function to migrate external blob data from 0.11 to 0.12. :param migration_schema: string of target schema to be migrated :param store: string of target dj.config['store'] to be migrated \"\"\" if not isinstance ( migration_schema , str ): raise ValueError ( \"Expected type {} for migration_schema, not {} .\" . format ( str , type ( migration_schema ) ) ) do_migration = False do_migration = ( user_choice ( \"\"\" Warning: Ensure the following are completed before proceeding. - Appropriate backups have been taken, - Any existing DJ 0.11.X connections are suspended, and - External config has been updated to new dj.config['stores'] structure. Proceed? \"\"\" , default = \"no\" , ) == \"yes\" ) if do_migration : _migrate_dj011_blob ( dj . Schema ( migration_schema ), store ) print ( \"Migration completed for schema: {} , store: {} .\" . format ( migration_schema , store ) ) return print ( \"No migration performed.\" ) DataJointError \u00b6 Bases: Exception Base class for errors specific to DataJoint internal operation. Source code in datajoint/errors.py 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 class DataJointError ( Exception ): \"\"\" Base class for errors specific to DataJoint internal operation. \"\"\" def __init__ ( self , * args ): from .plugin import connection_plugins , type_plugins self . __cause__ = ( PluginWarning ( \"Unverified DataJoint plugin detected.\" ) if any ( [ any ([ not plugins [ k ][ \"verified\" ] for k in plugins ]) for plugins in [ connection_plugins , type_plugins ] if plugins ] ) else None ) def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args )) suggest ( * args ) \u00b6 regenerate the exception with additional arguments Parameters: Name Type Description Default args addition arguments required Returns: Type Description a new exception of the same type with the additional arguments Source code in datajoint/errors.py 34 35 36 37 38 39 40 41 def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args )) key \u00b6 object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key Source code in datajoint/fetch.py 18 19 20 21 22 23 24 class key : \"\"\" object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key \"\"\" pass AndList \u00b6 Bases: list A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 Source code in datajoint/condition.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 class AndList ( list ): \"\"\" A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 \"\"\" def append ( self , restriction ): if isinstance ( restriction , AndList ): # extend to reduce nesting self . extend ( restriction ) else : super () . append ( restriction ) kill ( restriction = None , connection = None , order_by = None ) \u00b6 view and kill database connections. Parameters: Name Type Description Default restriction restriction to be applied to processlist None connection a datajoint.Connection object. Default calls datajoint.conn() None order_by order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes None Source code in datajoint/admin.py 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 def kill ( restriction = None , connection = None , order_by = None ): # pragma: no cover \"\"\" view and kill database connections. :param restriction: restriction to be applied to processlist :param connection: a datajoint.Connection object. Default calls datajoint.conn() :param order_by: order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes \"\"\" if connection is None : connection = conn () if order_by is not None and not isinstance ( order_by , str ): order_by = \",\" . join ( order_by ) query = ( \"SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()\" + ( \"\" if restriction is None else \" AND ( %s )\" % restriction ) + ( \" ORDER BY %s \" % ( order_by or \"id\" )) ) while True : print ( \" ID USER HOST STATE TIME INFO\" ) print ( \"+--+ +----------+ +-----------+ +-----------+ +-----+\" ) cur = ( { k . lower (): v for k , v in elem . items ()} for elem in connection . query ( query , as_dict = True ) ) for process in cur : try : print ( \" {id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d} {info} \" . format ( ** process ) ) except TypeError : print ( process ) response = input ( 'process to kill or \"q\" to quit > ' ) if response == \"q\" : break if response : try : pid = int ( response ) except ValueError : pass # ignore non-numeric input else : try : connection . query ( \"kill %d \" % pid ) except pymysql . err . InternalError : print ( \"Process not found\" ) Schema \u00b6 A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace context in which other UserTable classes are defined. Source code in datajoint/schemas.py 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 class Schema : \"\"\" A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace `context` in which other UserTable classes are defined. \"\"\" def __init__ ( self , schema_name = None , context = None , * , connection = None , create_schema = True , create_tables = True , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. If the schema_name is omitted, then schema.activate(..) must be called later to associate with the database. :param schema_name: the database schema to associate. :param context: dictionary for looking up foreign key references, leave None to use local context. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: When False, do not create the schema and raise an error if missing. :param create_tables: When False, do not create tables and raise errors when accessing missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" self . _log = None self . connection = connection self . database = None self . context = context self . create_schema = create_schema self . create_tables = create_tables self . _jobs = None self . external = ExternalMapping ( self ) self . add_objects = add_objects self . declare_list = [] if schema_name : self . activate ( schema_name ) def is_activated ( self ): return self . database is not None def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context ) def _assert_exists ( self , message = None ): if not self . exists : raise DataJointError ( message or \"Schema ` {db} ` has not been created.\" . format ( db = self . database ) ) def __call__ ( self , cls , * , context = None ): \"\"\" Binds the supplied class to a schema. This is intended to be used as a decorator. :param cls: class to decorate. :param context: supplied when called from spawn_missing_classes \"\"\" context = context or self . context or inspect . currentframe () . f_back . f_locals if issubclass ( cls , Part ): raise DataJointError ( \"The schema decorator should not be applied to Part tables.\" ) if self . is_activated (): self . _decorate_master ( cls , context ) else : self . declare_list . append (( cls , context )) return cls def _decorate_master ( self , cls , context ): \"\"\" :param cls: the master class to process :param context: the class' declaration context \"\"\" self . _decorate_table ( cls , context = dict ( context , self = cls , ** { cls . __name__ : cls }) ) # Process part tables for part in ordered_dir ( cls ): if part [ 0 ] . isupper (): part = getattr ( cls , part ) if inspect . isclass ( part ) and issubclass ( part , Part ): part . _master = cls # allow addressing master by name or keyword 'master' self . _decorate_table ( part , context = dict ( context , master = cls , self = part , ** { cls . __name__ : cls } ), ) def _decorate_table ( self , table_class , context , assert_declared = False ): \"\"\" assign schema properties to the table class and declare the table \"\"\" table_class . database = self . database table_class . _connection = self . connection table_class . _heading = Heading ( table_info = dict ( conn = self . connection , database = self . database , table_name = table_class . table_name , context = context , ) ) table_class . _support = [ table_class . full_table_name ] table_class . declaration_context = context # instantiate the class, declare the table if not already instance = table_class () is_declared = instance . is_declared if not is_declared and not assert_declared and self . create_tables : instance . declare ( context ) self . connection . dependencies . clear () is_declared = is_declared or instance . is_declared # add table definition to the doc string if isinstance ( table_class . definition , str ): table_class . __doc__ = ( ( table_class . __doc__ or \"\" ) + \" \\n Table definition: \\n\\n \" + table_class . definition ) # fill values in Lookup tables from their contents property if ( isinstance ( instance , Lookup ) and hasattr ( instance , \"contents\" ) and is_declared ): contents = list ( instance . contents ) if len ( contents ) > len ( instance ): if instance . heading . has_autoincrement : warnings . warn ( ( \"Contents has changed but cannot be inserted because \" \" {table} has autoincrement.\" ) . format ( table = instance . __class__ . __name__ ) ) else : instance . insert ( contents , skip_duplicates = True ) @property def log ( self ): self . _assert_exists () if self . _log is None : self . _log = Log ( self . connection , self . database ) return self . _log def __repr__ ( self ): return \"Schema ` {name} ` \\n \" . format ( name = self . database ) @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] ) def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class ) def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) ) @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount ) @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs @property def code ( self ): self . _assert_exists () return self . save () def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code ) def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ] activate ( schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None ) \u00b6 Associate database schema schema_name . If the schema does not exist, attempt to create it on the server. Parameters: Name Type Description Default schema_name the database schema to associate. schema_name=None is used to assert that the schema has already been activated. None connection Connection object. Defaults to datajoint.conn(). None create_schema If False, do not create the schema and raise an error if missing. None create_tables If False, do not create tables and raise errors when attempting to access missing tables. None add_objects a mapping with additional objects to make available to the context in which table classes are declared. None Source code in datajoint/schemas.py 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context ) size_on_disk () property \u00b6 Returns: Type Description size of the entire schema in bytes Source code in datajoint/schemas.py 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] ) spawn_missing_classes ( context = None ) \u00b6 Creates the appropriate python user table classes from tables in the schema and places them in the context. Parameters: Name Type Description Default context alternative context to place the missing classes into, e.g. locals() None Source code in datajoint/schemas.py 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class ) drop ( force = False ) \u00b6 Drop the associated schema if it exists Source code in datajoint/schemas.py 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) ) exists () property \u00b6 Returns: Type Description true if the associated schema exists on the server Source code in datajoint/schemas.py 377 378 379 380 381 382 383 384 385 386 387 388 389 390 @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount ) jobs () property \u00b6 schema.jobs provides a view of the job reservation table for the schema Returns: Type Description jobs table Source code in datajoint/schemas.py 392 393 394 395 396 397 398 399 400 401 402 @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs save ( python_filename = None ) \u00b6 Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. Returns: Type Description a string containing the body of a complete Python module defining this schema. Source code in datajoint/schemas.py 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code ) list_tables () \u00b6 Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job Returns: Type Description A list of table names from the database schema. Source code in datajoint/schemas.py 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ] Not \u00b6 invert restriction Source code in datajoint/condition.py 43 44 45 46 47 class Not : \"\"\"invert restriction\"\"\" def __init__ ( self , restriction ): self . restriction = restriction Table \u00b6 Bases: QueryExpression Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. Source code in datajoint/table.py 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 class Table ( QueryExpression ): \"\"\" Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. \"\"\" _table_name = None # must be defined in subclass _log_ = None # placeholder for the Log table object # These properties must be set by the schema decorator (schemas.py) at class level # or by FreeTable at instance level database = None declaration_context = None @property def table_name ( self ): return self . _table_name @property def definition ( self ): raise NotImplementedError ( \"Subclasses of Table must implement the `definition` property\" ) def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name ) def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name ) def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql ) def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ] def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ] def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 ) @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name ) @property def _log ( self ): if self . _log_ is None : self . _log_ = Log ( self . connection , database = self . database , skip_logging = self . table_name . startswith ( \"~\" ), ) return self . _log_ @property def external ( self ): return self . connection . schemas [ self . database ] . external def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None )) def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs ) def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" ) def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name ) def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" ) @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ] def show_definition ( self ): raise AttributeError ( \"show_definition is deprecated. Use the describe method instead.\" ) def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition def _update ( self , attrname , value = None ): \"\"\" This is a deprecated function to be removed in datajoint 0.14. Use ``.update1`` instead. Updates a field in one existing tuple. self must be restricted to exactly one entry. In DataJoint the principal way of updating data is to delete and re-insert the entire record and updates are reserved for corrective actions. This is because referential integrity is observed on the level of entire records rather than individual attributes. Safety constraints: 1. self must be restricted to exactly one tuple 2. the update attribute must not be in primary key Example: >>> (v2p.Mice() & key)._update('mouse_dob', '2011-01-01') >>> (v2p.Mice() & key)._update( 'lens') # set the value to NULL \"\"\" logger . warning ( \"`_update` is a deprecated function to be removed in datajoint 0.14. \" \"Use `.update1` instead.\" ) if len ( self ) != 1 : raise DataJointError ( \"Update is only allowed on one tuple at a time\" ) if attrname not in self . heading : raise DataJointError ( \"Invalid attribute name\" ) if attrname in self . heading . primary_key : raise DataJointError ( \"Cannot update a key value.\" ) attr = self . heading [ attrname ] if attr . is_blob : value = blob . pack ( value ) placeholder = \" %s \" elif attr . numeric : if value is None or np . isnan ( float ( value )): # nans are turned into NULLs placeholder = \"NULL\" value = None else : placeholder = \" %s \" value = str ( int ( value ) if isinstance ( value , bool ) else value ) else : placeholder = \" %s \" if value is not None else \"NULL\" command = \"UPDATE {full_table_name} SET ` {attrname} `= {placeholder} {where_clause} \" . format ( full_table_name = self . from_clause (), attrname = attrname , placeholder = placeholder , where_clause = self . where_clause (), ) self . connection . query ( command , args = ( value ,) if value is not None else ()) # --- private helper functions ---- def __make_placeholder ( self , name , value , ignore_extra_fields = False ): \"\"\" For a given attribute `name` with `value`, return its processed value or value placeholder as a string to be included in the query and the value, if any, to be submitted for processing by mysql API. :param name: name of attribute to be inserted :param value: value of attribute to be inserted \"\"\" if ignore_extra_fields and name not in self . heading : return None attr = self . heading [ name ] if attr . adapter : value = attr . adapter . put ( value ) if value is None or ( attr . numeric and ( value == \"\" or np . isnan ( float ( value )))): # set default value placeholder , value = \"DEFAULT\" , None else : # not NULL placeholder = \" %s \" if attr . uuid : if not isinstance ( value , uuid . UUID ): try : value = uuid . UUID ( value ) except ( AttributeError , ValueError ): raise DataJointError ( \"badly formed UUID value {v} for attribute ` {n} `\" . format ( v = value , n = name ) ) value = value . bytes elif attr . is_blob : value = blob . pack ( value ) value = ( self . external [ attr . store ] . put ( value ) . bytes if attr . is_external else value ) elif attr . is_attachment : attachment_path = Path ( value ) if attr . is_external : # value is hash of contents value = ( self . external [ attr . store ] . upload_attachment ( attachment_path ) . bytes ) else : # value is filename + contents value = ( str . encode ( attachment_path . name ) + b \" \\0 \" + attachment_path . read_bytes () ) elif attr . is_filepath : value = self . external [ attr . store ] . upload_filepath ( value ) . bytes elif attr . numeric : value = str ( int ( value ) if isinstance ( value , bool ) else value ) return name , placeholder , value def __make_row_to_insert ( self , row , field_list , ignore_extra_fields ): \"\"\" Helper function for insert and update :param row: A tuple to insert :return: a dict with fields 'names', 'placeholders', 'values' \"\"\" def check_fields ( fields ): \"\"\" Validates that all items in `fields` are valid attributes in the heading :param fields: field names of a tuple \"\"\" if not field_list : if not ignore_extra_fields : for field in fields : if field not in self . heading : raise KeyError ( \"` {0:s} ` is not in the table heading\" . format ( field ) ) elif set ( field_list ) != set ( fields ) . intersection ( self . heading . names ): raise DataJointError ( \"Attempt to insert rows with different fields.\" ) if isinstance ( row , np . void ): # np.array check_fields ( row . dtype . fields ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row . dtype . fields ] elif isinstance ( row , collections . abc . Mapping ): # dict-based check_fields ( row ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row ] else : # positional try : if len ( row ) != len ( self . heading ): raise DataJointError ( \"Invalid insert argument. Incorrect number of attributes: \" \" {given} given; {expected} expected\" . format ( given = len ( row ), expected = len ( self . heading ) ) ) except TypeError : raise DataJointError ( \"Datatype %s cannot be inserted\" % type ( row )) else : attributes = [ self . __make_placeholder ( name , value , ignore_extra_fields ) for name , value in zip ( self . heading , row ) ] if ignore_extra_fields : attributes = [ a for a in attributes if a is not None ] assert len ( attributes ), \"Empty tuple\" row_to_insert = dict ( zip (( \"names\" , \"placeholders\" , \"values\" ), zip ( * attributes ))) if not field_list : # first row sets the composition of the field list field_list . extend ( row_to_insert [ \"names\" ]) else : # reorder attributes in row_to_insert to match field_list order = list ( row_to_insert [ \"names\" ] . index ( field ) for field in field_list ) row_to_insert [ \"names\" ] = list ( row_to_insert [ \"names\" ][ i ] for i in order ) row_to_insert [ \"placeholders\" ] = list ( row_to_insert [ \"placeholders\" ][ i ] for i in order ) row_to_insert [ \"values\" ] = list ( row_to_insert [ \"values\" ][ i ] for i in order ) return row_to_insert declare ( context = None ) \u00b6 Declare the table in the schema based on self.definition. Parameters: Name Type Description Default context the context for foreign key resolution. If None, foreign keys are not allowed. None Source code in datajoint/table.py 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name ) alter ( prompt = True , context = None ) \u00b6 Alter the table definition from self.definition Source code in datajoint/table.py 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name ) from_clause () \u00b6 Returns: Type Description the FROM clause of SQL SELECT statements. Source code in datajoint/table.py 147 148 149 150 151 def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name get_select_fields ( select_fields = None ) \u00b6 Returns: Type Description the selected attributes from the SQL SELECT statement. Source code in datajoint/table.py 153 154 155 156 157 158 159 def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql ) parents ( primary = None , as_objects = False , foreign_key_info = False ) \u00b6 Parameters: Name Type Description Default primary if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of parents as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes children ( primary = None , as_objects = False , foreign_key_info = False ) \u00b6 Parameters: Name Type Description Default primary if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of children as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes descendants ( as_objects = False ) \u00b6 Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables descendants in topological order. Source code in datajoint/table.py 205 206 207 208 209 210 211 212 213 214 215 def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ] ancestors ( as_objects = False ) \u00b6 Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables ancestors in topological order. Source code in datajoint/table.py 217 218 219 220 221 222 223 224 225 226 227 def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ] parts ( as_objects = False ) \u00b6 return part tables either as entries in a dict with foreign key informaiton or a list of objects Parameters: Name Type Description Default as_objects if False (default), the output is a dict describing the foreign keys. If True, return table objects. False Source code in datajoint/table.py 229 230 231 232 233 234 235 236 237 238 239 240 def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes is_declared () property \u00b6 Returns: Type Description True is the table is declared in the schema. Source code in datajoint/table.py 242 243 244 245 246 247 248 249 250 251 252 253 254 @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 ) full_table_name () property \u00b6 Returns: Type Description full table name in the schema Source code in datajoint/table.py 256 257 258 259 260 261 @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name ) update1 ( row ) \u00b6 update1 updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to insert and delete entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. Parameters: Name Type Description Default row a dict containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default required Source code in datajoint/table.py 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None )) insert1 ( row , ** kwargs ) \u00b6 Insert one data record into the table. For kwargs , see insert() . Parameters: Name Type Description Default row a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. required Source code in datajoint/table.py 328 329 330 331 332 333 334 335 def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs ) insert ( rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None ) \u00b6 Insert a collection of rows. Parameters: Name Type Description Default rows An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. required replace If True, replaces the existing tuple. False skip_duplicates If True, silently skip duplicate inserts. False ignore_extra_fields If False, fields that are not in the heading raise error. False allow_direct_insert applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) None Source code in datajoint/table.py 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" ) delete_quick ( get_count = False ) \u00b6 Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. Source code in datajoint/table.py 448 449 450 451 452 453 454 455 456 457 458 459 460 461 def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count delete ( transaction = True , safemode = None , force_parts = False ) \u00b6 Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If True , use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to False if this delete is nested within another transaction. safemode: If True , prohibit nested transactions and prompt to confirm. Default is dj.config['safemode'] . force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. Source code in datajoint/table.py 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count drop_quick () \u00b6 Drops the table without cascading to dependent tables and without user prompt. Source code in datajoint/table.py 614 615 616 617 618 619 620 621 622 623 624 625 626 def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name ) drop () \u00b6 Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. Source code in datajoint/table.py 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" ) size_on_disk () property \u00b6 Returns: Type Description size of data and indices in bytes on the storage device Source code in datajoint/table.py 664 665 666 667 668 669 670 671 672 673 674 675 @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ] describe ( context = None , printout = True ) \u00b6 Returns: Type Description the definition string for the query using DataJoint DDL. Source code in datajoint/table.py 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition Diagram \u00b6 Bases: nx . DiGraph Entity relationship diagram. Usage: diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed Source code in datajoint/diagram.py 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 class Diagram ( nx . DiGraph ): \"\"\" Entity relationship diagram. Usage: >>> diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. >>> diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed \"\"\" def __init__ ( self , source , context = None ): if isinstance ( source , Diagram ): # copy constructor self . nodes_to_show = set ( source . nodes_to_show ) self . context = source . context super () . __init__ ( source ) return # get the caller's context if context is None : frame = inspect . currentframe () . f_back self . context = dict ( frame . f_globals , ** frame . f_locals ) del frame else : self . context = context # find connection in the source try : connection = source . connection except AttributeError : try : connection = source . schema . connection except AttributeError : raise DataJointError ( \"Could not find database connection in %s \" % repr ( source [ 0 ]) ) # initialize graph from dependencies connection . dependencies . load () super () . __init__ ( connection . dependencies ) # Enumerate nodes from all the items in the list self . nodes_to_show = set () try : self . nodes_to_show . add ( source . full_table_name ) except AttributeError : try : database = source . database except AttributeError : try : database = source . schema . database except AttributeError : raise DataJointError ( \"Cannot plot Diagram for %s \" % repr ( source ) ) for node in self : if node . startswith ( \"` %s `\" % database ): self . nodes_to_show . add ( node ) @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence )) def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) ) def __add__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Union of the diagrams when arg is another Diagram or an expansion downstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . add ( arg . full_table_name ) except AttributeError : for i in range ( arg ): new = nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( self , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __sub__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Difference of the diagrams when arg is another Diagram or an expansion upstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . difference_update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . remove ( arg . full_table_name ) except AttributeError : for i in range ( arg ): graph = nx . DiGraph ( self ) . reverse () new = nx . algorithms . boundary . node_boundary ( graph , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( graph , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __mul__ ( self , arg ): \"\"\" Intersection of two diagrams :param arg: another Diagram :return: a new Diagram comprising nodes that are present in both operands. \"\"\" self = Diagram ( self ) # copy self . nodes_to_show . intersection_update ( arg . nodes_to_show ) return self def _make_graph ( self ): \"\"\" Make the self.graph - a graph object ready for drawing \"\"\" # mark \"distinguished\" tables, i.e. those that introduce new primary key # attributes for name in self . nodes_to_show : foreign_attributes = set ( attr for p in self . in_edges ( name , data = True ) for attr in p [ 2 ][ \"attr_map\" ] if p [ 2 ][ \"primary\" ] ) self . nodes [ name ][ \"distinguished\" ] = ( \"primary_key\" in self . nodes [ name ] and foreign_attributes < self . nodes [ name ][ \"primary_key\" ] ) # include aliased nodes that are sandwiched between two displayed nodes gaps = set ( nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) ) . intersection ( nx . algorithms . boundary . node_boundary ( nx . DiGraph ( self ) . reverse (), self . nodes_to_show ) ) nodes = self . nodes_to_show . union ( a for a in gaps if a . isdigit ) # construct subgraph and rename nodes to class names graph = nx . DiGraph ( nx . DiGraph ( self ) . subgraph ( nodes )) nx . set_node_attributes ( graph , name = \"node_type\" , values = { n : _get_tier ( n ) for n in graph } ) # relabel nodes to class names mapping = { node : lookup_class_name ( node , self . context ) or node for node in graph . nodes () } new_names = [ mapping . values ()] if len ( new_names ) > len ( set ( new_names )): raise DataJointError ( \"Some classes have identical names. The Diagram cannot be plotted.\" ) nx . relabel_nodes ( graph , mapping , copy = False ) return graph def make_dot ( self ): graph = self . _make_graph () graph . nodes () scale = 1.2 # scaling factor for fonts and boxes label_props = { # http://matplotlib.org/examples/color/named_colors.html None : dict ( shape = \"circle\" , color = \"#FFFF0040\" , fontcolor = \"yellow\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), _AliasNode : dict ( shape = \"circle\" , color = \"#FF880080\" , fontcolor = \"#FF880080\" , fontsize = round ( scale * 0 ), size = 0.05 * scale , fixed = True , ), Manual : dict ( shape = \"box\" , color = \"#00FF0030\" , fontcolor = \"darkgreen\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Lookup : dict ( shape = \"plaintext\" , color = \"#00000020\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), Computed : dict ( shape = \"ellipse\" , color = \"#FF000020\" , fontcolor = \"#7F0000A0\" , fontsize = round ( scale * 10 ), size = 0.3 * scale , fixed = True , ), Imported : dict ( shape = \"ellipse\" , color = \"#00007F40\" , fontcolor = \"#00007FA0\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Part : dict ( shape = \"plaintext\" , color = \"#0000000\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.1 * scale , fixed = False , ), } node_props = { node : label_props [ d [ \"node_type\" ]] for node , d in dict ( graph . nodes ( data = True )) . items () } dot = nx . drawing . nx_pydot . to_pydot ( graph ) for node in dot . get_nodes (): node . set_shape ( \"circle\" ) name = node . get_name () . strip ( '\"' ) props = node_props [ name ] node . set_fontsize ( props [ \"fontsize\" ]) node . set_fontcolor ( props [ \"fontcolor\" ]) node . set_shape ( props [ \"shape\" ]) node . set_fontname ( \"arial\" ) node . set_fixedsize ( \"shape\" if props [ \"fixed\" ] else False ) node . set_width ( props [ \"size\" ]) node . set_height ( props [ \"size\" ]) if name . split ( \".\" )[ 0 ] in self . context : cls = eval ( name , self . context ) assert issubclass ( cls , Table ) description = ( cls () . describe ( context = self . context , printout = False ) . split ( \" \\n \" ) ) description = ( \"-\" * 30 if q . startswith ( \"---\" ) else q . replace ( \"->\" , \"→\" ) if \"->\" in q else q . split ( \":\" )[ 0 ] for q in description if not q . startswith ( \"#\" ) ) node . set_tooltip ( \" \" . join ( description )) node . set_label ( \"<\" + name + \">\" if node . get ( \"distinguished\" ) == \"True\" else name ) node . set_color ( props [ \"color\" ]) node . set_style ( \"filled\" ) for edge in dot . get_edges (): # see https://graphviz.org/doc/info/attrs.html src = edge . get_source () . strip ( '\"' ) dest = edge . get_destination () . strip ( '\"' ) props = graph . get_edge_data ( src , dest ) edge . set_color ( \"#00000040\" ) edge . set_style ( \"solid\" if props [ \"primary\" ] else \"dashed\" ) master_part = graph . nodes [ dest ][ \"node_type\" ] is Part and dest . startswith ( src + \".\" ) edge . set_weight ( 3 if master_part else 1 ) edge . set_arrowhead ( \"none\" ) edge . set_penwidth ( 0.75 if props [ \"multi\" ] else 2 ) return dot def make_svg ( self ): from IPython.display import SVG return SVG ( self . make_dot () . create_svg ()) def make_png ( self ): return io . BytesIO ( self . make_dot () . create_png ()) def make_image ( self ): if plot_active : return plt . imread ( self . make_png ()) else : raise DataJointError ( \"pyplot was not imported\" ) def _repr_svg_ ( self ): return self . make_svg () . _repr_svg_ () def draw ( self ): if plot_active : plt . imshow ( self . make_image ()) plt . gca () . axis ( \"off\" ) plt . show () else : raise DataJointError ( \"pyplot was not imported\" ) def save ( self , filename , format = None ): if format is None : if filename . lower () . endswith ( \".png\" ): format = \"png\" elif filename . lower () . endswith ( \".svg\" ): format = \"svg\" if format . lower () == \"png\" : with open ( filename , \"wb\" ) as f : f . write ( self . make_png () . getbuffer () . tobytes ()) elif format . lower () == \"svg\" : with open ( filename , \"w\" ) as f : f . write ( self . make_svg () . data ) else : raise DataJointError ( \"Unsupported file format\" ) @staticmethod def _layout ( graph , ** kwargs ): return pydot_layout ( graph , prog = \"dot\" , ** kwargs ) from_sequence ( sequence ) classmethod \u00b6 The join Diagram for all objects in sequence Parameters: Name Type Description Default sequence a sequence (e.g. list, tuple) required Returns: Type Description Diagram(arg1) + ... + Diagram(argn) Source code in datajoint/diagram.py 146 147 148 149 150 151 152 153 154 @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence )) add_parts () \u00b6 Adds to the diagram the part tables of tables already included in the diagram Returns: Type Description Source code in datajoint/diagram.py 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self topological_sort () \u00b6 Returns: Type Description list of nodes in topological order Source code in datajoint/diagram.py 183 184 185 186 187 188 189 190 191 def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) ) MatCell \u00b6 Bases: np . ndarray a numpy ndarray representing a Matlab cell array Source code in datajoint/blob.py 73 74 75 76 class MatCell ( np . ndarray ): \"\"\"a numpy ndarray representing a Matlab cell array\"\"\" pass MatStruct \u00b6 Bases: np . recarray numpy.recarray representing a Matlab struct array Source code in datajoint/blob.py 79 80 81 82 class MatStruct ( np . recarray ): \"\"\"numpy.recarray representing a Matlab struct array\"\"\" pass conn ( host = None , user = None , password = None , * , init_fun = None , reset = False , use_tls = None ) \u00b6 Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. Parameters: Name Type Description Default host hostname None user mysql user None password mysql password None init_fun initialization function None reset whether the connection should be reset or not False use_tls TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). None Source code in datajoint/connection.py 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 def conn ( host = None , user = None , password = None , * , init_fun = None , reset = False , use_tls = None ): \"\"\" Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. :param host: hostname :param user: mysql user :param password: mysql password :param init_fun: initialization function :param reset: whether the connection should be reset or not :param use_tls: TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). \"\"\" if not hasattr ( conn , \"connection\" ) or reset : host = host if host is not None else config [ \"database.host\" ] user = user if user is not None else config [ \"database.user\" ] password = password if password is not None else config [ \"database.password\" ] if user is None : # pragma: no cover user = input ( \"Please enter DataJoint username: \" ) if password is None : # pragma: no cover password = getpass ( prompt = \"Please enter DataJoint password: \" ) init_fun = ( init_fun if init_fun is not None else config [ \"connection.init_function\" ] ) use_tls = use_tls if use_tls is not None else config [ \"database.use_tls\" ] conn . connection = Connection ( host , user , password , None , init_fun , use_tls ) return conn . connection Manual \u00b6 Bases: UserTable Inherit from this class if the table's values are entered manually. Source code in datajoint/user_tables.py 133 134 135 136 137 138 139 class Manual ( UserTable ): \"\"\" Inherit from this class if the table's values are entered manually. \"\"\" _prefix = r \"\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\" Lookup \u00b6 Bases: UserTable Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. Source code in datajoint/user_tables.py 142 143 144 145 146 147 148 149 150 151 152 class Lookup ( UserTable ): \"\"\" Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. \"\"\" _prefix = \"#\" tier_regexp = ( r \"(?P\" + _prefix + _base_regexp . replace ( \"TIER\" , \"lookup\" ) + \")\" ) Imported \u00b6 Bases: UserTable , AutoPopulate Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 155 156 157 158 159 160 161 162 class Imported ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"_\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\" Connection \u00b6 A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. Parameters: Name Type Description Default host host name, may include port number as hostname:port, in which case it overrides the value in port required user user name required password password required port port number None init_fun connection initialization function (SQL) None use_tls TLS encryption option None Source code in datajoint/connection.py 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 class Connection : \"\"\" A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. :param host: host name, may include port number as hostname:port, in which case it overrides the value in port :param user: user name :param password: password :param port: port number :param init_fun: connection initialization function (SQL) :param use_tls: TLS encryption option \"\"\" def __init__ ( self , host , user , password , port = None , init_fun = None , use_tls = None ): host_input , host = ( host , get_host_hook ( host )) if \":\" in host : # the port in the hostname overrides the port argument host , port = host . split ( \":\" ) port = int ( port ) elif port is None : port = config [ \"database.port\" ] self . conn_info = dict ( host = host , port = port , user = user , passwd = password ) if use_tls is not False : self . conn_info [ \"ssl\" ] = ( use_tls if isinstance ( use_tls , dict ) else { \"ssl\" : {}} ) self . conn_info [ \"ssl_input\" ] = use_tls self . conn_info [ \"host_input\" ] = host_input self . init_fun = init_fun logger . info ( \"Connecting {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . _conn = None self . _query_cache = None connect_host_hook ( self ) if self . is_connected : logger . info ( \"Connected {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . connection_id = self . query ( \"SELECT connection_id()\" ) . fetchone ()[ 0 ] else : raise errors . LostConnectionError ( \"Connection failed.\" ) self . _in_transaction = False self . schemas = dict () self . dependencies = Dependencies ( self ) def __eq__ ( self , other ): return self . conn_info == other . conn_info def __repr__ ( self ): connected = \"connected\" if self . is_connected else \"disconnected\" return \"DataJoint connection ( {connected} ) {user} @ {host} : {port} \" . format ( connected = connected , ** self . conn_info ) def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True ) def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink () def close ( self ): self . _conn . close () def register ( self , schema ): self . schemas [ schema . database ] = schema self . dependencies . clear () def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False ) @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True @staticmethod def _execute_query ( cursor , query , args , suppress_warnings ): try : with warnings . catch_warnings (): if suppress_warnings : # suppress all warnings arising from underlying SQL library warnings . simplefilter ( \"ignore\" ) cursor . execute ( query , args ) except client . err . Error as err : raise translate_query_error ( err , query ) def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ] # ---------- transaction processing @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" ) def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" ) def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" ) # -------- context manager for transactions @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction () connect () \u00b6 Connect to the database server. Source code in datajoint/connection.py 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True ) set_query_cache ( query_cache = None ) \u00b6 When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. Parameters: Name Type Description Default query_cache a string to initialize the hash for query results None Source code in datajoint/connection.py 246 247 248 249 250 251 252 253 254 255 def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache purge_query_cache () \u00b6 Purges all query cache. Source code in datajoint/connection.py 257 258 259 260 261 262 263 264 265 def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink () ping () \u00b6 Ping the connection or raises an exception if the connection is closed. Source code in datajoint/connection.py 274 275 276 def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False ) is_connected () property \u00b6 Return true if the object is connected to the database server. Source code in datajoint/connection.py 278 279 280 281 282 283 284 285 @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True query ( query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ) \u00b6 Execute the specified query and return the tuple generator (cursor). Parameters: Name Type Description Default query SQL query required args additional arguments for the client.cursor () as_dict If as_dict is set to True, the returned cursor objects returns query results as dictionary. False suppress_warnings If True, suppress all warnings arising from underlying query library True reconnect when None, get from config, when True, attempt to reconnect if disconnected None Source code in datajoint/connection.py 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor get_user () \u00b6 Returns: Type Description the user name and host name provided by the client to the server. Source code in datajoint/connection.py 362 363 364 365 366 def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ] in_transaction () property \u00b6 Returns: Type Description True if there is an open transaction. Source code in datajoint/connection.py 369 370 371 372 373 374 375 @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction start_transaction () \u00b6 Starts a transaction error. Source code in datajoint/connection.py 377 378 379 380 381 382 383 384 385 def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" ) cancel_transaction () \u00b6 Cancels the current transaction and rolls back all changes made during the transaction. Source code in datajoint/connection.py 387 388 389 390 391 392 393 def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" ) commit_transaction () \u00b6 Commit all changes made during the transaction and close it. Source code in datajoint/connection.py 395 396 397 398 399 400 401 402 def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" ) transaction () property \u00b6 Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: import datajoint as dj with dj.conn().transaction as conn: # transaction is open here Source code in datajoint/connection.py 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction () Computed \u00b6 Bases: UserTable , AutoPopulate Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 165 166 167 168 169 170 171 172 class Computed ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"__\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\" Part \u00b6 Bases: UserTable Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. Source code in datajoint/user_tables.py 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 class Part ( UserTable ): \"\"\" Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. \"\"\" _connection = None _master = None tier_regexp = ( r \"(?P\" + \"|\" . join ([ c . tier_regexp for c in ( Manual , Lookup , Imported , Computed )]) + r \"){1,1}\" + \"__\" + r \"(?P\" + _base_regexp + \")\" ) @ClassProperty def connection ( cls ): return cls . _connection @ClassProperty def full_table_name ( cls ): return ( None if cls . database is None or cls . table_name is None else r \"` {0:s} `.` {1:s} `\" . format ( cls . database , cls . table_name ) ) @ClassProperty def master ( cls ): return cls . _master @ClassProperty def table_name ( cls ): return ( None if cls . master is None else cls . master . table_name + \"__\" + from_camel_case ( cls . __name__ ) ) def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" ) def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" ) delete ( force = False ) \u00b6 unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 220 221 222 223 224 225 226 227 228 229 def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" ) drop ( force = False ) \u00b6 unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 231 232 233 234 235 236 237 238 239 240 def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" ) VirtualModule \u00b6 Bases: types . ModuleType A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. Source code in datajoint/schemas.py 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 class VirtualModule ( types . ModuleType ): \"\"\" A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. \"\"\" def __init__ ( self , module_name , schema_name , * , create_schema = False , create_tables = False , connection = None , add_objects = None , ): \"\"\" Creates a python module with the given name from the name of a schema on the server and automatically adds classes to it corresponding to the tables in the schema. :param module_name: displayed module name :param schema_name: name of the database in mysql :param create_schema: if True, create the schema on the database server :param create_tables: if True, module.schema can be used as the decorator for declaring new :param connection: a dj.Connection object to pass into the schema :param add_objects: additional objects to add to the module :return: the python module containing classes from the schema object and the table classes \"\"\" super ( VirtualModule , self ) . __init__ ( name = module_name ) _schema = Schema ( schema_name , create_schema = create_schema , create_tables = create_tables , connection = connection , ) if add_objects : self . __dict__ . update ( add_objects ) self . __dict__ [ \"schema\" ] = _schema _schema . spawn_missing_classes ( context = self . __dict__ ) list_schemas ( connection = None ) \u00b6 Parameters: Name Type Description Default connection a dj.Connection object None Returns: Type Description list of all accessible schemas on the server Source code in datajoint/schemas.py 534 535 536 537 538 539 540 541 542 543 544 545 546 547 def list_schemas ( connection = None ): \"\"\" :param connection: a dj.Connection object :return: list of all accessible schemas on the server \"\"\" return [ r [ 0 ] for r in ( connection or conn ()) . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" 'WHERE schema_name <> \"information_schema\"' ) ] U \u00b6 dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the stimulus set: dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute s containing the total number of elements in query expression expr : dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number n of distinct values of attribute attr in query expressio expr . dj.U().aggr(expr, n='count(distinct attr)') dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute s containing the sum of values of attribute attr over entire result set of expression expr : dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes attr1 , attr2 and the number of their occurrences in the result set of query expression expr . dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression expr has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as expr but attr1 and attr2 are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if attr is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename attr in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. Source code in datajoint/expression.py 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 class U : \"\"\" dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the `stimulus` set: >>> dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute `s` containing the total number of elements in query expression `expr`: >>> dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number `n` of distinct values of attribute `attr` in query expressio `expr`. >>> dj.U().aggr(expr, n='count(distinct attr)') >>> dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute `s` containing the sum of values of attribute `attr` over entire result set of expression `expr`: >>> dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes `attr1`, `attr2` and the number of their occurrences in the result set of query expression `expr`. >>> dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression `expr` has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as `expr` but `attr1` and `attr2` are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if `attr` is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename `attr` in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. \"\"\" def __init__ ( self , * primary_key ): self . _primary_key = primary_key @property def primary_key ( self ): return self . _primary_key def __and__ ( self , other ): if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be restricted with a QueryExpression.\" ) result = copy . copy ( other ) result . _distinct = True result . _heading = result . heading . set_primary_key ( self . primary_key ) result = result . proj () return result def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result def __mul__ ( self , other ): \"\"\"shorthand for join\"\"\" return self . join ( other ) def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes ) aggregate = aggr # alias for aggr join ( other , left = False ) \u00b6 Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. Parameters: Name Type Description Default other the other query expression to join with. required left ignored. dj.U always acts as if left=False False Returns: Type Description a copy of the other query expression with the primary key extended. Source code in datajoint/expression.py 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result aggr ( group , ** named_attributes ) \u00b6 Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of group . Parameters: Name Type Description Default group The query expression to be aggregated. required named_attributes computations of the form new_attribute=\"sql expression on attributes of group\" required Returns: Type Description The derived query expression Source code in datajoint/expression.py 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes ) FreeTable \u00b6 Bases: Table A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. Parameters: Name Type Description Default conn a dj.Connection object required full_table_name in format database . table_name required Source code in datajoint/table.py 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 class FreeTable ( Table ): \"\"\" A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. :param conn: a dj.Connection object :param full_table_name: in format `database`.`table_name` \"\"\" def __init__ ( self , conn , full_table_name ): self . database , self . _table_name = ( s . strip ( \"`\" ) for s in full_table_name . split ( \".\" ) ) self . _connection = conn self . _support = [ full_table_name ] self . _heading = Heading ( table_info = dict ( conn = conn , database = self . database , table_name = self . table_name , context = None , ) ) def __repr__ ( self ): return ( \"FreeTable(` %s `.` %s `) \\n \" % ( self . database , self . _table_name ) + super () . __repr__ () )", "title": "__init__.py"}, {"location": "api/datajoint/__init__/#datajoint.AttributeAdapter", "text": "Base class for adapter objects for user-defined attribute types. Source code in datajoint/attribute_adapter.py 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 class AttributeAdapter : \"\"\" Base class for adapter objects for user-defined attribute types. \"\"\" @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "AttributeAdapter"}, {"location": "api/datajoint/__init__/#datajoint.attribute_adapter.AttributeAdapter.attribute_type", "text": "Returns: Type Description a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" Source code in datajoint/attribute_adapter.py 11 12 13 14 15 16 @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "attribute_type()"}, {"location": "api/datajoint/__init__/#datajoint.attribute_adapter.AttributeAdapter.get", "text": "convert value retrieved from the the attribute in a table into the adapted type Parameters: Name Type Description Default value value from the database required Returns: Type Description object of the adapted type Source code in datajoint/attribute_adapter.py 18 19 20 21 22 23 24 25 26 def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "get()"}, {"location": "api/datajoint/__init__/#datajoint.attribute_adapter.AttributeAdapter.put", "text": "convert an object of the adapted type into a value that DataJoint can store in a table attribute Parameters: Name Type Description Default obj an object of the adapted type required Returns: Type Description value to store in the database Source code in datajoint/attribute_adapter.py 28 29 30 31 32 33 34 35 def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "put()"}, {"location": "api/datajoint/__init__/#datajoint.key_hash", "text": "32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. Source code in datajoint/hash.py 7 8 9 10 11 12 13 14 15 16 def key_hash ( mapping ): \"\"\" 32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. \"\"\" hashed = hashlib . md5 () for k , v in sorted ( mapping . items ()): hashed . update ( str ( v ) . encode ()) return hashed . hexdigest ()", "title": "key_hash()"}, {"location": "api/datajoint/__init__/#datajoint.migrate_dj011_external_blob_storage_to_dj012", "text": "Utility function to migrate external blob data from 0.11 to 0.12. Parameters: Name Type Description Default migration_schema string of target schema to be migrated required store string of target dj.config['store'] to be migrated required Source code in datajoint/migrate.py 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 def migrate_dj011_external_blob_storage_to_dj012 ( migration_schema , store ): \"\"\" Utility function to migrate external blob data from 0.11 to 0.12. :param migration_schema: string of target schema to be migrated :param store: string of target dj.config['store'] to be migrated \"\"\" if not isinstance ( migration_schema , str ): raise ValueError ( \"Expected type {} for migration_schema, not {} .\" . format ( str , type ( migration_schema ) ) ) do_migration = False do_migration = ( user_choice ( \"\"\" Warning: Ensure the following are completed before proceeding. - Appropriate backups have been taken, - Any existing DJ 0.11.X connections are suspended, and - External config has been updated to new dj.config['stores'] structure. Proceed? \"\"\" , default = \"no\" , ) == \"yes\" ) if do_migration : _migrate_dj011_blob ( dj . Schema ( migration_schema ), store ) print ( \"Migration completed for schema: {} , store: {} .\" . format ( migration_schema , store ) ) return print ( \"No migration performed.\" )", "title": "migrate_dj011_external_blob_storage_to_dj012()"}, {"location": "api/datajoint/__init__/#datajoint.DataJointError", "text": "Bases: Exception Base class for errors specific to DataJoint internal operation. Source code in datajoint/errors.py 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 class DataJointError ( Exception ): \"\"\" Base class for errors specific to DataJoint internal operation. \"\"\" def __init__ ( self , * args ): from .plugin import connection_plugins , type_plugins self . __cause__ = ( PluginWarning ( \"Unverified DataJoint plugin detected.\" ) if any ( [ any ([ not plugins [ k ][ \"verified\" ] for k in plugins ]) for plugins in [ connection_plugins , type_plugins ] if plugins ] ) else None ) def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args ))", "title": "DataJointError"}, {"location": "api/datajoint/__init__/#datajoint.errors.DataJointError.suggest", "text": "regenerate the exception with additional arguments Parameters: Name Type Description Default args addition arguments required Returns: Type Description a new exception of the same type with the additional arguments Source code in datajoint/errors.py 34 35 36 37 38 39 40 41 def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args ))", "title": "suggest()"}, {"location": "api/datajoint/__init__/#datajoint.key", "text": "object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key Source code in datajoint/fetch.py 18 19 20 21 22 23 24 class key : \"\"\" object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key \"\"\" pass", "title": "key"}, {"location": "api/datajoint/__init__/#datajoint.AndList", "text": "Bases: list A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 Source code in datajoint/condition.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 class AndList ( list ): \"\"\" A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 \"\"\" def append ( self , restriction ): if isinstance ( restriction , AndList ): # extend to reduce nesting self . extend ( restriction ) else : super () . append ( restriction )", "title": "AndList"}, {"location": "api/datajoint/__init__/#datajoint.kill", "text": "view and kill database connections. Parameters: Name Type Description Default restriction restriction to be applied to processlist None connection a datajoint.Connection object. Default calls datajoint.conn() None order_by order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes None Source code in datajoint/admin.py 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 def kill ( restriction = None , connection = None , order_by = None ): # pragma: no cover \"\"\" view and kill database connections. :param restriction: restriction to be applied to processlist :param connection: a datajoint.Connection object. Default calls datajoint.conn() :param order_by: order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes \"\"\" if connection is None : connection = conn () if order_by is not None and not isinstance ( order_by , str ): order_by = \",\" . join ( order_by ) query = ( \"SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()\" + ( \"\" if restriction is None else \" AND ( %s )\" % restriction ) + ( \" ORDER BY %s \" % ( order_by or \"id\" )) ) while True : print ( \" ID USER HOST STATE TIME INFO\" ) print ( \"+--+ +----------+ +-----------+ +-----------+ +-----+\" ) cur = ( { k . lower (): v for k , v in elem . items ()} for elem in connection . query ( query , as_dict = True ) ) for process in cur : try : print ( \" {id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d} {info} \" . format ( ** process ) ) except TypeError : print ( process ) response = input ( 'process to kill or \"q\" to quit > ' ) if response == \"q\" : break if response : try : pid = int ( response ) except ValueError : pass # ignore non-numeric input else : try : connection . query ( \"kill %d \" % pid ) except pymysql . err . InternalError : print ( \"Process not found\" )", "title": "kill()"}, {"location": "api/datajoint/__init__/#datajoint.Schema", "text": "A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace context in which other UserTable classes are defined. Source code in datajoint/schemas.py 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 class Schema : \"\"\" A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace `context` in which other UserTable classes are defined. \"\"\" def __init__ ( self , schema_name = None , context = None , * , connection = None , create_schema = True , create_tables = True , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. If the schema_name is omitted, then schema.activate(..) must be called later to associate with the database. :param schema_name: the database schema to associate. :param context: dictionary for looking up foreign key references, leave None to use local context. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: When False, do not create the schema and raise an error if missing. :param create_tables: When False, do not create tables and raise errors when accessing missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" self . _log = None self . connection = connection self . database = None self . context = context self . create_schema = create_schema self . create_tables = create_tables self . _jobs = None self . external = ExternalMapping ( self ) self . add_objects = add_objects self . declare_list = [] if schema_name : self . activate ( schema_name ) def is_activated ( self ): return self . database is not None def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context ) def _assert_exists ( self , message = None ): if not self . exists : raise DataJointError ( message or \"Schema ` {db} ` has not been created.\" . format ( db = self . database ) ) def __call__ ( self , cls , * , context = None ): \"\"\" Binds the supplied class to a schema. This is intended to be used as a decorator. :param cls: class to decorate. :param context: supplied when called from spawn_missing_classes \"\"\" context = context or self . context or inspect . currentframe () . f_back . f_locals if issubclass ( cls , Part ): raise DataJointError ( \"The schema decorator should not be applied to Part tables.\" ) if self . is_activated (): self . _decorate_master ( cls , context ) else : self . declare_list . append (( cls , context )) return cls def _decorate_master ( self , cls , context ): \"\"\" :param cls: the master class to process :param context: the class' declaration context \"\"\" self . _decorate_table ( cls , context = dict ( context , self = cls , ** { cls . __name__ : cls }) ) # Process part tables for part in ordered_dir ( cls ): if part [ 0 ] . isupper (): part = getattr ( cls , part ) if inspect . isclass ( part ) and issubclass ( part , Part ): part . _master = cls # allow addressing master by name or keyword 'master' self . _decorate_table ( part , context = dict ( context , master = cls , self = part , ** { cls . __name__ : cls } ), ) def _decorate_table ( self , table_class , context , assert_declared = False ): \"\"\" assign schema properties to the table class and declare the table \"\"\" table_class . database = self . database table_class . _connection = self . connection table_class . _heading = Heading ( table_info = dict ( conn = self . connection , database = self . database , table_name = table_class . table_name , context = context , ) ) table_class . _support = [ table_class . full_table_name ] table_class . declaration_context = context # instantiate the class, declare the table if not already instance = table_class () is_declared = instance . is_declared if not is_declared and not assert_declared and self . create_tables : instance . declare ( context ) self . connection . dependencies . clear () is_declared = is_declared or instance . is_declared # add table definition to the doc string if isinstance ( table_class . definition , str ): table_class . __doc__ = ( ( table_class . __doc__ or \"\" ) + \" \\n Table definition: \\n\\n \" + table_class . definition ) # fill values in Lookup tables from their contents property if ( isinstance ( instance , Lookup ) and hasattr ( instance , \"contents\" ) and is_declared ): contents = list ( instance . contents ) if len ( contents ) > len ( instance ): if instance . heading . has_autoincrement : warnings . warn ( ( \"Contents has changed but cannot be inserted because \" \" {table} has autoincrement.\" ) . format ( table = instance . __class__ . __name__ ) ) else : instance . insert ( contents , skip_duplicates = True ) @property def log ( self ): self . _assert_exists () if self . _log is None : self . _log = Log ( self . connection , self . database ) return self . _log def __repr__ ( self ): return \"Schema ` {name} ` \\n \" . format ( name = self . database ) @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] ) def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class ) def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) ) @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount ) @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs @property def code ( self ): self . _assert_exists () return self . save () def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code ) def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ]", "title": "Schema"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.activate", "text": "Associate database schema schema_name . If the schema does not exist, attempt to create it on the server. Parameters: Name Type Description Default schema_name the database schema to associate. schema_name=None is used to assert that the schema has already been activated. None connection Connection object. Defaults to datajoint.conn(). None create_schema If False, do not create the schema and raise an error if missing. None create_tables If False, do not create tables and raise errors when attempting to access missing tables. None add_objects a mapping with additional objects to make available to the context in which table classes are declared. None Source code in datajoint/schemas.py 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context )", "title": "activate()"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.size_on_disk", "text": "Returns: Type Description size of the entire schema in bytes Source code in datajoint/schemas.py 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] )", "title": "size_on_disk()"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.spawn_missing_classes", "text": "Creates the appropriate python user table classes from tables in the schema and places them in the context. Parameters: Name Type Description Default context alternative context to place the missing classes into, e.g. locals() None Source code in datajoint/schemas.py 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class )", "title": "spawn_missing_classes()"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.drop", "text": "Drop the associated schema if it exists Source code in datajoint/schemas.py 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) )", "title": "drop()"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.exists", "text": "Returns: Type Description true if the associated schema exists on the server Source code in datajoint/schemas.py 377 378 379 380 381 382 383 384 385 386 387 388 389 390 @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount )", "title": "exists()"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.jobs", "text": "schema.jobs provides a view of the job reservation table for the schema Returns: Type Description jobs table Source code in datajoint/schemas.py 392 393 394 395 396 397 398 399 400 401 402 @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs", "title": "jobs()"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.save", "text": "Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. Returns: Type Description a string containing the body of a complete Python module defining this schema. Source code in datajoint/schemas.py 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code )", "title": "save()"}, {"location": "api/datajoint/__init__/#datajoint.schemas.Schema.list_tables", "text": "Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job Returns: Type Description A list of table names from the database schema. Source code in datajoint/schemas.py 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ]", "title": "list_tables()"}, {"location": "api/datajoint/__init__/#datajoint.Not", "text": "invert restriction Source code in datajoint/condition.py 43 44 45 46 47 class Not : \"\"\"invert restriction\"\"\" def __init__ ( self , restriction ): self . restriction = restriction", "title": "Not"}, {"location": "api/datajoint/__init__/#datajoint.Table", "text": "Bases: QueryExpression Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. Source code in datajoint/table.py 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 class Table ( QueryExpression ): \"\"\" Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. \"\"\" _table_name = None # must be defined in subclass _log_ = None # placeholder for the Log table object # These properties must be set by the schema decorator (schemas.py) at class level # or by FreeTable at instance level database = None declaration_context = None @property def table_name ( self ): return self . _table_name @property def definition ( self ): raise NotImplementedError ( \"Subclasses of Table must implement the `definition` property\" ) def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name ) def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name ) def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql ) def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ] def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ] def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 ) @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name ) @property def _log ( self ): if self . _log_ is None : self . _log_ = Log ( self . connection , database = self . database , skip_logging = self . table_name . startswith ( \"~\" ), ) return self . _log_ @property def external ( self ): return self . connection . schemas [ self . database ] . external def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None )) def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs ) def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" ) def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name ) def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" ) @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ] def show_definition ( self ): raise AttributeError ( \"show_definition is deprecated. Use the describe method instead.\" ) def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition def _update ( self , attrname , value = None ): \"\"\" This is a deprecated function to be removed in datajoint 0.14. Use ``.update1`` instead. Updates a field in one existing tuple. self must be restricted to exactly one entry. In DataJoint the principal way of updating data is to delete and re-insert the entire record and updates are reserved for corrective actions. This is because referential integrity is observed on the level of entire records rather than individual attributes. Safety constraints: 1. self must be restricted to exactly one tuple 2. the update attribute must not be in primary key Example: >>> (v2p.Mice() & key)._update('mouse_dob', '2011-01-01') >>> (v2p.Mice() & key)._update( 'lens') # set the value to NULL \"\"\" logger . warning ( \"`_update` is a deprecated function to be removed in datajoint 0.14. \" \"Use `.update1` instead.\" ) if len ( self ) != 1 : raise DataJointError ( \"Update is only allowed on one tuple at a time\" ) if attrname not in self . heading : raise DataJointError ( \"Invalid attribute name\" ) if attrname in self . heading . primary_key : raise DataJointError ( \"Cannot update a key value.\" ) attr = self . heading [ attrname ] if attr . is_blob : value = blob . pack ( value ) placeholder = \" %s \" elif attr . numeric : if value is None or np . isnan ( float ( value )): # nans are turned into NULLs placeholder = \"NULL\" value = None else : placeholder = \" %s \" value = str ( int ( value ) if isinstance ( value , bool ) else value ) else : placeholder = \" %s \" if value is not None else \"NULL\" command = \"UPDATE {full_table_name} SET ` {attrname} `= {placeholder} {where_clause} \" . format ( full_table_name = self . from_clause (), attrname = attrname , placeholder = placeholder , where_clause = self . where_clause (), ) self . connection . query ( command , args = ( value ,) if value is not None else ()) # --- private helper functions ---- def __make_placeholder ( self , name , value , ignore_extra_fields = False ): \"\"\" For a given attribute `name` with `value`, return its processed value or value placeholder as a string to be included in the query and the value, if any, to be submitted for processing by mysql API. :param name: name of attribute to be inserted :param value: value of attribute to be inserted \"\"\" if ignore_extra_fields and name not in self . heading : return None attr = self . heading [ name ] if attr . adapter : value = attr . adapter . put ( value ) if value is None or ( attr . numeric and ( value == \"\" or np . isnan ( float ( value )))): # set default value placeholder , value = \"DEFAULT\" , None else : # not NULL placeholder = \" %s \" if attr . uuid : if not isinstance ( value , uuid . UUID ): try : value = uuid . UUID ( value ) except ( AttributeError , ValueError ): raise DataJointError ( \"badly formed UUID value {v} for attribute ` {n} `\" . format ( v = value , n = name ) ) value = value . bytes elif attr . is_blob : value = blob . pack ( value ) value = ( self . external [ attr . store ] . put ( value ) . bytes if attr . is_external else value ) elif attr . is_attachment : attachment_path = Path ( value ) if attr . is_external : # value is hash of contents value = ( self . external [ attr . store ] . upload_attachment ( attachment_path ) . bytes ) else : # value is filename + contents value = ( str . encode ( attachment_path . name ) + b \" \\0 \" + attachment_path . read_bytes () ) elif attr . is_filepath : value = self . external [ attr . store ] . upload_filepath ( value ) . bytes elif attr . numeric : value = str ( int ( value ) if isinstance ( value , bool ) else value ) return name , placeholder , value def __make_row_to_insert ( self , row , field_list , ignore_extra_fields ): \"\"\" Helper function for insert and update :param row: A tuple to insert :return: a dict with fields 'names', 'placeholders', 'values' \"\"\" def check_fields ( fields ): \"\"\" Validates that all items in `fields` are valid attributes in the heading :param fields: field names of a tuple \"\"\" if not field_list : if not ignore_extra_fields : for field in fields : if field not in self . heading : raise KeyError ( \"` {0:s} ` is not in the table heading\" . format ( field ) ) elif set ( field_list ) != set ( fields ) . intersection ( self . heading . names ): raise DataJointError ( \"Attempt to insert rows with different fields.\" ) if isinstance ( row , np . void ): # np.array check_fields ( row . dtype . fields ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row . dtype . fields ] elif isinstance ( row , collections . abc . Mapping ): # dict-based check_fields ( row ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row ] else : # positional try : if len ( row ) != len ( self . heading ): raise DataJointError ( \"Invalid insert argument. Incorrect number of attributes: \" \" {given} given; {expected} expected\" . format ( given = len ( row ), expected = len ( self . heading ) ) ) except TypeError : raise DataJointError ( \"Datatype %s cannot be inserted\" % type ( row )) else : attributes = [ self . __make_placeholder ( name , value , ignore_extra_fields ) for name , value in zip ( self . heading , row ) ] if ignore_extra_fields : attributes = [ a for a in attributes if a is not None ] assert len ( attributes ), \"Empty tuple\" row_to_insert = dict ( zip (( \"names\" , \"placeholders\" , \"values\" ), zip ( * attributes ))) if not field_list : # first row sets the composition of the field list field_list . extend ( row_to_insert [ \"names\" ]) else : # reorder attributes in row_to_insert to match field_list order = list ( row_to_insert [ \"names\" ] . index ( field ) for field in field_list ) row_to_insert [ \"names\" ] = list ( row_to_insert [ \"names\" ][ i ] for i in order ) row_to_insert [ \"placeholders\" ] = list ( row_to_insert [ \"placeholders\" ][ i ] for i in order ) row_to_insert [ \"values\" ] = list ( row_to_insert [ \"values\" ][ i ] for i in order ) return row_to_insert", "title": "Table"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.declare", "text": "Declare the table in the schema based on self.definition. Parameters: Name Type Description Default context the context for foreign key resolution. If None, foreign keys are not allowed. None Source code in datajoint/table.py 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name )", "title": "declare()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.alter", "text": "Alter the table definition from self.definition Source code in datajoint/table.py 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name )", "title": "alter()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.from_clause", "text": "Returns: Type Description the FROM clause of SQL SELECT statements. Source code in datajoint/table.py 147 148 149 150 151 def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name", "title": "from_clause()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.get_select_fields", "text": "Returns: Type Description the selected attributes from the SQL SELECT statement. Source code in datajoint/table.py 153 154 155 156 157 158 159 def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql )", "title": "get_select_fields()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.parents", "text": "Parameters: Name Type Description Default primary if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of parents as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes", "title": "parents()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.children", "text": "Parameters: Name Type Description Default primary if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of children as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes", "title": "children()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.descendants", "text": "Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables descendants in topological order. Source code in datajoint/table.py 205 206 207 208 209 210 211 212 213 214 215 def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ]", "title": "descendants()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.ancestors", "text": "Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables ancestors in topological order. Source code in datajoint/table.py 217 218 219 220 221 222 223 224 225 226 227 def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ]", "title": "ancestors()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.parts", "text": "return part tables either as entries in a dict with foreign key informaiton or a list of objects Parameters: Name Type Description Default as_objects if False (default), the output is a dict describing the foreign keys. If True, return table objects. False Source code in datajoint/table.py 229 230 231 232 233 234 235 236 237 238 239 240 def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes", "title": "parts()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.is_declared", "text": "Returns: Type Description True is the table is declared in the schema. Source code in datajoint/table.py 242 243 244 245 246 247 248 249 250 251 252 253 254 @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 )", "title": "is_declared()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.full_table_name", "text": "Returns: Type Description full table name in the schema Source code in datajoint/table.py 256 257 258 259 260 261 @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name )", "title": "full_table_name()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.update1", "text": "update1 updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to insert and delete entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. Parameters: Name Type Description Default row a dict containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default required Source code in datajoint/table.py 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None ))", "title": "update1()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.insert1", "text": "Insert one data record into the table. For kwargs , see insert() . Parameters: Name Type Description Default row a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. required Source code in datajoint/table.py 328 329 330 331 332 333 334 335 def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs )", "title": "insert1()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.insert", "text": "Insert a collection of rows. Parameters: Name Type Description Default rows An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. required replace If True, replaces the existing tuple. False skip_duplicates If True, silently skip duplicate inserts. False ignore_extra_fields If False, fields that are not in the heading raise error. False allow_direct_insert applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) None Source code in datajoint/table.py 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" )", "title": "insert()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.delete_quick", "text": "Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. Source code in datajoint/table.py 448 449 450 451 452 453 454 455 456 457 458 459 460 461 def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count", "title": "delete_quick()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.delete", "text": "Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If True , use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to False if this delete is nested within another transaction. safemode: If True , prohibit nested transactions and prompt to confirm. Default is dj.config['safemode'] . force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. Source code in datajoint/table.py 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count", "title": "delete()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.drop_quick", "text": "Drops the table without cascading to dependent tables and without user prompt. Source code in datajoint/table.py 614 615 616 617 618 619 620 621 622 623 624 625 626 def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name )", "title": "drop_quick()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.drop", "text": "Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. Source code in datajoint/table.py 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" )", "title": "drop()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.size_on_disk", "text": "Returns: Type Description size of data and indices in bytes on the storage device Source code in datajoint/table.py 664 665 666 667 668 669 670 671 672 673 674 675 @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ]", "title": "size_on_disk()"}, {"location": "api/datajoint/__init__/#datajoint.table.Table.describe", "text": "Returns: Type Description the definition string for the query using DataJoint DDL. Source code in datajoint/table.py 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition", "title": "describe()"}, {"location": "api/datajoint/__init__/#datajoint.Diagram", "text": "Bases: nx . DiGraph Entity relationship diagram. Usage: diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed Source code in datajoint/diagram.py 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 class Diagram ( nx . DiGraph ): \"\"\" Entity relationship diagram. Usage: >>> diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. >>> diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed \"\"\" def __init__ ( self , source , context = None ): if isinstance ( source , Diagram ): # copy constructor self . nodes_to_show = set ( source . nodes_to_show ) self . context = source . context super () . __init__ ( source ) return # get the caller's context if context is None : frame = inspect . currentframe () . f_back self . context = dict ( frame . f_globals , ** frame . f_locals ) del frame else : self . context = context # find connection in the source try : connection = source . connection except AttributeError : try : connection = source . schema . connection except AttributeError : raise DataJointError ( \"Could not find database connection in %s \" % repr ( source [ 0 ]) ) # initialize graph from dependencies connection . dependencies . load () super () . __init__ ( connection . dependencies ) # Enumerate nodes from all the items in the list self . nodes_to_show = set () try : self . nodes_to_show . add ( source . full_table_name ) except AttributeError : try : database = source . database except AttributeError : try : database = source . schema . database except AttributeError : raise DataJointError ( \"Cannot plot Diagram for %s \" % repr ( source ) ) for node in self : if node . startswith ( \"` %s `\" % database ): self . nodes_to_show . add ( node ) @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence )) def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) ) def __add__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Union of the diagrams when arg is another Diagram or an expansion downstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . add ( arg . full_table_name ) except AttributeError : for i in range ( arg ): new = nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( self , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __sub__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Difference of the diagrams when arg is another Diagram or an expansion upstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . difference_update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . remove ( arg . full_table_name ) except AttributeError : for i in range ( arg ): graph = nx . DiGraph ( self ) . reverse () new = nx . algorithms . boundary . node_boundary ( graph , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( graph , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __mul__ ( self , arg ): \"\"\" Intersection of two diagrams :param arg: another Diagram :return: a new Diagram comprising nodes that are present in both operands. \"\"\" self = Diagram ( self ) # copy self . nodes_to_show . intersection_update ( arg . nodes_to_show ) return self def _make_graph ( self ): \"\"\" Make the self.graph - a graph object ready for drawing \"\"\" # mark \"distinguished\" tables, i.e. those that introduce new primary key # attributes for name in self . nodes_to_show : foreign_attributes = set ( attr for p in self . in_edges ( name , data = True ) for attr in p [ 2 ][ \"attr_map\" ] if p [ 2 ][ \"primary\" ] ) self . nodes [ name ][ \"distinguished\" ] = ( \"primary_key\" in self . nodes [ name ] and foreign_attributes < self . nodes [ name ][ \"primary_key\" ] ) # include aliased nodes that are sandwiched between two displayed nodes gaps = set ( nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) ) . intersection ( nx . algorithms . boundary . node_boundary ( nx . DiGraph ( self ) . reverse (), self . nodes_to_show ) ) nodes = self . nodes_to_show . union ( a for a in gaps if a . isdigit ) # construct subgraph and rename nodes to class names graph = nx . DiGraph ( nx . DiGraph ( self ) . subgraph ( nodes )) nx . set_node_attributes ( graph , name = \"node_type\" , values = { n : _get_tier ( n ) for n in graph } ) # relabel nodes to class names mapping = { node : lookup_class_name ( node , self . context ) or node for node in graph . nodes () } new_names = [ mapping . values ()] if len ( new_names ) > len ( set ( new_names )): raise DataJointError ( \"Some classes have identical names. The Diagram cannot be plotted.\" ) nx . relabel_nodes ( graph , mapping , copy = False ) return graph def make_dot ( self ): graph = self . _make_graph () graph . nodes () scale = 1.2 # scaling factor for fonts and boxes label_props = { # http://matplotlib.org/examples/color/named_colors.html None : dict ( shape = \"circle\" , color = \"#FFFF0040\" , fontcolor = \"yellow\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), _AliasNode : dict ( shape = \"circle\" , color = \"#FF880080\" , fontcolor = \"#FF880080\" , fontsize = round ( scale * 0 ), size = 0.05 * scale , fixed = True , ), Manual : dict ( shape = \"box\" , color = \"#00FF0030\" , fontcolor = \"darkgreen\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Lookup : dict ( shape = \"plaintext\" , color = \"#00000020\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), Computed : dict ( shape = \"ellipse\" , color = \"#FF000020\" , fontcolor = \"#7F0000A0\" , fontsize = round ( scale * 10 ), size = 0.3 * scale , fixed = True , ), Imported : dict ( shape = \"ellipse\" , color = \"#00007F40\" , fontcolor = \"#00007FA0\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Part : dict ( shape = \"plaintext\" , color = \"#0000000\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.1 * scale , fixed = False , ), } node_props = { node : label_props [ d [ \"node_type\" ]] for node , d in dict ( graph . nodes ( data = True )) . items () } dot = nx . drawing . nx_pydot . to_pydot ( graph ) for node in dot . get_nodes (): node . set_shape ( \"circle\" ) name = node . get_name () . strip ( '\"' ) props = node_props [ name ] node . set_fontsize ( props [ \"fontsize\" ]) node . set_fontcolor ( props [ \"fontcolor\" ]) node . set_shape ( props [ \"shape\" ]) node . set_fontname ( \"arial\" ) node . set_fixedsize ( \"shape\" if props [ \"fixed\" ] else False ) node . set_width ( props [ \"size\" ]) node . set_height ( props [ \"size\" ]) if name . split ( \".\" )[ 0 ] in self . context : cls = eval ( name , self . context ) assert issubclass ( cls , Table ) description = ( cls () . describe ( context = self . context , printout = False ) . split ( \" \\n \" ) ) description = ( \"-\" * 30 if q . startswith ( \"---\" ) else q . replace ( \"->\" , \"→\" ) if \"->\" in q else q . split ( \":\" )[ 0 ] for q in description if not q . startswith ( \"#\" ) ) node . set_tooltip ( \" \" . join ( description )) node . set_label ( \"<\" + name + \">\" if node . get ( \"distinguished\" ) == \"True\" else name ) node . set_color ( props [ \"color\" ]) node . set_style ( \"filled\" ) for edge in dot . get_edges (): # see https://graphviz.org/doc/info/attrs.html src = edge . get_source () . strip ( '\"' ) dest = edge . get_destination () . strip ( '\"' ) props = graph . get_edge_data ( src , dest ) edge . set_color ( \"#00000040\" ) edge . set_style ( \"solid\" if props [ \"primary\" ] else \"dashed\" ) master_part = graph . nodes [ dest ][ \"node_type\" ] is Part and dest . startswith ( src + \".\" ) edge . set_weight ( 3 if master_part else 1 ) edge . set_arrowhead ( \"none\" ) edge . set_penwidth ( 0.75 if props [ \"multi\" ] else 2 ) return dot def make_svg ( self ): from IPython.display import SVG return SVG ( self . make_dot () . create_svg ()) def make_png ( self ): return io . BytesIO ( self . make_dot () . create_png ()) def make_image ( self ): if plot_active : return plt . imread ( self . make_png ()) else : raise DataJointError ( \"pyplot was not imported\" ) def _repr_svg_ ( self ): return self . make_svg () . _repr_svg_ () def draw ( self ): if plot_active : plt . imshow ( self . make_image ()) plt . gca () . axis ( \"off\" ) plt . show () else : raise DataJointError ( \"pyplot was not imported\" ) def save ( self , filename , format = None ): if format is None : if filename . lower () . endswith ( \".png\" ): format = \"png\" elif filename . lower () . endswith ( \".svg\" ): format = \"svg\" if format . lower () == \"png\" : with open ( filename , \"wb\" ) as f : f . write ( self . make_png () . getbuffer () . tobytes ()) elif format . lower () == \"svg\" : with open ( filename , \"w\" ) as f : f . write ( self . make_svg () . data ) else : raise DataJointError ( \"Unsupported file format\" ) @staticmethod def _layout ( graph , ** kwargs ): return pydot_layout ( graph , prog = \"dot\" , ** kwargs )", "title": "Diagram"}, {"location": "api/datajoint/__init__/#datajoint.diagram.Diagram.from_sequence", "text": "The join Diagram for all objects in sequence Parameters: Name Type Description Default sequence a sequence (e.g. list, tuple) required Returns: Type Description Diagram(arg1) + ... + Diagram(argn) Source code in datajoint/diagram.py 146 147 148 149 150 151 152 153 154 @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence ))", "title": "from_sequence()"}, {"location": "api/datajoint/__init__/#datajoint.diagram.Diagram.add_parts", "text": "Adds to the diagram the part tables of tables already included in the diagram Returns: Type Description Source code in datajoint/diagram.py 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self", "title": "add_parts()"}, {"location": "api/datajoint/__init__/#datajoint.diagram.Diagram.topological_sort", "text": "Returns: Type Description list of nodes in topological order Source code in datajoint/diagram.py 183 184 185 186 187 188 189 190 191 def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) )", "title": "topological_sort()"}, {"location": "api/datajoint/__init__/#datajoint.MatCell", "text": "Bases: np . ndarray a numpy ndarray representing a Matlab cell array Source code in datajoint/blob.py 73 74 75 76 class MatCell ( np . ndarray ): \"\"\"a numpy ndarray representing a Matlab cell array\"\"\" pass", "title": "MatCell"}, {"location": "api/datajoint/__init__/#datajoint.MatStruct", "text": "Bases: np . recarray numpy.recarray representing a Matlab struct array Source code in datajoint/blob.py 79 80 81 82 class MatStruct ( np . recarray ): \"\"\"numpy.recarray representing a Matlab struct array\"\"\" pass", "title": "MatStruct"}, {"location": "api/datajoint/__init__/#datajoint.conn", "text": "Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. Parameters: Name Type Description Default host hostname None user mysql user None password mysql password None init_fun initialization function None reset whether the connection should be reset or not False use_tls TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). None Source code in datajoint/connection.py 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 def conn ( host = None , user = None , password = None , * , init_fun = None , reset = False , use_tls = None ): \"\"\" Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. :param host: hostname :param user: mysql user :param password: mysql password :param init_fun: initialization function :param reset: whether the connection should be reset or not :param use_tls: TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). \"\"\" if not hasattr ( conn , \"connection\" ) or reset : host = host if host is not None else config [ \"database.host\" ] user = user if user is not None else config [ \"database.user\" ] password = password if password is not None else config [ \"database.password\" ] if user is None : # pragma: no cover user = input ( \"Please enter DataJoint username: \" ) if password is None : # pragma: no cover password = getpass ( prompt = \"Please enter DataJoint password: \" ) init_fun = ( init_fun if init_fun is not None else config [ \"connection.init_function\" ] ) use_tls = use_tls if use_tls is not None else config [ \"database.use_tls\" ] conn . connection = Connection ( host , user , password , None , init_fun , use_tls ) return conn . connection", "title": "conn()"}, {"location": "api/datajoint/__init__/#datajoint.Manual", "text": "Bases: UserTable Inherit from this class if the table's values are entered manually. Source code in datajoint/user_tables.py 133 134 135 136 137 138 139 class Manual ( UserTable ): \"\"\" Inherit from this class if the table's values are entered manually. \"\"\" _prefix = r \"\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\"", "title": "Manual"}, {"location": "api/datajoint/__init__/#datajoint.Lookup", "text": "Bases: UserTable Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. Source code in datajoint/user_tables.py 142 143 144 145 146 147 148 149 150 151 152 class Lookup ( UserTable ): \"\"\" Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. \"\"\" _prefix = \"#\" tier_regexp = ( r \"(?P\" + _prefix + _base_regexp . replace ( \"TIER\" , \"lookup\" ) + \")\" )", "title": "Lookup"}, {"location": "api/datajoint/__init__/#datajoint.Imported", "text": "Bases: UserTable , AutoPopulate Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 155 156 157 158 159 160 161 162 class Imported ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"_\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\"", "title": "Imported"}, {"location": "api/datajoint/__init__/#datajoint.Connection", "text": "A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. Parameters: Name Type Description Default host host name, may include port number as hostname:port, in which case it overrides the value in port required user user name required password password required port port number None init_fun connection initialization function (SQL) None use_tls TLS encryption option None Source code in datajoint/connection.py 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 class Connection : \"\"\" A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. :param host: host name, may include port number as hostname:port, in which case it overrides the value in port :param user: user name :param password: password :param port: port number :param init_fun: connection initialization function (SQL) :param use_tls: TLS encryption option \"\"\" def __init__ ( self , host , user , password , port = None , init_fun = None , use_tls = None ): host_input , host = ( host , get_host_hook ( host )) if \":\" in host : # the port in the hostname overrides the port argument host , port = host . split ( \":\" ) port = int ( port ) elif port is None : port = config [ \"database.port\" ] self . conn_info = dict ( host = host , port = port , user = user , passwd = password ) if use_tls is not False : self . conn_info [ \"ssl\" ] = ( use_tls if isinstance ( use_tls , dict ) else { \"ssl\" : {}} ) self . conn_info [ \"ssl_input\" ] = use_tls self . conn_info [ \"host_input\" ] = host_input self . init_fun = init_fun logger . info ( \"Connecting {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . _conn = None self . _query_cache = None connect_host_hook ( self ) if self . is_connected : logger . info ( \"Connected {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . connection_id = self . query ( \"SELECT connection_id()\" ) . fetchone ()[ 0 ] else : raise errors . LostConnectionError ( \"Connection failed.\" ) self . _in_transaction = False self . schemas = dict () self . dependencies = Dependencies ( self ) def __eq__ ( self , other ): return self . conn_info == other . conn_info def __repr__ ( self ): connected = \"connected\" if self . is_connected else \"disconnected\" return \"DataJoint connection ( {connected} ) {user} @ {host} : {port} \" . format ( connected = connected , ** self . conn_info ) def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True ) def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink () def close ( self ): self . _conn . close () def register ( self , schema ): self . schemas [ schema . database ] = schema self . dependencies . clear () def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False ) @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True @staticmethod def _execute_query ( cursor , query , args , suppress_warnings ): try : with warnings . catch_warnings (): if suppress_warnings : # suppress all warnings arising from underlying SQL library warnings . simplefilter ( \"ignore\" ) cursor . execute ( query , args ) except client . err . Error as err : raise translate_query_error ( err , query ) def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ] # ---------- transaction processing @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" ) def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" ) def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" ) # -------- context manager for transactions @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction ()", "title": "Connection"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.connect", "text": "Connect to the database server. Source code in datajoint/connection.py 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True )", "title": "connect()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.set_query_cache", "text": "When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. Parameters: Name Type Description Default query_cache a string to initialize the hash for query results None Source code in datajoint/connection.py 246 247 248 249 250 251 252 253 254 255 def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache", "title": "set_query_cache()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.purge_query_cache", "text": "Purges all query cache. Source code in datajoint/connection.py 257 258 259 260 261 262 263 264 265 def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink ()", "title": "purge_query_cache()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.ping", "text": "Ping the connection or raises an exception if the connection is closed. Source code in datajoint/connection.py 274 275 276 def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False )", "title": "ping()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.is_connected", "text": "Return true if the object is connected to the database server. Source code in datajoint/connection.py 278 279 280 281 282 283 284 285 @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True", "title": "is_connected()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.query", "text": "Execute the specified query and return the tuple generator (cursor). Parameters: Name Type Description Default query SQL query required args additional arguments for the client.cursor () as_dict If as_dict is set to True, the returned cursor objects returns query results as dictionary. False suppress_warnings If True, suppress all warnings arising from underlying query library True reconnect when None, get from config, when True, attempt to reconnect if disconnected None Source code in datajoint/connection.py 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor", "title": "query()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.get_user", "text": "Returns: Type Description the user name and host name provided by the client to the server. Source code in datajoint/connection.py 362 363 364 365 366 def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ]", "title": "get_user()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.in_transaction", "text": "Returns: Type Description True if there is an open transaction. Source code in datajoint/connection.py 369 370 371 372 373 374 375 @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction", "title": "in_transaction()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.start_transaction", "text": "Starts a transaction error. Source code in datajoint/connection.py 377 378 379 380 381 382 383 384 385 def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" )", "title": "start_transaction()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.cancel_transaction", "text": "Cancels the current transaction and rolls back all changes made during the transaction. Source code in datajoint/connection.py 387 388 389 390 391 392 393 def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" )", "title": "cancel_transaction()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.commit_transaction", "text": "Commit all changes made during the transaction and close it. Source code in datajoint/connection.py 395 396 397 398 399 400 401 402 def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" )", "title": "commit_transaction()"}, {"location": "api/datajoint/__init__/#datajoint.connection.Connection.transaction", "text": "Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: import datajoint as dj with dj.conn().transaction as conn: # transaction is open here Source code in datajoint/connection.py 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction ()", "title": "transaction()"}, {"location": "api/datajoint/__init__/#datajoint.Computed", "text": "Bases: UserTable , AutoPopulate Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 165 166 167 168 169 170 171 172 class Computed ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"__\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\"", "title": "Computed"}, {"location": "api/datajoint/__init__/#datajoint.Part", "text": "Bases: UserTable Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. Source code in datajoint/user_tables.py 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 class Part ( UserTable ): \"\"\" Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. \"\"\" _connection = None _master = None tier_regexp = ( r \"(?P\" + \"|\" . join ([ c . tier_regexp for c in ( Manual , Lookup , Imported , Computed )]) + r \"){1,1}\" + \"__\" + r \"(?P\" + _base_regexp + \")\" ) @ClassProperty def connection ( cls ): return cls . _connection @ClassProperty def full_table_name ( cls ): return ( None if cls . database is None or cls . table_name is None else r \"` {0:s} `.` {1:s} `\" . format ( cls . database , cls . table_name ) ) @ClassProperty def master ( cls ): return cls . _master @ClassProperty def table_name ( cls ): return ( None if cls . master is None else cls . master . table_name + \"__\" + from_camel_case ( cls . __name__ ) ) def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" ) def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" )", "title": "Part"}, {"location": "api/datajoint/__init__/#datajoint.user_tables.Part.delete", "text": "unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 220 221 222 223 224 225 226 227 228 229 def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" )", "title": "delete()"}, {"location": "api/datajoint/__init__/#datajoint.user_tables.Part.drop", "text": "unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 231 232 233 234 235 236 237 238 239 240 def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" )", "title": "drop()"}, {"location": "api/datajoint/__init__/#datajoint.VirtualModule", "text": "Bases: types . ModuleType A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. Source code in datajoint/schemas.py 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 class VirtualModule ( types . ModuleType ): \"\"\" A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. \"\"\" def __init__ ( self , module_name , schema_name , * , create_schema = False , create_tables = False , connection = None , add_objects = None , ): \"\"\" Creates a python module with the given name from the name of a schema on the server and automatically adds classes to it corresponding to the tables in the schema. :param module_name: displayed module name :param schema_name: name of the database in mysql :param create_schema: if True, create the schema on the database server :param create_tables: if True, module.schema can be used as the decorator for declaring new :param connection: a dj.Connection object to pass into the schema :param add_objects: additional objects to add to the module :return: the python module containing classes from the schema object and the table classes \"\"\" super ( VirtualModule , self ) . __init__ ( name = module_name ) _schema = Schema ( schema_name , create_schema = create_schema , create_tables = create_tables , connection = connection , ) if add_objects : self . __dict__ . update ( add_objects ) self . __dict__ [ \"schema\" ] = _schema _schema . spawn_missing_classes ( context = self . __dict__ )", "title": "VirtualModule"}, {"location": "api/datajoint/__init__/#datajoint.list_schemas", "text": "Parameters: Name Type Description Default connection a dj.Connection object None Returns: Type Description list of all accessible schemas on the server Source code in datajoint/schemas.py 534 535 536 537 538 539 540 541 542 543 544 545 546 547 def list_schemas ( connection = None ): \"\"\" :param connection: a dj.Connection object :return: list of all accessible schemas on the server \"\"\" return [ r [ 0 ] for r in ( connection or conn ()) . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" 'WHERE schema_name <> \"information_schema\"' ) ]", "title": "list_schemas()"}, {"location": "api/datajoint/__init__/#datajoint.U", "text": "dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the stimulus set: dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute s containing the total number of elements in query expression expr : dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number n of distinct values of attribute attr in query expressio expr . dj.U().aggr(expr, n='count(distinct attr)') dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute s containing the sum of values of attribute attr over entire result set of expression expr : dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes attr1 , attr2 and the number of their occurrences in the result set of query expression expr . dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression expr has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as expr but attr1 and attr2 are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if attr is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename attr in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. Source code in datajoint/expression.py 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 class U : \"\"\" dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the `stimulus` set: >>> dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute `s` containing the total number of elements in query expression `expr`: >>> dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number `n` of distinct values of attribute `attr` in query expressio `expr`. >>> dj.U().aggr(expr, n='count(distinct attr)') >>> dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute `s` containing the sum of values of attribute `attr` over entire result set of expression `expr`: >>> dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes `attr1`, `attr2` and the number of their occurrences in the result set of query expression `expr`. >>> dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression `expr` has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as `expr` but `attr1` and `attr2` are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if `attr` is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename `attr` in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. \"\"\" def __init__ ( self , * primary_key ): self . _primary_key = primary_key @property def primary_key ( self ): return self . _primary_key def __and__ ( self , other ): if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be restricted with a QueryExpression.\" ) result = copy . copy ( other ) result . _distinct = True result . _heading = result . heading . set_primary_key ( self . primary_key ) result = result . proj () return result def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result def __mul__ ( self , other ): \"\"\"shorthand for join\"\"\" return self . join ( other ) def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes ) aggregate = aggr # alias for aggr", "title": "U"}, {"location": "api/datajoint/__init__/#datajoint.expression.U.join", "text": "Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. Parameters: Name Type Description Default other the other query expression to join with. required left ignored. dj.U always acts as if left=False False Returns: Type Description a copy of the other query expression with the primary key extended. Source code in datajoint/expression.py 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result", "title": "join()"}, {"location": "api/datajoint/__init__/#datajoint.expression.U.aggr", "text": "Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of group . Parameters: Name Type Description Default group The query expression to be aggregated. required named_attributes computations of the form new_attribute=\"sql expression on attributes of group\" required Returns: Type Description The derived query expression Source code in datajoint/expression.py 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes )", "title": "aggr()"}, {"location": "api/datajoint/__init__/#datajoint.FreeTable", "text": "Bases: Table A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. Parameters: Name Type Description Default conn a dj.Connection object required full_table_name in format database . table_name required Source code in datajoint/table.py 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 class FreeTable ( Table ): \"\"\" A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. :param conn: a dj.Connection object :param full_table_name: in format `database`.`table_name` \"\"\" def __init__ ( self , conn , full_table_name ): self . database , self . _table_name = ( s . strip ( \"`\" ) for s in full_table_name . split ( \".\" ) ) self . _connection = conn self . _support = [ full_table_name ] self . _heading = Heading ( table_info = dict ( conn = conn , database = self . database , table_name = self . table_name , context = None , ) ) def __repr__ ( self ): return ( \"FreeTable(` %s `.` %s `) \\n \" % ( self . database , self . _table_name ) + super () . __repr__ () )", "title": "FreeTable"}, {"location": "api/datajoint/admin/", "text": "kill ( restriction = None , connection = None , order_by = None ) \u00b6 view and kill database connections. Parameters: Name Type Description Default restriction restriction to be applied to processlist None connection a datajoint.Connection object. Default calls datajoint.conn() None order_by order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes None Source code in datajoint/admin.py 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 def kill ( restriction = None , connection = None , order_by = None ): # pragma: no cover \"\"\" view and kill database connections. :param restriction: restriction to be applied to processlist :param connection: a datajoint.Connection object. Default calls datajoint.conn() :param order_by: order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes \"\"\" if connection is None : connection = conn () if order_by is not None and not isinstance ( order_by , str ): order_by = \",\" . join ( order_by ) query = ( \"SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()\" + ( \"\" if restriction is None else \" AND ( %s )\" % restriction ) + ( \" ORDER BY %s \" % ( order_by or \"id\" )) ) while True : print ( \" ID USER HOST STATE TIME INFO\" ) print ( \"+--+ +----------+ +-----------+ +-----------+ +-----+\" ) cur = ( { k . lower (): v for k , v in elem . items ()} for elem in connection . query ( query , as_dict = True ) ) for process in cur : try : print ( \" {id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d} {info} \" . format ( ** process ) ) except TypeError : print ( process ) response = input ( 'process to kill or \"q\" to quit > ' ) if response == \"q\" : break if response : try : pid = int ( response ) except ValueError : pass # ignore non-numeric input else : try : connection . query ( \"kill %d \" % pid ) except pymysql . err . InternalError : print ( \"Process not found\" ) kill_quick ( restriction = None , connection = None ) \u00b6 Kill database connections without prompting. Returns number of terminated connections. Parameters: Name Type Description Default restriction restriction to be applied to processlist None connection a datajoint.Connection object. Default calls datajoint.conn() Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') terminates connections from hosts containing \"compute\". None Source code in datajoint/admin.py 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 def kill_quick ( restriction = None , connection = None ): \"\"\" Kill database connections without prompting. Returns number of terminated connections. :param restriction: restriction to be applied to processlist :param connection: a datajoint.Connection object. Default calls datajoint.conn() Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') terminates connections from hosts containing \"compute\". \"\"\" if connection is None : connection = conn () query = ( \"SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()\" + ( \"\" if restriction is None else \" AND ( %s )\" % restriction ) ) cur = ( { k . lower (): v for k , v in elem . items ()} for elem in connection . query ( query , as_dict = True ) ) nkill = 0 for process in cur : connection . query ( \"kill %d \" % process [ \"id\" ]) nkill += 1 return nkill", "title": "admin.py"}, {"location": "api/datajoint/admin/#datajoint.admin.kill", "text": "view and kill database connections. Parameters: Name Type Description Default restriction restriction to be applied to processlist None connection a datajoint.Connection object. Default calls datajoint.conn() None order_by order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes None Source code in datajoint/admin.py 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 def kill ( restriction = None , connection = None , order_by = None ): # pragma: no cover \"\"\" view and kill database connections. :param restriction: restriction to be applied to processlist :param connection: a datajoint.Connection object. Default calls datajoint.conn() :param order_by: order by a single attribute or the list of attributes. defaults to 'id'. Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') lists only connections from hosts containing \"compute\". dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes \"\"\" if connection is None : connection = conn () if order_by is not None and not isinstance ( order_by , str ): order_by = \",\" . join ( order_by ) query = ( \"SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()\" + ( \"\" if restriction is None else \" AND ( %s )\" % restriction ) + ( \" ORDER BY %s \" % ( order_by or \"id\" )) ) while True : print ( \" ID USER HOST STATE TIME INFO\" ) print ( \"+--+ +----------+ +-----------+ +-----------+ +-----+\" ) cur = ( { k . lower (): v for k , v in elem . items ()} for elem in connection . query ( query , as_dict = True ) ) for process in cur : try : print ( \" {id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d} {info} \" . format ( ** process ) ) except TypeError : print ( process ) response = input ( 'process to kill or \"q\" to quit > ' ) if response == \"q\" : break if response : try : pid = int ( response ) except ValueError : pass # ignore non-numeric input else : try : connection . query ( \"kill %d \" % pid ) except pymysql . err . InternalError : print ( \"Process not found\" )", "title": "kill()"}, {"location": "api/datajoint/admin/#datajoint.admin.kill_quick", "text": "Kill database connections without prompting. Returns number of terminated connections. Parameters: Name Type Description Default restriction restriction to be applied to processlist None connection a datajoint.Connection object. Default calls datajoint.conn() Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') terminates connections from hosts containing \"compute\". None Source code in datajoint/admin.py 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 def kill_quick ( restriction = None , connection = None ): \"\"\" Kill database connections without prompting. Returns number of terminated connections. :param restriction: restriction to be applied to processlist :param connection: a datajoint.Connection object. Default calls datajoint.conn() Restrictions are specified as strings and can involve any of the attributes of information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. Examples: dj.kill('HOST LIKE \"%compute%\"') terminates connections from hosts containing \"compute\". \"\"\" if connection is None : connection = conn () query = ( \"SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()\" + ( \"\" if restriction is None else \" AND ( %s )\" % restriction ) ) cur = ( { k . lower (): v for k , v in elem . items ()} for elem in connection . query ( query , as_dict = True ) ) nkill = 0 for process in cur : connection . query ( \"kill %d \" % process [ \"id\" ]) nkill += 1 return nkill", "title": "kill_quick()"}, {"location": "api/datajoint/attribute_adapter/", "text": "AttributeAdapter \u00b6 Base class for adapter objects for user-defined attribute types. Source code in datajoint/attribute_adapter.py 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 class AttributeAdapter : \"\"\" Base class for adapter objects for user-defined attribute types. \"\"\" @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) attribute_type () property \u00b6 Returns: Type Description a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" Source code in datajoint/attribute_adapter.py 11 12 13 14 15 16 @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) get ( value ) \u00b6 convert value retrieved from the the attribute in a table into the adapted type Parameters: Name Type Description Default value value from the database required Returns: Type Description object of the adapted type Source code in datajoint/attribute_adapter.py 18 19 20 21 22 23 24 25 26 def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) put ( obj ) \u00b6 convert an object of the adapted type into a value that DataJoint can store in a table attribute Parameters: Name Type Description Default obj an object of the adapted type required Returns: Type Description value to store in the database Source code in datajoint/attribute_adapter.py 28 29 30 31 32 33 34 35 def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) get_adapter ( context , adapter_name ) \u00b6 Extract the AttributeAdapter object by its name from the context and validate. Source code in datajoint/attribute_adapter.py 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 def get_adapter ( context , adapter_name ): \"\"\" Extract the AttributeAdapter object by its name from the context and validate. \"\"\" if not _support_adapted_types (): raise DataJointError ( \"Support for Adapted Attribute types is disabled.\" ) adapter_name = adapter_name . lstrip ( \"<\" ) . rstrip ( \">\" ) try : adapter = ( context [ adapter_name ] if adapter_name in context else type_plugins [ adapter_name ][ \"object\" ] . load () ) except KeyError : raise DataJointError ( \"Attribute adapter ' {adapter_name} ' is not defined.\" . format ( adapter_name = adapter_name ) ) if not isinstance ( adapter , AttributeAdapter ): raise DataJointError ( \"Attribute adapter ' {adapter_name} ' must be an instance of datajoint.AttributeAdapter\" . format ( adapter_name = adapter_name ) ) if not isinstance ( adapter . attribute_type , str ) or not re . match ( r \"^\\w\" , adapter . attribute_type ): raise DataJointError ( \"Invalid attribute type {type} in attribute adapter ' {adapter_name} '\" . format ( type = adapter . attribute_type , adapter_name = adapter_name ) ) return adapter", "title": "attribute_adapter.py"}, {"location": "api/datajoint/attribute_adapter/#datajoint.attribute_adapter.AttributeAdapter", "text": "Base class for adapter objects for user-defined attribute types. Source code in datajoint/attribute_adapter.py 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 class AttributeAdapter : \"\"\" Base class for adapter objects for user-defined attribute types. \"\"\" @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" ) def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "AttributeAdapter"}, {"location": "api/datajoint/attribute_adapter/#datajoint.attribute_adapter.AttributeAdapter.attribute_type", "text": "Returns: Type Description a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" Source code in datajoint/attribute_adapter.py 11 12 13 14 15 16 @property def attribute_type ( self ): \"\"\" :return: a supported DataJoint attribute type to use; e.g. \"longblob\", \"blob@store\" \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "attribute_type()"}, {"location": "api/datajoint/attribute_adapter/#datajoint.attribute_adapter.AttributeAdapter.get", "text": "convert value retrieved from the the attribute in a table into the adapted type Parameters: Name Type Description Default value value from the database required Returns: Type Description object of the adapted type Source code in datajoint/attribute_adapter.py 18 19 20 21 22 23 24 25 26 def get ( self , value ): \"\"\" convert value retrieved from the the attribute in a table into the adapted type :param value: value from the database :return: object of the adapted type \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "get()"}, {"location": "api/datajoint/attribute_adapter/#datajoint.attribute_adapter.AttributeAdapter.put", "text": "convert an object of the adapted type into a value that DataJoint can store in a table attribute Parameters: Name Type Description Default obj an object of the adapted type required Returns: Type Description value to store in the database Source code in datajoint/attribute_adapter.py 28 29 30 31 32 33 34 35 def put ( self , obj ): \"\"\" convert an object of the adapted type into a value that DataJoint can store in a table attribute :param obj: an object of the adapted type :return: value to store in the database \"\"\" raise NotImplementedError ( \"Undefined attribute adapter\" )", "title": "put()"}, {"location": "api/datajoint/attribute_adapter/#datajoint.attribute_adapter.get_adapter", "text": "Extract the AttributeAdapter object by its name from the context and validate. Source code in datajoint/attribute_adapter.py 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 def get_adapter ( context , adapter_name ): \"\"\" Extract the AttributeAdapter object by its name from the context and validate. \"\"\" if not _support_adapted_types (): raise DataJointError ( \"Support for Adapted Attribute types is disabled.\" ) adapter_name = adapter_name . lstrip ( \"<\" ) . rstrip ( \">\" ) try : adapter = ( context [ adapter_name ] if adapter_name in context else type_plugins [ adapter_name ][ \"object\" ] . load () ) except KeyError : raise DataJointError ( \"Attribute adapter ' {adapter_name} ' is not defined.\" . format ( adapter_name = adapter_name ) ) if not isinstance ( adapter , AttributeAdapter ): raise DataJointError ( \"Attribute adapter ' {adapter_name} ' must be an instance of datajoint.AttributeAdapter\" . format ( adapter_name = adapter_name ) ) if not isinstance ( adapter . attribute_type , str ) or not re . match ( r \"^\\w\" , adapter . attribute_type ): raise DataJointError ( \"Invalid attribute type {type} in attribute adapter ' {adapter_name} '\" . format ( type = adapter . attribute_type , adapter_name = adapter_name ) ) return adapter", "title": "get_adapter()"}, {"location": "api/datajoint/autopopulate/", "text": "This module defines class dj.AutoPopulate AutoPopulate \u00b6 AutoPopulate is a mixin class that adds the method populate() to a Table class. Auto-populated tables must inherit from both Table and AutoPopulate, must define the property key_source , and must define the callback method make . Source code in datajoint/autopopulate.py 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 class AutoPopulate : \"\"\" AutoPopulate is a mixin class that adds the method populate() to a Table class. Auto-populated tables must inherit from both Table and AutoPopulate, must define the property `key_source`, and must define the callback method `make`. \"\"\" _key_source = None _allow_insert = False @property def key_source ( self ): \"\"\" :return: the query expression that yields primary key values to be passed, sequentially, to the ``make`` method when populate() is called. The default value is the join of the parent tables references from the primary key. Subclasses may override they key_source to change the scope or the granularity of the make calls. \"\"\" def _rename_attributes ( table , props ): return ( table . proj ( ** { attr : ref for attr , ref in props [ \"attr_map\" ] . items () if attr != ref } ) if props [ \"aliased\" ] else table . proj () ) if self . _key_source is None : parents = self . target . parents ( primary = True , as_objects = True , foreign_key_info = True ) if not parents : raise DataJointError ( \"A table must have dependencies \" \"from its primary key for auto-populate to work\" ) self . _key_source = _rename_attributes ( * parents [ 0 ]) for q in parents [ 1 :]: self . _key_source *= _rename_attributes ( * q ) return self . _key_source def make ( self , key ): \"\"\" Derived classes must implement method `make` that fetches data from tables above them in the dependency hierarchy, restricting by the given key, computes secondary attributes, and inserts the new tuples into self. \"\"\" raise NotImplementedError ( \"Subclasses of AutoPopulate must implement the method `make`\" ) @property def target ( self ): \"\"\" :return: table to be populated. In the typical case, dj.AutoPopulate is mixed into a dj.Table class by inheritance and the target is self. \"\"\" return self def _job_key ( self , key ): \"\"\" :param key: they key returned for the job from the key source :return: the dict to use to generate the job reservation hash This method allows subclasses to control the job reservation granularity. \"\"\" return key def _jobs_to_do ( self , restrictions ): \"\"\" :return: the query yeilding the keys to be computed (derived from self.key_source) \"\"\" if self . restriction : raise DataJointError ( \"Cannot call populate on a restricted table. \" \"Instead, pass conditions to populate() as arguments.\" ) todo = self . key_source # key_source is a QueryExpression subclass -- trigger instantiation if inspect . isclass ( todo ) and issubclass ( todo , QueryExpression ): todo = todo () if not isinstance ( todo , QueryExpression ): raise DataJointError ( \"Invalid key_source value\" ) try : # check if target lacks any attributes from the primary key of key_source raise DataJointError ( \"The populate target lacks attribute %s \" \"from the primary key of key_source\" % next ( name for name in todo . heading . primary_key if name not in self . target . heading ) ) except StopIteration : pass return ( todo & AndList ( restrictions )) . proj () def populate ( self , * restrictions , suppress_errors = False , return_exception_objects = False , reserve_jobs = False , order = \"original\" , limit = None , max_calls = None , display_progress = False , processes = 1 , make_kwargs = None , ): \"\"\" ``table.populate()`` calls ``table.make(key)`` for every primary key in ``self.key_source`` for which there is not already a tuple in table. :param restrictions: a list of restrictions each restrict (table.key_source - target.proj()) :param suppress_errors: if True, do not terminate execution. :param return_exception_objects: return error objects instead of just error messages :param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion :param order: \"original\"|\"reverse\"|\"random\" - the order of execution :param limit: if not None, check at most this many keys :param max_calls: if not None, populate at most this many keys :param display_progress: if True, report progress_bar :param processes: number of processes to use. Set to None to use all cores :param make_kwargs: Keyword arguments which do not affect the result of computation to be passed down to each ``make()`` call. Computation arguments should be specified within the pipeline e.g. using a `dj.Lookup` table. :type make_kwargs: dict, optional \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Populate cannot be called during a transaction.\" ) valid_order = [ \"original\" , \"reverse\" , \"random\" ] if order not in valid_order : raise DataJointError ( \"The order argument must be one of %s \" % str ( valid_order ) ) jobs = ( self . connection . schemas [ self . target . database ] . jobs if reserve_jobs else None ) # define and set up signal handler for SIGTERM: if reserve_jobs : def handler ( signum , frame ): logger . info ( \"Populate terminated by SIGTERM\" ) raise SystemExit ( \"SIGTERM received\" ) old_handler = signal . signal ( signal . SIGTERM , handler ) keys = ( self . _jobs_to_do ( restrictions ) - self . target ) . fetch ( \"KEY\" , limit = limit ) if order == \"reverse\" : keys . reverse () elif order == \"random\" : random . shuffle ( keys ) logger . debug ( \"Found %d keys to populate\" % len ( keys )) keys = keys [: max_calls ] nkeys = len ( keys ) if not nkeys : return processes = min ( _ for _ in ( processes , nkeys , mp . cpu_count ()) if _ ) error_list = [] populate_kwargs = dict ( suppress_errors = suppress_errors , return_exception_objects = return_exception_objects , make_kwargs = make_kwargs , ) if processes == 1 : for key in ( tqdm ( keys , desc = self . __class__ . __name__ ) if display_progress else keys ): error = self . _populate1 ( key , jobs , ** populate_kwargs ) if error is not None : error_list . append ( error ) else : # spawn multiple processes self . connection . close () # disconnect parent process from MySQL server del self . connection . _conn . ctx # SSLContext is not pickleable with mp . Pool ( processes , _initialize_populate , ( self , jobs , populate_kwargs ) ) as pool , ( tqdm ( desc = \"Processes: \" , total = nkeys ) if display_progress else contextlib . nullcontext () ) as progress_bar : for error in pool . imap ( _call_populate1 , keys , chunksize = 1 ): if error is not None : error_list . append ( error ) if display_progress : progress_bar . update () self . connection . connect () # reconnect parent process to MySQL server # restore original signal handler: if reserve_jobs : signal . signal ( signal . SIGTERM , old_handler ) if suppress_errors : return error_list def _populate1 ( self , key , jobs , suppress_errors , return_exception_objects , make_kwargs = None ): \"\"\" populates table for one source key, calling self.make inside a transaction. :param jobs: the jobs table or None if not reserve_jobs :param key: dict specifying job to populate :param suppress_errors: bool if errors should be suppressed and returned :param return_exception_objects: if True, errors must be returned as objects :return: (key, error) when suppress_errors=True, otherwise None \"\"\" make = self . _make_tuples if hasattr ( self , \"_make_tuples\" ) else self . make if jobs is None or jobs . reserve ( self . target . table_name , self . _job_key ( key )): self . connection . start_transaction () if key in self . target : # already populated self . connection . cancel_transaction () if jobs is not None : jobs . complete ( self . target . table_name , self . _job_key ( key )) else : logger . debug ( f \"Making { key } -> { self . target . full_table_name } \" ) self . __class__ . _allow_insert = True try : make ( dict ( key ), ** ( make_kwargs or {})) except ( KeyboardInterrupt , SystemExit , Exception ) as error : try : self . connection . cancel_transaction () except LostConnectionError : pass error_message = \" {exception}{msg} \" . format ( exception = error . __class__ . __name__ , msg = \": \" + str ( error ) if str ( error ) else \"\" , ) logger . debug ( f \"Error making { key } -> { self . target . full_table_name } - { error_message } \" ) if jobs is not None : # show error name and error message (if any) jobs . error ( self . target . table_name , self . _job_key ( key ), error_message = error_message , error_stack = traceback . format_exc (), ) if not suppress_errors or isinstance ( error , SystemExit ): raise else : logger . error ( error ) return key , error if return_exception_objects else error_message else : self . connection . commit_transaction () logger . debug ( f \"Success making { key } -> { self . target . full_table_name } \" ) if jobs is not None : jobs . complete ( self . target . table_name , self . _job_key ( key )) finally : self . __class__ . _allow_insert = False def progress ( self , * restrictions , display = True ): \"\"\" Report the progress of populating the table. :return: (remaining, total) -- numbers of tuples to be populated \"\"\" todo = self . _jobs_to_do ( restrictions ) total = len ( todo ) remaining = len ( todo - self . target ) if display : print ( \" %-20s \" % self . __class__ . __name__ , \"Completed %d of %d ( %2.1f%% ) %s \" % ( total - remaining , total , 100 - 100 * remaining / ( total + 1e-12 ), datetime . datetime . strftime ( datetime . datetime . now (), \"%Y-%m- %d %H:%M:%S\" ), ), flush = True , ) return remaining , total key_source () property \u00b6 Returns: Type Description the query expression that yields primary key values to be passed, sequentially, to the make method when populate() is called. The default value is the join of the parent tables references from the primary key. Subclasses may override they key_source to change the scope or the granularity of the make calls. Source code in datajoint/autopopulate.py 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 @property def key_source ( self ): \"\"\" :return: the query expression that yields primary key values to be passed, sequentially, to the ``make`` method when populate() is called. The default value is the join of the parent tables references from the primary key. Subclasses may override they key_source to change the scope or the granularity of the make calls. \"\"\" def _rename_attributes ( table , props ): return ( table . proj ( ** { attr : ref for attr , ref in props [ \"attr_map\" ] . items () if attr != ref } ) if props [ \"aliased\" ] else table . proj () ) if self . _key_source is None : parents = self . target . parents ( primary = True , as_objects = True , foreign_key_info = True ) if not parents : raise DataJointError ( \"A table must have dependencies \" \"from its primary key for auto-populate to work\" ) self . _key_source = _rename_attributes ( * parents [ 0 ]) for q in parents [ 1 :]: self . _key_source *= _rename_attributes ( * q ) return self . _key_source make ( key ) \u00b6 Derived classes must implement method make that fetches data from tables above them in the dependency hierarchy, restricting by the given key, computes secondary attributes, and inserts the new tuples into self. Source code in datajoint/autopopulate.py 91 92 93 94 95 96 97 98 99 def make ( self , key ): \"\"\" Derived classes must implement method `make` that fetches data from tables above them in the dependency hierarchy, restricting by the given key, computes secondary attributes, and inserts the new tuples into self. \"\"\" raise NotImplementedError ( \"Subclasses of AutoPopulate must implement the method `make`\" ) target () property \u00b6 Returns: Type Description table to be populated. In the typical case, dj.AutoPopulate is mixed into a dj.Table class by inheritance and the target is self. Source code in datajoint/autopopulate.py 101 102 103 104 105 106 107 108 @property def target ( self ): \"\"\" :return: table to be populated. In the typical case, dj.AutoPopulate is mixed into a dj.Table class by inheritance and the target is self. \"\"\" return self populate ( * restrictions , suppress_errors = False , return_exception_objects = False , reserve_jobs = False , order = 'original' , limit = None , max_calls = None , display_progress = False , processes = 1 , make_kwargs = None ) \u00b6 table.populate() calls table.make(key) for every primary key in self.key_source for which there is not already a tuple in table. Parameters: Name Type Description Default restrictions a list of restrictions each restrict (table.key_source - target.proj()) required suppress_errors if True, do not terminate execution. False return_exception_objects return error objects instead of just error messages False reserve_jobs if True, reserve jobs to populate in asynchronous fashion False order \"original\"|\"reverse\"|\"random\" - the order of execution 'original' limit if not None, check at most this many keys None max_calls if not None, populate at most this many keys None display_progress if True, report progress_bar False processes number of processes to use. Set to None to use all cores 1 make_kwargs dict, optional Keyword arguments which do not affect the result of computation to be passed down to each make() call. Computation arguments should be specified within the pipeline e.g. using a dj.Lookup table. None Source code in datajoint/autopopulate.py 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 def populate ( self , * restrictions , suppress_errors = False , return_exception_objects = False , reserve_jobs = False , order = \"original\" , limit = None , max_calls = None , display_progress = False , processes = 1 , make_kwargs = None , ): \"\"\" ``table.populate()`` calls ``table.make(key)`` for every primary key in ``self.key_source`` for which there is not already a tuple in table. :param restrictions: a list of restrictions each restrict (table.key_source - target.proj()) :param suppress_errors: if True, do not terminate execution. :param return_exception_objects: return error objects instead of just error messages :param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion :param order: \"original\"|\"reverse\"|\"random\" - the order of execution :param limit: if not None, check at most this many keys :param max_calls: if not None, populate at most this many keys :param display_progress: if True, report progress_bar :param processes: number of processes to use. Set to None to use all cores :param make_kwargs: Keyword arguments which do not affect the result of computation to be passed down to each ``make()`` call. Computation arguments should be specified within the pipeline e.g. using a `dj.Lookup` table. :type make_kwargs: dict, optional \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Populate cannot be called during a transaction.\" ) valid_order = [ \"original\" , \"reverse\" , \"random\" ] if order not in valid_order : raise DataJointError ( \"The order argument must be one of %s \" % str ( valid_order ) ) jobs = ( self . connection . schemas [ self . target . database ] . jobs if reserve_jobs else None ) # define and set up signal handler for SIGTERM: if reserve_jobs : def handler ( signum , frame ): logger . info ( \"Populate terminated by SIGTERM\" ) raise SystemExit ( \"SIGTERM received\" ) old_handler = signal . signal ( signal . SIGTERM , handler ) keys = ( self . _jobs_to_do ( restrictions ) - self . target ) . fetch ( \"KEY\" , limit = limit ) if order == \"reverse\" : keys . reverse () elif order == \"random\" : random . shuffle ( keys ) logger . debug ( \"Found %d keys to populate\" % len ( keys )) keys = keys [: max_calls ] nkeys = len ( keys ) if not nkeys : return processes = min ( _ for _ in ( processes , nkeys , mp . cpu_count ()) if _ ) error_list = [] populate_kwargs = dict ( suppress_errors = suppress_errors , return_exception_objects = return_exception_objects , make_kwargs = make_kwargs , ) if processes == 1 : for key in ( tqdm ( keys , desc = self . __class__ . __name__ ) if display_progress else keys ): error = self . _populate1 ( key , jobs , ** populate_kwargs ) if error is not None : error_list . append ( error ) else : # spawn multiple processes self . connection . close () # disconnect parent process from MySQL server del self . connection . _conn . ctx # SSLContext is not pickleable with mp . Pool ( processes , _initialize_populate , ( self , jobs , populate_kwargs ) ) as pool , ( tqdm ( desc = \"Processes: \" , total = nkeys ) if display_progress else contextlib . nullcontext () ) as progress_bar : for error in pool . imap ( _call_populate1 , keys , chunksize = 1 ): if error is not None : error_list . append ( error ) if display_progress : progress_bar . update () self . connection . connect () # reconnect parent process to MySQL server # restore original signal handler: if reserve_jobs : signal . signal ( signal . SIGTERM , old_handler ) if suppress_errors : return error_list progress ( * restrictions , display = True ) \u00b6 Report the progress of populating the table. Returns: Type Description (remaining, total) -- numbers of tuples to be populated Source code in datajoint/autopopulate.py 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 def progress ( self , * restrictions , display = True ): \"\"\" Report the progress of populating the table. :return: (remaining, total) -- numbers of tuples to be populated \"\"\" todo = self . _jobs_to_do ( restrictions ) total = len ( todo ) remaining = len ( todo - self . target ) if display : print ( \" %-20s \" % self . __class__ . __name__ , \"Completed %d of %d ( %2.1f%% ) %s \" % ( total - remaining , total , 100 - 100 * remaining / ( total + 1e-12 ), datetime . datetime . strftime ( datetime . datetime . now (), \"%Y-%m- %d %H:%M:%S\" ), ), flush = True , ) return remaining , total", "title": "autopopulate.py"}, {"location": "api/datajoint/autopopulate/#datajoint.autopopulate.AutoPopulate", "text": "AutoPopulate is a mixin class that adds the method populate() to a Table class. Auto-populated tables must inherit from both Table and AutoPopulate, must define the property key_source , and must define the callback method make . Source code in datajoint/autopopulate.py 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 class AutoPopulate : \"\"\" AutoPopulate is a mixin class that adds the method populate() to a Table class. Auto-populated tables must inherit from both Table and AutoPopulate, must define the property `key_source`, and must define the callback method `make`. \"\"\" _key_source = None _allow_insert = False @property def key_source ( self ): \"\"\" :return: the query expression that yields primary key values to be passed, sequentially, to the ``make`` method when populate() is called. The default value is the join of the parent tables references from the primary key. Subclasses may override they key_source to change the scope or the granularity of the make calls. \"\"\" def _rename_attributes ( table , props ): return ( table . proj ( ** { attr : ref for attr , ref in props [ \"attr_map\" ] . items () if attr != ref } ) if props [ \"aliased\" ] else table . proj () ) if self . _key_source is None : parents = self . target . parents ( primary = True , as_objects = True , foreign_key_info = True ) if not parents : raise DataJointError ( \"A table must have dependencies \" \"from its primary key for auto-populate to work\" ) self . _key_source = _rename_attributes ( * parents [ 0 ]) for q in parents [ 1 :]: self . _key_source *= _rename_attributes ( * q ) return self . _key_source def make ( self , key ): \"\"\" Derived classes must implement method `make` that fetches data from tables above them in the dependency hierarchy, restricting by the given key, computes secondary attributes, and inserts the new tuples into self. \"\"\" raise NotImplementedError ( \"Subclasses of AutoPopulate must implement the method `make`\" ) @property def target ( self ): \"\"\" :return: table to be populated. In the typical case, dj.AutoPopulate is mixed into a dj.Table class by inheritance and the target is self. \"\"\" return self def _job_key ( self , key ): \"\"\" :param key: they key returned for the job from the key source :return: the dict to use to generate the job reservation hash This method allows subclasses to control the job reservation granularity. \"\"\" return key def _jobs_to_do ( self , restrictions ): \"\"\" :return: the query yeilding the keys to be computed (derived from self.key_source) \"\"\" if self . restriction : raise DataJointError ( \"Cannot call populate on a restricted table. \" \"Instead, pass conditions to populate() as arguments.\" ) todo = self . key_source # key_source is a QueryExpression subclass -- trigger instantiation if inspect . isclass ( todo ) and issubclass ( todo , QueryExpression ): todo = todo () if not isinstance ( todo , QueryExpression ): raise DataJointError ( \"Invalid key_source value\" ) try : # check if target lacks any attributes from the primary key of key_source raise DataJointError ( \"The populate target lacks attribute %s \" \"from the primary key of key_source\" % next ( name for name in todo . heading . primary_key if name not in self . target . heading ) ) except StopIteration : pass return ( todo & AndList ( restrictions )) . proj () def populate ( self , * restrictions , suppress_errors = False , return_exception_objects = False , reserve_jobs = False , order = \"original\" , limit = None , max_calls = None , display_progress = False , processes = 1 , make_kwargs = None , ): \"\"\" ``table.populate()`` calls ``table.make(key)`` for every primary key in ``self.key_source`` for which there is not already a tuple in table. :param restrictions: a list of restrictions each restrict (table.key_source - target.proj()) :param suppress_errors: if True, do not terminate execution. :param return_exception_objects: return error objects instead of just error messages :param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion :param order: \"original\"|\"reverse\"|\"random\" - the order of execution :param limit: if not None, check at most this many keys :param max_calls: if not None, populate at most this many keys :param display_progress: if True, report progress_bar :param processes: number of processes to use. Set to None to use all cores :param make_kwargs: Keyword arguments which do not affect the result of computation to be passed down to each ``make()`` call. Computation arguments should be specified within the pipeline e.g. using a `dj.Lookup` table. :type make_kwargs: dict, optional \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Populate cannot be called during a transaction.\" ) valid_order = [ \"original\" , \"reverse\" , \"random\" ] if order not in valid_order : raise DataJointError ( \"The order argument must be one of %s \" % str ( valid_order ) ) jobs = ( self . connection . schemas [ self . target . database ] . jobs if reserve_jobs else None ) # define and set up signal handler for SIGTERM: if reserve_jobs : def handler ( signum , frame ): logger . info ( \"Populate terminated by SIGTERM\" ) raise SystemExit ( \"SIGTERM received\" ) old_handler = signal . signal ( signal . SIGTERM , handler ) keys = ( self . _jobs_to_do ( restrictions ) - self . target ) . fetch ( \"KEY\" , limit = limit ) if order == \"reverse\" : keys . reverse () elif order == \"random\" : random . shuffle ( keys ) logger . debug ( \"Found %d keys to populate\" % len ( keys )) keys = keys [: max_calls ] nkeys = len ( keys ) if not nkeys : return processes = min ( _ for _ in ( processes , nkeys , mp . cpu_count ()) if _ ) error_list = [] populate_kwargs = dict ( suppress_errors = suppress_errors , return_exception_objects = return_exception_objects , make_kwargs = make_kwargs , ) if processes == 1 : for key in ( tqdm ( keys , desc = self . __class__ . __name__ ) if display_progress else keys ): error = self . _populate1 ( key , jobs , ** populate_kwargs ) if error is not None : error_list . append ( error ) else : # spawn multiple processes self . connection . close () # disconnect parent process from MySQL server del self . connection . _conn . ctx # SSLContext is not pickleable with mp . Pool ( processes , _initialize_populate , ( self , jobs , populate_kwargs ) ) as pool , ( tqdm ( desc = \"Processes: \" , total = nkeys ) if display_progress else contextlib . nullcontext () ) as progress_bar : for error in pool . imap ( _call_populate1 , keys , chunksize = 1 ): if error is not None : error_list . append ( error ) if display_progress : progress_bar . update () self . connection . connect () # reconnect parent process to MySQL server # restore original signal handler: if reserve_jobs : signal . signal ( signal . SIGTERM , old_handler ) if suppress_errors : return error_list def _populate1 ( self , key , jobs , suppress_errors , return_exception_objects , make_kwargs = None ): \"\"\" populates table for one source key, calling self.make inside a transaction. :param jobs: the jobs table or None if not reserve_jobs :param key: dict specifying job to populate :param suppress_errors: bool if errors should be suppressed and returned :param return_exception_objects: if True, errors must be returned as objects :return: (key, error) when suppress_errors=True, otherwise None \"\"\" make = self . _make_tuples if hasattr ( self , \"_make_tuples\" ) else self . make if jobs is None or jobs . reserve ( self . target . table_name , self . _job_key ( key )): self . connection . start_transaction () if key in self . target : # already populated self . connection . cancel_transaction () if jobs is not None : jobs . complete ( self . target . table_name , self . _job_key ( key )) else : logger . debug ( f \"Making { key } -> { self . target . full_table_name } \" ) self . __class__ . _allow_insert = True try : make ( dict ( key ), ** ( make_kwargs or {})) except ( KeyboardInterrupt , SystemExit , Exception ) as error : try : self . connection . cancel_transaction () except LostConnectionError : pass error_message = \" {exception}{msg} \" . format ( exception = error . __class__ . __name__ , msg = \": \" + str ( error ) if str ( error ) else \"\" , ) logger . debug ( f \"Error making { key } -> { self . target . full_table_name } - { error_message } \" ) if jobs is not None : # show error name and error message (if any) jobs . error ( self . target . table_name , self . _job_key ( key ), error_message = error_message , error_stack = traceback . format_exc (), ) if not suppress_errors or isinstance ( error , SystemExit ): raise else : logger . error ( error ) return key , error if return_exception_objects else error_message else : self . connection . commit_transaction () logger . debug ( f \"Success making { key } -> { self . target . full_table_name } \" ) if jobs is not None : jobs . complete ( self . target . table_name , self . _job_key ( key )) finally : self . __class__ . _allow_insert = False def progress ( self , * restrictions , display = True ): \"\"\" Report the progress of populating the table. :return: (remaining, total) -- numbers of tuples to be populated \"\"\" todo = self . _jobs_to_do ( restrictions ) total = len ( todo ) remaining = len ( todo - self . target ) if display : print ( \" %-20s \" % self . __class__ . __name__ , \"Completed %d of %d ( %2.1f%% ) %s \" % ( total - remaining , total , 100 - 100 * remaining / ( total + 1e-12 ), datetime . datetime . strftime ( datetime . datetime . now (), \"%Y-%m- %d %H:%M:%S\" ), ), flush = True , ) return remaining , total", "title": "AutoPopulate"}, {"location": "api/datajoint/autopopulate/#datajoint.autopopulate.AutoPopulate.key_source", "text": "Returns: Type Description the query expression that yields primary key values to be passed, sequentially, to the make method when populate() is called. The default value is the join of the parent tables references from the primary key. Subclasses may override they key_source to change the scope or the granularity of the make calls. Source code in datajoint/autopopulate.py 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 @property def key_source ( self ): \"\"\" :return: the query expression that yields primary key values to be passed, sequentially, to the ``make`` method when populate() is called. The default value is the join of the parent tables references from the primary key. Subclasses may override they key_source to change the scope or the granularity of the make calls. \"\"\" def _rename_attributes ( table , props ): return ( table . proj ( ** { attr : ref for attr , ref in props [ \"attr_map\" ] . items () if attr != ref } ) if props [ \"aliased\" ] else table . proj () ) if self . _key_source is None : parents = self . target . parents ( primary = True , as_objects = True , foreign_key_info = True ) if not parents : raise DataJointError ( \"A table must have dependencies \" \"from its primary key for auto-populate to work\" ) self . _key_source = _rename_attributes ( * parents [ 0 ]) for q in parents [ 1 :]: self . _key_source *= _rename_attributes ( * q ) return self . _key_source", "title": "key_source()"}, {"location": "api/datajoint/autopopulate/#datajoint.autopopulate.AutoPopulate.make", "text": "Derived classes must implement method make that fetches data from tables above them in the dependency hierarchy, restricting by the given key, computes secondary attributes, and inserts the new tuples into self. Source code in datajoint/autopopulate.py 91 92 93 94 95 96 97 98 99 def make ( self , key ): \"\"\" Derived classes must implement method `make` that fetches data from tables above them in the dependency hierarchy, restricting by the given key, computes secondary attributes, and inserts the new tuples into self. \"\"\" raise NotImplementedError ( \"Subclasses of AutoPopulate must implement the method `make`\" )", "title": "make()"}, {"location": "api/datajoint/autopopulate/#datajoint.autopopulate.AutoPopulate.target", "text": "Returns: Type Description table to be populated. In the typical case, dj.AutoPopulate is mixed into a dj.Table class by inheritance and the target is self. Source code in datajoint/autopopulate.py 101 102 103 104 105 106 107 108 @property def target ( self ): \"\"\" :return: table to be populated. In the typical case, dj.AutoPopulate is mixed into a dj.Table class by inheritance and the target is self. \"\"\" return self", "title": "target()"}, {"location": "api/datajoint/autopopulate/#datajoint.autopopulate.AutoPopulate.populate", "text": "table.populate() calls table.make(key) for every primary key in self.key_source for which there is not already a tuple in table. Parameters: Name Type Description Default restrictions a list of restrictions each restrict (table.key_source - target.proj()) required suppress_errors if True, do not terminate execution. False return_exception_objects return error objects instead of just error messages False reserve_jobs if True, reserve jobs to populate in asynchronous fashion False order \"original\"|\"reverse\"|\"random\" - the order of execution 'original' limit if not None, check at most this many keys None max_calls if not None, populate at most this many keys None display_progress if True, report progress_bar False processes number of processes to use. Set to None to use all cores 1 make_kwargs dict, optional Keyword arguments which do not affect the result of computation to be passed down to each make() call. Computation arguments should be specified within the pipeline e.g. using a dj.Lookup table. None Source code in datajoint/autopopulate.py 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 def populate ( self , * restrictions , suppress_errors = False , return_exception_objects = False , reserve_jobs = False , order = \"original\" , limit = None , max_calls = None , display_progress = False , processes = 1 , make_kwargs = None , ): \"\"\" ``table.populate()`` calls ``table.make(key)`` for every primary key in ``self.key_source`` for which there is not already a tuple in table. :param restrictions: a list of restrictions each restrict (table.key_source - target.proj()) :param suppress_errors: if True, do not terminate execution. :param return_exception_objects: return error objects instead of just error messages :param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion :param order: \"original\"|\"reverse\"|\"random\" - the order of execution :param limit: if not None, check at most this many keys :param max_calls: if not None, populate at most this many keys :param display_progress: if True, report progress_bar :param processes: number of processes to use. Set to None to use all cores :param make_kwargs: Keyword arguments which do not affect the result of computation to be passed down to each ``make()`` call. Computation arguments should be specified within the pipeline e.g. using a `dj.Lookup` table. :type make_kwargs: dict, optional \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Populate cannot be called during a transaction.\" ) valid_order = [ \"original\" , \"reverse\" , \"random\" ] if order not in valid_order : raise DataJointError ( \"The order argument must be one of %s \" % str ( valid_order ) ) jobs = ( self . connection . schemas [ self . target . database ] . jobs if reserve_jobs else None ) # define and set up signal handler for SIGTERM: if reserve_jobs : def handler ( signum , frame ): logger . info ( \"Populate terminated by SIGTERM\" ) raise SystemExit ( \"SIGTERM received\" ) old_handler = signal . signal ( signal . SIGTERM , handler ) keys = ( self . _jobs_to_do ( restrictions ) - self . target ) . fetch ( \"KEY\" , limit = limit ) if order == \"reverse\" : keys . reverse () elif order == \"random\" : random . shuffle ( keys ) logger . debug ( \"Found %d keys to populate\" % len ( keys )) keys = keys [: max_calls ] nkeys = len ( keys ) if not nkeys : return processes = min ( _ for _ in ( processes , nkeys , mp . cpu_count ()) if _ ) error_list = [] populate_kwargs = dict ( suppress_errors = suppress_errors , return_exception_objects = return_exception_objects , make_kwargs = make_kwargs , ) if processes == 1 : for key in ( tqdm ( keys , desc = self . __class__ . __name__ ) if display_progress else keys ): error = self . _populate1 ( key , jobs , ** populate_kwargs ) if error is not None : error_list . append ( error ) else : # spawn multiple processes self . connection . close () # disconnect parent process from MySQL server del self . connection . _conn . ctx # SSLContext is not pickleable with mp . Pool ( processes , _initialize_populate , ( self , jobs , populate_kwargs ) ) as pool , ( tqdm ( desc = \"Processes: \" , total = nkeys ) if display_progress else contextlib . nullcontext () ) as progress_bar : for error in pool . imap ( _call_populate1 , keys , chunksize = 1 ): if error is not None : error_list . append ( error ) if display_progress : progress_bar . update () self . connection . connect () # reconnect parent process to MySQL server # restore original signal handler: if reserve_jobs : signal . signal ( signal . SIGTERM , old_handler ) if suppress_errors : return error_list", "title": "populate()"}, {"location": "api/datajoint/autopopulate/#datajoint.autopopulate.AutoPopulate.progress", "text": "Report the progress of populating the table. Returns: Type Description (remaining, total) -- numbers of tuples to be populated Source code in datajoint/autopopulate.py 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 def progress ( self , * restrictions , display = True ): \"\"\" Report the progress of populating the table. :return: (remaining, total) -- numbers of tuples to be populated \"\"\" todo = self . _jobs_to_do ( restrictions ) total = len ( todo ) remaining = len ( todo - self . target ) if display : print ( \" %-20s \" % self . __class__ . __name__ , \"Completed %d of %d ( %2.1f%% ) %s \" % ( total - remaining , total , 100 - 100 * remaining / ( total + 1e-12 ), datetime . datetime . strftime ( datetime . datetime . now (), \"%Y-%m- %d %H:%M:%S\" ), ), flush = True , ) return remaining , total", "title": "progress()"}, {"location": "api/datajoint/blob/", "text": "(De)serialization methods for basic datatypes and numpy.ndarrays with provisions for mutual compatibility with Matlab-based serialization implemented by mYm. MatCell \u00b6 Bases: np . ndarray a numpy ndarray representing a Matlab cell array Source code in datajoint/blob.py 73 74 75 76 class MatCell ( np . ndarray ): \"\"\"a numpy ndarray representing a Matlab cell array\"\"\" pass MatStruct \u00b6 Bases: np . recarray numpy.recarray representing a Matlab struct array Source code in datajoint/blob.py 79 80 81 82 class MatStruct ( np . recarray ): \"\"\"numpy.recarray representing a Matlab struct array\"\"\" pass Blob \u00b6 Source code in datajoint/blob.py 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 class Blob : def __init__ ( self , squeeze = False ): self . _squeeze = squeeze self . _blob = None self . _pos = 0 self . protocol = None def set_dj0 ( self ): if not config . get ( \"enable_python_native_blobs\" ): raise DataJointError ( \"\"\"v0.12+ python native blobs disabled. See also: https://github.com/datajoint/datajoint-python#python-native-blobs\"\"\" ) self . protocol = b \"dj0 \\0 \" # when using new blob features def squeeze ( self , array , convert_to_scalar = True ): \"\"\" Simplify the input array - squeeze out all singleton dimensions. If convert_to_scalar, then convert zero-dimensional arrays to scalars \"\"\" if not self . _squeeze : return array array = array . squeeze () return array . item () if array . ndim == 0 and convert_to_scalar else array def unpack ( self , blob ): self . _blob = blob try : # decompress prefix = next ( p for p in compression if self . _blob [ self . _pos :] . startswith ( p ) ) except StopIteration : pass # assume uncompressed but could be unrecognized compression else : self . _pos += len ( prefix ) blob_size = self . read_value () blob = compression [ prefix ]( self . _blob [ self . _pos :]) assert len ( blob ) == blob_size self . _blob = blob self . _pos = 0 blob_format = self . read_zero_terminated_string () if blob_format in ( \"mYm\" , \"dj0\" ): return self . read_blob ( n_bytes = len ( self . _blob ) - self . _pos ) def read_blob ( self , n_bytes = None ): start = self . _pos data_structure_code = chr ( self . read_value ( \"uint8\" )) try : call = { # MATLAB-compatible, inherited from original mYm \"A\" : self . read_array , # matlab-compatible numeric arrays and scalars with ndim==0 \"P\" : self . read_sparse_array , # matlab sparse array -- not supported yet \"S\" : self . read_struct , # matlab struct array \"C\" : self . read_cell_array , # matlab cell array # basic data types \" \\xFF \" : self . read_none , # None \" \\x01 \" : self . read_tuple , # a Sequence (e.g. tuple) \" \\x02 \" : self . read_list , # a MutableSequence (e.g. list) \" \\x03 \" : self . read_set , # a Set \" \\x04 \" : self . read_dict , # a Mapping (e.g. dict) \" \\x05 \" : self . read_string , # a UTF8-encoded string \" \\x06 \" : self . read_bytes , # a ByteString \" \\x0a \" : self . read_int , # unbounded scalar int \" \\x0b \" : self . read_bool , # scalar boolean \" \\x0c \" : self . read_complex , # scalar 128-bit complex number \" \\x0d \" : self . read_float , # scalar 64-bit float \"F\" : self . read_recarray , # numpy array with fields, including recarrays \"d\" : self . read_decimal , # a decimal \"t\" : self . read_datetime , # date, time, or datetime \"u\" : self . read_uuid , # UUID }[ data_structure_code ] except KeyError : raise DataJointError ( 'Unknown data structure code \" %s \". Upgrade datajoint.' % data_structure_code ) v = call () if n_bytes is not None and self . _pos - start != n_bytes : raise DataJointError ( \"Blob length check failed! Invalid blob\" ) return v def pack_blob ( self , obj ): # original mYm-based serialization from datajoint-matlab if isinstance ( obj , MatCell ): return self . pack_cell_array ( obj ) if isinstance ( obj , MatStruct ): return self . pack_struct ( obj ) if isinstance ( obj , np . ndarray ) and obj . dtype . fields is None : return self . pack_array ( obj ) # blob types in the expanded dj0 blob format self . set_dj0 () if not isinstance ( obj , ( np . ndarray , np . number )): # python built-in data types if isinstance ( obj , bool ): return self . pack_bool ( obj ) if isinstance ( obj , int ): return self . pack_int ( obj ) if isinstance ( obj , complex ): return self . pack_complex ( obj ) if isinstance ( obj , float ): return self . pack_float ( obj ) if isinstance ( obj , np . ndarray ) and obj . dtype . fields : return self . pack_recarray ( np . array ( obj )) if isinstance ( obj , ( np . number , np . datetime64 )): return self . pack_array ( np . array ( obj )) if isinstance ( obj , ( bool , np . bool_ )): return self . pack_array ( np . array ( obj )) if isinstance ( obj , ( float , int , complex )): return self . pack_array ( np . array ( obj )) if isinstance ( obj , ( datetime . datetime , datetime . date , datetime . time )): return self . pack_datetime ( obj ) if isinstance ( obj , Decimal ): return self . pack_decimal ( obj ) if isinstance ( obj , uuid . UUID ): return self . pack_uuid ( obj ) if isinstance ( obj , collections . abc . Mapping ): return self . pack_dict ( obj ) if isinstance ( obj , str ): return self . pack_string ( obj ) if isinstance ( obj , collections . abc . ByteString ): return self . pack_bytes ( obj ) if isinstance ( obj , collections . abc . MutableSequence ): return self . pack_list ( obj ) if isinstance ( obj , collections . abc . Sequence ): return self . pack_tuple ( obj ) if isinstance ( obj , collections . abc . Set ): return self . pack_set ( obj ) if obj is None : return self . pack_none () raise DataJointError ( \"Packing object of type %s currently not supported!\" % type ( obj ) ) def read_array ( self ): n_dims = int ( self . read_value ()) shape = self . read_value ( count = n_dims ) n_elem = np . prod ( shape , dtype = int ) dtype_id , is_complex = self . read_value ( \"uint32\" , 2 ) # Get dtype from type id dtype = deserialize_lookup [ dtype_id ][ \"dtype\" ] # Check if name is void if deserialize_lookup [ dtype_id ][ \"scalar_type\" ] == \"VOID\" : data = np . array ( list ( self . read_blob ( self . read_value ()) for _ in range ( n_elem )), dtype = np . dtype ( \"O\" ), ) # Check if name is char elif deserialize_lookup [ dtype_id ][ \"scalar_type\" ] == \"CHAR\" : # compensate for MATLAB packing of char arrays data = self . read_value ( dtype , count = 2 * n_elem ) data = data [:: 2 ] . astype ( \"U1\" ) if n_dims == 2 and shape [ 0 ] == 1 or n_dims == 1 : compact = data . squeeze () data = ( compact if compact . shape == () else np . array ( \"\" . join ( data . squeeze ())) ) shape = ( 1 ,) else : data = self . read_value ( dtype , count = n_elem ) if is_complex : data = data + 1 j * self . read_value ( dtype , count = n_elem ) return self . squeeze ( data . reshape ( shape , order = \"F\" )) def pack_array ( self , array ): \"\"\" Serialize an np.ndarray into bytes. Scalars are encoded with ndim=0. \"\"\" if \"datetime64\" in array . dtype . name : self . set_dj0 () blob = ( b \"A\" + np . uint64 ( array . ndim ) . tobytes () + np . array ( array . shape , dtype = np . uint64 ) . tobytes () ) is_complex = np . iscomplexobj ( array ) if is_complex : array , imaginary = np . real ( array ), np . imag ( array ) try : type_id = serialize_lookup [ array . dtype ][ \"type_id\" ] except KeyError : # U is for unicode string if array . dtype . char == \"U\" : type_id = serialize_lookup [ np . dtype ( \"O\" )][ \"type_id\" ] else : raise DataJointError ( f \"Type { array . dtype } is ambiguous or unknown\" ) blob += np . array ([ type_id , is_complex ], dtype = np . uint32 ) . tobytes () if ( array . dtype . char == \"U\" or serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"VOID\" ): blob += b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for e in array . flatten ( order = \"F\" )) ) self . set_dj0 () # not supported by original mym elif serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"CHAR\" : blob += ( array . view ( np . uint8 ) . astype ( np . uint16 ) . tobytes () ) # convert to 16-bit chars for MATLAB else : # numeric arrays if array . ndim == 0 : # not supported by original mym self . set_dj0 () blob += array . tobytes ( order = \"F\" ) if is_complex : blob += imaginary . tobytes ( order = \"F\" ) return blob def read_recarray ( self ): \"\"\" Serialize an np.ndarray with fields, including recarrays \"\"\" n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] arrays = [ self . read_blob () for _ in range ( n_fields )] rec = np . empty ( arrays [ 0 ] . shape , np . dtype ([( f , t . dtype ) for f , t in zip ( field_names , arrays )]), ) for f , t in zip ( field_names , arrays ): rec [ f ] = t return rec . view ( np . recarray ) def pack_recarray ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"F\" + len_u32 ( array . dtype ) + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names self . pack_recarray ( array [ f ]) if array [ f ] . dtype . fields else self . pack_array ( array [ f ]) for f in array . dtype . names ) ) def read_sparse_array ( self ): raise DataJointError ( \"datajoint-python does not yet support sparse arrays. Issue (#590)\" ) def read_int ( self ): return int . from_bytes ( self . read_binary ( self . read_value ( \"uint16\" )), byteorder = \"little\" , signed = True ) @staticmethod def pack_int ( v ): n_bytes = v . bit_length () // 8 + 1 assert 0 < n_bytes <= 0xFFFF , \"Integers are limited to 65535 bytes\" return ( b \" \\x0a \" + np . uint16 ( n_bytes ) . tobytes () + v . to_bytes ( n_bytes , byteorder = \"little\" , signed = True ) ) def read_bool ( self ): return bool ( self . read_value ( \"bool\" )) @staticmethod def pack_bool ( v ): return b \" \\x0b \" + np . array ( v , dtype = \"bool\" ) . tobytes () def read_complex ( self ): return complex ( self . read_value ( \"complex128\" )) @staticmethod def pack_complex ( v ): return b \" \\x0c \" + np . array ( v , dtype = \"complex128\" ) . tobytes () def read_float ( self ): return float ( self . read_value ( \"float64\" )) @staticmethod def pack_float ( v ): return b \" \\x0d \" + np . array ( v , dtype = \"float64\" ) . tobytes () def read_decimal ( self ): return Decimal ( self . read_string ()) @staticmethod def pack_decimal ( d ): s = str ( d ) return b \"d\" + len_u64 ( s ) + s . encode () def read_string ( self ): return self . read_binary ( self . read_value ()) . decode () @staticmethod def pack_string ( s ): blob = s . encode () return b \" \\5 \" + len_u64 ( blob ) + blob def read_bytes ( self ): return self . read_binary ( self . read_value ()) @staticmethod def pack_bytes ( s ): return b \" \\6 \" + len_u64 ( s ) + s def read_none ( self ): pass @staticmethod def pack_none (): return b \" \\xFF \" def read_tuple ( self ): return tuple ( self . read_blob ( self . read_value ()) for _ in range ( self . read_value ()) ) def pack_tuple ( self , t ): return ( b \" \\1 \" + len_u64 ( t ) + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( i ) for i in t )) ) def read_list ( self ): return list ( self . read_blob ( self . read_value ()) for _ in range ( self . read_value ())) def pack_list ( self , t ): return ( b \" \\2 \" + len_u64 ( t ) + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( i ) for i in t )) ) def read_set ( self ): return set ( self . read_blob ( self . read_value ()) for _ in range ( self . read_value ())) def pack_set ( self , t ): return ( b \" \\3 \" + len_u64 ( t ) + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( i ) for i in t )) ) def read_dict ( self ): return dict ( ( self . read_blob ( self . read_value ()), self . read_blob ( self . read_value ())) for _ in range ( self . read_value ()) ) def pack_dict ( self , d ): return ( b \" \\4 \" + len_u64 ( d ) + b \"\" . join ( b \"\" . join (( len_u64 ( it ) + it ) for it in packed ) for packed in ( map ( self . pack_blob , pair ) for pair in d . items ()) ) ) def read_struct ( self ): \"\"\"deserialize matlab stuct\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = np . prod ( shape , dtype = int ) n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] raw_data = [ tuple ( self . read_blob ( n_bytes = int ( self . read_value ())) for _ in range ( n_fields ) ) for __ in range ( n_elem ) ] data = np . array ( raw_data , dtype = list ( zip ( field_names , repeat ( object )))) return self . squeeze ( data . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) . view ( MatStruct ) def pack_struct ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"S\" + np . array (( array . ndim ,) + array . shape , dtype = np . uint64 ) . tobytes () + len_u32 ( array . dtype . names ) # dimensionality + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for rec in array . flatten ( order = \"F\" ) for e in rec ) ) ) # values def read_cell_array ( self ): \"\"\"deserialize MATLAB cell array\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = int ( np . prod ( shape )) result = [ self . read_blob ( n_bytes = self . read_value ()) for _ in range ( n_elem )] return ( self . squeeze ( np . array ( result ) . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) ) . view ( MatCell ) def pack_cell_array ( self , array ): return ( b \"C\" + np . array (( array . ndim ,) + array . shape , dtype = np . uint64 ) . tobytes () + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for e in array . flatten ( order = \"F\" )) ) ) def read_datetime ( self ): \"\"\"deserialize datetime.date, .time, or .datetime\"\"\" date , time = self . read_value ( \"int32\" ), self . read_value ( \"int64\" ) date = ( datetime . date ( year = date // 10000 , month = ( date // 100 ) % 100 , day = date % 100 ) if date >= 0 else None ) time = ( datetime . time ( hour = ( time // 10000000000 ) % 100 , minute = ( time // 100000000 ) % 100 , second = ( time // 1000000 ) % 100 , microsecond = time % 1000000 , ) if time >= 0 else None ) return time and date and datetime . datetime . combine ( date , time ) or time or date @staticmethod def pack_datetime ( d ): if isinstance ( d , datetime . datetime ): date , time = d . date (), d . time () elif isinstance ( d , datetime . date ): date , time = d , None else : date , time = None , d return b \"t\" + ( np . int32 ( - 1 if date is None else ( date . year * 100 + date . month ) * 100 + date . day ) . tobytes () + np . int64 ( - 1 if time is None else (( time . hour * 100 + time . minute ) * 100 + time . second ) * 1000000 + time . microsecond ) . tobytes () ) def read_uuid ( self ): q = self . read_binary ( 16 ) return uuid . UUID ( bytes = q ) @staticmethod def pack_uuid ( obj ): return b \"u\" + obj . bytes def read_zero_terminated_string ( self ): target = self . _blob . find ( b \" \\0 \" , self . _pos ) data = self . _blob [ self . _pos : target ] . decode () self . _pos = target + 1 return data def read_value ( self , dtype = None , count = 1 ): if dtype is None : dtype = \"uint32\" if use_32bit_dims else \"uint64\" data = np . frombuffer ( self . _blob , dtype = dtype , count = count , offset = self . _pos ) self . _pos += data . dtype . itemsize * data . size return data [ 0 ] if count == 1 else data def read_binary ( self , size ): self . _pos += int ( size ) return self . _blob [ self . _pos - int ( size ) : self . _pos ] def pack ( self , obj , compress ): self . protocol = b \"mYm \\0 \" # will be replaced with dj0 if new features are used blob = self . pack_blob ( obj ) # this may reset the protocol and must precede protocol evaluation blob = self . protocol + blob if compress and len ( blob ) > 1000 : compressed = b \"ZL123 \\0 \" + len_u64 ( blob ) + zlib . compress ( blob ) if len ( compressed ) < len ( blob ): blob = compressed return blob squeeze ( array , convert_to_scalar = True ) \u00b6 Simplify the input array - squeeze out all singleton dimensions. If convert_to_scalar, then convert zero-dimensional arrays to scalars Source code in datajoint/blob.py 101 102 103 104 105 106 107 108 109 def squeeze ( self , array , convert_to_scalar = True ): \"\"\" Simplify the input array - squeeze out all singleton dimensions. If convert_to_scalar, then convert zero-dimensional arrays to scalars \"\"\" if not self . _squeeze : return array array = array . squeeze () return array . item () if array . ndim == 0 and convert_to_scalar else array pack_array ( array ) \u00b6 Serialize an np.ndarray into bytes. Scalars are encoded with ndim=0. Source code in datajoint/blob.py 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 def pack_array ( self , array ): \"\"\" Serialize an np.ndarray into bytes. Scalars are encoded with ndim=0. \"\"\" if \"datetime64\" in array . dtype . name : self . set_dj0 () blob = ( b \"A\" + np . uint64 ( array . ndim ) . tobytes () + np . array ( array . shape , dtype = np . uint64 ) . tobytes () ) is_complex = np . iscomplexobj ( array ) if is_complex : array , imaginary = np . real ( array ), np . imag ( array ) try : type_id = serialize_lookup [ array . dtype ][ \"type_id\" ] except KeyError : # U is for unicode string if array . dtype . char == \"U\" : type_id = serialize_lookup [ np . dtype ( \"O\" )][ \"type_id\" ] else : raise DataJointError ( f \"Type { array . dtype } is ambiguous or unknown\" ) blob += np . array ([ type_id , is_complex ], dtype = np . uint32 ) . tobytes () if ( array . dtype . char == \"U\" or serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"VOID\" ): blob += b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for e in array . flatten ( order = \"F\" )) ) self . set_dj0 () # not supported by original mym elif serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"CHAR\" : blob += ( array . view ( np . uint8 ) . astype ( np . uint16 ) . tobytes () ) # convert to 16-bit chars for MATLAB else : # numeric arrays if array . ndim == 0 : # not supported by original mym self . set_dj0 () blob += array . tobytes ( order = \"F\" ) if is_complex : blob += imaginary . tobytes ( order = \"F\" ) return blob read_recarray () \u00b6 Serialize an np.ndarray with fields, including recarrays Source code in datajoint/blob.py 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 def read_recarray ( self ): \"\"\" Serialize an np.ndarray with fields, including recarrays \"\"\" n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] arrays = [ self . read_blob () for _ in range ( n_fields )] rec = np . empty ( arrays [ 0 ] . shape , np . dtype ([( f , t . dtype ) for f , t in zip ( field_names , arrays )]), ) for f , t in zip ( field_names , arrays ): rec [ f ] = t return rec . view ( np . recarray ) pack_recarray ( array ) \u00b6 Serialize a Matlab struct array Source code in datajoint/blob.py 317 318 319 320 321 322 323 324 325 326 327 328 329 330 def pack_recarray ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"F\" + len_u32 ( array . dtype ) + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names self . pack_recarray ( array [ f ]) if array [ f ] . dtype . fields else self . pack_array ( array [ f ]) for f in array . dtype . names ) ) read_struct () \u00b6 deserialize matlab stuct Source code in datajoint/blob.py 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 def read_struct ( self ): \"\"\"deserialize matlab stuct\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = np . prod ( shape , dtype = int ) n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] raw_data = [ tuple ( self . read_blob ( n_bytes = int ( self . read_value ())) for _ in range ( n_fields ) ) for __ in range ( n_elem ) ] data = np . array ( raw_data , dtype = list ( zip ( field_names , repeat ( object )))) return self . squeeze ( data . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) . view ( MatStruct ) pack_struct ( array ) \u00b6 Serialize a Matlab struct array Source code in datajoint/blob.py 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 def pack_struct ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"S\" + np . array (( array . ndim ,) + array . shape , dtype = np . uint64 ) . tobytes () + len_u32 ( array . dtype . names ) # dimensionality + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for rec in array . flatten ( order = \"F\" ) for e in rec ) ) ) # values read_cell_array () \u00b6 deserialize MATLAB cell array Source code in datajoint/blob.py 487 488 489 490 491 492 493 494 495 496 497 def read_cell_array ( self ): \"\"\"deserialize MATLAB cell array\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = int ( np . prod ( shape )) result = [ self . read_blob ( n_bytes = self . read_value ()) for _ in range ( n_elem )] return ( self . squeeze ( np . array ( result ) . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) ) . view ( MatCell ) read_datetime () \u00b6 deserialize datetime.date, .time, or .datetime Source code in datajoint/blob.py 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 def read_datetime ( self ): \"\"\"deserialize datetime.date, .time, or .datetime\"\"\" date , time = self . read_value ( \"int32\" ), self . read_value ( \"int64\" ) date = ( datetime . date ( year = date // 10000 , month = ( date // 100 ) % 100 , day = date % 100 ) if date >= 0 else None ) time = ( datetime . time ( hour = ( time // 10000000000 ) % 100 , minute = ( time // 100000000 ) % 100 , second = ( time // 1000000 ) % 100 , microsecond = time % 1000000 , ) if time >= 0 else None ) return time and date and datetime . datetime . combine ( date , time ) or time or date", "title": "blob.py"}, {"location": "api/datajoint/blob/#datajoint.blob.MatCell", "text": "Bases: np . ndarray a numpy ndarray representing a Matlab cell array Source code in datajoint/blob.py 73 74 75 76 class MatCell ( np . ndarray ): \"\"\"a numpy ndarray representing a Matlab cell array\"\"\" pass", "title": "MatCell"}, {"location": "api/datajoint/blob/#datajoint.blob.MatStruct", "text": "Bases: np . recarray numpy.recarray representing a Matlab struct array Source code in datajoint/blob.py 79 80 81 82 class MatStruct ( np . recarray ): \"\"\"numpy.recarray representing a Matlab struct array\"\"\" pass", "title": "MatStruct"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob", "text": "Source code in datajoint/blob.py 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 class Blob : def __init__ ( self , squeeze = False ): self . _squeeze = squeeze self . _blob = None self . _pos = 0 self . protocol = None def set_dj0 ( self ): if not config . get ( \"enable_python_native_blobs\" ): raise DataJointError ( \"\"\"v0.12+ python native blobs disabled. See also: https://github.com/datajoint/datajoint-python#python-native-blobs\"\"\" ) self . protocol = b \"dj0 \\0 \" # when using new blob features def squeeze ( self , array , convert_to_scalar = True ): \"\"\" Simplify the input array - squeeze out all singleton dimensions. If convert_to_scalar, then convert zero-dimensional arrays to scalars \"\"\" if not self . _squeeze : return array array = array . squeeze () return array . item () if array . ndim == 0 and convert_to_scalar else array def unpack ( self , blob ): self . _blob = blob try : # decompress prefix = next ( p for p in compression if self . _blob [ self . _pos :] . startswith ( p ) ) except StopIteration : pass # assume uncompressed but could be unrecognized compression else : self . _pos += len ( prefix ) blob_size = self . read_value () blob = compression [ prefix ]( self . _blob [ self . _pos :]) assert len ( blob ) == blob_size self . _blob = blob self . _pos = 0 blob_format = self . read_zero_terminated_string () if blob_format in ( \"mYm\" , \"dj0\" ): return self . read_blob ( n_bytes = len ( self . _blob ) - self . _pos ) def read_blob ( self , n_bytes = None ): start = self . _pos data_structure_code = chr ( self . read_value ( \"uint8\" )) try : call = { # MATLAB-compatible, inherited from original mYm \"A\" : self . read_array , # matlab-compatible numeric arrays and scalars with ndim==0 \"P\" : self . read_sparse_array , # matlab sparse array -- not supported yet \"S\" : self . read_struct , # matlab struct array \"C\" : self . read_cell_array , # matlab cell array # basic data types \" \\xFF \" : self . read_none , # None \" \\x01 \" : self . read_tuple , # a Sequence (e.g. tuple) \" \\x02 \" : self . read_list , # a MutableSequence (e.g. list) \" \\x03 \" : self . read_set , # a Set \" \\x04 \" : self . read_dict , # a Mapping (e.g. dict) \" \\x05 \" : self . read_string , # a UTF8-encoded string \" \\x06 \" : self . read_bytes , # a ByteString \" \\x0a \" : self . read_int , # unbounded scalar int \" \\x0b \" : self . read_bool , # scalar boolean \" \\x0c \" : self . read_complex , # scalar 128-bit complex number \" \\x0d \" : self . read_float , # scalar 64-bit float \"F\" : self . read_recarray , # numpy array with fields, including recarrays \"d\" : self . read_decimal , # a decimal \"t\" : self . read_datetime , # date, time, or datetime \"u\" : self . read_uuid , # UUID }[ data_structure_code ] except KeyError : raise DataJointError ( 'Unknown data structure code \" %s \". Upgrade datajoint.' % data_structure_code ) v = call () if n_bytes is not None and self . _pos - start != n_bytes : raise DataJointError ( \"Blob length check failed! Invalid blob\" ) return v def pack_blob ( self , obj ): # original mYm-based serialization from datajoint-matlab if isinstance ( obj , MatCell ): return self . pack_cell_array ( obj ) if isinstance ( obj , MatStruct ): return self . pack_struct ( obj ) if isinstance ( obj , np . ndarray ) and obj . dtype . fields is None : return self . pack_array ( obj ) # blob types in the expanded dj0 blob format self . set_dj0 () if not isinstance ( obj , ( np . ndarray , np . number )): # python built-in data types if isinstance ( obj , bool ): return self . pack_bool ( obj ) if isinstance ( obj , int ): return self . pack_int ( obj ) if isinstance ( obj , complex ): return self . pack_complex ( obj ) if isinstance ( obj , float ): return self . pack_float ( obj ) if isinstance ( obj , np . ndarray ) and obj . dtype . fields : return self . pack_recarray ( np . array ( obj )) if isinstance ( obj , ( np . number , np . datetime64 )): return self . pack_array ( np . array ( obj )) if isinstance ( obj , ( bool , np . bool_ )): return self . pack_array ( np . array ( obj )) if isinstance ( obj , ( float , int , complex )): return self . pack_array ( np . array ( obj )) if isinstance ( obj , ( datetime . datetime , datetime . date , datetime . time )): return self . pack_datetime ( obj ) if isinstance ( obj , Decimal ): return self . pack_decimal ( obj ) if isinstance ( obj , uuid . UUID ): return self . pack_uuid ( obj ) if isinstance ( obj , collections . abc . Mapping ): return self . pack_dict ( obj ) if isinstance ( obj , str ): return self . pack_string ( obj ) if isinstance ( obj , collections . abc . ByteString ): return self . pack_bytes ( obj ) if isinstance ( obj , collections . abc . MutableSequence ): return self . pack_list ( obj ) if isinstance ( obj , collections . abc . Sequence ): return self . pack_tuple ( obj ) if isinstance ( obj , collections . abc . Set ): return self . pack_set ( obj ) if obj is None : return self . pack_none () raise DataJointError ( \"Packing object of type %s currently not supported!\" % type ( obj ) ) def read_array ( self ): n_dims = int ( self . read_value ()) shape = self . read_value ( count = n_dims ) n_elem = np . prod ( shape , dtype = int ) dtype_id , is_complex = self . read_value ( \"uint32\" , 2 ) # Get dtype from type id dtype = deserialize_lookup [ dtype_id ][ \"dtype\" ] # Check if name is void if deserialize_lookup [ dtype_id ][ \"scalar_type\" ] == \"VOID\" : data = np . array ( list ( self . read_blob ( self . read_value ()) for _ in range ( n_elem )), dtype = np . dtype ( \"O\" ), ) # Check if name is char elif deserialize_lookup [ dtype_id ][ \"scalar_type\" ] == \"CHAR\" : # compensate for MATLAB packing of char arrays data = self . read_value ( dtype , count = 2 * n_elem ) data = data [:: 2 ] . astype ( \"U1\" ) if n_dims == 2 and shape [ 0 ] == 1 or n_dims == 1 : compact = data . squeeze () data = ( compact if compact . shape == () else np . array ( \"\" . join ( data . squeeze ())) ) shape = ( 1 ,) else : data = self . read_value ( dtype , count = n_elem ) if is_complex : data = data + 1 j * self . read_value ( dtype , count = n_elem ) return self . squeeze ( data . reshape ( shape , order = \"F\" )) def pack_array ( self , array ): \"\"\" Serialize an np.ndarray into bytes. Scalars are encoded with ndim=0. \"\"\" if \"datetime64\" in array . dtype . name : self . set_dj0 () blob = ( b \"A\" + np . uint64 ( array . ndim ) . tobytes () + np . array ( array . shape , dtype = np . uint64 ) . tobytes () ) is_complex = np . iscomplexobj ( array ) if is_complex : array , imaginary = np . real ( array ), np . imag ( array ) try : type_id = serialize_lookup [ array . dtype ][ \"type_id\" ] except KeyError : # U is for unicode string if array . dtype . char == \"U\" : type_id = serialize_lookup [ np . dtype ( \"O\" )][ \"type_id\" ] else : raise DataJointError ( f \"Type { array . dtype } is ambiguous or unknown\" ) blob += np . array ([ type_id , is_complex ], dtype = np . uint32 ) . tobytes () if ( array . dtype . char == \"U\" or serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"VOID\" ): blob += b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for e in array . flatten ( order = \"F\" )) ) self . set_dj0 () # not supported by original mym elif serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"CHAR\" : blob += ( array . view ( np . uint8 ) . astype ( np . uint16 ) . tobytes () ) # convert to 16-bit chars for MATLAB else : # numeric arrays if array . ndim == 0 : # not supported by original mym self . set_dj0 () blob += array . tobytes ( order = \"F\" ) if is_complex : blob += imaginary . tobytes ( order = \"F\" ) return blob def read_recarray ( self ): \"\"\" Serialize an np.ndarray with fields, including recarrays \"\"\" n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] arrays = [ self . read_blob () for _ in range ( n_fields )] rec = np . empty ( arrays [ 0 ] . shape , np . dtype ([( f , t . dtype ) for f , t in zip ( field_names , arrays )]), ) for f , t in zip ( field_names , arrays ): rec [ f ] = t return rec . view ( np . recarray ) def pack_recarray ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"F\" + len_u32 ( array . dtype ) + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names self . pack_recarray ( array [ f ]) if array [ f ] . dtype . fields else self . pack_array ( array [ f ]) for f in array . dtype . names ) ) def read_sparse_array ( self ): raise DataJointError ( \"datajoint-python does not yet support sparse arrays. Issue (#590)\" ) def read_int ( self ): return int . from_bytes ( self . read_binary ( self . read_value ( \"uint16\" )), byteorder = \"little\" , signed = True ) @staticmethod def pack_int ( v ): n_bytes = v . bit_length () // 8 + 1 assert 0 < n_bytes <= 0xFFFF , \"Integers are limited to 65535 bytes\" return ( b \" \\x0a \" + np . uint16 ( n_bytes ) . tobytes () + v . to_bytes ( n_bytes , byteorder = \"little\" , signed = True ) ) def read_bool ( self ): return bool ( self . read_value ( \"bool\" )) @staticmethod def pack_bool ( v ): return b \" \\x0b \" + np . array ( v , dtype = \"bool\" ) . tobytes () def read_complex ( self ): return complex ( self . read_value ( \"complex128\" )) @staticmethod def pack_complex ( v ): return b \" \\x0c \" + np . array ( v , dtype = \"complex128\" ) . tobytes () def read_float ( self ): return float ( self . read_value ( \"float64\" )) @staticmethod def pack_float ( v ): return b \" \\x0d \" + np . array ( v , dtype = \"float64\" ) . tobytes () def read_decimal ( self ): return Decimal ( self . read_string ()) @staticmethod def pack_decimal ( d ): s = str ( d ) return b \"d\" + len_u64 ( s ) + s . encode () def read_string ( self ): return self . read_binary ( self . read_value ()) . decode () @staticmethod def pack_string ( s ): blob = s . encode () return b \" \\5 \" + len_u64 ( blob ) + blob def read_bytes ( self ): return self . read_binary ( self . read_value ()) @staticmethod def pack_bytes ( s ): return b \" \\6 \" + len_u64 ( s ) + s def read_none ( self ): pass @staticmethod def pack_none (): return b \" \\xFF \" def read_tuple ( self ): return tuple ( self . read_blob ( self . read_value ()) for _ in range ( self . read_value ()) ) def pack_tuple ( self , t ): return ( b \" \\1 \" + len_u64 ( t ) + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( i ) for i in t )) ) def read_list ( self ): return list ( self . read_blob ( self . read_value ()) for _ in range ( self . read_value ())) def pack_list ( self , t ): return ( b \" \\2 \" + len_u64 ( t ) + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( i ) for i in t )) ) def read_set ( self ): return set ( self . read_blob ( self . read_value ()) for _ in range ( self . read_value ())) def pack_set ( self , t ): return ( b \" \\3 \" + len_u64 ( t ) + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( i ) for i in t )) ) def read_dict ( self ): return dict ( ( self . read_blob ( self . read_value ()), self . read_blob ( self . read_value ())) for _ in range ( self . read_value ()) ) def pack_dict ( self , d ): return ( b \" \\4 \" + len_u64 ( d ) + b \"\" . join ( b \"\" . join (( len_u64 ( it ) + it ) for it in packed ) for packed in ( map ( self . pack_blob , pair ) for pair in d . items ()) ) ) def read_struct ( self ): \"\"\"deserialize matlab stuct\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = np . prod ( shape , dtype = int ) n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] raw_data = [ tuple ( self . read_blob ( n_bytes = int ( self . read_value ())) for _ in range ( n_fields ) ) for __ in range ( n_elem ) ] data = np . array ( raw_data , dtype = list ( zip ( field_names , repeat ( object )))) return self . squeeze ( data . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) . view ( MatStruct ) def pack_struct ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"S\" + np . array (( array . ndim ,) + array . shape , dtype = np . uint64 ) . tobytes () + len_u32 ( array . dtype . names ) # dimensionality + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for rec in array . flatten ( order = \"F\" ) for e in rec ) ) ) # values def read_cell_array ( self ): \"\"\"deserialize MATLAB cell array\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = int ( np . prod ( shape )) result = [ self . read_blob ( n_bytes = self . read_value ()) for _ in range ( n_elem )] return ( self . squeeze ( np . array ( result ) . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) ) . view ( MatCell ) def pack_cell_array ( self , array ): return ( b \"C\" + np . array (( array . ndim ,) + array . shape , dtype = np . uint64 ) . tobytes () + b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for e in array . flatten ( order = \"F\" )) ) ) def read_datetime ( self ): \"\"\"deserialize datetime.date, .time, or .datetime\"\"\" date , time = self . read_value ( \"int32\" ), self . read_value ( \"int64\" ) date = ( datetime . date ( year = date // 10000 , month = ( date // 100 ) % 100 , day = date % 100 ) if date >= 0 else None ) time = ( datetime . time ( hour = ( time // 10000000000 ) % 100 , minute = ( time // 100000000 ) % 100 , second = ( time // 1000000 ) % 100 , microsecond = time % 1000000 , ) if time >= 0 else None ) return time and date and datetime . datetime . combine ( date , time ) or time or date @staticmethod def pack_datetime ( d ): if isinstance ( d , datetime . datetime ): date , time = d . date (), d . time () elif isinstance ( d , datetime . date ): date , time = d , None else : date , time = None , d return b \"t\" + ( np . int32 ( - 1 if date is None else ( date . year * 100 + date . month ) * 100 + date . day ) . tobytes () + np . int64 ( - 1 if time is None else (( time . hour * 100 + time . minute ) * 100 + time . second ) * 1000000 + time . microsecond ) . tobytes () ) def read_uuid ( self ): q = self . read_binary ( 16 ) return uuid . UUID ( bytes = q ) @staticmethod def pack_uuid ( obj ): return b \"u\" + obj . bytes def read_zero_terminated_string ( self ): target = self . _blob . find ( b \" \\0 \" , self . _pos ) data = self . _blob [ self . _pos : target ] . decode () self . _pos = target + 1 return data def read_value ( self , dtype = None , count = 1 ): if dtype is None : dtype = \"uint32\" if use_32bit_dims else \"uint64\" data = np . frombuffer ( self . _blob , dtype = dtype , count = count , offset = self . _pos ) self . _pos += data . dtype . itemsize * data . size return data [ 0 ] if count == 1 else data def read_binary ( self , size ): self . _pos += int ( size ) return self . _blob [ self . _pos - int ( size ) : self . _pos ] def pack ( self , obj , compress ): self . protocol = b \"mYm \\0 \" # will be replaced with dj0 if new features are used blob = self . pack_blob ( obj ) # this may reset the protocol and must precede protocol evaluation blob = self . protocol + blob if compress and len ( blob ) > 1000 : compressed = b \"ZL123 \\0 \" + len_u64 ( blob ) + zlib . compress ( blob ) if len ( compressed ) < len ( blob ): blob = compressed return blob", "title": "Blob"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.squeeze", "text": "Simplify the input array - squeeze out all singleton dimensions. If convert_to_scalar, then convert zero-dimensional arrays to scalars Source code in datajoint/blob.py 101 102 103 104 105 106 107 108 109 def squeeze ( self , array , convert_to_scalar = True ): \"\"\" Simplify the input array - squeeze out all singleton dimensions. If convert_to_scalar, then convert zero-dimensional arrays to scalars \"\"\" if not self . _squeeze : return array array = array . squeeze () return array . item () if array . ndim == 0 and convert_to_scalar else array", "title": "squeeze()"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.pack_array", "text": "Serialize an np.ndarray into bytes. Scalars are encoded with ndim=0. Source code in datajoint/blob.py 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 def pack_array ( self , array ): \"\"\" Serialize an np.ndarray into bytes. Scalars are encoded with ndim=0. \"\"\" if \"datetime64\" in array . dtype . name : self . set_dj0 () blob = ( b \"A\" + np . uint64 ( array . ndim ) . tobytes () + np . array ( array . shape , dtype = np . uint64 ) . tobytes () ) is_complex = np . iscomplexobj ( array ) if is_complex : array , imaginary = np . real ( array ), np . imag ( array ) try : type_id = serialize_lookup [ array . dtype ][ \"type_id\" ] except KeyError : # U is for unicode string if array . dtype . char == \"U\" : type_id = serialize_lookup [ np . dtype ( \"O\" )][ \"type_id\" ] else : raise DataJointError ( f \"Type { array . dtype } is ambiguous or unknown\" ) blob += np . array ([ type_id , is_complex ], dtype = np . uint32 ) . tobytes () if ( array . dtype . char == \"U\" or serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"VOID\" ): blob += b \"\" . join ( len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for e in array . flatten ( order = \"F\" )) ) self . set_dj0 () # not supported by original mym elif serialize_lookup [ array . dtype ][ \"scalar_type\" ] == \"CHAR\" : blob += ( array . view ( np . uint8 ) . astype ( np . uint16 ) . tobytes () ) # convert to 16-bit chars for MATLAB else : # numeric arrays if array . ndim == 0 : # not supported by original mym self . set_dj0 () blob += array . tobytes ( order = \"F\" ) if is_complex : blob += imaginary . tobytes ( order = \"F\" ) return blob", "title": "pack_array()"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.read_recarray", "text": "Serialize an np.ndarray with fields, including recarrays Source code in datajoint/blob.py 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 def read_recarray ( self ): \"\"\" Serialize an np.ndarray with fields, including recarrays \"\"\" n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] arrays = [ self . read_blob () for _ in range ( n_fields )] rec = np . empty ( arrays [ 0 ] . shape , np . dtype ([( f , t . dtype ) for f , t in zip ( field_names , arrays )]), ) for f , t in zip ( field_names , arrays ): rec [ f ] = t return rec . view ( np . recarray )", "title": "read_recarray()"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.pack_recarray", "text": "Serialize a Matlab struct array Source code in datajoint/blob.py 317 318 319 320 321 322 323 324 325 326 327 328 329 330 def pack_recarray ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"F\" + len_u32 ( array . dtype ) + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names self . pack_recarray ( array [ f ]) if array [ f ] . dtype . fields else self . pack_array ( array [ f ]) for f in array . dtype . names ) )", "title": "pack_recarray()"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.read_struct", "text": "deserialize matlab stuct Source code in datajoint/blob.py 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 def read_struct ( self ): \"\"\"deserialize matlab stuct\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = np . prod ( shape , dtype = int ) n_fields = self . read_value ( \"uint32\" ) if not n_fields : return np . array ( None ) # empty array field_names = [ self . read_zero_terminated_string () for _ in range ( n_fields )] raw_data = [ tuple ( self . read_blob ( n_bytes = int ( self . read_value ())) for _ in range ( n_fields ) ) for __ in range ( n_elem ) ] data = np . array ( raw_data , dtype = list ( zip ( field_names , repeat ( object )))) return self . squeeze ( data . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) . view ( MatStruct )", "title": "read_struct()"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.pack_struct", "text": "Serialize a Matlab struct array Source code in datajoint/blob.py 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 def pack_struct ( self , array ): \"\"\"Serialize a Matlab struct array\"\"\" return ( b \"S\" + np . array (( array . ndim ,) + array . shape , dtype = np . uint64 ) . tobytes () + len_u32 ( array . dtype . names ) # dimensionality + \" \\0 \" . join ( array . dtype . names ) . encode () # number of fields + b \" \\0 \" + b \"\" . join ( # field names len_u64 ( it ) + it for it in ( self . pack_blob ( e ) for rec in array . flatten ( order = \"F\" ) for e in rec ) ) ) # values", "title": "pack_struct()"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.read_cell_array", "text": "deserialize MATLAB cell array Source code in datajoint/blob.py 487 488 489 490 491 492 493 494 495 496 497 def read_cell_array ( self ): \"\"\"deserialize MATLAB cell array\"\"\" n_dims = self . read_value () shape = self . read_value ( count = n_dims ) n_elem = int ( np . prod ( shape )) result = [ self . read_blob ( n_bytes = self . read_value ()) for _ in range ( n_elem )] return ( self . squeeze ( np . array ( result ) . reshape ( shape , order = \"F\" ), convert_to_scalar = False ) ) . view ( MatCell )", "title": "read_cell_array()"}, {"location": "api/datajoint/blob/#datajoint.blob.Blob.read_datetime", "text": "deserialize datetime.date, .time, or .datetime Source code in datajoint/blob.py 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 def read_datetime ( self ): \"\"\"deserialize datetime.date, .time, or .datetime\"\"\" date , time = self . read_value ( \"int32\" ), self . read_value ( \"int64\" ) date = ( datetime . date ( year = date // 10000 , month = ( date // 100 ) % 100 , day = date % 100 ) if date >= 0 else None ) time = ( datetime . time ( hour = ( time // 10000000000 ) % 100 , minute = ( time // 100000000 ) % 100 , second = ( time // 1000000 ) % 100 , microsecond = time % 1000000 , ) if time >= 0 else None ) return time and date and datetime . datetime . combine ( date , time ) or time or date", "title": "read_datetime()"}, {"location": "api/datajoint/condition/", "text": "methods for generating SQL WHERE clauses from datajoint restriction conditions PromiscuousOperand \u00b6 A container for an operand to ignore join compatibility Source code in datajoint/condition.py 14 15 16 17 18 19 20 class PromiscuousOperand : \"\"\" A container for an operand to ignore join compatibility \"\"\" def __init__ ( self , operand ): self . operand = operand AndList \u00b6 Bases: list A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 Source code in datajoint/condition.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 class AndList ( list ): \"\"\" A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 \"\"\" def append ( self , restriction ): if isinstance ( restriction , AndList ): # extend to reduce nesting self . extend ( restriction ) else : super () . append ( restriction ) Not \u00b6 invert restriction Source code in datajoint/condition.py 43 44 45 46 47 class Not : \"\"\"invert restriction\"\"\" def __init__ ( self , restriction ): self . restriction = restriction assert_join_compatibility ( expr1 , expr2 ) \u00b6 Determine if expressions expr1 and expr2 are join-compatible. To be join-compatible, the matching attributes in the two expressions must be in the primary key of one or the other expression. Raises an exception if not compatible. Parameters: Name Type Description Default expr1 A QueryExpression object required expr2 A QueryExpression object required Source code in datajoint/condition.py 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 def assert_join_compatibility ( expr1 , expr2 ): \"\"\" Determine if expressions expr1 and expr2 are join-compatible. To be join-compatible, the matching attributes in the two expressions must be in the primary key of one or the other expression. Raises an exception if not compatible. :param expr1: A QueryExpression object :param expr2: A QueryExpression object \"\"\" from .expression import QueryExpression , U for rel in ( expr1 , expr2 ): if not isinstance ( rel , ( U , QueryExpression )): raise DataJointError ( \"Object %r is not a QueryExpression and cannot be joined.\" % rel ) if not isinstance ( expr1 , U ) and not isinstance ( expr2 , U ): # dj.U is always compatible try : raise DataJointError ( \"Cannot join query expressions on dependent attribute ` %s `\" % next ( r for r in set ( expr1 . heading . secondary_attributes ) . intersection ( expr2 . heading . secondary_attributes ) ) ) except StopIteration : pass # all ok make_condition ( query_expression , condition , columns ) \u00b6 Translate the input condition into the equivalent SQL condition (a string) Parameters: Name Type Description Default query_expression a dj.QueryExpression object to apply condition required condition any valid restriction object. required columns a set passed by reference to collect all column names used in the condition. required Returns: Type Description an SQL condition string or a boolean value. Source code in datajoint/condition.py 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 def make_condition ( query_expression , condition , columns ): \"\"\" Translate the input condition into the equivalent SQL condition (a string) :param query_expression: a dj.QueryExpression object to apply condition :param condition: any valid restriction object. :param columns: a set passed by reference to collect all column names used in the condition. :return: an SQL condition string or a boolean value. \"\"\" from .expression import QueryExpression , Aggregation , U def prep_value ( k , v ): \"\"\"prepare value v for inclusion as a string in an SQL condition\"\"\" if query_expression . heading [ k ] . uuid : if not isinstance ( v , uuid . UUID ): try : v = uuid . UUID ( v ) except ( AttributeError , ValueError ): raise DataJointError ( \"Badly formed UUID {v} in restriction by ` {k} `\" . format ( k = k , v = v ) ) return \"X' %s '\" % v . bytes . hex () if isinstance ( v , ( datetime . date , datetime . datetime , datetime . time , decimal . Decimal ) ): return '\" %s \"' % v if isinstance ( v , str ): return '\" %s \"' % v . replace ( \"%\" , \" %% \" ) . replace ( \" \\\\ \" , \" \\\\\\\\ \" ) return \" %r \" % v negate = False while isinstance ( condition , Not ): negate = not negate condition = condition . restriction template = \"NOT ( %s )\" if negate else \" %s \" # restrict by string if isinstance ( condition , str ): columns . update ( extract_column_names ( condition )) return template % condition . strip () . replace ( \"%\" , \" %% \" ) # escape %, see issue #376 # restrict by AndList if isinstance ( condition , AndList ): # omit all conditions that evaluate to True items = [ item for item in ( make_condition ( query_expression , cond , columns ) for cond in condition ) if item is not True ] if any ( item is False for item in items ): return negate # if any item is False, the whole thing is False if not items : return not negate # and empty AndList is True return template % ( \"(\" + \") AND (\" . join ( items ) + \")\" ) # restriction by dj.U evaluates to True if isinstance ( condition , U ): return not negate # restrict by boolean if isinstance ( condition , bool ): return negate != condition # restrict by a mapping/dict -- convert to an AndList of string equality conditions if isinstance ( condition , collections . abc . Mapping ): common_attributes = set ( condition ) . intersection ( query_expression . heading . names ) if not common_attributes : return not negate # no matching attributes -> evaluates to True columns . update ( common_attributes ) return template % ( \"(\" + \") AND (\" . join ( \"` %s ` %s \" % ( k , \" IS NULL\" if condition [ k ] is None else f \"= { prep_value ( k , condition [ k ]) } \" , ) for k in common_attributes ) + \")\" ) # restrict by a numpy record -- convert to an AndList of string equality conditions if isinstance ( condition , numpy . void ): common_attributes = set ( condition . dtype . fields ) . intersection ( query_expression . heading . names ) if not common_attributes : return not negate # no matching attributes -> evaluate to True columns . update ( common_attributes ) return template % ( \"(\" + \") AND (\" . join ( \"` %s `= %s \" % ( k , prep_value ( k , condition [ k ])) for k in common_attributes ) + \")\" ) # restrict by a QueryExpression subclass -- trigger instantiation and move on if inspect . isclass ( condition ) and issubclass ( condition , QueryExpression ): condition = condition () # restrict by another expression (aka semijoin and antijoin) check_compatibility = True if isinstance ( condition , PromiscuousOperand ): condition = condition . operand check_compatibility = False if isinstance ( condition , QueryExpression ): if check_compatibility : assert_join_compatibility ( query_expression , condition ) common_attributes = [ q for q in condition . heading . names if q in query_expression . heading . names ] columns . update ( common_attributes ) if isinstance ( condition , Aggregation ): condition = condition . make_subquery () return ( # without common attributes, any non-empty set matches everything ( not negate if condition else negate ) if not common_attributes else \"( {fields} ) {not_} in ( {subquery} )\" . format ( fields = \"`\" + \"`,`\" . join ( common_attributes ) + \"`\" , not_ = \"not \" if negate else \"\" , subquery = condition . make_sql ( common_attributes ), ) ) # restrict by pandas.DataFrames if isinstance ( condition , pandas . DataFrame ): condition = condition . to_records () # convert to numpy.recarray and move on # if iterable (but not a string, a QueryExpression, or an AndList), treat as an OrList try : or_list = [ make_condition ( query_expression , q , columns ) for q in condition ] except TypeError : raise DataJointError ( \"Invalid restriction type %r \" % condition ) else : or_list = [ item for item in or_list if item is not False ] # ignore False conditions if any ( item is True for item in or_list ): # if any item is True, entirely True return not negate return template % ( \"( %s )\" % \" OR \" . join ( or_list )) if or_list else negate extract_column_names ( sql_expression ) \u00b6 extract all presumed column names from an sql expression such as the WHERE clause, for example. Parameters: Name Type Description Default sql_expression a string containing an SQL expression required Returns: Type Description set of extracted column names This may be MySQL-specific for now. Source code in datajoint/condition.py 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 def extract_column_names ( sql_expression ): \"\"\" extract all presumed column names from an sql expression such as the WHERE clause, for example. :param sql_expression: a string containing an SQL expression :return: set of extracted column names This may be MySQL-specific for now. \"\"\" assert isinstance ( sql_expression , str ) result = set () s = sql_expression # for terseness # remove escaped quotes s = re . sub ( r \"( \\\\\\\" )|( \\\\ \\')\" , \"\" , s ) # remove quoted text s = re . sub ( r \"'[^']*'\" , \"\" , s ) s = re . sub ( r '\"[^\"]*\"' , \"\" , s ) # find all tokens in back quotes and remove them result . update ( re . findall ( r \"`([a-z][a-z_0-9]*)`\" , s )) s = re . sub ( r \"`[a-z][a-z_0-9]*`\" , \"\" , s ) # remove space before parentheses s = re . sub ( r \"\\s*\\(\" , \"(\" , s ) # remove tokens followed by ( since they must be functions s = re . sub ( r \"(\\b[a-z][a-z_0-9]*)\\(\" , \"(\" , s ) remaining_tokens = set ( re . findall ( r \"\\b[a-z][a-z_0-9]*\\b\" , s )) # update result removing reserved words result . update ( remaining_tokens - { \"is\" , \"in\" , \"between\" , \"like\" , \"and\" , \"or\" , \"null\" , \"not\" , \"interval\" , \"second\" , \"minute\" , \"hour\" , \"day\" , \"month\" , \"week\" , \"year\" , } ) return result", "title": "condition.py"}, {"location": "api/datajoint/condition/#datajoint.condition.PromiscuousOperand", "text": "A container for an operand to ignore join compatibility Source code in datajoint/condition.py 14 15 16 17 18 19 20 class PromiscuousOperand : \"\"\" A container for an operand to ignore join compatibility \"\"\" def __init__ ( self , operand ): self . operand = operand", "title": "PromiscuousOperand"}, {"location": "api/datajoint/condition/#datajoint.condition.AndList", "text": "Bases: list A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 Source code in datajoint/condition.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 class AndList ( list ): \"\"\" A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 \"\"\" def append ( self , restriction ): if isinstance ( restriction , AndList ): # extend to reduce nesting self . extend ( restriction ) else : super () . append ( restriction )", "title": "AndList"}, {"location": "api/datajoint/condition/#datajoint.condition.Not", "text": "invert restriction Source code in datajoint/condition.py 43 44 45 46 47 class Not : \"\"\"invert restriction\"\"\" def __init__ ( self , restriction ): self . restriction = restriction", "title": "Not"}, {"location": "api/datajoint/condition/#datajoint.condition.assert_join_compatibility", "text": "Determine if expressions expr1 and expr2 are join-compatible. To be join-compatible, the matching attributes in the two expressions must be in the primary key of one or the other expression. Raises an exception if not compatible. Parameters: Name Type Description Default expr1 A QueryExpression object required expr2 A QueryExpression object required Source code in datajoint/condition.py 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 def assert_join_compatibility ( expr1 , expr2 ): \"\"\" Determine if expressions expr1 and expr2 are join-compatible. To be join-compatible, the matching attributes in the two expressions must be in the primary key of one or the other expression. Raises an exception if not compatible. :param expr1: A QueryExpression object :param expr2: A QueryExpression object \"\"\" from .expression import QueryExpression , U for rel in ( expr1 , expr2 ): if not isinstance ( rel , ( U , QueryExpression )): raise DataJointError ( \"Object %r is not a QueryExpression and cannot be joined.\" % rel ) if not isinstance ( expr1 , U ) and not isinstance ( expr2 , U ): # dj.U is always compatible try : raise DataJointError ( \"Cannot join query expressions on dependent attribute ` %s `\" % next ( r for r in set ( expr1 . heading . secondary_attributes ) . intersection ( expr2 . heading . secondary_attributes ) ) ) except StopIteration : pass # all ok", "title": "assert_join_compatibility()"}, {"location": "api/datajoint/condition/#datajoint.condition.make_condition", "text": "Translate the input condition into the equivalent SQL condition (a string) Parameters: Name Type Description Default query_expression a dj.QueryExpression object to apply condition required condition any valid restriction object. required columns a set passed by reference to collect all column names used in the condition. required Returns: Type Description an SQL condition string or a boolean value. Source code in datajoint/condition.py 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 def make_condition ( query_expression , condition , columns ): \"\"\" Translate the input condition into the equivalent SQL condition (a string) :param query_expression: a dj.QueryExpression object to apply condition :param condition: any valid restriction object. :param columns: a set passed by reference to collect all column names used in the condition. :return: an SQL condition string or a boolean value. \"\"\" from .expression import QueryExpression , Aggregation , U def prep_value ( k , v ): \"\"\"prepare value v for inclusion as a string in an SQL condition\"\"\" if query_expression . heading [ k ] . uuid : if not isinstance ( v , uuid . UUID ): try : v = uuid . UUID ( v ) except ( AttributeError , ValueError ): raise DataJointError ( \"Badly formed UUID {v} in restriction by ` {k} `\" . format ( k = k , v = v ) ) return \"X' %s '\" % v . bytes . hex () if isinstance ( v , ( datetime . date , datetime . datetime , datetime . time , decimal . Decimal ) ): return '\" %s \"' % v if isinstance ( v , str ): return '\" %s \"' % v . replace ( \"%\" , \" %% \" ) . replace ( \" \\\\ \" , \" \\\\\\\\ \" ) return \" %r \" % v negate = False while isinstance ( condition , Not ): negate = not negate condition = condition . restriction template = \"NOT ( %s )\" if negate else \" %s \" # restrict by string if isinstance ( condition , str ): columns . update ( extract_column_names ( condition )) return template % condition . strip () . replace ( \"%\" , \" %% \" ) # escape %, see issue #376 # restrict by AndList if isinstance ( condition , AndList ): # omit all conditions that evaluate to True items = [ item for item in ( make_condition ( query_expression , cond , columns ) for cond in condition ) if item is not True ] if any ( item is False for item in items ): return negate # if any item is False, the whole thing is False if not items : return not negate # and empty AndList is True return template % ( \"(\" + \") AND (\" . join ( items ) + \")\" ) # restriction by dj.U evaluates to True if isinstance ( condition , U ): return not negate # restrict by boolean if isinstance ( condition , bool ): return negate != condition # restrict by a mapping/dict -- convert to an AndList of string equality conditions if isinstance ( condition , collections . abc . Mapping ): common_attributes = set ( condition ) . intersection ( query_expression . heading . names ) if not common_attributes : return not negate # no matching attributes -> evaluates to True columns . update ( common_attributes ) return template % ( \"(\" + \") AND (\" . join ( \"` %s ` %s \" % ( k , \" IS NULL\" if condition [ k ] is None else f \"= { prep_value ( k , condition [ k ]) } \" , ) for k in common_attributes ) + \")\" ) # restrict by a numpy record -- convert to an AndList of string equality conditions if isinstance ( condition , numpy . void ): common_attributes = set ( condition . dtype . fields ) . intersection ( query_expression . heading . names ) if not common_attributes : return not negate # no matching attributes -> evaluate to True columns . update ( common_attributes ) return template % ( \"(\" + \") AND (\" . join ( \"` %s `= %s \" % ( k , prep_value ( k , condition [ k ])) for k in common_attributes ) + \")\" ) # restrict by a QueryExpression subclass -- trigger instantiation and move on if inspect . isclass ( condition ) and issubclass ( condition , QueryExpression ): condition = condition () # restrict by another expression (aka semijoin and antijoin) check_compatibility = True if isinstance ( condition , PromiscuousOperand ): condition = condition . operand check_compatibility = False if isinstance ( condition , QueryExpression ): if check_compatibility : assert_join_compatibility ( query_expression , condition ) common_attributes = [ q for q in condition . heading . names if q in query_expression . heading . names ] columns . update ( common_attributes ) if isinstance ( condition , Aggregation ): condition = condition . make_subquery () return ( # without common attributes, any non-empty set matches everything ( not negate if condition else negate ) if not common_attributes else \"( {fields} ) {not_} in ( {subquery} )\" . format ( fields = \"`\" + \"`,`\" . join ( common_attributes ) + \"`\" , not_ = \"not \" if negate else \"\" , subquery = condition . make_sql ( common_attributes ), ) ) # restrict by pandas.DataFrames if isinstance ( condition , pandas . DataFrame ): condition = condition . to_records () # convert to numpy.recarray and move on # if iterable (but not a string, a QueryExpression, or an AndList), treat as an OrList try : or_list = [ make_condition ( query_expression , q , columns ) for q in condition ] except TypeError : raise DataJointError ( \"Invalid restriction type %r \" % condition ) else : or_list = [ item for item in or_list if item is not False ] # ignore False conditions if any ( item is True for item in or_list ): # if any item is True, entirely True return not negate return template % ( \"( %s )\" % \" OR \" . join ( or_list )) if or_list else negate", "title": "make_condition()"}, {"location": "api/datajoint/condition/#datajoint.condition.extract_column_names", "text": "extract all presumed column names from an sql expression such as the WHERE clause, for example. Parameters: Name Type Description Default sql_expression a string containing an SQL expression required Returns: Type Description set of extracted column names This may be MySQL-specific for now. Source code in datajoint/condition.py 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 def extract_column_names ( sql_expression ): \"\"\" extract all presumed column names from an sql expression such as the WHERE clause, for example. :param sql_expression: a string containing an SQL expression :return: set of extracted column names This may be MySQL-specific for now. \"\"\" assert isinstance ( sql_expression , str ) result = set () s = sql_expression # for terseness # remove escaped quotes s = re . sub ( r \"( \\\\\\\" )|( \\\\ \\')\" , \"\" , s ) # remove quoted text s = re . sub ( r \"'[^']*'\" , \"\" , s ) s = re . sub ( r '\"[^\"]*\"' , \"\" , s ) # find all tokens in back quotes and remove them result . update ( re . findall ( r \"`([a-z][a-z_0-9]*)`\" , s )) s = re . sub ( r \"`[a-z][a-z_0-9]*`\" , \"\" , s ) # remove space before parentheses s = re . sub ( r \"\\s*\\(\" , \"(\" , s ) # remove tokens followed by ( since they must be functions s = re . sub ( r \"(\\b[a-z][a-z_0-9]*)\\(\" , \"(\" , s ) remaining_tokens = set ( re . findall ( r \"\\b[a-z][a-z_0-9]*\\b\" , s )) # update result removing reserved words result . update ( remaining_tokens - { \"is\" , \"in\" , \"between\" , \"like\" , \"and\" , \"or\" , \"null\" , \"not\" , \"interval\" , \"second\" , \"minute\" , \"hour\" , \"day\" , \"month\" , \"week\" , \"year\" , } ) return result", "title": "extract_column_names()"}, {"location": "api/datajoint/connection/", "text": "This module contains the Connection class that manages the connection to the database, and the conn function that provides access to a persistent connection in datajoint. translate_query_error ( client_error , query ) \u00b6 Take client error and original query and return the corresponding DataJoint exception. Parameters: Name Type Description Default client_error the exception raised by the client interface required query sql query with placeholders required Returns: Type Description an instance of the corresponding subclass of datajoint.errors.DataJointError Source code in datajoint/connection.py 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 def translate_query_error ( client_error , query ): \"\"\" Take client error and original query and return the corresponding DataJoint exception. :param client_error: the exception raised by the client interface :param query: sql query with placeholders :return: an instance of the corresponding subclass of datajoint.errors.DataJointError \"\"\" logger . debug ( \"type: {} , args: {} \" . format ( type ( client_error ), client_error . args )) err , * args = client_error . args # Loss of connection errors if err in ( 0 , \"(0, '')\" ): return errors . LostConnectionError ( \"Server connection lost due to an interface error.\" , * args ) if err == 2006 : return errors . LostConnectionError ( \"Connection timed out\" , * args ) if err == 2013 : return errors . LostConnectionError ( \"Server connection lost\" , * args ) # Access errors if err in ( 1044 , 1142 ): return errors . AccessError ( \"Insufficient privileges.\" , args [ 0 ], query ) # Integrity errors if err == 1062 : return errors . DuplicateError ( * args ) if err == 1451 : return errors . IntegrityError ( * args ) if err == 1452 : return errors . IntegrityError ( * args ) # Syntax errors if err == 1064 : return errors . QuerySyntaxError ( args [ 0 ], query ) # Existence errors if err == 1146 : return errors . MissingTableError ( args [ 0 ], query ) if err == 1364 : return errors . MissingAttributeError ( * args ) if err == 1054 : return errors . UnknownAttributeError ( * args ) # all the other errors are re-raised in original form return client_error conn ( host = None , user = None , password = None , * , init_fun = None , reset = False , use_tls = None ) \u00b6 Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. Parameters: Name Type Description Default host hostname None user mysql user None password mysql password None init_fun initialization function None reset whether the connection should be reset or not False use_tls TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). None Source code in datajoint/connection.py 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 def conn ( host = None , user = None , password = None , * , init_fun = None , reset = False , use_tls = None ): \"\"\" Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. :param host: hostname :param user: mysql user :param password: mysql password :param init_fun: initialization function :param reset: whether the connection should be reset or not :param use_tls: TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). \"\"\" if not hasattr ( conn , \"connection\" ) or reset : host = host if host is not None else config [ \"database.host\" ] user = user if user is not None else config [ \"database.user\" ] password = password if password is not None else config [ \"database.password\" ] if user is None : # pragma: no cover user = input ( \"Please enter DataJoint username: \" ) if password is None : # pragma: no cover password = getpass ( prompt = \"Please enter DataJoint password: \" ) init_fun = ( init_fun if init_fun is not None else config [ \"connection.init_function\" ] ) use_tls = use_tls if use_tls is not None else config [ \"database.use_tls\" ] conn . connection = Connection ( host , user , password , None , init_fun , use_tls ) return conn . connection EmulatedCursor \u00b6 acts like a cursor Source code in datajoint/connection.py 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 class EmulatedCursor : \"\"\"acts like a cursor\"\"\" def __init__ ( self , data ): self . _data = data self . _iter = iter ( self . _data ) def __iter__ ( self ): return self def __next__ ( self ): return next ( self . _iter ) def fetchall ( self ): return self . _data def fetchone ( self ): return next ( self . _iter ) @property def rowcount ( self ): return len ( self . _data ) Connection \u00b6 A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. Parameters: Name Type Description Default host host name, may include port number as hostname:port, in which case it overrides the value in port required user user name required password password required port port number None init_fun connection initialization function (SQL) None use_tls TLS encryption option None Source code in datajoint/connection.py 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 class Connection : \"\"\" A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. :param host: host name, may include port number as hostname:port, in which case it overrides the value in port :param user: user name :param password: password :param port: port number :param init_fun: connection initialization function (SQL) :param use_tls: TLS encryption option \"\"\" def __init__ ( self , host , user , password , port = None , init_fun = None , use_tls = None ): host_input , host = ( host , get_host_hook ( host )) if \":\" in host : # the port in the hostname overrides the port argument host , port = host . split ( \":\" ) port = int ( port ) elif port is None : port = config [ \"database.port\" ] self . conn_info = dict ( host = host , port = port , user = user , passwd = password ) if use_tls is not False : self . conn_info [ \"ssl\" ] = ( use_tls if isinstance ( use_tls , dict ) else { \"ssl\" : {}} ) self . conn_info [ \"ssl_input\" ] = use_tls self . conn_info [ \"host_input\" ] = host_input self . init_fun = init_fun logger . info ( \"Connecting {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . _conn = None self . _query_cache = None connect_host_hook ( self ) if self . is_connected : logger . info ( \"Connected {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . connection_id = self . query ( \"SELECT connection_id()\" ) . fetchone ()[ 0 ] else : raise errors . LostConnectionError ( \"Connection failed.\" ) self . _in_transaction = False self . schemas = dict () self . dependencies = Dependencies ( self ) def __eq__ ( self , other ): return self . conn_info == other . conn_info def __repr__ ( self ): connected = \"connected\" if self . is_connected else \"disconnected\" return \"DataJoint connection ( {connected} ) {user} @ {host} : {port} \" . format ( connected = connected , ** self . conn_info ) def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True ) def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink () def close ( self ): self . _conn . close () def register ( self , schema ): self . schemas [ schema . database ] = schema self . dependencies . clear () def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False ) @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True @staticmethod def _execute_query ( cursor , query , args , suppress_warnings ): try : with warnings . catch_warnings (): if suppress_warnings : # suppress all warnings arising from underlying SQL library warnings . simplefilter ( \"ignore\" ) cursor . execute ( query , args ) except client . err . Error as err : raise translate_query_error ( err , query ) def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ] # ---------- transaction processing @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" ) def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" ) def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" ) # -------- context manager for transactions @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction () connect () \u00b6 Connect to the database server. Source code in datajoint/connection.py 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True ) set_query_cache ( query_cache = None ) \u00b6 When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. Parameters: Name Type Description Default query_cache a string to initialize the hash for query results None Source code in datajoint/connection.py 246 247 248 249 250 251 252 253 254 255 def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache purge_query_cache () \u00b6 Purges all query cache. Source code in datajoint/connection.py 257 258 259 260 261 262 263 264 265 def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink () ping () \u00b6 Ping the connection or raises an exception if the connection is closed. Source code in datajoint/connection.py 274 275 276 def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False ) is_connected () property \u00b6 Return true if the object is connected to the database server. Source code in datajoint/connection.py 278 279 280 281 282 283 284 285 @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True query ( query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ) \u00b6 Execute the specified query and return the tuple generator (cursor). Parameters: Name Type Description Default query SQL query required args additional arguments for the client.cursor () as_dict If as_dict is set to True, the returned cursor objects returns query results as dictionary. False suppress_warnings If True, suppress all warnings arising from underlying query library True reconnect when None, get from config, when True, attempt to reconnect if disconnected None Source code in datajoint/connection.py 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor get_user () \u00b6 Returns: Type Description the user name and host name provided by the client to the server. Source code in datajoint/connection.py 362 363 364 365 366 def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ] in_transaction () property \u00b6 Returns: Type Description True if there is an open transaction. Source code in datajoint/connection.py 369 370 371 372 373 374 375 @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction start_transaction () \u00b6 Starts a transaction error. Source code in datajoint/connection.py 377 378 379 380 381 382 383 384 385 def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" ) cancel_transaction () \u00b6 Cancels the current transaction and rolls back all changes made during the transaction. Source code in datajoint/connection.py 387 388 389 390 391 392 393 def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" ) commit_transaction () \u00b6 Commit all changes made during the transaction and close it. Source code in datajoint/connection.py 395 396 397 398 399 400 401 402 def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" ) transaction () property \u00b6 Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: import datajoint as dj with dj.conn().transaction as conn: # transaction is open here Source code in datajoint/connection.py 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction ()", "title": "connection.py"}, {"location": "api/datajoint/connection/#datajoint.connection.translate_query_error", "text": "Take client error and original query and return the corresponding DataJoint exception. Parameters: Name Type Description Default client_error the exception raised by the client interface required query sql query with placeholders required Returns: Type Description an instance of the corresponding subclass of datajoint.errors.DataJointError Source code in datajoint/connection.py 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 def translate_query_error ( client_error , query ): \"\"\" Take client error and original query and return the corresponding DataJoint exception. :param client_error: the exception raised by the client interface :param query: sql query with placeholders :return: an instance of the corresponding subclass of datajoint.errors.DataJointError \"\"\" logger . debug ( \"type: {} , args: {} \" . format ( type ( client_error ), client_error . args )) err , * args = client_error . args # Loss of connection errors if err in ( 0 , \"(0, '')\" ): return errors . LostConnectionError ( \"Server connection lost due to an interface error.\" , * args ) if err == 2006 : return errors . LostConnectionError ( \"Connection timed out\" , * args ) if err == 2013 : return errors . LostConnectionError ( \"Server connection lost\" , * args ) # Access errors if err in ( 1044 , 1142 ): return errors . AccessError ( \"Insufficient privileges.\" , args [ 0 ], query ) # Integrity errors if err == 1062 : return errors . DuplicateError ( * args ) if err == 1451 : return errors . IntegrityError ( * args ) if err == 1452 : return errors . IntegrityError ( * args ) # Syntax errors if err == 1064 : return errors . QuerySyntaxError ( args [ 0 ], query ) # Existence errors if err == 1146 : return errors . MissingTableError ( args [ 0 ], query ) if err == 1364 : return errors . MissingAttributeError ( * args ) if err == 1054 : return errors . UnknownAttributeError ( * args ) # all the other errors are re-raised in original form return client_error", "title": "translate_query_error()"}, {"location": "api/datajoint/connection/#datajoint.connection.conn", "text": "Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. Parameters: Name Type Description Default host hostname None user mysql user None password mysql password None init_fun initialization function None reset whether the connection should be reset or not False use_tls TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). None Source code in datajoint/connection.py 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 def conn ( host = None , user = None , password = None , * , init_fun = None , reset = False , use_tls = None ): \"\"\" Returns a persistent connection object to be shared by multiple modules. If the connection is not yet established or reset=True, a new connection is set up. If connection information is not provided, it is taken from config which takes the information from dj_local_conf.json. If the password is not specified in that file datajoint prompts for the password. :param host: hostname :param user: mysql user :param password: mysql password :param init_fun: initialization function :param reset: whether the connection should be reset or not :param use_tls: TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). \"\"\" if not hasattr ( conn , \"connection\" ) or reset : host = host if host is not None else config [ \"database.host\" ] user = user if user is not None else config [ \"database.user\" ] password = password if password is not None else config [ \"database.password\" ] if user is None : # pragma: no cover user = input ( \"Please enter DataJoint username: \" ) if password is None : # pragma: no cover password = getpass ( prompt = \"Please enter DataJoint password: \" ) init_fun = ( init_fun if init_fun is not None else config [ \"connection.init_function\" ] ) use_tls = use_tls if use_tls is not None else config [ \"database.use_tls\" ] conn . connection = Connection ( host , user , password , None , init_fun , use_tls ) return conn . connection", "title": "conn()"}, {"location": "api/datajoint/connection/#datajoint.connection.EmulatedCursor", "text": "acts like a cursor Source code in datajoint/connection.py 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 class EmulatedCursor : \"\"\"acts like a cursor\"\"\" def __init__ ( self , data ): self . _data = data self . _iter = iter ( self . _data ) def __iter__ ( self ): return self def __next__ ( self ): return next ( self . _iter ) def fetchall ( self ): return self . _data def fetchone ( self ): return next ( self . _iter ) @property def rowcount ( self ): return len ( self . _data )", "title": "EmulatedCursor"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection", "text": "A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. Parameters: Name Type Description Default host host name, may include port number as hostname:port, in which case it overrides the value in port required user user name required password password required port port number None init_fun connection initialization function (SQL) None use_tls TLS encryption option None Source code in datajoint/connection.py 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 class Connection : \"\"\" A dj.Connection object manages a connection to a database server. It also catalogues modules, schemas, tables, and their dependencies (foreign keys). Most of the parameters below should be set in the local configuration file. :param host: host name, may include port number as hostname:port, in which case it overrides the value in port :param user: user name :param password: password :param port: port number :param init_fun: connection initialization function (SQL) :param use_tls: TLS encryption option \"\"\" def __init__ ( self , host , user , password , port = None , init_fun = None , use_tls = None ): host_input , host = ( host , get_host_hook ( host )) if \":\" in host : # the port in the hostname overrides the port argument host , port = host . split ( \":\" ) port = int ( port ) elif port is None : port = config [ \"database.port\" ] self . conn_info = dict ( host = host , port = port , user = user , passwd = password ) if use_tls is not False : self . conn_info [ \"ssl\" ] = ( use_tls if isinstance ( use_tls , dict ) else { \"ssl\" : {}} ) self . conn_info [ \"ssl_input\" ] = use_tls self . conn_info [ \"host_input\" ] = host_input self . init_fun = init_fun logger . info ( \"Connecting {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . _conn = None self . _query_cache = None connect_host_hook ( self ) if self . is_connected : logger . info ( \"Connected {user} @ {host} : {port} \" . format ( ** self . conn_info )) self . connection_id = self . query ( \"SELECT connection_id()\" ) . fetchone ()[ 0 ] else : raise errors . LostConnectionError ( \"Connection failed.\" ) self . _in_transaction = False self . schemas = dict () self . dependencies = Dependencies ( self ) def __eq__ ( self , other ): return self . conn_info == other . conn_info def __repr__ ( self ): connected = \"connected\" if self . is_connected else \"disconnected\" return \"DataJoint connection ( {connected} ) {user} @ {host} : {port} \" . format ( connected = connected , ** self . conn_info ) def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True ) def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink () def close ( self ): self . _conn . close () def register ( self , schema ): self . schemas [ schema . database ] = schema self . dependencies . clear () def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False ) @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True @staticmethod def _execute_query ( cursor , query , args , suppress_warnings ): try : with warnings . catch_warnings (): if suppress_warnings : # suppress all warnings arising from underlying SQL library warnings . simplefilter ( \"ignore\" ) cursor . execute ( query , args ) except client . err . Error as err : raise translate_query_error ( err , query ) def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ] # ---------- transaction processing @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" ) def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" ) def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" ) # -------- context manager for transactions @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction ()", "title": "Connection"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.connect", "text": "Connect to the database server. Source code in datajoint/connection.py 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 def connect ( self ): \"\"\"Connect to the database server.\"\"\" with warnings . catch_warnings (): warnings . filterwarnings ( \"ignore\" , \".*deprecated.*\" ) try : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if k not in [ \"ssl_input\" , \"host_input\" ] }, ) except client . err . InternalError : self . _conn = client . connect ( init_command = self . init_fun , sql_mode = \"NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,\" \"STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY\" , charset = config [ \"connection.charset\" ], ** { k : v for k , v in self . conn_info . items () if not ( k in [ \"ssl_input\" , \"host_input\" ] or k == \"ssl\" and self . conn_info [ \"ssl_input\" ] is None ) }, ) self . _conn . autocommit ( True )", "title": "connect()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.set_query_cache", "text": "When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. Parameters: Name Type Description Default query_cache a string to initialize the hash for query results None Source code in datajoint/connection.py 246 247 248 249 250 251 252 253 254 255 def set_query_cache ( self , query_cache = None ): \"\"\" When query_cache is not None, the connection switches into the query caching mode, which entails: 1. Only SELECT queries are allowed. 2. The results of queries are cached under the path indicated by dj.config['query_cache'] 3. query_cache is a string that differentiates different cache states. :param query_cache: a string to initialize the hash for query results \"\"\" self . _query_cache = query_cache", "title": "set_query_cache()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.purge_query_cache", "text": "Purges all query cache. Source code in datajoint/connection.py 257 258 259 260 261 262 263 264 265 def purge_query_cache ( self ): \"\"\"Purges all query cache.\"\"\" if ( isinstance ( config . get ( cache_key ), str ) and pathlib . Path ( config [ cache_key ]) . is_dir () ): for path in pathlib . Path ( config [ cache_key ]) . iterdir (): if not path . is_dir (): path . unlink ()", "title": "purge_query_cache()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.ping", "text": "Ping the connection or raises an exception if the connection is closed. Source code in datajoint/connection.py 274 275 276 def ping ( self ): \"\"\"Ping the connection or raises an exception if the connection is closed.\"\"\" self . _conn . ping ( reconnect = False )", "title": "ping()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.is_connected", "text": "Return true if the object is connected to the database server. Source code in datajoint/connection.py 278 279 280 281 282 283 284 285 @property def is_connected ( self ): \"\"\"Return true if the object is connected to the database server.\"\"\" try : self . ping () except : return False return True", "title": "is_connected()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.query", "text": "Execute the specified query and return the tuple generator (cursor). Parameters: Name Type Description Default query SQL query required args additional arguments for the client.cursor () as_dict If as_dict is set to True, the returned cursor objects returns query results as dictionary. False suppress_warnings If True, suppress all warnings arising from underlying query library True reconnect when None, get from config, when True, attempt to reconnect if disconnected None Source code in datajoint/connection.py 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 def query ( self , query , args = (), * , as_dict = False , suppress_warnings = True , reconnect = None ): \"\"\" Execute the specified query and return the tuple generator (cursor). :param query: SQL query :param args: additional arguments for the client.cursor :param as_dict: If as_dict is set to True, the returned cursor objects returns query results as dictionary. :param suppress_warnings: If True, suppress all warnings arising from underlying query library :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected \"\"\" # check cache first: use_query_cache = bool ( self . _query_cache ) if use_query_cache and not re . match ( r \"\\s*(SELECT|SHOW)\" , query ): raise errors . DataJointError ( \"Only SELECT queries are allowed when query caching is on.\" ) if use_query_cache : if not config [ cache_key ]: raise errors . DataJointError ( f \"Provide filepath dj.config[' { cache_key } '] when using query caching.\" ) hash_ = uuid_from_buffer ( ( str ( self . _query_cache ) + re . sub ( r \"`\\$\\w+`\" , \"\" , query )) . encode () + pack ( args ) ) cache_path = pathlib . Path ( config [ cache_key ]) / str ( hash_ ) try : buffer = cache_path . read_bytes () except FileNotFoundError : pass # proceed to query the database else : return EmulatedCursor ( unpack ( buffer )) if reconnect is None : reconnect = config [ \"database.reconnect\" ] logger . debug ( \"Executing SQL:\" + query [: query_log_max_length ]) cursor_class = client . cursors . DictCursor if as_dict else client . cursors . Cursor cursor = self . _conn . cursor ( cursor = cursor_class ) try : self . _execute_query ( cursor , query , args , suppress_warnings ) except errors . LostConnectionError : if not reconnect : raise logger . warning ( \"MySQL server has gone away. Reconnecting to the server.\" ) connect_host_hook ( self ) if self . _in_transaction : self . cancel_transaction () raise errors . LostConnectionError ( \"Connection was lost during a transaction.\" ) logger . debug ( \"Re-executing\" ) cursor = self . _conn . cursor ( cursor = cursor_class ) self . _execute_query ( cursor , query , args , suppress_warnings ) if use_query_cache : data = cursor . fetchall () cache_path . write_bytes ( pack ( data )) return EmulatedCursor ( data ) return cursor", "title": "query()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.get_user", "text": "Returns: Type Description the user name and host name provided by the client to the server. Source code in datajoint/connection.py 362 363 364 365 366 def get_user ( self ): \"\"\" :return: the user name and host name provided by the client to the server. \"\"\" return self . query ( \"SELECT user()\" ) . fetchone ()[ 0 ]", "title": "get_user()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.in_transaction", "text": "Returns: Type Description True if there is an open transaction. Source code in datajoint/connection.py 369 370 371 372 373 374 375 @property def in_transaction ( self ): \"\"\" :return: True if there is an open transaction. \"\"\" self . _in_transaction = self . _in_transaction and self . is_connected return self . _in_transaction", "title": "in_transaction()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.start_transaction", "text": "Starts a transaction error. Source code in datajoint/connection.py 377 378 379 380 381 382 383 384 385 def start_transaction ( self ): \"\"\" Starts a transaction error. \"\"\" if self . in_transaction : raise errors . DataJointError ( \"Nested connections are not supported.\" ) self . query ( \"START TRANSACTION WITH CONSISTENT SNAPSHOT\" ) self . _in_transaction = True logger . debug ( \"Transaction started\" )", "title": "start_transaction()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.cancel_transaction", "text": "Cancels the current transaction and rolls back all changes made during the transaction. Source code in datajoint/connection.py 387 388 389 390 391 392 393 def cancel_transaction ( self ): \"\"\" Cancels the current transaction and rolls back all changes made during the transaction. \"\"\" self . query ( \"ROLLBACK\" ) self . _in_transaction = False logger . debug ( \"Transaction cancelled. Rolling back ...\" )", "title": "cancel_transaction()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.commit_transaction", "text": "Commit all changes made during the transaction and close it. Source code in datajoint/connection.py 395 396 397 398 399 400 401 402 def commit_transaction ( self ): \"\"\" Commit all changes made during the transaction and close it. \"\"\" self . query ( \"COMMIT\" ) self . _in_transaction = False logger . debug ( \"Transaction committed and closed.\" )", "title": "commit_transaction()"}, {"location": "api/datajoint/connection/#datajoint.connection.Connection.transaction", "text": "Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: import datajoint as dj with dj.conn().transaction as conn: # transaction is open here Source code in datajoint/connection.py 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 @property @contextmanager def transaction ( self ): \"\"\" Context manager for transactions. Opens an transaction and closes it after the with statement. If an error is caught during the transaction, the commits are automatically rolled back. All errors are raised again. Example: >>> import datajoint as dj >>> with dj.conn().transaction as conn: >>> # transaction is open here \"\"\" try : self . start_transaction () yield self except : self . cancel_transaction () raise else : self . commit_transaction ()", "title": "transaction()"}, {"location": "api/datajoint/declare/", "text": "This module hosts functions to convert DataJoint table definitions into mysql table definitions, and to declare the corresponding mysql tables. is_foreign_key ( line ) \u00b6 Parameters: Name Type Description Default line a line from the table definition required Returns: Type Description true if the line appears to be a foreign key definition Source code in datajoint/declare.py 153 154 155 156 157 158 159 160 def is_foreign_key ( line ): \"\"\" :param line: a line from the table definition :return: true if the line appears to be a foreign key definition \"\"\" arrow_position = line . find ( \"->\" ) return arrow_position >= 0 and not any ( c in line [: arrow_position ] for c in \" \\\" #'\" ) compile_foreign_key ( line , context , attributes , primary_key , attr_sql , foreign_key_sql , index_sql ) \u00b6 Parameters: Name Type Description Default line a line from a table definition required context namespace containing referenced objects required attributes list of attribute names already in the declaration -- to be updated by this function required primary_key None if the current foreign key is made from the dependent section. Otherwise it is the list of primary key attributes thus far -- to be updated by the function required attr_sql list of sql statements defining attributes -- to be updated by this function. required foreign_key_sql list of sql statements specifying foreign key constraints -- to be updated by this function. required index_sql list of INDEX declaration statements, duplicate or redundant indexes are ok. required Source code in datajoint/declare.py 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 def compile_foreign_key ( line , context , attributes , primary_key , attr_sql , foreign_key_sql , index_sql ): \"\"\" :param line: a line from a table definition :param context: namespace containing referenced objects :param attributes: list of attribute names already in the declaration -- to be updated by this function :param primary_key: None if the current foreign key is made from the dependent section. Otherwise it is the list of primary key attributes thus far -- to be updated by the function :param attr_sql: list of sql statements defining attributes -- to be updated by this function. :param foreign_key_sql: list of sql statements specifying foreign key constraints -- to be updated by this function. :param index_sql: list of INDEX declaration statements, duplicate or redundant indexes are ok. \"\"\" # Parse and validate from .table import Table from .expression import QueryExpression obsolete = False # See issue #436. Old style to be deprecated in a future release try : result = foreign_key_parser . parseString ( line ) except pp . ParseException : try : result = foreign_key_parser_old . parseString ( line ) except pp . ParseBaseException as err : raise DataJointError ( 'Parsing error in line \" %s \". %s .' % ( line , err )) else : obsolete = True try : ref = eval ( result . ref_table , context ) except NameError if obsolete else Exception : raise DataJointError ( \"Foreign key reference %s could not be resolved\" % result . ref_table ) options = [ opt . upper () for opt in result . options ] for opt in options : # check for invalid options if opt not in { \"NULLABLE\" , \"UNIQUE\" }: raise DataJointError ( 'Invalid foreign key option \" {opt} \"' . format ( opt = opt )) is_nullable = \"NULLABLE\" in options is_unique = \"UNIQUE\" in options if is_nullable and primary_key is not None : raise DataJointError ( 'Primary dependencies cannot be nullable in line \" {line} \"' . format ( line = line ) ) if obsolete : logger . warning ( 'Line \" {line} \" uses obsolete syntax that will no longer be supported in datajoint 0.14. ' \"For details, see issue #780 https://github.com/datajoint/datajoint-python/issues/780\" . format ( line = line ) ) if not isinstance ( ref , type ) or not issubclass ( ref , Table ): raise DataJointError ( \"Foreign key reference %r must be a valid query\" % result . ref_table ) if isinstance ( ref , type ) and issubclass ( ref , Table ): ref = ref () # check that dependency is of a supported type if ( not isinstance ( ref , QueryExpression ) or len ( ref . restriction ) or len ( ref . support ) != 1 or not isinstance ( ref . support [ 0 ], str ) ): raise DataJointError ( 'Dependency \" %s \" is not supported (yet). Use a base table or its projection.' % result . ref_table ) if obsolete : # for backward compatibility with old-style dependency declarations. See issue #436 if not isinstance ( ref , Table ): DataJointError ( 'Dependency \" %s \" is not supported. Check documentation.' % result . ref_table ) if not all ( r in ref . primary_key for r in result . ref_attrs ): raise DataJointError ( 'Invalid foreign key attributes in \" %s \"' % line ) try : raise DataJointError ( 'Duplicate attributes \" {attr} \" in \" {line} \"' . format ( attr = next ( attr for attr in result . new_attrs if attr in attributes ), line = line , ) ) except StopIteration : pass # the normal outcome # Match the primary attributes of the referenced table to local attributes new_attrs = list ( result . new_attrs ) ref_attrs = list ( result . ref_attrs ) # special case, the renamed attribute is implicit if new_attrs and not ref_attrs : if len ( new_attrs ) != 1 : raise DataJointError ( 'Renamed foreign key must be mapped to the primary key in \" %s \"' % line ) if len ( ref . primary_key ) == 1 : # if the primary key has one attribute, allow implicit renaming ref_attrs = ref . primary_key else : # if only one primary key attribute remains, then allow implicit renaming ref_attrs = [ attr for attr in ref . primary_key if attr not in attributes ] if len ( ref_attrs ) != 1 : raise DataJointError ( 'Could not resolve which primary key attribute should be referenced in \" %s \"' % line ) if len ( new_attrs ) != len ( ref_attrs ): raise DataJointError ( 'Mismatched attributes in foreign key \" %s \"' % line ) if ref_attrs : # convert to projected dependency ref = ref . proj ( ** dict ( zip ( new_attrs , ref_attrs ))) # declare new foreign key attributes for attr in ref . primary_key : if attr not in attributes : attributes . append ( attr ) if primary_key is not None : primary_key . append ( attr ) attr_sql . append ( ref . heading [ attr ] . sql . replace ( \"NOT NULL \" , \"\" , int ( is_nullable )) ) # declare the foreign key foreign_key_sql . append ( \"FOREIGN KEY (` {fk} `) REFERENCES {ref} (` {pk} `) ON UPDATE CASCADE ON DELETE RESTRICT\" . format ( fk = \"`,`\" . join ( ref . primary_key ), pk = \"`,`\" . join ( ref . heading [ name ] . original_name for name in ref . primary_key ), ref = ref . support [ 0 ], ) ) # declare unique index if is_unique : index_sql . append ( \"UNIQUE INDEX ( {attrs} )\" . format ( attrs = \",\" . join ( \"` %s `\" % attr for attr in ref . primary_key ) ) ) declare ( full_table_name , definition , context ) \u00b6 Parse declaration and generate the SQL CREATE TABLE code Parameters: Name Type Description Default full_table_name full name of the table required definition DataJoint table definition required context dictionary of objects that might be referred to in the table required Returns: Type Description SQL CREATE TABLE statement, list of external stores used Source code in datajoint/declare.py 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 def declare ( full_table_name , definition , context ): \"\"\" Parse declaration and generate the SQL CREATE TABLE code :param full_table_name: full name of the table :param definition: DataJoint table definition :param context: dictionary of objects that might be referred to in the table :return: SQL CREATE TABLE statement, list of external stores used \"\"\" table_name = full_table_name . strip ( \"`\" ) . split ( \".\" )[ 1 ] if len ( table_name ) > MAX_TABLE_NAME_LENGTH : raise DataJointError ( \"Table name ` {name} ` exceeds the max length of {max_length} \" . format ( name = table_name , max_length = MAX_TABLE_NAME_LENGTH ) ) ( table_comment , primary_key , attribute_sql , foreign_key_sql , index_sql , external_stores , ) = prepare_declare ( definition , context ) if not primary_key : raise DataJointError ( \"Table must have a primary key\" ) return ( \"CREATE TABLE IF NOT EXISTS %s ( \\n \" % full_table_name + \", \\n \" . join ( attribute_sql + [ \"PRIMARY KEY (`\" + \"`,`\" . join ( primary_key ) + \"`)\" ] + foreign_key_sql + index_sql ) + ' \\n ) ENGINE=InnoDB, COMMENT \" %s \"' % table_comment ), external_stores alter ( definition , old_definition , context ) \u00b6 Parameters: Name Type Description Default definition new table definition required old_definition current table definition required context the context in which to evaluate foreign key definitions required Returns: Type Description string SQL ALTER command, list of new stores used for external storage Source code in datajoint/declare.py 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 def alter ( definition , old_definition , context ): \"\"\" :param definition: new table definition :param old_definition: current table definition :param context: the context in which to evaluate foreign key definitions :return: string SQL ALTER command, list of new stores used for external storage \"\"\" ( table_comment , primary_key , attribute_sql , foreign_key_sql , index_sql , external_stores , ) = prepare_declare ( definition , context ) ( table_comment_ , primary_key_ , attribute_sql_ , foreign_key_sql_ , index_sql_ , external_stores_ , ) = prepare_declare ( old_definition , context ) # analyze differences between declarations sql = list () if primary_key != primary_key_ : raise NotImplementedError ( \"table.alter cannot alter the primary key (yet).\" ) if foreign_key_sql != foreign_key_sql_ : raise NotImplementedError ( \"table.alter cannot alter foreign keys (yet).\" ) if index_sql != index_sql_ : raise NotImplementedError ( \"table.alter cannot alter indexes (yet)\" ) if attribute_sql != attribute_sql_ : sql . extend ( _make_attribute_alter ( attribute_sql , attribute_sql_ , primary_key )) if table_comment != table_comment_ : sql . append ( 'COMMENT=\" %s \"' % table_comment ) return sql , [ e for e in external_stores if e not in external_stores_ ] substitute_special_type ( match , category , foreign_key_sql , context ) \u00b6 Parameters: Name Type Description Default match dict containing with keys \"type\" and \"comment\" -- will be modified in place required category attribute type category from TYPE_PATTERN required foreign_key_sql list of foreign key declarations to add to required context context for looking up user-defined attribute_type adapters required Source code in datajoint/declare.py 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 def substitute_special_type ( match , category , foreign_key_sql , context ): \"\"\" :param match: dict containing with keys \"type\" and \"comment\" -- will be modified in place :param category: attribute type category from TYPE_PATTERN :param foreign_key_sql: list of foreign key declarations to add to :param context: context for looking up user-defined attribute_type adapters \"\"\" if category == \"UUID\" : match [ \"type\" ] = UUID_DATA_TYPE elif category == \"INTERNAL_ATTACH\" : match [ \"type\" ] = \"LONGBLOB\" elif category in EXTERNAL_TYPES : if category == \"FILEPATH\" and not _support_filepath_types (): raise DataJointError ( \"\"\" The filepath data type is disabled until complete validation. To turn it on as experimental feature, set the environment variable {env} = TRUE or upgrade datajoint. \"\"\" . format ( env = FILEPATH_FEATURE_SWITCH ) ) match [ \"store\" ] = match [ \"type\" ] . split ( \"@\" , 1 )[ 1 ] match [ \"type\" ] = UUID_DATA_TYPE foreign_key_sql . append ( \"FOREIGN KEY (` {name} `) REFERENCES `{{database}}`.` {external_table_root} _ {store} ` (`hash`) \" \"ON UPDATE RESTRICT ON DELETE RESTRICT\" . format ( external_table_root = EXTERNAL_TABLE_ROOT , ** match ) ) elif category == \"ADAPTED\" : adapter = get_adapter ( context , match [ \"type\" ]) match [ \"type\" ] = adapter . attribute_type category = match_type ( match [ \"type\" ]) if category in SPECIAL_TYPES : # recursive redefinition from user-defined datatypes. substitute_special_type ( match , category , foreign_key_sql , context ) else : assert False , \"Unknown special type\" compile_attribute ( line , in_key , foreign_key_sql , context ) \u00b6 Convert attribute definition from DataJoint format to SQL Parameters: Name Type Description Default line attribution line required in_key set to True if attribute is in primary key set required foreign_key_sql the list of foreign key declarations to add to required context context in which to look up user-defined attribute type adapterss required Returns: Type Description (name, sql, is_external) -- attribute name and sql code for its declaration Source code in datajoint/declare.py 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 def compile_attribute ( line , in_key , foreign_key_sql , context ): \"\"\" Convert attribute definition from DataJoint format to SQL :param line: attribution line :param in_key: set to True if attribute is in primary key set :param foreign_key_sql: the list of foreign key declarations to add to :param context: context in which to look up user-defined attribute type adapterss :returns: (name, sql, is_external) -- attribute name and sql code for its declaration \"\"\" try : match = attribute_parser . parseString ( line + \"#\" , parseAll = True ) except pp . ParseException as err : raise DataJointError ( \"Declaration error in position {pos} in line: \\n {line} \\n {msg} \" . format ( line = err . args [ 0 ], pos = err . args [ 1 ], msg = err . args [ 2 ] ) ) match [ \"comment\" ] = match [ \"comment\" ] . rstrip ( \"#\" ) if \"default\" not in match : match [ \"default\" ] = \"\" match = { k : v . strip () for k , v in match . items ()} match [ \"nullable\" ] = match [ \"default\" ] . lower () == \"null\" if match [ \"nullable\" ]: if in_key : raise DataJointError ( 'Primary key attributes cannot be nullable in line \" %s \"' % line ) match [ \"default\" ] = \"DEFAULT NULL\" # nullable attributes default to null else : if match [ \"default\" ]: quote = ( match [ \"default\" ] . split ( \"(\" )[ 0 ] . upper () not in CONSTANT_LITERALS and match [ \"default\" ][ 0 ] not in \" \\\" '\" ) match [ \"default\" ] = ( \"NOT NULL DEFAULT \" + ( '\" %s \"' if quote else \" %s \" ) % match [ \"default\" ] ) else : match [ \"default\" ] = \"NOT NULL\" match [ \"comment\" ] = match [ \"comment\" ] . replace ( '\"' , ' \\\\ \"' ) # escape double quotes in comment if match [ \"comment\" ] . startswith ( \":\" ): raise DataJointError ( 'An attribute comment must not start with a colon in comment \" {comment} \"' . format ( ** match ) ) category = match_type ( match [ \"type\" ]) if category in SPECIAL_TYPES : match [ \"comment\" ] = \": {type} : {comment} \" . format ( ** match ) # insert custom type into comment substitute_special_type ( match , category , foreign_key_sql , context ) if category in SERIALIZED_TYPES and match [ \"default\" ] not in { \"DEFAULT NULL\" , \"NOT NULL\" , }: raise DataJointError ( \"The default value for a blob or attachment attributes can only be NULL in: \\n {line} \" . format ( line = line ) ) sql = ( \"` {name} ` {type} {default} \" + ( ' COMMENT \" {comment} \"' if match [ \"comment\" ] else \"\" ) ) . format ( ** match ) return match [ \"name\" ], sql , match . get ( \"store\" )", "title": "declare.py"}, {"location": "api/datajoint/declare/#datajoint.declare.is_foreign_key", "text": "Parameters: Name Type Description Default line a line from the table definition required Returns: Type Description true if the line appears to be a foreign key definition Source code in datajoint/declare.py 153 154 155 156 157 158 159 160 def is_foreign_key ( line ): \"\"\" :param line: a line from the table definition :return: true if the line appears to be a foreign key definition \"\"\" arrow_position = line . find ( \"->\" ) return arrow_position >= 0 and not any ( c in line [: arrow_position ] for c in \" \\\" #'\" )", "title": "is_foreign_key()"}, {"location": "api/datajoint/declare/#datajoint.declare.compile_foreign_key", "text": "Parameters: Name Type Description Default line a line from a table definition required context namespace containing referenced objects required attributes list of attribute names already in the declaration -- to be updated by this function required primary_key None if the current foreign key is made from the dependent section. Otherwise it is the list of primary key attributes thus far -- to be updated by the function required attr_sql list of sql statements defining attributes -- to be updated by this function. required foreign_key_sql list of sql statements specifying foreign key constraints -- to be updated by this function. required index_sql list of INDEX declaration statements, duplicate or redundant indexes are ok. required Source code in datajoint/declare.py 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 def compile_foreign_key ( line , context , attributes , primary_key , attr_sql , foreign_key_sql , index_sql ): \"\"\" :param line: a line from a table definition :param context: namespace containing referenced objects :param attributes: list of attribute names already in the declaration -- to be updated by this function :param primary_key: None if the current foreign key is made from the dependent section. Otherwise it is the list of primary key attributes thus far -- to be updated by the function :param attr_sql: list of sql statements defining attributes -- to be updated by this function. :param foreign_key_sql: list of sql statements specifying foreign key constraints -- to be updated by this function. :param index_sql: list of INDEX declaration statements, duplicate or redundant indexes are ok. \"\"\" # Parse and validate from .table import Table from .expression import QueryExpression obsolete = False # See issue #436. Old style to be deprecated in a future release try : result = foreign_key_parser . parseString ( line ) except pp . ParseException : try : result = foreign_key_parser_old . parseString ( line ) except pp . ParseBaseException as err : raise DataJointError ( 'Parsing error in line \" %s \". %s .' % ( line , err )) else : obsolete = True try : ref = eval ( result . ref_table , context ) except NameError if obsolete else Exception : raise DataJointError ( \"Foreign key reference %s could not be resolved\" % result . ref_table ) options = [ opt . upper () for opt in result . options ] for opt in options : # check for invalid options if opt not in { \"NULLABLE\" , \"UNIQUE\" }: raise DataJointError ( 'Invalid foreign key option \" {opt} \"' . format ( opt = opt )) is_nullable = \"NULLABLE\" in options is_unique = \"UNIQUE\" in options if is_nullable and primary_key is not None : raise DataJointError ( 'Primary dependencies cannot be nullable in line \" {line} \"' . format ( line = line ) ) if obsolete : logger . warning ( 'Line \" {line} \" uses obsolete syntax that will no longer be supported in datajoint 0.14. ' \"For details, see issue #780 https://github.com/datajoint/datajoint-python/issues/780\" . format ( line = line ) ) if not isinstance ( ref , type ) or not issubclass ( ref , Table ): raise DataJointError ( \"Foreign key reference %r must be a valid query\" % result . ref_table ) if isinstance ( ref , type ) and issubclass ( ref , Table ): ref = ref () # check that dependency is of a supported type if ( not isinstance ( ref , QueryExpression ) or len ( ref . restriction ) or len ( ref . support ) != 1 or not isinstance ( ref . support [ 0 ], str ) ): raise DataJointError ( 'Dependency \" %s \" is not supported (yet). Use a base table or its projection.' % result . ref_table ) if obsolete : # for backward compatibility with old-style dependency declarations. See issue #436 if not isinstance ( ref , Table ): DataJointError ( 'Dependency \" %s \" is not supported. Check documentation.' % result . ref_table ) if not all ( r in ref . primary_key for r in result . ref_attrs ): raise DataJointError ( 'Invalid foreign key attributes in \" %s \"' % line ) try : raise DataJointError ( 'Duplicate attributes \" {attr} \" in \" {line} \"' . format ( attr = next ( attr for attr in result . new_attrs if attr in attributes ), line = line , ) ) except StopIteration : pass # the normal outcome # Match the primary attributes of the referenced table to local attributes new_attrs = list ( result . new_attrs ) ref_attrs = list ( result . ref_attrs ) # special case, the renamed attribute is implicit if new_attrs and not ref_attrs : if len ( new_attrs ) != 1 : raise DataJointError ( 'Renamed foreign key must be mapped to the primary key in \" %s \"' % line ) if len ( ref . primary_key ) == 1 : # if the primary key has one attribute, allow implicit renaming ref_attrs = ref . primary_key else : # if only one primary key attribute remains, then allow implicit renaming ref_attrs = [ attr for attr in ref . primary_key if attr not in attributes ] if len ( ref_attrs ) != 1 : raise DataJointError ( 'Could not resolve which primary key attribute should be referenced in \" %s \"' % line ) if len ( new_attrs ) != len ( ref_attrs ): raise DataJointError ( 'Mismatched attributes in foreign key \" %s \"' % line ) if ref_attrs : # convert to projected dependency ref = ref . proj ( ** dict ( zip ( new_attrs , ref_attrs ))) # declare new foreign key attributes for attr in ref . primary_key : if attr not in attributes : attributes . append ( attr ) if primary_key is not None : primary_key . append ( attr ) attr_sql . append ( ref . heading [ attr ] . sql . replace ( \"NOT NULL \" , \"\" , int ( is_nullable )) ) # declare the foreign key foreign_key_sql . append ( \"FOREIGN KEY (` {fk} `) REFERENCES {ref} (` {pk} `) ON UPDATE CASCADE ON DELETE RESTRICT\" . format ( fk = \"`,`\" . join ( ref . primary_key ), pk = \"`,`\" . join ( ref . heading [ name ] . original_name for name in ref . primary_key ), ref = ref . support [ 0 ], ) ) # declare unique index if is_unique : index_sql . append ( \"UNIQUE INDEX ( {attrs} )\" . format ( attrs = \",\" . join ( \"` %s `\" % attr for attr in ref . primary_key ) ) )", "title": "compile_foreign_key()"}, {"location": "api/datajoint/declare/#datajoint.declare.declare", "text": "Parse declaration and generate the SQL CREATE TABLE code Parameters: Name Type Description Default full_table_name full name of the table required definition DataJoint table definition required context dictionary of objects that might be referred to in the table required Returns: Type Description SQL CREATE TABLE statement, list of external stores used Source code in datajoint/declare.py 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 def declare ( full_table_name , definition , context ): \"\"\" Parse declaration and generate the SQL CREATE TABLE code :param full_table_name: full name of the table :param definition: DataJoint table definition :param context: dictionary of objects that might be referred to in the table :return: SQL CREATE TABLE statement, list of external stores used \"\"\" table_name = full_table_name . strip ( \"`\" ) . split ( \".\" )[ 1 ] if len ( table_name ) > MAX_TABLE_NAME_LENGTH : raise DataJointError ( \"Table name ` {name} ` exceeds the max length of {max_length} \" . format ( name = table_name , max_length = MAX_TABLE_NAME_LENGTH ) ) ( table_comment , primary_key , attribute_sql , foreign_key_sql , index_sql , external_stores , ) = prepare_declare ( definition , context ) if not primary_key : raise DataJointError ( \"Table must have a primary key\" ) return ( \"CREATE TABLE IF NOT EXISTS %s ( \\n \" % full_table_name + \", \\n \" . join ( attribute_sql + [ \"PRIMARY KEY (`\" + \"`,`\" . join ( primary_key ) + \"`)\" ] + foreign_key_sql + index_sql ) + ' \\n ) ENGINE=InnoDB, COMMENT \" %s \"' % table_comment ), external_stores", "title": "declare()"}, {"location": "api/datajoint/declare/#datajoint.declare.alter", "text": "Parameters: Name Type Description Default definition new table definition required old_definition current table definition required context the context in which to evaluate foreign key definitions required Returns: Type Description string SQL ALTER command, list of new stores used for external storage Source code in datajoint/declare.py 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 def alter ( definition , old_definition , context ): \"\"\" :param definition: new table definition :param old_definition: current table definition :param context: the context in which to evaluate foreign key definitions :return: string SQL ALTER command, list of new stores used for external storage \"\"\" ( table_comment , primary_key , attribute_sql , foreign_key_sql , index_sql , external_stores , ) = prepare_declare ( definition , context ) ( table_comment_ , primary_key_ , attribute_sql_ , foreign_key_sql_ , index_sql_ , external_stores_ , ) = prepare_declare ( old_definition , context ) # analyze differences between declarations sql = list () if primary_key != primary_key_ : raise NotImplementedError ( \"table.alter cannot alter the primary key (yet).\" ) if foreign_key_sql != foreign_key_sql_ : raise NotImplementedError ( \"table.alter cannot alter foreign keys (yet).\" ) if index_sql != index_sql_ : raise NotImplementedError ( \"table.alter cannot alter indexes (yet)\" ) if attribute_sql != attribute_sql_ : sql . extend ( _make_attribute_alter ( attribute_sql , attribute_sql_ , primary_key )) if table_comment != table_comment_ : sql . append ( 'COMMENT=\" %s \"' % table_comment ) return sql , [ e for e in external_stores if e not in external_stores_ ]", "title": "alter()"}, {"location": "api/datajoint/declare/#datajoint.declare.substitute_special_type", "text": "Parameters: Name Type Description Default match dict containing with keys \"type\" and \"comment\" -- will be modified in place required category attribute type category from TYPE_PATTERN required foreign_key_sql list of foreign key declarations to add to required context context for looking up user-defined attribute_type adapters required Source code in datajoint/declare.py 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 def substitute_special_type ( match , category , foreign_key_sql , context ): \"\"\" :param match: dict containing with keys \"type\" and \"comment\" -- will be modified in place :param category: attribute type category from TYPE_PATTERN :param foreign_key_sql: list of foreign key declarations to add to :param context: context for looking up user-defined attribute_type adapters \"\"\" if category == \"UUID\" : match [ \"type\" ] = UUID_DATA_TYPE elif category == \"INTERNAL_ATTACH\" : match [ \"type\" ] = \"LONGBLOB\" elif category in EXTERNAL_TYPES : if category == \"FILEPATH\" and not _support_filepath_types (): raise DataJointError ( \"\"\" The filepath data type is disabled until complete validation. To turn it on as experimental feature, set the environment variable {env} = TRUE or upgrade datajoint. \"\"\" . format ( env = FILEPATH_FEATURE_SWITCH ) ) match [ \"store\" ] = match [ \"type\" ] . split ( \"@\" , 1 )[ 1 ] match [ \"type\" ] = UUID_DATA_TYPE foreign_key_sql . append ( \"FOREIGN KEY (` {name} `) REFERENCES `{{database}}`.` {external_table_root} _ {store} ` (`hash`) \" \"ON UPDATE RESTRICT ON DELETE RESTRICT\" . format ( external_table_root = EXTERNAL_TABLE_ROOT , ** match ) ) elif category == \"ADAPTED\" : adapter = get_adapter ( context , match [ \"type\" ]) match [ \"type\" ] = adapter . attribute_type category = match_type ( match [ \"type\" ]) if category in SPECIAL_TYPES : # recursive redefinition from user-defined datatypes. substitute_special_type ( match , category , foreign_key_sql , context ) else : assert False , \"Unknown special type\"", "title": "substitute_special_type()"}, {"location": "api/datajoint/declare/#datajoint.declare.compile_attribute", "text": "Convert attribute definition from DataJoint format to SQL Parameters: Name Type Description Default line attribution line required in_key set to True if attribute is in primary key set required foreign_key_sql the list of foreign key declarations to add to required context context in which to look up user-defined attribute type adapterss required Returns: Type Description (name, sql, is_external) -- attribute name and sql code for its declaration Source code in datajoint/declare.py 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 def compile_attribute ( line , in_key , foreign_key_sql , context ): \"\"\" Convert attribute definition from DataJoint format to SQL :param line: attribution line :param in_key: set to True if attribute is in primary key set :param foreign_key_sql: the list of foreign key declarations to add to :param context: context in which to look up user-defined attribute type adapterss :returns: (name, sql, is_external) -- attribute name and sql code for its declaration \"\"\" try : match = attribute_parser . parseString ( line + \"#\" , parseAll = True ) except pp . ParseException as err : raise DataJointError ( \"Declaration error in position {pos} in line: \\n {line} \\n {msg} \" . format ( line = err . args [ 0 ], pos = err . args [ 1 ], msg = err . args [ 2 ] ) ) match [ \"comment\" ] = match [ \"comment\" ] . rstrip ( \"#\" ) if \"default\" not in match : match [ \"default\" ] = \"\" match = { k : v . strip () for k , v in match . items ()} match [ \"nullable\" ] = match [ \"default\" ] . lower () == \"null\" if match [ \"nullable\" ]: if in_key : raise DataJointError ( 'Primary key attributes cannot be nullable in line \" %s \"' % line ) match [ \"default\" ] = \"DEFAULT NULL\" # nullable attributes default to null else : if match [ \"default\" ]: quote = ( match [ \"default\" ] . split ( \"(\" )[ 0 ] . upper () not in CONSTANT_LITERALS and match [ \"default\" ][ 0 ] not in \" \\\" '\" ) match [ \"default\" ] = ( \"NOT NULL DEFAULT \" + ( '\" %s \"' if quote else \" %s \" ) % match [ \"default\" ] ) else : match [ \"default\" ] = \"NOT NULL\" match [ \"comment\" ] = match [ \"comment\" ] . replace ( '\"' , ' \\\\ \"' ) # escape double quotes in comment if match [ \"comment\" ] . startswith ( \":\" ): raise DataJointError ( 'An attribute comment must not start with a colon in comment \" {comment} \"' . format ( ** match ) ) category = match_type ( match [ \"type\" ]) if category in SPECIAL_TYPES : match [ \"comment\" ] = \": {type} : {comment} \" . format ( ** match ) # insert custom type into comment substitute_special_type ( match , category , foreign_key_sql , context ) if category in SERIALIZED_TYPES and match [ \"default\" ] not in { \"DEFAULT NULL\" , \"NOT NULL\" , }: raise DataJointError ( \"The default value for a blob or attachment attributes can only be NULL in: \\n {line} \" . format ( line = line ) ) sql = ( \"` {name} ` {type} {default} \" + ( ' COMMENT \" {comment} \"' if match [ \"comment\" ] else \"\" ) ) . format ( ** match ) return match [ \"name\" ], sql , match . get ( \"store\" )", "title": "compile_attribute()"}, {"location": "api/datajoint/dependencies/", "text": "unite_master_parts ( lst ) \u00b6 re-order a list of table names so that part tables immediately follow their master tables without breaking the topological order. Without this correction, a simple topological sort may insert other descendants between master and parts. The input list must be topologically sorted. :example: unite_master_parts( [' s . a ', ' s . a__q ', ' s . b ', ' s . c ', ' s . c__q ', ' s . b__q ', ' s . d ', ' s . a__r ']) -> [' s . a ', ' s . a__q ', ' s . a__r ', ' s . b ', ' s . b__q ', ' s . c ', ' s . c__q ', ' s . d '] Source code in datajoint/dependencies.py 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 def unite_master_parts ( lst ): \"\"\" re-order a list of table names so that part tables immediately follow their master tables without breaking the topological order. Without this correction, a simple topological sort may insert other descendants between master and parts. The input list must be topologically sorted. :example: unite_master_parts( ['`s`.`a`', '`s`.`a__q`', '`s`.`b`', '`s`.`c`', '`s`.`c__q`', '`s`.`b__q`', '`s`.`d`', '`s`.`a__r`']) -> ['`s`.`a`', '`s`.`a__q`', '`s`.`a__r`', '`s`.`b`', '`s`.`b__q`', '`s`.`c`', '`s`.`c__q`', '`s`.`d`'] \"\"\" for i in range ( 2 , len ( lst )): name = lst [ i ] match = re . match ( r \"(?P`\\w+`.`#?\\w+)__\\w+`\" , name ) if match : # name is a part table master = match . group ( \"master\" ) for j in range ( i - 1 , - 1 , - 1 ): if lst [ j ] == master + \"`\" or lst [ j ] . startswith ( master + \"__\" ): # move from the ith position to the (j+1)th position lst [ j + 1 : i + 1 ] = [ name ] + lst [ j + 1 : i ] break return lst Dependencies \u00b6 Bases: nx . DiGraph The graph of dependencies (foreign keys) between loaded tables. Note: the 'connection' argument should normally be supplied; Empty use is permitted to facilitate use of networkx algorithms which internally create objects with the expectation of empty constructors. See also: https://github.com/datajoint/datajoint-python/pull/443 Source code in datajoint/dependencies.py 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 class Dependencies ( nx . DiGraph ): \"\"\" The graph of dependencies (foreign keys) between loaded tables. Note: the 'connection' argument should normally be supplied; Empty use is permitted to facilitate use of networkx algorithms which internally create objects with the expectation of empty constructors. See also: https://github.com/datajoint/datajoint-python/pull/443 \"\"\" def __init__ ( self , connection = None ): self . _conn = connection self . _node_alias_count = itertools . count () self . _loaded = False super () . __init__ ( self ) def clear ( self ): self . _loaded = False super () . clear () def load ( self , force = True ): \"\"\" Load dependencies for all loaded schemas. This method gets called before any operation that requires dependencies: delete, drop, populate, progress. \"\"\" # reload from scratch to prevent duplication of renamed edges if self . _loaded and not force : return self . clear () # load primary key info keys = self . _conn . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as tab, column_name FROM information_schema.key_column_usage WHERE table_name not LIKE \"~%%\" AND table_schema in ('{schemas}') AND constraint_name=\"PRIMARY\" \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ) ) pks = defaultdict ( set ) for key in keys : pks [ key [ 0 ]] . add ( key [ 1 ]) # add nodes to the graph for n , pk in pks . items (): self . add_node ( n , primary_key = pk ) # load foreign keys keys = ( { k . lower (): v for k , v in elem . items ()} for elem in self . _conn . query ( \"\"\" SELECT constraint_name, concat('`', table_schema, '`.`', table_name, '`') as referencing_table, concat('`', referenced_table_schema, '`.`', referenced_table_name, '`') as referenced_table, column_name, referenced_column_name FROM information_schema.key_column_usage WHERE referenced_table_name NOT LIKE \"~%%\" AND (referenced_table_schema in ('{schemas}') OR referenced_table_schema is not NULL AND table_schema in ('{schemas}')) \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ), as_dict = True , ) ) fks = defaultdict ( lambda : dict ( attr_map = dict ())) for key in keys : d = fks [ ( key [ \"constraint_name\" ], key [ \"referencing_table\" ], key [ \"referenced_table\" ], ) ] d [ \"referencing_table\" ] = key [ \"referencing_table\" ] d [ \"referenced_table\" ] = key [ \"referenced_table\" ] d [ \"attr_map\" ][ key [ \"column_name\" ]] = key [ \"referenced_column_name\" ] # add edges to the graph for fk in fks . values (): props = dict ( primary = set ( fk [ \"attr_map\" ]) <= set ( pks [ fk [ \"referencing_table\" ]]), attr_map = fk [ \"attr_map\" ], aliased = any ( k != v for k , v in fk [ \"attr_map\" ] . items ()), multi = set ( fk [ \"attr_map\" ]) != set ( pks [ fk [ \"referencing_table\" ]]), ) if not props [ \"aliased\" ]: self . add_edge ( fk [ \"referenced_table\" ], fk [ \"referencing_table\" ], ** props ) else : # for aliased dependencies, add an extra node in the format '1', '2', etc alias_node = \" %d \" % next ( self . _node_alias_count ) self . add_node ( alias_node ) self . add_edge ( fk [ \"referenced_table\" ], alias_node , ** props ) self . add_edge ( alias_node , fk [ \"referencing_table\" ], ** props ) if not nx . is_directed_acyclic_graph ( self ): # pragma: no cover raise DataJointError ( \"DataJoint can only work with acyclic dependencies\" ) self . _loaded = True def parents ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referenced by the foreign keys of table \"\"\" self . load ( force = False ) return { p [ 0 ]: p [ 2 ] for p in self . in_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary } def children ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referencing the table through foreign keys \"\"\" self . load ( force = False ) return { p [ 1 ]: p [ 2 ] for p in self . out_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary } def descendants ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . descendants ( self , full_table_name )) return unite_master_parts ( [ full_table_name ] + list ( nx . algorithms . dag . topological_sort ( nodes )) ) def ancestors ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . ancestors ( self , full_table_name )) return list ( reversed ( unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nodes )) + [ full_table_name ] ) ) ) load ( force = True ) \u00b6 Load dependencies for all loaded schemas. This method gets called before any operation that requires dependencies: delete, drop, populate, progress. Source code in datajoint/dependencies.py 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 def load ( self , force = True ): \"\"\" Load dependencies for all loaded schemas. This method gets called before any operation that requires dependencies: delete, drop, populate, progress. \"\"\" # reload from scratch to prevent duplication of renamed edges if self . _loaded and not force : return self . clear () # load primary key info keys = self . _conn . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as tab, column_name FROM information_schema.key_column_usage WHERE table_name not LIKE \"~%%\" AND table_schema in ('{schemas}') AND constraint_name=\"PRIMARY\" \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ) ) pks = defaultdict ( set ) for key in keys : pks [ key [ 0 ]] . add ( key [ 1 ]) # add nodes to the graph for n , pk in pks . items (): self . add_node ( n , primary_key = pk ) # load foreign keys keys = ( { k . lower (): v for k , v in elem . items ()} for elem in self . _conn . query ( \"\"\" SELECT constraint_name, concat('`', table_schema, '`.`', table_name, '`') as referencing_table, concat('`', referenced_table_schema, '`.`', referenced_table_name, '`') as referenced_table, column_name, referenced_column_name FROM information_schema.key_column_usage WHERE referenced_table_name NOT LIKE \"~%%\" AND (referenced_table_schema in ('{schemas}') OR referenced_table_schema is not NULL AND table_schema in ('{schemas}')) \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ), as_dict = True , ) ) fks = defaultdict ( lambda : dict ( attr_map = dict ())) for key in keys : d = fks [ ( key [ \"constraint_name\" ], key [ \"referencing_table\" ], key [ \"referenced_table\" ], ) ] d [ \"referencing_table\" ] = key [ \"referencing_table\" ] d [ \"referenced_table\" ] = key [ \"referenced_table\" ] d [ \"attr_map\" ][ key [ \"column_name\" ]] = key [ \"referenced_column_name\" ] # add edges to the graph for fk in fks . values (): props = dict ( primary = set ( fk [ \"attr_map\" ]) <= set ( pks [ fk [ \"referencing_table\" ]]), attr_map = fk [ \"attr_map\" ], aliased = any ( k != v for k , v in fk [ \"attr_map\" ] . items ()), multi = set ( fk [ \"attr_map\" ]) != set ( pks [ fk [ \"referencing_table\" ]]), ) if not props [ \"aliased\" ]: self . add_edge ( fk [ \"referenced_table\" ], fk [ \"referencing_table\" ], ** props ) else : # for aliased dependencies, add an extra node in the format '1', '2', etc alias_node = \" %d \" % next ( self . _node_alias_count ) self . add_node ( alias_node ) self . add_edge ( fk [ \"referenced_table\" ], alias_node , ** props ) self . add_edge ( alias_node , fk [ \"referencing_table\" ], ** props ) if not nx . is_directed_acyclic_graph ( self ): # pragma: no cover raise DataJointError ( \"DataJoint can only work with acyclic dependencies\" ) self . _loaded = True parents ( table_name , primary = None ) \u00b6 Parameters: Name Type Description Default table_name schema . table required primary if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. None Returns: Type Description dict of tables referenced by the foreign keys of table Source code in datajoint/dependencies.py 134 135 136 137 138 139 140 141 142 143 144 145 146 147 def parents ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referenced by the foreign keys of table \"\"\" self . load ( force = False ) return { p [ 0 ]: p [ 2 ] for p in self . in_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary } children ( table_name , primary = None ) \u00b6 Parameters: Name Type Description Default table_name schema . table required primary if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. None Returns: Type Description dict of tables referencing the table through foreign keys Source code in datajoint/dependencies.py 149 150 151 152 153 154 155 156 157 158 159 160 161 162 def children ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referencing the table through foreign keys \"\"\" self . load ( force = False ) return { p [ 1 ]: p [ 2 ] for p in self . out_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary } descendants ( full_table_name ) \u00b6 Parameters: Name Type Description Default full_table_name In form schema . table_name required Returns: Type Description all dependent tables sorted in topological order. Self is included. Source code in datajoint/dependencies.py 164 165 166 167 168 169 170 171 172 173 def descendants ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . descendants ( self , full_table_name )) return unite_master_parts ( [ full_table_name ] + list ( nx . algorithms . dag . topological_sort ( nodes )) ) ancestors ( full_table_name ) \u00b6 Parameters: Name Type Description Default full_table_name In form schema . table_name required Returns: Type Description all dependent tables sorted in topological order. Self is included. Source code in datajoint/dependencies.py 175 176 177 178 179 180 181 182 183 184 185 186 187 188 def ancestors ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . ancestors ( self , full_table_name )) return list ( reversed ( unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nodes )) + [ full_table_name ] ) ) )", "title": "dependencies.py"}, {"location": "api/datajoint/dependencies/#datajoint.dependencies.unite_master_parts", "text": "re-order a list of table names so that part tables immediately follow their master tables without breaking the topological order. Without this correction, a simple topological sort may insert other descendants between master and parts. The input list must be topologically sorted. :example: unite_master_parts( [' s . a ', ' s . a__q ', ' s . b ', ' s . c ', ' s . c__q ', ' s . b__q ', ' s . d ', ' s . a__r ']) -> [' s . a ', ' s . a__q ', ' s . a__r ', ' s . b ', ' s . b__q ', ' s . c ', ' s . c__q ', ' s . d '] Source code in datajoint/dependencies.py 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 def unite_master_parts ( lst ): \"\"\" re-order a list of table names so that part tables immediately follow their master tables without breaking the topological order. Without this correction, a simple topological sort may insert other descendants between master and parts. The input list must be topologically sorted. :example: unite_master_parts( ['`s`.`a`', '`s`.`a__q`', '`s`.`b`', '`s`.`c`', '`s`.`c__q`', '`s`.`b__q`', '`s`.`d`', '`s`.`a__r`']) -> ['`s`.`a`', '`s`.`a__q`', '`s`.`a__r`', '`s`.`b`', '`s`.`b__q`', '`s`.`c`', '`s`.`c__q`', '`s`.`d`'] \"\"\" for i in range ( 2 , len ( lst )): name = lst [ i ] match = re . match ( r \"(?P`\\w+`.`#?\\w+)__\\w+`\" , name ) if match : # name is a part table master = match . group ( \"master\" ) for j in range ( i - 1 , - 1 , - 1 ): if lst [ j ] == master + \"`\" or lst [ j ] . startswith ( master + \"__\" ): # move from the ith position to the (j+1)th position lst [ j + 1 : i + 1 ] = [ name ] + lst [ j + 1 : i ] break return lst", "title": "unite_master_parts()"}, {"location": "api/datajoint/dependencies/#datajoint.dependencies.Dependencies", "text": "Bases: nx . DiGraph The graph of dependencies (foreign keys) between loaded tables. Note: the 'connection' argument should normally be supplied; Empty use is permitted to facilitate use of networkx algorithms which internally create objects with the expectation of empty constructors. See also: https://github.com/datajoint/datajoint-python/pull/443 Source code in datajoint/dependencies.py 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 class Dependencies ( nx . DiGraph ): \"\"\" The graph of dependencies (foreign keys) between loaded tables. Note: the 'connection' argument should normally be supplied; Empty use is permitted to facilitate use of networkx algorithms which internally create objects with the expectation of empty constructors. See also: https://github.com/datajoint/datajoint-python/pull/443 \"\"\" def __init__ ( self , connection = None ): self . _conn = connection self . _node_alias_count = itertools . count () self . _loaded = False super () . __init__ ( self ) def clear ( self ): self . _loaded = False super () . clear () def load ( self , force = True ): \"\"\" Load dependencies for all loaded schemas. This method gets called before any operation that requires dependencies: delete, drop, populate, progress. \"\"\" # reload from scratch to prevent duplication of renamed edges if self . _loaded and not force : return self . clear () # load primary key info keys = self . _conn . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as tab, column_name FROM information_schema.key_column_usage WHERE table_name not LIKE \"~%%\" AND table_schema in ('{schemas}') AND constraint_name=\"PRIMARY\" \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ) ) pks = defaultdict ( set ) for key in keys : pks [ key [ 0 ]] . add ( key [ 1 ]) # add nodes to the graph for n , pk in pks . items (): self . add_node ( n , primary_key = pk ) # load foreign keys keys = ( { k . lower (): v for k , v in elem . items ()} for elem in self . _conn . query ( \"\"\" SELECT constraint_name, concat('`', table_schema, '`.`', table_name, '`') as referencing_table, concat('`', referenced_table_schema, '`.`', referenced_table_name, '`') as referenced_table, column_name, referenced_column_name FROM information_schema.key_column_usage WHERE referenced_table_name NOT LIKE \"~%%\" AND (referenced_table_schema in ('{schemas}') OR referenced_table_schema is not NULL AND table_schema in ('{schemas}')) \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ), as_dict = True , ) ) fks = defaultdict ( lambda : dict ( attr_map = dict ())) for key in keys : d = fks [ ( key [ \"constraint_name\" ], key [ \"referencing_table\" ], key [ \"referenced_table\" ], ) ] d [ \"referencing_table\" ] = key [ \"referencing_table\" ] d [ \"referenced_table\" ] = key [ \"referenced_table\" ] d [ \"attr_map\" ][ key [ \"column_name\" ]] = key [ \"referenced_column_name\" ] # add edges to the graph for fk in fks . values (): props = dict ( primary = set ( fk [ \"attr_map\" ]) <= set ( pks [ fk [ \"referencing_table\" ]]), attr_map = fk [ \"attr_map\" ], aliased = any ( k != v for k , v in fk [ \"attr_map\" ] . items ()), multi = set ( fk [ \"attr_map\" ]) != set ( pks [ fk [ \"referencing_table\" ]]), ) if not props [ \"aliased\" ]: self . add_edge ( fk [ \"referenced_table\" ], fk [ \"referencing_table\" ], ** props ) else : # for aliased dependencies, add an extra node in the format '1', '2', etc alias_node = \" %d \" % next ( self . _node_alias_count ) self . add_node ( alias_node ) self . add_edge ( fk [ \"referenced_table\" ], alias_node , ** props ) self . add_edge ( alias_node , fk [ \"referencing_table\" ], ** props ) if not nx . is_directed_acyclic_graph ( self ): # pragma: no cover raise DataJointError ( \"DataJoint can only work with acyclic dependencies\" ) self . _loaded = True def parents ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referenced by the foreign keys of table \"\"\" self . load ( force = False ) return { p [ 0 ]: p [ 2 ] for p in self . in_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary } def children ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referencing the table through foreign keys \"\"\" self . load ( force = False ) return { p [ 1 ]: p [ 2 ] for p in self . out_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary } def descendants ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . descendants ( self , full_table_name )) return unite_master_parts ( [ full_table_name ] + list ( nx . algorithms . dag . topological_sort ( nodes )) ) def ancestors ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . ancestors ( self , full_table_name )) return list ( reversed ( unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nodes )) + [ full_table_name ] ) ) )", "title": "Dependencies"}, {"location": "api/datajoint/dependencies/#datajoint.dependencies.Dependencies.load", "text": "Load dependencies for all loaded schemas. This method gets called before any operation that requires dependencies: delete, drop, populate, progress. Source code in datajoint/dependencies.py 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 def load ( self , force = True ): \"\"\" Load dependencies for all loaded schemas. This method gets called before any operation that requires dependencies: delete, drop, populate, progress. \"\"\" # reload from scratch to prevent duplication of renamed edges if self . _loaded and not force : return self . clear () # load primary key info keys = self . _conn . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as tab, column_name FROM information_schema.key_column_usage WHERE table_name not LIKE \"~%%\" AND table_schema in ('{schemas}') AND constraint_name=\"PRIMARY\" \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ) ) pks = defaultdict ( set ) for key in keys : pks [ key [ 0 ]] . add ( key [ 1 ]) # add nodes to the graph for n , pk in pks . items (): self . add_node ( n , primary_key = pk ) # load foreign keys keys = ( { k . lower (): v for k , v in elem . items ()} for elem in self . _conn . query ( \"\"\" SELECT constraint_name, concat('`', table_schema, '`.`', table_name, '`') as referencing_table, concat('`', referenced_table_schema, '`.`', referenced_table_name, '`') as referenced_table, column_name, referenced_column_name FROM information_schema.key_column_usage WHERE referenced_table_name NOT LIKE \"~%%\" AND (referenced_table_schema in ('{schemas}') OR referenced_table_schema is not NULL AND table_schema in ('{schemas}')) \"\"\" . format ( schemas = \"','\" . join ( self . _conn . schemas ) ), as_dict = True , ) ) fks = defaultdict ( lambda : dict ( attr_map = dict ())) for key in keys : d = fks [ ( key [ \"constraint_name\" ], key [ \"referencing_table\" ], key [ \"referenced_table\" ], ) ] d [ \"referencing_table\" ] = key [ \"referencing_table\" ] d [ \"referenced_table\" ] = key [ \"referenced_table\" ] d [ \"attr_map\" ][ key [ \"column_name\" ]] = key [ \"referenced_column_name\" ] # add edges to the graph for fk in fks . values (): props = dict ( primary = set ( fk [ \"attr_map\" ]) <= set ( pks [ fk [ \"referencing_table\" ]]), attr_map = fk [ \"attr_map\" ], aliased = any ( k != v for k , v in fk [ \"attr_map\" ] . items ()), multi = set ( fk [ \"attr_map\" ]) != set ( pks [ fk [ \"referencing_table\" ]]), ) if not props [ \"aliased\" ]: self . add_edge ( fk [ \"referenced_table\" ], fk [ \"referencing_table\" ], ** props ) else : # for aliased dependencies, add an extra node in the format '1', '2', etc alias_node = \" %d \" % next ( self . _node_alias_count ) self . add_node ( alias_node ) self . add_edge ( fk [ \"referenced_table\" ], alias_node , ** props ) self . add_edge ( alias_node , fk [ \"referencing_table\" ], ** props ) if not nx . is_directed_acyclic_graph ( self ): # pragma: no cover raise DataJointError ( \"DataJoint can only work with acyclic dependencies\" ) self . _loaded = True", "title": "load()"}, {"location": "api/datajoint/dependencies/#datajoint.dependencies.Dependencies.parents", "text": "Parameters: Name Type Description Default table_name schema . table required primary if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. None Returns: Type Description dict of tables referenced by the foreign keys of table Source code in datajoint/dependencies.py 134 135 136 137 138 139 140 141 142 143 144 145 146 147 def parents ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referenced by the foreign keys of table \"\"\" self . load ( force = False ) return { p [ 0 ]: p [ 2 ] for p in self . in_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary }", "title": "parents()"}, {"location": "api/datajoint/dependencies/#datajoint.dependencies.Dependencies.children", "text": "Parameters: Name Type Description Default table_name schema . table required primary if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. None Returns: Type Description dict of tables referencing the table through foreign keys Source code in datajoint/dependencies.py 149 150 151 152 153 154 155 156 157 158 159 160 161 162 def children ( self , table_name , primary = None ): \"\"\" :param table_name: `schema`.`table` :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered. :return: dict of tables referencing the table through foreign keys \"\"\" self . load ( force = False ) return { p [ 1 ]: p [ 2 ] for p in self . out_edges ( table_name , data = True ) if primary is None or p [ 2 ][ \"primary\" ] == primary }", "title": "children()"}, {"location": "api/datajoint/dependencies/#datajoint.dependencies.Dependencies.descendants", "text": "Parameters: Name Type Description Default full_table_name In form schema . table_name required Returns: Type Description all dependent tables sorted in topological order. Self is included. Source code in datajoint/dependencies.py 164 165 166 167 168 169 170 171 172 173 def descendants ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . descendants ( self , full_table_name )) return unite_master_parts ( [ full_table_name ] + list ( nx . algorithms . dag . topological_sort ( nodes )) )", "title": "descendants()"}, {"location": "api/datajoint/dependencies/#datajoint.dependencies.Dependencies.ancestors", "text": "Parameters: Name Type Description Default full_table_name In form schema . table_name required Returns: Type Description all dependent tables sorted in topological order. Self is included. Source code in datajoint/dependencies.py 175 176 177 178 179 180 181 182 183 184 185 186 187 188 def ancestors ( self , full_table_name ): \"\"\" :param full_table_name: In form `schema`.`table_name` :return: all dependent tables sorted in topological order. Self is included. \"\"\" self . load ( force = False ) nodes = self . subgraph ( nx . algorithms . dag . ancestors ( self , full_table_name )) return list ( reversed ( unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nodes )) + [ full_table_name ] ) ) )", "title": "ancestors()"}, {"location": "api/datajoint/diagram/", "text": "Diagram \u00b6 Bases: nx . DiGraph Entity relationship diagram. Usage: diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed Source code in datajoint/diagram.py 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 class Diagram ( nx . DiGraph ): \"\"\" Entity relationship diagram. Usage: >>> diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. >>> diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed \"\"\" def __init__ ( self , source , context = None ): if isinstance ( source , Diagram ): # copy constructor self . nodes_to_show = set ( source . nodes_to_show ) self . context = source . context super () . __init__ ( source ) return # get the caller's context if context is None : frame = inspect . currentframe () . f_back self . context = dict ( frame . f_globals , ** frame . f_locals ) del frame else : self . context = context # find connection in the source try : connection = source . connection except AttributeError : try : connection = source . schema . connection except AttributeError : raise DataJointError ( \"Could not find database connection in %s \" % repr ( source [ 0 ]) ) # initialize graph from dependencies connection . dependencies . load () super () . __init__ ( connection . dependencies ) # Enumerate nodes from all the items in the list self . nodes_to_show = set () try : self . nodes_to_show . add ( source . full_table_name ) except AttributeError : try : database = source . database except AttributeError : try : database = source . schema . database except AttributeError : raise DataJointError ( \"Cannot plot Diagram for %s \" % repr ( source ) ) for node in self : if node . startswith ( \"` %s `\" % database ): self . nodes_to_show . add ( node ) @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence )) def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) ) def __add__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Union of the diagrams when arg is another Diagram or an expansion downstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . add ( arg . full_table_name ) except AttributeError : for i in range ( arg ): new = nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( self , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __sub__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Difference of the diagrams when arg is another Diagram or an expansion upstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . difference_update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . remove ( arg . full_table_name ) except AttributeError : for i in range ( arg ): graph = nx . DiGraph ( self ) . reverse () new = nx . algorithms . boundary . node_boundary ( graph , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( graph , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __mul__ ( self , arg ): \"\"\" Intersection of two diagrams :param arg: another Diagram :return: a new Diagram comprising nodes that are present in both operands. \"\"\" self = Diagram ( self ) # copy self . nodes_to_show . intersection_update ( arg . nodes_to_show ) return self def _make_graph ( self ): \"\"\" Make the self.graph - a graph object ready for drawing \"\"\" # mark \"distinguished\" tables, i.e. those that introduce new primary key # attributes for name in self . nodes_to_show : foreign_attributes = set ( attr for p in self . in_edges ( name , data = True ) for attr in p [ 2 ][ \"attr_map\" ] if p [ 2 ][ \"primary\" ] ) self . nodes [ name ][ \"distinguished\" ] = ( \"primary_key\" in self . nodes [ name ] and foreign_attributes < self . nodes [ name ][ \"primary_key\" ] ) # include aliased nodes that are sandwiched between two displayed nodes gaps = set ( nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) ) . intersection ( nx . algorithms . boundary . node_boundary ( nx . DiGraph ( self ) . reverse (), self . nodes_to_show ) ) nodes = self . nodes_to_show . union ( a for a in gaps if a . isdigit ) # construct subgraph and rename nodes to class names graph = nx . DiGraph ( nx . DiGraph ( self ) . subgraph ( nodes )) nx . set_node_attributes ( graph , name = \"node_type\" , values = { n : _get_tier ( n ) for n in graph } ) # relabel nodes to class names mapping = { node : lookup_class_name ( node , self . context ) or node for node in graph . nodes () } new_names = [ mapping . values ()] if len ( new_names ) > len ( set ( new_names )): raise DataJointError ( \"Some classes have identical names. The Diagram cannot be plotted.\" ) nx . relabel_nodes ( graph , mapping , copy = False ) return graph def make_dot ( self ): graph = self . _make_graph () graph . nodes () scale = 1.2 # scaling factor for fonts and boxes label_props = { # http://matplotlib.org/examples/color/named_colors.html None : dict ( shape = \"circle\" , color = \"#FFFF0040\" , fontcolor = \"yellow\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), _AliasNode : dict ( shape = \"circle\" , color = \"#FF880080\" , fontcolor = \"#FF880080\" , fontsize = round ( scale * 0 ), size = 0.05 * scale , fixed = True , ), Manual : dict ( shape = \"box\" , color = \"#00FF0030\" , fontcolor = \"darkgreen\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Lookup : dict ( shape = \"plaintext\" , color = \"#00000020\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), Computed : dict ( shape = \"ellipse\" , color = \"#FF000020\" , fontcolor = \"#7F0000A0\" , fontsize = round ( scale * 10 ), size = 0.3 * scale , fixed = True , ), Imported : dict ( shape = \"ellipse\" , color = \"#00007F40\" , fontcolor = \"#00007FA0\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Part : dict ( shape = \"plaintext\" , color = \"#0000000\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.1 * scale , fixed = False , ), } node_props = { node : label_props [ d [ \"node_type\" ]] for node , d in dict ( graph . nodes ( data = True )) . items () } dot = nx . drawing . nx_pydot . to_pydot ( graph ) for node in dot . get_nodes (): node . set_shape ( \"circle\" ) name = node . get_name () . strip ( '\"' ) props = node_props [ name ] node . set_fontsize ( props [ \"fontsize\" ]) node . set_fontcolor ( props [ \"fontcolor\" ]) node . set_shape ( props [ \"shape\" ]) node . set_fontname ( \"arial\" ) node . set_fixedsize ( \"shape\" if props [ \"fixed\" ] else False ) node . set_width ( props [ \"size\" ]) node . set_height ( props [ \"size\" ]) if name . split ( \".\" )[ 0 ] in self . context : cls = eval ( name , self . context ) assert issubclass ( cls , Table ) description = ( cls () . describe ( context = self . context , printout = False ) . split ( \" \\n \" ) ) description = ( \"-\" * 30 if q . startswith ( \"---\" ) else q . replace ( \"->\" , \"→\" ) if \"->\" in q else q . split ( \":\" )[ 0 ] for q in description if not q . startswith ( \"#\" ) ) node . set_tooltip ( \" \" . join ( description )) node . set_label ( \"<\" + name + \">\" if node . get ( \"distinguished\" ) == \"True\" else name ) node . set_color ( props [ \"color\" ]) node . set_style ( \"filled\" ) for edge in dot . get_edges (): # see https://graphviz.org/doc/info/attrs.html src = edge . get_source () . strip ( '\"' ) dest = edge . get_destination () . strip ( '\"' ) props = graph . get_edge_data ( src , dest ) edge . set_color ( \"#00000040\" ) edge . set_style ( \"solid\" if props [ \"primary\" ] else \"dashed\" ) master_part = graph . nodes [ dest ][ \"node_type\" ] is Part and dest . startswith ( src + \".\" ) edge . set_weight ( 3 if master_part else 1 ) edge . set_arrowhead ( \"none\" ) edge . set_penwidth ( 0.75 if props [ \"multi\" ] else 2 ) return dot def make_svg ( self ): from IPython.display import SVG return SVG ( self . make_dot () . create_svg ()) def make_png ( self ): return io . BytesIO ( self . make_dot () . create_png ()) def make_image ( self ): if plot_active : return plt . imread ( self . make_png ()) else : raise DataJointError ( \"pyplot was not imported\" ) def _repr_svg_ ( self ): return self . make_svg () . _repr_svg_ () def draw ( self ): if plot_active : plt . imshow ( self . make_image ()) plt . gca () . axis ( \"off\" ) plt . show () else : raise DataJointError ( \"pyplot was not imported\" ) def save ( self , filename , format = None ): if format is None : if filename . lower () . endswith ( \".png\" ): format = \"png\" elif filename . lower () . endswith ( \".svg\" ): format = \"svg\" if format . lower () == \"png\" : with open ( filename , \"wb\" ) as f : f . write ( self . make_png () . getbuffer () . tobytes ()) elif format . lower () == \"svg\" : with open ( filename , \"w\" ) as f : f . write ( self . make_svg () . data ) else : raise DataJointError ( \"Unsupported file format\" ) @staticmethod def _layout ( graph , ** kwargs ): return pydot_layout ( graph , prog = \"dot\" , ** kwargs ) from_sequence ( sequence ) classmethod \u00b6 The join Diagram for all objects in sequence Parameters: Name Type Description Default sequence a sequence (e.g. list, tuple) required Returns: Type Description Diagram(arg1) + ... + Diagram(argn) Source code in datajoint/diagram.py 146 147 148 149 150 151 152 153 154 @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence )) add_parts () \u00b6 Adds to the diagram the part tables of tables already included in the diagram Returns: Type Description Source code in datajoint/diagram.py 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self topological_sort () \u00b6 Returns: Type Description list of nodes in topological order Source code in datajoint/diagram.py 183 184 185 186 187 188 189 190 191 def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) )", "title": "diagram.py"}, {"location": "api/datajoint/diagram/#datajoint.diagram.Diagram", "text": "Bases: nx . DiGraph Entity relationship diagram. Usage: diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed Source code in datajoint/diagram.py 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 class Diagram ( nx . DiGraph ): \"\"\" Entity relationship diagram. Usage: >>> diag = Diagram(source) source can be a base table object, a base table class, a schema, or a module that has a schema. >>> diag.draw() draws the diagram using pyplot diag1 + diag2 - combines the two diagrams. diag + n - expands n levels of successors diag - n - expands n levels of predecessors Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. Only those tables that are loaded in the connection object are displayed \"\"\" def __init__ ( self , source , context = None ): if isinstance ( source , Diagram ): # copy constructor self . nodes_to_show = set ( source . nodes_to_show ) self . context = source . context super () . __init__ ( source ) return # get the caller's context if context is None : frame = inspect . currentframe () . f_back self . context = dict ( frame . f_globals , ** frame . f_locals ) del frame else : self . context = context # find connection in the source try : connection = source . connection except AttributeError : try : connection = source . schema . connection except AttributeError : raise DataJointError ( \"Could not find database connection in %s \" % repr ( source [ 0 ]) ) # initialize graph from dependencies connection . dependencies . load () super () . __init__ ( connection . dependencies ) # Enumerate nodes from all the items in the list self . nodes_to_show = set () try : self . nodes_to_show . add ( source . full_table_name ) except AttributeError : try : database = source . database except AttributeError : try : database = source . schema . database except AttributeError : raise DataJointError ( \"Cannot plot Diagram for %s \" % repr ( source ) ) for node in self : if node . startswith ( \"` %s `\" % database ): self . nodes_to_show . add ( node ) @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence )) def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) ) def __add__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Union of the diagrams when arg is another Diagram or an expansion downstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . add ( arg . full_table_name ) except AttributeError : for i in range ( arg ): new = nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( self , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __sub__ ( self , arg ): \"\"\" :param arg: either another Diagram or a positive integer. :return: Difference of the diagrams when arg is another Diagram or an expansion upstream when arg is a positive integer. \"\"\" self = Diagram ( self ) # copy try : self . nodes_to_show . difference_update ( arg . nodes_to_show ) except AttributeError : try : self . nodes_to_show . remove ( arg . full_table_name ) except AttributeError : for i in range ( arg ): graph = nx . DiGraph ( self ) . reverse () new = nx . algorithms . boundary . node_boundary ( graph , self . nodes_to_show ) if not new : break # add nodes referenced by aliased nodes new . update ( nx . algorithms . boundary . node_boundary ( graph , ( a for a in new if a . isdigit ()) ) ) self . nodes_to_show . update ( new ) return self def __mul__ ( self , arg ): \"\"\" Intersection of two diagrams :param arg: another Diagram :return: a new Diagram comprising nodes that are present in both operands. \"\"\" self = Diagram ( self ) # copy self . nodes_to_show . intersection_update ( arg . nodes_to_show ) return self def _make_graph ( self ): \"\"\" Make the self.graph - a graph object ready for drawing \"\"\" # mark \"distinguished\" tables, i.e. those that introduce new primary key # attributes for name in self . nodes_to_show : foreign_attributes = set ( attr for p in self . in_edges ( name , data = True ) for attr in p [ 2 ][ \"attr_map\" ] if p [ 2 ][ \"primary\" ] ) self . nodes [ name ][ \"distinguished\" ] = ( \"primary_key\" in self . nodes [ name ] and foreign_attributes < self . nodes [ name ][ \"primary_key\" ] ) # include aliased nodes that are sandwiched between two displayed nodes gaps = set ( nx . algorithms . boundary . node_boundary ( self , self . nodes_to_show ) ) . intersection ( nx . algorithms . boundary . node_boundary ( nx . DiGraph ( self ) . reverse (), self . nodes_to_show ) ) nodes = self . nodes_to_show . union ( a for a in gaps if a . isdigit ) # construct subgraph and rename nodes to class names graph = nx . DiGraph ( nx . DiGraph ( self ) . subgraph ( nodes )) nx . set_node_attributes ( graph , name = \"node_type\" , values = { n : _get_tier ( n ) for n in graph } ) # relabel nodes to class names mapping = { node : lookup_class_name ( node , self . context ) or node for node in graph . nodes () } new_names = [ mapping . values ()] if len ( new_names ) > len ( set ( new_names )): raise DataJointError ( \"Some classes have identical names. The Diagram cannot be plotted.\" ) nx . relabel_nodes ( graph , mapping , copy = False ) return graph def make_dot ( self ): graph = self . _make_graph () graph . nodes () scale = 1.2 # scaling factor for fonts and boxes label_props = { # http://matplotlib.org/examples/color/named_colors.html None : dict ( shape = \"circle\" , color = \"#FFFF0040\" , fontcolor = \"yellow\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), _AliasNode : dict ( shape = \"circle\" , color = \"#FF880080\" , fontcolor = \"#FF880080\" , fontsize = round ( scale * 0 ), size = 0.05 * scale , fixed = True , ), Manual : dict ( shape = \"box\" , color = \"#00FF0030\" , fontcolor = \"darkgreen\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Lookup : dict ( shape = \"plaintext\" , color = \"#00000020\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.4 * scale , fixed = False , ), Computed : dict ( shape = \"ellipse\" , color = \"#FF000020\" , fontcolor = \"#7F0000A0\" , fontsize = round ( scale * 10 ), size = 0.3 * scale , fixed = True , ), Imported : dict ( shape = \"ellipse\" , color = \"#00007F40\" , fontcolor = \"#00007FA0\" , fontsize = round ( scale * 10 ), size = 0.4 * scale , fixed = False , ), Part : dict ( shape = \"plaintext\" , color = \"#0000000\" , fontcolor = \"black\" , fontsize = round ( scale * 8 ), size = 0.1 * scale , fixed = False , ), } node_props = { node : label_props [ d [ \"node_type\" ]] for node , d in dict ( graph . nodes ( data = True )) . items () } dot = nx . drawing . nx_pydot . to_pydot ( graph ) for node in dot . get_nodes (): node . set_shape ( \"circle\" ) name = node . get_name () . strip ( '\"' ) props = node_props [ name ] node . set_fontsize ( props [ \"fontsize\" ]) node . set_fontcolor ( props [ \"fontcolor\" ]) node . set_shape ( props [ \"shape\" ]) node . set_fontname ( \"arial\" ) node . set_fixedsize ( \"shape\" if props [ \"fixed\" ] else False ) node . set_width ( props [ \"size\" ]) node . set_height ( props [ \"size\" ]) if name . split ( \".\" )[ 0 ] in self . context : cls = eval ( name , self . context ) assert issubclass ( cls , Table ) description = ( cls () . describe ( context = self . context , printout = False ) . split ( \" \\n \" ) ) description = ( \"-\" * 30 if q . startswith ( \"---\" ) else q . replace ( \"->\" , \"→\" ) if \"->\" in q else q . split ( \":\" )[ 0 ] for q in description if not q . startswith ( \"#\" ) ) node . set_tooltip ( \" \" . join ( description )) node . set_label ( \"<\" + name + \">\" if node . get ( \"distinguished\" ) == \"True\" else name ) node . set_color ( props [ \"color\" ]) node . set_style ( \"filled\" ) for edge in dot . get_edges (): # see https://graphviz.org/doc/info/attrs.html src = edge . get_source () . strip ( '\"' ) dest = edge . get_destination () . strip ( '\"' ) props = graph . get_edge_data ( src , dest ) edge . set_color ( \"#00000040\" ) edge . set_style ( \"solid\" if props [ \"primary\" ] else \"dashed\" ) master_part = graph . nodes [ dest ][ \"node_type\" ] is Part and dest . startswith ( src + \".\" ) edge . set_weight ( 3 if master_part else 1 ) edge . set_arrowhead ( \"none\" ) edge . set_penwidth ( 0.75 if props [ \"multi\" ] else 2 ) return dot def make_svg ( self ): from IPython.display import SVG return SVG ( self . make_dot () . create_svg ()) def make_png ( self ): return io . BytesIO ( self . make_dot () . create_png ()) def make_image ( self ): if plot_active : return plt . imread ( self . make_png ()) else : raise DataJointError ( \"pyplot was not imported\" ) def _repr_svg_ ( self ): return self . make_svg () . _repr_svg_ () def draw ( self ): if plot_active : plt . imshow ( self . make_image ()) plt . gca () . axis ( \"off\" ) plt . show () else : raise DataJointError ( \"pyplot was not imported\" ) def save ( self , filename , format = None ): if format is None : if filename . lower () . endswith ( \".png\" ): format = \"png\" elif filename . lower () . endswith ( \".svg\" ): format = \"svg\" if format . lower () == \"png\" : with open ( filename , \"wb\" ) as f : f . write ( self . make_png () . getbuffer () . tobytes ()) elif format . lower () == \"svg\" : with open ( filename , \"w\" ) as f : f . write ( self . make_svg () . data ) else : raise DataJointError ( \"Unsupported file format\" ) @staticmethod def _layout ( graph , ** kwargs ): return pydot_layout ( graph , prog = \"dot\" , ** kwargs )", "title": "Diagram"}, {"location": "api/datajoint/diagram/#datajoint.diagram.Diagram.from_sequence", "text": "The join Diagram for all objects in sequence Parameters: Name Type Description Default sequence a sequence (e.g. list, tuple) required Returns: Type Description Diagram(arg1) + ... + Diagram(argn) Source code in datajoint/diagram.py 146 147 148 149 150 151 152 153 154 @classmethod def from_sequence ( cls , sequence ): \"\"\" The join Diagram for all objects in sequence :param sequence: a sequence (e.g. list, tuple) :return: Diagram(arg1) + ... + Diagram(argn) \"\"\" return functools . reduce ( lambda x , y : x + y , map ( Diagram , sequence ))", "title": "from_sequence()"}, {"location": "api/datajoint/diagram/#datajoint.diagram.Diagram.add_parts", "text": "Adds to the diagram the part tables of tables already included in the diagram Returns: Type Description Source code in datajoint/diagram.py 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def add_parts ( self ): \"\"\" Adds to the diagram the part tables of tables already included in the diagram :return: \"\"\" def is_part ( part , master ): \"\"\" :param part: `database`.`table_name` :param master: `database`.`table_name` :return: True if part is part of master. \"\"\" part = [ s . strip ( \"`\" ) for s in part . split ( \".\" )] master = [ s . strip ( \"`\" ) for s in master . split ( \".\" )] return ( master [ 0 ] == part [ 0 ] and master [ 1 ] + \"__\" == part [ 1 ][: len ( master [ 1 ]) + 2 ] ) self = Diagram ( self ) # copy self . nodes_to_show . update ( n for n in self . nodes () if any ( is_part ( n , m ) for m in self . nodes_to_show ) ) return self", "title": "add_parts()"}, {"location": "api/datajoint/diagram/#datajoint.diagram.Diagram.topological_sort", "text": "Returns: Type Description list of nodes in topological order Source code in datajoint/diagram.py 183 184 185 186 187 188 189 190 191 def topological_sort ( self ): \"\"\":return: list of nodes in topological order\"\"\" return unite_master_parts ( list ( nx . algorithms . dag . topological_sort ( nx . DiGraph ( self ) . subgraph ( self . nodes_to_show ) ) ) )", "title": "topological_sort()"}, {"location": "api/datajoint/errors/", "text": "Exception classes for the DataJoint library DataJointError \u00b6 Bases: Exception Base class for errors specific to DataJoint internal operation. Source code in datajoint/errors.py 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 class DataJointError ( Exception ): \"\"\" Base class for errors specific to DataJoint internal operation. \"\"\" def __init__ ( self , * args ): from .plugin import connection_plugins , type_plugins self . __cause__ = ( PluginWarning ( \"Unverified DataJoint plugin detected.\" ) if any ( [ any ([ not plugins [ k ][ \"verified\" ] for k in plugins ]) for plugins in [ connection_plugins , type_plugins ] if plugins ] ) else None ) def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args )) suggest ( * args ) \u00b6 regenerate the exception with additional arguments Parameters: Name Type Description Default args addition arguments required Returns: Type Description a new exception of the same type with the additional arguments Source code in datajoint/errors.py 34 35 36 37 38 39 40 41 def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args )) LostConnectionError \u00b6 Bases: DataJointError Loss of server connection Source code in datajoint/errors.py 45 46 47 48 class LostConnectionError ( DataJointError ): \"\"\" Loss of server connection \"\"\" QueryError \u00b6 Bases: DataJointError Errors arising from queries to the database Source code in datajoint/errors.py 51 52 53 54 class QueryError ( DataJointError ): \"\"\" Errors arising from queries to the database \"\"\" QuerySyntaxError \u00b6 Bases: QueryError Errors arising from incorrect query syntax Source code in datajoint/errors.py 58 59 60 61 class QuerySyntaxError ( QueryError ): \"\"\" Errors arising from incorrect query syntax \"\"\" AccessError \u00b6 Bases: QueryError User access error: insufficient privileges. Source code in datajoint/errors.py 64 65 66 67 class AccessError ( QueryError ): \"\"\" User access error: insufficient privileges. \"\"\" MissingTableError \u00b6 Bases: DataJointError Query on a table that has not been declared Source code in datajoint/errors.py 70 71 72 73 class MissingTableError ( DataJointError ): \"\"\" Query on a table that has not been declared \"\"\" DuplicateError \u00b6 Bases: QueryError An integrity error caused by a duplicate entry into a unique key Source code in datajoint/errors.py 76 77 78 79 class DuplicateError ( QueryError ): \"\"\" An integrity error caused by a duplicate entry into a unique key \"\"\" IntegrityError \u00b6 Bases: QueryError An integrity error triggered by foreign key constraints Source code in datajoint/errors.py 82 83 84 85 class IntegrityError ( QueryError ): \"\"\" An integrity error triggered by foreign key constraints \"\"\" UnknownAttributeError \u00b6 Bases: QueryError User requests an attribute name not found in query heading Source code in datajoint/errors.py 88 89 90 91 class UnknownAttributeError ( QueryError ): \"\"\" User requests an attribute name not found in query heading \"\"\" MissingAttributeError \u00b6 Bases: QueryError An error arising when a required attribute value is not provided in INSERT Source code in datajoint/errors.py 94 95 96 97 class MissingAttributeError ( QueryError ): \"\"\" An error arising when a required attribute value is not provided in INSERT \"\"\" MissingExternalFile \u00b6 Bases: DataJointError Error raised when an external file managed by DataJoint is no longer accessible Source code in datajoint/errors.py 100 101 102 103 class MissingExternalFile ( DataJointError ): \"\"\" Error raised when an external file managed by DataJoint is no longer accessible \"\"\" BucketInaccessible \u00b6 Bases: DataJointError Error raised when a S3 bucket is inaccessible Source code in datajoint/errors.py 106 107 108 109 class BucketInaccessible ( DataJointError ): \"\"\" Error raised when a S3 bucket is inaccessible \"\"\"", "title": "errors.py"}, {"location": "api/datajoint/errors/#datajoint.errors.DataJointError", "text": "Bases: Exception Base class for errors specific to DataJoint internal operation. Source code in datajoint/errors.py 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 class DataJointError ( Exception ): \"\"\" Base class for errors specific to DataJoint internal operation. \"\"\" def __init__ ( self , * args ): from .plugin import connection_plugins , type_plugins self . __cause__ = ( PluginWarning ( \"Unverified DataJoint plugin detected.\" ) if any ( [ any ([ not plugins [ k ][ \"verified\" ] for k in plugins ]) for plugins in [ connection_plugins , type_plugins ] if plugins ] ) else None ) def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args ))", "title": "DataJointError"}, {"location": "api/datajoint/errors/#datajoint.errors.DataJointError.suggest", "text": "regenerate the exception with additional arguments Parameters: Name Type Description Default args addition arguments required Returns: Type Description a new exception of the same type with the additional arguments Source code in datajoint/errors.py 34 35 36 37 38 39 40 41 def suggest ( self , * args ): \"\"\" regenerate the exception with additional arguments :param args: addition arguments :return: a new exception of the same type with the additional arguments \"\"\" return self . __class__ ( * ( self . args + args ))", "title": "suggest()"}, {"location": "api/datajoint/errors/#datajoint.errors.LostConnectionError", "text": "Bases: DataJointError Loss of server connection Source code in datajoint/errors.py 45 46 47 48 class LostConnectionError ( DataJointError ): \"\"\" Loss of server connection \"\"\"", "title": "LostConnectionError"}, {"location": "api/datajoint/errors/#datajoint.errors.QueryError", "text": "Bases: DataJointError Errors arising from queries to the database Source code in datajoint/errors.py 51 52 53 54 class QueryError ( DataJointError ): \"\"\" Errors arising from queries to the database \"\"\"", "title": "QueryError"}, {"location": "api/datajoint/errors/#datajoint.errors.QuerySyntaxError", "text": "Bases: QueryError Errors arising from incorrect query syntax Source code in datajoint/errors.py 58 59 60 61 class QuerySyntaxError ( QueryError ): \"\"\" Errors arising from incorrect query syntax \"\"\"", "title": "QuerySyntaxError"}, {"location": "api/datajoint/errors/#datajoint.errors.AccessError", "text": "Bases: QueryError User access error: insufficient privileges. Source code in datajoint/errors.py 64 65 66 67 class AccessError ( QueryError ): \"\"\" User access error: insufficient privileges. \"\"\"", "title": "AccessError"}, {"location": "api/datajoint/errors/#datajoint.errors.MissingTableError", "text": "Bases: DataJointError Query on a table that has not been declared Source code in datajoint/errors.py 70 71 72 73 class MissingTableError ( DataJointError ): \"\"\" Query on a table that has not been declared \"\"\"", "title": "MissingTableError"}, {"location": "api/datajoint/errors/#datajoint.errors.DuplicateError", "text": "Bases: QueryError An integrity error caused by a duplicate entry into a unique key Source code in datajoint/errors.py 76 77 78 79 class DuplicateError ( QueryError ): \"\"\" An integrity error caused by a duplicate entry into a unique key \"\"\"", "title": "DuplicateError"}, {"location": "api/datajoint/errors/#datajoint.errors.IntegrityError", "text": "Bases: QueryError An integrity error triggered by foreign key constraints Source code in datajoint/errors.py 82 83 84 85 class IntegrityError ( QueryError ): \"\"\" An integrity error triggered by foreign key constraints \"\"\"", "title": "IntegrityError"}, {"location": "api/datajoint/errors/#datajoint.errors.UnknownAttributeError", "text": "Bases: QueryError User requests an attribute name not found in query heading Source code in datajoint/errors.py 88 89 90 91 class UnknownAttributeError ( QueryError ): \"\"\" User requests an attribute name not found in query heading \"\"\"", "title": "UnknownAttributeError"}, {"location": "api/datajoint/errors/#datajoint.errors.MissingAttributeError", "text": "Bases: QueryError An error arising when a required attribute value is not provided in INSERT Source code in datajoint/errors.py 94 95 96 97 class MissingAttributeError ( QueryError ): \"\"\" An error arising when a required attribute value is not provided in INSERT \"\"\"", "title": "MissingAttributeError"}, {"location": "api/datajoint/errors/#datajoint.errors.MissingExternalFile", "text": "Bases: DataJointError Error raised when an external file managed by DataJoint is no longer accessible Source code in datajoint/errors.py 100 101 102 103 class MissingExternalFile ( DataJointError ): \"\"\" Error raised when an external file managed by DataJoint is no longer accessible \"\"\"", "title": "MissingExternalFile"}, {"location": "api/datajoint/errors/#datajoint.errors.BucketInaccessible", "text": "Bases: DataJointError Error raised when a S3 bucket is inaccessible Source code in datajoint/errors.py 106 107 108 109 class BucketInaccessible ( DataJointError ): \"\"\" Error raised when a S3 bucket is inaccessible \"\"\"", "title": "BucketInaccessible"}, {"location": "api/datajoint/expression/", "text": "AndList \u00b6 Bases: list A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 Source code in datajoint/condition.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 class AndList ( list ): \"\"\" A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 \"\"\" def append ( self , restriction ): if isinstance ( restriction , AndList ): # extend to reduce nesting self . extend ( restriction ) else : super () . append ( restriction ) QueryExpression \u00b6 QueryExpression implements query operators to derive new entity set from its input. A QueryExpression object generates a SELECT statement in SQL. QueryExpression operators are restrict, join, proj, aggr, and union. A QueryExpression object has a support, a restriction (an AndList), and heading. Property heading (type dj.Heading) contains information about the attributes. It is loaded from the database and updated by proj. Property support is the list of table names or other QueryExpressions to be joined. The restriction is applied first without having access to the attributes generated by the projection. Then projection is applied by selecting modifying the heading attribute. Application of operators does not always lead to the creation of a subquery. A subquery is generated when: 1. A restriction is applied on any computed or renamed attributes 2. A projection is applied remapping remapped attributes 3. Subclasses: Join, Aggregation, and Union have additional specific rules. Source code in datajoint/expression.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 class QueryExpression : \"\"\" QueryExpression implements query operators to derive new entity set from its input. A QueryExpression object generates a SELECT statement in SQL. QueryExpression operators are restrict, join, proj, aggr, and union. A QueryExpression object has a support, a restriction (an AndList), and heading. Property `heading` (type dj.Heading) contains information about the attributes. It is loaded from the database and updated by proj. Property `support` is the list of table names or other QueryExpressions to be joined. The restriction is applied first without having access to the attributes generated by the projection. Then projection is applied by selecting modifying the heading attribute. Application of operators does not always lead to the creation of a subquery. A subquery is generated when: 1. A restriction is applied on any computed or renamed attributes 2. A projection is applied remapping remapped attributes 3. Subclasses: Join, Aggregation, and Union have additional specific rules. \"\"\" _restriction = None _restriction_attributes = None _left = [] # list of booleans True for left joins, False for inner joins _original_heading = None # heading before projections # subclasses or instantiators must provide values _connection = None _heading = None _support = None # If the query will be using distinct _distinct = False @property def connection ( self ): \"\"\"a dj.Connection object\"\"\" assert self . _connection is not None return self . _connection @property def support ( self ): \"\"\"A list of table names or subqueries to from the FROM clause\"\"\" assert self . _support is not None return self . _support @property def heading ( self ): \"\"\"a dj.Heading object, reflects the effects of the projection operator .proj\"\"\" return self . _heading @property def original_heading ( self ): \"\"\"a dj.Heading object reflecting the attributes before projection\"\"\" return self . _original_heading or self . heading @property def restriction ( self ): \"\"\"a AndList object of restrictions applied to input to produce the result\"\"\" if self . _restriction is None : self . _restriction = AndList () return self . _restriction @property def restriction_attributes ( self ): \"\"\"the set of attribute names invoked in the WHERE clause\"\"\" if self . _restriction_attributes is None : self . _restriction_attributes = set () return self . _restriction_attributes @property def primary_key ( self ): return self . heading . primary_key _subquery_alias_count = count () # count for alias names used in the FROM clause def from_clause ( self ): support = ( \"(\" + src . make_sql () + \") as `$ %x `\" % next ( self . _subquery_alias_count ) if isinstance ( src , QueryExpression ) else src for src in self . support ) clause = next ( support ) for s , left in zip ( support , self . _left ): clause += \" NATURAL {left} JOIN {clause} \" . format ( left = \" LEFT\" if left else \"\" , clause = s ) return clause def where_clause ( self ): return ( \"\" if not self . restriction else \" WHERE ( %s )\" % \")AND(\" . join ( str ( s ) for s in self . restriction ) ) def make_sql ( self , fields = None ): \"\"\" Make the SQL SELECT statement. :param fields: used to explicitly set the select attributes \"\"\" return \"SELECT {distinct}{fields} FROM {from_}{where} \" . format ( distinct = \"DISTINCT \" if self . _distinct else \"\" , fields = self . heading . as_sql ( fields or self . heading . names ), from_ = self . from_clause (), where = self . where_clause (), ) # --------- query operators ----------- def make_subquery ( self ): \"\"\"create a new SELECT statement where self is the FROM clause\"\"\" result = QueryExpression () result . _connection = self . connection result . _support = [ self ] result . _heading = self . heading . make_subquery_heading () return result def restrict ( self , restriction ): \"\"\" Produces a new expression with the new restriction applied. rel.restrict(restriction) is equivalent to rel & restriction. rel.restrict(Not(restriction)) is equivalent to rel - restriction The primary key of the result is unaffected. Successive restrictions are combined as logical AND: r & a & b is equivalent to r & AndList((a, b)) Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists (logical disjunction of conditions) Inverse restriction is accomplished by either using the subtraction operator or the Not class. The expressions in each row equivalent: rel & True rel rel & False the empty entity set rel & 'TRUE' rel rel & 'FALSE' the empty entity set rel - cond rel & Not(cond) rel - 'TRUE' rel & False rel - 'FALSE' rel rel & AndList((cond1,cond2)) rel & cond1 & cond2 rel & AndList() rel rel & [cond1, cond2] rel & OrList((cond1, cond2)) rel & [] rel & False rel & None rel & False rel & any_empty_entity_set rel & False rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)] rel - [cond1, cond2] rel & Not(cond1) & Not(cond2) rel - AndList() rel & False rel - [] rel rel - None rel rel - any_empty_entity_set rel When arg is another QueryExpression, the restriction rel & arg restricts rel to elements that match at least one element in arg (hence arg is treated as an OrList). Conversely, rel - arg restricts rel to elements that do not match any elements in arg. Two elements match when their common attributes have equal values or when they have no common attributes. All shared attributes must be in the primary key of either rel or arg or both or an error will be raised. QueryExpression.restrict is the only access point that modifies restrictions. All other operators must ultimately call restrict() :param restriction: a sequence or an array (treated as OR list), another QueryExpression, an SQL condition string, or an AndList. \"\"\" attributes = set () new_condition = make_condition ( self , restriction , attributes ) if new_condition is True : return self # restriction has no effect, return the same object # check that all attributes in condition are present in the query try : raise DataJointError ( \"Attribute ` %s ` is not found in query.\" % next ( attr for attr in attributes if attr not in self . heading . names ) ) except StopIteration : pass # all ok # If the new condition uses any new attributes, a subquery is required. # However, Aggregation's HAVING statement works fine with aliased attributes. need_subquery = isinstance ( self , Union ) or ( not isinstance ( self , Aggregation ) and self . heading . new_attributes ) if need_subquery : result = self . make_subquery () else : result = copy . copy ( self ) result . _restriction = AndList ( self . restriction ) # copy to preserve the original result . restriction . append ( new_condition ) result . restriction_attributes . update ( attributes ) return result def restrict_in_place ( self , restriction ): self . __dict__ . update ( self . restrict ( restriction ) . __dict__ ) def __and__ ( self , restriction ): \"\"\" Restriction operator e.g. ``q1 & q2``. :return: a restricted copy of the input argument See QueryExpression.restrict for more detail. \"\"\" return self . restrict ( restriction ) def __xor__ ( self , restriction ): \"\"\" Permissive restriction operator ignoring compatibility check e.g. ``q1 ^ q2``. \"\"\" if inspect . isclass ( restriction ) and issubclass ( restriction , QueryExpression ): restriction = restriction () if isinstance ( restriction , Not ): return self . restrict ( Not ( PromiscuousOperand ( restriction . restriction ))) return self . restrict ( PromiscuousOperand ( restriction )) def __sub__ ( self , restriction ): \"\"\" Inverted restriction e.g. ``q1 - q2``. :return: a restricted copy of the input argument See QueryExpression.restrict for more detail. \"\"\" return self . restrict ( Not ( restriction )) def __neg__ ( self ): \"\"\" Convert between restriction and inverted restriction e.g. ``-q1``. :return: target restriction See QueryExpression.restrict for more detail. \"\"\" if isinstance ( self , Not ): return self . restriction return Not ( self ) def __mul__ ( self , other ): \"\"\" join of query expressions `self` and `other` e.g. ``q1 * q2``. \"\"\" return self . join ( other ) def __matmul__ ( self , other ): \"\"\" Permissive join of query expressions `self` and `other` ignoring compatibility check e.g. ``q1 @ q2``. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate return self . join ( other , semantic_check = False ) def join ( self , other , semantic_check = True , left = False ): \"\"\" create the joined QueryExpression. a * b is short for A.join(B) a @ b is short for A.join(B, semantic_check=False) Additionally, left=True will retain the rows of self, effectively performing a left join. \"\"\" # trigger subqueries if joining on renamed attributes if isinstance ( other , U ): return other * self if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if not isinstance ( other , QueryExpression ): raise DataJointError ( \"The argument of join must be a QueryExpression\" ) if semantic_check : assert_join_compatibility ( self , other ) join_attributes = set ( n for n in self . heading . names if n in other . heading . names ) # needs subquery if self's FROM clause has common attributes with other's FROM clause need_subquery1 = need_subquery2 = bool ( ( set ( self . original_heading . names ) & set ( other . original_heading . names )) - join_attributes ) # need subquery if any of the join attributes are derived need_subquery1 = ( need_subquery1 or isinstance ( self , Aggregation ) or any ( n in self . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) need_subquery2 = ( need_subquery2 or isinstance ( other , Aggregation ) or any ( n in other . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) if need_subquery1 : self = self . make_subquery () if need_subquery2 : other = other . make_subquery () result = QueryExpression () result . _connection = self . connection result . _support = self . support + other . support result . _left = self . _left + [ left ] + other . _left result . _heading = self . heading . join ( other . heading ) result . _restriction = AndList ( self . restriction ) result . _restriction . append ( other . restriction ) result . _original_heading = self . original_heading . join ( other . original_heading ) assert len ( result . support ) == len ( result . _left ) + 1 return result def __add__ ( self , other ): \"\"\"union e.g. ``q1 + q2``.\"\"\" return Union . create ( self , other ) def proj ( self , * attributes , ** named_attributes ): \"\"\" Projection operator. :param attributes: attributes to be included in the result. (The primary key is already included). :param named_attributes: new attributes computed or renamed from existing attributes. :return: the projected expression. Primary key attributes cannot be excluded but may be renamed. If the attribute list contains an Ellipsis ..., then all secondary attributes are included too Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present. Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self) self.proj() -- include only primary key self.proj('attr1', 'attr2') -- include primary key and attributes attr1 and attr2 self.proj(..., '-attr1', '-attr2') -- include all attributes except attr1 and attr2 self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1 self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup' self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax) from other attributes available before the projection. Each attribute name can only be used once. \"\"\" # new attributes in parentheses are included again with the new name without removing original duplication_pattern = re . compile ( rf '^\\s*\$\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*\$\\s*$' ) # attributes without parentheses renamed rename_pattern = re . compile ( rf '^\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*$' ) replicate_map = { k : m . group ( \"name\" ) for k , m in ( ( k , duplication_pattern . match ( v )) for k , v in named_attributes . items () ) if m } rename_map = { k : m . group ( \"name\" ) for k , m in ( ( k , rename_pattern . match ( v )) for k , v in named_attributes . items () ) if m } compute_map = { k : v for k , v in named_attributes . items () if not duplication_pattern . match ( v ) and not rename_pattern . match ( v ) } attributes = set ( attributes ) # include primary key attributes . update (( k for k in self . primary_key if k not in rename_map . values ())) # include all secondary attributes with Ellipsis if Ellipsis in attributes : attributes . discard ( Ellipsis ) attributes . update ( ( a for a in self . heading . secondary_attributes if a not in attributes and a not in rename_map . values () ) ) try : raise DataJointError ( \" %s is not a valid data type for an attribute in .proj\" % next ( a for a in attributes if not isinstance ( a , str )) ) except StopIteration : pass # normal case # remove excluded attributes, specified as `-attr' excluded = set ( a for a in attributes if a . strip () . startswith ( \"-\" )) attributes . difference_update ( excluded ) excluded = set ( a . lstrip ( \"-\" ) . strip () for a in excluded ) attributes . difference_update ( excluded ) try : raise DataJointError ( \"Cannot exclude primary key attribute %s \" , next ( a for a in excluded if a in self . primary_key ), ) except StopIteration : pass # all ok # check that all attributes exist in heading try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( a for a in attributes if a not in self . heading . names ) ) except StopIteration : pass # all ok # check that all mentioned names are present in heading mentions = attributes . union ( replicate_map . values ()) . union ( rename_map . values ()) try : raise DataJointError ( \"Attribute ' %s ' not found.\" % next ( a for a in mentions if not self . heading . names ) ) except StopIteration : pass # all ok # check that newly created attributes do not clash with any other selected attributes try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in rename_map if a in attributes . union ( compute_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in compute_map if a in attributes . union ( rename_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in replicate_map if a in attributes . union ( rename_map ) . union ( compute_map ) ) ) except StopIteration : pass # all ok # need a subquery if the projection remaps any remapped attributes used = set ( q for v in compute_map . values () for q in extract_column_names ( v )) used . update ( rename_map . values ()) used . update ( replicate_map . values ()) used . intersection_update ( self . heading . names ) need_subquery = isinstance ( self , Union ) or any ( self . heading [ name ] . attribute_expression is not None for name in used ) if not need_subquery and self . restriction : # need a subquery if the restriction applies to attributes that have been renamed need_subquery = any ( name in self . restriction_attributes for name in self . heading . new_attributes ) result = self . make_subquery () if need_subquery else copy . copy ( self ) result . _original_heading = result . original_heading result . _heading = result . heading . select ( attributes , rename_map = dict ( ** rename_map , ** replicate_map ), compute_map = compute_map , ) return result def aggr ( self , group , * attributes , keep_all_rows = False , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param keep_all_rows: True=keep all the rows from self. False=keep only rows that match entries in group. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if Ellipsis in attributes : # expand ellipsis to include only attributes from the left table attributes = set ( attributes ) attributes . discard ( Ellipsis ) attributes . update ( self . heading . secondary_attributes ) return Aggregation . create ( self , group = group , keep_all_rows = keep_all_rows ) . proj ( * attributes , ** named_attributes ) aggregate = aggr # alias for aggr # ---------- Fetch operators -------------------- @property def fetch1 ( self ): return Fetch1 ( self ) @property def fetch ( self ): return Fetch ( self ) def head ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the first few entries from query expression. Equivalent to fetch(order_by=\"KEY\", limit=25) :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY\" , limit = limit , ** fetch_kwargs ) def tail ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the last few entries from query expression. Equivalent to fetch(order_by=\"KEY DESC\", limit=25)[::-1] :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY DESC\" , limit = limit , ** fetch_kwargs )[:: - 1 ] def __len__ ( self ): \"\"\":return: number of elements in the result set e.g. ``len(q1)``.\"\"\" return self . connection . query ( \"SELECT {select_} FROM {from_}{where} \" . format ( select_ = ( \"count(*)\" if any ( self . _left ) else \"count(DISTINCT {fields} )\" . format ( fields = self . heading . as_sql ( self . primary_key , include_aliases = False ) ) ), from_ = self . from_clause (), where = self . where_clause (), ) ) . fetchone ()[ 0 ] def __bool__ ( self ): \"\"\" :return: True if the result is not empty. Equivalent to len(self) > 0 but often faster e.g. ``bool(q1)``. \"\"\" return bool ( self . connection . query ( \"SELECT EXISTS(SELECT 1 FROM {from_}{where} )\" . format ( from_ = self . from_clause (), where = self . where_clause () ) ) . fetchone ()[ 0 ] ) def __contains__ ( self , item ): \"\"\" returns True if the restriction in item matches any entries in self e.g. ``restriction in q1``. :param item: any restriction (item in query_expression) is equivalent to bool(query_expression & item) but may be executed more efficiently. \"\"\" return bool ( self & item ) # May be optimized e.g. using an EXISTS query def __iter__ ( self ): \"\"\" returns an iterator-compatible QueryExpression object e.g. ``iter(q1)``. :param self: iterator-compatible QueryExpression object \"\"\" self . _iter_only_key = all ( v . in_key for v in self . heading . attributes . values ()) self . _iter_keys = self . fetch ( \"KEY\" ) return self def __next__ ( self ): \"\"\" returns the next record on an iterator-compatible QueryExpression object e.g. ``next(q1)``. :param self: A query expression :type self: :class:`QueryExpression` :rtype: dict \"\"\" try : key = self . _iter_keys . pop ( 0 ) except AttributeError : # self._iter_keys is missing because __iter__ has not been called. raise TypeError ( \"A QueryExpression object is not an iterator. \" \"Use iter(obj) to create an iterator.\" ) except IndexError : raise StopIteration else : if self . _iter_only_key : return key else : try : return ( self & key ) . fetch1 () except DataJointError : # The data may have been deleted since the moment the keys were fetched # -- move on to next entry. return next ( self ) def cursor ( self , offset = 0 , limit = None , order_by = None , as_dict = False ): \"\"\" See expression.fetch() for input description. :return: query cursor \"\"\" if offset and limit is None : raise DataJointError ( \"limit is required when offset is set\" ) sql = self . make_sql () if order_by is not None : sql += \" ORDER BY \" + \", \" . join ( order_by ) if limit is not None : sql += \" LIMIT %d \" % limit + ( \" OFFSET %d \" % offset if offset else \"\" ) logger . debug ( sql ) return self . connection . query ( sql , as_dict = as_dict ) def __repr__ ( self ): \"\"\" returns the string representation of a QueryExpression object e.g. ``str(q1)``. :param self: A query expression :type self: :class:`QueryExpression` :rtype: str \"\"\" return ( super () . __repr__ () if config [ \"loglevel\" ] . lower () == \"debug\" else self . preview () ) def preview ( self , limit = None , width = None ): \"\"\":return: a string of preview of the contents of the query.\"\"\" return preview ( self , limit , width ) def _repr_html_ ( self ): \"\"\":return: HTML to display table in Jupyter notebook.\"\"\" return repr_html ( self ) connection () property \u00b6 a dj.Connection object Source code in datajoint/expression.py 58 59 60 61 62 @property def connection ( self ): \"\"\"a dj.Connection object\"\"\" assert self . _connection is not None return self . _connection support () property \u00b6 A list of table names or subqueries to from the FROM clause Source code in datajoint/expression.py 64 65 66 67 68 @property def support ( self ): \"\"\"A list of table names or subqueries to from the FROM clause\"\"\" assert self . _support is not None return self . _support heading () property \u00b6 a dj.Heading object, reflects the effects of the projection operator .proj Source code in datajoint/expression.py 70 71 72 73 @property def heading ( self ): \"\"\"a dj.Heading object, reflects the effects of the projection operator .proj\"\"\" return self . _heading original_heading () property \u00b6 a dj.Heading object reflecting the attributes before projection Source code in datajoint/expression.py 75 76 77 78 @property def original_heading ( self ): \"\"\"a dj.Heading object reflecting the attributes before projection\"\"\" return self . _original_heading or self . heading restriction () property \u00b6 a AndList object of restrictions applied to input to produce the result Source code in datajoint/expression.py 80 81 82 83 84 85 @property def restriction ( self ): \"\"\"a AndList object of restrictions applied to input to produce the result\"\"\" if self . _restriction is None : self . _restriction = AndList () return self . _restriction restriction_attributes () property \u00b6 the set of attribute names invoked in the WHERE clause Source code in datajoint/expression.py 87 88 89 90 91 92 @property def restriction_attributes ( self ): \"\"\"the set of attribute names invoked in the WHERE clause\"\"\" if self . _restriction_attributes is None : self . _restriction_attributes = set () return self . _restriction_attributes make_sql ( fields = None ) \u00b6 Make the SQL SELECT statement. Parameters: Name Type Description Default fields used to explicitly set the select attributes None Source code in datajoint/expression.py 121 122 123 124 125 126 127 128 129 130 131 132 def make_sql ( self , fields = None ): \"\"\" Make the SQL SELECT statement. :param fields: used to explicitly set the select attributes \"\"\" return \"SELECT {distinct}{fields} FROM {from_}{where} \" . format ( distinct = \"DISTINCT \" if self . _distinct else \"\" , fields = self . heading . as_sql ( fields or self . heading . names ), from_ = self . from_clause (), where = self . where_clause (), ) make_subquery () \u00b6 create a new SELECT statement where self is the FROM clause Source code in datajoint/expression.py 135 136 137 138 139 140 141 def make_subquery ( self ): \"\"\"create a new SELECT statement where self is the FROM clause\"\"\" result = QueryExpression () result . _connection = self . connection result . _support = [ self ] result . _heading = self . heading . make_subquery_heading () return result restrict ( restriction ) \u00b6 Produces a new expression with the new restriction applied. rel.restrict(restriction) is equivalent to rel & restriction. rel.restrict(Not(restriction)) is equivalent to rel - restriction The primary key of the result is unaffected. Successive restrictions are combined as logical AND: r & a & b is equivalent to r & AndList((a, b)) Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists (logical disjunction of conditions) Inverse restriction is accomplished by either using the subtraction operator or the Not class. The expressions in each row equivalent: rel & True rel rel & False the empty entity set rel & 'TRUE' rel rel & 'FALSE' the empty entity set rel - cond rel & Not(cond) rel - 'TRUE' rel & False rel - 'FALSE' rel rel & AndList((cond1,cond2)) rel & cond1 & cond2 rel & AndList() rel rel & [cond1, cond2] rel & OrList((cond1, cond2)) rel & [] rel & False rel & None rel & False rel & any_empty_entity_set rel & False rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)] rel - [cond1, cond2] rel & Not(cond1) & Not(cond2) rel - AndList() rel & False rel - [] rel rel - None rel rel - any_empty_entity_set rel When arg is another QueryExpression, the restriction rel & arg restricts rel to elements that match at least one element in arg (hence arg is treated as an OrList). Conversely, rel - arg restricts rel to elements that do not match any elements in arg. Two elements match when their common attributes have equal values or when they have no common attributes. All shared attributes must be in the primary key of either rel or arg or both or an error will be raised. QueryExpression.restrict is the only access point that modifies restrictions. All other operators must ultimately call restrict() Parameters: Name Type Description Default restriction a sequence or an array (treated as OR list), another QueryExpression, an SQL condition string, or an AndList. required Source code in datajoint/expression.py 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 def restrict ( self , restriction ): \"\"\" Produces a new expression with the new restriction applied. rel.restrict(restriction) is equivalent to rel & restriction. rel.restrict(Not(restriction)) is equivalent to rel - restriction The primary key of the result is unaffected. Successive restrictions are combined as logical AND: r & a & b is equivalent to r & AndList((a, b)) Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists (logical disjunction of conditions) Inverse restriction is accomplished by either using the subtraction operator or the Not class. The expressions in each row equivalent: rel & True rel rel & False the empty entity set rel & 'TRUE' rel rel & 'FALSE' the empty entity set rel - cond rel & Not(cond) rel - 'TRUE' rel & False rel - 'FALSE' rel rel & AndList((cond1,cond2)) rel & cond1 & cond2 rel & AndList() rel rel & [cond1, cond2] rel & OrList((cond1, cond2)) rel & [] rel & False rel & None rel & False rel & any_empty_entity_set rel & False rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)] rel - [cond1, cond2] rel & Not(cond1) & Not(cond2) rel - AndList() rel & False rel - [] rel rel - None rel rel - any_empty_entity_set rel When arg is another QueryExpression, the restriction rel & arg restricts rel to elements that match at least one element in arg (hence arg is treated as an OrList). Conversely, rel - arg restricts rel to elements that do not match any elements in arg. Two elements match when their common attributes have equal values or when they have no common attributes. All shared attributes must be in the primary key of either rel or arg or both or an error will be raised. QueryExpression.restrict is the only access point that modifies restrictions. All other operators must ultimately call restrict() :param restriction: a sequence or an array (treated as OR list), another QueryExpression, an SQL condition string, or an AndList. \"\"\" attributes = set () new_condition = make_condition ( self , restriction , attributes ) if new_condition is True : return self # restriction has no effect, return the same object # check that all attributes in condition are present in the query try : raise DataJointError ( \"Attribute ` %s ` is not found in query.\" % next ( attr for attr in attributes if attr not in self . heading . names ) ) except StopIteration : pass # all ok # If the new condition uses any new attributes, a subquery is required. # However, Aggregation's HAVING statement works fine with aliased attributes. need_subquery = isinstance ( self , Union ) or ( not isinstance ( self , Aggregation ) and self . heading . new_attributes ) if need_subquery : result = self . make_subquery () else : result = copy . copy ( self ) result . _restriction = AndList ( self . restriction ) # copy to preserve the original result . restriction . append ( new_condition ) result . restriction_attributes . update ( attributes ) return result join ( other , semantic_check = True , left = False ) \u00b6 create the joined QueryExpression. a * b is short for A.join(B) a @ b is short for A.join(B, semantic_check=False) Additionally, left=True will retain the rows of self, effectively performing a left join. Source code in datajoint/expression.py 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 def join ( self , other , semantic_check = True , left = False ): \"\"\" create the joined QueryExpression. a * b is short for A.join(B) a @ b is short for A.join(B, semantic_check=False) Additionally, left=True will retain the rows of self, effectively performing a left join. \"\"\" # trigger subqueries if joining on renamed attributes if isinstance ( other , U ): return other * self if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if not isinstance ( other , QueryExpression ): raise DataJointError ( \"The argument of join must be a QueryExpression\" ) if semantic_check : assert_join_compatibility ( self , other ) join_attributes = set ( n for n in self . heading . names if n in other . heading . names ) # needs subquery if self's FROM clause has common attributes with other's FROM clause need_subquery1 = need_subquery2 = bool ( ( set ( self . original_heading . names ) & set ( other . original_heading . names )) - join_attributes ) # need subquery if any of the join attributes are derived need_subquery1 = ( need_subquery1 or isinstance ( self , Aggregation ) or any ( n in self . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) need_subquery2 = ( need_subquery2 or isinstance ( other , Aggregation ) or any ( n in other . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) if need_subquery1 : self = self . make_subquery () if need_subquery2 : other = other . make_subquery () result = QueryExpression () result . _connection = self . connection result . _support = self . support + other . support result . _left = self . _left + [ left ] + other . _left result . _heading = self . heading . join ( other . heading ) result . _restriction = AndList ( self . restriction ) result . _restriction . append ( other . restriction ) result . _original_heading = self . original_heading . join ( other . original_heading ) assert len ( result . support ) == len ( result . _left ) + 1 return result proj ( * attributes , ** named_attributes ) \u00b6 Projection operator. Parameters: Name Type Description Default attributes attributes to be included in the result. (The primary key is already included). required named_attributes new attributes computed or renamed from existing attributes. required Returns: Type Description the projected expression. Primary key attributes cannot be excluded but may be renamed. If the attribute list contains an Ellipsis ..., then all secondary attributes are included too Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present. Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self) self.proj() -- include only primary key self.proj('attr1', 'attr2') -- include primary key and attributes attr1 and attr2 self.proj(..., '-attr1', '-attr2') -- include all attributes except attr1 and attr2 self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1 self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup' self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax) from other attributes available before the projection. Each attribute name can only be used once. Source code in datajoint/expression.py 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 def proj ( self , * attributes , ** named_attributes ): \"\"\" Projection operator. :param attributes: attributes to be included in the result. (The primary key is already included). :param named_attributes: new attributes computed or renamed from existing attributes. :return: the projected expression. Primary key attributes cannot be excluded but may be renamed. If the attribute list contains an Ellipsis ..., then all secondary attributes are included too Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present. Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self) self.proj() -- include only primary key self.proj('attr1', 'attr2') -- include primary key and attributes attr1 and attr2 self.proj(..., '-attr1', '-attr2') -- include all attributes except attr1 and attr2 self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1 self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup' self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax) from other attributes available before the projection. Each attribute name can only be used once. \"\"\" # new attributes in parentheses are included again with the new name without removing original duplication_pattern = re . compile ( rf '^\\s*\$\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*\$\\s*$' ) # attributes without parentheses renamed rename_pattern = re . compile ( rf '^\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*$' ) replicate_map = { k : m . group ( \"name\" ) for k , m in ( ( k , duplication_pattern . match ( v )) for k , v in named_attributes . items () ) if m } rename_map = { k : m . group ( \"name\" ) for k , m in ( ( k , rename_pattern . match ( v )) for k , v in named_attributes . items () ) if m } compute_map = { k : v for k , v in named_attributes . items () if not duplication_pattern . match ( v ) and not rename_pattern . match ( v ) } attributes = set ( attributes ) # include primary key attributes . update (( k for k in self . primary_key if k not in rename_map . values ())) # include all secondary attributes with Ellipsis if Ellipsis in attributes : attributes . discard ( Ellipsis ) attributes . update ( ( a for a in self . heading . secondary_attributes if a not in attributes and a not in rename_map . values () ) ) try : raise DataJointError ( \" %s is not a valid data type for an attribute in .proj\" % next ( a for a in attributes if not isinstance ( a , str )) ) except StopIteration : pass # normal case # remove excluded attributes, specified as `-attr' excluded = set ( a for a in attributes if a . strip () . startswith ( \"-\" )) attributes . difference_update ( excluded ) excluded = set ( a . lstrip ( \"-\" ) . strip () for a in excluded ) attributes . difference_update ( excluded ) try : raise DataJointError ( \"Cannot exclude primary key attribute %s \" , next ( a for a in excluded if a in self . primary_key ), ) except StopIteration : pass # all ok # check that all attributes exist in heading try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( a for a in attributes if a not in self . heading . names ) ) except StopIteration : pass # all ok # check that all mentioned names are present in heading mentions = attributes . union ( replicate_map . values ()) . union ( rename_map . values ()) try : raise DataJointError ( \"Attribute ' %s ' not found.\" % next ( a for a in mentions if not self . heading . names ) ) except StopIteration : pass # all ok # check that newly created attributes do not clash with any other selected attributes try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in rename_map if a in attributes . union ( compute_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in compute_map if a in attributes . union ( rename_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in replicate_map if a in attributes . union ( rename_map ) . union ( compute_map ) ) ) except StopIteration : pass # all ok # need a subquery if the projection remaps any remapped attributes used = set ( q for v in compute_map . values () for q in extract_column_names ( v )) used . update ( rename_map . values ()) used . update ( replicate_map . values ()) used . intersection_update ( self . heading . names ) need_subquery = isinstance ( self , Union ) or any ( self . heading [ name ] . attribute_expression is not None for name in used ) if not need_subquery and self . restriction : # need a subquery if the restriction applies to attributes that have been renamed need_subquery = any ( name in self . restriction_attributes for name in self . heading . new_attributes ) result = self . make_subquery () if need_subquery else copy . copy ( self ) result . _original_heading = result . original_heading result . _heading = result . heading . select ( attributes , rename_map = dict ( ** rename_map , ** replicate_map ), compute_map = compute_map , ) return result aggr ( group , * attributes , keep_all_rows = False , ** named_attributes ) \u00b6 Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of group . Parameters: Name Type Description Default group The query expression to be aggregated. required keep_all_rows True=keep all the rows from self. False=keep only rows that match entries in group. False named_attributes computations of the form new_attribute=\"sql expression on attributes of group\" required Returns: Type Description The derived query expression Source code in datajoint/expression.py 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 def aggr ( self , group , * attributes , keep_all_rows = False , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param keep_all_rows: True=keep all the rows from self. False=keep only rows that match entries in group. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if Ellipsis in attributes : # expand ellipsis to include only attributes from the left table attributes = set ( attributes ) attributes . discard ( Ellipsis ) attributes . update ( self . heading . secondary_attributes ) return Aggregation . create ( self , group = group , keep_all_rows = keep_all_rows ) . proj ( * attributes , ** named_attributes ) head ( limit = 25 , ** fetch_kwargs ) \u00b6 shortcut to fetch the first few entries from query expression. Equivalent to fetch(order_by=\"KEY\", limit=25) Parameters: Name Type Description Default limit number of entries 25 fetch_kwargs kwargs for fetch required Returns: Type Description query result Source code in datajoint/expression.py 512 513 514 515 516 517 518 519 520 521 def head ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the first few entries from query expression. Equivalent to fetch(order_by=\"KEY\", limit=25) :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY\" , limit = limit , ** fetch_kwargs ) tail ( limit = 25 , ** fetch_kwargs ) \u00b6 shortcut to fetch the last few entries from query expression. Equivalent to fetch(order_by=\"KEY DESC\", limit=25)[::-1] Parameters: Name Type Description Default limit number of entries 25 fetch_kwargs kwargs for fetch required Returns: Type Description query result Source code in datajoint/expression.py 523 524 525 526 527 528 529 530 531 532 def tail ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the last few entries from query expression. Equivalent to fetch(order_by=\"KEY DESC\", limit=25)[::-1] :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY DESC\" , limit = limit , ** fetch_kwargs )[:: - 1 ] cursor ( offset = 0 , limit = None , order_by = None , as_dict = False ) \u00b6 See expression.fetch() for input description. Returns: Type Description query cursor Source code in datajoint/expression.py 616 617 618 619 620 621 622 623 624 625 626 627 628 629 def cursor ( self , offset = 0 , limit = None , order_by = None , as_dict = False ): \"\"\" See expression.fetch() for input description. :return: query cursor \"\"\" if offset and limit is None : raise DataJointError ( \"limit is required when offset is set\" ) sql = self . make_sql () if order_by is not None : sql += \" ORDER BY \" + \", \" . join ( order_by ) if limit is not None : sql += \" LIMIT %d \" % limit + ( \" OFFSET %d \" % offset if offset else \"\" ) logger . debug ( sql ) return self . connection . query ( sql , as_dict = as_dict ) preview ( limit = None , width = None ) \u00b6 Returns: Type Description a string of preview of the contents of the query. Source code in datajoint/expression.py 645 646 647 def preview ( self , limit = None , width = None ): \"\"\":return: a string of preview of the contents of the query.\"\"\" return preview ( self , limit , width ) Not \u00b6 invert restriction Source code in datajoint/condition.py 43 44 45 46 47 class Not : \"\"\"invert restriction\"\"\" def __init__ ( self , restriction ): self . restriction = restriction Aggregation \u00b6 Bases: QueryExpression Aggregation.create(arg, group, comp1='calc1', ..., compn='calcn') yields an entity set with primary key from arg. The computed arguments comp1, ..., compn use aggregation calculations on the attributes of group or simple projections and calculations on the attributes of arg. Aggregation is used QueryExpression.aggr and U.aggr. Aggregation is a private class in DataJoint, not exposed to users. Source code in datajoint/expression.py 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 class Aggregation ( QueryExpression ): \"\"\" Aggregation.create(arg, group, comp1='calc1', ..., compn='calcn') yields an entity set with primary key from arg. The computed arguments comp1, ..., compn use aggregation calculations on the attributes of group or simple projections and calculations on the attributes of arg. Aggregation is used QueryExpression.aggr and U.aggr. Aggregation is a private class in DataJoint, not exposed to users. \"\"\" _left_restrict = None # the pre-GROUP BY conditions for the WHERE clause _subquery_alias_count = count () @classmethod def create ( cls , arg , group , keep_all_rows = False ): if inspect . isclass ( group ) and issubclass ( group , QueryExpression ): group = group () # instantiate if a class assert isinstance ( group , QueryExpression ) if keep_all_rows and len ( group . support ) > 1 or group . heading . new_attributes : group = group . make_subquery () # subquery if left joining a join join = arg . join ( group , left = keep_all_rows ) # reuse the join logic result = cls () result . _connection = join . connection result . _heading = join . heading . set_primary_key ( arg . primary_key ) # use left operand's primary key result . _support = join . support result . _left = join . _left result . _left_restrict = join . restriction # WHERE clause applied before GROUP BY result . _grouping_attributes = result . primary_key return result def where_clause ( self ): return ( \"\" if not self . _left_restrict else \" WHERE ( %s )\" % \")AND(\" . join ( str ( s ) for s in self . _left_restrict ) ) def make_sql ( self , fields = None ): fields = self . heading . as_sql ( fields or self . heading . names ) assert self . _grouping_attributes or not self . restriction distinct = set ( self . heading . names ) == set ( self . primary_key ) return \"SELECT {distinct}{fields} FROM {from_}{where}{group_by} \" . format ( distinct = \"DISTINCT \" if distinct else \"\" , fields = fields , from_ = self . from_clause (), where = self . where_clause (), group_by = \"\" if not self . primary_key else ( \" GROUP BY ` %s `\" % \"`,`\" . join ( self . _grouping_attributes ) + ( \"\" if not self . restriction else \" HAVING ( %s )\" % \")AND(\" . join ( self . restriction ) ) ), ) def __len__ ( self ): return self . connection . query ( \"SELECT count(1) FROM ( {subquery} ) `$ {alias:x} `\" . format ( subquery = self . make_sql (), alias = next ( self . _subquery_alias_count ) ) ) . fetchone ()[ 0 ] def __bool__ ( self ): return bool ( self . connection . query ( \"SELECT EXISTS( {sql} )\" . format ( sql = self . make_sql ())) ) Union \u00b6 Bases: QueryExpression Union is the private DataJoint class that implements the union operator. Source code in datajoint/expression.py 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 class Union ( QueryExpression ): \"\"\" Union is the private DataJoint class that implements the union operator. \"\"\" __count = count () @classmethod def create ( cls , arg1 , arg2 ): if inspect . isclass ( arg2 ) and issubclass ( arg2 , QueryExpression ): arg2 = arg2 () # instantiate if a class if not isinstance ( arg2 , QueryExpression ): raise DataJointError ( \"A QueryExpression can only be unioned with another QueryExpression\" ) if arg1 . connection != arg2 . connection : raise DataJointError ( \"Cannot operate on QueryExpressions originating from different connections.\" ) if set ( arg1 . primary_key ) != set ( arg2 . primary_key ): raise DataJointError ( \"The operands of a union must share the same primary key.\" ) if set ( arg1 . heading . secondary_attributes ) & set ( arg2 . heading . secondary_attributes ): raise DataJointError ( \"The operands of a union must not share any secondary attributes.\" ) result = cls () result . _connection = arg1 . connection result . _heading = arg1 . heading . join ( arg2 . heading ) result . _support = [ arg1 , arg2 ] return result def make_sql ( self ): arg1 , arg2 = self . _support if ( not arg1 . heading . secondary_attributes and not arg2 . heading . secondary_attributes ): # no secondary attributes: use UNION DISTINCT fields = arg1 . primary_key return \"SELECT * FROM (( {sql1} ) UNION ( {sql2} )) as `_u {alias} `\" . format ( sql1 = arg1 . make_sql () if isinstance ( arg1 , Union ) else arg1 . make_sql ( fields ), sql2 = arg2 . make_sql () if isinstance ( arg2 , Union ) else arg2 . make_sql ( fields ), alias = next ( self . __count ), ) # with secondary attributes, use union of left join with antijoin fields = self . heading . names sql1 = arg1 . join ( arg2 , left = True ) . make_sql ( fields ) sql2 = ( ( arg2 - arg1 ) . proj ( ... , ** { k : \"NULL\" for k in arg1 . heading . secondary_attributes }) . make_sql ( fields ) ) return \"( {sql1} ) UNION ( {sql2} )\" . format ( sql1 = sql1 , sql2 = sql2 ) def from_clause ( self ): \"\"\"The union does not use a FROM clause\"\"\" assert False def where_clause ( self ): \"\"\"The union does not use a WHERE clause\"\"\" assert False def __len__ ( self ): return self . connection . query ( \"SELECT count(1) FROM ( {subquery} ) `$ {alias:x} `\" . format ( subquery = self . make_sql (), alias = next ( QueryExpression . _subquery_alias_count ), ) ) . fetchone ()[ 0 ] def __bool__ ( self ): return bool ( self . connection . query ( \"SELECT EXISTS( {sql} )\" . format ( sql = self . make_sql ())) ) from_clause () \u00b6 The union does not use a FROM clause Source code in datajoint/expression.py 790 791 792 def from_clause ( self ): \"\"\"The union does not use a FROM clause\"\"\" assert False where_clause () \u00b6 The union does not use a WHERE clause Source code in datajoint/expression.py 794 795 796 def where_clause ( self ): \"\"\"The union does not use a WHERE clause\"\"\" assert False U \u00b6 dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the stimulus set: dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute s containing the total number of elements in query expression expr : dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number n of distinct values of attribute attr in query expressio expr . dj.U().aggr(expr, n='count(distinct attr)') dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute s containing the sum of values of attribute attr over entire result set of expression expr : dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes attr1 , attr2 and the number of their occurrences in the result set of query expression expr . dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression expr has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as expr but attr1 and attr2 are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if attr is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename attr in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. Source code in datajoint/expression.py 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 class U : \"\"\" dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the `stimulus` set: >>> dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute `s` containing the total number of elements in query expression `expr`: >>> dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number `n` of distinct values of attribute `attr` in query expressio `expr`. >>> dj.U().aggr(expr, n='count(distinct attr)') >>> dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute `s` containing the sum of values of attribute `attr` over entire result set of expression `expr`: >>> dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes `attr1`, `attr2` and the number of their occurrences in the result set of query expression `expr`. >>> dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression `expr` has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as `expr` but `attr1` and `attr2` are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if `attr` is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename `attr` in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. \"\"\" def __init__ ( self , * primary_key ): self . _primary_key = primary_key @property def primary_key ( self ): return self . _primary_key def __and__ ( self , other ): if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be restricted with a QueryExpression.\" ) result = copy . copy ( other ) result . _distinct = True result . _heading = result . heading . set_primary_key ( self . primary_key ) result = result . proj () return result def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result def __mul__ ( self , other ): \"\"\"shorthand for join\"\"\" return self . join ( other ) def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes ) aggregate = aggr # alias for aggr join ( other , left = False ) \u00b6 Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. Parameters: Name Type Description Default other the other query expression to join with. required left ignored. dj.U always acts as if left=False False Returns: Type Description a copy of the other query expression with the primary key extended. Source code in datajoint/expression.py 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result aggr ( group , ** named_attributes ) \u00b6 Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of group . Parameters: Name Type Description Default group The query expression to be aggregated. required named_attributes computations of the form new_attribute=\"sql expression on attributes of group\" required Returns: Type Description The derived query expression Source code in datajoint/expression.py 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes )", "title": "expression.py"}, {"location": "api/datajoint/expression/#datajoint.expression.AndList", "text": "Bases: list A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 Source code in datajoint/condition.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 class AndList ( list ): \"\"\" A list of conditions to by applied to a query expression by logical conjunction: the conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are applied by logical disjunction (OR). Example: expr2 = expr & dj.AndList((cond1, cond2, cond3)) is equivalent to expr2 = expr & cond1 & cond2 & cond3 \"\"\" def append ( self , restriction ): if isinstance ( restriction , AndList ): # extend to reduce nesting self . extend ( restriction ) else : super () . append ( restriction )", "title": "AndList"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression", "text": "QueryExpression implements query operators to derive new entity set from its input. A QueryExpression object generates a SELECT statement in SQL. QueryExpression operators are restrict, join, proj, aggr, and union. A QueryExpression object has a support, a restriction (an AndList), and heading. Property heading (type dj.Heading) contains information about the attributes. It is loaded from the database and updated by proj. Property support is the list of table names or other QueryExpressions to be joined. The restriction is applied first without having access to the attributes generated by the projection. Then projection is applied by selecting modifying the heading attribute. Application of operators does not always lead to the creation of a subquery. A subquery is generated when: 1. A restriction is applied on any computed or renamed attributes 2. A projection is applied remapping remapped attributes 3. Subclasses: Join, Aggregation, and Union have additional specific rules. Source code in datajoint/expression.py 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 class QueryExpression : \"\"\" QueryExpression implements query operators to derive new entity set from its input. A QueryExpression object generates a SELECT statement in SQL. QueryExpression operators are restrict, join, proj, aggr, and union. A QueryExpression object has a support, a restriction (an AndList), and heading. Property `heading` (type dj.Heading) contains information about the attributes. It is loaded from the database and updated by proj. Property `support` is the list of table names or other QueryExpressions to be joined. The restriction is applied first without having access to the attributes generated by the projection. Then projection is applied by selecting modifying the heading attribute. Application of operators does not always lead to the creation of a subquery. A subquery is generated when: 1. A restriction is applied on any computed or renamed attributes 2. A projection is applied remapping remapped attributes 3. Subclasses: Join, Aggregation, and Union have additional specific rules. \"\"\" _restriction = None _restriction_attributes = None _left = [] # list of booleans True for left joins, False for inner joins _original_heading = None # heading before projections # subclasses or instantiators must provide values _connection = None _heading = None _support = None # If the query will be using distinct _distinct = False @property def connection ( self ): \"\"\"a dj.Connection object\"\"\" assert self . _connection is not None return self . _connection @property def support ( self ): \"\"\"A list of table names or subqueries to from the FROM clause\"\"\" assert self . _support is not None return self . _support @property def heading ( self ): \"\"\"a dj.Heading object, reflects the effects of the projection operator .proj\"\"\" return self . _heading @property def original_heading ( self ): \"\"\"a dj.Heading object reflecting the attributes before projection\"\"\" return self . _original_heading or self . heading @property def restriction ( self ): \"\"\"a AndList object of restrictions applied to input to produce the result\"\"\" if self . _restriction is None : self . _restriction = AndList () return self . _restriction @property def restriction_attributes ( self ): \"\"\"the set of attribute names invoked in the WHERE clause\"\"\" if self . _restriction_attributes is None : self . _restriction_attributes = set () return self . _restriction_attributes @property def primary_key ( self ): return self . heading . primary_key _subquery_alias_count = count () # count for alias names used in the FROM clause def from_clause ( self ): support = ( \"(\" + src . make_sql () + \") as `$ %x `\" % next ( self . _subquery_alias_count ) if isinstance ( src , QueryExpression ) else src for src in self . support ) clause = next ( support ) for s , left in zip ( support , self . _left ): clause += \" NATURAL {left} JOIN {clause} \" . format ( left = \" LEFT\" if left else \"\" , clause = s ) return clause def where_clause ( self ): return ( \"\" if not self . restriction else \" WHERE ( %s )\" % \")AND(\" . join ( str ( s ) for s in self . restriction ) ) def make_sql ( self , fields = None ): \"\"\" Make the SQL SELECT statement. :param fields: used to explicitly set the select attributes \"\"\" return \"SELECT {distinct}{fields} FROM {from_}{where} \" . format ( distinct = \"DISTINCT \" if self . _distinct else \"\" , fields = self . heading . as_sql ( fields or self . heading . names ), from_ = self . from_clause (), where = self . where_clause (), ) # --------- query operators ----------- def make_subquery ( self ): \"\"\"create a new SELECT statement where self is the FROM clause\"\"\" result = QueryExpression () result . _connection = self . connection result . _support = [ self ] result . _heading = self . heading . make_subquery_heading () return result def restrict ( self , restriction ): \"\"\" Produces a new expression with the new restriction applied. rel.restrict(restriction) is equivalent to rel & restriction. rel.restrict(Not(restriction)) is equivalent to rel - restriction The primary key of the result is unaffected. Successive restrictions are combined as logical AND: r & a & b is equivalent to r & AndList((a, b)) Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists (logical disjunction of conditions) Inverse restriction is accomplished by either using the subtraction operator or the Not class. The expressions in each row equivalent: rel & True rel rel & False the empty entity set rel & 'TRUE' rel rel & 'FALSE' the empty entity set rel - cond rel & Not(cond) rel - 'TRUE' rel & False rel - 'FALSE' rel rel & AndList((cond1,cond2)) rel & cond1 & cond2 rel & AndList() rel rel & [cond1, cond2] rel & OrList((cond1, cond2)) rel & [] rel & False rel & None rel & False rel & any_empty_entity_set rel & False rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)] rel - [cond1, cond2] rel & Not(cond1) & Not(cond2) rel - AndList() rel & False rel - [] rel rel - None rel rel - any_empty_entity_set rel When arg is another QueryExpression, the restriction rel & arg restricts rel to elements that match at least one element in arg (hence arg is treated as an OrList). Conversely, rel - arg restricts rel to elements that do not match any elements in arg. Two elements match when their common attributes have equal values or when they have no common attributes. All shared attributes must be in the primary key of either rel or arg or both or an error will be raised. QueryExpression.restrict is the only access point that modifies restrictions. All other operators must ultimately call restrict() :param restriction: a sequence or an array (treated as OR list), another QueryExpression, an SQL condition string, or an AndList. \"\"\" attributes = set () new_condition = make_condition ( self , restriction , attributes ) if new_condition is True : return self # restriction has no effect, return the same object # check that all attributes in condition are present in the query try : raise DataJointError ( \"Attribute ` %s ` is not found in query.\" % next ( attr for attr in attributes if attr not in self . heading . names ) ) except StopIteration : pass # all ok # If the new condition uses any new attributes, a subquery is required. # However, Aggregation's HAVING statement works fine with aliased attributes. need_subquery = isinstance ( self , Union ) or ( not isinstance ( self , Aggregation ) and self . heading . new_attributes ) if need_subquery : result = self . make_subquery () else : result = copy . copy ( self ) result . _restriction = AndList ( self . restriction ) # copy to preserve the original result . restriction . append ( new_condition ) result . restriction_attributes . update ( attributes ) return result def restrict_in_place ( self , restriction ): self . __dict__ . update ( self . restrict ( restriction ) . __dict__ ) def __and__ ( self , restriction ): \"\"\" Restriction operator e.g. ``q1 & q2``. :return: a restricted copy of the input argument See QueryExpression.restrict for more detail. \"\"\" return self . restrict ( restriction ) def __xor__ ( self , restriction ): \"\"\" Permissive restriction operator ignoring compatibility check e.g. ``q1 ^ q2``. \"\"\" if inspect . isclass ( restriction ) and issubclass ( restriction , QueryExpression ): restriction = restriction () if isinstance ( restriction , Not ): return self . restrict ( Not ( PromiscuousOperand ( restriction . restriction ))) return self . restrict ( PromiscuousOperand ( restriction )) def __sub__ ( self , restriction ): \"\"\" Inverted restriction e.g. ``q1 - q2``. :return: a restricted copy of the input argument See QueryExpression.restrict for more detail. \"\"\" return self . restrict ( Not ( restriction )) def __neg__ ( self ): \"\"\" Convert between restriction and inverted restriction e.g. ``-q1``. :return: target restriction See QueryExpression.restrict for more detail. \"\"\" if isinstance ( self , Not ): return self . restriction return Not ( self ) def __mul__ ( self , other ): \"\"\" join of query expressions `self` and `other` e.g. ``q1 * q2``. \"\"\" return self . join ( other ) def __matmul__ ( self , other ): \"\"\" Permissive join of query expressions `self` and `other` ignoring compatibility check e.g. ``q1 @ q2``. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate return self . join ( other , semantic_check = False ) def join ( self , other , semantic_check = True , left = False ): \"\"\" create the joined QueryExpression. a * b is short for A.join(B) a @ b is short for A.join(B, semantic_check=False) Additionally, left=True will retain the rows of self, effectively performing a left join. \"\"\" # trigger subqueries if joining on renamed attributes if isinstance ( other , U ): return other * self if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if not isinstance ( other , QueryExpression ): raise DataJointError ( \"The argument of join must be a QueryExpression\" ) if semantic_check : assert_join_compatibility ( self , other ) join_attributes = set ( n for n in self . heading . names if n in other . heading . names ) # needs subquery if self's FROM clause has common attributes with other's FROM clause need_subquery1 = need_subquery2 = bool ( ( set ( self . original_heading . names ) & set ( other . original_heading . names )) - join_attributes ) # need subquery if any of the join attributes are derived need_subquery1 = ( need_subquery1 or isinstance ( self , Aggregation ) or any ( n in self . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) need_subquery2 = ( need_subquery2 or isinstance ( other , Aggregation ) or any ( n in other . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) if need_subquery1 : self = self . make_subquery () if need_subquery2 : other = other . make_subquery () result = QueryExpression () result . _connection = self . connection result . _support = self . support + other . support result . _left = self . _left + [ left ] + other . _left result . _heading = self . heading . join ( other . heading ) result . _restriction = AndList ( self . restriction ) result . _restriction . append ( other . restriction ) result . _original_heading = self . original_heading . join ( other . original_heading ) assert len ( result . support ) == len ( result . _left ) + 1 return result def __add__ ( self , other ): \"\"\"union e.g. ``q1 + q2``.\"\"\" return Union . create ( self , other ) def proj ( self , * attributes , ** named_attributes ): \"\"\" Projection operator. :param attributes: attributes to be included in the result. (The primary key is already included). :param named_attributes: new attributes computed or renamed from existing attributes. :return: the projected expression. Primary key attributes cannot be excluded but may be renamed. If the attribute list contains an Ellipsis ..., then all secondary attributes are included too Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present. Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self) self.proj() -- include only primary key self.proj('attr1', 'attr2') -- include primary key and attributes attr1 and attr2 self.proj(..., '-attr1', '-attr2') -- include all attributes except attr1 and attr2 self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1 self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup' self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax) from other attributes available before the projection. Each attribute name can only be used once. \"\"\" # new attributes in parentheses are included again with the new name without removing original duplication_pattern = re . compile ( rf '^\\s*\$\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*\$\\s*$' ) # attributes without parentheses renamed rename_pattern = re . compile ( rf '^\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*$' ) replicate_map = { k : m . group ( \"name\" ) for k , m in ( ( k , duplication_pattern . match ( v )) for k , v in named_attributes . items () ) if m } rename_map = { k : m . group ( \"name\" ) for k , m in ( ( k , rename_pattern . match ( v )) for k , v in named_attributes . items () ) if m } compute_map = { k : v for k , v in named_attributes . items () if not duplication_pattern . match ( v ) and not rename_pattern . match ( v ) } attributes = set ( attributes ) # include primary key attributes . update (( k for k in self . primary_key if k not in rename_map . values ())) # include all secondary attributes with Ellipsis if Ellipsis in attributes : attributes . discard ( Ellipsis ) attributes . update ( ( a for a in self . heading . secondary_attributes if a not in attributes and a not in rename_map . values () ) ) try : raise DataJointError ( \" %s is not a valid data type for an attribute in .proj\" % next ( a for a in attributes if not isinstance ( a , str )) ) except StopIteration : pass # normal case # remove excluded attributes, specified as `-attr' excluded = set ( a for a in attributes if a . strip () . startswith ( \"-\" )) attributes . difference_update ( excluded ) excluded = set ( a . lstrip ( \"-\" ) . strip () for a in excluded ) attributes . difference_update ( excluded ) try : raise DataJointError ( \"Cannot exclude primary key attribute %s \" , next ( a for a in excluded if a in self . primary_key ), ) except StopIteration : pass # all ok # check that all attributes exist in heading try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( a for a in attributes if a not in self . heading . names ) ) except StopIteration : pass # all ok # check that all mentioned names are present in heading mentions = attributes . union ( replicate_map . values ()) . union ( rename_map . values ()) try : raise DataJointError ( \"Attribute ' %s ' not found.\" % next ( a for a in mentions if not self . heading . names ) ) except StopIteration : pass # all ok # check that newly created attributes do not clash with any other selected attributes try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in rename_map if a in attributes . union ( compute_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in compute_map if a in attributes . union ( rename_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in replicate_map if a in attributes . union ( rename_map ) . union ( compute_map ) ) ) except StopIteration : pass # all ok # need a subquery if the projection remaps any remapped attributes used = set ( q for v in compute_map . values () for q in extract_column_names ( v )) used . update ( rename_map . values ()) used . update ( replicate_map . values ()) used . intersection_update ( self . heading . names ) need_subquery = isinstance ( self , Union ) or any ( self . heading [ name ] . attribute_expression is not None for name in used ) if not need_subquery and self . restriction : # need a subquery if the restriction applies to attributes that have been renamed need_subquery = any ( name in self . restriction_attributes for name in self . heading . new_attributes ) result = self . make_subquery () if need_subquery else copy . copy ( self ) result . _original_heading = result . original_heading result . _heading = result . heading . select ( attributes , rename_map = dict ( ** rename_map , ** replicate_map ), compute_map = compute_map , ) return result def aggr ( self , group , * attributes , keep_all_rows = False , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param keep_all_rows: True=keep all the rows from self. False=keep only rows that match entries in group. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if Ellipsis in attributes : # expand ellipsis to include only attributes from the left table attributes = set ( attributes ) attributes . discard ( Ellipsis ) attributes . update ( self . heading . secondary_attributes ) return Aggregation . create ( self , group = group , keep_all_rows = keep_all_rows ) . proj ( * attributes , ** named_attributes ) aggregate = aggr # alias for aggr # ---------- Fetch operators -------------------- @property def fetch1 ( self ): return Fetch1 ( self ) @property def fetch ( self ): return Fetch ( self ) def head ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the first few entries from query expression. Equivalent to fetch(order_by=\"KEY\", limit=25) :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY\" , limit = limit , ** fetch_kwargs ) def tail ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the last few entries from query expression. Equivalent to fetch(order_by=\"KEY DESC\", limit=25)[::-1] :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY DESC\" , limit = limit , ** fetch_kwargs )[:: - 1 ] def __len__ ( self ): \"\"\":return: number of elements in the result set e.g. ``len(q1)``.\"\"\" return self . connection . query ( \"SELECT {select_} FROM {from_}{where} \" . format ( select_ = ( \"count(*)\" if any ( self . _left ) else \"count(DISTINCT {fields} )\" . format ( fields = self . heading . as_sql ( self . primary_key , include_aliases = False ) ) ), from_ = self . from_clause (), where = self . where_clause (), ) ) . fetchone ()[ 0 ] def __bool__ ( self ): \"\"\" :return: True if the result is not empty. Equivalent to len(self) > 0 but often faster e.g. ``bool(q1)``. \"\"\" return bool ( self . connection . query ( \"SELECT EXISTS(SELECT 1 FROM {from_}{where} )\" . format ( from_ = self . from_clause (), where = self . where_clause () ) ) . fetchone ()[ 0 ] ) def __contains__ ( self , item ): \"\"\" returns True if the restriction in item matches any entries in self e.g. ``restriction in q1``. :param item: any restriction (item in query_expression) is equivalent to bool(query_expression & item) but may be executed more efficiently. \"\"\" return bool ( self & item ) # May be optimized e.g. using an EXISTS query def __iter__ ( self ): \"\"\" returns an iterator-compatible QueryExpression object e.g. ``iter(q1)``. :param self: iterator-compatible QueryExpression object \"\"\" self . _iter_only_key = all ( v . in_key for v in self . heading . attributes . values ()) self . _iter_keys = self . fetch ( \"KEY\" ) return self def __next__ ( self ): \"\"\" returns the next record on an iterator-compatible QueryExpression object e.g. ``next(q1)``. :param self: A query expression :type self: :class:`QueryExpression` :rtype: dict \"\"\" try : key = self . _iter_keys . pop ( 0 ) except AttributeError : # self._iter_keys is missing because __iter__ has not been called. raise TypeError ( \"A QueryExpression object is not an iterator. \" \"Use iter(obj) to create an iterator.\" ) except IndexError : raise StopIteration else : if self . _iter_only_key : return key else : try : return ( self & key ) . fetch1 () except DataJointError : # The data may have been deleted since the moment the keys were fetched # -- move on to next entry. return next ( self ) def cursor ( self , offset = 0 , limit = None , order_by = None , as_dict = False ): \"\"\" See expression.fetch() for input description. :return: query cursor \"\"\" if offset and limit is None : raise DataJointError ( \"limit is required when offset is set\" ) sql = self . make_sql () if order_by is not None : sql += \" ORDER BY \" + \", \" . join ( order_by ) if limit is not None : sql += \" LIMIT %d \" % limit + ( \" OFFSET %d \" % offset if offset else \"\" ) logger . debug ( sql ) return self . connection . query ( sql , as_dict = as_dict ) def __repr__ ( self ): \"\"\" returns the string representation of a QueryExpression object e.g. ``str(q1)``. :param self: A query expression :type self: :class:`QueryExpression` :rtype: str \"\"\" return ( super () . __repr__ () if config [ \"loglevel\" ] . lower () == \"debug\" else self . preview () ) def preview ( self , limit = None , width = None ): \"\"\":return: a string of preview of the contents of the query.\"\"\" return preview ( self , limit , width ) def _repr_html_ ( self ): \"\"\":return: HTML to display table in Jupyter notebook.\"\"\" return repr_html ( self )", "title": "QueryExpression"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.connection", "text": "a dj.Connection object Source code in datajoint/expression.py 58 59 60 61 62 @property def connection ( self ): \"\"\"a dj.Connection object\"\"\" assert self . _connection is not None return self . _connection", "title": "connection()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.support", "text": "A list of table names or subqueries to from the FROM clause Source code in datajoint/expression.py 64 65 66 67 68 @property def support ( self ): \"\"\"A list of table names or subqueries to from the FROM clause\"\"\" assert self . _support is not None return self . _support", "title": "support()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.heading", "text": "a dj.Heading object, reflects the effects of the projection operator .proj Source code in datajoint/expression.py 70 71 72 73 @property def heading ( self ): \"\"\"a dj.Heading object, reflects the effects of the projection operator .proj\"\"\" return self . _heading", "title": "heading()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.original_heading", "text": "a dj.Heading object reflecting the attributes before projection Source code in datajoint/expression.py 75 76 77 78 @property def original_heading ( self ): \"\"\"a dj.Heading object reflecting the attributes before projection\"\"\" return self . _original_heading or self . heading", "title": "original_heading()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.restriction", "text": "a AndList object of restrictions applied to input to produce the result Source code in datajoint/expression.py 80 81 82 83 84 85 @property def restriction ( self ): \"\"\"a AndList object of restrictions applied to input to produce the result\"\"\" if self . _restriction is None : self . _restriction = AndList () return self . _restriction", "title": "restriction()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.restriction_attributes", "text": "the set of attribute names invoked in the WHERE clause Source code in datajoint/expression.py 87 88 89 90 91 92 @property def restriction_attributes ( self ): \"\"\"the set of attribute names invoked in the WHERE clause\"\"\" if self . _restriction_attributes is None : self . _restriction_attributes = set () return self . _restriction_attributes", "title": "restriction_attributes()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.make_sql", "text": "Make the SQL SELECT statement. Parameters: Name Type Description Default fields used to explicitly set the select attributes None Source code in datajoint/expression.py 121 122 123 124 125 126 127 128 129 130 131 132 def make_sql ( self , fields = None ): \"\"\" Make the SQL SELECT statement. :param fields: used to explicitly set the select attributes \"\"\" return \"SELECT {distinct}{fields} FROM {from_}{where} \" . format ( distinct = \"DISTINCT \" if self . _distinct else \"\" , fields = self . heading . as_sql ( fields or self . heading . names ), from_ = self . from_clause (), where = self . where_clause (), )", "title": "make_sql()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.make_subquery", "text": "create a new SELECT statement where self is the FROM clause Source code in datajoint/expression.py 135 136 137 138 139 140 141 def make_subquery ( self ): \"\"\"create a new SELECT statement where self is the FROM clause\"\"\" result = QueryExpression () result . _connection = self . connection result . _support = [ self ] result . _heading = self . heading . make_subquery_heading () return result", "title": "make_subquery()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.restrict", "text": "Produces a new expression with the new restriction applied. rel.restrict(restriction) is equivalent to rel & restriction. rel.restrict(Not(restriction)) is equivalent to rel - restriction The primary key of the result is unaffected. Successive restrictions are combined as logical AND: r & a & b is equivalent to r & AndList((a, b)) Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists (logical disjunction of conditions) Inverse restriction is accomplished by either using the subtraction operator or the Not class. The expressions in each row equivalent: rel & True rel rel & False the empty entity set rel & 'TRUE' rel rel & 'FALSE' the empty entity set rel - cond rel & Not(cond) rel - 'TRUE' rel & False rel - 'FALSE' rel rel & AndList((cond1,cond2)) rel & cond1 & cond2 rel & AndList() rel rel & [cond1, cond2] rel & OrList((cond1, cond2)) rel & [] rel & False rel & None rel & False rel & any_empty_entity_set rel & False rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)] rel - [cond1, cond2] rel & Not(cond1) & Not(cond2) rel - AndList() rel & False rel - [] rel rel - None rel rel - any_empty_entity_set rel When arg is another QueryExpression, the restriction rel & arg restricts rel to elements that match at least one element in arg (hence arg is treated as an OrList). Conversely, rel - arg restricts rel to elements that do not match any elements in arg. Two elements match when their common attributes have equal values or when they have no common attributes. All shared attributes must be in the primary key of either rel or arg or both or an error will be raised. QueryExpression.restrict is the only access point that modifies restrictions. All other operators must ultimately call restrict() Parameters: Name Type Description Default restriction a sequence or an array (treated as OR list), another QueryExpression, an SQL condition string, or an AndList. required Source code in datajoint/expression.py 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 def restrict ( self , restriction ): \"\"\" Produces a new expression with the new restriction applied. rel.restrict(restriction) is equivalent to rel & restriction. rel.restrict(Not(restriction)) is equivalent to rel - restriction The primary key of the result is unaffected. Successive restrictions are combined as logical AND: r & a & b is equivalent to r & AndList((a, b)) Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists (logical disjunction of conditions) Inverse restriction is accomplished by either using the subtraction operator or the Not class. The expressions in each row equivalent: rel & True rel rel & False the empty entity set rel & 'TRUE' rel rel & 'FALSE' the empty entity set rel - cond rel & Not(cond) rel - 'TRUE' rel & False rel - 'FALSE' rel rel & AndList((cond1,cond2)) rel & cond1 & cond2 rel & AndList() rel rel & [cond1, cond2] rel & OrList((cond1, cond2)) rel & [] rel & False rel & None rel & False rel & any_empty_entity_set rel & False rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)] rel - [cond1, cond2] rel & Not(cond1) & Not(cond2) rel - AndList() rel & False rel - [] rel rel - None rel rel - any_empty_entity_set rel When arg is another QueryExpression, the restriction rel & arg restricts rel to elements that match at least one element in arg (hence arg is treated as an OrList). Conversely, rel - arg restricts rel to elements that do not match any elements in arg. Two elements match when their common attributes have equal values or when they have no common attributes. All shared attributes must be in the primary key of either rel or arg or both or an error will be raised. QueryExpression.restrict is the only access point that modifies restrictions. All other operators must ultimately call restrict() :param restriction: a sequence or an array (treated as OR list), another QueryExpression, an SQL condition string, or an AndList. \"\"\" attributes = set () new_condition = make_condition ( self , restriction , attributes ) if new_condition is True : return self # restriction has no effect, return the same object # check that all attributes in condition are present in the query try : raise DataJointError ( \"Attribute ` %s ` is not found in query.\" % next ( attr for attr in attributes if attr not in self . heading . names ) ) except StopIteration : pass # all ok # If the new condition uses any new attributes, a subquery is required. # However, Aggregation's HAVING statement works fine with aliased attributes. need_subquery = isinstance ( self , Union ) or ( not isinstance ( self , Aggregation ) and self . heading . new_attributes ) if need_subquery : result = self . make_subquery () else : result = copy . copy ( self ) result . _restriction = AndList ( self . restriction ) # copy to preserve the original result . restriction . append ( new_condition ) result . restriction_attributes . update ( attributes ) return result", "title": "restrict()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.join", "text": "create the joined QueryExpression. a * b is short for A.join(B) a @ b is short for A.join(B, semantic_check=False) Additionally, left=True will retain the rows of self, effectively performing a left join. Source code in datajoint/expression.py 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 def join ( self , other , semantic_check = True , left = False ): \"\"\" create the joined QueryExpression. a * b is short for A.join(B) a @ b is short for A.join(B, semantic_check=False) Additionally, left=True will retain the rows of self, effectively performing a left join. \"\"\" # trigger subqueries if joining on renamed attributes if isinstance ( other , U ): return other * self if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if not isinstance ( other , QueryExpression ): raise DataJointError ( \"The argument of join must be a QueryExpression\" ) if semantic_check : assert_join_compatibility ( self , other ) join_attributes = set ( n for n in self . heading . names if n in other . heading . names ) # needs subquery if self's FROM clause has common attributes with other's FROM clause need_subquery1 = need_subquery2 = bool ( ( set ( self . original_heading . names ) & set ( other . original_heading . names )) - join_attributes ) # need subquery if any of the join attributes are derived need_subquery1 = ( need_subquery1 or isinstance ( self , Aggregation ) or any ( n in self . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) need_subquery2 = ( need_subquery2 or isinstance ( other , Aggregation ) or any ( n in other . heading . new_attributes for n in join_attributes ) or isinstance ( self , Union ) ) if need_subquery1 : self = self . make_subquery () if need_subquery2 : other = other . make_subquery () result = QueryExpression () result . _connection = self . connection result . _support = self . support + other . support result . _left = self . _left + [ left ] + other . _left result . _heading = self . heading . join ( other . heading ) result . _restriction = AndList ( self . restriction ) result . _restriction . append ( other . restriction ) result . _original_heading = self . original_heading . join ( other . original_heading ) assert len ( result . support ) == len ( result . _left ) + 1 return result", "title": "join()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.proj", "text": "Projection operator. Parameters: Name Type Description Default attributes attributes to be included in the result. (The primary key is already included). required named_attributes new attributes computed or renamed from existing attributes. required Returns: Type Description the projected expression. Primary key attributes cannot be excluded but may be renamed. If the attribute list contains an Ellipsis ..., then all secondary attributes are included too Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present. Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self) self.proj() -- include only primary key self.proj('attr1', 'attr2') -- include primary key and attributes attr1 and attr2 self.proj(..., '-attr1', '-attr2') -- include all attributes except attr1 and attr2 self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1 self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup' self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax) from other attributes available before the projection. Each attribute name can only be used once. Source code in datajoint/expression.py 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 def proj ( self , * attributes , ** named_attributes ): \"\"\" Projection operator. :param attributes: attributes to be included in the result. (The primary key is already included). :param named_attributes: new attributes computed or renamed from existing attributes. :return: the projected expression. Primary key attributes cannot be excluded but may be renamed. If the attribute list contains an Ellipsis ..., then all secondary attributes are included too Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present. Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self) self.proj() -- include only primary key self.proj('attr1', 'attr2') -- include primary key and attributes attr1 and attr2 self.proj(..., '-attr1', '-attr2') -- include all attributes except attr1 and attr2 self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1 self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup' self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax) from other attributes available before the projection. Each attribute name can only be used once. \"\"\" # new attributes in parentheses are included again with the new name without removing original duplication_pattern = re . compile ( rf '^\\s*\$\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*\$\\s*$' ) # attributes without parentheses renamed rename_pattern = re . compile ( rf '^\\s*(?! { \"|\" . join ( CONSTANT_LITERALS ) } )(?P[a-zA-Z_]\\w*)\\s*$' ) replicate_map = { k : m . group ( \"name\" ) for k , m in ( ( k , duplication_pattern . match ( v )) for k , v in named_attributes . items () ) if m } rename_map = { k : m . group ( \"name\" ) for k , m in ( ( k , rename_pattern . match ( v )) for k , v in named_attributes . items () ) if m } compute_map = { k : v for k , v in named_attributes . items () if not duplication_pattern . match ( v ) and not rename_pattern . match ( v ) } attributes = set ( attributes ) # include primary key attributes . update (( k for k in self . primary_key if k not in rename_map . values ())) # include all secondary attributes with Ellipsis if Ellipsis in attributes : attributes . discard ( Ellipsis ) attributes . update ( ( a for a in self . heading . secondary_attributes if a not in attributes and a not in rename_map . values () ) ) try : raise DataJointError ( \" %s is not a valid data type for an attribute in .proj\" % next ( a for a in attributes if not isinstance ( a , str )) ) except StopIteration : pass # normal case # remove excluded attributes, specified as `-attr' excluded = set ( a for a in attributes if a . strip () . startswith ( \"-\" )) attributes . difference_update ( excluded ) excluded = set ( a . lstrip ( \"-\" ) . strip () for a in excluded ) attributes . difference_update ( excluded ) try : raise DataJointError ( \"Cannot exclude primary key attribute %s \" , next ( a for a in excluded if a in self . primary_key ), ) except StopIteration : pass # all ok # check that all attributes exist in heading try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( a for a in attributes if a not in self . heading . names ) ) except StopIteration : pass # all ok # check that all mentioned names are present in heading mentions = attributes . union ( replicate_map . values ()) . union ( rename_map . values ()) try : raise DataJointError ( \"Attribute ' %s ' not found.\" % next ( a for a in mentions if not self . heading . names ) ) except StopIteration : pass # all ok # check that newly created attributes do not clash with any other selected attributes try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in rename_map if a in attributes . union ( compute_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in compute_map if a in attributes . union ( rename_map ) . union ( replicate_map ) ) ) except StopIteration : pass # all ok try : raise DataJointError ( \"Attribute ` %s ` already exists\" % next ( a for a in replicate_map if a in attributes . union ( rename_map ) . union ( compute_map ) ) ) except StopIteration : pass # all ok # need a subquery if the projection remaps any remapped attributes used = set ( q for v in compute_map . values () for q in extract_column_names ( v )) used . update ( rename_map . values ()) used . update ( replicate_map . values ()) used . intersection_update ( self . heading . names ) need_subquery = isinstance ( self , Union ) or any ( self . heading [ name ] . attribute_expression is not None for name in used ) if not need_subquery and self . restriction : # need a subquery if the restriction applies to attributes that have been renamed need_subquery = any ( name in self . restriction_attributes for name in self . heading . new_attributes ) result = self . make_subquery () if need_subquery else copy . copy ( self ) result . _original_heading = result . original_heading result . _heading = result . heading . select ( attributes , rename_map = dict ( ** rename_map , ** replicate_map ), compute_map = compute_map , ) return result", "title": "proj()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.aggr", "text": "Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of group . Parameters: Name Type Description Default group The query expression to be aggregated. required keep_all_rows True=keep all the rows from self. False=keep only rows that match entries in group. False named_attributes computations of the form new_attribute=\"sql expression on attributes of group\" required Returns: Type Description The derived query expression Source code in datajoint/expression.py 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 def aggr ( self , group , * attributes , keep_all_rows = False , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param keep_all_rows: True=keep all the rows from self. False=keep only rows that match entries in group. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if Ellipsis in attributes : # expand ellipsis to include only attributes from the left table attributes = set ( attributes ) attributes . discard ( Ellipsis ) attributes . update ( self . heading . secondary_attributes ) return Aggregation . create ( self , group = group , keep_all_rows = keep_all_rows ) . proj ( * attributes , ** named_attributes )", "title": "aggr()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.head", "text": "shortcut to fetch the first few entries from query expression. Equivalent to fetch(order_by=\"KEY\", limit=25) Parameters: Name Type Description Default limit number of entries 25 fetch_kwargs kwargs for fetch required Returns: Type Description query result Source code in datajoint/expression.py 512 513 514 515 516 517 518 519 520 521 def head ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the first few entries from query expression. Equivalent to fetch(order_by=\"KEY\", limit=25) :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY\" , limit = limit , ** fetch_kwargs )", "title": "head()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.tail", "text": "shortcut to fetch the last few entries from query expression. Equivalent to fetch(order_by=\"KEY DESC\", limit=25)[::-1] Parameters: Name Type Description Default limit number of entries 25 fetch_kwargs kwargs for fetch required Returns: Type Description query result Source code in datajoint/expression.py 523 524 525 526 527 528 529 530 531 532 def tail ( self , limit = 25 , ** fetch_kwargs ): \"\"\" shortcut to fetch the last few entries from query expression. Equivalent to fetch(order_by=\"KEY DESC\", limit=25)[::-1] :param limit: number of entries :param fetch_kwargs: kwargs for fetch :return: query result \"\"\" return self . fetch ( order_by = \"KEY DESC\" , limit = limit , ** fetch_kwargs )[:: - 1 ]", "title": "tail()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.cursor", "text": "See expression.fetch() for input description. Returns: Type Description query cursor Source code in datajoint/expression.py 616 617 618 619 620 621 622 623 624 625 626 627 628 629 def cursor ( self , offset = 0 , limit = None , order_by = None , as_dict = False ): \"\"\" See expression.fetch() for input description. :return: query cursor \"\"\" if offset and limit is None : raise DataJointError ( \"limit is required when offset is set\" ) sql = self . make_sql () if order_by is not None : sql += \" ORDER BY \" + \", \" . join ( order_by ) if limit is not None : sql += \" LIMIT %d \" % limit + ( \" OFFSET %d \" % offset if offset else \"\" ) logger . debug ( sql ) return self . connection . query ( sql , as_dict = as_dict )", "title": "cursor()"}, {"location": "api/datajoint/expression/#datajoint.expression.QueryExpression.preview", "text": "Returns: Type Description a string of preview of the contents of the query. Source code in datajoint/expression.py 645 646 647 def preview ( self , limit = None , width = None ): \"\"\":return: a string of preview of the contents of the query.\"\"\" return preview ( self , limit , width )", "title": "preview()"}, {"location": "api/datajoint/expression/#datajoint.expression.Not", "text": "invert restriction Source code in datajoint/condition.py 43 44 45 46 47 class Not : \"\"\"invert restriction\"\"\" def __init__ ( self , restriction ): self . restriction = restriction", "title": "Not"}, {"location": "api/datajoint/expression/#datajoint.expression.Aggregation", "text": "Bases: QueryExpression Aggregation.create(arg, group, comp1='calc1', ..., compn='calcn') yields an entity set with primary key from arg. The computed arguments comp1, ..., compn use aggregation calculations on the attributes of group or simple projections and calculations on the attributes of arg. Aggregation is used QueryExpression.aggr and U.aggr. Aggregation is a private class in DataJoint, not exposed to users. Source code in datajoint/expression.py 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 class Aggregation ( QueryExpression ): \"\"\" Aggregation.create(arg, group, comp1='calc1', ..., compn='calcn') yields an entity set with primary key from arg. The computed arguments comp1, ..., compn use aggregation calculations on the attributes of group or simple projections and calculations on the attributes of arg. Aggregation is used QueryExpression.aggr and U.aggr. Aggregation is a private class in DataJoint, not exposed to users. \"\"\" _left_restrict = None # the pre-GROUP BY conditions for the WHERE clause _subquery_alias_count = count () @classmethod def create ( cls , arg , group , keep_all_rows = False ): if inspect . isclass ( group ) and issubclass ( group , QueryExpression ): group = group () # instantiate if a class assert isinstance ( group , QueryExpression ) if keep_all_rows and len ( group . support ) > 1 or group . heading . new_attributes : group = group . make_subquery () # subquery if left joining a join join = arg . join ( group , left = keep_all_rows ) # reuse the join logic result = cls () result . _connection = join . connection result . _heading = join . heading . set_primary_key ( arg . primary_key ) # use left operand's primary key result . _support = join . support result . _left = join . _left result . _left_restrict = join . restriction # WHERE clause applied before GROUP BY result . _grouping_attributes = result . primary_key return result def where_clause ( self ): return ( \"\" if not self . _left_restrict else \" WHERE ( %s )\" % \")AND(\" . join ( str ( s ) for s in self . _left_restrict ) ) def make_sql ( self , fields = None ): fields = self . heading . as_sql ( fields or self . heading . names ) assert self . _grouping_attributes or not self . restriction distinct = set ( self . heading . names ) == set ( self . primary_key ) return \"SELECT {distinct}{fields} FROM {from_}{where}{group_by} \" . format ( distinct = \"DISTINCT \" if distinct else \"\" , fields = fields , from_ = self . from_clause (), where = self . where_clause (), group_by = \"\" if not self . primary_key else ( \" GROUP BY ` %s `\" % \"`,`\" . join ( self . _grouping_attributes ) + ( \"\" if not self . restriction else \" HAVING ( %s )\" % \")AND(\" . join ( self . restriction ) ) ), ) def __len__ ( self ): return self . connection . query ( \"SELECT count(1) FROM ( {subquery} ) `$ {alias:x} `\" . format ( subquery = self . make_sql (), alias = next ( self . _subquery_alias_count ) ) ) . fetchone ()[ 0 ] def __bool__ ( self ): return bool ( self . connection . query ( \"SELECT EXISTS( {sql} )\" . format ( sql = self . make_sql ())) )", "title": "Aggregation"}, {"location": "api/datajoint/expression/#datajoint.expression.Union", "text": "Bases: QueryExpression Union is the private DataJoint class that implements the union operator. Source code in datajoint/expression.py 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 class Union ( QueryExpression ): \"\"\" Union is the private DataJoint class that implements the union operator. \"\"\" __count = count () @classmethod def create ( cls , arg1 , arg2 ): if inspect . isclass ( arg2 ) and issubclass ( arg2 , QueryExpression ): arg2 = arg2 () # instantiate if a class if not isinstance ( arg2 , QueryExpression ): raise DataJointError ( \"A QueryExpression can only be unioned with another QueryExpression\" ) if arg1 . connection != arg2 . connection : raise DataJointError ( \"Cannot operate on QueryExpressions originating from different connections.\" ) if set ( arg1 . primary_key ) != set ( arg2 . primary_key ): raise DataJointError ( \"The operands of a union must share the same primary key.\" ) if set ( arg1 . heading . secondary_attributes ) & set ( arg2 . heading . secondary_attributes ): raise DataJointError ( \"The operands of a union must not share any secondary attributes.\" ) result = cls () result . _connection = arg1 . connection result . _heading = arg1 . heading . join ( arg2 . heading ) result . _support = [ arg1 , arg2 ] return result def make_sql ( self ): arg1 , arg2 = self . _support if ( not arg1 . heading . secondary_attributes and not arg2 . heading . secondary_attributes ): # no secondary attributes: use UNION DISTINCT fields = arg1 . primary_key return \"SELECT * FROM (( {sql1} ) UNION ( {sql2} )) as `_u {alias} `\" . format ( sql1 = arg1 . make_sql () if isinstance ( arg1 , Union ) else arg1 . make_sql ( fields ), sql2 = arg2 . make_sql () if isinstance ( arg2 , Union ) else arg2 . make_sql ( fields ), alias = next ( self . __count ), ) # with secondary attributes, use union of left join with antijoin fields = self . heading . names sql1 = arg1 . join ( arg2 , left = True ) . make_sql ( fields ) sql2 = ( ( arg2 - arg1 ) . proj ( ... , ** { k : \"NULL\" for k in arg1 . heading . secondary_attributes }) . make_sql ( fields ) ) return \"( {sql1} ) UNION ( {sql2} )\" . format ( sql1 = sql1 , sql2 = sql2 ) def from_clause ( self ): \"\"\"The union does not use a FROM clause\"\"\" assert False def where_clause ( self ): \"\"\"The union does not use a WHERE clause\"\"\" assert False def __len__ ( self ): return self . connection . query ( \"SELECT count(1) FROM ( {subquery} ) `$ {alias:x} `\" . format ( subquery = self . make_sql (), alias = next ( QueryExpression . _subquery_alias_count ), ) ) . fetchone ()[ 0 ] def __bool__ ( self ): return bool ( self . connection . query ( \"SELECT EXISTS( {sql} )\" . format ( sql = self . make_sql ())) )", "title": "Union"}, {"location": "api/datajoint/expression/#datajoint.expression.Union.from_clause", "text": "The union does not use a FROM clause Source code in datajoint/expression.py 790 791 792 def from_clause ( self ): \"\"\"The union does not use a FROM clause\"\"\" assert False", "title": "from_clause()"}, {"location": "api/datajoint/expression/#datajoint.expression.Union.where_clause", "text": "The union does not use a WHERE clause Source code in datajoint/expression.py 794 795 796 def where_clause ( self ): \"\"\"The union does not use a WHERE clause\"\"\" assert False", "title": "where_clause()"}, {"location": "api/datajoint/expression/#datajoint.expression.U", "text": "dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the stimulus set: dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute s containing the total number of elements in query expression expr : dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number n of distinct values of attribute attr in query expressio expr . dj.U().aggr(expr, n='count(distinct attr)') dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute s containing the sum of values of attribute attr over entire result set of expression expr : dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes attr1 , attr2 and the number of their occurrences in the result set of query expression expr . dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression expr has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as expr but attr1 and attr2 are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if attr is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename attr in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. Source code in datajoint/expression.py 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 class U : \"\"\" dj.U objects are the universal sets representing all possible values of their attributes. dj.U objects cannot be queried on their own but are useful for forming some queries. dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. The universal set is the set of all possible combinations of values of the attributes. Without any attributes, dj.U() represents the set with one element that has no attributes. Restriction: dj.U can be used to enumerate unique combinations of values of attributes from other expressions. The following expression yields all unique combinations of contrast and brightness found in the `stimulus` set: >>> dj.U('contrast', 'brightness') & stimulus Aggregation: In aggregation, dj.U is used for summary calculation over an entire set: The following expression yields one element with one attribute `s` containing the total number of elements in query expression `expr`: >>> dj.U().aggr(expr, n='count(*)') The following expressions both yield one element containing the number `n` of distinct values of attribute `attr` in query expressio `expr`. >>> dj.U().aggr(expr, n='count(distinct attr)') >>> dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)') The following expression yields one element and one attribute `s` containing the sum of values of attribute `attr` over entire result set of expression `expr`: >>> dj.U().aggr(expr, s='sum(attr)') The following expression yields the set of all unique combinations of attributes `attr1`, `attr2` and the number of their occurrences in the result set of query expression `expr`. >>> dj.U(attr1,attr2).aggr(expr, n='count(*)') Joins: If expression `expr` has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result as `expr` but `attr1` and `attr2` are promoted to the the primary key. This is useful for producing a join on non-primary key attributes. For example, if `attr` is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw an error because in most cases, it does not make sense to join on non-primary key attributes and users must first rename `attr` in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint. \"\"\" def __init__ ( self , * primary_key ): self . _primary_key = primary_key @property def primary_key ( self ): return self . _primary_key def __and__ ( self , other ): if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be restricted with a QueryExpression.\" ) result = copy . copy ( other ) result . _distinct = True result . _heading = result . heading . set_primary_key ( self . primary_key ) result = result . proj () return result def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result def __mul__ ( self , other ): \"\"\"shorthand for join\"\"\" return self . join ( other ) def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes ) aggregate = aggr # alias for aggr", "title": "U"}, {"location": "api/datajoint/expression/#datajoint.expression.U.join", "text": "Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. Parameters: Name Type Description Default other the other query expression to join with. required left ignored. dj.U always acts as if left=False False Returns: Type Description a copy of the other query expression with the primary key extended. Source code in datajoint/expression.py 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 def join ( self , other , left = False ): \"\"\" Joining U with a query expression has the effect of promoting the attributes of U to the primary key of the other query expression. :param other: the other query expression to join with. :param left: ignored. dj.U always acts as if left=False :return: a copy of the other query expression with the primary key extended. \"\"\" if inspect . isclass ( other ) and issubclass ( other , QueryExpression ): other = other () # instantiate if a class if not isinstance ( other , QueryExpression ): raise DataJointError ( \"Set U can only be joined with a QueryExpression.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found\" % next ( k for k in self . primary_key if k not in other . heading . names ) ) except StopIteration : pass # all ok result = copy . copy ( other ) result . _heading = result . heading . set_primary_key ( other . primary_key + [ k for k in self . primary_key if k not in other . primary_key ] ) return result", "title": "join()"}, {"location": "api/datajoint/expression/#datajoint.expression.U.aggr", "text": "Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of group . Parameters: Name Type Description Default group The query expression to be aggregated. required named_attributes computations of the form new_attribute=\"sql expression on attributes of group\" required Returns: Type Description The derived query expression Source code in datajoint/expression.py 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 def aggr ( self , group , ** named_attributes ): \"\"\" Aggregation of the type U('attr1','attr2').aggr(group, computation=\"QueryExpression\") has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`. :param group: The query expression to be aggregated. :param named_attributes: computations of the form new_attribute=\"sql expression on attributes of group\" :return: The derived query expression \"\"\" if named_attributes . get ( \"keep_all_rows\" , False ): raise DataJointError ( \"Cannot set keep_all_rows=True when aggregating on a universal set.\" ) return Aggregation . create ( self , group = group , keep_all_rows = False ) . proj ( ** named_attributes )", "title": "aggr()"}, {"location": "api/datajoint/external/", "text": "subfold ( name , folds ) \u00b6 subfolding for external storage: e.g. subfold('aBCdefg', (2, 3)) --> ['ab','cde'] Source code in datajoint/external.py 23 24 25 26 27 28 29 30 31 def subfold ( name , folds ): \"\"\" subfolding for external storage: e.g. subfold('aBCdefg', (2, 3)) --> ['ab','cde'] \"\"\" return ( ( name [: folds [ 0 ]] . lower (),) + subfold ( name [ folds [ 0 ] :], folds [ 1 :]) if folds else () ) ExternalTable \u00b6 Bases: Table The table tracking externally stored objects. Declare as ExternalTable(connection, database) Source code in datajoint/external.py 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 class ExternalTable ( Table ): \"\"\" The table tracking externally stored objects. Declare as ExternalTable(connection, database) \"\"\" def __init__ ( self , connection , store , database ): self . store = store self . spec = config . get_store_spec ( store ) self . _s3 = None self . database = database self . _connection = connection self . _heading = Heading ( table_info = dict ( conn = connection , database = database , table_name = self . table_name , context = None , ) ) self . _support = [ self . full_table_name ] if not self . is_declared : self . declare () self . _s3 = None if self . spec [ \"protocol\" ] == \"file\" and not Path ( self . spec [ \"location\" ]) . is_dir (): raise FileNotFoundError ( \"Inaccessible local directory %s \" % self . spec [ \"location\" ] ) from None @property def definition ( self ): return \"\"\" # external storage tracking hash : uuid # hash of contents (blob), of filename + contents (attach), or relative filepath (filepath) --- size :bigint unsigned # size of object in bytes attachment_name=null : varchar(255) # the filename of an attachment filepath=null : varchar(1000) # relative filepath or attachment filename contents_hash=null : uuid # used for the filepath datatype timestamp=CURRENT_TIMESTAMP :timestamp # automatic timestamp \"\"\" @property def table_name ( self ): return f \" { EXTERNAL_TABLE_ROOT } _ { self . store } \" @property def s3 ( self ): if self . _s3 is None : self . _s3 = s3 . Folder ( ** self . spec ) return self . _s3 # - low-level operations - private def _make_external_filepath ( self , relative_filepath ): \"\"\"resolve the complete external path based on the relative path\"\"\" # Strip root if self . spec [ \"protocol\" ] == \"s3\" : posix_path = PurePosixPath ( PureWindowsPath ( self . spec [ \"location\" ])) location_path = ( Path ( * posix_path . parts [ 1 :]) if len ( self . spec [ \"location\" ]) > 0 and any ( case in posix_path . parts [ 0 ] for case in ( \" \\\\ \" , \":\" )) else Path ( posix_path ) ) return PurePosixPath ( location_path , relative_filepath ) # Preserve root elif self . spec [ \"protocol\" ] == \"file\" : return PurePosixPath ( Path ( self . spec [ \"location\" ]), relative_filepath ) else : assert False def _make_uuid_path ( self , uuid , suffix = \"\" ): \"\"\"create external path based on the uuid hash\"\"\" return self . _make_external_filepath ( PurePosixPath ( self . database , \"/\" . join ( subfold ( uuid . hex , self . spec [ \"subfolding\" ])), uuid . hex , ) . with_suffix ( suffix ) ) def _upload_file ( self , local_path , external_path , metadata = None ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . fput ( local_path , external_path , metadata ) elif self . spec [ \"protocol\" ] == \"file\" : safe_copy ( local_path , external_path , overwrite = True ) else : assert False def _download_file ( self , external_path , download_path ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . fget ( external_path , download_path ) elif self . spec [ \"protocol\" ] == \"file\" : safe_copy ( external_path , download_path ) else : assert False def _upload_buffer ( self , buffer , external_path ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . put ( external_path , buffer ) elif self . spec [ \"protocol\" ] == \"file\" : safe_write ( external_path , buffer ) else : assert False def _download_buffer ( self , external_path ): if self . spec [ \"protocol\" ] == \"s3\" : return self . s3 . get ( external_path ) if self . spec [ \"protocol\" ] == \"file\" : return Path ( external_path ) . read_bytes () assert False def _remove_external_file ( self , external_path ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . remove_object ( external_path ) elif self . spec [ \"protocol\" ] == \"file\" : try : Path ( external_path ) . unlink () except FileNotFoundError : pass def exists ( self , external_filepath ): \"\"\" :return: True if the external file is accessible \"\"\" if self . spec [ \"protocol\" ] == \"s3\" : return self . s3 . exists ( external_filepath ) if self . spec [ \"protocol\" ] == \"file\" : return Path ( external_filepath ) . is_file () assert False # --- BLOBS ---- def put ( self , blob ): \"\"\" put a binary string (blob) in external store \"\"\" uuid = uuid_from_buffer ( blob ) self . _upload_buffer ( blob , self . _make_uuid_path ( uuid )) # insert tracking info self . connection . query ( \"INSERT INTO {tab} (hash, size) VALUES ( %s , {size} ) ON DUPLICATE KEY \" \"UPDATE timestamp=CURRENT_TIMESTAMP\" . format ( tab = self . full_table_name , size = len ( blob ) ), args = ( uuid . bytes ,), ) return uuid def get ( self , uuid ): \"\"\" get an object from external store. \"\"\" if uuid is None : return None # attempt to get object from cache blob = None cache_folder = config . get ( \"cache\" , None ) if cache_folder : try : cache_path = Path ( cache_folder , * subfold ( uuid . hex , CACHE_SUBFOLDING )) cache_file = Path ( cache_path , uuid . hex ) blob = cache_file . read_bytes () except FileNotFoundError : pass # not cached # download blob from external store if blob is None : try : blob = self . _download_buffer ( self . _make_uuid_path ( uuid )) except MissingExternalFile : if not SUPPORT_MIGRATED_BLOBS : raise # blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths relative_filepath , contents_hash = ( self & { \"hash\" : uuid }) . fetch1 ( \"filepath\" , \"contents_hash\" ) if relative_filepath is None : raise blob = self . _download_buffer ( self . _make_external_filepath ( relative_filepath ) ) if cache_folder : cache_path . mkdir ( parents = True , exist_ok = True ) safe_write ( cache_path / uuid . hex , blob ) return blob # --- ATTACHMENTS --- def upload_attachment ( self , local_path ): attachment_name = Path ( local_path ) . name uuid = uuid_from_file ( local_path , init_string = attachment_name + \" \\0 \" ) external_path = self . _make_uuid_path ( uuid , \".\" + attachment_name ) self . _upload_file ( local_path , external_path ) # insert tracking info self . connection . query ( \"\"\" INSERT INTO {tab} (hash, size, attachment_name) VALUES (%s, {size}, \"{attachment_name}\") ON DUPLICATE KEY UPDATE timestamp=CURRENT_TIMESTAMP\"\"\" . format ( tab = self . full_table_name , size = Path ( local_path ) . stat () . st_size , attachment_name = attachment_name , ), args = [ uuid . bytes ], ) return uuid def get_attachment_name ( self , uuid ): return ( self & { \"hash\" : uuid }) . fetch1 ( \"attachment_name\" ) def download_attachment ( self , uuid , attachment_name , download_path ): \"\"\"save attachment from memory buffer into the save_path\"\"\" external_path = self . _make_uuid_path ( uuid , \".\" + attachment_name ) self . _download_file ( external_path , download_path ) # --- FILEPATH --- def upload_filepath ( self , local_filepath ): \"\"\" Raise exception if an external entry already exists with a different contents checksum. Otherwise, copy (with overwrite) file to remote and If an external entry exists with the same checksum, then no copying should occur \"\"\" local_filepath = Path ( local_filepath ) try : relative_filepath = str ( local_filepath . relative_to ( self . spec [ \"stage\" ]) . as_posix () ) except ValueError : raise DataJointError ( \"The path {path} is not in stage {stage} \" . format ( path = local_filepath . parent , ** self . spec ) ) uuid = uuid_from_buffer ( init_string = relative_filepath ) # hash relative path, not contents contents_hash = uuid_from_file ( local_filepath ) # check if the remote file already exists and verify that it matches check_hash = ( self & { \"hash\" : uuid }) . fetch ( \"contents_hash\" ) if check_hash : # the tracking entry exists, check that it's the same file as before if contents_hash != check_hash [ 0 ]: raise DataJointError ( f \"A different version of ' { relative_filepath } ' has already been placed.\" ) else : # upload the file and create its tracking entry self . _upload_file ( local_filepath , self . _make_external_filepath ( relative_filepath ), metadata = { \"contents_hash\" : str ( contents_hash )}, ) self . connection . query ( \"INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES ( %s , {size} , ' {filepath} ', %s )\" . format ( tab = self . full_table_name , size = Path ( local_filepath ) . stat () . st_size , filepath = relative_filepath , ), args = ( uuid . bytes , contents_hash . bytes ), ) return uuid def download_filepath ( self , filepath_hash ): \"\"\" sync a file from external store to the local stage :param filepath_hash: The hash (UUID) of the relative_path :return: hash (UUID) of the contents of the downloaded file or Nones \"\"\" def _need_checksum ( local_filepath , expected_size ): limit = config . get ( \"filepath_checksum_size_limit\" ) actual_size = Path ( local_filepath ) . stat () . st_size if expected_size != actual_size : # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but size did not match.\" ) return limit is None or actual_size < limit if filepath_hash is not None : relative_filepath , contents_hash , size = ( self & { \"hash\" : filepath_hash } ) . fetch1 ( \"filepath\" , \"contents_hash\" , \"size\" ) external_path = self . _make_external_filepath ( relative_filepath ) local_filepath = Path ( self . spec [ \"stage\" ]) . absolute () / relative_filepath file_exists = Path ( local_filepath ) . is_file () and ( not _need_checksum ( local_filepath , size ) or uuid_from_file ( local_filepath ) == contents_hash ) if not file_exists : self . _download_file ( external_path , local_filepath ) if ( _need_checksum ( local_filepath , size ) and uuid_from_file ( local_filepath ) != contents_hash ): # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but did not pass checksum.\" ) if not _need_checksum ( local_filepath , size ): logger . warning ( f \"Skipped checksum for file with hash: { contents_hash } , and path: { local_filepath } \" ) return str ( local_filepath ), contents_hash # --- UTILITIES --- @property def references ( self ): \"\"\" :return: generator of referencing table names and their referencing columns \"\"\" return ( { k . lower (): v for k , v in elem . items ()} for elem in self . connection . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name FROM information_schema.key_column_usage WHERE referenced_table_name=\"{tab}\" and referenced_table_schema=\"{db}\" \"\"\" . format ( tab = self . table_name , db = self . database ), as_dict = True , ) ) def fetch_external_paths ( self , ** fetch_kwargs ): \"\"\" generate complete external filepaths from the query. Each element is a tuple: (uuid, path) :param fetch_kwargs: keyword arguments to pass to fetch \"\"\" fetch_kwargs . update ( as_dict = True ) paths = [] for item in self . fetch ( \"hash\" , \"attachment_name\" , \"filepath\" , ** fetch_kwargs ): if item [ \"attachment_name\" ]: # attachments path = self . _make_uuid_path ( item [ \"hash\" ], \".\" + item [ \"attachment_name\" ]) elif item [ \"filepath\" ]: # external filepaths path = self . _make_external_filepath ( item [ \"filepath\" ]) else : # blobs path = self . _make_uuid_path ( item [ \"hash\" ]) paths . append (( item [ \"hash\" ], path )) return paths def unused ( self ): \"\"\" query expression for unused hashes :return: self restricted to elements that are not in use by any tables in the schema \"\"\" return self - [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ] def used ( self ): \"\"\" query expression for used hashes :return: self restricted to elements that in use by tables in the schema \"\"\" return self & [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ] def delete ( self , * , delete_external_files = None , limit = None , display_progress = True , errors_as_string = True , ): \"\"\" :param delete_external_files: True or False. If False, only the tracking info is removed from the external store table but the external files remain intact. If True, then the external files themselves are deleted too. :param errors_as_string: If True any errors returned when deleting from external files will be strings :param limit: (integer) limit the number of items to delete :param display_progress: if True, display progress as files are cleaned up :return: if deleting external files, returns errors \"\"\" if delete_external_files not in ( True , False ): raise DataJointError ( \"The delete_external_files argument must be set to either \" \"True or False in delete()\" ) if not delete_external_files : self . unused () . delete_quick () else : items = self . unused () . fetch_external_paths ( limit = limit ) if display_progress : items = tqdm ( items ) # delete items one by one, close to transaction-safe error_list = [] for uuid , external_path in items : row = ( self & { \"hash\" : uuid }) . fetch () if row . size : try : ( self & { \"hash\" : uuid }) . delete_quick () except Exception : pass # if delete failed, do not remove the external file else : try : self . _remove_external_file ( external_path ) except Exception as error : # adding row back into table after failed delete self . insert1 ( row [ 0 ], skip_duplicates = True ) error_list . append ( ( uuid , external_path , str ( error ) if errors_as_string else error , ) ) return error_list exists ( external_filepath ) \u00b6 Returns: Type Description True if the external file is accessible Source code in datajoint/external.py 156 157 158 159 160 161 162 163 164 def exists ( self , external_filepath ): \"\"\" :return: True if the external file is accessible \"\"\" if self . spec [ \"protocol\" ] == \"s3\" : return self . s3 . exists ( external_filepath ) if self . spec [ \"protocol\" ] == \"file\" : return Path ( external_filepath ) . is_file () assert False put ( blob ) \u00b6 put a binary string (blob) in external store Source code in datajoint/external.py 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 def put ( self , blob ): \"\"\" put a binary string (blob) in external store \"\"\" uuid = uuid_from_buffer ( blob ) self . _upload_buffer ( blob , self . _make_uuid_path ( uuid )) # insert tracking info self . connection . query ( \"INSERT INTO {tab} (hash, size) VALUES ( %s , {size} ) ON DUPLICATE KEY \" \"UPDATE timestamp=CURRENT_TIMESTAMP\" . format ( tab = self . full_table_name , size = len ( blob ) ), args = ( uuid . bytes ,), ) return uuid get ( uuid ) \u00b6 get an object from external store. Source code in datajoint/external.py 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 def get ( self , uuid ): \"\"\" get an object from external store. \"\"\" if uuid is None : return None # attempt to get object from cache blob = None cache_folder = config . get ( \"cache\" , None ) if cache_folder : try : cache_path = Path ( cache_folder , * subfold ( uuid . hex , CACHE_SUBFOLDING )) cache_file = Path ( cache_path , uuid . hex ) blob = cache_file . read_bytes () except FileNotFoundError : pass # not cached # download blob from external store if blob is None : try : blob = self . _download_buffer ( self . _make_uuid_path ( uuid )) except MissingExternalFile : if not SUPPORT_MIGRATED_BLOBS : raise # blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths relative_filepath , contents_hash = ( self & { \"hash\" : uuid }) . fetch1 ( \"filepath\" , \"contents_hash\" ) if relative_filepath is None : raise blob = self . _download_buffer ( self . _make_external_filepath ( relative_filepath ) ) if cache_folder : cache_path . mkdir ( parents = True , exist_ok = True ) safe_write ( cache_path / uuid . hex , blob ) return blob download_attachment ( uuid , attachment_name , download_path ) \u00b6 save attachment from memory buffer into the save_path Source code in datajoint/external.py 245 246 247 248 def download_attachment ( self , uuid , attachment_name , download_path ): \"\"\"save attachment from memory buffer into the save_path\"\"\" external_path = self . _make_uuid_path ( uuid , \".\" + attachment_name ) self . _download_file ( external_path , download_path ) upload_filepath ( local_filepath ) \u00b6 Raise exception if an external entry already exists with a different contents checksum. Otherwise, copy (with overwrite) file to remote and If an external entry exists with the same checksum, then no copying should occur Source code in datajoint/external.py 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 def upload_filepath ( self , local_filepath ): \"\"\" Raise exception if an external entry already exists with a different contents checksum. Otherwise, copy (with overwrite) file to remote and If an external entry exists with the same checksum, then no copying should occur \"\"\" local_filepath = Path ( local_filepath ) try : relative_filepath = str ( local_filepath . relative_to ( self . spec [ \"stage\" ]) . as_posix () ) except ValueError : raise DataJointError ( \"The path {path} is not in stage {stage} \" . format ( path = local_filepath . parent , ** self . spec ) ) uuid = uuid_from_buffer ( init_string = relative_filepath ) # hash relative path, not contents contents_hash = uuid_from_file ( local_filepath ) # check if the remote file already exists and verify that it matches check_hash = ( self & { \"hash\" : uuid }) . fetch ( \"contents_hash\" ) if check_hash : # the tracking entry exists, check that it's the same file as before if contents_hash != check_hash [ 0 ]: raise DataJointError ( f \"A different version of ' { relative_filepath } ' has already been placed.\" ) else : # upload the file and create its tracking entry self . _upload_file ( local_filepath , self . _make_external_filepath ( relative_filepath ), metadata = { \"contents_hash\" : str ( contents_hash )}, ) self . connection . query ( \"INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES ( %s , {size} , ' {filepath} ', %s )\" . format ( tab = self . full_table_name , size = Path ( local_filepath ) . stat () . st_size , filepath = relative_filepath , ), args = ( uuid . bytes , contents_hash . bytes ), ) return uuid download_filepath ( filepath_hash ) \u00b6 sync a file from external store to the local stage Parameters: Name Type Description Default filepath_hash The hash (UUID) of the relative_path required Returns: Type Description hash (UUID) of the contents of the downloaded file or Nones Source code in datajoint/external.py 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 def download_filepath ( self , filepath_hash ): \"\"\" sync a file from external store to the local stage :param filepath_hash: The hash (UUID) of the relative_path :return: hash (UUID) of the contents of the downloaded file or Nones \"\"\" def _need_checksum ( local_filepath , expected_size ): limit = config . get ( \"filepath_checksum_size_limit\" ) actual_size = Path ( local_filepath ) . stat () . st_size if expected_size != actual_size : # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but size did not match.\" ) return limit is None or actual_size < limit if filepath_hash is not None : relative_filepath , contents_hash , size = ( self & { \"hash\" : filepath_hash } ) . fetch1 ( \"filepath\" , \"contents_hash\" , \"size\" ) external_path = self . _make_external_filepath ( relative_filepath ) local_filepath = Path ( self . spec [ \"stage\" ]) . absolute () / relative_filepath file_exists = Path ( local_filepath ) . is_file () and ( not _need_checksum ( local_filepath , size ) or uuid_from_file ( local_filepath ) == contents_hash ) if not file_exists : self . _download_file ( external_path , local_filepath ) if ( _need_checksum ( local_filepath , size ) and uuid_from_file ( local_filepath ) != contents_hash ): # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but did not pass checksum.\" ) if not _need_checksum ( local_filepath , size ): logger . warning ( f \"Skipped checksum for file with hash: { contents_hash } , and path: { local_filepath } \" ) return str ( local_filepath ), contents_hash references () property \u00b6 Returns: Type Description generator of referencing table names and their referencing columns Source code in datajoint/external.py 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 @property def references ( self ): \"\"\" :return: generator of referencing table names and their referencing columns \"\"\" return ( { k . lower (): v for k , v in elem . items ()} for elem in self . connection . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name FROM information_schema.key_column_usage WHERE referenced_table_name=\"{tab}\" and referenced_table_schema=\"{db}\" \"\"\" . format ( tab = self . table_name , db = self . database ), as_dict = True , ) ) fetch_external_paths ( ** fetch_kwargs ) \u00b6 generate complete external filepaths from the query. Each element is a tuple: (uuid, path) Parameters: Name Type Description Default fetch_kwargs keyword arguments to pass to fetch required Source code in datajoint/external.py 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 def fetch_external_paths ( self , ** fetch_kwargs ): \"\"\" generate complete external filepaths from the query. Each element is a tuple: (uuid, path) :param fetch_kwargs: keyword arguments to pass to fetch \"\"\" fetch_kwargs . update ( as_dict = True ) paths = [] for item in self . fetch ( \"hash\" , \"attachment_name\" , \"filepath\" , ** fetch_kwargs ): if item [ \"attachment_name\" ]: # attachments path = self . _make_uuid_path ( item [ \"hash\" ], \".\" + item [ \"attachment_name\" ]) elif item [ \"filepath\" ]: # external filepaths path = self . _make_external_filepath ( item [ \"filepath\" ]) else : # blobs path = self . _make_uuid_path ( item [ \"hash\" ]) paths . append (( item [ \"hash\" ], path )) return paths unused () \u00b6 query expression for unused hashes Returns: Type Description self restricted to elements that are not in use by any tables in the schema Source code in datajoint/external.py 388 389 390 391 392 393 394 395 396 397 398 399 def unused ( self ): \"\"\" query expression for unused hashes :return: self restricted to elements that are not in use by any tables in the schema \"\"\" return self - [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ] used () \u00b6 query expression for used hashes Returns: Type Description self restricted to elements that in use by tables in the schema Source code in datajoint/external.py 401 402 403 404 405 406 407 408 409 410 411 412 def used ( self ): \"\"\" query expression for used hashes :return: self restricted to elements that in use by tables in the schema \"\"\" return self & [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ] delete ( * , delete_external_files = None , limit = None , display_progress = True , errors_as_string = True ) \u00b6 Parameters: Name Type Description Default delete_external_files True or False. If False, only the tracking info is removed from the external store table but the external files remain intact. If True, then the external files themselves are deleted too. None errors_as_string If True any errors returned when deleting from external files will be strings True limit (integer) limit the number of items to delete None display_progress if True, display progress as files are cleaned up True Returns: Type Description if deleting external files, returns errors Source code in datajoint/external.py 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 def delete ( self , * , delete_external_files = None , limit = None , display_progress = True , errors_as_string = True , ): \"\"\" :param delete_external_files: True or False. If False, only the tracking info is removed from the external store table but the external files remain intact. If True, then the external files themselves are deleted too. :param errors_as_string: If True any errors returned when deleting from external files will be strings :param limit: (integer) limit the number of items to delete :param display_progress: if True, display progress as files are cleaned up :return: if deleting external files, returns errors \"\"\" if delete_external_files not in ( True , False ): raise DataJointError ( \"The delete_external_files argument must be set to either \" \"True or False in delete()\" ) if not delete_external_files : self . unused () . delete_quick () else : items = self . unused () . fetch_external_paths ( limit = limit ) if display_progress : items = tqdm ( items ) # delete items one by one, close to transaction-safe error_list = [] for uuid , external_path in items : row = ( self & { \"hash\" : uuid }) . fetch () if row . size : try : ( self & { \"hash\" : uuid }) . delete_quick () except Exception : pass # if delete failed, do not remove the external file else : try : self . _remove_external_file ( external_path ) except Exception as error : # adding row back into table after failed delete self . insert1 ( row [ 0 ], skip_duplicates = True ) error_list . append ( ( uuid , external_path , str ( error ) if errors_as_string else error , ) ) return error_list ExternalMapping \u00b6 Bases: Mapping The external manager contains all the tables for all external stores for a given schema :Example: e = ExternalMapping(schema) external_table = e[store] Source code in datajoint/external.py 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 class ExternalMapping ( Mapping ): \"\"\" The external manager contains all the tables for all external stores for a given schema :Example: e = ExternalMapping(schema) external_table = e[store] \"\"\" def __init__ ( self , schema ): self . schema = schema self . _tables = {} def __repr__ ( self ): return \"External file tables for schema ` {schema} `: \\n \" . format ( schema = self . schema . database ) + \" \\n \" . join ( '\" {store} \" {protocol} : {location} ' . format ( store = k , ** v . spec ) for k , v in self . items () ) def __getitem__ ( self , store ): \"\"\" Triggers the creation of an external table. Should only be used when ready to save or read from external storage. :param store: the name of the store :return: the ExternalTable object for the store \"\"\" if store not in self . _tables : self . _tables [ store ] = ExternalTable ( connection = self . schema . connection , store = store , database = self . schema . database , ) return self . _tables [ store ] def __len__ ( self ): return len ( self . _tables ) def __iter__ ( self ): return iter ( self . _tables )", "title": "external.py"}, {"location": "api/datajoint/external/#datajoint.external.subfold", "text": "subfolding for external storage: e.g. subfold('aBCdefg', (2, 3)) --> ['ab','cde'] Source code in datajoint/external.py 23 24 25 26 27 28 29 30 31 def subfold ( name , folds ): \"\"\" subfolding for external storage: e.g. subfold('aBCdefg', (2, 3)) --> ['ab','cde'] \"\"\" return ( ( name [: folds [ 0 ]] . lower (),) + subfold ( name [ folds [ 0 ] :], folds [ 1 :]) if folds else () )", "title": "subfold()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable", "text": "Bases: Table The table tracking externally stored objects. Declare as ExternalTable(connection, database) Source code in datajoint/external.py 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 class ExternalTable ( Table ): \"\"\" The table tracking externally stored objects. Declare as ExternalTable(connection, database) \"\"\" def __init__ ( self , connection , store , database ): self . store = store self . spec = config . get_store_spec ( store ) self . _s3 = None self . database = database self . _connection = connection self . _heading = Heading ( table_info = dict ( conn = connection , database = database , table_name = self . table_name , context = None , ) ) self . _support = [ self . full_table_name ] if not self . is_declared : self . declare () self . _s3 = None if self . spec [ \"protocol\" ] == \"file\" and not Path ( self . spec [ \"location\" ]) . is_dir (): raise FileNotFoundError ( \"Inaccessible local directory %s \" % self . spec [ \"location\" ] ) from None @property def definition ( self ): return \"\"\" # external storage tracking hash : uuid # hash of contents (blob), of filename + contents (attach), or relative filepath (filepath) --- size :bigint unsigned # size of object in bytes attachment_name=null : varchar(255) # the filename of an attachment filepath=null : varchar(1000) # relative filepath or attachment filename contents_hash=null : uuid # used for the filepath datatype timestamp=CURRENT_TIMESTAMP :timestamp # automatic timestamp \"\"\" @property def table_name ( self ): return f \" { EXTERNAL_TABLE_ROOT } _ { self . store } \" @property def s3 ( self ): if self . _s3 is None : self . _s3 = s3 . Folder ( ** self . spec ) return self . _s3 # - low-level operations - private def _make_external_filepath ( self , relative_filepath ): \"\"\"resolve the complete external path based on the relative path\"\"\" # Strip root if self . spec [ \"protocol\" ] == \"s3\" : posix_path = PurePosixPath ( PureWindowsPath ( self . spec [ \"location\" ])) location_path = ( Path ( * posix_path . parts [ 1 :]) if len ( self . spec [ \"location\" ]) > 0 and any ( case in posix_path . parts [ 0 ] for case in ( \" \\\\ \" , \":\" )) else Path ( posix_path ) ) return PurePosixPath ( location_path , relative_filepath ) # Preserve root elif self . spec [ \"protocol\" ] == \"file\" : return PurePosixPath ( Path ( self . spec [ \"location\" ]), relative_filepath ) else : assert False def _make_uuid_path ( self , uuid , suffix = \"\" ): \"\"\"create external path based on the uuid hash\"\"\" return self . _make_external_filepath ( PurePosixPath ( self . database , \"/\" . join ( subfold ( uuid . hex , self . spec [ \"subfolding\" ])), uuid . hex , ) . with_suffix ( suffix ) ) def _upload_file ( self , local_path , external_path , metadata = None ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . fput ( local_path , external_path , metadata ) elif self . spec [ \"protocol\" ] == \"file\" : safe_copy ( local_path , external_path , overwrite = True ) else : assert False def _download_file ( self , external_path , download_path ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . fget ( external_path , download_path ) elif self . spec [ \"protocol\" ] == \"file\" : safe_copy ( external_path , download_path ) else : assert False def _upload_buffer ( self , buffer , external_path ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . put ( external_path , buffer ) elif self . spec [ \"protocol\" ] == \"file\" : safe_write ( external_path , buffer ) else : assert False def _download_buffer ( self , external_path ): if self . spec [ \"protocol\" ] == \"s3\" : return self . s3 . get ( external_path ) if self . spec [ \"protocol\" ] == \"file\" : return Path ( external_path ) . read_bytes () assert False def _remove_external_file ( self , external_path ): if self . spec [ \"protocol\" ] == \"s3\" : self . s3 . remove_object ( external_path ) elif self . spec [ \"protocol\" ] == \"file\" : try : Path ( external_path ) . unlink () except FileNotFoundError : pass def exists ( self , external_filepath ): \"\"\" :return: True if the external file is accessible \"\"\" if self . spec [ \"protocol\" ] == \"s3\" : return self . s3 . exists ( external_filepath ) if self . spec [ \"protocol\" ] == \"file\" : return Path ( external_filepath ) . is_file () assert False # --- BLOBS ---- def put ( self , blob ): \"\"\" put a binary string (blob) in external store \"\"\" uuid = uuid_from_buffer ( blob ) self . _upload_buffer ( blob , self . _make_uuid_path ( uuid )) # insert tracking info self . connection . query ( \"INSERT INTO {tab} (hash, size) VALUES ( %s , {size} ) ON DUPLICATE KEY \" \"UPDATE timestamp=CURRENT_TIMESTAMP\" . format ( tab = self . full_table_name , size = len ( blob ) ), args = ( uuid . bytes ,), ) return uuid def get ( self , uuid ): \"\"\" get an object from external store. \"\"\" if uuid is None : return None # attempt to get object from cache blob = None cache_folder = config . get ( \"cache\" , None ) if cache_folder : try : cache_path = Path ( cache_folder , * subfold ( uuid . hex , CACHE_SUBFOLDING )) cache_file = Path ( cache_path , uuid . hex ) blob = cache_file . read_bytes () except FileNotFoundError : pass # not cached # download blob from external store if blob is None : try : blob = self . _download_buffer ( self . _make_uuid_path ( uuid )) except MissingExternalFile : if not SUPPORT_MIGRATED_BLOBS : raise # blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths relative_filepath , contents_hash = ( self & { \"hash\" : uuid }) . fetch1 ( \"filepath\" , \"contents_hash\" ) if relative_filepath is None : raise blob = self . _download_buffer ( self . _make_external_filepath ( relative_filepath ) ) if cache_folder : cache_path . mkdir ( parents = True , exist_ok = True ) safe_write ( cache_path / uuid . hex , blob ) return blob # --- ATTACHMENTS --- def upload_attachment ( self , local_path ): attachment_name = Path ( local_path ) . name uuid = uuid_from_file ( local_path , init_string = attachment_name + \" \\0 \" ) external_path = self . _make_uuid_path ( uuid , \".\" + attachment_name ) self . _upload_file ( local_path , external_path ) # insert tracking info self . connection . query ( \"\"\" INSERT INTO {tab} (hash, size, attachment_name) VALUES (%s, {size}, \"{attachment_name}\") ON DUPLICATE KEY UPDATE timestamp=CURRENT_TIMESTAMP\"\"\" . format ( tab = self . full_table_name , size = Path ( local_path ) . stat () . st_size , attachment_name = attachment_name , ), args = [ uuid . bytes ], ) return uuid def get_attachment_name ( self , uuid ): return ( self & { \"hash\" : uuid }) . fetch1 ( \"attachment_name\" ) def download_attachment ( self , uuid , attachment_name , download_path ): \"\"\"save attachment from memory buffer into the save_path\"\"\" external_path = self . _make_uuid_path ( uuid , \".\" + attachment_name ) self . _download_file ( external_path , download_path ) # --- FILEPATH --- def upload_filepath ( self , local_filepath ): \"\"\" Raise exception if an external entry already exists with a different contents checksum. Otherwise, copy (with overwrite) file to remote and If an external entry exists with the same checksum, then no copying should occur \"\"\" local_filepath = Path ( local_filepath ) try : relative_filepath = str ( local_filepath . relative_to ( self . spec [ \"stage\" ]) . as_posix () ) except ValueError : raise DataJointError ( \"The path {path} is not in stage {stage} \" . format ( path = local_filepath . parent , ** self . spec ) ) uuid = uuid_from_buffer ( init_string = relative_filepath ) # hash relative path, not contents contents_hash = uuid_from_file ( local_filepath ) # check if the remote file already exists and verify that it matches check_hash = ( self & { \"hash\" : uuid }) . fetch ( \"contents_hash\" ) if check_hash : # the tracking entry exists, check that it's the same file as before if contents_hash != check_hash [ 0 ]: raise DataJointError ( f \"A different version of ' { relative_filepath } ' has already been placed.\" ) else : # upload the file and create its tracking entry self . _upload_file ( local_filepath , self . _make_external_filepath ( relative_filepath ), metadata = { \"contents_hash\" : str ( contents_hash )}, ) self . connection . query ( \"INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES ( %s , {size} , ' {filepath} ', %s )\" . format ( tab = self . full_table_name , size = Path ( local_filepath ) . stat () . st_size , filepath = relative_filepath , ), args = ( uuid . bytes , contents_hash . bytes ), ) return uuid def download_filepath ( self , filepath_hash ): \"\"\" sync a file from external store to the local stage :param filepath_hash: The hash (UUID) of the relative_path :return: hash (UUID) of the contents of the downloaded file or Nones \"\"\" def _need_checksum ( local_filepath , expected_size ): limit = config . get ( \"filepath_checksum_size_limit\" ) actual_size = Path ( local_filepath ) . stat () . st_size if expected_size != actual_size : # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but size did not match.\" ) return limit is None or actual_size < limit if filepath_hash is not None : relative_filepath , contents_hash , size = ( self & { \"hash\" : filepath_hash } ) . fetch1 ( \"filepath\" , \"contents_hash\" , \"size\" ) external_path = self . _make_external_filepath ( relative_filepath ) local_filepath = Path ( self . spec [ \"stage\" ]) . absolute () / relative_filepath file_exists = Path ( local_filepath ) . is_file () and ( not _need_checksum ( local_filepath , size ) or uuid_from_file ( local_filepath ) == contents_hash ) if not file_exists : self . _download_file ( external_path , local_filepath ) if ( _need_checksum ( local_filepath , size ) and uuid_from_file ( local_filepath ) != contents_hash ): # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but did not pass checksum.\" ) if not _need_checksum ( local_filepath , size ): logger . warning ( f \"Skipped checksum for file with hash: { contents_hash } , and path: { local_filepath } \" ) return str ( local_filepath ), contents_hash # --- UTILITIES --- @property def references ( self ): \"\"\" :return: generator of referencing table names and their referencing columns \"\"\" return ( { k . lower (): v for k , v in elem . items ()} for elem in self . connection . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name FROM information_schema.key_column_usage WHERE referenced_table_name=\"{tab}\" and referenced_table_schema=\"{db}\" \"\"\" . format ( tab = self . table_name , db = self . database ), as_dict = True , ) ) def fetch_external_paths ( self , ** fetch_kwargs ): \"\"\" generate complete external filepaths from the query. Each element is a tuple: (uuid, path) :param fetch_kwargs: keyword arguments to pass to fetch \"\"\" fetch_kwargs . update ( as_dict = True ) paths = [] for item in self . fetch ( \"hash\" , \"attachment_name\" , \"filepath\" , ** fetch_kwargs ): if item [ \"attachment_name\" ]: # attachments path = self . _make_uuid_path ( item [ \"hash\" ], \".\" + item [ \"attachment_name\" ]) elif item [ \"filepath\" ]: # external filepaths path = self . _make_external_filepath ( item [ \"filepath\" ]) else : # blobs path = self . _make_uuid_path ( item [ \"hash\" ]) paths . append (( item [ \"hash\" ], path )) return paths def unused ( self ): \"\"\" query expression for unused hashes :return: self restricted to elements that are not in use by any tables in the schema \"\"\" return self - [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ] def used ( self ): \"\"\" query expression for used hashes :return: self restricted to elements that in use by tables in the schema \"\"\" return self & [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ] def delete ( self , * , delete_external_files = None , limit = None , display_progress = True , errors_as_string = True , ): \"\"\" :param delete_external_files: True or False. If False, only the tracking info is removed from the external store table but the external files remain intact. If True, then the external files themselves are deleted too. :param errors_as_string: If True any errors returned when deleting from external files will be strings :param limit: (integer) limit the number of items to delete :param display_progress: if True, display progress as files are cleaned up :return: if deleting external files, returns errors \"\"\" if delete_external_files not in ( True , False ): raise DataJointError ( \"The delete_external_files argument must be set to either \" \"True or False in delete()\" ) if not delete_external_files : self . unused () . delete_quick () else : items = self . unused () . fetch_external_paths ( limit = limit ) if display_progress : items = tqdm ( items ) # delete items one by one, close to transaction-safe error_list = [] for uuid , external_path in items : row = ( self & { \"hash\" : uuid }) . fetch () if row . size : try : ( self & { \"hash\" : uuid }) . delete_quick () except Exception : pass # if delete failed, do not remove the external file else : try : self . _remove_external_file ( external_path ) except Exception as error : # adding row back into table after failed delete self . insert1 ( row [ 0 ], skip_duplicates = True ) error_list . append ( ( uuid , external_path , str ( error ) if errors_as_string else error , ) ) return error_list", "title": "ExternalTable"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.exists", "text": "Returns: Type Description True if the external file is accessible Source code in datajoint/external.py 156 157 158 159 160 161 162 163 164 def exists ( self , external_filepath ): \"\"\" :return: True if the external file is accessible \"\"\" if self . spec [ \"protocol\" ] == \"s3\" : return self . s3 . exists ( external_filepath ) if self . spec [ \"protocol\" ] == \"file\" : return Path ( external_filepath ) . is_file () assert False", "title": "exists()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.put", "text": "put a binary string (blob) in external store Source code in datajoint/external.py 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 def put ( self , blob ): \"\"\" put a binary string (blob) in external store \"\"\" uuid = uuid_from_buffer ( blob ) self . _upload_buffer ( blob , self . _make_uuid_path ( uuid )) # insert tracking info self . connection . query ( \"INSERT INTO {tab} (hash, size) VALUES ( %s , {size} ) ON DUPLICATE KEY \" \"UPDATE timestamp=CURRENT_TIMESTAMP\" . format ( tab = self . full_table_name , size = len ( blob ) ), args = ( uuid . bytes ,), ) return uuid", "title": "put()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.get", "text": "get an object from external store. Source code in datajoint/external.py 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 def get ( self , uuid ): \"\"\" get an object from external store. \"\"\" if uuid is None : return None # attempt to get object from cache blob = None cache_folder = config . get ( \"cache\" , None ) if cache_folder : try : cache_path = Path ( cache_folder , * subfold ( uuid . hex , CACHE_SUBFOLDING )) cache_file = Path ( cache_path , uuid . hex ) blob = cache_file . read_bytes () except FileNotFoundError : pass # not cached # download blob from external store if blob is None : try : blob = self . _download_buffer ( self . _make_uuid_path ( uuid )) except MissingExternalFile : if not SUPPORT_MIGRATED_BLOBS : raise # blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths relative_filepath , contents_hash = ( self & { \"hash\" : uuid }) . fetch1 ( \"filepath\" , \"contents_hash\" ) if relative_filepath is None : raise blob = self . _download_buffer ( self . _make_external_filepath ( relative_filepath ) ) if cache_folder : cache_path . mkdir ( parents = True , exist_ok = True ) safe_write ( cache_path / uuid . hex , blob ) return blob", "title": "get()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.download_attachment", "text": "save attachment from memory buffer into the save_path Source code in datajoint/external.py 245 246 247 248 def download_attachment ( self , uuid , attachment_name , download_path ): \"\"\"save attachment from memory buffer into the save_path\"\"\" external_path = self . _make_uuid_path ( uuid , \".\" + attachment_name ) self . _download_file ( external_path , download_path )", "title": "download_attachment()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.upload_filepath", "text": "Raise exception if an external entry already exists with a different contents checksum. Otherwise, copy (with overwrite) file to remote and If an external entry exists with the same checksum, then no copying should occur Source code in datajoint/external.py 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 def upload_filepath ( self , local_filepath ): \"\"\" Raise exception if an external entry already exists with a different contents checksum. Otherwise, copy (with overwrite) file to remote and If an external entry exists with the same checksum, then no copying should occur \"\"\" local_filepath = Path ( local_filepath ) try : relative_filepath = str ( local_filepath . relative_to ( self . spec [ \"stage\" ]) . as_posix () ) except ValueError : raise DataJointError ( \"The path {path} is not in stage {stage} \" . format ( path = local_filepath . parent , ** self . spec ) ) uuid = uuid_from_buffer ( init_string = relative_filepath ) # hash relative path, not contents contents_hash = uuid_from_file ( local_filepath ) # check if the remote file already exists and verify that it matches check_hash = ( self & { \"hash\" : uuid }) . fetch ( \"contents_hash\" ) if check_hash : # the tracking entry exists, check that it's the same file as before if contents_hash != check_hash [ 0 ]: raise DataJointError ( f \"A different version of ' { relative_filepath } ' has already been placed.\" ) else : # upload the file and create its tracking entry self . _upload_file ( local_filepath , self . _make_external_filepath ( relative_filepath ), metadata = { \"contents_hash\" : str ( contents_hash )}, ) self . connection . query ( \"INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES ( %s , {size} , ' {filepath} ', %s )\" . format ( tab = self . full_table_name , size = Path ( local_filepath ) . stat () . st_size , filepath = relative_filepath , ), args = ( uuid . bytes , contents_hash . bytes ), ) return uuid", "title": "upload_filepath()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.download_filepath", "text": "sync a file from external store to the local stage Parameters: Name Type Description Default filepath_hash The hash (UUID) of the relative_path required Returns: Type Description hash (UUID) of the contents of the downloaded file or Nones Source code in datajoint/external.py 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 def download_filepath ( self , filepath_hash ): \"\"\" sync a file from external store to the local stage :param filepath_hash: The hash (UUID) of the relative_path :return: hash (UUID) of the contents of the downloaded file or Nones \"\"\" def _need_checksum ( local_filepath , expected_size ): limit = config . get ( \"filepath_checksum_size_limit\" ) actual_size = Path ( local_filepath ) . stat () . st_size if expected_size != actual_size : # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but size did not match.\" ) return limit is None or actual_size < limit if filepath_hash is not None : relative_filepath , contents_hash , size = ( self & { \"hash\" : filepath_hash } ) . fetch1 ( \"filepath\" , \"contents_hash\" , \"size\" ) external_path = self . _make_external_filepath ( relative_filepath ) local_filepath = Path ( self . spec [ \"stage\" ]) . absolute () / relative_filepath file_exists = Path ( local_filepath ) . is_file () and ( not _need_checksum ( local_filepath , size ) or uuid_from_file ( local_filepath ) == contents_hash ) if not file_exists : self . _download_file ( external_path , local_filepath ) if ( _need_checksum ( local_filepath , size ) and uuid_from_file ( local_filepath ) != contents_hash ): # this should never happen without outside interference raise DataJointError ( f \"' { local_filepath } ' downloaded but did not pass checksum.\" ) if not _need_checksum ( local_filepath , size ): logger . warning ( f \"Skipped checksum for file with hash: { contents_hash } , and path: { local_filepath } \" ) return str ( local_filepath ), contents_hash", "title": "download_filepath()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.references", "text": "Returns: Type Description generator of referencing table names and their referencing columns Source code in datajoint/external.py 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 @property def references ( self ): \"\"\" :return: generator of referencing table names and their referencing columns \"\"\" return ( { k . lower (): v for k , v in elem . items ()} for elem in self . connection . query ( \"\"\" SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name FROM information_schema.key_column_usage WHERE referenced_table_name=\"{tab}\" and referenced_table_schema=\"{db}\" \"\"\" . format ( tab = self . table_name , db = self . database ), as_dict = True , ) )", "title": "references()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.fetch_external_paths", "text": "generate complete external filepaths from the query. Each element is a tuple: (uuid, path) Parameters: Name Type Description Default fetch_kwargs keyword arguments to pass to fetch required Source code in datajoint/external.py 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 def fetch_external_paths ( self , ** fetch_kwargs ): \"\"\" generate complete external filepaths from the query. Each element is a tuple: (uuid, path) :param fetch_kwargs: keyword arguments to pass to fetch \"\"\" fetch_kwargs . update ( as_dict = True ) paths = [] for item in self . fetch ( \"hash\" , \"attachment_name\" , \"filepath\" , ** fetch_kwargs ): if item [ \"attachment_name\" ]: # attachments path = self . _make_uuid_path ( item [ \"hash\" ], \".\" + item [ \"attachment_name\" ]) elif item [ \"filepath\" ]: # external filepaths path = self . _make_external_filepath ( item [ \"filepath\" ]) else : # blobs path = self . _make_uuid_path ( item [ \"hash\" ]) paths . append (( item [ \"hash\" ], path )) return paths", "title": "fetch_external_paths()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.unused", "text": "query expression for unused hashes Returns: Type Description self restricted to elements that are not in use by any tables in the schema Source code in datajoint/external.py 388 389 390 391 392 393 394 395 396 397 398 399 def unused ( self ): \"\"\" query expression for unused hashes :return: self restricted to elements that are not in use by any tables in the schema \"\"\" return self - [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ]", "title": "unused()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.used", "text": "query expression for used hashes Returns: Type Description self restricted to elements that in use by tables in the schema Source code in datajoint/external.py 401 402 403 404 405 406 407 408 409 410 411 412 def used ( self ): \"\"\" query expression for used hashes :return: self restricted to elements that in use by tables in the schema \"\"\" return self & [ FreeTable ( self . connection , ref [ \"referencing_table\" ]) . proj ( hash = ref [ \"column_name\" ] ) for ref in self . references ]", "title": "used()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalTable.delete", "text": "Parameters: Name Type Description Default delete_external_files True or False. If False, only the tracking info is removed from the external store table but the external files remain intact. If True, then the external files themselves are deleted too. None errors_as_string If True any errors returned when deleting from external files will be strings True limit (integer) limit the number of items to delete None display_progress if True, display progress as files are cleaned up True Returns: Type Description if deleting external files, returns errors Source code in datajoint/external.py 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 def delete ( self , * , delete_external_files = None , limit = None , display_progress = True , errors_as_string = True , ): \"\"\" :param delete_external_files: True or False. If False, only the tracking info is removed from the external store table but the external files remain intact. If True, then the external files themselves are deleted too. :param errors_as_string: If True any errors returned when deleting from external files will be strings :param limit: (integer) limit the number of items to delete :param display_progress: if True, display progress as files are cleaned up :return: if deleting external files, returns errors \"\"\" if delete_external_files not in ( True , False ): raise DataJointError ( \"The delete_external_files argument must be set to either \" \"True or False in delete()\" ) if not delete_external_files : self . unused () . delete_quick () else : items = self . unused () . fetch_external_paths ( limit = limit ) if display_progress : items = tqdm ( items ) # delete items one by one, close to transaction-safe error_list = [] for uuid , external_path in items : row = ( self & { \"hash\" : uuid }) . fetch () if row . size : try : ( self & { \"hash\" : uuid }) . delete_quick () except Exception : pass # if delete failed, do not remove the external file else : try : self . _remove_external_file ( external_path ) except Exception as error : # adding row back into table after failed delete self . insert1 ( row [ 0 ], skip_duplicates = True ) error_list . append ( ( uuid , external_path , str ( error ) if errors_as_string else error , ) ) return error_list", "title": "delete()"}, {"location": "api/datajoint/external/#datajoint.external.ExternalMapping", "text": "Bases: Mapping The external manager contains all the tables for all external stores for a given schema :Example: e = ExternalMapping(schema) external_table = e[store] Source code in datajoint/external.py 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 class ExternalMapping ( Mapping ): \"\"\" The external manager contains all the tables for all external stores for a given schema :Example: e = ExternalMapping(schema) external_table = e[store] \"\"\" def __init__ ( self , schema ): self . schema = schema self . _tables = {} def __repr__ ( self ): return \"External file tables for schema ` {schema} `: \\n \" . format ( schema = self . schema . database ) + \" \\n \" . join ( '\" {store} \" {protocol} : {location} ' . format ( store = k , ** v . spec ) for k , v in self . items () ) def __getitem__ ( self , store ): \"\"\" Triggers the creation of an external table. Should only be used when ready to save or read from external storage. :param store: the name of the store :return: the ExternalTable object for the store \"\"\" if store not in self . _tables : self . _tables [ store ] = ExternalTable ( connection = self . schema . connection , store = store , database = self . schema . database , ) return self . _tables [ store ] def __len__ ( self ): return len ( self . _tables ) def __iter__ ( self ): return iter ( self . _tables )", "title": "ExternalMapping"}, {"location": "api/datajoint/fetch/", "text": "key \u00b6 object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key Source code in datajoint/fetch.py 18 19 20 21 22 23 24 class key : \"\"\" object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key \"\"\" pass to_dicts ( recarray ) \u00b6 convert record array to a dictionaries Source code in datajoint/fetch.py 31 32 33 34 def to_dicts ( recarray ): \"\"\"convert record array to a dictionaries\"\"\" for rec in recarray : yield dict ( zip ( recarray . dtype . names , rec . tolist ())) Fetch \u00b6 A fetch object that handles retrieving elements from the table expression. Parameters: Name Type Description Default expression the QueryExpression object to fetch from. required Source code in datajoint/fetch.py 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 class Fetch : \"\"\" A fetch object that handles retrieving elements from the table expression. :param expression: the QueryExpression object to fetch from. \"\"\" def __init__ ( self , expression ): self . _expression = expression def __call__ ( self , * attrs , offset = None , limit = None , order_by = None , format = None , as_dict = None , squeeze = False , download_path = \".\" ): \"\"\" Fetches the expression results from the database into an np.array or list of dictionaries and unpacks blob attributes. :param attrs: zero or more attributes to fetch. If not provided, the call will return all attributes of this table. If provided, returns tuples with an entry for each attribute. :param offset: the number of tuples to skip in the returned result :param limit: the maximum number of tuples to return :param order_by: a single attribute or the list of attributes to order the results. No ordering should be assumed if order_by=None. To reverse the order, add DESC to the attribute name or names: e.g. (\"age DESC\", \"frequency\") To order by primary key, use \"KEY\" or \"KEY DESC\" :param format: Effective when as_dict=None and when attrs is empty None: default from config['fetch_format'] or 'array' if not configured \"array\": use numpy.key_array \"frame\": output pandas.DataFrame. . :param as_dict: returns a list of dictionaries instead of a record array. Defaults to False for .fetch() and to True for .fetch('KEY') :param squeeze: if True, remove extra dimensions from arrays :param download_path: for fetches that download data, e.g. attachments :return: the contents of the table in the form of a structured numpy.array or a dict list \"\"\" if order_by is not None : # if 'order_by' passed in a string, make into list if isinstance ( order_by , str ): order_by = [ order_by ] # expand \"KEY\" or \"KEY DESC\" order_by = list ( _flatten_attribute_list ( self . _expression . primary_key , order_by ) ) attrs_as_dict = as_dict and attrs if attrs_as_dict : # absorb KEY into attrs and prepare to return attributes as dict (issue #595) if any ( is_key ( k ) for k in attrs ): attrs = list ( self . _expression . primary_key ) + [ a for a in attrs if a not in self . _expression . primary_key ] if as_dict is None : as_dict = bool ( attrs ) # default to True for \"KEY\" and False otherwise # format should not be specified with attrs or is_dict=True if format is not None and ( as_dict or attrs ): raise DataJointError ( \"Cannot specify output format when as_dict=True or \" \"when attributes are selected to be fetched separately.\" ) if format not in { None , \"array\" , \"frame\" }: raise DataJointError ( \"Fetch output format must be in \" '{{\"array\", \"frame\"}} but \" {} \" was given' . format ( format ) ) if not ( attrs or as_dict ) and format is None : format = config [ \"fetch_format\" ] # default to array if format not in { \"array\" , \"frame\" }: raise DataJointError ( 'Invalid entry \" {} \" in datajoint.config[\"fetch_format\"]: ' 'use \"array\" or \"frame\"' . format ( format ) ) if limit is None and offset is not None : logger . warning ( \"Offset set, but no limit. Setting limit to a large number. \" \"Consider setting a limit explicitly.\" ) limit = 8000000000 # just a very large number to effect no limit get = partial ( _get , self . _expression . connection , squeeze = squeeze , download_path = download_path , ) if attrs : # a list of attributes provided attributes = [ a for a in attrs if not is_key ( a )] ret = self . _expression . proj ( * attributes ) ret = ret . fetch ( offset = offset , limit = limit , order_by = order_by , as_dict = False , squeeze = squeeze , download_path = download_path , format = \"array\" , ) if attrs_as_dict : ret = [ { k : v for k , v in zip ( ret . dtype . names , x ) if k in attrs } for x in ret ] else : return_values = [ list ( ( to_dicts if as_dict else lambda x : x )( ret [ self . _expression . primary_key ] ) ) if is_key ( attribute ) else ret [ attribute ] for attribute in attrs ] ret = return_values [ 0 ] if len ( attrs ) == 1 else return_values else : # fetch all attributes as a numpy.record_array or pandas.DataFrame cur = self . _expression . cursor ( as_dict = as_dict , limit = limit , offset = offset , order_by = order_by ) heading = self . _expression . heading if as_dict : ret = [ dict (( name , get ( heading [ name ], d [ name ])) for name in heading . names ) for d in cur ] else : ret = list ( cur . fetchall ()) record_type = ( heading . as_dtype if not ret else np . dtype ( [ ( name , type ( value ), ) # use the first element to determine blob type if heading [ name ] . is_blob and isinstance ( value , numbers . Number ) else ( name , heading . as_dtype [ name ]) for value , name in zip ( ret [ 0 ], heading . as_dtype . names ) ] ) ) try : ret = np . array ( ret , dtype = record_type ) except Exception as e : raise e for name in heading : # unpack blobs and externals ret [ name ] = list ( map ( partial ( get , heading [ name ]), ret [ name ])) if format == \"frame\" : ret = pandas . DataFrame ( ret ) . set_index ( heading . primary_key ) return ret Fetch1 \u00b6 Fetch object for fetching the result of a query yielding one row. Parameters: Name Type Description Default expression a query expression to fetch from. required Source code in datajoint/fetch.py 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 class Fetch1 : \"\"\" Fetch object for fetching the result of a query yielding one row. :param expression: a query expression to fetch from. \"\"\" def __init__ ( self , expression ): self . _expression = expression def __call__ ( self , * attrs , squeeze = False , download_path = \".\" ): \"\"\" Fetches the result of a query expression that yields one entry. If no attributes are specified, returns the result as a dict. If attributes are specified returns the corresponding results as a tuple. Examples: d = rel.fetch1() # as a dictionary a, b = rel.fetch1('a', 'b') # as a tuple :params *attrs: attributes to return when expanding into a tuple. If attrs is empty, the return result is a dict :param squeeze: When true, remove extra dimensions from arrays in attributes :param download_path: for fetches that download data, e.g. attachments :return: the one tuple in the table in the form of a dict \"\"\" heading = self . _expression . heading if not attrs : # fetch all attributes, return as ordered dict cur = self . _expression . cursor ( as_dict = True ) ret = cur . fetchone () if not ret or cur . fetchone (): raise DataJointError ( \"fetch1 requires exactly one tuple in the input set.\" ) ret = dict ( ( name , _get ( self . _expression . connection , heading [ name ], ret [ name ], squeeze = squeeze , download_path = download_path , ), ) for name in heading . names ) else : # fetch some attributes, return as tuple attributes = [ a for a in attrs if not is_key ( a )] result = self . _expression . proj ( * attributes ) . fetch ( squeeze = squeeze , download_path = download_path , format = \"array\" ) if len ( result ) != 1 : raise DataJointError ( \"fetch1 should only return one tuple. %d tuples found\" % len ( result ) ) return_values = tuple ( next ( to_dicts ( result [ self . _expression . primary_key ])) if is_key ( attribute ) else result [ attribute ][ 0 ] for attribute in attrs ) ret = return_values [ 0 ] if len ( attrs ) == 1 else return_values return ret", "title": "fetch.py"}, {"location": "api/datajoint/fetch/#datajoint.fetch.key", "text": "object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key Source code in datajoint/fetch.py 18 19 20 21 22 23 24 class key : \"\"\" object that allows requesting the primary key as an argument in expression.fetch() The string \"KEY\" can be used instead of the class key \"\"\" pass", "title": "key"}, {"location": "api/datajoint/fetch/#datajoint.fetch.to_dicts", "text": "convert record array to a dictionaries Source code in datajoint/fetch.py 31 32 33 34 def to_dicts ( recarray ): \"\"\"convert record array to a dictionaries\"\"\" for rec in recarray : yield dict ( zip ( recarray . dtype . names , rec . tolist ()))", "title": "to_dicts()"}, {"location": "api/datajoint/fetch/#datajoint.fetch.Fetch", "text": "A fetch object that handles retrieving elements from the table expression. Parameters: Name Type Description Default expression the QueryExpression object to fetch from. required Source code in datajoint/fetch.py 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 class Fetch : \"\"\" A fetch object that handles retrieving elements from the table expression. :param expression: the QueryExpression object to fetch from. \"\"\" def __init__ ( self , expression ): self . _expression = expression def __call__ ( self , * attrs , offset = None , limit = None , order_by = None , format = None , as_dict = None , squeeze = False , download_path = \".\" ): \"\"\" Fetches the expression results from the database into an np.array or list of dictionaries and unpacks blob attributes. :param attrs: zero or more attributes to fetch. If not provided, the call will return all attributes of this table. If provided, returns tuples with an entry for each attribute. :param offset: the number of tuples to skip in the returned result :param limit: the maximum number of tuples to return :param order_by: a single attribute or the list of attributes to order the results. No ordering should be assumed if order_by=None. To reverse the order, add DESC to the attribute name or names: e.g. (\"age DESC\", \"frequency\") To order by primary key, use \"KEY\" or \"KEY DESC\" :param format: Effective when as_dict=None and when attrs is empty None: default from config['fetch_format'] or 'array' if not configured \"array\": use numpy.key_array \"frame\": output pandas.DataFrame. . :param as_dict: returns a list of dictionaries instead of a record array. Defaults to False for .fetch() and to True for .fetch('KEY') :param squeeze: if True, remove extra dimensions from arrays :param download_path: for fetches that download data, e.g. attachments :return: the contents of the table in the form of a structured numpy.array or a dict list \"\"\" if order_by is not None : # if 'order_by' passed in a string, make into list if isinstance ( order_by , str ): order_by = [ order_by ] # expand \"KEY\" or \"KEY DESC\" order_by = list ( _flatten_attribute_list ( self . _expression . primary_key , order_by ) ) attrs_as_dict = as_dict and attrs if attrs_as_dict : # absorb KEY into attrs and prepare to return attributes as dict (issue #595) if any ( is_key ( k ) for k in attrs ): attrs = list ( self . _expression . primary_key ) + [ a for a in attrs if a not in self . _expression . primary_key ] if as_dict is None : as_dict = bool ( attrs ) # default to True for \"KEY\" and False otherwise # format should not be specified with attrs or is_dict=True if format is not None and ( as_dict or attrs ): raise DataJointError ( \"Cannot specify output format when as_dict=True or \" \"when attributes are selected to be fetched separately.\" ) if format not in { None , \"array\" , \"frame\" }: raise DataJointError ( \"Fetch output format must be in \" '{{\"array\", \"frame\"}} but \" {} \" was given' . format ( format ) ) if not ( attrs or as_dict ) and format is None : format = config [ \"fetch_format\" ] # default to array if format not in { \"array\" , \"frame\" }: raise DataJointError ( 'Invalid entry \" {} \" in datajoint.config[\"fetch_format\"]: ' 'use \"array\" or \"frame\"' . format ( format ) ) if limit is None and offset is not None : logger . warning ( \"Offset set, but no limit. Setting limit to a large number. \" \"Consider setting a limit explicitly.\" ) limit = 8000000000 # just a very large number to effect no limit get = partial ( _get , self . _expression . connection , squeeze = squeeze , download_path = download_path , ) if attrs : # a list of attributes provided attributes = [ a for a in attrs if not is_key ( a )] ret = self . _expression . proj ( * attributes ) ret = ret . fetch ( offset = offset , limit = limit , order_by = order_by , as_dict = False , squeeze = squeeze , download_path = download_path , format = \"array\" , ) if attrs_as_dict : ret = [ { k : v for k , v in zip ( ret . dtype . names , x ) if k in attrs } for x in ret ] else : return_values = [ list ( ( to_dicts if as_dict else lambda x : x )( ret [ self . _expression . primary_key ] ) ) if is_key ( attribute ) else ret [ attribute ] for attribute in attrs ] ret = return_values [ 0 ] if len ( attrs ) == 1 else return_values else : # fetch all attributes as a numpy.record_array or pandas.DataFrame cur = self . _expression . cursor ( as_dict = as_dict , limit = limit , offset = offset , order_by = order_by ) heading = self . _expression . heading if as_dict : ret = [ dict (( name , get ( heading [ name ], d [ name ])) for name in heading . names ) for d in cur ] else : ret = list ( cur . fetchall ()) record_type = ( heading . as_dtype if not ret else np . dtype ( [ ( name , type ( value ), ) # use the first element to determine blob type if heading [ name ] . is_blob and isinstance ( value , numbers . Number ) else ( name , heading . as_dtype [ name ]) for value , name in zip ( ret [ 0 ], heading . as_dtype . names ) ] ) ) try : ret = np . array ( ret , dtype = record_type ) except Exception as e : raise e for name in heading : # unpack blobs and externals ret [ name ] = list ( map ( partial ( get , heading [ name ]), ret [ name ])) if format == \"frame\" : ret = pandas . DataFrame ( ret ) . set_index ( heading . primary_key ) return ret", "title": "Fetch"}, {"location": "api/datajoint/fetch/#datajoint.fetch.Fetch1", "text": "Fetch object for fetching the result of a query yielding one row. Parameters: Name Type Description Default expression a query expression to fetch from. required Source code in datajoint/fetch.py 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 class Fetch1 : \"\"\" Fetch object for fetching the result of a query yielding one row. :param expression: a query expression to fetch from. \"\"\" def __init__ ( self , expression ): self . _expression = expression def __call__ ( self , * attrs , squeeze = False , download_path = \".\" ): \"\"\" Fetches the result of a query expression that yields one entry. If no attributes are specified, returns the result as a dict. If attributes are specified returns the corresponding results as a tuple. Examples: d = rel.fetch1() # as a dictionary a, b = rel.fetch1('a', 'b') # as a tuple :params *attrs: attributes to return when expanding into a tuple. If attrs is empty, the return result is a dict :param squeeze: When true, remove extra dimensions from arrays in attributes :param download_path: for fetches that download data, e.g. attachments :return: the one tuple in the table in the form of a dict \"\"\" heading = self . _expression . heading if not attrs : # fetch all attributes, return as ordered dict cur = self . _expression . cursor ( as_dict = True ) ret = cur . fetchone () if not ret or cur . fetchone (): raise DataJointError ( \"fetch1 requires exactly one tuple in the input set.\" ) ret = dict ( ( name , _get ( self . _expression . connection , heading [ name ], ret [ name ], squeeze = squeeze , download_path = download_path , ), ) for name in heading . names ) else : # fetch some attributes, return as tuple attributes = [ a for a in attrs if not is_key ( a )] result = self . _expression . proj ( * attributes ) . fetch ( squeeze = squeeze , download_path = download_path , format = \"array\" ) if len ( result ) != 1 : raise DataJointError ( \"fetch1 should only return one tuple. %d tuples found\" % len ( result ) ) return_values = tuple ( next ( to_dicts ( result [ self . _expression . primary_key ])) if is_key ( attribute ) else result [ attribute ][ 0 ] for attribute in attrs ) ret = return_values [ 0 ] if len ( attrs ) == 1 else return_values return ret", "title": "Fetch1"}, {"location": "api/datajoint/hash/", "text": "key_hash ( mapping ) \u00b6 32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. Source code in datajoint/hash.py 7 8 9 10 11 12 13 14 15 16 def key_hash ( mapping ): \"\"\" 32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. \"\"\" hashed = hashlib . md5 () for k , v in sorted ( mapping . items ()): hashed . update ( str ( v ) . encode ()) return hashed . hexdigest () uuid_from_stream ( stream , * , init_string = '' ) \u00b6 :stream: stream object or open file handle :init_string: string to initialize the checksum Returns: Type Description 16-byte digest of stream data Source code in datajoint/hash.py 19 20 21 22 23 24 25 26 27 28 29 30 31 def uuid_from_stream ( stream , * , init_string = \"\" ): \"\"\" :return: 16-byte digest of stream data :stream: stream object or open file handle :init_string: string to initialize the checksum \"\"\" hashed = hashlib . md5 ( init_string . encode ()) chunk = True chunk_size = 1 << 14 while chunk : chunk = stream . read ( chunk_size ) hashed . update ( chunk ) return uuid . UUID ( bytes = hashed . digest ())", "title": "hash.py"}, {"location": "api/datajoint/hash/#datajoint.hash.key_hash", "text": "32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. Source code in datajoint/hash.py 7 8 9 10 11 12 13 14 15 16 def key_hash ( mapping ): \"\"\" 32-byte hash of the mapping's key values sorted by the key name. This is often used to convert a long primary key value into a shorter hash. For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables. \"\"\" hashed = hashlib . md5 () for k , v in sorted ( mapping . items ()): hashed . update ( str ( v ) . encode ()) return hashed . hexdigest ()", "title": "key_hash()"}, {"location": "api/datajoint/hash/#datajoint.hash.uuid_from_stream", "text": ":stream: stream object or open file handle :init_string: string to initialize the checksum Returns: Type Description 16-byte digest of stream data Source code in datajoint/hash.py 19 20 21 22 23 24 25 26 27 28 29 30 31 def uuid_from_stream ( stream , * , init_string = \"\" ): \"\"\" :return: 16-byte digest of stream data :stream: stream object or open file handle :init_string: string to initialize the checksum \"\"\" hashed = hashlib . md5 ( init_string . encode ()) chunk = True chunk_size = 1 << 14 while chunk : chunk = stream . read ( chunk_size ) hashed . update ( chunk ) return uuid . UUID ( bytes = hashed . digest ())", "title": "uuid_from_stream()"}, {"location": "api/datajoint/heading/", "text": "Attribute \u00b6 Bases: namedtuple ( _Attribute , default_attribute_properties ) Properties of a table column (attribute) Source code in datajoint/heading.py 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 class Attribute ( namedtuple ( \"_Attribute\" , default_attribute_properties )): \"\"\" Properties of a table column (attribute) \"\"\" def todict ( self ): \"\"\"Convert namedtuple to dict.\"\"\" return dict (( name , self [ i ]) for i , name in enumerate ( self . _fields )) @property def sql_type ( self ): \"\"\":return: datatype (as string) in database. In most cases, it is the same as self.type\"\"\" return UUID_DATA_TYPE if self . uuid else self . type @property def sql_comment ( self ): \"\"\":return: full comment for the SQL declaration. Includes custom type specification\"\"\" return ( \":uuid:\" if self . uuid else \"\" ) + self . comment @property def sql ( self ): \"\"\" Convert primary key attribute tuple into its SQL CREATE TABLE clause. Default values are not reflected. This is used for declaring foreign keys in referencing tables :return: SQL code for attribute declaration \"\"\" return '` {name} ` {type} NOT NULL COMMENT \" {comment} \"' . format ( name = self . name , type = self . sql_type , comment = self . sql_comment ) @property def original_name ( self ): if self . attribute_expression is None : return self . name assert self . attribute_expression . startswith ( \"`\" ) return self . attribute_expression . strip ( \"`\" ) todict () \u00b6 Convert namedtuple to dict. Source code in datajoint/heading.py 50 51 52 def todict ( self ): \"\"\"Convert namedtuple to dict.\"\"\" return dict (( name , self [ i ]) for i , name in enumerate ( self . _fields )) sql_type () property \u00b6 Returns: Type Description datatype (as string) in database. In most cases, it is the same as self.type Source code in datajoint/heading.py 54 55 56 57 @property def sql_type ( self ): \"\"\":return: datatype (as string) in database. In most cases, it is the same as self.type\"\"\" return UUID_DATA_TYPE if self . uuid else self . type sql_comment () property \u00b6 Returns: Type Description full comment for the SQL declaration. Includes custom type specification Source code in datajoint/heading.py 59 60 61 62 @property def sql_comment ( self ): \"\"\":return: full comment for the SQL declaration. Includes custom type specification\"\"\" return ( \":uuid:\" if self . uuid else \"\" ) + self . comment sql () property \u00b6 Convert primary key attribute tuple into its SQL CREATE TABLE clause. Default values are not reflected. This is used for declaring foreign keys in referencing tables Returns: Type Description SQL code for attribute declaration Source code in datajoint/heading.py 64 65 66 67 68 69 70 71 72 73 74 75 @property def sql ( self ): \"\"\" Convert primary key attribute tuple into its SQL CREATE TABLE clause. Default values are not reflected. This is used for declaring foreign keys in referencing tables :return: SQL code for attribute declaration \"\"\" return '` {name} ` {type} NOT NULL COMMENT \" {comment} \"' . format ( name = self . name , type = self . sql_type , comment = self . sql_comment ) Heading \u00b6 Local class for table headings. Heading contains the property attributes, which is an dict in which the keys are the attribute names and the values are Attributes. Source code in datajoint/heading.py 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 class Heading : \"\"\" Local class for table headings. Heading contains the property attributes, which is an dict in which the keys are the attribute names and the values are Attributes. \"\"\" def __init__ ( self , attribute_specs = None , table_info = None ): \"\"\" :param attribute_specs: a list of dicts with the same keys as Attribute :param table_info: a dict with information to load the heading from the database \"\"\" self . indexes = None self . table_info = table_info self . _table_status = None self . _attributes = ( None if attribute_specs is None else dict (( q [ \"name\" ], Attribute ( ** q )) for q in attribute_specs ) ) def __len__ ( self ): return 0 if self . attributes is None else len ( self . attributes ) @property def table_status ( self ): if self . table_info is None : return None if self . _table_status is None : self . _init_from_database () return self . _table_status @property def attributes ( self ): if self . _attributes is None : self . _init_from_database () # lazy loading from database return self . _attributes @property def names ( self ): return [ k for k in self . attributes ] @property def primary_key ( self ): return [ k for k , v in self . attributes . items () if v . in_key ] @property def secondary_attributes ( self ): return [ k for k , v in self . attributes . items () if not v . in_key ] @property def blobs ( self ): return [ k for k , v in self . attributes . items () if v . is_blob ] @property def non_blobs ( self ): return [ k for k , v in self . attributes . items () if not v . is_blob and not v . is_attachment and not v . is_filepath ] @property def new_attributes ( self ): return [ k for k , v in self . attributes . items () if v . attribute_expression is not None ] def __getitem__ ( self , name ): \"\"\"shortcut to the attribute\"\"\" return self . attributes [ name ] def __repr__ ( self ): \"\"\" :return: heading representation in DataJoint declaration format but without foreign key expansion \"\"\" in_key = True ret = \"\" if self . _table_status is not None : ret += \"# \" + self . table_status [ \"comment\" ] + \" \\n \" for v in self . attributes . values (): if in_key and not v . in_key : ret += \"--- \\n \" in_key = False ret += \" %-20s : %-28s # %s \\n \" % ( v . name if v . default is None else \" %s = %s \" % ( v . name , v . default ), \" %s%s \" % ( v . type , \"auto_increment\" if v . autoincrement else \"\" ), v . comment , ) return ret @property def has_autoincrement ( self ): return any ( e . autoincrement for e in self . attributes . values ()) @property def as_dtype ( self ): \"\"\" represent the heading as a numpy dtype \"\"\" return np . dtype ( dict ( names = self . names , formats = [ v . dtype for v in self . attributes . values ()]) ) def as_sql ( self , fields , include_aliases = True ): \"\"\" represent heading as the SQL SELECT clause. \"\"\" return \",\" . join ( \"` %s `\" % name if self . attributes [ name ] . attribute_expression is None else self . attributes [ name ] . attribute_expression + ( \" as ` %s `\" % name if include_aliases else \"\" ) for name in fields ) def __iter__ ( self ): return iter ( self . attributes ) def _init_from_database ( self ): \"\"\"initialize heading from an existing database table.\"\"\" conn , database , table_name , context = ( self . table_info [ k ] for k in ( \"conn\" , \"database\" , \"table_name\" , \"context\" ) ) info = conn . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE name=\" {table_name} \"' . format ( table_name = table_name , database = database ), as_dict = True , ) . fetchone () if info is None : if table_name == \"~log\" : logger . warning ( \"Could not create the ~log table\" ) return raise DataJointError ( \"The table ` {database} `.` {table_name} ` is not defined.\" . format ( table_name = table_name , database = database ) ) self . _table_status = { k . lower (): v for k , v in info . items ()} cur = conn . query ( \"SHOW FULL COLUMNS FROM ` {table_name} ` IN ` {database} `\" . format ( table_name = table_name , database = database ), as_dict = True , ) attributes = cur . fetchall () rename_map = { \"Field\" : \"name\" , \"Type\" : \"type\" , \"Null\" : \"nullable\" , \"Default\" : \"default\" , \"Key\" : \"in_key\" , \"Comment\" : \"comment\" , } fields_to_drop = ( \"Privileges\" , \"Collation\" ) # rename and drop attributes attributes = [ { rename_map [ k ] if k in rename_map else k : v for k , v in x . items () if k not in fields_to_drop } for x in attributes ] numeric_types = { ( \"float\" , False ): np . float64 , ( \"float\" , True ): np . float64 , ( \"double\" , False ): np . float64 , ( \"double\" , True ): np . float64 , ( \"tinyint\" , False ): np . int64 , ( \"tinyint\" , True ): np . int64 , ( \"smallint\" , False ): np . int64 , ( \"smallint\" , True ): np . int64 , ( \"mediumint\" , False ): np . int64 , ( \"mediumint\" , True ): np . int64 , ( \"int\" , False ): np . int64 , ( \"int\" , True ): np . int64 , ( \"bigint\" , False ): np . int64 , ( \"bigint\" , True ): np . uint64 , } sql_literals = [ \"CURRENT_TIMESTAMP\" ] # additional attribute properties for attr in attributes : attr . update ( in_key = ( attr [ \"in_key\" ] == \"PRI\" ), database = database , nullable = attr [ \"nullable\" ] == \"YES\" , autoincrement = bool ( re . search ( r \"auto_increment\" , attr [ \"Extra\" ], flags = re . I ) ), numeric = any ( TYPE_PATTERN [ t ] . match ( attr [ \"type\" ]) for t in ( \"DECIMAL\" , \"INTEGER\" , \"FLOAT\" ) ), string = any ( TYPE_PATTERN [ t ] . match ( attr [ \"type\" ]) for t in ( \"ENUM\" , \"TEMPORAL\" , \"STRING\" ) ), is_blob = bool ( TYPE_PATTERN [ \"INTERNAL_BLOB\" ] . match ( attr [ \"type\" ])), uuid = False , is_attachment = False , is_filepath = False , adapter = None , store = None , is_external = False , attribute_expression = None , ) if any ( TYPE_PATTERN [ t ] . match ( attr [ \"type\" ]) for t in ( \"INTEGER\" , \"FLOAT\" )): attr [ \"type\" ] = re . sub ( r \"\$\\d+\$\" , \"\" , attr [ \"type\" ], count = 1 ) # strip size off integers and floats attr [ \"unsupported\" ] = not any ( ( attr [ \"is_blob\" ], attr [ \"numeric\" ], attr [ \"numeric\" ]) ) attr . pop ( \"Extra\" ) # process custom DataJoint types special = re . match ( r \":(?P[^:]+):(?P.*)\" , attr [ \"comment\" ]) if special : special = special . groupdict () attr . update ( special ) # process adapted attribute types if special and TYPE_PATTERN [ \"ADAPTED\" ] . match ( attr [ \"type\" ]): assert context is not None , \"Declaration context is not set\" adapter_name = special [ \"type\" ] try : attr . update ( adapter = get_adapter ( context , adapter_name )) except DataJointError : # if no adapter, then delay the error until the first invocation attr . update ( adapter = AttributeAdapter ()) else : attr . update ( type = attr [ \"adapter\" ] . attribute_type ) if not any ( r . match ( attr [ \"type\" ]) for r in TYPE_PATTERN . values ()): raise DataJointError ( \"Invalid attribute type ' {type} ' in adapter object < {adapter_name} >.\" . format ( adapter_name = adapter_name , ** attr ) ) special = not any ( TYPE_PATTERN [ c ] . match ( attr [ \"type\" ]) for c in NATIVE_TYPES ) if special : try : category = next ( c for c in SPECIAL_TYPES if TYPE_PATTERN [ c ] . match ( attr [ \"type\" ]) ) except StopIteration : if attr [ \"type\" ] . startswith ( \"external\" ): url = ( \"https://docs.datajoint.io/python/admin/5-blob-config.html\" \"#migration-between-datajoint-v0-11-and-v0-12\" ) raise DataJointError ( \"Legacy datatype ` {type} `. Migrate your external stores to \" \"datajoint 0.12: {url} \" . format ( url = url , ** attr ) ) raise DataJointError ( \"Unknown attribute type ` {type} `\" . format ( ** attr ) ) if category == \"FILEPATH\" and not _support_filepath_types (): raise DataJointError ( \"\"\" The filepath data type is disabled until complete validation. To turn it on as experimental feature, set the environment variable {env} = TRUE or upgrade datajoint. \"\"\" . format ( env = FILEPATH_FEATURE_SWITCH ) ) attr . update ( unsupported = False , is_attachment = category in ( \"INTERNAL_ATTACH\" , \"EXTERNAL_ATTACH\" ), is_filepath = category == \"FILEPATH\" , # INTERNAL_BLOB is not a custom type but is included for completeness is_blob = category in ( \"INTERNAL_BLOB\" , \"EXTERNAL_BLOB\" ), uuid = category == \"UUID\" , is_external = category in EXTERNAL_TYPES , store = attr [ \"type\" ] . split ( \"@\" )[ 1 ] if category in EXTERNAL_TYPES else None , ) if attr [ \"in_key\" ] and any ( ( attr [ \"is_blob\" ], attr [ \"is_attachment\" ], attr [ \"is_filepath\" ]) ): raise DataJointError ( \"Blob, attachment, or filepath attributes are not allowed in the primary key\" ) if ( attr [ \"string\" ] and attr [ \"default\" ] is not None and attr [ \"default\" ] not in sql_literals ): attr [ \"default\" ] = '\" %s \"' % attr [ \"default\" ] if attr [ \"nullable\" ]: # nullable fields always default to null attr [ \"default\" ] = \"null\" # fill out dtype. All floats and non-nullable integers are turned into specific dtypes attr [ \"dtype\" ] = object if attr [ \"numeric\" ] and not attr [ \"adapter\" ]: is_integer = TYPE_PATTERN [ \"INTEGER\" ] . match ( attr [ \"type\" ]) is_float = TYPE_PATTERN [ \"FLOAT\" ] . match ( attr [ \"type\" ]) if is_integer and not attr [ \"nullable\" ] or is_float : is_unsigned = bool ( re . match ( \"sunsigned\" , attr [ \"type\" ], flags = re . I )) t = re . sub ( r \"\$.*\$\" , \"\" , attr [ \"type\" ]) # remove parentheses t = re . sub ( r \" unsigned$\" , \"\" , t ) # remove unsigned assert ( t , is_unsigned ) in numeric_types , ( \"dtype not found for type %s \" % t ) attr [ \"dtype\" ] = numeric_types [( t , is_unsigned )] if attr [ \"adapter\" ]: # restore adapted type name attr [ \"type\" ] = adapter_name self . _attributes = dict ((( q [ \"name\" ], Attribute ( ** q )) for q in attributes )) # Read and tabulate secondary indexes keys = defaultdict ( dict ) for item in conn . query ( \"SHOW KEYS FROM ` {db} `.` {tab} `\" . format ( db = database , tab = table_name ), as_dict = True , ): if item [ \"Key_name\" ] != \"PRIMARY\" : keys [ item [ \"Key_name\" ]][ item [ \"Seq_in_index\" ]] = dict ( column = item [ \"Column_name\" ], unique = ( item [ \"Non_unique\" ] == 0 ), nullable = item [ \"Null\" ] . lower () == \"yes\" , ) self . indexes = { tuple ( item [ k ][ \"column\" ] for k in sorted ( item . keys ())): dict ( unique = item [ 1 ][ \"unique\" ], nullable = any ( v [ \"nullable\" ] for v in item . values ()), ) for item in keys . values () } def select ( self , select_list , rename_map = None , compute_map = None ): \"\"\" derive a new heading by selecting, renaming, or computing attributes. In relational algebra these operators are known as project, rename, and extend. :param select_list: the full list of existing attributes to include :param rename_map: dictionary of renamed attributes: keys=new names, values=old names :param compute_map: a direction of computed attributes This low-level method performs no error checking. \"\"\" rename_map = rename_map or {} compute_map = compute_map or {} copy_attrs = list () for name in self . attributes : if name in select_list : copy_attrs . append ( self . attributes [ name ] . todict ()) copy_attrs . extend ( ( dict ( self . attributes [ old_name ] . todict (), name = new_name , attribute_expression = \"` %s `\" % old_name , ) for new_name , old_name in rename_map . items () if old_name == name ) ) compute_attrs = ( dict ( default_attribute_properties , name = new_name , attribute_expression = expr ) for new_name , expr in compute_map . items () ) return Heading ( chain ( copy_attrs , compute_attrs )) def join ( self , other ): \"\"\" Join two headings into a new one. It assumes that self and other are headings that share no common dependent attributes. \"\"\" return Heading ( [ self . attributes [ name ] . todict () for name in self . primary_key ] + [ other . attributes [ name ] . todict () for name in other . primary_key if name not in self . primary_key ] + [ self . attributes [ name ] . todict () for name in self . secondary_attributes if name not in other . primary_key ] + [ other . attributes [ name ] . todict () for name in other . secondary_attributes if name not in self . primary_key ] ) def set_primary_key ( self , primary_key ): \"\"\" Create a new heading with the specified primary key. This low-level method performs no error checking. \"\"\" return Heading ( chain ( ( dict ( self . attributes [ name ] . todict (), in_key = True ) for name in primary_key ), ( dict ( self . attributes [ name ] . todict (), in_key = False ) for name in self . names if name not in primary_key ), ) ) def make_subquery_heading ( self ): \"\"\" Create a new heading with removed attribute sql_expressions. Used by subqueries, which resolve the sql_expressions. \"\"\" return Heading ( dict ( v . todict (), attribute_expression = None ) for v in self . attributes . values () ) as_dtype () property \u00b6 represent the heading as a numpy dtype Source code in datajoint/heading.py 181 182 183 184 185 186 187 188 @property def as_dtype ( self ): \"\"\" represent the heading as a numpy dtype \"\"\" return np . dtype ( dict ( names = self . names , formats = [ v . dtype for v in self . attributes . values ()]) ) as_sql ( fields , include_aliases = True ) \u00b6 represent heading as the SQL SELECT clause. Source code in datajoint/heading.py 190 191 192 193 194 195 196 197 198 199 200 def as_sql ( self , fields , include_aliases = True ): \"\"\" represent heading as the SQL SELECT clause. \"\"\" return \",\" . join ( \"` %s `\" % name if self . attributes [ name ] . attribute_expression is None else self . attributes [ name ] . attribute_expression + ( \" as ` %s `\" % name if include_aliases else \"\" ) for name in fields ) select ( select_list , rename_map = None , compute_map = None ) \u00b6 derive a new heading by selecting, renaming, or computing attributes. In relational algebra these operators are known as project, rename, and extend. Parameters: Name Type Description Default select_list the full list of existing attributes to include required rename_map dictionary of renamed attributes: keys=new names, values=old names None compute_map a direction of computed attributes This low-level method performs no error checking. None Source code in datajoint/heading.py 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 def select ( self , select_list , rename_map = None , compute_map = None ): \"\"\" derive a new heading by selecting, renaming, or computing attributes. In relational algebra these operators are known as project, rename, and extend. :param select_list: the full list of existing attributes to include :param rename_map: dictionary of renamed attributes: keys=new names, values=old names :param compute_map: a direction of computed attributes This low-level method performs no error checking. \"\"\" rename_map = rename_map or {} compute_map = compute_map or {} copy_attrs = list () for name in self . attributes : if name in select_list : copy_attrs . append ( self . attributes [ name ] . todict ()) copy_attrs . extend ( ( dict ( self . attributes [ old_name ] . todict (), name = new_name , attribute_expression = \"` %s `\" % old_name , ) for new_name , old_name in rename_map . items () if old_name == name ) ) compute_attrs = ( dict ( default_attribute_properties , name = new_name , attribute_expression = expr ) for new_name , expr in compute_map . items () ) return Heading ( chain ( copy_attrs , compute_attrs )) join ( other ) \u00b6 Join two headings into a new one. It assumes that self and other are headings that share no common dependent attributes. Source code in datajoint/heading.py 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 def join ( self , other ): \"\"\" Join two headings into a new one. It assumes that self and other are headings that share no common dependent attributes. \"\"\" return Heading ( [ self . attributes [ name ] . todict () for name in self . primary_key ] + [ other . attributes [ name ] . todict () for name in other . primary_key if name not in self . primary_key ] + [ self . attributes [ name ] . todict () for name in self . secondary_attributes if name not in other . primary_key ] + [ other . attributes [ name ] . todict () for name in other . secondary_attributes if name not in self . primary_key ] ) set_primary_key ( primary_key ) \u00b6 Create a new heading with the specified primary key. This low-level method performs no error checking. Source code in datajoint/heading.py 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 def set_primary_key ( self , primary_key ): \"\"\" Create a new heading with the specified primary key. This low-level method performs no error checking. \"\"\" return Heading ( chain ( ( dict ( self . attributes [ name ] . todict (), in_key = True ) for name in primary_key ), ( dict ( self . attributes [ name ] . todict (), in_key = False ) for name in self . names if name not in primary_key ), ) ) make_subquery_heading () \u00b6 Create a new heading with removed attribute sql_expressions. Used by subqueries, which resolve the sql_expressions. Source code in datajoint/heading.py 511 512 513 514 515 516 517 518 519 def make_subquery_heading ( self ): \"\"\" Create a new heading with removed attribute sql_expressions. Used by subqueries, which resolve the sql_expressions. \"\"\" return Heading ( dict ( v . todict (), attribute_expression = None ) for v in self . attributes . values () )", "title": "heading.py"}, {"location": "api/datajoint/heading/#datajoint.heading.Attribute", "text": "Bases: namedtuple ( _Attribute , default_attribute_properties ) Properties of a table column (attribute) Source code in datajoint/heading.py 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 class Attribute ( namedtuple ( \"_Attribute\" , default_attribute_properties )): \"\"\" Properties of a table column (attribute) \"\"\" def todict ( self ): \"\"\"Convert namedtuple to dict.\"\"\" return dict (( name , self [ i ]) for i , name in enumerate ( self . _fields )) @property def sql_type ( self ): \"\"\":return: datatype (as string) in database. In most cases, it is the same as self.type\"\"\" return UUID_DATA_TYPE if self . uuid else self . type @property def sql_comment ( self ): \"\"\":return: full comment for the SQL declaration. Includes custom type specification\"\"\" return ( \":uuid:\" if self . uuid else \"\" ) + self . comment @property def sql ( self ): \"\"\" Convert primary key attribute tuple into its SQL CREATE TABLE clause. Default values are not reflected. This is used for declaring foreign keys in referencing tables :return: SQL code for attribute declaration \"\"\" return '` {name} ` {type} NOT NULL COMMENT \" {comment} \"' . format ( name = self . name , type = self . sql_type , comment = self . sql_comment ) @property def original_name ( self ): if self . attribute_expression is None : return self . name assert self . attribute_expression . startswith ( \"`\" ) return self . attribute_expression . strip ( \"`\" )", "title": "Attribute"}, {"location": "api/datajoint/heading/#datajoint.heading.Attribute.todict", "text": "Convert namedtuple to dict. Source code in datajoint/heading.py 50 51 52 def todict ( self ): \"\"\"Convert namedtuple to dict.\"\"\" return dict (( name , self [ i ]) for i , name in enumerate ( self . _fields ))", "title": "todict()"}, {"location": "api/datajoint/heading/#datajoint.heading.Attribute.sql_type", "text": "Returns: Type Description datatype (as string) in database. In most cases, it is the same as self.type Source code in datajoint/heading.py 54 55 56 57 @property def sql_type ( self ): \"\"\":return: datatype (as string) in database. In most cases, it is the same as self.type\"\"\" return UUID_DATA_TYPE if self . uuid else self . type", "title": "sql_type()"}, {"location": "api/datajoint/heading/#datajoint.heading.Attribute.sql_comment", "text": "Returns: Type Description full comment for the SQL declaration. Includes custom type specification Source code in datajoint/heading.py 59 60 61 62 @property def sql_comment ( self ): \"\"\":return: full comment for the SQL declaration. Includes custom type specification\"\"\" return ( \":uuid:\" if self . uuid else \"\" ) + self . comment", "title": "sql_comment()"}, {"location": "api/datajoint/heading/#datajoint.heading.Attribute.sql", "text": "Convert primary key attribute tuple into its SQL CREATE TABLE clause. Default values are not reflected. This is used for declaring foreign keys in referencing tables Returns: Type Description SQL code for attribute declaration Source code in datajoint/heading.py 64 65 66 67 68 69 70 71 72 73 74 75 @property def sql ( self ): \"\"\" Convert primary key attribute tuple into its SQL CREATE TABLE clause. Default values are not reflected. This is used for declaring foreign keys in referencing tables :return: SQL code for attribute declaration \"\"\" return '` {name} ` {type} NOT NULL COMMENT \" {comment} \"' . format ( name = self . name , type = self . sql_type , comment = self . sql_comment )", "title": "sql()"}, {"location": "api/datajoint/heading/#datajoint.heading.Heading", "text": "Local class for table headings. Heading contains the property attributes, which is an dict in which the keys are the attribute names and the values are Attributes. Source code in datajoint/heading.py 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 class Heading : \"\"\" Local class for table headings. Heading contains the property attributes, which is an dict in which the keys are the attribute names and the values are Attributes. \"\"\" def __init__ ( self , attribute_specs = None , table_info = None ): \"\"\" :param attribute_specs: a list of dicts with the same keys as Attribute :param table_info: a dict with information to load the heading from the database \"\"\" self . indexes = None self . table_info = table_info self . _table_status = None self . _attributes = ( None if attribute_specs is None else dict (( q [ \"name\" ], Attribute ( ** q )) for q in attribute_specs ) ) def __len__ ( self ): return 0 if self . attributes is None else len ( self . attributes ) @property def table_status ( self ): if self . table_info is None : return None if self . _table_status is None : self . _init_from_database () return self . _table_status @property def attributes ( self ): if self . _attributes is None : self . _init_from_database () # lazy loading from database return self . _attributes @property def names ( self ): return [ k for k in self . attributes ] @property def primary_key ( self ): return [ k for k , v in self . attributes . items () if v . in_key ] @property def secondary_attributes ( self ): return [ k for k , v in self . attributes . items () if not v . in_key ] @property def blobs ( self ): return [ k for k , v in self . attributes . items () if v . is_blob ] @property def non_blobs ( self ): return [ k for k , v in self . attributes . items () if not v . is_blob and not v . is_attachment and not v . is_filepath ] @property def new_attributes ( self ): return [ k for k , v in self . attributes . items () if v . attribute_expression is not None ] def __getitem__ ( self , name ): \"\"\"shortcut to the attribute\"\"\" return self . attributes [ name ] def __repr__ ( self ): \"\"\" :return: heading representation in DataJoint declaration format but without foreign key expansion \"\"\" in_key = True ret = \"\" if self . _table_status is not None : ret += \"# \" + self . table_status [ \"comment\" ] + \" \\n \" for v in self . attributes . values (): if in_key and not v . in_key : ret += \"--- \\n \" in_key = False ret += \" %-20s : %-28s # %s \\n \" % ( v . name if v . default is None else \" %s = %s \" % ( v . name , v . default ), \" %s%s \" % ( v . type , \"auto_increment\" if v . autoincrement else \"\" ), v . comment , ) return ret @property def has_autoincrement ( self ): return any ( e . autoincrement for e in self . attributes . values ()) @property def as_dtype ( self ): \"\"\" represent the heading as a numpy dtype \"\"\" return np . dtype ( dict ( names = self . names , formats = [ v . dtype for v in self . attributes . values ()]) ) def as_sql ( self , fields , include_aliases = True ): \"\"\" represent heading as the SQL SELECT clause. \"\"\" return \",\" . join ( \"` %s `\" % name if self . attributes [ name ] . attribute_expression is None else self . attributes [ name ] . attribute_expression + ( \" as ` %s `\" % name if include_aliases else \"\" ) for name in fields ) def __iter__ ( self ): return iter ( self . attributes ) def _init_from_database ( self ): \"\"\"initialize heading from an existing database table.\"\"\" conn , database , table_name , context = ( self . table_info [ k ] for k in ( \"conn\" , \"database\" , \"table_name\" , \"context\" ) ) info = conn . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE name=\" {table_name} \"' . format ( table_name = table_name , database = database ), as_dict = True , ) . fetchone () if info is None : if table_name == \"~log\" : logger . warning ( \"Could not create the ~log table\" ) return raise DataJointError ( \"The table ` {database} `.` {table_name} ` is not defined.\" . format ( table_name = table_name , database = database ) ) self . _table_status = { k . lower (): v for k , v in info . items ()} cur = conn . query ( \"SHOW FULL COLUMNS FROM ` {table_name} ` IN ` {database} `\" . format ( table_name = table_name , database = database ), as_dict = True , ) attributes = cur . fetchall () rename_map = { \"Field\" : \"name\" , \"Type\" : \"type\" , \"Null\" : \"nullable\" , \"Default\" : \"default\" , \"Key\" : \"in_key\" , \"Comment\" : \"comment\" , } fields_to_drop = ( \"Privileges\" , \"Collation\" ) # rename and drop attributes attributes = [ { rename_map [ k ] if k in rename_map else k : v for k , v in x . items () if k not in fields_to_drop } for x in attributes ] numeric_types = { ( \"float\" , False ): np . float64 , ( \"float\" , True ): np . float64 , ( \"double\" , False ): np . float64 , ( \"double\" , True ): np . float64 , ( \"tinyint\" , False ): np . int64 , ( \"tinyint\" , True ): np . int64 , ( \"smallint\" , False ): np . int64 , ( \"smallint\" , True ): np . int64 , ( \"mediumint\" , False ): np . int64 , ( \"mediumint\" , True ): np . int64 , ( \"int\" , False ): np . int64 , ( \"int\" , True ): np . int64 , ( \"bigint\" , False ): np . int64 , ( \"bigint\" , True ): np . uint64 , } sql_literals = [ \"CURRENT_TIMESTAMP\" ] # additional attribute properties for attr in attributes : attr . update ( in_key = ( attr [ \"in_key\" ] == \"PRI\" ), database = database , nullable = attr [ \"nullable\" ] == \"YES\" , autoincrement = bool ( re . search ( r \"auto_increment\" , attr [ \"Extra\" ], flags = re . I ) ), numeric = any ( TYPE_PATTERN [ t ] . match ( attr [ \"type\" ]) for t in ( \"DECIMAL\" , \"INTEGER\" , \"FLOAT\" ) ), string = any ( TYPE_PATTERN [ t ] . match ( attr [ \"type\" ]) for t in ( \"ENUM\" , \"TEMPORAL\" , \"STRING\" ) ), is_blob = bool ( TYPE_PATTERN [ \"INTERNAL_BLOB\" ] . match ( attr [ \"type\" ])), uuid = False , is_attachment = False , is_filepath = False , adapter = None , store = None , is_external = False , attribute_expression = None , ) if any ( TYPE_PATTERN [ t ] . match ( attr [ \"type\" ]) for t in ( \"INTEGER\" , \"FLOAT\" )): attr [ \"type\" ] = re . sub ( r \"\$\\d+\$\" , \"\" , attr [ \"type\" ], count = 1 ) # strip size off integers and floats attr [ \"unsupported\" ] = not any ( ( attr [ \"is_blob\" ], attr [ \"numeric\" ], attr [ \"numeric\" ]) ) attr . pop ( \"Extra\" ) # process custom DataJoint types special = re . match ( r \":(?P[^:]+):(?P.*)\" , attr [ \"comment\" ]) if special : special = special . groupdict () attr . update ( special ) # process adapted attribute types if special and TYPE_PATTERN [ \"ADAPTED\" ] . match ( attr [ \"type\" ]): assert context is not None , \"Declaration context is not set\" adapter_name = special [ \"type\" ] try : attr . update ( adapter = get_adapter ( context , adapter_name )) except DataJointError : # if no adapter, then delay the error until the first invocation attr . update ( adapter = AttributeAdapter ()) else : attr . update ( type = attr [ \"adapter\" ] . attribute_type ) if not any ( r . match ( attr [ \"type\" ]) for r in TYPE_PATTERN . values ()): raise DataJointError ( \"Invalid attribute type ' {type} ' in adapter object < {adapter_name} >.\" . format ( adapter_name = adapter_name , ** attr ) ) special = not any ( TYPE_PATTERN [ c ] . match ( attr [ \"type\" ]) for c in NATIVE_TYPES ) if special : try : category = next ( c for c in SPECIAL_TYPES if TYPE_PATTERN [ c ] . match ( attr [ \"type\" ]) ) except StopIteration : if attr [ \"type\" ] . startswith ( \"external\" ): url = ( \"https://docs.datajoint.io/python/admin/5-blob-config.html\" \"#migration-between-datajoint-v0-11-and-v0-12\" ) raise DataJointError ( \"Legacy datatype ` {type} `. Migrate your external stores to \" \"datajoint 0.12: {url} \" . format ( url = url , ** attr ) ) raise DataJointError ( \"Unknown attribute type ` {type} `\" . format ( ** attr ) ) if category == \"FILEPATH\" and not _support_filepath_types (): raise DataJointError ( \"\"\" The filepath data type is disabled until complete validation. To turn it on as experimental feature, set the environment variable {env} = TRUE or upgrade datajoint. \"\"\" . format ( env = FILEPATH_FEATURE_SWITCH ) ) attr . update ( unsupported = False , is_attachment = category in ( \"INTERNAL_ATTACH\" , \"EXTERNAL_ATTACH\" ), is_filepath = category == \"FILEPATH\" , # INTERNAL_BLOB is not a custom type but is included for completeness is_blob = category in ( \"INTERNAL_BLOB\" , \"EXTERNAL_BLOB\" ), uuid = category == \"UUID\" , is_external = category in EXTERNAL_TYPES , store = attr [ \"type\" ] . split ( \"@\" )[ 1 ] if category in EXTERNAL_TYPES else None , ) if attr [ \"in_key\" ] and any ( ( attr [ \"is_blob\" ], attr [ \"is_attachment\" ], attr [ \"is_filepath\" ]) ): raise DataJointError ( \"Blob, attachment, or filepath attributes are not allowed in the primary key\" ) if ( attr [ \"string\" ] and attr [ \"default\" ] is not None and attr [ \"default\" ] not in sql_literals ): attr [ \"default\" ] = '\" %s \"' % attr [ \"default\" ] if attr [ \"nullable\" ]: # nullable fields always default to null attr [ \"default\" ] = \"null\" # fill out dtype. All floats and non-nullable integers are turned into specific dtypes attr [ \"dtype\" ] = object if attr [ \"numeric\" ] and not attr [ \"adapter\" ]: is_integer = TYPE_PATTERN [ \"INTEGER\" ] . match ( attr [ \"type\" ]) is_float = TYPE_PATTERN [ \"FLOAT\" ] . match ( attr [ \"type\" ]) if is_integer and not attr [ \"nullable\" ] or is_float : is_unsigned = bool ( re . match ( \"sunsigned\" , attr [ \"type\" ], flags = re . I )) t = re . sub ( r \"\$.*\$\" , \"\" , attr [ \"type\" ]) # remove parentheses t = re . sub ( r \" unsigned$\" , \"\" , t ) # remove unsigned assert ( t , is_unsigned ) in numeric_types , ( \"dtype not found for type %s \" % t ) attr [ \"dtype\" ] = numeric_types [( t , is_unsigned )] if attr [ \"adapter\" ]: # restore adapted type name attr [ \"type\" ] = adapter_name self . _attributes = dict ((( q [ \"name\" ], Attribute ( ** q )) for q in attributes )) # Read and tabulate secondary indexes keys = defaultdict ( dict ) for item in conn . query ( \"SHOW KEYS FROM ` {db} `.` {tab} `\" . format ( db = database , tab = table_name ), as_dict = True , ): if item [ \"Key_name\" ] != \"PRIMARY\" : keys [ item [ \"Key_name\" ]][ item [ \"Seq_in_index\" ]] = dict ( column = item [ \"Column_name\" ], unique = ( item [ \"Non_unique\" ] == 0 ), nullable = item [ \"Null\" ] . lower () == \"yes\" , ) self . indexes = { tuple ( item [ k ][ \"column\" ] for k in sorted ( item . keys ())): dict ( unique = item [ 1 ][ \"unique\" ], nullable = any ( v [ \"nullable\" ] for v in item . values ()), ) for item in keys . values () } def select ( self , select_list , rename_map = None , compute_map = None ): \"\"\" derive a new heading by selecting, renaming, or computing attributes. In relational algebra these operators are known as project, rename, and extend. :param select_list: the full list of existing attributes to include :param rename_map: dictionary of renamed attributes: keys=new names, values=old names :param compute_map: a direction of computed attributes This low-level method performs no error checking. \"\"\" rename_map = rename_map or {} compute_map = compute_map or {} copy_attrs = list () for name in self . attributes : if name in select_list : copy_attrs . append ( self . attributes [ name ] . todict ()) copy_attrs . extend ( ( dict ( self . attributes [ old_name ] . todict (), name = new_name , attribute_expression = \"` %s `\" % old_name , ) for new_name , old_name in rename_map . items () if old_name == name ) ) compute_attrs = ( dict ( default_attribute_properties , name = new_name , attribute_expression = expr ) for new_name , expr in compute_map . items () ) return Heading ( chain ( copy_attrs , compute_attrs )) def join ( self , other ): \"\"\" Join two headings into a new one. It assumes that self and other are headings that share no common dependent attributes. \"\"\" return Heading ( [ self . attributes [ name ] . todict () for name in self . primary_key ] + [ other . attributes [ name ] . todict () for name in other . primary_key if name not in self . primary_key ] + [ self . attributes [ name ] . todict () for name in self . secondary_attributes if name not in other . primary_key ] + [ other . attributes [ name ] . todict () for name in other . secondary_attributes if name not in self . primary_key ] ) def set_primary_key ( self , primary_key ): \"\"\" Create a new heading with the specified primary key. This low-level method performs no error checking. \"\"\" return Heading ( chain ( ( dict ( self . attributes [ name ] . todict (), in_key = True ) for name in primary_key ), ( dict ( self . attributes [ name ] . todict (), in_key = False ) for name in self . names if name not in primary_key ), ) ) def make_subquery_heading ( self ): \"\"\" Create a new heading with removed attribute sql_expressions. Used by subqueries, which resolve the sql_expressions. \"\"\" return Heading ( dict ( v . todict (), attribute_expression = None ) for v in self . attributes . values () )", "title": "Heading"}, {"location": "api/datajoint/heading/#datajoint.heading.Heading.as_dtype", "text": "represent the heading as a numpy dtype Source code in datajoint/heading.py 181 182 183 184 185 186 187 188 @property def as_dtype ( self ): \"\"\" represent the heading as a numpy dtype \"\"\" return np . dtype ( dict ( names = self . names , formats = [ v . dtype for v in self . attributes . values ()]) )", "title": "as_dtype()"}, {"location": "api/datajoint/heading/#datajoint.heading.Heading.as_sql", "text": "represent heading as the SQL SELECT clause. Source code in datajoint/heading.py 190 191 192 193 194 195 196 197 198 199 200 def as_sql ( self , fields , include_aliases = True ): \"\"\" represent heading as the SQL SELECT clause. \"\"\" return \",\" . join ( \"` %s `\" % name if self . attributes [ name ] . attribute_expression is None else self . attributes [ name ] . attribute_expression + ( \" as ` %s `\" % name if include_aliases else \"\" ) for name in fields )", "title": "as_sql()"}, {"location": "api/datajoint/heading/#datajoint.heading.Heading.select", "text": "derive a new heading by selecting, renaming, or computing attributes. In relational algebra these operators are known as project, rename, and extend. Parameters: Name Type Description Default select_list the full list of existing attributes to include required rename_map dictionary of renamed attributes: keys=new names, values=old names None compute_map a direction of computed attributes This low-level method performs no error checking. None Source code in datajoint/heading.py 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 def select ( self , select_list , rename_map = None , compute_map = None ): \"\"\" derive a new heading by selecting, renaming, or computing attributes. In relational algebra these operators are known as project, rename, and extend. :param select_list: the full list of existing attributes to include :param rename_map: dictionary of renamed attributes: keys=new names, values=old names :param compute_map: a direction of computed attributes This low-level method performs no error checking. \"\"\" rename_map = rename_map or {} compute_map = compute_map or {} copy_attrs = list () for name in self . attributes : if name in select_list : copy_attrs . append ( self . attributes [ name ] . todict ()) copy_attrs . extend ( ( dict ( self . attributes [ old_name ] . todict (), name = new_name , attribute_expression = \"` %s `\" % old_name , ) for new_name , old_name in rename_map . items () if old_name == name ) ) compute_attrs = ( dict ( default_attribute_properties , name = new_name , attribute_expression = expr ) for new_name , expr in compute_map . items () ) return Heading ( chain ( copy_attrs , compute_attrs ))", "title": "select()"}, {"location": "api/datajoint/heading/#datajoint.heading.Heading.join", "text": "Join two headings into a new one. It assumes that self and other are headings that share no common dependent attributes. Source code in datajoint/heading.py 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 def join ( self , other ): \"\"\" Join two headings into a new one. It assumes that self and other are headings that share no common dependent attributes. \"\"\" return Heading ( [ self . attributes [ name ] . todict () for name in self . primary_key ] + [ other . attributes [ name ] . todict () for name in other . primary_key if name not in self . primary_key ] + [ self . attributes [ name ] . todict () for name in self . secondary_attributes if name not in other . primary_key ] + [ other . attributes [ name ] . todict () for name in other . secondary_attributes if name not in self . primary_key ] )", "title": "join()"}, {"location": "api/datajoint/heading/#datajoint.heading.Heading.set_primary_key", "text": "Create a new heading with the specified primary key. This low-level method performs no error checking. Source code in datajoint/heading.py 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 def set_primary_key ( self , primary_key ): \"\"\" Create a new heading with the specified primary key. This low-level method performs no error checking. \"\"\" return Heading ( chain ( ( dict ( self . attributes [ name ] . todict (), in_key = True ) for name in primary_key ), ( dict ( self . attributes [ name ] . todict (), in_key = False ) for name in self . names if name not in primary_key ), ) )", "title": "set_primary_key()"}, {"location": "api/datajoint/heading/#datajoint.heading.Heading.make_subquery_heading", "text": "Create a new heading with removed attribute sql_expressions. Used by subqueries, which resolve the sql_expressions. Source code in datajoint/heading.py 511 512 513 514 515 516 517 518 519 def make_subquery_heading ( self ): \"\"\" Create a new heading with removed attribute sql_expressions. Used by subqueries, which resolve the sql_expressions. \"\"\" return Heading ( dict ( v . todict (), attribute_expression = None ) for v in self . attributes . values () )", "title": "make_subquery_heading()"}, {"location": "api/datajoint/jobs/", "text": "JobTable \u00b6 Bases: Table A base table with no definition. Allows reserving jobs Source code in datajoint/jobs.py 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 class JobTable ( Table ): \"\"\" A base table with no definition. Allows reserving jobs \"\"\" def __init__ ( self , conn , database ): self . database = database self . _connection = conn self . _heading = Heading ( table_info = dict ( conn = conn , database = database , table_name = self . table_name , context = None ) ) self . _support = [ self . full_table_name ] self . _definition = \"\"\" # job reservation table for ` {database} ` table_name :varchar(255) # className of the table key_hash :char(32) # key hash --- status :enum('reserved','error','ignore') # if tuple is missing, the job is available key=null :blob # structure containing the key error_message=\"\" :varchar( {error_message_length} ) # error message returned if failed error_stack=null :mediumblob # error stack if failed user=\"\" :varchar(255) # database user host=\"\" :varchar(255) # system hostname pid=0 :int unsigned # system process id connection_id = 0 : bigint unsigned # connection_id() timestamp=CURRENT_TIMESTAMP :timestamp # automatic timestamp \"\"\" . format ( database = database , error_message_length = ERROR_MESSAGE_LENGTH ) if not self . is_declared : self . declare () self . _user = self . connection . get_user () @property def definition ( self ): return self . _definition @property def table_name ( self ): return \"~jobs\" def delete ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . delete_quick () def drop ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . drop_quick () def reserve ( self , table_name , key ): \"\"\" Reserve a job for computation. When a job is reserved, the job table contains an entry for the job key, identified by its hash. When jobs are completed, the entry is removed. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :return: True if reserved job successfully. False = the jobs is already taken \"\"\" job = dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"reserved\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , key = key , user = self . _user , ) try : with config ( enable_python_native_blobs = True ): self . insert1 ( job , ignore_extra_fields = True ) except DuplicateError : return False return True def complete ( self , table_name , key ): \"\"\" Log a completed job. When a job is completed, its reservation entry is deleted. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key \"\"\" job_key = dict ( table_name = table_name , key_hash = key_hash ( key )) ( self & job_key ) . delete_quick () def error ( self , table_name , key , error_message , error_stack = None ): \"\"\" Log an error message. The job reservation is replaced with an error entry. if an error occurs, leave an entry describing the problem :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :param error_message: string error message :param error_stack: stack trace \"\"\" if len ( error_message ) > ERROR_MESSAGE_LENGTH : error_message = ( error_message [: ERROR_MESSAGE_LENGTH - len ( TRUNCATION_APPENDIX )] + TRUNCATION_APPENDIX ) with config ( enable_python_native_blobs = True ): self . insert1 ( dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"error\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , user = self . _user , key = key , error_message = error_message , error_stack = error_stack , ), replace = True , ignore_extra_fields = True , ) delete () \u00b6 bypass interactive prompts and dependencies Source code in datajoint/jobs.py 56 57 58 def delete ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . delete_quick () drop () \u00b6 bypass interactive prompts and dependencies Source code in datajoint/jobs.py 60 61 62 def drop ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . drop_quick () reserve ( table_name , key ) \u00b6 Reserve a job for computation. When a job is reserved, the job table contains an entry for the job key, identified by its hash. When jobs are completed, the entry is removed. Parameters: Name Type Description Default table_name database . table_name required key the dict of the job's primary key required Returns: Type Description True if reserved job successfully. False = the jobs is already taken Source code in datajoint/jobs.py 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 def reserve ( self , table_name , key ): \"\"\" Reserve a job for computation. When a job is reserved, the job table contains an entry for the job key, identified by its hash. When jobs are completed, the entry is removed. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :return: True if reserved job successfully. False = the jobs is already taken \"\"\" job = dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"reserved\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , key = key , user = self . _user , ) try : with config ( enable_python_native_blobs = True ): self . insert1 ( job , ignore_extra_fields = True ) except DuplicateError : return False return True complete ( table_name , key ) \u00b6 Log a completed job. When a job is completed, its reservation entry is deleted. Parameters: Name Type Description Default table_name database . table_name required key the dict of the job's primary key required Source code in datajoint/jobs.py 90 91 92 93 94 95 96 97 98 def complete ( self , table_name , key ): \"\"\" Log a completed job. When a job is completed, its reservation entry is deleted. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key \"\"\" job_key = dict ( table_name = table_name , key_hash = key_hash ( key )) ( self & job_key ) . delete_quick () error ( table_name , key , error_message , error_stack = None ) \u00b6 Log an error message. The job reservation is replaced with an error entry. if an error occurs, leave an entry describing the problem Parameters: Name Type Description Default table_name database . table_name required key the dict of the job's primary key required error_message string error message required error_stack stack trace None Source code in datajoint/jobs.py 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 def error ( self , table_name , key , error_message , error_stack = None ): \"\"\" Log an error message. The job reservation is replaced with an error entry. if an error occurs, leave an entry describing the problem :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :param error_message: string error message :param error_stack: stack trace \"\"\" if len ( error_message ) > ERROR_MESSAGE_LENGTH : error_message = ( error_message [: ERROR_MESSAGE_LENGTH - len ( TRUNCATION_APPENDIX )] + TRUNCATION_APPENDIX ) with config ( enable_python_native_blobs = True ): self . insert1 ( dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"error\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , user = self . _user , key = key , error_message = error_message , error_stack = error_stack , ), replace = True , ignore_extra_fields = True , )", "title": "jobs.py"}, {"location": "api/datajoint/jobs/#datajoint.jobs.JobTable", "text": "Bases: Table A base table with no definition. Allows reserving jobs Source code in datajoint/jobs.py 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 class JobTable ( Table ): \"\"\" A base table with no definition. Allows reserving jobs \"\"\" def __init__ ( self , conn , database ): self . database = database self . _connection = conn self . _heading = Heading ( table_info = dict ( conn = conn , database = database , table_name = self . table_name , context = None ) ) self . _support = [ self . full_table_name ] self . _definition = \"\"\" # job reservation table for ` {database} ` table_name :varchar(255) # className of the table key_hash :char(32) # key hash --- status :enum('reserved','error','ignore') # if tuple is missing, the job is available key=null :blob # structure containing the key error_message=\"\" :varchar( {error_message_length} ) # error message returned if failed error_stack=null :mediumblob # error stack if failed user=\"\" :varchar(255) # database user host=\"\" :varchar(255) # system hostname pid=0 :int unsigned # system process id connection_id = 0 : bigint unsigned # connection_id() timestamp=CURRENT_TIMESTAMP :timestamp # automatic timestamp \"\"\" . format ( database = database , error_message_length = ERROR_MESSAGE_LENGTH ) if not self . is_declared : self . declare () self . _user = self . connection . get_user () @property def definition ( self ): return self . _definition @property def table_name ( self ): return \"~jobs\" def delete ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . delete_quick () def drop ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . drop_quick () def reserve ( self , table_name , key ): \"\"\" Reserve a job for computation. When a job is reserved, the job table contains an entry for the job key, identified by its hash. When jobs are completed, the entry is removed. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :return: True if reserved job successfully. False = the jobs is already taken \"\"\" job = dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"reserved\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , key = key , user = self . _user , ) try : with config ( enable_python_native_blobs = True ): self . insert1 ( job , ignore_extra_fields = True ) except DuplicateError : return False return True def complete ( self , table_name , key ): \"\"\" Log a completed job. When a job is completed, its reservation entry is deleted. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key \"\"\" job_key = dict ( table_name = table_name , key_hash = key_hash ( key )) ( self & job_key ) . delete_quick () def error ( self , table_name , key , error_message , error_stack = None ): \"\"\" Log an error message. The job reservation is replaced with an error entry. if an error occurs, leave an entry describing the problem :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :param error_message: string error message :param error_stack: stack trace \"\"\" if len ( error_message ) > ERROR_MESSAGE_LENGTH : error_message = ( error_message [: ERROR_MESSAGE_LENGTH - len ( TRUNCATION_APPENDIX )] + TRUNCATION_APPENDIX ) with config ( enable_python_native_blobs = True ): self . insert1 ( dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"error\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , user = self . _user , key = key , error_message = error_message , error_stack = error_stack , ), replace = True , ignore_extra_fields = True , )", "title": "JobTable"}, {"location": "api/datajoint/jobs/#datajoint.jobs.JobTable.delete", "text": "bypass interactive prompts and dependencies Source code in datajoint/jobs.py 56 57 58 def delete ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . delete_quick ()", "title": "delete()"}, {"location": "api/datajoint/jobs/#datajoint.jobs.JobTable.drop", "text": "bypass interactive prompts and dependencies Source code in datajoint/jobs.py 60 61 62 def drop ( self ): \"\"\"bypass interactive prompts and dependencies\"\"\" self . drop_quick ()", "title": "drop()"}, {"location": "api/datajoint/jobs/#datajoint.jobs.JobTable.reserve", "text": "Reserve a job for computation. When a job is reserved, the job table contains an entry for the job key, identified by its hash. When jobs are completed, the entry is removed. Parameters: Name Type Description Default table_name database . table_name required key the dict of the job's primary key required Returns: Type Description True if reserved job successfully. False = the jobs is already taken Source code in datajoint/jobs.py 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 def reserve ( self , table_name , key ): \"\"\" Reserve a job for computation. When a job is reserved, the job table contains an entry for the job key, identified by its hash. When jobs are completed, the entry is removed. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :return: True if reserved job successfully. False = the jobs is already taken \"\"\" job = dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"reserved\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , key = key , user = self . _user , ) try : with config ( enable_python_native_blobs = True ): self . insert1 ( job , ignore_extra_fields = True ) except DuplicateError : return False return True", "title": "reserve()"}, {"location": "api/datajoint/jobs/#datajoint.jobs.JobTable.complete", "text": "Log a completed job. When a job is completed, its reservation entry is deleted. Parameters: Name Type Description Default table_name database . table_name required key the dict of the job's primary key required Source code in datajoint/jobs.py 90 91 92 93 94 95 96 97 98 def complete ( self , table_name , key ): \"\"\" Log a completed job. When a job is completed, its reservation entry is deleted. :param table_name: `database`.`table_name` :param key: the dict of the job's primary key \"\"\" job_key = dict ( table_name = table_name , key_hash = key_hash ( key )) ( self & job_key ) . delete_quick ()", "title": "complete()"}, {"location": "api/datajoint/jobs/#datajoint.jobs.JobTable.error", "text": "Log an error message. The job reservation is replaced with an error entry. if an error occurs, leave an entry describing the problem Parameters: Name Type Description Default table_name database . table_name required key the dict of the job's primary key required error_message string error message required error_stack stack trace None Source code in datajoint/jobs.py 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 def error ( self , table_name , key , error_message , error_stack = None ): \"\"\" Log an error message. The job reservation is replaced with an error entry. if an error occurs, leave an entry describing the problem :param table_name: `database`.`table_name` :param key: the dict of the job's primary key :param error_message: string error message :param error_stack: stack trace \"\"\" if len ( error_message ) > ERROR_MESSAGE_LENGTH : error_message = ( error_message [: ERROR_MESSAGE_LENGTH - len ( TRUNCATION_APPENDIX )] + TRUNCATION_APPENDIX ) with config ( enable_python_native_blobs = True ): self . insert1 ( dict ( table_name = table_name , key_hash = key_hash ( key ), status = \"error\" , host = platform . node (), pid = os . getpid (), connection_id = self . connection . connection_id , user = self . _user , key = key , error_message = error_message , error_stack = error_stack , ), replace = True , ignore_extra_fields = True , )", "title": "error()"}, {"location": "api/datajoint/logging/", "text": "", "title": "logging.py"}, {"location": "api/datajoint/migrate/", "text": "migrate_dj011_external_blob_storage_to_dj012 ( migration_schema , store ) \u00b6 Utility function to migrate external blob data from 0.11 to 0.12. Parameters: Name Type Description Default migration_schema string of target schema to be migrated required store string of target dj.config['store'] to be migrated required Source code in datajoint/migrate.py 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 def migrate_dj011_external_blob_storage_to_dj012 ( migration_schema , store ): \"\"\" Utility function to migrate external blob data from 0.11 to 0.12. :param migration_schema: string of target schema to be migrated :param store: string of target dj.config['store'] to be migrated \"\"\" if not isinstance ( migration_schema , str ): raise ValueError ( \"Expected type {} for migration_schema, not {} .\" . format ( str , type ( migration_schema ) ) ) do_migration = False do_migration = ( user_choice ( \"\"\" Warning: Ensure the following are completed before proceeding. - Appropriate backups have been taken, - Any existing DJ 0.11.X connections are suspended, and - External config has been updated to new dj.config['stores'] structure. Proceed? \"\"\" , default = \"no\" , ) == \"yes\" ) if do_migration : _migrate_dj011_blob ( dj . Schema ( migration_schema ), store ) print ( \"Migration completed for schema: {} , store: {} .\" . format ( migration_schema , store ) ) return print ( \"No migration performed.\" )", "title": "migrate.py"}, {"location": "api/datajoint/migrate/#datajoint.migrate.migrate_dj011_external_blob_storage_to_dj012", "text": "Utility function to migrate external blob data from 0.11 to 0.12. Parameters: Name Type Description Default migration_schema string of target schema to be migrated required store string of target dj.config['store'] to be migrated required Source code in datajoint/migrate.py 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 def migrate_dj011_external_blob_storage_to_dj012 ( migration_schema , store ): \"\"\" Utility function to migrate external blob data from 0.11 to 0.12. :param migration_schema: string of target schema to be migrated :param store: string of target dj.config['store'] to be migrated \"\"\" if not isinstance ( migration_schema , str ): raise ValueError ( \"Expected type {} for migration_schema, not {} .\" . format ( str , type ( migration_schema ) ) ) do_migration = False do_migration = ( user_choice ( \"\"\" Warning: Ensure the following are completed before proceeding. - Appropriate backups have been taken, - Any existing DJ 0.11.X connections are suspended, and - External config has been updated to new dj.config['stores'] structure. Proceed? \"\"\" , default = \"no\" , ) == \"yes\" ) if do_migration : _migrate_dj011_blob ( dj . Schema ( migration_schema ), store ) print ( \"Migration completed for schema: {} , store: {} .\" . format ( migration_schema , store ) ) return print ( \"No migration performed.\" )", "title": "migrate_dj011_external_blob_storage_to_dj012()"}, {"location": "api/datajoint/plugin/", "text": "", "title": "plugin.py"}, {"location": "api/datajoint/preview/", "text": "methods for generating previews of query expression results in python command line and Jupyter", "title": "preview.py"}, {"location": "api/datajoint/s3/", "text": "AWS S3 operations Folder \u00b6 A Folder instance manipulates a flat folder of objects within an S3-compatible object store Source code in datajoint/s3.py 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 class Folder : \"\"\" A Folder instance manipulates a flat folder of objects within an S3-compatible object store \"\"\" def __init__ ( self , endpoint , bucket , access_key , secret_key , * , secure = False , proxy_server = None , ** _ ): # from https://docs.min.io/docs/python-client-api-reference self . client = minio . Minio ( endpoint , access_key = access_key , secret_key = secret_key , secure = secure , http_client = ( urllib3 . ProxyManager ( proxy_server , timeout = urllib3 . Timeout . DEFAULT_TIMEOUT , cert_reqs = \"CERT_REQUIRED\" , retries = urllib3 . Retry ( total = 5 , backoff_factor = 0.2 , status_forcelist = [ 500 , 502 , 503 , 504 ], ), ) if proxy_server else None ), ) self . bucket = bucket if not self . client . bucket_exists ( bucket ): raise errors . BucketInaccessible ( \"Inaccessible s3 bucket %s \" % bucket ) def put ( self , name , buffer ): logger . debug ( \"put: {} : {} \" . format ( self . bucket , name )) return self . client . put_object ( self . bucket , str ( name ), BytesIO ( buffer ), length = len ( buffer ) ) def fput ( self , local_file , name , metadata = None ): logger . debug ( \"fput: {} -> {} : {} \" . format ( self . bucket , local_file , name )) return self . client . fput_object ( self . bucket , str ( name ), str ( local_file ), metadata = metadata ) def get ( self , name ): logger . debug ( \"get: {} : {} \" . format ( self . bucket , name )) try : return self . client . get_object ( self . bucket , str ( name )) . data except minio . error . S3Error as e : if e . code == \"NoSuchKey\" : raise errors . MissingExternalFile ( \"Missing s3 key %s \" % name ) else : raise e def fget ( self , name , local_filepath ): \"\"\"get file from object name to local filepath\"\"\" logger . debug ( \"fget: {} : {} \" . format ( self . bucket , name )) name = str ( name ) stat = self . client . stat_object ( self . bucket , name ) meta = { k . lower () . lstrip ( \"x-amz-meta\" ): v for k , v in stat . metadata . items ()} data = self . client . get_object ( self . bucket , name ) local_filepath = Path ( local_filepath ) local_filepath . parent . mkdir ( parents = True , exist_ok = True ) with local_filepath . open ( \"wb\" ) as f : for d in data . stream ( 1 << 16 ): f . write ( d ) if \"contents_hash\" in meta : return uuid . UUID ( meta [ \"contents_hash\" ]) def exists ( self , name ): logger . debug ( \"exists: {} : {} \" . format ( self . bucket , name )) try : self . client . stat_object ( self . bucket , str ( name )) except minio . error . S3Error as e : if e . code == \"NoSuchKey\" : return False else : raise e return True def get_size ( self , name ): logger . debug ( \"get_size: {} : {} \" . format ( self . bucket , name )) try : return self . client . stat_object ( self . bucket , str ( name )) . size except minio . error . S3Error as e : if e . code == \"NoSuchKey\" : raise errors . MissingExternalFile raise e def remove_object ( self , name ): logger . debug ( \"remove_object: {} : {} \" . format ( self . bucket , name )) try : self . client . remove_object ( self . bucket , str ( name )) except minio . error . MinioException : raise errors . DataJointError ( \"Failed to delete %s from s3 storage\" % name ) fget ( name , local_filepath ) \u00b6 get file from object name to local filepath Source code in datajoint/s3.py 78 79 80 81 82 83 84 85 86 87 88 89 90 91 def fget ( self , name , local_filepath ): \"\"\"get file from object name to local filepath\"\"\" logger . debug ( \"fget: {} : {} \" . format ( self . bucket , name )) name = str ( name ) stat = self . client . stat_object ( self . bucket , name ) meta = { k . lower () . lstrip ( \"x-amz-meta\" ): v for k , v in stat . metadata . items ()} data = self . client . get_object ( self . bucket , name ) local_filepath = Path ( local_filepath ) local_filepath . parent . mkdir ( parents = True , exist_ok = True ) with local_filepath . open ( \"wb\" ) as f : for d in data . stream ( 1 << 16 ): f . write ( d ) if \"contents_hash\" in meta : return uuid . UUID ( meta [ \"contents_hash\" ])", "title": "s3.py"}, {"location": "api/datajoint/s3/#datajoint.s3.Folder", "text": "A Folder instance manipulates a flat folder of objects within an S3-compatible object store Source code in datajoint/s3.py 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 class Folder : \"\"\" A Folder instance manipulates a flat folder of objects within an S3-compatible object store \"\"\" def __init__ ( self , endpoint , bucket , access_key , secret_key , * , secure = False , proxy_server = None , ** _ ): # from https://docs.min.io/docs/python-client-api-reference self . client = minio . Minio ( endpoint , access_key = access_key , secret_key = secret_key , secure = secure , http_client = ( urllib3 . ProxyManager ( proxy_server , timeout = urllib3 . Timeout . DEFAULT_TIMEOUT , cert_reqs = \"CERT_REQUIRED\" , retries = urllib3 . Retry ( total = 5 , backoff_factor = 0.2 , status_forcelist = [ 500 , 502 , 503 , 504 ], ), ) if proxy_server else None ), ) self . bucket = bucket if not self . client . bucket_exists ( bucket ): raise errors . BucketInaccessible ( \"Inaccessible s3 bucket %s \" % bucket ) def put ( self , name , buffer ): logger . debug ( \"put: {} : {} \" . format ( self . bucket , name )) return self . client . put_object ( self . bucket , str ( name ), BytesIO ( buffer ), length = len ( buffer ) ) def fput ( self , local_file , name , metadata = None ): logger . debug ( \"fput: {} -> {} : {} \" . format ( self . bucket , local_file , name )) return self . client . fput_object ( self . bucket , str ( name ), str ( local_file ), metadata = metadata ) def get ( self , name ): logger . debug ( \"get: {} : {} \" . format ( self . bucket , name )) try : return self . client . get_object ( self . bucket , str ( name )) . data except minio . error . S3Error as e : if e . code == \"NoSuchKey\" : raise errors . MissingExternalFile ( \"Missing s3 key %s \" % name ) else : raise e def fget ( self , name , local_filepath ): \"\"\"get file from object name to local filepath\"\"\" logger . debug ( \"fget: {} : {} \" . format ( self . bucket , name )) name = str ( name ) stat = self . client . stat_object ( self . bucket , name ) meta = { k . lower () . lstrip ( \"x-amz-meta\" ): v for k , v in stat . metadata . items ()} data = self . client . get_object ( self . bucket , name ) local_filepath = Path ( local_filepath ) local_filepath . parent . mkdir ( parents = True , exist_ok = True ) with local_filepath . open ( \"wb\" ) as f : for d in data . stream ( 1 << 16 ): f . write ( d ) if \"contents_hash\" in meta : return uuid . UUID ( meta [ \"contents_hash\" ]) def exists ( self , name ): logger . debug ( \"exists: {} : {} \" . format ( self . bucket , name )) try : self . client . stat_object ( self . bucket , str ( name )) except minio . error . S3Error as e : if e . code == \"NoSuchKey\" : return False else : raise e return True def get_size ( self , name ): logger . debug ( \"get_size: {} : {} \" . format ( self . bucket , name )) try : return self . client . stat_object ( self . bucket , str ( name )) . size except minio . error . S3Error as e : if e . code == \"NoSuchKey\" : raise errors . MissingExternalFile raise e def remove_object ( self , name ): logger . debug ( \"remove_object: {} : {} \" . format ( self . bucket , name )) try : self . client . remove_object ( self . bucket , str ( name )) except minio . error . MinioException : raise errors . DataJointError ( \"Failed to delete %s from s3 storage\" % name )", "title": "Folder"}, {"location": "api/datajoint/s3/#datajoint.s3.Folder.fget", "text": "get file from object name to local filepath Source code in datajoint/s3.py 78 79 80 81 82 83 84 85 86 87 88 89 90 91 def fget ( self , name , local_filepath ): \"\"\"get file from object name to local filepath\"\"\" logger . debug ( \"fget: {} : {} \" . format ( self . bucket , name )) name = str ( name ) stat = self . client . stat_object ( self . bucket , name ) meta = { k . lower () . lstrip ( \"x-amz-meta\" ): v for k , v in stat . metadata . items ()} data = self . client . get_object ( self . bucket , name ) local_filepath = Path ( local_filepath ) local_filepath . parent . mkdir ( parents = True , exist_ok = True ) with local_filepath . open ( \"wb\" ) as f : for d in data . stream ( 1 << 16 ): f . write ( d ) if \"contents_hash\" in meta : return uuid . UUID ( meta [ \"contents_hash\" ])", "title": "fget()"}, {"location": "api/datajoint/schemas/", "text": "ordered_dir ( class_ ) \u00b6 List (most) attributes of the class including inherited ones, similar to dir build-in function, but respects order of attribute declaration as much as possible. Parameters: Name Type Description Default class_ class to list members for required Returns: Type Description a list of attributes declared in class_ and its superclasses Source code in datajoint/schemas.py 22 23 24 25 26 27 28 29 30 31 32 33 def ordered_dir ( class_ ): \"\"\" List (most) attributes of the class including inherited ones, similar to `dir` build-in function, but respects order of attribute declaration as much as possible. :param class_: class to list members for :return: a list of attributes declared in class_ and its superclasses \"\"\" attr_list = list () for c in reversed ( class_ . mro ()): attr_list . extend ( e for e in c . __dict__ if e not in attr_list ) return attr_list Schema \u00b6 A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace context in which other UserTable classes are defined. Source code in datajoint/schemas.py 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 class Schema : \"\"\" A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace `context` in which other UserTable classes are defined. \"\"\" def __init__ ( self , schema_name = None , context = None , * , connection = None , create_schema = True , create_tables = True , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. If the schema_name is omitted, then schema.activate(..) must be called later to associate with the database. :param schema_name: the database schema to associate. :param context: dictionary for looking up foreign key references, leave None to use local context. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: When False, do not create the schema and raise an error if missing. :param create_tables: When False, do not create tables and raise errors when accessing missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" self . _log = None self . connection = connection self . database = None self . context = context self . create_schema = create_schema self . create_tables = create_tables self . _jobs = None self . external = ExternalMapping ( self ) self . add_objects = add_objects self . declare_list = [] if schema_name : self . activate ( schema_name ) def is_activated ( self ): return self . database is not None def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context ) def _assert_exists ( self , message = None ): if not self . exists : raise DataJointError ( message or \"Schema ` {db} ` has not been created.\" . format ( db = self . database ) ) def __call__ ( self , cls , * , context = None ): \"\"\" Binds the supplied class to a schema. This is intended to be used as a decorator. :param cls: class to decorate. :param context: supplied when called from spawn_missing_classes \"\"\" context = context or self . context or inspect . currentframe () . f_back . f_locals if issubclass ( cls , Part ): raise DataJointError ( \"The schema decorator should not be applied to Part tables.\" ) if self . is_activated (): self . _decorate_master ( cls , context ) else : self . declare_list . append (( cls , context )) return cls def _decorate_master ( self , cls , context ): \"\"\" :param cls: the master class to process :param context: the class' declaration context \"\"\" self . _decorate_table ( cls , context = dict ( context , self = cls , ** { cls . __name__ : cls }) ) # Process part tables for part in ordered_dir ( cls ): if part [ 0 ] . isupper (): part = getattr ( cls , part ) if inspect . isclass ( part ) and issubclass ( part , Part ): part . _master = cls # allow addressing master by name or keyword 'master' self . _decorate_table ( part , context = dict ( context , master = cls , self = part , ** { cls . __name__ : cls } ), ) def _decorate_table ( self , table_class , context , assert_declared = False ): \"\"\" assign schema properties to the table class and declare the table \"\"\" table_class . database = self . database table_class . _connection = self . connection table_class . _heading = Heading ( table_info = dict ( conn = self . connection , database = self . database , table_name = table_class . table_name , context = context , ) ) table_class . _support = [ table_class . full_table_name ] table_class . declaration_context = context # instantiate the class, declare the table if not already instance = table_class () is_declared = instance . is_declared if not is_declared and not assert_declared and self . create_tables : instance . declare ( context ) self . connection . dependencies . clear () is_declared = is_declared or instance . is_declared # add table definition to the doc string if isinstance ( table_class . definition , str ): table_class . __doc__ = ( ( table_class . __doc__ or \"\" ) + \" \\n Table definition: \\n\\n \" + table_class . definition ) # fill values in Lookup tables from their contents property if ( isinstance ( instance , Lookup ) and hasattr ( instance , \"contents\" ) and is_declared ): contents = list ( instance . contents ) if len ( contents ) > len ( instance ): if instance . heading . has_autoincrement : warnings . warn ( ( \"Contents has changed but cannot be inserted because \" \" {table} has autoincrement.\" ) . format ( table = instance . __class__ . __name__ ) ) else : instance . insert ( contents , skip_duplicates = True ) @property def log ( self ): self . _assert_exists () if self . _log is None : self . _log = Log ( self . connection , self . database ) return self . _log def __repr__ ( self ): return \"Schema ` {name} ` \\n \" . format ( name = self . database ) @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] ) def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class ) def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) ) @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount ) @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs @property def code ( self ): self . _assert_exists () return self . save () def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code ) def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ] activate ( schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None ) \u00b6 Associate database schema schema_name . If the schema does not exist, attempt to create it on the server. Parameters: Name Type Description Default schema_name the database schema to associate. schema_name=None is used to assert that the schema has already been activated. None connection Connection object. Defaults to datajoint.conn(). None create_schema If False, do not create the schema and raise an error if missing. None create_tables If False, do not create tables and raise errors when attempting to access missing tables. None add_objects a mapping with additional objects to make available to the context in which table classes are declared. None Source code in datajoint/schemas.py 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context ) size_on_disk () property \u00b6 Returns: Type Description size of the entire schema in bytes Source code in datajoint/schemas.py 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] ) spawn_missing_classes ( context = None ) \u00b6 Creates the appropriate python user table classes from tables in the schema and places them in the context. Parameters: Name Type Description Default context alternative context to place the missing classes into, e.g. locals() None Source code in datajoint/schemas.py 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class ) drop ( force = False ) \u00b6 Drop the associated schema if it exists Source code in datajoint/schemas.py 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) ) exists () property \u00b6 Returns: Type Description true if the associated schema exists on the server Source code in datajoint/schemas.py 377 378 379 380 381 382 383 384 385 386 387 388 389 390 @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount ) jobs () property \u00b6 schema.jobs provides a view of the job reservation table for the schema Returns: Type Description jobs table Source code in datajoint/schemas.py 392 393 394 395 396 397 398 399 400 401 402 @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs save ( python_filename = None ) \u00b6 Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. Returns: Type Description a string containing the body of a complete Python module defining this schema. Source code in datajoint/schemas.py 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code ) list_tables () \u00b6 Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job Returns: Type Description A list of table names from the database schema. Source code in datajoint/schemas.py 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ] VirtualModule \u00b6 Bases: types . ModuleType A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. Source code in datajoint/schemas.py 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 class VirtualModule ( types . ModuleType ): \"\"\" A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. \"\"\" def __init__ ( self , module_name , schema_name , * , create_schema = False , create_tables = False , connection = None , add_objects = None , ): \"\"\" Creates a python module with the given name from the name of a schema on the server and automatically adds classes to it corresponding to the tables in the schema. :param module_name: displayed module name :param schema_name: name of the database in mysql :param create_schema: if True, create the schema on the database server :param create_tables: if True, module.schema can be used as the decorator for declaring new :param connection: a dj.Connection object to pass into the schema :param add_objects: additional objects to add to the module :return: the python module containing classes from the schema object and the table classes \"\"\" super ( VirtualModule , self ) . __init__ ( name = module_name ) _schema = Schema ( schema_name , create_schema = create_schema , create_tables = create_tables , connection = connection , ) if add_objects : self . __dict__ . update ( add_objects ) self . __dict__ [ \"schema\" ] = _schema _schema . spawn_missing_classes ( context = self . __dict__ ) list_schemas ( connection = None ) \u00b6 Parameters: Name Type Description Default connection a dj.Connection object None Returns: Type Description list of all accessible schemas on the server Source code in datajoint/schemas.py 534 535 536 537 538 539 540 541 542 543 544 545 546 547 def list_schemas ( connection = None ): \"\"\" :param connection: a dj.Connection object :return: list of all accessible schemas on the server \"\"\" return [ r [ 0 ] for r in ( connection or conn ()) . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" 'WHERE schema_name <> \"information_schema\"' ) ]", "title": "schemas.py"}, {"location": "api/datajoint/schemas/#datajoint.schemas.ordered_dir", "text": "List (most) attributes of the class including inherited ones, similar to dir build-in function, but respects order of attribute declaration as much as possible. Parameters: Name Type Description Default class_ class to list members for required Returns: Type Description a list of attributes declared in class_ and its superclasses Source code in datajoint/schemas.py 22 23 24 25 26 27 28 29 30 31 32 33 def ordered_dir ( class_ ): \"\"\" List (most) attributes of the class including inherited ones, similar to `dir` build-in function, but respects order of attribute declaration as much as possible. :param class_: class to list members for :return: a list of attributes declared in class_ and its superclasses \"\"\" attr_list = list () for c in reversed ( class_ . mro ()): attr_list . extend ( e for e in c . __dict__ if e not in attr_list ) return attr_list", "title": "ordered_dir()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema", "text": "A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace context in which other UserTable classes are defined. Source code in datajoint/schemas.py 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 class Schema : \"\"\" A schema object is a decorator for UserTable classes that binds them to their database. It also specifies the namespace `context` in which other UserTable classes are defined. \"\"\" def __init__ ( self , schema_name = None , context = None , * , connection = None , create_schema = True , create_tables = True , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. If the schema_name is omitted, then schema.activate(..) must be called later to associate with the database. :param schema_name: the database schema to associate. :param context: dictionary for looking up foreign key references, leave None to use local context. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: When False, do not create the schema and raise an error if missing. :param create_tables: When False, do not create tables and raise errors when accessing missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" self . _log = None self . connection = connection self . database = None self . context = context self . create_schema = create_schema self . create_tables = create_tables self . _jobs = None self . external = ExternalMapping ( self ) self . add_objects = add_objects self . declare_list = [] if schema_name : self . activate ( schema_name ) def is_activated ( self ): return self . database is not None def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context ) def _assert_exists ( self , message = None ): if not self . exists : raise DataJointError ( message or \"Schema ` {db} ` has not been created.\" . format ( db = self . database ) ) def __call__ ( self , cls , * , context = None ): \"\"\" Binds the supplied class to a schema. This is intended to be used as a decorator. :param cls: class to decorate. :param context: supplied when called from spawn_missing_classes \"\"\" context = context or self . context or inspect . currentframe () . f_back . f_locals if issubclass ( cls , Part ): raise DataJointError ( \"The schema decorator should not be applied to Part tables.\" ) if self . is_activated (): self . _decorate_master ( cls , context ) else : self . declare_list . append (( cls , context )) return cls def _decorate_master ( self , cls , context ): \"\"\" :param cls: the master class to process :param context: the class' declaration context \"\"\" self . _decorate_table ( cls , context = dict ( context , self = cls , ** { cls . __name__ : cls }) ) # Process part tables for part in ordered_dir ( cls ): if part [ 0 ] . isupper (): part = getattr ( cls , part ) if inspect . isclass ( part ) and issubclass ( part , Part ): part . _master = cls # allow addressing master by name or keyword 'master' self . _decorate_table ( part , context = dict ( context , master = cls , self = part , ** { cls . __name__ : cls } ), ) def _decorate_table ( self , table_class , context , assert_declared = False ): \"\"\" assign schema properties to the table class and declare the table \"\"\" table_class . database = self . database table_class . _connection = self . connection table_class . _heading = Heading ( table_info = dict ( conn = self . connection , database = self . database , table_name = table_class . table_name , context = context , ) ) table_class . _support = [ table_class . full_table_name ] table_class . declaration_context = context # instantiate the class, declare the table if not already instance = table_class () is_declared = instance . is_declared if not is_declared and not assert_declared and self . create_tables : instance . declare ( context ) self . connection . dependencies . clear () is_declared = is_declared or instance . is_declared # add table definition to the doc string if isinstance ( table_class . definition , str ): table_class . __doc__ = ( ( table_class . __doc__ or \"\" ) + \" \\n Table definition: \\n\\n \" + table_class . definition ) # fill values in Lookup tables from their contents property if ( isinstance ( instance , Lookup ) and hasattr ( instance , \"contents\" ) and is_declared ): contents = list ( instance . contents ) if len ( contents ) > len ( instance ): if instance . heading . has_autoincrement : warnings . warn ( ( \"Contents has changed but cannot be inserted because \" \" {table} has autoincrement.\" ) . format ( table = instance . __class__ . __name__ ) ) else : instance . insert ( contents , skip_duplicates = True ) @property def log ( self ): self . _assert_exists () if self . _log is None : self . _log = Log ( self . connection , self . database ) return self . _log def __repr__ ( self ): return \"Schema ` {name} ` \\n \" . format ( name = self . database ) @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] ) def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class ) def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) ) @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount ) @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs @property def code ( self ): self . _assert_exists () return self . save () def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code ) def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ]", "title": "Schema"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.activate", "text": "Associate database schema schema_name . If the schema does not exist, attempt to create it on the server. Parameters: Name Type Description Default schema_name the database schema to associate. schema_name=None is used to assert that the schema has already been activated. None connection Connection object. Defaults to datajoint.conn(). None create_schema If False, do not create the schema and raise an error if missing. None create_tables If False, do not create tables and raise errors when attempting to access missing tables. None add_objects a mapping with additional objects to make available to the context in which table classes are declared. None Source code in datajoint/schemas.py 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 def activate ( self , schema_name = None , * , connection = None , create_schema = None , create_tables = None , add_objects = None , ): \"\"\" Associate database schema `schema_name`. If the schema does not exist, attempt to create it on the server. :param schema_name: the database schema to associate. schema_name=None is used to assert that the schema has already been activated. :param connection: Connection object. Defaults to datajoint.conn(). :param create_schema: If False, do not create the schema and raise an error if missing. :param create_tables: If False, do not create tables and raise errors when attempting to access missing tables. :param add_objects: a mapping with additional objects to make available to the context in which table classes are declared. \"\"\" if schema_name is None : if self . exists : return raise DataJointError ( \"Please provide a schema_name to activate the schema.\" ) if self . database is not None and self . exists : if self . database == schema_name : # already activated return raise DataJointError ( \"The schema is already activated for schema {db} .\" . format ( db = self . database ) ) if connection is not None : self . connection = connection if self . connection is None : self . connection = conn () self . database = schema_name if create_schema is not None : self . create_schema = create_schema if create_tables is not None : self . create_tables = create_tables if add_objects : self . add_objects = add_objects if not self . exists : if not self . create_schema or not self . database : raise DataJointError ( \"Database ` {name} ` has not yet been declared. \" \"Set argument create_schema=True to create it.\" . format ( name = schema_name ) ) # create database logger . debug ( \"Creating schema ` {name} `.\" . format ( name = schema_name )) try : self . connection . query ( \"CREATE DATABASE ` {name} `\" . format ( name = schema_name ) ) except AccessError : raise DataJointError ( \"Schema ` {name} ` does not exist and could not be created. \" \"Check permissions.\" . format ( name = schema_name ) ) else : self . log ( \"created\" ) self . connection . register ( self ) # decorate all tables already decorated for cls , context in self . declare_list : if self . add_objects : context = dict ( context , ** self . add_objects ) self . _decorate_master ( cls , context )", "title": "activate()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.size_on_disk", "text": "Returns: Type Description size of the entire schema in bytes Source code in datajoint/schemas.py 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 @property def size_on_disk ( self ): \"\"\" :return: size of the entire schema in bytes \"\"\" self . _assert_exists () return int ( self . connection . query ( \"\"\" SELECT SUM(data_length + index_length) FROM information_schema.tables WHERE table_schema='{db}' \"\"\" . format ( db = self . database ) ) . fetchone ()[ 0 ] )", "title": "size_on_disk()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.spawn_missing_classes", "text": "Creates the appropriate python user table classes from tables in the schema and places them in the context. Parameters: Name Type Description Default context alternative context to place the missing classes into, e.g. locals() None Source code in datajoint/schemas.py 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 def spawn_missing_classes ( self , context = None ): \"\"\" Creates the appropriate python user table classes from tables in the schema and places them in the context. :param context: alternative context to place the missing classes into, e.g. locals() \"\"\" self . _assert_exists () if context is None : if self . context is not None : context = self . context else : # if context is missing, use the calling namespace frame = inspect . currentframe () . f_back context = frame . f_locals del frame tables = [ row [ 0 ] for row in self . connection . query ( \"SHOW TABLES in ` %s `\" % self . database ) if lookup_class_name ( \"` {db} `.` {tab} `\" . format ( db = self . database , tab = row [ 0 ]), context , 0 ) is None ] master_classes = ( Lookup , Manual , Imported , Computed ) part_tables = [] for table_name in tables : class_name = to_camel_case ( table_name ) if class_name not in context : try : cls = next ( cls for cls in master_classes if re . fullmatch ( cls . tier_regexp , table_name ) ) except StopIteration : if re . fullmatch ( Part . tier_regexp , table_name ): part_tables . append ( table_name ) else : # declare and decorate master table classes context [ class_name ] = self ( type ( class_name , ( cls ,), dict ()), context = context ) # attach parts to masters for table_name in part_tables : groups = re . fullmatch ( Part . tier_regexp , table_name ) . groupdict () class_name = to_camel_case ( groups [ \"part\" ]) try : master_class = context [ to_camel_case ( groups [ \"master\" ])] except KeyError : raise DataJointError ( \"The table %s does not follow DataJoint naming conventions\" % table_name ) part_class = type ( class_name , ( Part ,), dict ( definition =... )) part_class . _master = master_class self . _decorate_table ( part_class , context = context , assert_declared = True ) setattr ( master_class , class_name , part_class )", "title": "spawn_missing_classes()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.drop", "text": "Drop the associated schema if it exists Source code in datajoint/schemas.py 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 def drop ( self , force = False ): \"\"\" Drop the associated schema if it exists \"\"\" if not self . exists : logger . info ( \"Schema named ` {database} ` does not exist. Doing nothing.\" . format ( database = self . database ) ) elif ( not config [ \"safemode\" ] or force or user_choice ( \"Proceed to delete entire schema ` %s `?\" % self . database , default = \"no\" ) == \"yes\" ): logger . debug ( \"Dropping ` {database} `.\" . format ( database = self . database )) try : self . connection . query ( \"DROP DATABASE ` {database} `\" . format ( database = self . database ) ) logger . debug ( \"Schema ` {database} ` was dropped successfully.\" . format ( database = self . database ) ) except AccessError : raise AccessError ( \"An attempt to drop schema ` {database} ` \" \"has failed. Check permissions.\" . format ( database = self . database ) )", "title": "drop()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.exists", "text": "Returns: Type Description true if the associated schema exists on the server Source code in datajoint/schemas.py 377 378 379 380 381 382 383 384 385 386 387 388 389 390 @property def exists ( self ): \"\"\" :return: true if the associated schema exists on the server \"\"\" if self . database is None : raise DataJointError ( \"Schema must be activated first.\" ) return bool ( self . connection . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" \"WHERE schema_name = ' {database} '\" . format ( database = self . database ) ) . rowcount )", "title": "exists()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.jobs", "text": "schema.jobs provides a view of the job reservation table for the schema Returns: Type Description jobs table Source code in datajoint/schemas.py 392 393 394 395 396 397 398 399 400 401 402 @property def jobs ( self ): \"\"\" schema.jobs provides a view of the job reservation table for the schema :return: jobs table \"\"\" self . _assert_exists () if self . _jobs is None : self . _jobs = JobTable ( self . connection , self . database ) return self . _jobs", "title": "jobs()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.save", "text": "Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. Returns: Type Description a string containing the body of a complete Python module defining this schema. Source code in datajoint/schemas.py 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 def save ( self , python_filename = None ): \"\"\" Generate the code for a module that recreates the schema. This method is in preparation for a future release and is not officially supported. :return: a string containing the body of a complete Python module defining this schema. \"\"\" self . _assert_exists () module_count = itertools . count () # add virtual modules for referenced modules with names vmod0, vmod1, ... module_lookup = collections . defaultdict ( lambda : \"vmod\" + str ( next ( module_count )) ) db = self . database def make_class_definition ( table ): tier = _get_tier ( table ) . __name__ class_name = table . split ( \".\" )[ 1 ] . strip ( \"`\" ) indent = \"\" if tier == \"Part\" : class_name = class_name . split ( \"__\" )[ - 1 ] indent += \" \" class_name = to_camel_case ( class_name ) def replace ( s ): d , tabs = s . group ( 1 ), s . group ( 2 ) return ( \"\" if d == db else ( module_lookup [ d ] + \".\" )) + \".\" . join ( to_camel_case ( tab ) for tab in tabs . lstrip ( \"__\" ) . split ( \"__\" ) ) return ( \"\" if tier == \"Part\" else \" \\n @schema \\n \" ) + ( \" {indent} class {class_name} (dj. {tier} ): \\n \" ' {indent} definition = \"\"\" \\n ' ' {indent} {defi} \"\"\"' ) . format ( class_name = class_name , indent = indent , tier = tier , defi = re . sub ( r \"`([^`]+)`.`([^`]+)`\" , replace , FreeTable ( self . connection , table ) . describe ( printout = False ), ) . replace ( \" \\n \" , \" \\n \" + indent ), ) diagram = Diagram ( self ) body = \" \\n\\n \" . join ( make_class_definition ( table ) for table in diagram . topological_sort () ) python_code = \" \\n\\n \" . join ( ( '\"\"\"This module was auto-generated by datajoint from an existing schema\"\"\"' , \"import datajoint as dj \\n\\n schema = dj.Schema(' {db} ')\" . format ( db = db ), \" \\n \" . join ( \" {module} = dj.VirtualModule(' {module} ', ' {schema_name} ')\" . format ( module = v , schema_name = k ) for k , v in module_lookup . items () ), body , ) ) if python_filename is None : return python_code with open ( python_filename , \"wt\" ) as f : f . write ( python_code )", "title": "save()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.Schema.list_tables", "text": "Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job Returns: Type Description A list of table names from the database schema. Source code in datajoint/schemas.py 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 def list_tables ( self ): \"\"\" Return a list of all tables in the schema except tables with ~ in first character such as ~logs and ~job :return: A list of table names from the database schema. \"\"\" return [ t for d , t in ( full_t . replace ( \"`\" , \"\" ) . split ( \".\" ) for full_t in Diagram ( self ) . topological_sort () ) if d == self . database ]", "title": "list_tables()"}, {"location": "api/datajoint/schemas/#datajoint.schemas.VirtualModule", "text": "Bases: types . ModuleType A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. Source code in datajoint/schemas.py 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 class VirtualModule ( types . ModuleType ): \"\"\" A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. It declares the schema objects and a class for each table. \"\"\" def __init__ ( self , module_name , schema_name , * , create_schema = False , create_tables = False , connection = None , add_objects = None , ): \"\"\" Creates a python module with the given name from the name of a schema on the server and automatically adds classes to it corresponding to the tables in the schema. :param module_name: displayed module name :param schema_name: name of the database in mysql :param create_schema: if True, create the schema on the database server :param create_tables: if True, module.schema can be used as the decorator for declaring new :param connection: a dj.Connection object to pass into the schema :param add_objects: additional objects to add to the module :return: the python module containing classes from the schema object and the table classes \"\"\" super ( VirtualModule , self ) . __init__ ( name = module_name ) _schema = Schema ( schema_name , create_schema = create_schema , create_tables = create_tables , connection = connection , ) if add_objects : self . __dict__ . update ( add_objects ) self . __dict__ [ \"schema\" ] = _schema _schema . spawn_missing_classes ( context = self . __dict__ )", "title": "VirtualModule"}, {"location": "api/datajoint/schemas/#datajoint.schemas.list_schemas", "text": "Parameters: Name Type Description Default connection a dj.Connection object None Returns: Type Description list of all accessible schemas on the server Source code in datajoint/schemas.py 534 535 536 537 538 539 540 541 542 543 544 545 546 547 def list_schemas ( connection = None ): \"\"\" :param connection: a dj.Connection object :return: list of all accessible schemas on the server \"\"\" return [ r [ 0 ] for r in ( connection or conn ()) . query ( \"SELECT schema_name \" \"FROM information_schema.schemata \" 'WHERE schema_name <> \"information_schema\"' ) ]", "title": "list_schemas()"}, {"location": "api/datajoint/settings/", "text": "Settings for DataJoint. Config \u00b6 Bases: collections . abc . MutableMapping Source code in datajoint/settings.py 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 class Config ( collections . abc . MutableMapping ): instance = None def __init__ ( self , * args , ** kwargs ): if not Config . instance : Config . instance = Config . __Config ( * args , ** kwargs ) else : Config . instance . _conf . update ( dict ( * args , ** kwargs )) def __getattr__ ( self , name ): return getattr ( self . instance , name ) def __getitem__ ( self , item ): return self . instance . __getitem__ ( item ) def __setitem__ ( self , item , value ): self . instance . __setitem__ ( item , value ) def __str__ ( self ): return pprint . pformat ( self . instance . _conf , indent = 4 ) def __repr__ ( self ): return self . __str__ () def __delitem__ ( self , key ): del self . instance . _conf [ key ] def __iter__ ( self ): return iter ( self . instance . _conf ) def __len__ ( self ): return len ( self . instance . _conf ) def save ( self , filename , verbose = False ): \"\"\" Saves the settings in JSON format to the given file path. :param filename: filename of the local JSON settings file. :param verbose: report having saved the settings file \"\"\" with open ( filename , \"w\" ) as fid : json . dump ( self . _conf , fid , indent = 4 ) if verbose : logger . info ( \"Saved settings in \" + filename ) def load ( self , filename ): \"\"\" Updates the setting from config file in JSON format. :param filename: filename of the local JSON settings file. If None, the local config file is used. \"\"\" if filename is None : filename = LOCALCONFIG with open ( filename , \"r\" ) as fid : self . _conf . update ( json . load ( fid )) def save_local ( self , verbose = False ): \"\"\" saves the settings in the local config file \"\"\" self . save ( LOCALCONFIG , verbose ) def save_global ( self , verbose = False ): \"\"\" saves the settings in the global config file \"\"\" self . save ( os . path . expanduser ( os . path . join ( \"~\" , GLOBALCONFIG )), verbose ) def get_store_spec ( self , store ): \"\"\" find configuration of external stores for blobs and attachments \"\"\" try : spec = self [ \"stores\" ][ store ] except KeyError : raise DataJointError ( \"Storage {store} is requested but not configured\" . format ( store = store ) ) spec [ \"subfolding\" ] = spec . get ( \"subfolding\" , DEFAULT_SUBFOLDING ) spec_keys = { # REQUIRED in uppercase and allowed in lowercase \"file\" : ( \"PROTOCOL\" , \"LOCATION\" , \"subfolding\" , \"stage\" ), \"s3\" : ( \"PROTOCOL\" , \"ENDPOINT\" , \"BUCKET\" , \"ACCESS_KEY\" , \"SECRET_KEY\" , \"LOCATION\" , \"secure\" , \"subfolding\" , \"stage\" , \"proxy_server\" , ), } try : spec_keys = spec_keys [ spec . get ( \"protocol\" , \"\" ) . lower ()] except KeyError : raise DataJointError ( 'Missing or invalid protocol in dj.config[\"stores\"][\" {store} \"]' . format ( store = store ) ) # check that all required keys are present in spec try : raise DataJointError ( 'dj.config[\"stores\"][\" {store} \"] is missing \" {k} \"' . format ( store = store , k = next ( k . lower () for k in spec_keys if k . isupper () and k . lower () not in spec ), ) ) except StopIteration : pass # check that only allowed keys are present in spec try : raise DataJointError ( 'Invalid key \" {k} \" in dj.config[\"stores\"][\" {store} \"]' . format ( store = store , k = next ( k for k in spec if k . upper () not in spec_keys and k . lower () not in spec_keys ), ) ) except StopIteration : pass # no invalid keys return spec @contextmanager def __call__ ( self , ** kwargs ): \"\"\" The config object can also be used in a with statement to change the state of the configuration temporarily. kwargs to the context manager are the keys into config, where '.' is replaced by a double underscore '__'. The context manager yields the changed config object. Example: >>> import datajoint as dj >>> with dj.config(safemode=False, database__host=\"localhost\") as cfg: >>> # do dangerous stuff here \"\"\" try : backup = self . instance self . instance = Config . __Config ( self . instance . _conf ) new = { k . replace ( \"__\" , \".\" ): v for k , v in kwargs . items ()} self . instance . _conf . update ( new ) yield self except : self . instance = backup raise else : self . instance = backup class __Config : \"\"\" Stores datajoint settings. Behaves like a dictionary, but applies validator functions when certain keys are set. The default parameters are stored in datajoint.settings.default . If a local config file exists, the settings specified in this file override the default settings. \"\"\" def __init__ ( self , * args , ** kwargs ): self . _conf = dict ( default ) self . _conf . update ( dict ( * args , ** kwargs )) # use the free update to set keys def __getitem__ ( self , key ): return self . _conf [ key ] def __setitem__ ( self , key , value ): logger . debug ( \"Setting {0:s} to {1:s} \" . format ( str ( key ), str ( value ))) if validators [ key ]( value ): self . _conf [ key ] = value else : raise DataJointError ( \"Validator for {0:s} did not pass\" . format ( key )) save ( filename , verbose = False ) \u00b6 Saves the settings in JSON format to the given file path. Parameters: Name Type Description Default filename filename of the local JSON settings file. required verbose report having saved the settings file False Source code in datajoint/settings.py 98 99 100 101 102 103 104 105 106 107 108 def save ( self , filename , verbose = False ): \"\"\" Saves the settings in JSON format to the given file path. :param filename: filename of the local JSON settings file. :param verbose: report having saved the settings file \"\"\" with open ( filename , \"w\" ) as fid : json . dump ( self . _conf , fid , indent = 4 ) if verbose : logger . info ( \"Saved settings in \" + filename ) load ( filename ) \u00b6 Updates the setting from config file in JSON format. Parameters: Name Type Description Default filename filename of the local JSON settings file. If None, the local config file is used. required Source code in datajoint/settings.py 110 111 112 113 114 115 116 117 118 119 def load ( self , filename ): \"\"\" Updates the setting from config file in JSON format. :param filename: filename of the local JSON settings file. If None, the local config file is used. \"\"\" if filename is None : filename = LOCALCONFIG with open ( filename , \"r\" ) as fid : self . _conf . update ( json . load ( fid )) save_local ( verbose = False ) \u00b6 saves the settings in the local config file Source code in datajoint/settings.py 121 122 123 124 125 def save_local ( self , verbose = False ): \"\"\" saves the settings in the local config file \"\"\" self . save ( LOCALCONFIG , verbose ) save_global ( verbose = False ) \u00b6 saves the settings in the global config file Source code in datajoint/settings.py 127 128 129 130 131 def save_global ( self , verbose = False ): \"\"\" saves the settings in the global config file \"\"\" self . save ( os . path . expanduser ( os . path . join ( \"~\" , GLOBALCONFIG )), verbose ) get_store_spec ( store ) \u00b6 find configuration of external stores for blobs and attachments Source code in datajoint/settings.py 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 def get_store_spec ( self , store ): \"\"\" find configuration of external stores for blobs and attachments \"\"\" try : spec = self [ \"stores\" ][ store ] except KeyError : raise DataJointError ( \"Storage {store} is requested but not configured\" . format ( store = store ) ) spec [ \"subfolding\" ] = spec . get ( \"subfolding\" , DEFAULT_SUBFOLDING ) spec_keys = { # REQUIRED in uppercase and allowed in lowercase \"file\" : ( \"PROTOCOL\" , \"LOCATION\" , \"subfolding\" , \"stage\" ), \"s3\" : ( \"PROTOCOL\" , \"ENDPOINT\" , \"BUCKET\" , \"ACCESS_KEY\" , \"SECRET_KEY\" , \"LOCATION\" , \"secure\" , \"subfolding\" , \"stage\" , \"proxy_server\" , ), } try : spec_keys = spec_keys [ spec . get ( \"protocol\" , \"\" ) . lower ()] except KeyError : raise DataJointError ( 'Missing or invalid protocol in dj.config[\"stores\"][\" {store} \"]' . format ( store = store ) ) # check that all required keys are present in spec try : raise DataJointError ( 'dj.config[\"stores\"][\" {store} \"] is missing \" {k} \"' . format ( store = store , k = next ( k . lower () for k in spec_keys if k . isupper () and k . lower () not in spec ), ) ) except StopIteration : pass # check that only allowed keys are present in spec try : raise DataJointError ( 'Invalid key \" {k} \" in dj.config[\"stores\"][\" {store} \"]' . format ( store = store , k = next ( k for k in spec if k . upper () not in spec_keys and k . lower () not in spec_keys ), ) ) except StopIteration : pass # no invalid keys return spec", "title": "settings.py"}, {"location": "api/datajoint/settings/#datajoint.settings.Config", "text": "Bases: collections . abc . MutableMapping Source code in datajoint/settings.py 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 class Config ( collections . abc . MutableMapping ): instance = None def __init__ ( self , * args , ** kwargs ): if not Config . instance : Config . instance = Config . __Config ( * args , ** kwargs ) else : Config . instance . _conf . update ( dict ( * args , ** kwargs )) def __getattr__ ( self , name ): return getattr ( self . instance , name ) def __getitem__ ( self , item ): return self . instance . __getitem__ ( item ) def __setitem__ ( self , item , value ): self . instance . __setitem__ ( item , value ) def __str__ ( self ): return pprint . pformat ( self . instance . _conf , indent = 4 ) def __repr__ ( self ): return self . __str__ () def __delitem__ ( self , key ): del self . instance . _conf [ key ] def __iter__ ( self ): return iter ( self . instance . _conf ) def __len__ ( self ): return len ( self . instance . _conf ) def save ( self , filename , verbose = False ): \"\"\" Saves the settings in JSON format to the given file path. :param filename: filename of the local JSON settings file. :param verbose: report having saved the settings file \"\"\" with open ( filename , \"w\" ) as fid : json . dump ( self . _conf , fid , indent = 4 ) if verbose : logger . info ( \"Saved settings in \" + filename ) def load ( self , filename ): \"\"\" Updates the setting from config file in JSON format. :param filename: filename of the local JSON settings file. If None, the local config file is used. \"\"\" if filename is None : filename = LOCALCONFIG with open ( filename , \"r\" ) as fid : self . _conf . update ( json . load ( fid )) def save_local ( self , verbose = False ): \"\"\" saves the settings in the local config file \"\"\" self . save ( LOCALCONFIG , verbose ) def save_global ( self , verbose = False ): \"\"\" saves the settings in the global config file \"\"\" self . save ( os . path . expanduser ( os . path . join ( \"~\" , GLOBALCONFIG )), verbose ) def get_store_spec ( self , store ): \"\"\" find configuration of external stores for blobs and attachments \"\"\" try : spec = self [ \"stores\" ][ store ] except KeyError : raise DataJointError ( \"Storage {store} is requested but not configured\" . format ( store = store ) ) spec [ \"subfolding\" ] = spec . get ( \"subfolding\" , DEFAULT_SUBFOLDING ) spec_keys = { # REQUIRED in uppercase and allowed in lowercase \"file\" : ( \"PROTOCOL\" , \"LOCATION\" , \"subfolding\" , \"stage\" ), \"s3\" : ( \"PROTOCOL\" , \"ENDPOINT\" , \"BUCKET\" , \"ACCESS_KEY\" , \"SECRET_KEY\" , \"LOCATION\" , \"secure\" , \"subfolding\" , \"stage\" , \"proxy_server\" , ), } try : spec_keys = spec_keys [ spec . get ( \"protocol\" , \"\" ) . lower ()] except KeyError : raise DataJointError ( 'Missing or invalid protocol in dj.config[\"stores\"][\" {store} \"]' . format ( store = store ) ) # check that all required keys are present in spec try : raise DataJointError ( 'dj.config[\"stores\"][\" {store} \"] is missing \" {k} \"' . format ( store = store , k = next ( k . lower () for k in spec_keys if k . isupper () and k . lower () not in spec ), ) ) except StopIteration : pass # check that only allowed keys are present in spec try : raise DataJointError ( 'Invalid key \" {k} \" in dj.config[\"stores\"][\" {store} \"]' . format ( store = store , k = next ( k for k in spec if k . upper () not in spec_keys and k . lower () not in spec_keys ), ) ) except StopIteration : pass # no invalid keys return spec @contextmanager def __call__ ( self , ** kwargs ): \"\"\" The config object can also be used in a with statement to change the state of the configuration temporarily. kwargs to the context manager are the keys into config, where '.' is replaced by a double underscore '__'. The context manager yields the changed config object. Example: >>> import datajoint as dj >>> with dj.config(safemode=False, database__host=\"localhost\") as cfg: >>> # do dangerous stuff here \"\"\" try : backup = self . instance self . instance = Config . __Config ( self . instance . _conf ) new = { k . replace ( \"__\" , \".\" ): v for k , v in kwargs . items ()} self . instance . _conf . update ( new ) yield self except : self . instance = backup raise else : self . instance = backup class __Config : \"\"\" Stores datajoint settings. Behaves like a dictionary, but applies validator functions when certain keys are set. The default parameters are stored in datajoint.settings.default . If a local config file exists, the settings specified in this file override the default settings. \"\"\" def __init__ ( self , * args , ** kwargs ): self . _conf = dict ( default ) self . _conf . update ( dict ( * args , ** kwargs )) # use the free update to set keys def __getitem__ ( self , key ): return self . _conf [ key ] def __setitem__ ( self , key , value ): logger . debug ( \"Setting {0:s} to {1:s} \" . format ( str ( key ), str ( value ))) if validators [ key ]( value ): self . _conf [ key ] = value else : raise DataJointError ( \"Validator for {0:s} did not pass\" . format ( key ))", "title": "Config"}, {"location": "api/datajoint/settings/#datajoint.settings.Config.save", "text": "Saves the settings in JSON format to the given file path. Parameters: Name Type Description Default filename filename of the local JSON settings file. required verbose report having saved the settings file False Source code in datajoint/settings.py 98 99 100 101 102 103 104 105 106 107 108 def save ( self , filename , verbose = False ): \"\"\" Saves the settings in JSON format to the given file path. :param filename: filename of the local JSON settings file. :param verbose: report having saved the settings file \"\"\" with open ( filename , \"w\" ) as fid : json . dump ( self . _conf , fid , indent = 4 ) if verbose : logger . info ( \"Saved settings in \" + filename )", "title": "save()"}, {"location": "api/datajoint/settings/#datajoint.settings.Config.load", "text": "Updates the setting from config file in JSON format. Parameters: Name Type Description Default filename filename of the local JSON settings file. If None, the local config file is used. required Source code in datajoint/settings.py 110 111 112 113 114 115 116 117 118 119 def load ( self , filename ): \"\"\" Updates the setting from config file in JSON format. :param filename: filename of the local JSON settings file. If None, the local config file is used. \"\"\" if filename is None : filename = LOCALCONFIG with open ( filename , \"r\" ) as fid : self . _conf . update ( json . load ( fid ))", "title": "load()"}, {"location": "api/datajoint/settings/#datajoint.settings.Config.save_local", "text": "saves the settings in the local config file Source code in datajoint/settings.py 121 122 123 124 125 def save_local ( self , verbose = False ): \"\"\" saves the settings in the local config file \"\"\" self . save ( LOCALCONFIG , verbose )", "title": "save_local()"}, {"location": "api/datajoint/settings/#datajoint.settings.Config.save_global", "text": "saves the settings in the global config file Source code in datajoint/settings.py 127 128 129 130 131 def save_global ( self , verbose = False ): \"\"\" saves the settings in the global config file \"\"\" self . save ( os . path . expanduser ( os . path . join ( \"~\" , GLOBALCONFIG )), verbose )", "title": "save_global()"}, {"location": "api/datajoint/settings/#datajoint.settings.Config.get_store_spec", "text": "find configuration of external stores for blobs and attachments Source code in datajoint/settings.py 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 def get_store_spec ( self , store ): \"\"\" find configuration of external stores for blobs and attachments \"\"\" try : spec = self [ \"stores\" ][ store ] except KeyError : raise DataJointError ( \"Storage {store} is requested but not configured\" . format ( store = store ) ) spec [ \"subfolding\" ] = spec . get ( \"subfolding\" , DEFAULT_SUBFOLDING ) spec_keys = { # REQUIRED in uppercase and allowed in lowercase \"file\" : ( \"PROTOCOL\" , \"LOCATION\" , \"subfolding\" , \"stage\" ), \"s3\" : ( \"PROTOCOL\" , \"ENDPOINT\" , \"BUCKET\" , \"ACCESS_KEY\" , \"SECRET_KEY\" , \"LOCATION\" , \"secure\" , \"subfolding\" , \"stage\" , \"proxy_server\" , ), } try : spec_keys = spec_keys [ spec . get ( \"protocol\" , \"\" ) . lower ()] except KeyError : raise DataJointError ( 'Missing or invalid protocol in dj.config[\"stores\"][\" {store} \"]' . format ( store = store ) ) # check that all required keys are present in spec try : raise DataJointError ( 'dj.config[\"stores\"][\" {store} \"] is missing \" {k} \"' . format ( store = store , k = next ( k . lower () for k in spec_keys if k . isupper () and k . lower () not in spec ), ) ) except StopIteration : pass # check that only allowed keys are present in spec try : raise DataJointError ( 'Invalid key \" {k} \" in dj.config[\"stores\"][\" {store} \"]' . format ( store = store , k = next ( k for k in spec if k . upper () not in spec_keys and k . lower () not in spec_keys ), ) ) except StopIteration : pass # no invalid keys return spec", "title": "get_store_spec()"}, {"location": "api/datajoint/table/", "text": "Table \u00b6 Bases: QueryExpression Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. Source code in datajoint/table.py 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 class Table ( QueryExpression ): \"\"\" Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. \"\"\" _table_name = None # must be defined in subclass _log_ = None # placeholder for the Log table object # These properties must be set by the schema decorator (schemas.py) at class level # or by FreeTable at instance level database = None declaration_context = None @property def table_name ( self ): return self . _table_name @property def definition ( self ): raise NotImplementedError ( \"Subclasses of Table must implement the `definition` property\" ) def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name ) def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name ) def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql ) def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ] def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ] def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 ) @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name ) @property def _log ( self ): if self . _log_ is None : self . _log_ = Log ( self . connection , database = self . database , skip_logging = self . table_name . startswith ( \"~\" ), ) return self . _log_ @property def external ( self ): return self . connection . schemas [ self . database ] . external def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None )) def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs ) def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" ) def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name ) def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" ) @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ] def show_definition ( self ): raise AttributeError ( \"show_definition is deprecated. Use the describe method instead.\" ) def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition def _update ( self , attrname , value = None ): \"\"\" This is a deprecated function to be removed in datajoint 0.14. Use ``.update1`` instead. Updates a field in one existing tuple. self must be restricted to exactly one entry. In DataJoint the principal way of updating data is to delete and re-insert the entire record and updates are reserved for corrective actions. This is because referential integrity is observed on the level of entire records rather than individual attributes. Safety constraints: 1. self must be restricted to exactly one tuple 2. the update attribute must not be in primary key Example: >>> (v2p.Mice() & key)._update('mouse_dob', '2011-01-01') >>> (v2p.Mice() & key)._update( 'lens') # set the value to NULL \"\"\" logger . warning ( \"`_update` is a deprecated function to be removed in datajoint 0.14. \" \"Use `.update1` instead.\" ) if len ( self ) != 1 : raise DataJointError ( \"Update is only allowed on one tuple at a time\" ) if attrname not in self . heading : raise DataJointError ( \"Invalid attribute name\" ) if attrname in self . heading . primary_key : raise DataJointError ( \"Cannot update a key value.\" ) attr = self . heading [ attrname ] if attr . is_blob : value = blob . pack ( value ) placeholder = \" %s \" elif attr . numeric : if value is None or np . isnan ( float ( value )): # nans are turned into NULLs placeholder = \"NULL\" value = None else : placeholder = \" %s \" value = str ( int ( value ) if isinstance ( value , bool ) else value ) else : placeholder = \" %s \" if value is not None else \"NULL\" command = \"UPDATE {full_table_name} SET ` {attrname} `= {placeholder} {where_clause} \" . format ( full_table_name = self . from_clause (), attrname = attrname , placeholder = placeholder , where_clause = self . where_clause (), ) self . connection . query ( command , args = ( value ,) if value is not None else ()) # --- private helper functions ---- def __make_placeholder ( self , name , value , ignore_extra_fields = False ): \"\"\" For a given attribute `name` with `value`, return its processed value or value placeholder as a string to be included in the query and the value, if any, to be submitted for processing by mysql API. :param name: name of attribute to be inserted :param value: value of attribute to be inserted \"\"\" if ignore_extra_fields and name not in self . heading : return None attr = self . heading [ name ] if attr . adapter : value = attr . adapter . put ( value ) if value is None or ( attr . numeric and ( value == \"\" or np . isnan ( float ( value )))): # set default value placeholder , value = \"DEFAULT\" , None else : # not NULL placeholder = \" %s \" if attr . uuid : if not isinstance ( value , uuid . UUID ): try : value = uuid . UUID ( value ) except ( AttributeError , ValueError ): raise DataJointError ( \"badly formed UUID value {v} for attribute ` {n} `\" . format ( v = value , n = name ) ) value = value . bytes elif attr . is_blob : value = blob . pack ( value ) value = ( self . external [ attr . store ] . put ( value ) . bytes if attr . is_external else value ) elif attr . is_attachment : attachment_path = Path ( value ) if attr . is_external : # value is hash of contents value = ( self . external [ attr . store ] . upload_attachment ( attachment_path ) . bytes ) else : # value is filename + contents value = ( str . encode ( attachment_path . name ) + b \" \\0 \" + attachment_path . read_bytes () ) elif attr . is_filepath : value = self . external [ attr . store ] . upload_filepath ( value ) . bytes elif attr . numeric : value = str ( int ( value ) if isinstance ( value , bool ) else value ) return name , placeholder , value def __make_row_to_insert ( self , row , field_list , ignore_extra_fields ): \"\"\" Helper function for insert and update :param row: A tuple to insert :return: a dict with fields 'names', 'placeholders', 'values' \"\"\" def check_fields ( fields ): \"\"\" Validates that all items in `fields` are valid attributes in the heading :param fields: field names of a tuple \"\"\" if not field_list : if not ignore_extra_fields : for field in fields : if field not in self . heading : raise KeyError ( \"` {0:s} ` is not in the table heading\" . format ( field ) ) elif set ( field_list ) != set ( fields ) . intersection ( self . heading . names ): raise DataJointError ( \"Attempt to insert rows with different fields.\" ) if isinstance ( row , np . void ): # np.array check_fields ( row . dtype . fields ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row . dtype . fields ] elif isinstance ( row , collections . abc . Mapping ): # dict-based check_fields ( row ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row ] else : # positional try : if len ( row ) != len ( self . heading ): raise DataJointError ( \"Invalid insert argument. Incorrect number of attributes: \" \" {given} given; {expected} expected\" . format ( given = len ( row ), expected = len ( self . heading ) ) ) except TypeError : raise DataJointError ( \"Datatype %s cannot be inserted\" % type ( row )) else : attributes = [ self . __make_placeholder ( name , value , ignore_extra_fields ) for name , value in zip ( self . heading , row ) ] if ignore_extra_fields : attributes = [ a for a in attributes if a is not None ] assert len ( attributes ), \"Empty tuple\" row_to_insert = dict ( zip (( \"names\" , \"placeholders\" , \"values\" ), zip ( * attributes ))) if not field_list : # first row sets the composition of the field list field_list . extend ( row_to_insert [ \"names\" ]) else : # reorder attributes in row_to_insert to match field_list order = list ( row_to_insert [ \"names\" ] . index ( field ) for field in field_list ) row_to_insert [ \"names\" ] = list ( row_to_insert [ \"names\" ][ i ] for i in order ) row_to_insert [ \"placeholders\" ] = list ( row_to_insert [ \"placeholders\" ][ i ] for i in order ) row_to_insert [ \"values\" ] = list ( row_to_insert [ \"values\" ][ i ] for i in order ) return row_to_insert declare ( context = None ) \u00b6 Declare the table in the schema based on self.definition. Parameters: Name Type Description Default context the context for foreign key resolution. If None, foreign keys are not allowed. None Source code in datajoint/table.py 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name ) alter ( prompt = True , context = None ) \u00b6 Alter the table definition from self.definition Source code in datajoint/table.py 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name ) from_clause () \u00b6 Returns: Type Description the FROM clause of SQL SELECT statements. Source code in datajoint/table.py 147 148 149 150 151 def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name get_select_fields ( select_fields = None ) \u00b6 Returns: Type Description the selected attributes from the SQL SELECT statement. Source code in datajoint/table.py 153 154 155 156 157 158 159 def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql ) parents ( primary = None , as_objects = False , foreign_key_info = False ) \u00b6 Parameters: Name Type Description Default primary if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of parents as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes children ( primary = None , as_objects = False , foreign_key_info = False ) \u00b6 Parameters: Name Type Description Default primary if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of children as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes descendants ( as_objects = False ) \u00b6 Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables descendants in topological order. Source code in datajoint/table.py 205 206 207 208 209 210 211 212 213 214 215 def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ] ancestors ( as_objects = False ) \u00b6 Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables ancestors in topological order. Source code in datajoint/table.py 217 218 219 220 221 222 223 224 225 226 227 def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ] parts ( as_objects = False ) \u00b6 return part tables either as entries in a dict with foreign key informaiton or a list of objects Parameters: Name Type Description Default as_objects if False (default), the output is a dict describing the foreign keys. If True, return table objects. False Source code in datajoint/table.py 229 230 231 232 233 234 235 236 237 238 239 240 def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes is_declared () property \u00b6 Returns: Type Description True is the table is declared in the schema. Source code in datajoint/table.py 242 243 244 245 246 247 248 249 250 251 252 253 254 @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 ) full_table_name () property \u00b6 Returns: Type Description full table name in the schema Source code in datajoint/table.py 256 257 258 259 260 261 @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name ) update1 ( row ) \u00b6 update1 updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to insert and delete entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. Parameters: Name Type Description Default row a dict containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default required Source code in datajoint/table.py 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None )) insert1 ( row , ** kwargs ) \u00b6 Insert one data record into the table. For kwargs , see insert() . Parameters: Name Type Description Default row a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. required Source code in datajoint/table.py 328 329 330 331 332 333 334 335 def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs ) insert ( rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None ) \u00b6 Insert a collection of rows. Parameters: Name Type Description Default rows An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. required replace If True, replaces the existing tuple. False skip_duplicates If True, silently skip duplicate inserts. False ignore_extra_fields If False, fields that are not in the heading raise error. False allow_direct_insert applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) None Source code in datajoint/table.py 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" ) delete_quick ( get_count = False ) \u00b6 Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. Source code in datajoint/table.py 448 449 450 451 452 453 454 455 456 457 458 459 460 461 def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count delete ( transaction = True , safemode = None , force_parts = False ) \u00b6 Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If True , use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to False if this delete is nested within another transaction. safemode: If True , prohibit nested transactions and prompt to confirm. Default is dj.config['safemode'] . force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. Source code in datajoint/table.py 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count drop_quick () \u00b6 Drops the table without cascading to dependent tables and without user prompt. Source code in datajoint/table.py 614 615 616 617 618 619 620 621 622 623 624 625 626 def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name ) drop () \u00b6 Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. Source code in datajoint/table.py 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" ) size_on_disk () property \u00b6 Returns: Type Description size of data and indices in bytes on the storage device Source code in datajoint/table.py 664 665 666 667 668 669 670 671 672 673 674 675 @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ] describe ( context = None , printout = True ) \u00b6 Returns: Type Description the definition string for the query using DataJoint DDL. Source code in datajoint/table.py 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition lookup_class_name ( name , context , depth = 3 ) \u00b6 given a table name in the form schema_name . table_name , find its class in the context. Parameters: Name Type Description Default name schema_name . table_name required context dictionary representing the namespace required depth search depth into imported modules, helps avoid infinite recursion. 3 Returns: Type Description class name found in the context or None if not found Source code in datajoint/table.py 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 def lookup_class_name ( name , context , depth = 3 ): \"\"\" given a table name in the form `schema_name`.`table_name`, find its class in the context. :param name: `schema_name`.`table_name` :param context: dictionary representing the namespace :param depth: search depth into imported modules, helps avoid infinite recursion. :return: class name found in the context or None if not found \"\"\" # breadth-first search nodes = [ dict ( context = context , context_name = \"\" , depth = depth )] while nodes : node = nodes . pop ( 0 ) for member_name , member in node [ \"context\" ] . items (): if not member_name . startswith ( \"_\" ): # skip IPython's implicit variables if inspect . isclass ( member ) and issubclass ( member , Table ): if member . full_table_name == name : # found it! return \".\" . join ([ node [ \"context_name\" ], member_name ]) . lstrip ( \".\" ) try : # look for part tables parts = member . __dict__ except AttributeError : pass # not a UserTable -- cannot have part tables. else : for part in ( getattr ( member , p ) for p in parts if p [ 0 ] . isupper () and hasattr ( member , p ) ): if ( inspect . isclass ( part ) and issubclass ( part , Table ) and part . full_table_name == name ): return \".\" . join ( [ node [ \"context_name\" ], member_name , part . __name__ ] ) . lstrip ( \".\" ) elif ( node [ \"depth\" ] > 0 and inspect . ismodule ( member ) and member . __name__ != \"datajoint\" ): try : nodes . append ( dict ( context = dict ( inspect . getmembers ( member )), context_name = node [ \"context_name\" ] + \".\" + member_name , depth = node [ \"depth\" ] - 1 , ) ) except ImportError : pass # could not import, so do not attempt return None FreeTable \u00b6 Bases: Table A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. Parameters: Name Type Description Default conn a dj.Connection object required full_table_name in format database . table_name required Source code in datajoint/table.py 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 class FreeTable ( Table ): \"\"\" A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. :param conn: a dj.Connection object :param full_table_name: in format `database`.`table_name` \"\"\" def __init__ ( self , conn , full_table_name ): self . database , self . _table_name = ( s . strip ( \"`\" ) for s in full_table_name . split ( \".\" ) ) self . _connection = conn self . _support = [ full_table_name ] self . _heading = Heading ( table_info = dict ( conn = conn , database = self . database , table_name = self . table_name , context = None , ) ) def __repr__ ( self ): return ( \"FreeTable(` %s `.` %s `) \\n \" % ( self . database , self . _table_name ) + super () . __repr__ () ) Log \u00b6 Bases: Table The log table for each schema. Instances are callable. Calls log the time and identifying information along with the event. Parameters: Name Type Description Default skip_logging if True, then log entry is skipped by default. See call False Source code in datajoint/table.py 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 class Log ( Table ): \"\"\" The log table for each schema. Instances are callable. Calls log the time and identifying information along with the event. :param skip_logging: if True, then log entry is skipped by default. See __call__ \"\"\" _table_name = \"~log\" def __init__ ( self , conn , database , skip_logging = False ): self . database = database self . skip_logging = skip_logging self . _connection = conn self . _heading = Heading ( table_info = dict ( conn = conn , database = database , table_name = self . table_name , context = None ) ) self . _support = [ self . full_table_name ] self . _definition = \"\"\" # event logging table for ` {database} ` id :int unsigned auto_increment # event order id --- timestamp = CURRENT_TIMESTAMP : timestamp # event timestamp version :varchar(12) # datajoint version user :varchar(255) # user@host host=\"\" :varchar(255) # system hostname event=\"\" :varchar(255) # event message \"\"\" . format ( database = database ) super () . __init__ () if not self . is_declared : self . declare () self . connection . dependencies . clear () self . _user = self . connection . get_user () @property def definition ( self ): return self . _definition def __call__ ( self , event , skip_logging = None ): \"\"\" :param event: string to write into the log table :param skip_logging: If True then do not log. If None, then use self.skip_logging \"\"\" skip_logging = self . skip_logging if skip_logging is None else skip_logging if not skip_logging : try : self . insert1 ( dict ( user = self . _user , version = version + \"py\" , host = platform . uname () . node , event = event , ), skip_duplicates = True , ignore_extra_fields = True , ) except DataJointError : logger . info ( \"could not log event in table ~log\" ) def delete ( self ): \"\"\" bypass interactive prompts and cascading dependencies :return: number of deleted items \"\"\" return self . delete_quick ( get_count = True ) def drop ( self ): \"\"\"bypass interactive prompts and cascading dependencies\"\"\" self . drop_quick () delete () \u00b6 bypass interactive prompts and cascading dependencies Returns: Type Description number of deleted items Source code in datajoint/table.py 1102 1103 1104 1105 1106 1107 1108 def delete ( self ): \"\"\" bypass interactive prompts and cascading dependencies :return: number of deleted items \"\"\" return self . delete_quick ( get_count = True ) drop () \u00b6 bypass interactive prompts and cascading dependencies Source code in datajoint/table.py 1110 1111 1112 def drop ( self ): \"\"\"bypass interactive prompts and cascading dependencies\"\"\" self . drop_quick ()", "title": "table.py"}, {"location": "api/datajoint/table/#datajoint.table.Table", "text": "Bases: QueryExpression Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. Source code in datajoint/table.py 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 class Table ( QueryExpression ): \"\"\" Table is an abstract class that represents a table in the schema. It implements insert and delete methods and inherits query functionality. To make it a concrete class, override the abstract properties specifying the connection, table name, database, and definition. \"\"\" _table_name = None # must be defined in subclass _log_ = None # placeholder for the Log table object # These properties must be set by the schema decorator (schemas.py) at class level # or by FreeTable at instance level database = None declaration_context = None @property def table_name ( self ): return self . _table_name @property def definition ( self ): raise NotImplementedError ( \"Subclasses of Table must implement the `definition` property\" ) def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name ) def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name ) def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql ) def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ] def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ] def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 ) @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name ) @property def _log ( self ): if self . _log_ is None : self . _log_ = Log ( self . connection , database = self . database , skip_logging = self . table_name . startswith ( \"~\" ), ) return self . _log_ @property def external ( self ): return self . connection . schemas [ self . database ] . external def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None )) def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs ) def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" ) def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name ) def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" ) @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ] def show_definition ( self ): raise AttributeError ( \"show_definition is deprecated. Use the describe method instead.\" ) def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition def _update ( self , attrname , value = None ): \"\"\" This is a deprecated function to be removed in datajoint 0.14. Use ``.update1`` instead. Updates a field in one existing tuple. self must be restricted to exactly one entry. In DataJoint the principal way of updating data is to delete and re-insert the entire record and updates are reserved for corrective actions. This is because referential integrity is observed on the level of entire records rather than individual attributes. Safety constraints: 1. self must be restricted to exactly one tuple 2. the update attribute must not be in primary key Example: >>> (v2p.Mice() & key)._update('mouse_dob', '2011-01-01') >>> (v2p.Mice() & key)._update( 'lens') # set the value to NULL \"\"\" logger . warning ( \"`_update` is a deprecated function to be removed in datajoint 0.14. \" \"Use `.update1` instead.\" ) if len ( self ) != 1 : raise DataJointError ( \"Update is only allowed on one tuple at a time\" ) if attrname not in self . heading : raise DataJointError ( \"Invalid attribute name\" ) if attrname in self . heading . primary_key : raise DataJointError ( \"Cannot update a key value.\" ) attr = self . heading [ attrname ] if attr . is_blob : value = blob . pack ( value ) placeholder = \" %s \" elif attr . numeric : if value is None or np . isnan ( float ( value )): # nans are turned into NULLs placeholder = \"NULL\" value = None else : placeholder = \" %s \" value = str ( int ( value ) if isinstance ( value , bool ) else value ) else : placeholder = \" %s \" if value is not None else \"NULL\" command = \"UPDATE {full_table_name} SET ` {attrname} `= {placeholder} {where_clause} \" . format ( full_table_name = self . from_clause (), attrname = attrname , placeholder = placeholder , where_clause = self . where_clause (), ) self . connection . query ( command , args = ( value ,) if value is not None else ()) # --- private helper functions ---- def __make_placeholder ( self , name , value , ignore_extra_fields = False ): \"\"\" For a given attribute `name` with `value`, return its processed value or value placeholder as a string to be included in the query and the value, if any, to be submitted for processing by mysql API. :param name: name of attribute to be inserted :param value: value of attribute to be inserted \"\"\" if ignore_extra_fields and name not in self . heading : return None attr = self . heading [ name ] if attr . adapter : value = attr . adapter . put ( value ) if value is None or ( attr . numeric and ( value == \"\" or np . isnan ( float ( value )))): # set default value placeholder , value = \"DEFAULT\" , None else : # not NULL placeholder = \" %s \" if attr . uuid : if not isinstance ( value , uuid . UUID ): try : value = uuid . UUID ( value ) except ( AttributeError , ValueError ): raise DataJointError ( \"badly formed UUID value {v} for attribute ` {n} `\" . format ( v = value , n = name ) ) value = value . bytes elif attr . is_blob : value = blob . pack ( value ) value = ( self . external [ attr . store ] . put ( value ) . bytes if attr . is_external else value ) elif attr . is_attachment : attachment_path = Path ( value ) if attr . is_external : # value is hash of contents value = ( self . external [ attr . store ] . upload_attachment ( attachment_path ) . bytes ) else : # value is filename + contents value = ( str . encode ( attachment_path . name ) + b \" \\0 \" + attachment_path . read_bytes () ) elif attr . is_filepath : value = self . external [ attr . store ] . upload_filepath ( value ) . bytes elif attr . numeric : value = str ( int ( value ) if isinstance ( value , bool ) else value ) return name , placeholder , value def __make_row_to_insert ( self , row , field_list , ignore_extra_fields ): \"\"\" Helper function for insert and update :param row: A tuple to insert :return: a dict with fields 'names', 'placeholders', 'values' \"\"\" def check_fields ( fields ): \"\"\" Validates that all items in `fields` are valid attributes in the heading :param fields: field names of a tuple \"\"\" if not field_list : if not ignore_extra_fields : for field in fields : if field not in self . heading : raise KeyError ( \"` {0:s} ` is not in the table heading\" . format ( field ) ) elif set ( field_list ) != set ( fields ) . intersection ( self . heading . names ): raise DataJointError ( \"Attempt to insert rows with different fields.\" ) if isinstance ( row , np . void ): # np.array check_fields ( row . dtype . fields ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row . dtype . fields ] elif isinstance ( row , collections . abc . Mapping ): # dict-based check_fields ( row ) attributes = [ self . __make_placeholder ( name , row [ name ], ignore_extra_fields ) for name in self . heading if name in row ] else : # positional try : if len ( row ) != len ( self . heading ): raise DataJointError ( \"Invalid insert argument. Incorrect number of attributes: \" \" {given} given; {expected} expected\" . format ( given = len ( row ), expected = len ( self . heading ) ) ) except TypeError : raise DataJointError ( \"Datatype %s cannot be inserted\" % type ( row )) else : attributes = [ self . __make_placeholder ( name , value , ignore_extra_fields ) for name , value in zip ( self . heading , row ) ] if ignore_extra_fields : attributes = [ a for a in attributes if a is not None ] assert len ( attributes ), \"Empty tuple\" row_to_insert = dict ( zip (( \"names\" , \"placeholders\" , \"values\" ), zip ( * attributes ))) if not field_list : # first row sets the composition of the field list field_list . extend ( row_to_insert [ \"names\" ]) else : # reorder attributes in row_to_insert to match field_list order = list ( row_to_insert [ \"names\" ] . index ( field ) for field in field_list ) row_to_insert [ \"names\" ] = list ( row_to_insert [ \"names\" ][ i ] for i in order ) row_to_insert [ \"placeholders\" ] = list ( row_to_insert [ \"placeholders\" ][ i ] for i in order ) row_to_insert [ \"values\" ] = list ( row_to_insert [ \"values\" ][ i ] for i in order ) return row_to_insert", "title": "Table"}, {"location": "api/datajoint/table/#datajoint.table.Table.declare", "text": "Declare the table in the schema based on self.definition. Parameters: Name Type Description Default context the context for foreign key resolution. If None, foreign keys are not allowed. None Source code in datajoint/table.py 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 def declare ( self , context = None ): \"\"\" Declare the table in the schema based on self.definition. :param context: the context for foreign key resolution. If None, foreign keys are not allowed. \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot declare new tables inside a transaction, \" \"e.g. from inside a populate/make call\" ) sql , external_stores = declare ( self . full_table_name , self . definition , context ) sql = sql . format ( database = self . database ) try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : self . _log ( \"Declared \" + self . full_table_name )", "title": "declare()"}, {"location": "api/datajoint/table/#datajoint.table.Table.alter", "text": "Alter the table definition from self.definition Source code in datajoint/table.py 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 def alter ( self , prompt = True , context = None ): \"\"\" Alter the table definition from self.definition \"\"\" if self . connection . in_transaction : raise DataJointError ( \"Cannot update table declaration inside a transaction, \" \"e.g. from inside a populate/make call\" ) if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame old_definition = self . describe ( context = context , printout = False ) sql , external_stores = alter ( self . definition , old_definition , context ) if not sql : if prompt : print ( \"Nothing to alter.\" ) else : sql = \"ALTER TABLE {tab} \\n\\t \" . format ( tab = self . full_table_name ) + \", \\n\\t \" . join ( sql ) if not prompt or user_choice ( sql + \" \\n\\n Execute?\" ) == \"yes\" : try : # declare all external tables before declaring main table for store in external_stores : self . connection . schemas [ self . database ] . external [ store ] self . connection . query ( sql ) except AccessError : # skip if no create privilege pass else : # reset heading self . __class__ . _heading = Heading ( table_info = self . heading . table_info ) if prompt : print ( \"Table altered\" ) self . _log ( \"Altered \" + self . full_table_name )", "title": "alter()"}, {"location": "api/datajoint/table/#datajoint.table.Table.from_clause", "text": "Returns: Type Description the FROM clause of SQL SELECT statements. Source code in datajoint/table.py 147 148 149 150 151 def from_clause ( self ): \"\"\" :return: the FROM clause of SQL SELECT statements. \"\"\" return self . full_table_name", "title": "from_clause()"}, {"location": "api/datajoint/table/#datajoint.table.Table.get_select_fields", "text": "Returns: Type Description the selected attributes from the SQL SELECT statement. Source code in datajoint/table.py 153 154 155 156 157 158 159 def get_select_fields ( self , select_fields = None ): \"\"\" :return: the selected attributes from the SQL SELECT statement. \"\"\" return ( \"*\" if select_fields is None else self . heading . project ( select_fields ) . as_sql )", "title": "get_select_fields()"}, {"location": "api/datajoint/table/#datajoint.table.Table.parents", "text": "Parameters: Name Type Description Default primary if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of parents as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 def parents ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of parents as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . parents nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes", "title": "parents()"}, {"location": "api/datajoint/table/#datajoint.table.Table.children", "text": "Parameters: Name Type Description Default primary if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. None as_objects if False, return table names. If True, return table objects. False foreign_key_info if True, each element in result also includes foreign key info. False Returns: Type Description list of children as table names or table objects with (optional) foreign key information. Source code in datajoint/table.py 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 def children ( self , primary = None , as_objects = False , foreign_key_info = False ): \"\"\" :param primary: if None, then all children are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, return foreign keys including at least one secondary attribute. :param as_objects: if False, return table names. If True, return table objects. :param foreign_key_info: if True, each element in result also includes foreign key info. :return: list of children as table names or table objects with (optional) foreign key information. \"\"\" get_edge = self . connection . dependencies . children nodes = [ next ( iter ( get_edge ( name ) . items ())) if name . isdigit () else ( name , props ) for name , props in get_edge ( self . full_table_name , primary ) . items () ] if as_objects : nodes = [( FreeTable ( self . connection , name ), props ) for name , props in nodes ] if not foreign_key_info : nodes = [ name for name , props in nodes ] return nodes", "title": "children()"}, {"location": "api/datajoint/table/#datajoint.table.Table.descendants", "text": "Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables descendants in topological order. Source code in datajoint/table.py 205 206 207 208 209 210 211 212 213 214 215 def descendants ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables descendants in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . descendants ( self . full_table_name ) if not node . isdigit () ]", "title": "descendants()"}, {"location": "api/datajoint/table/#datajoint.table.Table.ancestors", "text": "Parameters: Name Type Description Default as_objects False - a list of table names; True - a list of table objects. False Returns: Type Description list of tables ancestors in topological order. Source code in datajoint/table.py 217 218 219 220 221 222 223 224 225 226 227 def ancestors ( self , as_objects = False ): \"\"\" :param as_objects: False - a list of table names; True - a list of table objects. :return: list of tables ancestors in topological order. \"\"\" return [ FreeTable ( self . connection , node ) if as_objects else node for node in self . connection . dependencies . ancestors ( self . full_table_name ) if not node . isdigit () ]", "title": "ancestors()"}, {"location": "api/datajoint/table/#datajoint.table.Table.parts", "text": "return part tables either as entries in a dict with foreign key informaiton or a list of objects Parameters: Name Type Description Default as_objects if False (default), the output is a dict describing the foreign keys. If True, return table objects. False Source code in datajoint/table.py 229 230 231 232 233 234 235 236 237 238 239 240 def parts ( self , as_objects = False ): \"\"\" return part tables either as entries in a dict with foreign key informaiton or a list of objects :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects. \"\"\" nodes = [ node for node in self . connection . dependencies . nodes if not node . isdigit () and node . startswith ( self . full_table_name [: - 1 ] + \"__\" ) ] return [ FreeTable ( self . connection , c ) for c in nodes ] if as_objects else nodes", "title": "parts()"}, {"location": "api/datajoint/table/#datajoint.table.Table.is_declared", "text": "Returns: Type Description True is the table is declared in the schema. Source code in datajoint/table.py 242 243 244 245 246 247 248 249 250 251 252 253 254 @property def is_declared ( self ): \"\"\" :return: True is the table is declared in the schema. \"\"\" return ( self . connection . query ( 'SHOW TABLES in ` {database} ` LIKE \" {table_name} \"' . format ( database = self . database , table_name = self . table_name ) ) . rowcount > 0 )", "title": "is_declared()"}, {"location": "api/datajoint/table/#datajoint.table.Table.full_table_name", "text": "Returns: Type Description full table name in the schema Source code in datajoint/table.py 256 257 258 259 260 261 @property def full_table_name ( self ): \"\"\" :return: full table name in the schema \"\"\" return r \"` {0:s} `.` {1:s} `\" . format ( self . database , self . table_name )", "title": "full_table_name()"}, {"location": "api/datajoint/table/#datajoint.table.Table.update1", "text": "update1 updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to insert and delete entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. Parameters: Name Type Description Default row a dict containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default required Source code in datajoint/table.py 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 def update1 ( self , row ): \"\"\" ``update1`` updates one existing entry in the table. Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and ``delete`` entire records since referential integrity works on the level of records, not fields. Therefore, updates are reserved for corrective operations outside of main workflow. Use UPDATE methods sparingly with full awareness of potential violations of assumptions. :param row: a ``dict`` containing the primary key values and the attributes to update. Setting an attribute value to None will reset it to the default value (if any). The primary key attributes must always be provided. Examples: >>> table.update1({'id': 1, 'value': 3}) # update value in record with id=1 >>> table.update1({'id': 1, 'value': None}) # reset value to default \"\"\" # argument validations if not isinstance ( row , collections . abc . Mapping ): raise DataJointError ( \"The argument of update1 must be dict-like.\" ) if not set ( row ) . issuperset ( self . primary_key ): raise DataJointError ( \"The argument of update1 must supply all primary key values.\" ) try : raise DataJointError ( \"Attribute ` %s ` not found.\" % next ( k for k in row if k not in self . heading . names ) ) except StopIteration : pass # ok if len ( self . restriction ): raise DataJointError ( \"Update cannot be applied to a restricted table.\" ) key = { k : row [ k ] for k in self . primary_key } if len ( self & key ) != 1 : raise DataJointError ( \"Update can only be applied to one existing entry.\" ) # UPDATE query row = [ self . __make_placeholder ( k , v ) for k , v in row . items () if k not in self . primary_key ] query = \"UPDATE {table} SET {assignments} WHERE {where} \" . format ( table = self . full_table_name , assignments = \",\" . join ( \"` %s `= %s \" % r [: 2 ] for r in row ), where = make_condition ( self , key , set ()), ) self . connection . query ( query , args = list ( r [ 2 ] for r in row if r [ 2 ] is not None ))", "title": "update1()"}, {"location": "api/datajoint/table/#datajoint.table.Table.insert1", "text": "Insert one data record into the table. For kwargs , see insert() . Parameters: Name Type Description Default row a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. required Source code in datajoint/table.py 328 329 330 331 332 333 334 335 def insert1 ( self , row , ** kwargs ): \"\"\" Insert one data record into the table. For ``kwargs``, see ``insert()``. :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row. \"\"\" self . insert (( row ,), ** kwargs )", "title": "insert1()"}, {"location": "api/datajoint/table/#datajoint.table.Table.insert", "text": "Insert a collection of rows. Parameters: Name Type Description Default rows An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. required replace If True, replaces the existing tuple. False skip_duplicates If True, silently skip duplicate inserts. False ignore_extra_fields If False, fields that are not in the heading raise error. False allow_direct_insert applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) None Source code in datajoint/table.py 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 def insert ( self , rows , replace = False , skip_duplicates = False , ignore_extra_fields = False , allow_direct_insert = None , ): \"\"\" Insert a collection of rows. :param rows: An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self. :param replace: If True, replaces the existing tuple. :param skip_duplicates: If True, silently skip duplicate inserts. :param ignore_extra_fields: If False, fields that are not in the heading raise error. :param allow_direct_insert: applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species=\"mouse\", date_of_birth=\"2014-09-01\"), >>> dict(subject_id=8, species=\"mouse\", date_of_birth=\"2014-09-02\")]) \"\"\" if isinstance ( rows , pandas . DataFrame ): # drop 'extra' synthetic index for 1-field index case - # frames with more advanced indices should be prepared by user. rows = rows . reset_index ( drop = len ( rows . index . names ) == 1 and not rows . index . names [ 0 ] ) . to_records ( index = False ) # prohibit direct inserts into auto-populated tables if not allow_direct_insert and not getattr ( self , \"_allow_insert\" , True ): raise DataJointError ( \"Inserts into an auto-populated table can only be done inside \" \"its make method during a populate call.\" \" To override, set keyword argument allow_direct_insert=True.\" ) if inspect . isclass ( rows ) and issubclass ( rows , QueryExpression ): rows = rows () # instantiate if a class if isinstance ( rows , QueryExpression ): # insert from select if not ignore_extra_fields : try : raise DataJointError ( \"Attribute %s not found. To ignore extra attributes in insert, \" \"set ignore_extra_fields=True.\" % next ( name for name in rows . heading if name not in self . heading ) ) except StopIteration : pass fields = list ( name for name in rows . heading if name in self . heading ) query = \" {command} INTO {table} ( {fields} ) {select}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , fields = \"`\" + \"`,`\" . join ( fields ) + \"`\" , table = self . full_table_name , select = rows . make_sql ( fields ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `= {table} .` {pk} `\" . format ( table = self . full_table_name , pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query ) return field_list = [] # collects the field list from first row (passed by reference) rows = list ( self . __make_row_to_insert ( row , field_list , ignore_extra_fields ) for row in rows ) if rows : try : query = \" {command} INTO {destination} (` {fields} `) VALUES {placeholders}{duplicate} \" . format ( command = \"REPLACE\" if replace else \"INSERT\" , destination = self . from_clause (), fields = \"`,`\" . join ( field_list ), placeholders = \",\" . join ( \"(\" + \",\" . join ( row [ \"placeholders\" ]) + \")\" for row in rows ), duplicate = ( \" ON DUPLICATE KEY UPDATE ` {pk} `=` {pk} `\" . format ( pk = self . primary_key [ 0 ] ) if skip_duplicates else \"\" ), ) self . connection . query ( query , args = list ( itertools . chain . from_iterable ( ( v for v in r [ \"values\" ] if v is not None ) for r in rows ) ), ) except UnknownAttributeError as err : raise err . suggest ( \"To ignore extra fields in insert, set ignore_extra_fields=True\" ) except DuplicateError as err : raise err . suggest ( \"To ignore duplicate entries in insert, set skip_duplicates=True\" )", "title": "insert()"}, {"location": "api/datajoint/table/#datajoint.table.Table.delete_quick", "text": "Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. Source code in datajoint/table.py 448 449 450 451 452 453 454 455 456 457 458 459 460 461 def delete_quick ( self , get_count = False ): \"\"\" Deletes the table without cascading and without user prompt. If this table has populated dependent tables, this will fail. \"\"\" query = \"DELETE FROM \" + self . full_table_name + self . where_clause () self . connection . query ( query ) count = ( self . connection . query ( \"SELECT ROW_COUNT()\" ) . fetchone ()[ 0 ] if get_count else None ) self . _log ( query [: 255 ]) return count", "title": "delete_quick()"}, {"location": "api/datajoint/table/#datajoint.table.Table.delete", "text": "Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If True , use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to False if this delete is nested within another transaction. safemode: If True , prohibit nested transactions and prompt to confirm. Default is dj.config['safemode'] . force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. Source code in datajoint/table.py 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 def delete ( self , transaction : bool = True , safemode : Union [ bool , None ] = None , force_parts : bool = False , ) -> int : \"\"\" Deletes the contents of the table and its dependent tables, recursively. Args: transaction: If `True`, use of the entire delete becomes an atomic transaction. This is the default and recommended behavior. Set to `False` if this delete is nested within another transaction. safemode: If `True`, prohibit nested transactions and prompt to confirm. Default is `dj.config['safemode']`. force_parts: Delete from parts even when not deleting from their masters. Returns: Number of deleted rows (excluding those from dependent tables). Raises: DataJointError: Delete exceeds maximum number of delete attempts. DataJointError: When deleting within an existing transaction. DataJointError: Deleting a part table before its master. \"\"\" deleted = set () def cascade ( table ): \"\"\"service function to perform cascading deletes recursively.\"\"\" max_attempts = 50 for _ in range ( max_attempts ): try : delete_count = table . delete_quick ( get_count = True ) except IntegrityError as error : match = foreign_key_error_regexp . match ( error . args [ 0 ]) . groupdict () if \"`.`\" not in match [ \"child\" ]: # if schema name missing, use table match [ \"child\" ] = \" {} . {} \" . format ( table . full_table_name . split ( \".\" )[ 0 ], match [ \"child\" ] ) if ( match [ \"pk_attrs\" ] is not None ): # fully matched, adjusting the keys match [ \"fk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"fk_attrs\" ] . split ( \",\" ) ] match [ \"pk_attrs\" ] = [ k . strip ( \"`\" ) for k in match [ \"pk_attrs\" ] . split ( \",\" ) ] else : # only partially matched, querying with constraint to determine keys match [ \"fk_attrs\" ], match [ \"parent\" ], match [ \"pk_attrs\" ] = list ( map ( list , zip ( * table . connection . query ( constraint_info_query , args = ( match [ \"name\" ] . strip ( \"`\" ), * [ _ . strip ( \"`\" ) for _ in match [ \"child\" ] . split ( \"`.`\" ) ], ), ) . fetchall () ), ) ) match [ \"parent\" ] = match [ \"parent\" ][ 0 ] # Restrict child by table if # 1. if table's restriction attributes are not in child's primary key # 2. if child renames any attributes # Otherwise restrict child by table's restriction. child = FreeTable ( table . connection , match [ \"child\" ]) if ( set ( table . restriction_attributes ) <= set ( child . primary_key ) and match [ \"fk_attrs\" ] == match [ \"pk_attrs\" ] ): child . _restriction = table . _restriction elif match [ \"fk_attrs\" ] != match [ \"pk_attrs\" ]: child &= table . proj ( ** dict ( zip ( match [ \"fk_attrs\" ], match [ \"pk_attrs\" ])) ) else : child &= table . proj () cascade ( child ) else : deleted . add ( table . full_table_name ) logger . info ( \"Deleting {count} rows from {table} \" . format ( count = delete_count , table = table . full_table_name ) ) break else : raise DataJointError ( \"Exceeded maximum number of delete attempts.\" ) return delete_count safemode = config [ \"safemode\" ] if safemode is None else safemode # Start transaction if transaction : if not self . connection . in_transaction : self . connection . start_transaction () else : if not safemode : transaction = False else : raise DataJointError ( \"Delete cannot use a transaction within an ongoing transaction. \" \"Set transaction=False or safemode=False).\" ) # Cascading delete try : delete_count = cascade ( self ) except : if transaction : self . connection . cancel_transaction () raise if not force_parts : # Avoid deleting from child before master (See issue #151) for part in deleted : master = get_master ( part ) if master and master not in deleted : if transaction : self . connection . cancel_transaction () raise DataJointError ( \"Attempt to delete part table {part} before deleting from \" \"its master {master} first.\" . format ( part = part , master = master ) ) # Confirm and commit if delete_count == 0 : if safemode : print ( \"Nothing to delete.\" ) if transaction : self . connection . cancel_transaction () else : if not safemode or user_choice ( \"Commit deletes?\" , default = \"no\" ) == \"yes\" : if transaction : self . connection . commit_transaction () if safemode : print ( \"Deletes committed.\" ) else : if transaction : self . connection . cancel_transaction () if safemode : print ( \"Deletes cancelled\" ) return delete_count", "title": "delete()"}, {"location": "api/datajoint/table/#datajoint.table.Table.drop_quick", "text": "Drops the table without cascading to dependent tables and without user prompt. Source code in datajoint/table.py 614 615 616 617 618 619 620 621 622 623 624 625 626 def drop_quick ( self ): \"\"\" Drops the table without cascading to dependent tables and without user prompt. \"\"\" if self . is_declared : query = \"DROP TABLE %s \" % self . full_table_name self . connection . query ( query ) logger . info ( \"Dropped table %s \" % self . full_table_name ) self . _log ( query [: 255 ]) else : logger . info ( \"Nothing to drop: table %s is not declared\" % self . full_table_name )", "title": "drop_quick()"}, {"location": "api/datajoint/table/#datajoint.table.Table.drop", "text": "Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. Source code in datajoint/table.py 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 def drop ( self ): \"\"\" Drop the table and all tables that reference it, recursively. User is prompted for confirmation if config['safemode'] is set to True. \"\"\" if self . restriction : raise DataJointError ( \"A table with an applied restriction cannot be dropped.\" \" Call drop() on the unrestricted Table.\" ) self . connection . dependencies . load () do_drop = True tables = [ table for table in self . connection . dependencies . descendants ( self . full_table_name ) if not table . isdigit () ] # avoid dropping part tables without their masters: See issue #374 for part in tables : master = get_master ( part ) if master and master not in tables : raise DataJointError ( \"Attempt to drop part table {part} before dropping \" \"its master. Drop {master} first.\" . format ( part = part , master = master ) ) if config [ \"safemode\" ]: for table in tables : print ( table , \"( %d tuples)\" % len ( FreeTable ( self . connection , table ))) do_drop = user_choice ( \"Proceed?\" , default = \"no\" ) == \"yes\" if do_drop : for table in reversed ( tables ): FreeTable ( self . connection , table ) . drop_quick () print ( \"Tables dropped. Restart kernel.\" )", "title": "drop()"}, {"location": "api/datajoint/table/#datajoint.table.Table.size_on_disk", "text": "Returns: Type Description size of data and indices in bytes on the storage device Source code in datajoint/table.py 664 665 666 667 668 669 670 671 672 673 674 675 @property def size_on_disk ( self ): \"\"\" :return: size of data and indices in bytes on the storage device \"\"\" ret = self . connection . query ( 'SHOW TABLE STATUS FROM ` {database} ` WHERE NAME=\" {table} \"' . format ( database = self . database , table = self . table_name ), as_dict = True , ) . fetchone () return ret [ \"Data_length\" ] + ret [ \"Index_length\" ]", "title": "size_on_disk()"}, {"location": "api/datajoint/table/#datajoint.table.Table.describe", "text": "Returns: Type Description the definition string for the query using DataJoint DDL. Source code in datajoint/table.py 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 def describe ( self , context = None , printout = True ): \"\"\" :return: the definition string for the query using DataJoint DDL. \"\"\" if context is None : frame = inspect . currentframe () . f_back context = dict ( frame . f_globals , ** frame . f_locals ) del frame if self . full_table_name not in self . connection . dependencies : self . connection . dependencies . load () parents = self . parents ( foreign_key_info = True ) in_key = True definition = ( \"# \" + self . heading . table_status [ \"comment\" ] + \" \\n \" if self . heading . table_status [ \"comment\" ] else \"\" ) attributes_thus_far = set () attributes_declared = set () indexes = self . heading . indexes . copy () for attr in self . heading . attributes . values (): if in_key and not attr . in_key : definition += \"--- \\n \" in_key = False attributes_thus_far . add ( attr . name ) do_include = True for parent_name , fk_props in parents : if attr . name in fk_props [ \"attr_map\" ]: do_include = False if attributes_thus_far . issuperset ( fk_props [ \"attr_map\" ]): # foreign key properties try : index_props = indexes . pop ( tuple ( fk_props [ \"attr_map\" ])) except KeyError : index_props = \"\" else : index_props = [ k for k , v in index_props . items () if v ] index_props = ( \" [ {} ]\" . format ( \", \" . join ( index_props )) if index_props else \"\" ) if not fk_props [ \"aliased\" ]: # simple foreign key definition += \"-> {props} {class_name} \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , ) else : # projected foreign key definition += ( \"-> {props} {class_name} .proj( {proj_list} ) \\n \" . format ( props = index_props , class_name = lookup_class_name ( parent_name , context ) or parent_name , proj_list = \",\" . join ( ' {} =\" {} \"' . format ( attr , ref ) for attr , ref in fk_props [ \"attr_map\" ] . items () if ref != attr ), ) ) attributes_declared . update ( fk_props [ \"attr_map\" ]) if do_include : attributes_declared . add ( attr . name ) definition += \" %-20s : %-28s %s \\n \" % ( attr . name if attr . default is None else \" %s = %s \" % ( attr . name , attr . default ), \" %s%s \" % ( attr . type , \" auto_increment\" if attr . autoincrement else \"\" ), \"# \" + attr . comment if attr . comment else \"\" , ) # add remaining indexes for k , v in indexes . items (): definition += \" {unique} INDEX ( {attrs} ) \\n \" . format ( unique = \"UNIQUE \" if v [ \"unique\" ] else \"\" , attrs = \", \" . join ( k ) ) if printout : print ( definition ) return definition", "title": "describe()"}, {"location": "api/datajoint/table/#datajoint.table.lookup_class_name", "text": "given a table name in the form schema_name . table_name , find its class in the context. Parameters: Name Type Description Default name schema_name . table_name required context dictionary representing the namespace required depth search depth into imported modules, helps avoid infinite recursion. 3 Returns: Type Description class name found in the context or None if not found Source code in datajoint/table.py 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 def lookup_class_name ( name , context , depth = 3 ): \"\"\" given a table name in the form `schema_name`.`table_name`, find its class in the context. :param name: `schema_name`.`table_name` :param context: dictionary representing the namespace :param depth: search depth into imported modules, helps avoid infinite recursion. :return: class name found in the context or None if not found \"\"\" # breadth-first search nodes = [ dict ( context = context , context_name = \"\" , depth = depth )] while nodes : node = nodes . pop ( 0 ) for member_name , member in node [ \"context\" ] . items (): if not member_name . startswith ( \"_\" ): # skip IPython's implicit variables if inspect . isclass ( member ) and issubclass ( member , Table ): if member . full_table_name == name : # found it! return \".\" . join ([ node [ \"context_name\" ], member_name ]) . lstrip ( \".\" ) try : # look for part tables parts = member . __dict__ except AttributeError : pass # not a UserTable -- cannot have part tables. else : for part in ( getattr ( member , p ) for p in parts if p [ 0 ] . isupper () and hasattr ( member , p ) ): if ( inspect . isclass ( part ) and issubclass ( part , Table ) and part . full_table_name == name ): return \".\" . join ( [ node [ \"context_name\" ], member_name , part . __name__ ] ) . lstrip ( \".\" ) elif ( node [ \"depth\" ] > 0 and inspect . ismodule ( member ) and member . __name__ != \"datajoint\" ): try : nodes . append ( dict ( context = dict ( inspect . getmembers ( member )), context_name = node [ \"context_name\" ] + \".\" + member_name , depth = node [ \"depth\" ] - 1 , ) ) except ImportError : pass # could not import, so do not attempt return None", "title": "lookup_class_name()"}, {"location": "api/datajoint/table/#datajoint.table.FreeTable", "text": "Bases: Table A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. Parameters: Name Type Description Default conn a dj.Connection object required full_table_name in format database . table_name required Source code in datajoint/table.py 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 class FreeTable ( Table ): \"\"\" A base table without a dedicated class. Each instance is associated with a table specified by full_table_name. :param conn: a dj.Connection object :param full_table_name: in format `database`.`table_name` \"\"\" def __init__ ( self , conn , full_table_name ): self . database , self . _table_name = ( s . strip ( \"`\" ) for s in full_table_name . split ( \".\" ) ) self . _connection = conn self . _support = [ full_table_name ] self . _heading = Heading ( table_info = dict ( conn = conn , database = self . database , table_name = self . table_name , context = None , ) ) def __repr__ ( self ): return ( \"FreeTable(` %s `.` %s `) \\n \" % ( self . database , self . _table_name ) + super () . __repr__ () )", "title": "FreeTable"}, {"location": "api/datajoint/table/#datajoint.table.Log", "text": "Bases: Table The log table for each schema. Instances are callable. Calls log the time and identifying information along with the event. Parameters: Name Type Description Default skip_logging if True, then log entry is skipped by default. See call False Source code in datajoint/table.py 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 class Log ( Table ): \"\"\" The log table for each schema. Instances are callable. Calls log the time and identifying information along with the event. :param skip_logging: if True, then log entry is skipped by default. See __call__ \"\"\" _table_name = \"~log\" def __init__ ( self , conn , database , skip_logging = False ): self . database = database self . skip_logging = skip_logging self . _connection = conn self . _heading = Heading ( table_info = dict ( conn = conn , database = database , table_name = self . table_name , context = None ) ) self . _support = [ self . full_table_name ] self . _definition = \"\"\" # event logging table for ` {database} ` id :int unsigned auto_increment # event order id --- timestamp = CURRENT_TIMESTAMP : timestamp # event timestamp version :varchar(12) # datajoint version user :varchar(255) # user@host host=\"\" :varchar(255) # system hostname event=\"\" :varchar(255) # event message \"\"\" . format ( database = database ) super () . __init__ () if not self . is_declared : self . declare () self . connection . dependencies . clear () self . _user = self . connection . get_user () @property def definition ( self ): return self . _definition def __call__ ( self , event , skip_logging = None ): \"\"\" :param event: string to write into the log table :param skip_logging: If True then do not log. If None, then use self.skip_logging \"\"\" skip_logging = self . skip_logging if skip_logging is None else skip_logging if not skip_logging : try : self . insert1 ( dict ( user = self . _user , version = version + \"py\" , host = platform . uname () . node , event = event , ), skip_duplicates = True , ignore_extra_fields = True , ) except DataJointError : logger . info ( \"could not log event in table ~log\" ) def delete ( self ): \"\"\" bypass interactive prompts and cascading dependencies :return: number of deleted items \"\"\" return self . delete_quick ( get_count = True ) def drop ( self ): \"\"\"bypass interactive prompts and cascading dependencies\"\"\" self . drop_quick ()", "title": "Log"}, {"location": "api/datajoint/table/#datajoint.table.Log.delete", "text": "bypass interactive prompts and cascading dependencies Returns: Type Description number of deleted items Source code in datajoint/table.py 1102 1103 1104 1105 1106 1107 1108 def delete ( self ): \"\"\" bypass interactive prompts and cascading dependencies :return: number of deleted items \"\"\" return self . delete_quick ( get_count = True )", "title": "delete()"}, {"location": "api/datajoint/table/#datajoint.table.Log.drop", "text": "bypass interactive prompts and cascading dependencies Source code in datajoint/table.py 1110 1111 1112 def drop ( self ): \"\"\"bypass interactive prompts and cascading dependencies\"\"\" self . drop_quick ()", "title": "drop()"}, {"location": "api/datajoint/user_tables/", "text": "Hosts the table tiers, user tables should be derived from. TableMeta \u00b6 Bases: type TableMeta subclasses allow applying some instance methods and properties directly at class level. For example, this allows Table.fetch() instead of Table().fetch(). Source code in datajoint/user_tables.py 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 class TableMeta ( type ): \"\"\" TableMeta subclasses allow applying some instance methods and properties directly at class level. For example, this allows Table.fetch() instead of Table().fetch(). \"\"\" def __getattribute__ ( cls , name ): # trigger instantiation for supported class attrs return ( cls () . __getattribute__ ( name ) if name in supported_class_attrs else super () . __getattribute__ ( name ) ) def __and__ ( cls , arg ): return cls () & arg def __xor__ ( cls , arg ): return cls () ^ arg def __sub__ ( cls , arg ): return cls () - arg def __neg__ ( cls ): return - cls () def __mul__ ( cls , arg ): return cls () * arg def __matmul__ ( cls , arg ): return cls () @ arg def __add__ ( cls , arg ): return cls () + arg def __iter__ ( cls ): return iter ( cls ()) UserTable \u00b6 Bases: Table A subclass of UserTable is a dedicated class interfacing a base table. UserTable is initialized by the decorator generated by schema(). Source code in datajoint/user_tables.py 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 class UserTable ( Table , metaclass = TableMeta ): \"\"\" A subclass of UserTable is a dedicated class interfacing a base table. UserTable is initialized by the decorator generated by schema(). \"\"\" # set by @schema _connection = None _heading = None _support = None # set by subclass tier_regexp = None _prefix = None @property def definition ( self ): \"\"\" :return: a string containing the table definition using the DataJoint DDL. \"\"\" raise NotImplementedError ( 'Subclasses of Table must implement the property \"definition\"' ) @ClassProperty def connection ( cls ): return cls . _connection @ClassProperty def table_name ( cls ): \"\"\" :return: the table name of the table formatted for mysql. \"\"\" if cls . _prefix is None : raise AttributeError ( \"Class prefix is not defined!\" ) return cls . _prefix + from_camel_case ( cls . __name__ ) @ClassProperty def full_table_name ( cls ): if cls not in { Manual , Imported , Lookup , Computed , Part , UserTable }: # for derived classes only if cls . database is None : raise DataJointError ( \"Class %s is not properly declared (schema decorator not applied?)\" % cls . __name__ ) return r \"` {0:s} `.` {1:s} `\" . format ( cls . database , cls . table_name ) definition () property \u00b6 Returns: Type Description a string containing the table definition using the DataJoint DDL. Source code in datajoint/user_tables.py 99 100 101 102 103 104 105 106 @property def definition ( self ): \"\"\" :return: a string containing the table definition using the DataJoint DDL. \"\"\" raise NotImplementedError ( 'Subclasses of Table must implement the property \"definition\"' ) table_name () \u00b6 Returns: Type Description the table name of the table formatted for mysql. Source code in datajoint/user_tables.py 112 113 114 115 116 117 118 119 @ClassProperty def table_name ( cls ): \"\"\" :return: the table name of the table formatted for mysql. \"\"\" if cls . _prefix is None : raise AttributeError ( \"Class prefix is not defined!\" ) return cls . _prefix + from_camel_case ( cls . __name__ ) Manual \u00b6 Bases: UserTable Inherit from this class if the table's values are entered manually. Source code in datajoint/user_tables.py 133 134 135 136 137 138 139 class Manual ( UserTable ): \"\"\" Inherit from this class if the table's values are entered manually. \"\"\" _prefix = r \"\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\" Lookup \u00b6 Bases: UserTable Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. Source code in datajoint/user_tables.py 142 143 144 145 146 147 148 149 150 151 152 class Lookup ( UserTable ): \"\"\" Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. \"\"\" _prefix = \"#\" tier_regexp = ( r \"(?P\" + _prefix + _base_regexp . replace ( \"TIER\" , \"lookup\" ) + \")\" ) Imported \u00b6 Bases: UserTable , AutoPopulate Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 155 156 157 158 159 160 161 162 class Imported ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"_\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\" Computed \u00b6 Bases: UserTable , AutoPopulate Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 165 166 167 168 169 170 171 172 class Computed ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"__\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\" Part \u00b6 Bases: UserTable Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. Source code in datajoint/user_tables.py 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 class Part ( UserTable ): \"\"\" Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. \"\"\" _connection = None _master = None tier_regexp = ( r \"(?P\" + \"|\" . join ([ c . tier_regexp for c in ( Manual , Lookup , Imported , Computed )]) + r \"){1,1}\" + \"__\" + r \"(?P\" + _base_regexp + \")\" ) @ClassProperty def connection ( cls ): return cls . _connection @ClassProperty def full_table_name ( cls ): return ( None if cls . database is None or cls . table_name is None else r \"` {0:s} `.` {1:s} `\" . format ( cls . database , cls . table_name ) ) @ClassProperty def master ( cls ): return cls . _master @ClassProperty def table_name ( cls ): return ( None if cls . master is None else cls . master . table_name + \"__\" + from_camel_case ( cls . __name__ ) ) def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" ) def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" ) delete ( force = False ) \u00b6 unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 220 221 222 223 224 225 226 227 228 229 def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" ) drop ( force = False ) \u00b6 unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 231 232 233 234 235 236 237 238 239 240 def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" )", "title": "user_tables.py"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.TableMeta", "text": "Bases: type TableMeta subclasses allow applying some instance methods and properties directly at class level. For example, this allows Table.fetch() instead of Table().fetch(). Source code in datajoint/user_tables.py 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 class TableMeta ( type ): \"\"\" TableMeta subclasses allow applying some instance methods and properties directly at class level. For example, this allows Table.fetch() instead of Table().fetch(). \"\"\" def __getattribute__ ( cls , name ): # trigger instantiation for supported class attrs return ( cls () . __getattribute__ ( name ) if name in supported_class_attrs else super () . __getattribute__ ( name ) ) def __and__ ( cls , arg ): return cls () & arg def __xor__ ( cls , arg ): return cls () ^ arg def __sub__ ( cls , arg ): return cls () - arg def __neg__ ( cls ): return - cls () def __mul__ ( cls , arg ): return cls () * arg def __matmul__ ( cls , arg ): return cls () @ arg def __add__ ( cls , arg ): return cls () + arg def __iter__ ( cls ): return iter ( cls ())", "title": "TableMeta"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.UserTable", "text": "Bases: Table A subclass of UserTable is a dedicated class interfacing a base table. UserTable is initialized by the decorator generated by schema(). Source code in datajoint/user_tables.py 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 class UserTable ( Table , metaclass = TableMeta ): \"\"\" A subclass of UserTable is a dedicated class interfacing a base table. UserTable is initialized by the decorator generated by schema(). \"\"\" # set by @schema _connection = None _heading = None _support = None # set by subclass tier_regexp = None _prefix = None @property def definition ( self ): \"\"\" :return: a string containing the table definition using the DataJoint DDL. \"\"\" raise NotImplementedError ( 'Subclasses of Table must implement the property \"definition\"' ) @ClassProperty def connection ( cls ): return cls . _connection @ClassProperty def table_name ( cls ): \"\"\" :return: the table name of the table formatted for mysql. \"\"\" if cls . _prefix is None : raise AttributeError ( \"Class prefix is not defined!\" ) return cls . _prefix + from_camel_case ( cls . __name__ ) @ClassProperty def full_table_name ( cls ): if cls not in { Manual , Imported , Lookup , Computed , Part , UserTable }: # for derived classes only if cls . database is None : raise DataJointError ( \"Class %s is not properly declared (schema decorator not applied?)\" % cls . __name__ ) return r \"` {0:s} `.` {1:s} `\" . format ( cls . database , cls . table_name )", "title": "UserTable"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.UserTable.definition", "text": "Returns: Type Description a string containing the table definition using the DataJoint DDL. Source code in datajoint/user_tables.py 99 100 101 102 103 104 105 106 @property def definition ( self ): \"\"\" :return: a string containing the table definition using the DataJoint DDL. \"\"\" raise NotImplementedError ( 'Subclasses of Table must implement the property \"definition\"' )", "title": "definition()"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.UserTable.table_name", "text": "Returns: Type Description the table name of the table formatted for mysql. Source code in datajoint/user_tables.py 112 113 114 115 116 117 118 119 @ClassProperty def table_name ( cls ): \"\"\" :return: the table name of the table formatted for mysql. \"\"\" if cls . _prefix is None : raise AttributeError ( \"Class prefix is not defined!\" ) return cls . _prefix + from_camel_case ( cls . __name__ )", "title": "table_name()"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.Manual", "text": "Bases: UserTable Inherit from this class if the table's values are entered manually. Source code in datajoint/user_tables.py 133 134 135 136 137 138 139 class Manual ( UserTable ): \"\"\" Inherit from this class if the table's values are entered manually. \"\"\" _prefix = r \"\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\"", "title": "Manual"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.Lookup", "text": "Bases: UserTable Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. Source code in datajoint/user_tables.py 142 143 144 145 146 147 148 149 150 151 152 class Lookup ( UserTable ): \"\"\" Inherit from this class if the table's values are for lookup. This is currently equivalent to defining the table as Manual and serves semantic purposes only. \"\"\" _prefix = \"#\" tier_regexp = ( r \"(?P\" + _prefix + _base_regexp . replace ( \"TIER\" , \"lookup\" ) + \")\" )", "title": "Lookup"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.Imported", "text": "Bases: UserTable , AutoPopulate Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 155 156 157 158 159 160 161 162 class Imported ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are imported from external data sources. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"_\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\"", "title": "Imported"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.Computed", "text": "Bases: UserTable , AutoPopulate Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function _make_tuples . Source code in datajoint/user_tables.py 165 166 167 168 169 170 171 172 class Computed ( UserTable , AutoPopulate ): \"\"\" Inherit from this class if the table's values are computed from other tables in the schema. The inherited class must at least provide the function `_make_tuples`. \"\"\" _prefix = \"__\" tier_regexp = r \"(?P\" + _prefix + _base_regexp + \")\"", "title": "Computed"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.Part", "text": "Bases: UserTable Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. Source code in datajoint/user_tables.py 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 class Part ( UserTable ): \"\"\" Inherit from this class if the table's values are details of an entry in another table and if this table is populated by the other table. For example, the entries inheriting from dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. Part tables are implemented as classes inside classes. \"\"\" _connection = None _master = None tier_regexp = ( r \"(?P\" + \"|\" . join ([ c . tier_regexp for c in ( Manual , Lookup , Imported , Computed )]) + r \"){1,1}\" + \"__\" + r \"(?P\" + _base_regexp + \")\" ) @ClassProperty def connection ( cls ): return cls . _connection @ClassProperty def full_table_name ( cls ): return ( None if cls . database is None or cls . table_name is None else r \"` {0:s} `.` {1:s} `\" . format ( cls . database , cls . table_name ) ) @ClassProperty def master ( cls ): return cls . _master @ClassProperty def table_name ( cls ): return ( None if cls . master is None else cls . master . table_name + \"__\" + from_camel_case ( cls . __name__ ) ) def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" ) def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" )", "title": "Part"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.Part.delete", "text": "unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 220 221 222 223 224 225 226 227 228 229 def delete ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . delete ( force_parts = True ) else : raise DataJointError ( \"Cannot delete from a Part directly. Delete from master instead\" )", "title": "delete()"}, {"location": "api/datajoint/user_tables/#datajoint.user_tables.Part.drop", "text": "unless force is True, prohibits direct deletes from parts. Source code in datajoint/user_tables.py 231 232 233 234 235 236 237 238 239 240 def drop ( self , force = False ): \"\"\" unless force is True, prohibits direct deletes from parts. \"\"\" if force : super () . drop () else : raise DataJointError ( \"Cannot drop a Part directly. Delete from master instead\" )", "title": "drop()"}, {"location": "api/datajoint/utils/", "text": "General-purpose utilities user_choice ( prompt , choices = ( 'yes' , 'no' ), default = None ) \u00b6 Prompts the user for confirmation. The default value, if any, is capitalized. Parameters: Name Type Description Default prompt Information to display to the user. required choices an iterable of possible choices. ('yes', 'no') default default choice None Returns: Type Description the user's choice Source code in datajoint/utils.py 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 def user_choice ( prompt , choices = ( \"yes\" , \"no\" ), default = None ): \"\"\" Prompts the user for confirmation. The default value, if any, is capitalized. :param prompt: Information to display to the user. :param choices: an iterable of possible choices. :param default: default choice :return: the user's choice \"\"\" assert default is None or default in choices choice_list = \", \" . join ( ( choice . title () if choice == default else choice for choice in choices ) ) response = None while response not in choices : response = input ( prompt + \" [\" + choice_list + \"]: \" ) response = response . lower () if response else default return response get_master ( full_table_name ) \u00b6 If the table name is that of a part table, then return what the master table name would be. This follows DataJoint's table naming convention where a master and a part must be in the same schema and the part table is prefixed with the master table name + __ . Example: ephys . session -- master ephys . session__recording -- part Parameters: Name Type Description Default full_table_name str Full table name including part. required Returns: Type Description str Supposed master full table name or empty string if not a part table name. Source code in datajoint/utils.py 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 def get_master ( full_table_name : str ) -> str : \"\"\" If the table name is that of a part table, then return what the master table name would be. This follows DataJoint's table naming convention where a master and a part must be in the same schema and the part table is prefixed with the master table name + ``__``. Example: `ephys`.`session` -- master `ephys`.`session__recording` -- part :param full_table_name: Full table name including part. :type full_table_name: str :return: Supposed master full table name or empty string if not a part table name. :rtype: str \"\"\" match = re . match ( r \"(?P`\\w+`.`\\w+)__(?P\\w+)`\" , full_table_name ) return match [ \"master\" ] + \"`\" if match else \"\" to_camel_case ( s ) \u00b6 Convert names with under score (_) separation into camel case names. Parameters: Name Type Description Default s string in under_score notation required Returns: Type Description string in CamelCase notation Example: >>> to_camel_case(\"table_name\") # returns \"TableName\" Source code in datajoint/utils.py 56 57 58 59 60 61 62 63 64 65 66 67 68 69 def to_camel_case ( s ): \"\"\" Convert names with under score (_) separation into camel case names. :param s: string in under_score notation :returns: string in CamelCase notation Example: >>> to_camel_case(\"table_name\") # returns \"TableName\" \"\"\" def to_upper ( match ): return match . group ( 0 )[ - 1 ] . upper () return re . sub ( r \"(^|[_\\W])+[a-zA-Z]\" , to_upper , s ) from_camel_case ( s ) \u00b6 Convert names in camel case into underscore (_) separated names Parameters: Name Type Description Default s string in CamelCase notation required Returns: Type Description string in under_score notation Example: >>> from_camel_case(\"TableName\") # yields \"table_name\" Source code in datajoint/utils.py 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 def from_camel_case ( s ): \"\"\" Convert names in camel case into underscore (_) separated names :param s: string in CamelCase notation :returns: string in under_score notation Example: >>> from_camel_case(\"TableName\") # yields \"table_name\" \"\"\" def convert ( match ): return ( \"_\" if match . groups ()[ 0 ] else \"\" ) + match . group ( 0 ) . lower () if not re . match ( r \"[A-Z][a-zA-Z0-9]*\" , s ): raise DataJointError ( \"ClassName must be alphanumeric in CamelCase, begin with a capital letter\" ) return re . sub ( r \"(\\B[A-Z])|(\\b[A-Z])\" , convert , s ) safe_write ( filepath , blob ) \u00b6 A two-step write. Parameters: Name Type Description Default filename full path required blob binary data required Source code in datajoint/utils.py 92 93 94 95 96 97 98 99 100 101 102 103 104 def safe_write ( filepath , blob ): \"\"\" A two-step write. :param filename: full path :param blob: binary data \"\"\" filepath = Path ( filepath ) if not filepath . is_file (): filepath . parent . mkdir ( parents = True , exist_ok = True ) temp_file = filepath . with_suffix ( filepath . suffix + \".saving\" ) temp_file . write_bytes ( blob ) temp_file . rename ( filepath ) safe_copy ( src , dest , overwrite = False ) \u00b6 Copy the contents of src file into dest file as a two-step process. Skip if dest exists already Source code in datajoint/utils.py 107 108 109 110 111 112 113 114 115 116 def safe_copy ( src , dest , overwrite = False ): \"\"\" Copy the contents of src file into dest file as a two-step process. Skip if dest exists already \"\"\" src , dest = Path ( src ), Path ( dest ) if not ( dest . exists () and src . samefile ( dest )) and ( overwrite or not dest . is_file ()): dest . parent . mkdir ( parents = True , exist_ok = True ) temp_file = dest . with_suffix ( dest . suffix + \".copying\" ) shutil . copyfile ( str ( src ), str ( temp_file )) temp_file . rename ( dest ) parse_sql ( filepath ) \u00b6 yield SQL statements from an SQL file Source code in datajoint/utils.py 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 def parse_sql ( filepath ): \"\"\" yield SQL statements from an SQL file \"\"\" delimiter = \";\" statement = [] with Path ( filepath ) . open ( \"rt\" ) as f : for line in f : line = line . strip () if not line . startswith ( \"--\" ) and len ( line ) > 1 : if line . startswith ( \"delimiter\" ): delimiter = line . split ()[ 1 ] else : statement . append ( line ) if line . endswith ( delimiter ): yield \" \" . join ( statement ) statement = []", "title": "utils.py"}, {"location": "api/datajoint/utils/#datajoint.utils.user_choice", "text": "Prompts the user for confirmation. The default value, if any, is capitalized. Parameters: Name Type Description Default prompt Information to display to the user. required choices an iterable of possible choices. ('yes', 'no') default default choice None Returns: Type Description the user's choice Source code in datajoint/utils.py 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 def user_choice ( prompt , choices = ( \"yes\" , \"no\" ), default = None ): \"\"\" Prompts the user for confirmation. The default value, if any, is capitalized. :param prompt: Information to display to the user. :param choices: an iterable of possible choices. :param default: default choice :return: the user's choice \"\"\" assert default is None or default in choices choice_list = \", \" . join ( ( choice . title () if choice == default else choice for choice in choices ) ) response = None while response not in choices : response = input ( prompt + \" [\" + choice_list + \"]: \" ) response = response . lower () if response else default return response", "title": "user_choice()"}, {"location": "api/datajoint/utils/#datajoint.utils.get_master", "text": "If the table name is that of a part table, then return what the master table name would be. This follows DataJoint's table naming convention where a master and a part must be in the same schema and the part table is prefixed with the master table name + __ . Example: ephys . session -- master ephys . session__recording -- part Parameters: Name Type Description Default full_table_name str Full table name including part. required Returns: Type Description str Supposed master full table name or empty string if not a part table name. Source code in datajoint/utils.py 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 def get_master ( full_table_name : str ) -> str : \"\"\" If the table name is that of a part table, then return what the master table name would be. This follows DataJoint's table naming convention where a master and a part must be in the same schema and the part table is prefixed with the master table name + ``__``. Example: `ephys`.`session` -- master `ephys`.`session__recording` -- part :param full_table_name: Full table name including part. :type full_table_name: str :return: Supposed master full table name or empty string if not a part table name. :rtype: str \"\"\" match = re . match ( r \"(?P`\\w+`.`\\w+)__(?P\\w+)`\" , full_table_name ) return match [ \"master\" ] + \"`\" if match else \"\"", "title": "get_master()"}, {"location": "api/datajoint/utils/#datajoint.utils.to_camel_case", "text": "Convert names with under score (_) separation into camel case names. Parameters: Name Type Description Default s string in under_score notation required Returns: Type Description string in CamelCase notation Example: >>> to_camel_case(\"table_name\") # returns \"TableName\" Source code in datajoint/utils.py 56 57 58 59 60 61 62 63 64 65 66 67 68 69 def to_camel_case ( s ): \"\"\" Convert names with under score (_) separation into camel case names. :param s: string in under_score notation :returns: string in CamelCase notation Example: >>> to_camel_case(\"table_name\") # returns \"TableName\" \"\"\" def to_upper ( match ): return match . group ( 0 )[ - 1 ] . upper () return re . sub ( r \"(^|[_\\W])+[a-zA-Z]\" , to_upper , s )", "title": "to_camel_case()"}, {"location": "api/datajoint/utils/#datajoint.utils.from_camel_case", "text": "Convert names in camel case into underscore (_) separated names Parameters: Name Type Description Default s string in CamelCase notation required Returns: Type Description string in under_score notation Example: >>> from_camel_case(\"TableName\") # yields \"table_name\" Source code in datajoint/utils.py 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 def from_camel_case ( s ): \"\"\" Convert names in camel case into underscore (_) separated names :param s: string in CamelCase notation :returns: string in under_score notation Example: >>> from_camel_case(\"TableName\") # yields \"table_name\" \"\"\" def convert ( match ): return ( \"_\" if match . groups ()[ 0 ] else \"\" ) + match . group ( 0 ) . lower () if not re . match ( r \"[A-Z][a-zA-Z0-9]*\" , s ): raise DataJointError ( \"ClassName must be alphanumeric in CamelCase, begin with a capital letter\" ) return re . sub ( r \"(\\B[A-Z])|(\\b[A-Z])\" , convert , s )", "title": "from_camel_case()"}, {"location": "api/datajoint/utils/#datajoint.utils.safe_write", "text": "A two-step write. Parameters: Name Type Description Default filename full path required blob binary data required Source code in datajoint/utils.py 92 93 94 95 96 97 98 99 100 101 102 103 104 def safe_write ( filepath , blob ): \"\"\" A two-step write. :param filename: full path :param blob: binary data \"\"\" filepath = Path ( filepath ) if not filepath . is_file (): filepath . parent . mkdir ( parents = True , exist_ok = True ) temp_file = filepath . with_suffix ( filepath . suffix + \".saving\" ) temp_file . write_bytes ( blob ) temp_file . rename ( filepath )", "title": "safe_write()"}, {"location": "api/datajoint/utils/#datajoint.utils.safe_copy", "text": "Copy the contents of src file into dest file as a two-step process. Skip if dest exists already Source code in datajoint/utils.py 107 108 109 110 111 112 113 114 115 116 def safe_copy ( src , dest , overwrite = False ): \"\"\" Copy the contents of src file into dest file as a two-step process. Skip if dest exists already \"\"\" src , dest = Path ( src ), Path ( dest ) if not ( dest . exists () and src . samefile ( dest )) and ( overwrite or not dest . is_file ()): dest . parent . mkdir ( parents = True , exist_ok = True ) temp_file = dest . with_suffix ( dest . suffix + \".copying\" ) shutil . copyfile ( str ( src ), str ( temp_file )) temp_file . rename ( dest )", "title": "safe_copy()"}, {"location": "api/datajoint/utils/#datajoint.utils.parse_sql", "text": "yield SQL statements from an SQL file Source code in datajoint/utils.py 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 def parse_sql ( filepath ): \"\"\" yield SQL statements from an SQL file \"\"\" delimiter = \";\" statement = [] with Path ( filepath ) . open ( \"rt\" ) as f : for line in f : line = line . strip () if not line . startswith ( \"--\" ) and len ( line ) > 1 : if line . startswith ( \"delimiter\" ): delimiter = line . split ()[ 1 ] else : statement . append ( line ) if line . endswith ( delimiter ): yield \" \" . join ( statement ) statement = []", "title": "parse_sql()"}, {"location": "api/datajoint/version/", "text": "", "title": "version.py"}, {"location": "concepts/existing-pipelines/", "text": "Existing Pipelines \u00b6 This section describes how to work with database schemas without access to the original code that generated the schema. These situations often arise when the database is created by another user who has not shared the generating code yet or when the database schema is created from a programming language other than Python. Loading Classes \u00b6 Typically, a DataJoint schema is created as a dedicated Python module. This module defines a schema object that is used to link classes declared in the module to tables in the database schema. With the module installed, you can simply import it to interact with its tables: import datajoint as dj from element_calcium_imaging import scan # (1) This and other DataJoint Elements are installable via pip or downloadable via their respective GitHub repositories. To visualize an unfamiliar schema, see commands for generating diagrams . Spawning Missing Classes \u00b6 Now, imagine we do not have access to the Python definition of Scan , or we're unsure if the version on our server matches the definition available. We can use the dj.list_schemas function to list the available database schemas. import datajoint as dj dj . conn () # (1) dj . list_schemas () # (2) dj . Schema ( 'schema_name' ) . list_tables () # (3) Establish a connection to the server. List the available schemas on the server. List the tables for a given schema from the previous step. These will appear in their raw database form, with underscores instead of camelcase and special characters for Part tables. Just as with a new schema, we can create a schema object to connect to the chosen database schema. If the schema already exists, dj.Schema is initialized as usual. If a diagram will shows a mixture of class names and database table names, the spawn_missing_classes method will spawn classes into the local namespace for any tables missing their classes. This will allow us to interact with all tables as if they were declared in the current namespace. schema . spawn_missing_classes () Virtual Modules \u00b6 While spawn_missing_classes creates the new classes in the local namespace, it is often more convenient to import a schema with its Python module, equivalent to the Python command. We can mimmick this import without having access to the schema using the VirtualModule class object: import datajoint as dj subject = dj . create_virtual_module ( module_name = 'subject' , schema_name = 'db_subject' ) Now, subject behaves as an imported module complete with the schema object and all the table classes. The class object VirtualModule of the dj.Schema class provides access to virtual modules. It creates a python module with the given name from the name of a schema on the server, automatically adds classes to it corresponding to the tables in the schema. The function can take several parameters: module_name : displayed module name. schema_name : name of the database in MySQL. create_schema : if True , create the schema on the database server if it does not already exist; if False (default), raise an error when the schema is not found. create_tables : if True , module.schema can be used as the decorator for declaring new classes; if False , such use will raise an error stating that the module is intend only to work with existing tables. The function returns the Python module containing classes from the schema object with all the table classes already declared inside it. create_schema=False may be useful if we want to make sure that the schema already exists. If none exists, create_schema=True will create an empty schema. dj . VirtualModule ( 'what' , 'nonexistent' ) Returns DataJointError : Database named ` nonexistent ` was not defined . Set argument create_schema = True to create it . create_tables=False prevents the use of the schema object of the virtual module for creating new tables in the existing schema. This is a precautionary measure since virtual modules are often used for completed schemas. create_tables=True will new tables to the existing schema. A more common approach in this scenario would be to create a new schema object and to use the spawn_missing_classes function to make the classes available. However, you if do decide to create new tables in an existing tables using the virtual module, you may do so by using the schema object from the module as the decorator for declaring new tables: uni = dj . VirtualModule ( 'university.py' , 'dimitri_university' , create_tables = True ) @uni . schema class Example ( dj . Manual ): definition = \"\"\" -> uni.Student --- example : varchar(255) \"\"\" dj . Diagram ( uni )", "title": "Existing Pipelines"}, {"location": "concepts/existing-pipelines/#existing-pipelines", "text": "This section describes how to work with database schemas without access to the original code that generated the schema. These situations often arise when the database is created by another user who has not shared the generating code yet or when the database schema is created from a programming language other than Python.", "title": "Existing Pipelines"}, {"location": "concepts/existing-pipelines/#loading-classes", "text": "Typically, a DataJoint schema is created as a dedicated Python module. This module defines a schema object that is used to link classes declared in the module to tables in the database schema. With the module installed, you can simply import it to interact with its tables: import datajoint as dj from element_calcium_imaging import scan # (1) This and other DataJoint Elements are installable via pip or downloadable via their respective GitHub repositories. To visualize an unfamiliar schema, see commands for generating diagrams .", "title": "Loading Classes"}, {"location": "concepts/existing-pipelines/#spawning-missing-classes", "text": "Now, imagine we do not have access to the Python definition of Scan , or we're unsure if the version on our server matches the definition available. We can use the dj.list_schemas function to list the available database schemas. import datajoint as dj dj . conn () # (1) dj . list_schemas () # (2) dj . Schema ( 'schema_name' ) . list_tables () # (3) Establish a connection to the server. List the available schemas on the server. List the tables for a given schema from the previous step. These will appear in their raw database form, with underscores instead of camelcase and special characters for Part tables. Just as with a new schema, we can create a schema object to connect to the chosen database schema. If the schema already exists, dj.Schema is initialized as usual. If a diagram will shows a mixture of class names and database table names, the spawn_missing_classes method will spawn classes into the local namespace for any tables missing their classes. This will allow us to interact with all tables as if they were declared in the current namespace. schema . spawn_missing_classes ()", "title": "Spawning Missing Classes"}, {"location": "concepts/existing-pipelines/#virtual-modules", "text": "While spawn_missing_classes creates the new classes in the local namespace, it is often more convenient to import a schema with its Python module, equivalent to the Python command. We can mimmick this import without having access to the schema using the VirtualModule class object: import datajoint as dj subject = dj . create_virtual_module ( module_name = 'subject' , schema_name = 'db_subject' ) Now, subject behaves as an imported module complete with the schema object and all the table classes. The class object VirtualModule of the dj.Schema class provides access to virtual modules. It creates a python module with the given name from the name of a schema on the server, automatically adds classes to it corresponding to the tables in the schema. The function can take several parameters: module_name : displayed module name. schema_name : name of the database in MySQL. create_schema : if True , create the schema on the database server if it does not already exist; if False (default), raise an error when the schema is not found. create_tables : if True , module.schema can be used as the decorator for declaring new classes; if False , such use will raise an error stating that the module is intend only to work with existing tables. The function returns the Python module containing classes from the schema object with all the table classes already declared inside it. create_schema=False may be useful if we want to make sure that the schema already exists. If none exists, create_schema=True will create an empty schema. dj . VirtualModule ( 'what' , 'nonexistent' ) Returns DataJointError : Database named ` nonexistent ` was not defined . Set argument create_schema = True to create it . create_tables=False prevents the use of the schema object of the virtual module for creating new tables in the existing schema. This is a precautionary measure since virtual modules are often used for completed schemas. create_tables=True will new tables to the existing schema. A more common approach in this scenario would be to create a new schema object and to use the spawn_missing_classes function to make the classes available. However, you if do decide to create new tables in an existing tables using the virtual module, you may do so by using the schema object from the module as the decorator for declaring new tables: uni = dj . VirtualModule ( 'university.py' , 'dimitri_university' , create_tables = True ) @uni . schema class Example ( dj . Manual ): definition = \"\"\" -> uni.Student --- example : varchar(255) \"\"\" dj . Diagram ( uni )", "title": "Virtual Modules"}, {"location": "getting-started/", "text": "Getting Started \u00b6 Installation \u00b6 First, please install Python version 3.7 or later. We recommend 3.8. Next, please install DataJoint via one of the following: conda pip + pip + pip + Pre-Requisites Ensure you have conda installed. To add the conda-forge channel: conda config --add channels conda-forge To install: conda install -c conda-forge datajoint Pre-Requisites Ensure you have pip installed. Install graphviz pre-requisite for diagram visualization. To install: pip install datajoint Pre-Requisites Ensure you have pip installed. Install graphviz pre-requisite for diagram visualization. To install: pip install datajoint Pre-Requisites Ensure you have pip installed. Install graphviz pre-requisite for diagram visualization. To install: pip install datajoint Connection \u00b6 Note Although you may connect to any MySQL server of your choice, the DataJoint company offers an online tutorial environment. Simply sign up for a free DataJoint account . You will be granted privileges to create schemas that are prefixed as {user}_ . environment variables memory file Before using datajoint , set the following environment variables like so: 1 2 3 DJ_HOST = tutorial-db.datajoint.io DJ_USER ={ user } DJ_PASS ={ password } To set connection settings within Python, perform: 1 2 3 4 5 import datajoint as dj dj . config [ \"database.host\" ] = \"tutorial-db.datajoint.io\" dj . config [ \"database.user\" ] = \" {user} \" dj . config [ \"database.password\" ] = \" {password} \" These configuration settings can be saved either locally or system-wide using one of the following commands: dj . config . save_local () dj . config . save_global () Before using datajoint , create a file named dj_local_conf.json in the current directory like so: 1 2 3 4 5 { \"database.host\" : \"tutorial-db.datajoint.io\" , \"database.user\" : \"{user}\" , \"database.password\" : \"{password}\" } These settings will be loaded whenever a Python instance is launched from this directory. To configure settings globally, save a similar file as .datajoint_config.json in your home directory. A local config, if present, will take precedent over global settings. Data Pipeline Definition \u00b6 Let's definite a simple data pipeline. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 import datajoint as dj schema = dj . Schema ( f \" { dj . config [ 'database.user' ] } _shapes\" ) # (1) @schema # (2) class Rectangle ( dj . Manual ): definition = \"\"\" # (3) shape_id: int --- shape_height: float shape_width: float \"\"\" @schema class Area ( dj . Computed ): definition = \"\"\" -> Rectangle --- shape_area: float \"\"\" def make ( self , key ): rectangle = ( Rectangle & key ) . fetch1 () Area . insert1 ( dict ( shape_id = rectangle [ \"shape_id\" ], shape_area = rectangle [ \"shape_height\" ] * rectangle [ \"shape_width\" ], ) ) This statement creates the database schema {username}_shapes on the server. The @schema decorator for DataJoint classes creates the table on the server. The table is defined by the the definition property. It is a common practice to have a separate Python module for each schema. Therefore, each such module has only one dj.Schema object defined and is usually named schema . The dj.Schema constructor can take a number of optional parameters after the schema name. context - Dictionary for looking up foreign key references. Defaults to None to use local context. connection - Specifies the DataJoint connection object. Defaults to dj.conn() . create_schema - When False , the schema object will not create a schema on the database and will raise an error if one does not already exist. Defaults to True . create_tables - When False , the schema object will not create tables on the database and will raise errors when accessing missing tables. Defaults to True . The @schema decorator uses the class name and the data tier to check whether an appropriate table exists on the database. If a table does not already exist, the decorator creates one on the database using the definition property. The decorator attaches the information about the table to the class, and then returns the class. Diagram \u00b6 Display \u00b6 The diagram displays the relationship of the data model in the data pipeline. This can be done for an entire schema: dj . Diagram ( schema ) Or for individual or sets of tables: dj . Diagram ( schema . Rectangle ) dj . Diagram ( schema . Rectangle ) + dj . Diagram ( schema . Area ) What if I don't see the diagram? Some Python interfaces may require additional draw method. dj . Diagram ( schema ) . draw () Calling the .draw() method is not necessary when working in a Jupyter notebook by entering dj.Diagram(schema) in a notebook cell. The Diagram will automatically render in the notebook by calling its _repr_html_ method. A Diagram displayed without .draw() will be rendered as an SVG, and hovering the mouse over a table will reveal a compact version of the output of the .describe() method. Customize \u00b6 Adding or substracting a number to a diagram object adds nodes downstream or upstream, respectively, in the pipeline. ( dj . Diagram ( schema . Rectangle ) + 1 ) . draw () # (1) Plot all the tables directly downstream from schema.Rectangle ( dj . Diagram ( 'my_schema' ) - 1 + 1 ) . draw () # (1) Plot all tables directly downstream of those directly upstream of this schema. Save \u00b6 The diagram can be saved as either png or svg . dj . Diagram ( schema ) . save ( filename = 'my-diagram' , format = 'png' ) Add data \u00b6 Let's add data for a rectangle: Rectangle . insert1 ( dict ( shape_id = 1 , shape_height = 2 , shape_width = 4 )) Run computation \u00b6 Let's start the computations on our entity: Area . Area . populate ( display_progress = True ) Query \u00b6 Let's inspect the results. Area & \"shape_area >= 8\" shaped_id shape_area 1 8.0", "title": "Getting Started"}, {"location": "getting-started/#getting-started", "text": "", "title": "Getting Started"}, {"location": "getting-started/#installation", "text": "First, please install Python version 3.7 or later. We recommend 3.8. Next, please install DataJoint via one of the following: conda pip + pip + pip + Pre-Requisites Ensure you have conda installed. To add the conda-forge channel: conda config --add channels conda-forge To install: conda install -c conda-forge datajoint Pre-Requisites Ensure you have pip installed. Install graphviz pre-requisite for diagram visualization. To install: pip install datajoint Pre-Requisites Ensure you have pip installed. Install graphviz pre-requisite for diagram visualization. To install: pip install datajoint Pre-Requisites Ensure you have pip installed. Install graphviz pre-requisite for diagram visualization. To install: pip install datajoint", "title": "Installation"}, {"location": "getting-started/#connection", "text": "Note Although you may connect to any MySQL server of your choice, the DataJoint company offers an online tutorial environment. Simply sign up for a free DataJoint account . You will be granted privileges to create schemas that are prefixed as {user}_ . environment variables memory file Before using datajoint , set the following environment variables like so: 1 2 3 DJ_HOST = tutorial-db.datajoint.io DJ_USER ={ user } DJ_PASS ={ password } To set connection settings within Python, perform: 1 2 3 4 5 import datajoint as dj dj . config [ \"database.host\" ] = \"tutorial-db.datajoint.io\" dj . config [ \"database.user\" ] = \" {user} \" dj . config [ \"database.password\" ] = \" {password} \" These configuration settings can be saved either locally or system-wide using one of the following commands: dj . config . save_local () dj . config . save_global () Before using datajoint , create a file named dj_local_conf.json in the current directory like so: 1 2 3 4 5 { \"database.host\" : \"tutorial-db.datajoint.io\" , \"database.user\" : \"{user}\" , \"database.password\" : \"{password}\" } These settings will be loaded whenever a Python instance is launched from this directory. To configure settings globally, save a similar file as .datajoint_config.json in your home directory. A local config, if present, will take precedent over global settings.", "title": "Connection"}, {"location": "getting-started/#data-pipeline-definition", "text": "Let's definite a simple data pipeline. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 import datajoint as dj schema = dj . Schema ( f \" { dj . config [ 'database.user' ] } _shapes\" ) # (1) @schema # (2) class Rectangle ( dj . Manual ): definition = \"\"\" # (3) shape_id: int --- shape_height: float shape_width: float \"\"\" @schema class Area ( dj . Computed ): definition = \"\"\" -> Rectangle --- shape_area: float \"\"\" def make ( self , key ): rectangle = ( Rectangle & key ) . fetch1 () Area . insert1 ( dict ( shape_id = rectangle [ \"shape_id\" ], shape_area = rectangle [ \"shape_height\" ] * rectangle [ \"shape_width\" ], ) ) This statement creates the database schema {username}_shapes on the server. The @schema decorator for DataJoint classes creates the table on the server. The table is defined by the the definition property. It is a common practice to have a separate Python module for each schema. Therefore, each such module has only one dj.Schema object defined and is usually named schema . The dj.Schema constructor can take a number of optional parameters after the schema name. context - Dictionary for looking up foreign key references. Defaults to None to use local context. connection - Specifies the DataJoint connection object. Defaults to dj.conn() . create_schema - When False , the schema object will not create a schema on the database and will raise an error if one does not already exist. Defaults to True . create_tables - When False , the schema object will not create tables on the database and will raise errors when accessing missing tables. Defaults to True . The @schema decorator uses the class name and the data tier to check whether an appropriate table exists on the database. If a table does not already exist, the decorator creates one on the database using the definition property. The decorator attaches the information about the table to the class, and then returns the class.", "title": "Data Pipeline Definition"}, {"location": "getting-started/#diagram", "text": "", "title": "Diagram"}, {"location": "getting-started/#display", "text": "The diagram displays the relationship of the data model in the data pipeline. This can be done for an entire schema: dj . Diagram ( schema ) Or for individual or sets of tables: dj . Diagram ( schema . Rectangle ) dj . Diagram ( schema . Rectangle ) + dj . Diagram ( schema . Area ) What if I don't see the diagram? Some Python interfaces may require additional draw method. dj . Diagram ( schema ) . draw () Calling the .draw() method is not necessary when working in a Jupyter notebook by entering dj.Diagram(schema) in a notebook cell. The Diagram will automatically render in the notebook by calling its _repr_html_ method. A Diagram displayed without .draw() will be rendered as an SVG, and hovering the mouse over a table will reveal a compact version of the output of the .describe() method.", "title": "Display"}, {"location": "getting-started/#customize", "text": "Adding or substracting a number to a diagram object adds nodes downstream or upstream, respectively, in the pipeline. ( dj . Diagram ( schema . Rectangle ) + 1 ) . draw () # (1) Plot all the tables directly downstream from schema.Rectangle ( dj . Diagram ( 'my_schema' ) - 1 + 1 ) . draw () # (1) Plot all tables directly downstream of those directly upstream of this schema.", "title": "Customize"}, {"location": "getting-started/#save", "text": "The diagram can be saved as either png or svg . dj . Diagram ( schema ) . save ( filename = 'my-diagram' , format = 'png' )", "title": "Save"}, {"location": "getting-started/#add-data", "text": "Let's add data for a rectangle: Rectangle . insert1 ( dict ( shape_id = 1 , shape_height = 2 , shape_width = 4 ))", "title": "Add data"}, {"location": "getting-started/#run-computation", "text": "Let's start the computations on our entity: Area . Area . populate ( display_progress = True )", "title": "Run computation"}, {"location": "getting-started/#query", "text": "Let's inspect the results. Area & \"shape_area >= 8\" shaped_id shape_area 1 8.0", "title": "Query"}, {"location": "query-lang/common-commands/", "text": "Make \u00b6 See the article on make methods Fetch \u00b6 Entire table \u00b6 A fetch command can either retrieve table data as a NumPy recarray or a as a list of dict data = query . fetch () # (1) data = query . fetch ( as_dict = True ) # (2) NumPy recarray List of dict : For very large tables... In some cases, the amount of data returned by fetch can be quite large; it can be useful to use the size_on_disk attribute to determine if running a bare fetch would be wise. Please note that it is only currently possible to query the size of entire tables stored directly in the database at this time. Separate variables \u00b6 name , img = query . fetch1 ( 'name' , 'image' ) # when query has exactly one entity name , img = query . fetch ( 'name' , 'image' ) # [name, ...] [image, ...] Primary key values \u00b6 keydict = tab . fetch1 ( \"KEY\" ) # single key dict when tab has exactly one entity keylist = tab . fetch ( \"KEY\" ) # list of key dictionaries [{}, ...] KEY can also used when returning attribute values as separate variables, such that one of the returned variables contains the entire primary keys. Sorting results \u00b6 To sort the result, use the order_by keyword argument. data = query . fetch ( order_by = 'name' ) # ascending order data = query . fetch ( order_by = 'name desc' ) # descending order data = query . fetch ( order_by = ( 'name desc' , 'year' )) # by name first, year second data = query . fetch ( order_by = 'KEY' ) # sort by the primary key data = query . fetch ( order_by = ( 'name' , 'KEY desc' )) # sort by name but for same names order by primary key The order_by argument can be a string specifying the attribute to sort by. By default the sort is in ascending order. Use 'attr desc' to sort in descending order by attribute attr . The value can also be a sequence of strings, in which case, the sort performed on all the attributes jointly in the order specified. The special attribute name 'KEY' represents the primary key attributes in order that they appear in the index. Otherwise, this name can be used as any other argument. If an attribute happens to be a SQL reserved word, it needs to be enclosed in backquotes. For example: data = query . fetch ( order_by = '`select` desc' ) The order_by value is eventually passed to the ORDER BY clause . Limiting results \u00b6 Similar to sorting, the limit and offset arguments can be used to limit the result to a subset of entities. data = query . fetch ( order_by = 'name' , limit = 10 , offset = 5 ) Note that an offset cannot be used without specifying a limit as well. Usage with Pandas \u00b6 The pandas library is a popular library for data analysis in Python which can easily be used with DataJoint query results. Since the records returned by fetch() are contained within a numpy.recarray , they can be easily converted to pandas.DataFrame objects by passing them into the pandas.DataFrame constructor. For example: import pandas as pd frame = pd . DataFrame ( tab . fetch ()) Calling fetch() with the argument format=\"frame\" returns results as pandas.DataFrame objects indexed by the table's primary key attributes. frame = tab . fetch ( format = \"frame\" ) Returning results as a DataFrame is not possible when fetching a particular subset of attributes or when as_dict is set to True .", "title": "Common Commands"}, {"location": "query-lang/common-commands/#make", "text": "See the article on make methods", "title": "Make"}, {"location": "query-lang/common-commands/#fetch", "text": "", "title": "Fetch"}, {"location": "query-lang/common-commands/#entire-table", "text": "A fetch command can either retrieve table data as a NumPy recarray or a as a list of dict data = query . fetch () # (1) data = query . fetch ( as_dict = True ) # (2) NumPy recarray List of dict : For very large tables... In some cases, the amount of data returned by fetch can be quite large; it can be useful to use the size_on_disk attribute to determine if running a bare fetch would be wise. Please note that it is only currently possible to query the size of entire tables stored directly in the database at this time.", "title": "Entire table"}, {"location": "query-lang/common-commands/#separate-variables", "text": "name , img = query . fetch1 ( 'name' , 'image' ) # when query has exactly one entity name , img = query . fetch ( 'name' , 'image' ) # [name, ...] [image, ...]", "title": "Separate variables"}, {"location": "query-lang/common-commands/#primary-key-values", "text": "keydict = tab . fetch1 ( \"KEY\" ) # single key dict when tab has exactly one entity keylist = tab . fetch ( \"KEY\" ) # list of key dictionaries [{}, ...] KEY can also used when returning attribute values as separate variables, such that one of the returned variables contains the entire primary keys.", "title": "Primary key values"}, {"location": "query-lang/common-commands/#sorting-results", "text": "To sort the result, use the order_by keyword argument. data = query . fetch ( order_by = 'name' ) # ascending order data = query . fetch ( order_by = 'name desc' ) # descending order data = query . fetch ( order_by = ( 'name desc' , 'year' )) # by name first, year second data = query . fetch ( order_by = 'KEY' ) # sort by the primary key data = query . fetch ( order_by = ( 'name' , 'KEY desc' )) # sort by name but for same names order by primary key The order_by argument can be a string specifying the attribute to sort by. By default the sort is in ascending order. Use 'attr desc' to sort in descending order by attribute attr . The value can also be a sequence of strings, in which case, the sort performed on all the attributes jointly in the order specified. The special attribute name 'KEY' represents the primary key attributes in order that they appear in the index. Otherwise, this name can be used as any other argument. If an attribute happens to be a SQL reserved word, it needs to be enclosed in backquotes. For example: data = query . fetch ( order_by = '`select` desc' ) The order_by value is eventually passed to the ORDER BY clause .", "title": "Sorting results"}, {"location": "query-lang/common-commands/#limiting-results", "text": "Similar to sorting, the limit and offset arguments can be used to limit the result to a subset of entities. data = query . fetch ( order_by = 'name' , limit = 10 , offset = 5 ) Note that an offset cannot be used without specifying a limit as well.", "title": "Limiting results"}, {"location": "query-lang/common-commands/#usage-with-pandas", "text": "The pandas library is a popular library for data analysis in Python which can easily be used with DataJoint query results. Since the records returned by fetch() are contained within a numpy.recarray , they can be easily converted to pandas.DataFrame objects by passing them into the pandas.DataFrame constructor. For example: import pandas as pd frame = pd . DataFrame ( tab . fetch ()) Calling fetch() with the argument format=\"frame\" returns results as pandas.DataFrame objects indexed by the table's primary key attributes. frame = tab . fetch ( format = \"frame\" ) Returning results as a DataFrame is not possible when fetching a particular subset of attributes or when as_dict is set to True .", "title": "Usage with Pandas"}, {"location": "query-lang/iteration/", "text": "Iteration \u00b6 The DataJoint model primarily handles data as sets, in the form of tables. However, it can sometimes be useful to access or to perform actions such as visualization upon individual entities sequentially. In DataJoint this is accomplished through iteration. In the simple example below, iteration is used to display the names and values of the attributes of each entity in the simple table or table expression. for entity in table : print ( entity ) This example illustrates the function of the iterator: DataJoint iterates through the whole table expression, returning the entire entity during each step. In this case, each entity will be returned as a dict containing all attributes. At the start of the above loop, DataJoint internally fetches only the primary keys of the entities. Since only the primary keys are needed to distinguish between entities, DataJoint can then iterate over the list of primary keys to execute the loop. At each step of the loop, DataJoint uses a single primary key to fetch an entire entity for use in the iteration, such that print(entity) will print all attributes of each entity. By first fetching only the primary keys and then fetching each entity individually, DataJoint saves memory at the cost of network overhead. This can be particularly useful for tables containing large amounts of data in secondary attributes. The memory savings of the above syntax may not be worth the additional network overhead in all cases, such as for tables with little data stored as secondary attributes. In the example below, DataJoint fetches all of the attributes of each entity in a single call and then iterates over the list of entities stored in memory. for entity in table . fetch ( as_dict = True ): print ( entity )", "title": "Iteration"}, {"location": "query-lang/iteration/#iteration", "text": "The DataJoint model primarily handles data as sets, in the form of tables. However, it can sometimes be useful to access or to perform actions such as visualization upon individual entities sequentially. In DataJoint this is accomplished through iteration. In the simple example below, iteration is used to display the names and values of the attributes of each entity in the simple table or table expression. for entity in table : print ( entity ) This example illustrates the function of the iterator: DataJoint iterates through the whole table expression, returning the entire entity during each step. In this case, each entity will be returned as a dict containing all attributes. At the start of the above loop, DataJoint internally fetches only the primary keys of the entities. Since only the primary keys are needed to distinguish between entities, DataJoint can then iterate over the list of primary keys to execute the loop. At each step of the loop, DataJoint uses a single primary key to fetch an entire entity for use in the iteration, such that print(entity) will print all attributes of each entity. By first fetching only the primary keys and then fetching each entity individually, DataJoint saves memory at the cost of network overhead. This can be particularly useful for tables containing large amounts of data in secondary attributes. The memory savings of the above syntax may not be worth the additional network overhead in all cases, such as for tables with little data stored as secondary attributes. In the example below, DataJoint fetches all of the attributes of each entity in a single call and then iterates over the list of entities stored in memory. for entity in table . fetch ( as_dict = True ): print ( entity )", "title": "Iteration"}, {"location": "query-lang/operators/", "text": "Operators \u00b6 The examples below will use the table definitions in table tiers . Restriction \u00b6 & and - operators permit restriction. By a mapping \u00b6 For a Session table , that has the attribute session_date , we can restrict to sessions from January 1st, 2022: Session & { 'session_date' : \"2022-01-01\" } If there were any typos (e.g., using sess_date instead of session_date ), our query will return all of the entities of Session . By a string \u00b6 Conditions may include arithmetic operations, functions, range tests, etc. Restriction of table A by a string containing an attribute not found in table A produces an error. Session & 'user = \"Alice\"' # (1) Session & 'session_date >= \"2022-01-01\"' # (2) All the sessions performed by Alice All of the sessions on or after January 1st, 2022 By a collection \u00b6 When cond is a collection of conditions, the conditions are applied by logical disjunction (logical OR). Restricting a table by a collection will return all entities that meet any of the conditions in the collection. For example, if we restrict the Session table by a collection containing two conditions, one for user and one for date, the query will return any sessions with a matching user or date. A collection can be a list, a tuple, or a Pandas DataFrame . cond_list = [ 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ] # (1) cond_tuple = ( 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ) # (2) import pandas as pd cond_frame = pd . DataFrame ( data = { 'user' : [ 'Alice' ], 'session_date' : [ '2022-01-01' ]}) # (3) Session () & [ 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ] A list A tuple A data frame dj.AndList represents logical conjunction(logical AND). Restricting a table by an AndList will return all entities that meet all of the conditions in the list. A & dj.AndList([c1, c2, c3]) is equivalent to A & c1 & c2 & c3 . Student () & dj . AndList ([ 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ]) The above will show all the sessions that Alice conducted on the given day. By a Not object \u00b6 The special function dj.Not represents logical negation, such that A & dj.Not (cond) is equivalent to A - cond . By a query \u00b6 Restriction by a query object is a generalization of restriction by a table. The example below creates a query object corresponding to all the users named Alice. The Session table is then restricted by the query object, returning all the sessions performed by Alice. query = User & 'user = \"Alice\"' Session & query Proj \u00b6 Renaming an attribute in python can be done via keyword arguments: table . proj ( new_attr = 'old_attr' ) This can be done in the context of a table definition: @schema class Session ( dj . Manual ): definition = \"\"\" # Experiment Session -> Animal session : smallint # session number for the animal --- session_datetime : datetime # YYYY-MM-DD HH:MM:SS session_start_time : float # seconds relative to session_datetime session_end_time : float # seconds relative to session_datetime -> User.proj(experimenter='username') -> User.proj(supervisor='username') \"\"\" Or to rename multiple values in a table with the following syntax: Table.proj(*existing_attributes,*renamed_attributes) Session . proj ( 'session' , 'session_date' , start = 'session_start_time' , end = 'session_end_time' ) Projection can also be used to to compute new attributes from existing ones. Session . proj ( duration = 'session_end_time-session_start_time' ) & 'duration > 10' Aggr \u00b6 For more complicated calculations, we can use aggregation. Subject . aggr ( Session , n = \"count(*)\" ) # (1) Subject . aggr ( Session , average_start = \"avg(session_start_time)\" ) # (2) Number of sessions per subject. Average session_start_time for each subject Universal set \u00b6 Universal sets offer the complete list of combinations of attributes. # All home cities of students dj . U ( 'laser_wavelength' , 'laser_power' ) & Scan # (1) dj . U ( 'laser_wavelength' , 'laser_power' ) . aggr ( Scan , n = \"count(*)\" ) # (2) dj . U () . aggr ( Session , n = \"max(session)\" ) # (3) All combinations of wavelength and power. Total number of scans for each combination. Largest session number. dj.U() , as shown in the last example above, is often useful for integer IDs. For an example of this process, see the source code for Element Array Electrophysiology's insert_new_params .", "title": "Operators"}, {"location": "query-lang/operators/#operators", "text": "The examples below will use the table definitions in table tiers .", "title": "Operators"}, {"location": "query-lang/operators/#restriction", "text": "& and - operators permit restriction.", "title": "Restriction"}, {"location": "query-lang/operators/#by-a-mapping", "text": "For a Session table , that has the attribute session_date , we can restrict to sessions from January 1st, 2022: Session & { 'session_date' : \"2022-01-01\" } If there were any typos (e.g., using sess_date instead of session_date ), our query will return all of the entities of Session .", "title": "By a mapping"}, {"location": "query-lang/operators/#by-a-string", "text": "Conditions may include arithmetic operations, functions, range tests, etc. Restriction of table A by a string containing an attribute not found in table A produces an error. Session & 'user = \"Alice\"' # (1) Session & 'session_date >= \"2022-01-01\"' # (2) All the sessions performed by Alice All of the sessions on or after January 1st, 2022", "title": "By a string"}, {"location": "query-lang/operators/#by-a-collection", "text": "When cond is a collection of conditions, the conditions are applied by logical disjunction (logical OR). Restricting a table by a collection will return all entities that meet any of the conditions in the collection. For example, if we restrict the Session table by a collection containing two conditions, one for user and one for date, the query will return any sessions with a matching user or date. A collection can be a list, a tuple, or a Pandas DataFrame . cond_list = [ 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ] # (1) cond_tuple = ( 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ) # (2) import pandas as pd cond_frame = pd . DataFrame ( data = { 'user' : [ 'Alice' ], 'session_date' : [ '2022-01-01' ]}) # (3) Session () & [ 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ] A list A tuple A data frame dj.AndList represents logical conjunction(logical AND). Restricting a table by an AndList will return all entities that meet all of the conditions in the list. A & dj.AndList([c1, c2, c3]) is equivalent to A & c1 & c2 & c3 . Student () & dj . AndList ([ 'user = \"Alice\"' , 'session_date = \"2022-01-01\"' ]) The above will show all the sessions that Alice conducted on the given day.", "title": "By a collection"}, {"location": "query-lang/operators/#by-a-not-object", "text": "The special function dj.Not represents logical negation, such that A & dj.Not (cond) is equivalent to A - cond .", "title": "By a Not object"}, {"location": "query-lang/operators/#by-a-query", "text": "Restriction by a query object is a generalization of restriction by a table. The example below creates a query object corresponding to all the users named Alice. The Session table is then restricted by the query object, returning all the sessions performed by Alice. query = User & 'user = \"Alice\"' Session & query", "title": "By a query"}, {"location": "query-lang/operators/#proj", "text": "Renaming an attribute in python can be done via keyword arguments: table . proj ( new_attr = 'old_attr' ) This can be done in the context of a table definition: @schema class Session ( dj . Manual ): definition = \"\"\" # Experiment Session -> Animal session : smallint # session number for the animal --- session_datetime : datetime # YYYY-MM-DD HH:MM:SS session_start_time : float # seconds relative to session_datetime session_end_time : float # seconds relative to session_datetime -> User.proj(experimenter='username') -> User.proj(supervisor='username') \"\"\" Or to rename multiple values in a table with the following syntax: Table.proj(*existing_attributes,*renamed_attributes) Session . proj ( 'session' , 'session_date' , start = 'session_start_time' , end = 'session_end_time' ) Projection can also be used to to compute new attributes from existing ones. Session . proj ( duration = 'session_end_time-session_start_time' ) & 'duration > 10'", "title": "Proj"}, {"location": "query-lang/operators/#aggr", "text": "For more complicated calculations, we can use aggregation. Subject . aggr ( Session , n = \"count(*)\" ) # (1) Subject . aggr ( Session , average_start = \"avg(session_start_time)\" ) # (2) Number of sessions per subject. Average session_start_time for each subject", "title": "Aggr"}, {"location": "query-lang/operators/#universal-set", "text": "Universal sets offer the complete list of combinations of attributes. # All home cities of students dj . U ( 'laser_wavelength' , 'laser_power' ) & Scan # (1) dj . U ( 'laser_wavelength' , 'laser_power' ) . aggr ( Scan , n = \"count(*)\" ) # (2) dj . U () . aggr ( Session , n = \"max(session)\" ) # (3) All combinations of wavelength and power. Total number of scans for each combination. Largest session number. dj.U() , as shown in the last example above, is often useful for integer IDs. For an example of this process, see the source code for Element Array Electrophysiology's insert_new_params .", "title": "Universal set"}, {"location": "query-lang/query-caching/", "text": "Query Caching \u00b6 Query caching allows avoiding repeated queries to the database by caching the results locally for faster retrieval. To enable queries, set the query cache local path in dj.config , create the directory, and activate the query caching. dj . config [ 'query_cache' ] = os . path . expanduser ( '~/dj_query_cache' ) # (1) # (2) conn = dj . conn () # if queries co-located with tables conn = module . schema . connection # if schema co-located with tables conn = module . table . connection # most flexible conn . set_query_cache ( query_cache = 'main' ) # (3) Set the query cache path Access the active connection object for the tables Activate query caching for a namespace called 'main' The query_cache argument is an arbitrary string serving to differentiate cache states; setting a new value will effectively start a new cache, triggering retrieval of new values once. To turn off query caching, use the following: conn . set_query_cache ( query_cache = None ) ## OR conn . set_query_cache () While query caching is enabled, any insert or delete calls and any transactions are disabled and will raise an error. This ensures that stale data are not used for updating the database in violation of data integrity. To clear and remove the query cache, use the following: conn . purge_query_cache () # Purge the cached queries", "title": "Query Caching"}, {"location": "query-lang/query-caching/#query-caching", "text": "Query caching allows avoiding repeated queries to the database by caching the results locally for faster retrieval. To enable queries, set the query cache local path in dj.config , create the directory, and activate the query caching. dj . config [ 'query_cache' ] = os . path . expanduser ( '~/dj_query_cache' ) # (1) # (2) conn = dj . conn () # if queries co-located with tables conn = module . schema . connection # if schema co-located with tables conn = module . table . connection # most flexible conn . set_query_cache ( query_cache = 'main' ) # (3) Set the query cache path Access the active connection object for the tables Activate query caching for a namespace called 'main' The query_cache argument is an arbitrary string serving to differentiate cache states; setting a new value will effectively start a new cache, triggering retrieval of new values once. To turn off query caching, use the following: conn . set_query_cache ( query_cache = None ) ## OR conn . set_query_cache () While query caching is enabled, any insert or delete calls and any transactions are disabled and will raise an error. This ensures that stale data are not used for updating the database in violation of data integrity. To clear and remove the query cache, use the following: conn . purge_query_cache () # Purge the cached queries", "title": "Query Caching"}, {"location": "reproduce/make-method/", "text": "Make Method \u00b6 Consider the following table definition from the article on table tiers : @schema class FilteredImage ( dj . Computed ): definition = \"\"\" # Filtered image -> Image --- filtered_image : longblob \"\"\" def make ( self , key ): img = ( test . Image & key ) . fetch1 ( 'image' ) key [ 'filtered_image' ] = my_filter ( img ) self . insert1 ( key ) The FilteredImage table can be populated as FilteredImage . populate () The make method receives one argument: the dict key containing the primary key value of an element of key source to be worked on. Optional Arguments \u00b6 The make method also accepts a number of optional arguments that provide more features and allow greater control over the method's behavior. Argument Default Description restrictions A list of restrictions, restricting as (tab.key_source & AndList (restrictions)) - tab.proj() . Here target is the table to be populated, usually tab itself. suppress_errors False If True , encountering an error will cancel the current make call, log the error, and continue to the next make call. Error messages will be logged in the job reservation table (if reserve_jobs is True ) and returned as a list. See also return_exception_objects and reserve_jobs . return_exception_objects False If True , error objects are returned instead of error messages. This applies only when suppress_errors is True . reserve_jobs False If True , reserves job to indicate to other distributed processes. The job reservation table may be access as schema.jobs . Errors are logged in the jobs table. order original The order of execution, either \"original\" , \"reverse\" , or \"random\" . limit None If not None , checks at most this number of keys. max_calls None If not None , populates at most this many keys. Defaults to no limit. display_progress False If True , displays a progress bar. processes 1 Number of processes to use. Set to None to use all cores make_kwargs None Keyword arguments which do not affect the result of computation to be passed down to each make() call. Computation arguments should be specified within the pipeline e.g. using a dj.Lookup table. Progress \u00b6 The method table.progress reports how many key_source entries have been populated and how many remain. Two optional parameters allow more advanced use of the method. A parameter of restriction conditions can be provided, specifying which entities to consider. A Boolean parameter display (default is True ) allows disabling the output, such that the numbers of remaining and total entities are returned but not printed.", "title": "Make Method"}, {"location": "reproduce/make-method/#make-method", "text": "Consider the following table definition from the article on table tiers : @schema class FilteredImage ( dj . Computed ): definition = \"\"\" # Filtered image -> Image --- filtered_image : longblob \"\"\" def make ( self , key ): img = ( test . Image & key ) . fetch1 ( 'image' ) key [ 'filtered_image' ] = my_filter ( img ) self . insert1 ( key ) The FilteredImage table can be populated as FilteredImage . populate () The make method receives one argument: the dict key containing the primary key value of an element of key source to be worked on.", "title": "Make Method"}, {"location": "reproduce/make-method/#optional-arguments", "text": "The make method also accepts a number of optional arguments that provide more features and allow greater control over the method's behavior. Argument Default Description restrictions A list of restrictions, restricting as (tab.key_source & AndList (restrictions)) - tab.proj() . Here target is the table to be populated, usually tab itself. suppress_errors False If True , encountering an error will cancel the current make call, log the error, and continue to the next make call. Error messages will be logged in the job reservation table (if reserve_jobs is True ) and returned as a list. See also return_exception_objects and reserve_jobs . return_exception_objects False If True , error objects are returned instead of error messages. This applies only when suppress_errors is True . reserve_jobs False If True , reserves job to indicate to other distributed processes. The job reservation table may be access as schema.jobs . Errors are logged in the jobs table. order original The order of execution, either \"original\" , \"reverse\" , or \"random\" . limit None If not None , checks at most this number of keys. max_calls None If not None , populates at most this many keys. Defaults to no limit. display_progress False If True , displays a progress bar. processes 1 Number of processes to use. Set to None to use all cores make_kwargs None Keyword arguments which do not affect the result of computation to be passed down to each make() call. Computation arguments should be specified within the pipeline e.g. using a dj.Lookup table.", "title": "Optional Arguments"}, {"location": "reproduce/make-method/#progress", "text": "The method table.progress reports how many key_source entries have been populated and how many remain. Two optional parameters allow more advanced use of the method. A parameter of restriction conditions can be provided, specifying which entities to consider. A Boolean parameter display (default is True ) allows disabling the output, such that the numbers of remaining and total entities are returned but not printed.", "title": "Progress"}, {"location": "reproduce/table-tiers/", "text": "Table Tiers \u00b6 To define a DataJoint table in Python: Define a class inheriting from the appropriate DataJoint class: dj.Lookup , dj.Manual , dj.Imported or dj.Computed . Decorate the class with the schema object (see schema ) Define the class property definition to define the table heading. DataJoint for Python is implemented through the use of classes providing access to the actual tables stored on the database. Since only a single table exists on the database for any class, interactions with all instances of the class are equivalent. As such, most methods can be called on the classes themselves rather than on an object, for convenience. Whether calling a DataJoint method on a class or on an instance, the result will only depend on or apply to the corresponding table. All of the basic functionality of DataJoint is built to operate on the classes themselves, even when called on an instance. For example, calling Person.insert(...) (on the class) and Person.insert(...) (on an instance) both have the identical effect of inserting data into the table on the database server. DataJoint does not prevent a user from working with instances, but the workflow is complete without the need for instantiation. It is up to the user whether to implement additional functionality as class methods or methods called on instances. Manual Tables \u00b6 The following code defines two manual tables, Animal and Session : @schema class Animal ( dj . Manual ): definition = \"\"\" # information about animal animal_id : int # animal id assigned by the lab --- -> Species date_of_birth=null : date # YYYY-MM-DD optional sex='' : enum('M', 'F', '') # leave empty if unspecified \"\"\" @schema class Session ( dj . Manual ): definition = \"\"\" # Experiment Session -> Animal session : smallint # session number for the animal --- session_datetime : datetime # YYYY-MM-DD HH:MM:SS session_start_time : float # seconds relative to session_datetime session_end_time : float # seconds relative to session_datetime -> [nullable] User \"\"\" Note that the notation to permit null entries differs for attributes versus foreign key references. Lookup Tables \u00b6 Lookup tables are commonly populated from their contents property. The table below is declared as a lookup table with its contents property provided to generate entities. @schema class User ( dj . Lookup ): definition = \"\"\" # users in the lab username : varchar(20) # user in the lab --- first_name : varchar(20) # user first name last_name : varchar(20) # user last name \"\"\" contents = [ [ 'cajal' , 'Santiago' , 'Cajal' ], [ 'hubel' , 'David' , 'Hubel' ], [ 'wiesel' , 'Torsten' , 'Wiesel' ] ] @schema class ProcessingParamSet ( dj . Lookup ): definition = \"\"\" # Parameter set used for processing of calcium imaging data paramset_idx: smallint --- -> ProcessingMethod paramset_desc: varchar(128) param_set_hash: uuid unique index (param_set_hash) (1) params: longblob # dictionary of all applicable parameters \"\"\" This syntax enforces uniqueness of a secondary attribute. Imported and Computed Tables \u00b6 Imported and Computed tables provide make methods to determine how they are populated, either from files or other tables. Imagine that there is a table test.Image that contains 2D grayscale images in its image attribute. We can define the Computed table, test.FilteredImage that filters the image in some way and saves the result in its filtered_image attribute. @schema class FilteredImage ( dj . Computed ): definition = \"\"\" # Filtered image -> Image --- filtered_image : longblob \"\"\" def make ( self , key ): img = ( test . Image & key ) . fetch1 ( 'image' ) key [ 'filtered_image' ] = my_filter ( img ) self . insert1 ( key ) Part Tables \u00b6 The following code defines a Imported table with an associated part table. In Python, the master-part relationship is expressed by making the part a nested class of the master. The part is subclassed from dj.Part and does not need the @schema decorator. @schema class Scan ( dj . Imported ): definition = \"\"\" # Two-photon imaging scan -> Session scan : smallint # scan number within the session --- -> Lens laser_wavelength : decimal(5,1) # um laser_power : decimal(4,1) # mW \"\"\" class ScanField ( dj . Part ): definition = \"\"\" -> master ROI: longblob # Region of interest \"\"\" def make ( self , key ): ... # (1) self . insert1 ( key ) self . ScanField . insert1 ( ROI_information ) This make method is truncated for the sake of brevity. For more detailed examples, please visit Element Calcium Imaging table definitions", "title": "Table Tiers"}, {"location": "reproduce/table-tiers/#table-tiers", "text": "To define a DataJoint table in Python: Define a class inheriting from the appropriate DataJoint class: dj.Lookup , dj.Manual , dj.Imported or dj.Computed . Decorate the class with the schema object (see schema ) Define the class property definition to define the table heading. DataJoint for Python is implemented through the use of classes providing access to the actual tables stored on the database. Since only a single table exists on the database for any class, interactions with all instances of the class are equivalent. As such, most methods can be called on the classes themselves rather than on an object, for convenience. Whether calling a DataJoint method on a class or on an instance, the result will only depend on or apply to the corresponding table. All of the basic functionality of DataJoint is built to operate on the classes themselves, even when called on an instance. For example, calling Person.insert(...) (on the class) and Person.insert(...) (on an instance) both have the identical effect of inserting data into the table on the database server. DataJoint does not prevent a user from working with instances, but the workflow is complete without the need for instantiation. It is up to the user whether to implement additional functionality as class methods or methods called on instances.", "title": "Table Tiers"}, {"location": "reproduce/table-tiers/#manual-tables", "text": "The following code defines two manual tables, Animal and Session : @schema class Animal ( dj . Manual ): definition = \"\"\" # information about animal animal_id : int # animal id assigned by the lab --- -> Species date_of_birth=null : date # YYYY-MM-DD optional sex='' : enum('M', 'F', '') # leave empty if unspecified \"\"\" @schema class Session ( dj . Manual ): definition = \"\"\" # Experiment Session -> Animal session : smallint # session number for the animal --- session_datetime : datetime # YYYY-MM-DD HH:MM:SS session_start_time : float # seconds relative to session_datetime session_end_time : float # seconds relative to session_datetime -> [nullable] User \"\"\" Note that the notation to permit null entries differs for attributes versus foreign key references.", "title": "Manual Tables"}, {"location": "reproduce/table-tiers/#lookup-tables", "text": "Lookup tables are commonly populated from their contents property. The table below is declared as a lookup table with its contents property provided to generate entities. @schema class User ( dj . Lookup ): definition = \"\"\" # users in the lab username : varchar(20) # user in the lab --- first_name : varchar(20) # user first name last_name : varchar(20) # user last name \"\"\" contents = [ [ 'cajal' , 'Santiago' , 'Cajal' ], [ 'hubel' , 'David' , 'Hubel' ], [ 'wiesel' , 'Torsten' , 'Wiesel' ] ] @schema class ProcessingParamSet ( dj . Lookup ): definition = \"\"\" # Parameter set used for processing of calcium imaging data paramset_idx: smallint --- -> ProcessingMethod paramset_desc: varchar(128) param_set_hash: uuid unique index (param_set_hash) (1) params: longblob # dictionary of all applicable parameters \"\"\" This syntax enforces uniqueness of a secondary attribute.", "title": "Lookup Tables"}, {"location": "reproduce/table-tiers/#imported-and-computed-tables", "text": "Imported and Computed tables provide make methods to determine how they are populated, either from files or other tables. Imagine that there is a table test.Image that contains 2D grayscale images in its image attribute. We can define the Computed table, test.FilteredImage that filters the image in some way and saves the result in its filtered_image attribute. @schema class FilteredImage ( dj . Computed ): definition = \"\"\" # Filtered image -> Image --- filtered_image : longblob \"\"\" def make ( self , key ): img = ( test . Image & key ) . fetch1 ( 'image' ) key [ 'filtered_image' ] = my_filter ( img ) self . insert1 ( key )", "title": "Imported and Computed Tables"}, {"location": "reproduce/table-tiers/#part-tables", "text": "The following code defines a Imported table with an associated part table. In Python, the master-part relationship is expressed by making the part a nested class of the master. The part is subclassed from dj.Part and does not need the @schema decorator. @schema class Scan ( dj . Imported ): definition = \"\"\" # Two-photon imaging scan -> Session scan : smallint # scan number within the session --- -> Lens laser_wavelength : decimal(5,1) # um laser_power : decimal(4,1) # mW \"\"\" class ScanField ( dj . Part ): definition = \"\"\" -> master ROI: longblob # Region of interest \"\"\" def make ( self , key ): ... # (1) self . insert1 ( key ) self . ScanField . insert1 ( ROI_information ) This make method is truncated for the sake of brevity. For more detailed examples, please visit Element Calcium Imaging table definitions", "title": "Part Tables"}]} \ No newline at end of file diff --git a/0.13/sitemap.xml b/0.13/sitemap.xml new file mode 100644 index 000000000..f9a01e6dd --- /dev/null +++ b/0.13/sitemap.xml @@ -0,0 +1,203 @@ + + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + + None + 2022-11-11 + daily + + \ No newline at end of file diff --git a/0.13/sitemap.xml.gz b/0.13/sitemap.xml.gz new file mode 100644 index 000000000..672c6dbc7 Binary files /dev/null and b/0.13/sitemap.xml.gz differ diff --git a/0.13/tutorials/index.html b/0.13/tutorials/index.html new file mode 100644 index 000000000..1615b9063 --- /dev/null +++ b/0.13/tutorials/index.html @@ -0,0 +1,1133 @@ + + + + + + + + + + + + + + + + Tutorials - DataJoint Python + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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DataJoint for Python is a framework for building data pipelines using MySQL databases +to represent pipeline structure and bulk storage systems for large objects. +DataJoint is built on the foundation of the relational data model and prescribes a +consistent method for organizing, populating, and querying data.

The DataJoint data model is described in https://arxiv.org/abs/1807.11104

DataJoint is free software under the LGPL License. In addition, we request +that any use of DataJoint leading to a publication be acknowledged in the publication.

Please cite:

- http://biorxiv.org/content/early/2015/11/14/031658 + - http://dx.doi.org/10.1101/031658

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+ + +

+ `kill(restriction=None, connection=None, order_by=None)` + +¶

+ + +

+ +

view and kill database connections.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `restriction` +	+	+ + restriction to be applied to processlist + +	+ `None` +
+ `connection` +	+	+ + a datajoint.Connection object. Default calls datajoint.conn() + +	+ `None` +
+ `order_by` +	+	+ + order by a single attribute or the list of attributes. defaults to 'id'. + Restrictions are specified as strings and can involve any of the attributes of +information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. + Examples: + dj.kill('HOST LIKE "%compute%"') lists only connections from hosts containing "compute". + dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes + +	+ `None` +

+ + +

Source code in datajoint/admin.py

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def kill(restriction=None, connection=None, order_by=None):
+    """
+    view and kill database connections.
+
+    :param restriction: restriction to be applied to processlist
+    :param connection: a datajoint.Connection object. Default calls datajoint.conn()
+    :param order_by: order by a single attribute or the list of attributes. defaults to 'id'.
+
+    Restrictions are specified as strings and can involve any of the attributes of
+    information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO.
+
+    Examples:
+        dj.kill('HOST LIKE "%compute%"') lists only connections from hosts containing "compute".
+        dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes
+    """
+
+    if connection is None:
+        connection = conn()
+
+    if order_by is not None and not isinstance(order_by, str):
+        order_by = ",".join(order_by)
+
+    query = (
+        "SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()"
+        + ("" if restriction is None else " AND (%s)" % restriction)
+        + (" ORDER BY %s" % (order_by or "id"))
+    )
+
+    while True:
+        print("  ID USER         HOST          STATE         TIME    INFO")
+        print("+--+ +----------+ +-----------+ +-----------+ +-----+")
+        cur = (
+            {k.lower(): v for k, v in elem.items()}
+            for elem in connection.query(query, as_dict=True)
+        )
+        for process in cur:
+            try:
+                print(
+                    "{id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d}  {info}".format(
+                        **process
+                    )
+                )
+            except TypeError:
+                print(process)
+        response = input('process to kill or "q" to quit > ')
+        if response == "q":
+            break
+        if response:
+            try:
+                pid = int(response)
+            except ValueError:
+                pass  # ignore non-numeric input
+            else:
+                try:
+                    connection.query("kill %d" % pid)
+                except pymysql.err.InternalError:
+                    logger.warn("Process not found")
+

+ +

+ + + + + + +

+ + + +

+ `AttributeAdapter` + + +¶

+ + +

+ + + +

Base class for adapter objects for user-defined attribute types.

+ + + + + + + + +

Source code in datajoint/attribute_adapter.py

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class AttributeAdapter:
+    """
+    Base class for adapter objects for user-defined attribute types.
+    """
+
+    @property
+    def attribute_type(self):
+        """
+        :return: a supported DataJoint attribute type to use; e.g. "longblob", "blob@store"
+        """
+        raise NotImplementedError("Undefined attribute adapter")
+
+    def get(self, value):
+        """
+        convert value retrieved from the the attribute in a table into the adapted type
+
+        :param value: value from the database
+
+        :return: object of the adapted type
+        """
+        raise NotImplementedError("Undefined attribute adapter")
+
+    def put(self, obj):
+        """
+        convert an object of the adapted type into a value that DataJoint can store in a table attribute
+
+        :param obj: an object of the adapted type
+        :return: value to store in the database
+        """
+        raise NotImplementedError("Undefined attribute adapter")
+

+ + + +

+ + + + + + + +

+ + + +

+ `attribute_type` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a supported DataJoint attribute type to use; e.g. "longblob", "blob@store" + +

+ +

+ + + + + + +

+ + +

+ `get(value)` + +¶

+ + +

+ +

convert value retrieved from the the attribute in a table into the adapted type

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `value` +	+	+ + value from the database + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + object of the adapted type + +

+ + +

Source code in datajoint/attribute_adapter.py

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def get(self, value):
+    """
+    convert value retrieved from the the attribute in a table into the adapted type
+
+    :param value: value from the database
+
+    :return: object of the adapted type
+    """
+    raise NotImplementedError("Undefined attribute adapter")
+

+ +

+ + + + + + +

+ + +

+ `put(obj)` + +¶

+ + +

+ +

convert an object of the adapted type into a value that DataJoint can store in a table attribute

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `obj` +	+	+ + an object of the adapted type + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + value to store in the database + +

+ + +

Source code in datajoint/attribute_adapter.py

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def put(self, obj):
+    """
+    convert an object of the adapted type into a value that DataJoint can store in a table attribute
+
+    :param obj: an object of the adapted type
+    :return: value to store in the database
+    """
+    raise NotImplementedError("Undefined attribute adapter")
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `MatCell` + + +¶

+ + +

+ Bases: ndarray

+ + + +

a numpy ndarray representing a Matlab cell array

+ + + + + + + + +

Source code in datajoint/blob.py

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class MatCell(np.ndarray):
+    """a numpy ndarray representing a Matlab cell array"""
+
+    pass
+

+ +

+ + + + + + +

+ + + +

+ `MatStruct` + + +¶

+ + +

+ Bases: recarray

+ + + +

numpy.recarray representing a Matlab struct array

+ + + + + + + + +

Source code in datajoint/blob.py

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class MatStruct(np.recarray):
+    """numpy.recarray representing a Matlab struct array"""
+
+    pass
+

+ +

+ + + + + + +

+ + + +

+ `Connection` + + +¶

+ + +

+ + + +

A dj.Connection object manages a connection to a database server. +It also catalogues modules, schemas, tables, and their dependencies (foreign keys).

Most of the parameters below should be set in the local configuration file.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `host` +	+	+ + host name, may include port number as hostname:port, in which case it overrides the value in port + +	+ required +
+ `user` +	+	+ + user name + +	+ required +
+ `password` +	+	+ + password + +	+ required +
+ `port` +	+	+ + port number + +	+ `None` +
+ `init_fun` +	+	+ + connection initialization function (SQL) + +	+ `None` +
+ `use_tls` +	+	+ + TLS encryption option + +	+ `None` +

+ + + + + + + + +

Source code in datajoint/connection.py

class Connection:
+    """
+    A dj.Connection object manages a connection to a database server.
+    It also catalogues modules, schemas, tables, and their dependencies (foreign keys).
+
+    Most of the parameters below should be set in the local configuration file.
+
+    :param host: host name, may include port number as hostname:port, in which case it overrides the value in port
+    :param user: user name
+    :param password: password
+    :param port: port number
+    :param init_fun: connection initialization function (SQL)
+    :param use_tls: TLS encryption option
+    """
+
+    def __init__(self, host, user, password, port=None, init_fun=None, use_tls=None):
+        host_input, host = (host, get_host_hook(host))
+        if ":" in host:
+            # the port in the hostname overrides the port argument
+            host, port = host.split(":")
+            port = int(port)
+        elif port is None:
+            port = config["database.port"]
+        self.conn_info = dict(host=host, port=port, user=user, passwd=password)
+        if use_tls is not False:
+            self.conn_info["ssl"] = (
+                use_tls if isinstance(use_tls, dict) else {"ssl": {}}
+            )
+        self.conn_info["ssl_input"] = use_tls
+        self.conn_info["host_input"] = host_input
+        self.init_fun = init_fun
+        self._conn = None
+        self._query_cache = None
+        connect_host_hook(self)
+        if self.is_connected:
+            logger.info(
+                "DataJoint {version} connected to {user}@{host}:{port}".format(
+                    version=__version__, **self.conn_info
+                )
+            )
+            self.connection_id = self.query("SELECT connection_id()").fetchone()[0]
+        else:
+            raise errors.LostConnectionError(
+                "Connection failed {user}@{host}:{port}".format(**self.conn_info)
+            )
+        self._in_transaction = False
+        self.schemas = dict()
+        self.dependencies = Dependencies(self)
+
+    def __eq__(self, other):
+        return self.conn_info == other.conn_info
+
+    def __repr__(self):
+        connected = "connected" if self.is_connected else "disconnected"
+        return "DataJoint connection ({connected}) {user}@{host}:{port}".format(
+            connected=connected, **self.conn_info
+        )
+
+    def connect(self):
+        """Connect to the database server."""
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", ".*deprecated.*")
+            try:
+                self._conn = client.connect(
+                    init_command=self.init_fun,
+                    sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                    "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                    charset=config["connection.charset"],
+                    **{
+                        k: v
+                        for k, v in self.conn_info.items()
+                        if k not in ["ssl_input", "host_input"]
+                    },
+                )
+            except client.err.InternalError:
+                self._conn = client.connect(
+                    init_command=self.init_fun,
+                    sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                    "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                    charset=config["connection.charset"],
+                    **{
+                        k: v
+                        for k, v in self.conn_info.items()
+                        if not (
+                            k in ["ssl_input", "host_input"]
+                            or k == "ssl"
+                            and self.conn_info["ssl_input"] is None
+                        )
+                    },
+                )
+        self._conn.autocommit(True)
+
+    def set_query_cache(self, query_cache=None):
+        """
+        When query_cache is not None, the connection switches into the query caching mode, which entails:
+        1. Only SELECT queries are allowed.
+        2. The results of queries are cached under the path indicated by dj.config['query_cache']
+        3. query_cache is a string that differentiates different cache states.
+
+        :param query_cache: a string to initialize the hash for query results
+        """
+        self._query_cache = query_cache
+
+    def purge_query_cache(self):
+        """Purges all query cache."""
+        if (
+            isinstance(config.get(cache_key), str)
+            and pathlib.Path(config[cache_key]).is_dir()
+        ):
+            for path in pathlib.Path(config[cache_key]).iterdir():
+                if not path.is_dir():
+                    path.unlink()
+
+    def close(self):
+        self._conn.close()
+
+    def register(self, schema):
+        self.schemas[schema.database] = schema
+        self.dependencies.clear()
+
+    def ping(self):
+        """Ping the connection or raises an exception if the connection is closed."""
+        self._conn.ping(reconnect=False)
+
+    @property
+    def is_connected(self):
+        """Return true if the object is connected to the database server."""
+        try:
+            self.ping()
+        except:
+            return False
+        return True
+
+    @staticmethod
+    def _execute_query(cursor, query, args, suppress_warnings):
+        try:
+            with warnings.catch_warnings():
+                if suppress_warnings:
+                    # suppress all warnings arising from underlying SQL library
+                    warnings.simplefilter("ignore")
+                cursor.execute(query, args)
+        except client.err.Error as err:
+            raise translate_query_error(err, query)
+
+    def query(
+        self, query, args=(), *, as_dict=False, suppress_warnings=True, reconnect=None
+    ):
+        """
+        Execute the specified query and return the tuple generator (cursor).
+
+        :param query: SQL query
+        :param args: additional arguments for the client.cursor
+        :param as_dict: If as_dict is set to True, the returned cursor objects returns
+                        query results as dictionary.
+        :param suppress_warnings: If True, suppress all warnings arising from underlying query library
+        :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected
+        """
+        # check cache first:
+        use_query_cache = bool(self._query_cache)
+        if use_query_cache and not re.match(r"\s*(SELECT|SHOW)", query):
+            raise errors.DataJointError(
+                "Only SELECT queries are allowed when query caching is on."
+            )
+        if use_query_cache:
+            if not config[cache_key]:
+                raise errors.DataJointError(
+                    f"Provide filepath dj.config['{cache_key}'] when using query caching."
+                )
+            hash_ = uuid_from_buffer(
+                (str(self._query_cache) + re.sub(r"`\$\w+`", "", query)).encode()
+                + pack(args)
+            )
+            cache_path = pathlib.Path(config[cache_key]) / str(hash_)
+            try:
+                buffer = cache_path.read_bytes()
+            except FileNotFoundError:
+                pass  # proceed to query the database
+            else:
+                return EmulatedCursor(unpack(buffer))
+
+        if reconnect is None:
+            reconnect = config["database.reconnect"]
+        logger.debug("Executing SQL:" + query[:query_log_max_length])
+        cursor_class = client.cursors.DictCursor if as_dict else client.cursors.Cursor
+        cursor = self._conn.cursor(cursor=cursor_class)
+        try:
+            self._execute_query(cursor, query, args, suppress_warnings)
+        except errors.LostConnectionError:
+            if not reconnect:
+                raise
+            logger.warning("Reconnecting to MySQL server.")
+            connect_host_hook(self)
+            if self._in_transaction:
+                self.cancel_transaction()
+                raise errors.LostConnectionError(
+                    "Connection was lost during a transaction."
+                )
+            logger.debug("Re-executing")
+            cursor = self._conn.cursor(cursor=cursor_class)
+            self._execute_query(cursor, query, args, suppress_warnings)
+
+        if use_query_cache:
+            data = cursor.fetchall()
+            cache_path.write_bytes(pack(data))
+            return EmulatedCursor(data)
+
+        return cursor
+
+    def get_user(self):
+        """
+        :return: the user name and host name provided by the client to the server.
+        """
+        return self.query("SELECT user()").fetchone()[0]
+
+    # ---------- transaction processing
+    @property
+    def in_transaction(self):
+        """
+        :return: True if there is an open transaction.
+        """
+        self._in_transaction = self._in_transaction and self.is_connected
+        return self._in_transaction
+
+    def start_transaction(self):
+        """
+        Starts a transaction error.
+        """
+        if self.in_transaction:
+            raise errors.DataJointError("Nested connections are not supported.")
+        self.query("START TRANSACTION WITH CONSISTENT SNAPSHOT")
+        self._in_transaction = True
+        logger.debug("Transaction started")
+
+    def cancel_transaction(self):
+        """
+        Cancels the current transaction and rolls back all changes made during the transaction.
+        """
+        self.query("ROLLBACK")
+        self._in_transaction = False
+        logger.debug("Transaction cancelled. Rolling back ...")
+
+    def commit_transaction(self):
+        """
+        Commit all changes made during the transaction and close it.
+
+        """
+        self.query("COMMIT")
+        self._in_transaction = False
+        logger.debug("Transaction committed and closed.")
+
+    # -------- context manager for transactions
+    @property
+    @contextmanager
+    def transaction(self):
+        """
+        Context manager for transactions. Opens an transaction and closes it after the with statement.
+        If an error is caught during the transaction, the commits are automatically rolled back.
+        All errors are raised again.
+
+        Example:
+        >>> import datajoint as dj
+        >>> with dj.conn().transaction as conn:
+        >>>     # transaction is open here
+        """
+        try:
+            self.start_transaction()
+            yield self
+        except:
+            self.cancel_transaction()
+            raise
+        else:
+            self.commit_transaction()
+

+ + + +

+ + + + + + + +

+ + +

+ `connect()` + +¶

+ + +

+ +

Connect to the database server.

+ + +

Source code in datajoint/connection.py

def connect(self):
+    """Connect to the database server."""
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", ".*deprecated.*")
+        try:
+            self._conn = client.connect(
+                init_command=self.init_fun,
+                sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                charset=config["connection.charset"],
+                **{
+                    k: v
+                    for k, v in self.conn_info.items()
+                    if k not in ["ssl_input", "host_input"]
+                },
+            )
+        except client.err.InternalError:
+            self._conn = client.connect(
+                init_command=self.init_fun,
+                sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                charset=config["connection.charset"],
+                **{
+                    k: v
+                    for k, v in self.conn_info.items()
+                    if not (
+                        k in ["ssl_input", "host_input"]
+                        or k == "ssl"
+                        and self.conn_info["ssl_input"] is None
+                    )
+                },
+            )
+    self._conn.autocommit(True)
+

+ +

+ + + + + + +

+ + +

+ `set_query_cache(query_cache=None)` + +¶

+ + +

+ +

When query_cache is not None, the connection switches into the query caching mode, which entails: +1. Only SELECT queries are allowed. +2. The results of queries are cached under the path indicated by dj.config['query_cache'] +3. query_cache is a string that differentiates different cache states.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `query_cache` +	+	+ + a string to initialize the hash for query results + +	+ `None` +

+ + +

Source code in datajoint/connection.py

def set_query_cache(self, query_cache=None):
+    """
+    When query_cache is not None, the connection switches into the query caching mode, which entails:
+    1. Only SELECT queries are allowed.
+    2. The results of queries are cached under the path indicated by dj.config['query_cache']
+    3. query_cache is a string that differentiates different cache states.
+
+    :param query_cache: a string to initialize the hash for query results
+    """
+    self._query_cache = query_cache
+

+ +

+ + + + + + +

+ + +

+ `purge_query_cache()` + +¶

+ + +

+ +

Purges all query cache.

+ + +

Source code in datajoint/connection.py

def purge_query_cache(self):
+    """Purges all query cache."""
+    if (
+        isinstance(config.get(cache_key), str)
+        and pathlib.Path(config[cache_key]).is_dir()
+    ):
+        for path in pathlib.Path(config[cache_key]).iterdir():
+            if not path.is_dir():
+                path.unlink()
+

+ +

+ + + + + + +

+ + +

+ `ping()` + +¶

+ + +

+ +

Ping the connection or raises an exception if the connection is closed.

+ + +

Source code in datajoint/connection.py

def ping(self):
+    """Ping the connection or raises an exception if the connection is closed."""
+    self._conn.ping(reconnect=False)
+

+ +

+ + + + + + +

+ + + +

+ `is_connected` + + + `property` + + +¶

+ + +

+ +

Return true if the object is connected to the database server.

+ +

+ + + + + + +

+ + +

+ `query(query, args=(), *, as_dict=False, suppress_warnings=True, reconnect=None)` + +¶

+ + +

+ +

Execute the specified query and return the tuple generator (cursor).

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `query` +	+	+ + SQL query + +	+ required +
+ `args` +	+	+ + additional arguments for the client.cursor + +	+ `()` +
+ `as_dict` +	+	+ + If as_dict is set to True, the returned cursor objects returns +query results as dictionary. + +	+ `False` +
+ `suppress_warnings` +	+	+ + If True, suppress all warnings arising from underlying query library + +	+ `True` +
+ `reconnect` +	+	+ + when None, get from config, when True, attempt to reconnect if disconnected + +	+ `None` +

+ + +

Source code in datajoint/connection.py

def query(
+    self, query, args=(), *, as_dict=False, suppress_warnings=True, reconnect=None
+):
+    """
+    Execute the specified query and return the tuple generator (cursor).
+
+    :param query: SQL query
+    :param args: additional arguments for the client.cursor
+    :param as_dict: If as_dict is set to True, the returned cursor objects returns
+                    query results as dictionary.
+    :param suppress_warnings: If True, suppress all warnings arising from underlying query library
+    :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected
+    """
+    # check cache first:
+    use_query_cache = bool(self._query_cache)
+    if use_query_cache and not re.match(r"\s*(SELECT|SHOW)", query):
+        raise errors.DataJointError(
+            "Only SELECT queries are allowed when query caching is on."
+        )
+    if use_query_cache:
+        if not config[cache_key]:
+            raise errors.DataJointError(
+                f"Provide filepath dj.config['{cache_key}'] when using query caching."
+            )
+        hash_ = uuid_from_buffer(
+            (str(self._query_cache) + re.sub(r"`\$\w+`", "", query)).encode()
+            + pack(args)
+        )
+        cache_path = pathlib.Path(config[cache_key]) / str(hash_)
+        try:
+            buffer = cache_path.read_bytes()
+        except FileNotFoundError:
+            pass  # proceed to query the database
+        else:
+            return EmulatedCursor(unpack(buffer))
+
+    if reconnect is None:
+        reconnect = config["database.reconnect"]
+    logger.debug("Executing SQL:" + query[:query_log_max_length])
+    cursor_class = client.cursors.DictCursor if as_dict else client.cursors.Cursor
+    cursor = self._conn.cursor(cursor=cursor_class)
+    try:
+        self._execute_query(cursor, query, args, suppress_warnings)
+    except errors.LostConnectionError:
+        if not reconnect:
+            raise
+        logger.warning("Reconnecting to MySQL server.")
+        connect_host_hook(self)
+        if self._in_transaction:
+            self.cancel_transaction()
+            raise errors.LostConnectionError(
+                "Connection was lost during a transaction."
+            )
+        logger.debug("Re-executing")
+        cursor = self._conn.cursor(cursor=cursor_class)
+        self._execute_query(cursor, query, args, suppress_warnings)
+
+    if use_query_cache:
+        data = cursor.fetchall()
+        cache_path.write_bytes(pack(data))
+        return EmulatedCursor(data)
+
+    return cursor
+

+ +

+ + + + + + +

+ + +

+ `get_user()` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the user name and host name provided by the client to the server. + +

+ + +

Source code in datajoint/connection.py

def get_user(self):
+    """
+    :return: the user name and host name provided by the client to the server.
+    """
+    return self.query("SELECT user()").fetchone()[0]
+

+ +

+ + + + + + +

+ + + +

+ `in_transaction` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + True if there is an open transaction. + +

+ +

+ + + + + + +

+ + +

+ `start_transaction()` + +¶

+ + +

+ +

Starts a transaction error.

+ + +

Source code in datajoint/connection.py

def start_transaction(self):
+    """
+    Starts a transaction error.
+    """
+    if self.in_transaction:
+        raise errors.DataJointError("Nested connections are not supported.")
+    self.query("START TRANSACTION WITH CONSISTENT SNAPSHOT")
+    self._in_transaction = True
+    logger.debug("Transaction started")
+

+ +

+ + + + + + +

+ + +

+ `cancel_transaction()` + +¶

+ + +

+ +

Cancels the current transaction and rolls back all changes made during the transaction.

+ + +

Source code in datajoint/connection.py

def cancel_transaction(self):
+    """
+    Cancels the current transaction and rolls back all changes made during the transaction.
+    """
+    self.query("ROLLBACK")
+    self._in_transaction = False
+    logger.debug("Transaction cancelled. Rolling back ...")
+

+ +

+ + + + + + +

+ + +

+ `commit_transaction()` + +¶

+ + +

+ +

Commit all changes made during the transaction and close it.

+ + +

Source code in datajoint/connection.py

def commit_transaction(self):
+    """
+    Commit all changes made during the transaction and close it.
+
+    """
+    self.query("COMMIT")
+    self._in_transaction = False
+    logger.debug("Transaction committed and closed.")
+

+ +

+ + + + + + +

+ + + +

+ `transaction` + + + `property` + + +¶

+ + +

+ +

Context manager for transactions. Opens an transaction and closes it after the with statement. +If an error is caught during the transaction, the commits are automatically rolled back. +All errors are raised again.

Example:

+
+
+
import datajoint as dj +with dj.conn().transaction as conn: + # transaction is open here
+
+
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + +

+ `conn(host=None, user=None, password=None, *, init_fun=None, reset=False, use_tls=None)` + +¶

+ + +

+ +

Returns a persistent connection object to be shared by multiple modules. +If the connection is not yet established or reset=True, a new connection is set up. +If connection information is not provided, it is taken from config which takes the +information from dj_local_conf.json. If the password is not specified in that file +datajoint prompts for the password.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `host` +	+	+ + hostname + +	+ `None` +
+ `user` +	+	+ + mysql user + +	+ `None` +
+ `password` +	+	+ + mysql password + +	+ `None` +
+ `init_fun` +	+	+ + initialization function + +	+ `None` +
+ `reset` +	+	+ + whether the connection should be reset or not + +	+ `False` +
+ `use_tls` +	+	+ + TLS encryption option. Valid options are: True (required), False +(required no TLS), None (TLS preferred, default), dict (Manually specify values per +https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). + +	+ `None` +

+ + +

Source code in datajoint/connection.py

def conn(
+    host=None, user=None, password=None, *, init_fun=None, reset=False, use_tls=None
+):
+    """
+    Returns a persistent connection object to be shared by multiple modules.
+    If the connection is not yet established or reset=True, a new connection is set up.
+    If connection information is not provided, it is taken from config which takes the
+    information from dj_local_conf.json. If the password is not specified in that file
+    datajoint prompts for the password.
+
+    :param host: hostname
+    :param user: mysql user
+    :param password: mysql password
+    :param init_fun: initialization function
+    :param reset: whether the connection should be reset or not
+    :param use_tls: TLS encryption option. Valid options are: True (required), False
+        (required no TLS), None (TLS preferred, default), dict (Manually specify values per
+        https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options).
+    """
+    if not hasattr(conn, "connection") or reset:
+        host = host if host is not None else config["database.host"]
+        user = user if user is not None else config["database.user"]
+        password = password if password is not None else config["database.password"]
+        if user is None:
+            user = input("Please enter DataJoint username: ")
+        if password is None:
+            password = getpass(prompt="Please enter DataJoint password: ")
+        init_fun = (
+            init_fun if init_fun is not None else config["connection.init_function"]
+        )
+        use_tls = use_tls if use_tls is not None else config["database.use_tls"]
+        conn.connection = Connection(host, user, password, None, init_fun, use_tls)
+    return conn.connection
+

+ +

+ + + + + + +

+ + + +

+ `Diagram` + + +¶

+ + +

+ Bases: DiGraph

+ + + +

Schema diagram showing tables and foreign keys between in the form of a directed +acyclic graph (DAG). The diagram is derived from the connection.dependencies object.

Usage:

+
+
+
diag = Diagram(source)
+
+
+

source can be a table object, a table class, a schema, or a module that has a schema.

+
+
+
diag.draw()
+
+
+

draws the diagram using pyplot

diag1 + diag2 - combines the two diagrams. +diag1 - diag2 - difference between diagrams +diag1 * diag2 - intersection of diagrams +diag + n - expands n levels of successors +diag - n - expands n levels of predecessors +Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table

Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. +Only those tables that are loaded in the connection object are displayed

+ + + + + + + + +

Source code in datajoint/diagram.py

class Diagram(nx.DiGraph):
+    """
+    Schema diagram showing tables and foreign keys between in the form of a directed
+    acyclic graph (DAG).  The diagram is derived from the connection.dependencies object.
+
+    Usage:
+
+    >>>  diag = Diagram(source)
+
+    source can be a table object, a table class, a schema, or a module that has a schema.
+
+    >>> diag.draw()
+
+    draws the diagram using pyplot
+
+    diag1 + diag2  - combines the two diagrams.
+    diag1 - diag2  - difference between diagrams
+    diag1 * diag2  - intersection of diagrams
+    diag + n   - expands n levels of successors
+    diag - n   - expands n levels of predecessors
+    Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table
+
+    Note that diagram + 1 - 1  may differ from diagram - 1 + 1 and so forth.
+    Only those tables that are loaded in the connection object are displayed
+    """
+
+    def __init__(self, source, context=None):
+
+        if isinstance(source, Diagram):
+            # copy constructor
+            self.nodes_to_show = set(source.nodes_to_show)
+            self.context = source.context
+            super().__init__(source)
+            return
+
+        # get the caller's context
+        if context is None:
+            frame = inspect.currentframe().f_back
+            self.context = dict(frame.f_globals, **frame.f_locals)
+            del frame
+        else:
+            self.context = context
+
+        # find connection in the source
+        try:
+            connection = source.connection
+        except AttributeError:
+            try:
+                connection = source.schema.connection
+            except AttributeError:
+                raise DataJointError(
+                    "Could not find database connection in %s" % repr(source[0])
+                )
+
+        # initialize graph from dependencies
+        connection.dependencies.load()
+        super().__init__(connection.dependencies)
+
+        # Enumerate nodes from all the items in the list
+        self.nodes_to_show = set()
+        try:
+            self.nodes_to_show.add(source.full_table_name)
+        except AttributeError:
+            try:
+                database = source.database
+            except AttributeError:
+                try:
+                    database = source.schema.database
+                except AttributeError:
+                    raise DataJointError(
+                        "Cannot plot Diagram for %s" % repr(source)
+                    )
+            for node in self:
+                if node.startswith("`%s`" % database):
+                    self.nodes_to_show.add(node)
+
+    @classmethod
+    def from_sequence(cls, sequence):
+        """
+        The join Diagram for all objects in sequence
+
+        :param sequence: a sequence (e.g. list, tuple)
+        :return: Diagram(arg1) + ... + Diagram(argn)
+        """
+        return functools.reduce(lambda x, y: x + y, map(Diagram, sequence))
+
+    def add_parts(self):
+        """
+        Adds to the diagram the part tables of all master tables already in the diagram
+        :return:
+        """
+
+        def is_part(part, master):
+            """
+            :param part:  `database`.`table_name`
+            :param master:   `database`.`table_name`
+            :return: True if part is part of master.
+            """
+            part = [s.strip("`") for s in part.split(".")]
+            master = [s.strip("`") for s in master.split(".")]
+            return (
+                master[0] == part[0]
+                and master[1] + "__" == part[1][: len(master[1]) + 2]
+            )
+
+        self = Diagram(self)  # copy
+        self.nodes_to_show.update(
+            n
+            for n in self.nodes()
+            if any(is_part(n, m) for m in self.nodes_to_show)
+        )
+        return self
+
+    def __add__(self, arg):
+        """
+        :param arg: either another Diagram or a positive integer.
+        :return: Union of the diagrams when arg is another Diagram
+                 or an expansion downstream when arg is a positive integer.
+        """
+        self = Diagram(self)  # copy
+        try:
+            self.nodes_to_show.update(arg.nodes_to_show)
+        except AttributeError:
+            try:
+                self.nodes_to_show.add(arg.full_table_name)
+            except AttributeError:
+                for i in range(arg):
+                    new = nx.algorithms.boundary.node_boundary(
+                        self, self.nodes_to_show
+                    )
+                    if not new:
+                        break
+                    # add nodes referenced by aliased nodes
+                    new.update(
+                        nx.algorithms.boundary.node_boundary(
+                            self, (a for a in new if a.isdigit())
+                        )
+                    )
+                    self.nodes_to_show.update(new)
+        return self
+
+    def __sub__(self, arg):
+        """
+        :param arg: either another Diagram or a positive integer.
+        :return: Difference of the diagrams when arg is another Diagram or
+                 an expansion upstream when arg is a positive integer.
+        """
+        self = Diagram(self)  # copy
+        try:
+            self.nodes_to_show.difference_update(arg.nodes_to_show)
+        except AttributeError:
+            try:
+                self.nodes_to_show.remove(arg.full_table_name)
+            except AttributeError:
+                for i in range(arg):
+                    graph = nx.DiGraph(self).reverse()
+                    new = nx.algorithms.boundary.node_boundary(
+                        graph, self.nodes_to_show
+                    )
+                    if not new:
+                        break
+                    # add nodes referenced by aliased nodes
+                    new.update(
+                        nx.algorithms.boundary.node_boundary(
+                            graph, (a for a in new if a.isdigit())
+                        )
+                    )
+                    self.nodes_to_show.update(new)
+        return self
+
+    def __mul__(self, arg):
+        """
+        Intersection of two diagrams
+        :param arg: another Diagram
+        :return: a new Diagram comprising nodes that are present in both operands.
+        """
+        self = Diagram(self)  # copy
+        self.nodes_to_show.intersection_update(arg.nodes_to_show)
+        return self
+
+    def topo_sort(self):
+        """return nodes in lexicographical topological order"""
+        return topo_sort(self)
+
+    def _make_graph(self):
+        """
+        Make the self.graph - a graph object ready for drawing
+        """
+        # mark "distinguished" tables, i.e. those that introduce new primary key
+        # attributes
+        for name in self.nodes_to_show:
+            foreign_attributes = set(
+                attr
+                for p in self.in_edges(name, data=True)
+                for attr in p[2]["attr_map"]
+                if p[2]["primary"]
+            )
+            self.nodes[name]["distinguished"] = (
+                "primary_key" in self.nodes[name]
+                and foreign_attributes < self.nodes[name]["primary_key"]
+            )
+        # include aliased nodes that are sandwiched between two displayed nodes
+        gaps = set(
+            nx.algorithms.boundary.node_boundary(self, self.nodes_to_show)
+        ).intersection(
+            nx.algorithms.boundary.node_boundary(
+                nx.DiGraph(self).reverse(), self.nodes_to_show
+            )
+        )
+        nodes = self.nodes_to_show.union(a for a in gaps if a.isdigit)
+        # construct subgraph and rename nodes to class names
+        graph = nx.DiGraph(nx.DiGraph(self).subgraph(nodes))
+        nx.set_node_attributes(
+            graph, name="node_type", values={n: _get_tier(n) for n in graph}
+        )
+        # relabel nodes to class names
+        mapping = {
+            node: lookup_class_name(node, self.context) or node
+            for node in graph.nodes()
+        }
+        new_names = [mapping.values()]
+        if len(new_names) > len(set(new_names)):
+            raise DataJointError(
+                "Some classes have identical names. The Diagram cannot be plotted."
+            )
+        nx.relabel_nodes(graph, mapping, copy=False)
+        return graph
+
+    @staticmethod
+    def _encapsulate_edge_attributes(graph):
+        """
+        Modifies the `nx.Graph`'s edge attribute `attr_map` to be a string representation
+        of the attribute map, and encapsulates the string in double quotes.
+        Changes the graph in place.
+
+        Implements workaround described in
+        https://github.com/pydot/pydot/issues/258#issuecomment-795798099
+        """
+        for u, v, *_, edgedata in graph.edges(data=True):
+            if "attr_map" in edgedata:
+                graph.edges[u, v]["attr_map"] = '"{0}"'.format(edgedata["attr_map"])
+
+    @staticmethod
+    def _encapsulate_node_names(graph):
+        """
+        Modifies the `nx.Graph`'s node names string representations encapsulated in
+        double quotes.
+        Changes the graph in place.
+
+        Implements workaround described in
+        https://github.com/datajoint/datajoint-python/pull/1176
+        """
+        nx.relabel_nodes(
+            graph,
+            {node: '"{0}"'.format(node) for node in graph.nodes()},
+            copy=False,
+        )
+
+    def make_dot(self):
+        graph = self._make_graph()
+        graph.nodes()
+
+        scale = 1.2  # scaling factor for fonts and boxes
+        label_props = {  # http://matplotlib.org/examples/color/named_colors.html
+            None: dict(
+                shape="circle",
+                color="#FFFF0040",
+                fontcolor="yellow",
+                fontsize=round(scale * 8),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            _AliasNode: dict(
+                shape="circle",
+                color="#FF880080",
+                fontcolor="#FF880080",
+                fontsize=round(scale * 0),
+                size=0.05 * scale,
+                fixed=True,
+            ),
+            Manual: dict(
+                shape="box",
+                color="#00FF0030",
+                fontcolor="darkgreen",
+                fontsize=round(scale * 10),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            Lookup: dict(
+                shape="plaintext",
+                color="#00000020",
+                fontcolor="black",
+                fontsize=round(scale * 8),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            Computed: dict(
+                shape="ellipse",
+                color="#FF000020",
+                fontcolor="#7F0000A0",
+                fontsize=round(scale * 10),
+                size=0.3 * scale,
+                fixed=True,
+            ),
+            Imported: dict(
+                shape="ellipse",
+                color="#00007F40",
+                fontcolor="#00007FA0",
+                fontsize=round(scale * 10),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            Part: dict(
+                shape="plaintext",
+                color="#0000000",
+                fontcolor="black",
+                fontsize=round(scale * 8),
+                size=0.1 * scale,
+                fixed=False,
+            ),
+        }
+        node_props = {
+            node: label_props[d["node_type"]]
+            for node, d in dict(graph.nodes(data=True)).items()
+        }
+
+        self._encapsulate_node_names(graph)
+        self._encapsulate_edge_attributes(graph)
+        dot = nx.drawing.nx_pydot.to_pydot(graph)
+        for node in dot.get_nodes():
+            node.set_shape("circle")
+            name = node.get_name().strip('"')
+            props = node_props[name]
+            node.set_fontsize(props["fontsize"])
+            node.set_fontcolor(props["fontcolor"])
+            node.set_shape(props["shape"])
+            node.set_fontname("arial")
+            node.set_fixedsize("shape" if props["fixed"] else False)
+            node.set_width(props["size"])
+            node.set_height(props["size"])
+            if name.split(".")[0] in self.context:
+                cls = eval(name, self.context)
+                assert issubclass(cls, Table)
+                description = cls().describe(context=self.context).split("\n")
+                description = (
+                    (
+                        "-" * 30
+                        if q.startswith("---")
+                        else (
+                            q.replace("->", "&#8594;")
+                            if "->" in q
+                            else q.split(":")[0]
+                        )
+                    )
+                    for q in description
+                    if not q.startswith("#")
+                )
+                node.set_tooltip("&#13;".join(description))
+            node.set_label(
+                "<<u>" + name + "</u>>"
+                if node.get("distinguished") == "True"
+                else name
+            )
+            node.set_color(props["color"])
+            node.set_style("filled")
+
+        for edge in dot.get_edges():
+            # see https://graphviz.org/doc/info/attrs.html
+            src = edge.get_source()
+            dest = edge.get_destination()
+            props = graph.get_edge_data(src, dest)
+            if props is None:
+                raise DataJointError(
+                    "Could not find edge with source "
+                    "'{}' and destination '{}'".format(src, dest)
+                )
+            edge.set_color("#00000040")
+            edge.set_style("solid" if props["primary"] else "dashed")
+            master_part = graph.nodes[dest][
+                "node_type"
+            ] is Part and dest.startswith(src + ".")
+            edge.set_weight(3 if master_part else 1)
+            edge.set_arrowhead("none")
+            edge.set_penwidth(0.75 if props["multi"] else 2)
+
+        return dot
+
+    def make_svg(self):
+        from IPython.display import SVG
+
+        return SVG(self.make_dot().create_svg())
+
+    def make_png(self):
+        return io.BytesIO(self.make_dot().create_png())
+
+    def make_image(self):
+        if plot_active:
+            return plt.imread(self.make_png())
+        else:
+            raise DataJointError("pyplot was not imported")
+
+    def _repr_svg_(self):
+        return self.make_svg()._repr_svg_()
+
+    def draw(self):
+        if plot_active:
+            plt.imshow(self.make_image())
+            plt.gca().axis("off")
+            plt.show()
+        else:
+            raise DataJointError("pyplot was not imported")
+
+    def save(self, filename, format=None):
+        if format is None:
+            if filename.lower().endswith(".png"):
+                format = "png"
+            elif filename.lower().endswith(".svg"):
+                format = "svg"
+        if format.lower() == "png":
+            with open(filename, "wb") as f:
+                f.write(self.make_png().getbuffer().tobytes())
+        elif format.lower() == "svg":
+            with open(filename, "w") as f:
+                f.write(self.make_svg().data)
+        else:
+            raise DataJointError("Unsupported file format")
+
+    @staticmethod
+    def _layout(graph, **kwargs):
+        return pydot_layout(graph, prog="dot", **kwargs)
+

+ + + +

+ + + + + + + +

+ + +

+ `from_sequence(sequence)` + + + `classmethod` + + +¶

+ + +

+ +

The join Diagram for all objects in sequence

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `sequence` +	+	+ + a sequence (e.g. list, tuple) + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + Diagram(arg1) + ... + Diagram(argn) + +

+ + +

Source code in datajoint/diagram.py

@classmethod
+def from_sequence(cls, sequence):
+    """
+    The join Diagram for all objects in sequence
+
+    :param sequence: a sequence (e.g. list, tuple)
+    :return: Diagram(arg1) + ... + Diagram(argn)
+    """
+    return functools.reduce(lambda x, y: x + y, map(Diagram, sequence))
+

+ +

+ + + + + + +

+ + +

+ `add_parts()` + +¶

+ + +

+ +

Adds to the diagram the part tables of all master tables already in the diagram

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + + +

+ + +

Source code in datajoint/diagram.py

def add_parts(self):
+    """
+    Adds to the diagram the part tables of all master tables already in the diagram
+    :return:
+    """
+
+    def is_part(part, master):
+        """
+        :param part:  `database`.`table_name`
+        :param master:   `database`.`table_name`
+        :return: True if part is part of master.
+        """
+        part = [s.strip("`") for s in part.split(".")]
+        master = [s.strip("`") for s in master.split(".")]
+        return (
+            master[0] == part[0]
+            and master[1] + "__" == part[1][: len(master[1]) + 2]
+        )
+
+    self = Diagram(self)  # copy
+    self.nodes_to_show.update(
+        n
+        for n in self.nodes()
+        if any(is_part(n, m) for m in self.nodes_to_show)
+    )
+    return self
+

+ +

+ + + + + + +

+ + +

+ `topo_sort()` + +¶

+ + +

+ +

return nodes in lexicographical topological order

+ + +

Source code in datajoint/diagram.py

def topo_sort(self):
+    """return nodes in lexicographical topological order"""
+    return topo_sort(self)
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `DataJointError` + + +¶

+ + +

+ Bases: Exception

+ + + +

Base class for errors specific to DataJoint internal operation.

+ + + + + + + + +

Source code in datajoint/errors.py

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class DataJointError(Exception):
+    """
+    Base class for errors specific to DataJoint internal operation.
+    """
+
+    def __init__(self, *args):
+        from .plugin import connection_plugins, type_plugins
+
+        self.__cause__ = (
+            PluginWarning("Unverified DataJoint plugin detected.")
+            if any(
+                [
+                    any([not plugins[k]["verified"] for k in plugins])
+                    for plugins in [connection_plugins, type_plugins]
+                    if plugins
+                ]
+            )
+            else None
+        )
+
+    def suggest(self, *args):
+        """
+        regenerate the exception with additional arguments
+
+        :param args: addition arguments
+        :return: a new exception of the same type with the additional arguments
+        """
+        return self.__class__(*(self.args + args))
+

+ + + +

+ + + + + + + +

+ + +

+ `suggest(*args)` + +¶

+ + +

+ +

regenerate the exception with additional arguments

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `args` +	+	+ + addition arguments + +	+ `()` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a new exception of the same type with the additional arguments + +

+ + +

Source code in datajoint/errors.py

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def suggest(self, *args):
+    """
+    regenerate the exception with additional arguments
+
+    :param args: addition arguments
+    :return: a new exception of the same type with the additional arguments
+    """
+    return self.__class__(*(self.args + args))
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `AndList` + + +¶

+ + +

+ Bases: list

+ + + +

A list of conditions to by applied to a query expression by logical conjunction: the +conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are +applied by logical disjunction (OR).

Example: +expr2 = expr & dj.AndList((cond1, cond2, cond3)) +is equivalent to +expr2 = expr & cond1 & cond2 & cond3

+ + + + + + + + +

Source code in datajoint/condition.py

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class AndList(list):
+    """
+    A list of conditions to by applied to a query expression by logical conjunction: the
+    conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are
+    applied by logical disjunction (OR).
+
+    Example:
+    expr2 = expr & dj.AndList((cond1, cond2, cond3))
+    is equivalent to
+    expr2 = expr & cond1 & cond2 & cond3
+    """
+
+    def append(self, restriction):
+        if isinstance(restriction, AndList):
+            # extend to reduce nesting
+            self.extend(restriction)
+        else:
+            super().append(restriction)
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Not` + + +¶

+ + +

+ + + +

invert restriction

+ + + + + + + + +

Source code in datajoint/condition.py

class Not:
+    """invert restriction"""
+
+    def __init__(self, restriction):
+        self.restriction = restriction
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Top` + + + + `dataclass` + + +¶

+ + +

+ + + +

A restriction to the top entities of a query. +In SQL, this corresponds to ORDER BY ... LIMIT ... OFFSET

+ + + + + + + + +

Source code in datajoint/condition.py

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@dataclass
+class Top:
+    """
+    A restriction to the top entities of a query.
+    In SQL, this corresponds to ORDER BY ... LIMIT ... OFFSET
+    """
+
+    limit: Union[int, None] = 1
+    order_by: Union[str, List[str]] = "KEY"
+    offset: int = 0
+
+    def __post_init__(self):
+        self.order_by = self.order_by or ["KEY"]
+        self.offset = self.offset or 0
+
+        if self.limit is not None and not isinstance(self.limit, int):
+            raise TypeError("Top limit must be an integer")
+        if not isinstance(self.order_by, (str, collections.abc.Sequence)) or not all(
+            isinstance(r, str) for r in self.order_by
+        ):
+            raise TypeError("Top order_by attributes must all be strings")
+        if not isinstance(self.offset, int):
+            raise TypeError("The offset argument must be an integer")
+        if self.offset and self.limit is None:
+            self.limit = 999999999999  # arbitrary large number to allow query
+        if isinstance(self.order_by, str):
+            self.order_by = [self.order_by]
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `U` + + +¶

+ + +

+ + + +

dj.U objects are the universal sets representing all possible values of their attributes. +dj.U objects cannot be queried on their own but are useful for forming some queries. +dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn. +The universal set is the set of all possible combinations of values of the attributes. +Without any attributes, dj.U() represents the set with one element that has no attributes.

Restriction:

dj.U can be used to enumerate unique combinations of values of attributes from other expressions.

The following expression yields all unique combinations of contrast and brightness found in the stimulus set:

+
+
+
dj.U('contrast', 'brightness') & stimulus
+
+
+

Aggregation:

In aggregation, dj.U is used for summary calculation over an entire set:

The following expression yields one element with one attribute s containing the total number of elements in +query expression expr:

+
+
+
dj.U().aggr(expr, n='count(*)')
+
+
+

The following expressions both yield one element containing the number n of distinct values of attribute attr in +query expression expr.

+
+
+
dj.U().aggr(expr, n='count(distinct attr)') +dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)')
+
+
+

The following expression yields one element and one attribute s containing the sum of values of attribute attr +over entire result set of expression expr:

+
+
+
dj.U().aggr(expr, s='sum(attr)')
+
+
+

The following expression yields the set of all unique combinations of attributes attr1, attr2 and the number of +their occurrences in the result set of query expression expr.

+
+
+
dj.U(attr1,attr2).aggr(expr, n='count(*)')
+
+
+

Joins:

If expression expr has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result +as expr but attr1 and attr2 are promoted to the the primary key. This is useful for producing a join on +non-primary key attributes. +For example, if attr is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw +an error because in most cases, it does not make sense to join on non-primary key attributes and users must first +rename attr in one of the operands. The expression dj.U('attr') * rel1 * rel2 overrides this constraint.

+ + + + + + + + +

Source code in datajoint/expression.py

class U:
+    """
+    dj.U objects are the universal sets representing all possible values of their attributes.
+    dj.U objects cannot be queried on their own but are useful for forming some queries.
+    dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn.
+    The universal set is the set of all possible combinations of values of the attributes.
+    Without any attributes, dj.U() represents the set with one element that has no attributes.
+
+    Restriction:
+
+    dj.U can be used to enumerate unique combinations of values of attributes from other expressions.
+
+    The following expression yields all unique combinations of contrast and brightness found in the `stimulus` set:
+
+    >>> dj.U('contrast', 'brightness') & stimulus
+
+    Aggregation:
+
+    In aggregation, dj.U is used for summary calculation over an entire set:
+
+    The following expression yields one element with one attribute `s` containing the total number of elements in
+    query expression `expr`:
+
+    >>> dj.U().aggr(expr, n='count(*)')
+
+    The following expressions both yield one element containing the number `n` of distinct values of attribute `attr` in
+    query expression `expr`.
+
+    >>> dj.U().aggr(expr, n='count(distinct attr)')
+    >>> dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)')
+
+    The following expression yields one element and one attribute `s` containing the sum of values of attribute `attr`
+    over entire result set of expression `expr`:
+
+    >>> dj.U().aggr(expr, s='sum(attr)')
+
+    The following expression yields the set of all unique combinations of attributes `attr1`, `attr2` and the number of
+    their occurrences in the result set of query expression `expr`.
+
+    >>> dj.U(attr1,attr2).aggr(expr, n='count(*)')
+
+    Joins:
+
+    If expression `expr` has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result
+    as `expr` but `attr1` and `attr2` are promoted to the the primary key.  This is useful for producing a join on
+    non-primary key attributes.
+    For example, if `attr` is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw
+    an error because in most cases, it does not make sense to join on non-primary key attributes and users must first
+    rename `attr` in one of the operands.  The expression dj.U('attr') * rel1 * rel2 overrides this constraint.
+    """
+
+    def __init__(self, *primary_key):
+        self._primary_key = primary_key
+
+    @property
+    def primary_key(self):
+        return self._primary_key
+
+    def __and__(self, other):
+        if inspect.isclass(other) and issubclass(other, QueryExpression):
+            other = other()  # instantiate if a class
+        if not isinstance(other, QueryExpression):
+            raise DataJointError("Set U can only be restricted with a QueryExpression.")
+        result = copy.copy(other)
+        result._distinct = True
+        result._heading = result.heading.set_primary_key(self.primary_key)
+        result = result.proj()
+        return result
+
+    def join(self, other, left=False):
+        """
+        Joining U with a query expression has the effect of promoting the attributes of U to
+        the primary key of the other query expression.
+
+        :param other: the other query expression to join with.
+        :param left: ignored. dj.U always acts as if left=False
+        :return: a copy of the other query expression with the primary key extended.
+        """
+        if inspect.isclass(other) and issubclass(other, QueryExpression):
+            other = other()  # instantiate if a class
+        if not isinstance(other, QueryExpression):
+            raise DataJointError("Set U can only be joined with a QueryExpression.")
+        try:
+            raise DataJointError(
+                "Attribute `%s` not found"
+                % next(k for k in self.primary_key if k not in other.heading.names)
+            )
+        except StopIteration:
+            pass  # all ok
+        result = copy.copy(other)
+        result._heading = result.heading.set_primary_key(
+            other.primary_key
+            + [k for k in self.primary_key if k not in other.primary_key]
+        )
+        return result
+
+    def __mul__(self, other):
+        """shorthand for join"""
+        return self.join(other)
+
+    def aggr(self, group, **named_attributes):
+        """
+        Aggregation of the type U('attr1','attr2').aggr(group, computation="QueryExpression")
+        has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`.
+
+        :param group:  The query expression to be aggregated.
+        :param named_attributes: computations of the form new_attribute="sql expression on attributes of group"
+        :return: The derived query expression
+        """
+        if named_attributes.get("keep_all_rows", False):
+            raise DataJointError(
+                "Cannot set keep_all_rows=True when aggregating on a universal set."
+            )
+        return Aggregation.create(self, group=group, keep_all_rows=False).proj(
+            **named_attributes
+        )
+
+    aggregate = aggr  # alias for aggr
+

+ + + +

+ + + + + + + +

+ + +

+ `join(other, left=False)` + +¶

+ + +

+ +

Joining U with a query expression has the effect of promoting the attributes of U to +the primary key of the other query expression.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `other` +	+	+ + the other query expression to join with. + +	+ required +
+ `left` +	+	+ + ignored. dj.U always acts as if left=False + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a copy of the other query expression with the primary key extended. + +

+ + +

Source code in datajoint/expression.py

def join(self, other, left=False):
+    """
+    Joining U with a query expression has the effect of promoting the attributes of U to
+    the primary key of the other query expression.
+
+    :param other: the other query expression to join with.
+    :param left: ignored. dj.U always acts as if left=False
+    :return: a copy of the other query expression with the primary key extended.
+    """
+    if inspect.isclass(other) and issubclass(other, QueryExpression):
+        other = other()  # instantiate if a class
+    if not isinstance(other, QueryExpression):
+        raise DataJointError("Set U can only be joined with a QueryExpression.")
+    try:
+        raise DataJointError(
+            "Attribute `%s` not found"
+            % next(k for k in self.primary_key if k not in other.heading.names)
+        )
+    except StopIteration:
+        pass  # all ok
+    result = copy.copy(other)
+    result._heading = result.heading.set_primary_key(
+        other.primary_key
+        + [k for k in self.primary_key if k not in other.primary_key]
+    )
+    return result
+

+ +

+ + + + + + +

+ + +

+ `aggr(group, **named_attributes)` + +¶

+ + +

+ +

Aggregation of the type U('attr1','attr2').aggr(group, computation="QueryExpression") +has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of group.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `group` +	+	+ + The query expression to be aggregated. + +	+ required +
+ `named_attributes` +	+	+ + computations of the form new_attribute="sql expression on attributes of group" + +	+ `{}` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + The derived query expression + +

+ + +

Source code in datajoint/expression.py

def aggr(self, group, **named_attributes):
+    """
+    Aggregation of the type U('attr1','attr2').aggr(group, computation="QueryExpression")
+    has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`.
+
+    :param group:  The query expression to be aggregated.
+    :param named_attributes: computations of the form new_attribute="sql expression on attributes of group"
+    :return: The derived query expression
+    """
+    if named_attributes.get("keep_all_rows", False):
+        raise DataJointError(
+            "Cannot set keep_all_rows=True when aggregating on a universal set."
+        )
+    return Aggregation.create(self, group=group, keep_all_rows=False).proj(
+        **named_attributes
+    )
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `key` + + +¶

+ + +

+ + + +

object that allows requesting the primary key as an argument in expression.fetch() +The string "KEY" can be used instead of the class key

+ + + + + + + + +

Source code in datajoint/fetch.py

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class key:
+    """
+    object that allows requesting the primary key as an argument in expression.fetch()
+    The string "KEY" can be used instead of the class key
+    """
+
+    pass
+

+ +

+ + + + + + +

+ + +

+ `key_hash(mapping)` + +¶

+ + +

+ +

32-byte hash of the mapping's key values sorted by the key name. +This is often used to convert a long primary key value into a shorter hash. +For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables.

+ + +

Source code in datajoint/hash.py

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def key_hash(mapping):
+    """
+    32-byte hash of the mapping's key values sorted by the key name.
+    This is often used to convert a long primary key value into a shorter hash.
+    For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables.
+    """
+    hashed = hashlib.md5()
+    for k, v in sorted(mapping.items()):
+        hashed.update(str(v).encode())
+    return hashed.hexdigest()
+

+ +

+ + + + + + +

+ + + +

+ `Schema` + + +¶

+ + +

+ + + +

A schema object is a decorator for UserTable classes that binds them to their database. +It also specifies the namespace context in which other UserTable classes are defined.

+ + + + + + + + +

Source code in datajoint/schemas.py

class Schema:
+    """
+    A schema object is a decorator for UserTable classes that binds them to their database.
+    It also specifies the namespace `context` in which other UserTable classes are defined.
+    """
+
+    def __init__(
+        self,
+        schema_name=None,
+        context=None,
+        *,
+        connection=None,
+        create_schema=True,
+        create_tables=True,
+        add_objects=None,
+    ):
+        """
+        Associate database schema `schema_name`. If the schema does not exist, attempt to
+        create it on the server.
+
+        If the schema_name is omitted, then schema.activate(..) must be called later
+        to associate with the database.
+
+        :param schema_name: the database schema to associate.
+        :param context: dictionary for looking up foreign key references, leave None to use local context.
+        :param connection: Connection object. Defaults to datajoint.conn().
+        :param create_schema: When False, do not create the schema and raise an error if missing.
+        :param create_tables: When False, do not create tables and raise errors when accessing missing tables.
+        :param add_objects: a mapping with additional objects to make available to the context in which table classes
+        are declared.
+        """
+        self._log = None
+        self.connection = connection
+        self.database = None
+        self.context = context
+        self.create_schema = create_schema
+        self.create_tables = create_tables
+        self._jobs = None
+        self.external = ExternalMapping(self)
+        self.add_objects = add_objects
+        self.declare_list = []
+        if schema_name:
+            self.activate(schema_name)
+
+    def is_activated(self):
+        return self.database is not None
+
+    def activate(
+        self,
+        schema_name=None,
+        *,
+        connection=None,
+        create_schema=None,
+        create_tables=None,
+        add_objects=None,
+    ):
+        """
+        Associate database schema `schema_name`. If the schema does not exist, attempt to
+        create it on the server.
+
+        :param schema_name: the database schema to associate.
+            schema_name=None is used to assert that the schema has already been activated.
+        :param connection: Connection object. Defaults to datajoint.conn().
+        :param create_schema: If False, do not create the schema and raise an error if missing.
+        :param create_tables: If False, do not create tables and raise errors when attempting
+            to access missing tables.
+        :param add_objects: a mapping with additional objects to make available to the context
+            in which table classes are declared.
+        """
+        if schema_name is None:
+            if self.exists:
+                return
+            raise DataJointError("Please provide a schema_name to activate the schema.")
+        if self.database is not None and self.exists:
+            if self.database == schema_name:  # already activated
+                return
+            raise DataJointError(
+                "The schema is already activated for schema {db}.".format(
+                    db=self.database
+                )
+            )
+        if connection is not None:
+            self.connection = connection
+        if self.connection is None:
+            self.connection = conn()
+        self.database = schema_name
+        if create_schema is not None:
+            self.create_schema = create_schema
+        if create_tables is not None:
+            self.create_tables = create_tables
+        if add_objects:
+            self.add_objects = add_objects
+        if not self.exists:
+            if not self.create_schema or not self.database:
+                raise DataJointError(
+                    "Database `{name}` has not yet been declared. "
+                    "Set argument create_schema=True to create it.".format(
+                        name=schema_name
+                    )
+                )
+            # create database
+            logger.debug("Creating schema `{name}`.".format(name=schema_name))
+            try:
+                self.connection.query(
+                    "CREATE DATABASE `{name}`".format(name=schema_name)
+                )
+            except AccessError:
+                raise DataJointError(
+                    "Schema `{name}` does not exist and could not be created. "
+                    "Check permissions.".format(name=schema_name)
+                )
+            else:
+                self.log("created")
+        self.connection.register(self)
+
+        # decorate all tables already decorated
+        for cls, context in self.declare_list:
+            if self.add_objects:
+                context = dict(context, **self.add_objects)
+            self._decorate_master(cls, context)
+
+    def _assert_exists(self, message=None):
+        if not self.exists:
+            raise DataJointError(
+                message
+                or "Schema `{db}` has not been created.".format(db=self.database)
+            )
+
+    def __call__(self, cls, *, context=None):
+        """
+        Binds the supplied class to a schema. This is intended to be used as a decorator.
+
+        :param cls: class to decorate.
+        :param context: supplied when called from spawn_missing_classes
+        """
+        context = context or self.context or inspect.currentframe().f_back.f_locals
+        if issubclass(cls, Part):
+            raise DataJointError(
+                "The schema decorator should not be applied to Part tables."
+            )
+        if self.is_activated():
+            self._decorate_master(cls, context)
+        else:
+            self.declare_list.append((cls, context))
+        return cls
+
+    def _decorate_master(self, cls, context):
+        """
+
+        :param cls: the master class to process
+        :param context: the class' declaration context
+        """
+        self._decorate_table(
+            cls, context=dict(context, self=cls, **{cls.__name__: cls})
+        )
+        # Process part tables
+        for part in ordered_dir(cls):
+            if part[0].isupper():
+                part = getattr(cls, part)
+                if inspect.isclass(part) and issubclass(part, Part):
+                    part._master = cls
+                    # allow addressing master by name or keyword 'master'
+                    self._decorate_table(
+                        part,
+                        context=dict(
+                            context, master=cls, self=part, **{cls.__name__: cls}
+                        ),
+                    )
+
+    def _decorate_table(self, table_class, context, assert_declared=False):
+        """
+        assign schema properties to the table class and declare the table
+        """
+        table_class.database = self.database
+        table_class._connection = self.connection
+        table_class._heading = Heading(
+            table_info=dict(
+                conn=self.connection,
+                database=self.database,
+                table_name=table_class.table_name,
+                context=context,
+            )
+        )
+        table_class._support = [table_class.full_table_name]
+        table_class.declaration_context = context
+
+        # instantiate the class, declare the table if not already
+        instance = table_class()
+        is_declared = instance.is_declared
+        if not is_declared and not assert_declared and self.create_tables:
+            instance.declare(context)
+            self.connection.dependencies.clear()
+        is_declared = is_declared or instance.is_declared
+
+        # add table definition to the doc string
+        if isinstance(table_class.definition, str):
+            table_class.__doc__ = (
+                (table_class.__doc__ or "")
+                + "\nTable definition:\n\n"
+                + table_class.definition
+            )
+
+        # fill values in Lookup tables from their contents property
+        if (
+            isinstance(instance, Lookup)
+            and hasattr(instance, "contents")
+            and is_declared
+        ):
+            contents = list(instance.contents)
+            if len(contents) > len(instance):
+                if instance.heading.has_autoincrement:
+                    warnings.warn(
+                        (
+                            "Contents has changed but cannot be inserted because "
+                            "{table} has autoincrement."
+                        ).format(table=instance.__class__.__name__)
+                    )
+                else:
+                    instance.insert(contents, skip_duplicates=True)
+
+    @property
+    def log(self):
+        self._assert_exists()
+        if self._log is None:
+            self._log = Log(self.connection, self.database)
+        return self._log
+
+    def __repr__(self):
+        return "Schema `{name}`\n".format(name=self.database)
+
+    @property
+    def size_on_disk(self):
+        """
+        :return: size of the entire schema in bytes
+        """
+        self._assert_exists()
+        return int(
+            self.connection.query(
+                """
+            SELECT SUM(data_length + index_length)
+            FROM information_schema.tables WHERE table_schema='{db}'
+            """.format(
+                    db=self.database
+                )
+            ).fetchone()[0]
+        )
+
+    def spawn_missing_classes(self, context=None):
+        """
+        Creates the appropriate python user table classes from tables in the schema and places them
+        in the context.
+
+        :param context: alternative context to place the missing classes into, e.g. locals()
+        """
+        self._assert_exists()
+        if context is None:
+            if self.context is not None:
+                context = self.context
+            else:
+                # if context is missing, use the calling namespace
+                frame = inspect.currentframe().f_back
+                context = frame.f_locals
+                del frame
+        tables = [
+            row[0]
+            for row in self.connection.query("SHOW TABLES in `%s`" % self.database)
+            if lookup_class_name(
+                "`{db}`.`{tab}`".format(db=self.database, tab=row[0]), context, 0
+            )
+            is None
+        ]
+        master_classes = (Lookup, Manual, Imported, Computed)
+        part_tables = []
+        for table_name in tables:
+            class_name = to_camel_case(table_name)
+            if class_name not in context:
+                try:
+                    cls = next(
+                        cls
+                        for cls in master_classes
+                        if re.fullmatch(cls.tier_regexp, table_name)
+                    )
+                except StopIteration:
+                    if re.fullmatch(Part.tier_regexp, table_name):
+                        part_tables.append(table_name)
+                else:
+                    # declare and decorate master table classes
+                    context[class_name] = self(
+                        type(class_name, (cls,), dict()), context=context
+                    )
+
+        # attach parts to masters
+        for table_name in part_tables:
+            groups = re.fullmatch(Part.tier_regexp, table_name).groupdict()
+            class_name = to_camel_case(groups["part"])
+            try:
+                master_class = context[to_camel_case(groups["master"])]
+            except KeyError:
+                raise DataJointError(
+                    "The table %s does not follow DataJoint naming conventions"
+                    % table_name
+                )
+            part_class = type(class_name, (Part,), dict(definition=...))
+            part_class._master = master_class
+            self._decorate_table(part_class, context=context, assert_declared=True)
+            setattr(master_class, class_name, part_class)
+
+    def drop(self, force=False):
+        """
+        Drop the associated schema if it exists
+        """
+        if not self.exists:
+            logger.info(
+                "Schema named `{database}` does not exist. Doing nothing.".format(
+                    database=self.database
+                )
+            )
+        elif (
+            not config["safemode"]
+            or force
+            or user_choice(
+                "Proceed to delete entire schema `%s`?" % self.database, default="no"
+            )
+            == "yes"
+        ):
+            logger.debug("Dropping `{database}`.".format(database=self.database))
+            try:
+                self.connection.query(
+                    "DROP DATABASE `{database}`".format(database=self.database)
+                )
+                logger.debug(
+                    "Schema `{database}` was dropped successfully.".format(
+                        database=self.database
+                    )
+                )
+            except AccessError:
+                raise AccessError(
+                    "An attempt to drop schema `{database}` "
+                    "has failed. Check permissions.".format(database=self.database)
+                )
+
+    @property
+    def exists(self):
+        """
+        :return: true if the associated schema exists on the server
+        """
+        if self.database is None:
+            raise DataJointError("Schema must be activated first.")
+        return bool(
+            self.connection.query(
+                "SELECT schema_name "
+                "FROM information_schema.schemata "
+                "WHERE schema_name = '{database}'".format(database=self.database)
+            ).rowcount
+        )
+
+    @property
+    def jobs(self):
+        """
+        schema.jobs provides a view of the job reservation table for the schema
+
+        :return: jobs table
+        """
+        self._assert_exists()
+        if self._jobs is None:
+            self._jobs = JobTable(self.connection, self.database)
+        return self._jobs
+
+    @property
+    def code(self):
+        self._assert_exists()
+        return self.save()
+
+    def save(self, python_filename=None):
+        """
+        Generate the code for a module that recreates the schema.
+        This method is in preparation for a future release and is not officially supported.
+
+        :return: a string containing the body of a complete Python module defining this schema.
+        """
+        self.connection.dependencies.load()
+        self._assert_exists()
+        module_count = itertools.count()
+        # add virtual modules for referenced modules with names vmod0, vmod1, ...
+        module_lookup = collections.defaultdict(
+            lambda: "vmod" + str(next(module_count))
+        )
+        db = self.database
+
+        def make_class_definition(table):
+            tier = _get_tier(table).__name__
+            class_name = table.split(".")[1].strip("`")
+            indent = ""
+            if tier == "Part":
+                class_name = class_name.split("__")[-1]
+                indent += "    "
+            class_name = to_camel_case(class_name)
+
+            def replace(s):
+                d, tabs = s.group(1), s.group(2)
+                return ("" if d == db else (module_lookup[d] + ".")) + ".".join(
+                    to_camel_case(tab) for tab in tabs.lstrip("__").split("__")
+                )
+
+            return ("" if tier == "Part" else "\n@schema\n") + (
+                "{indent}class {class_name}(dj.{tier}):\n"
+                '{indent}    definition = """\n'
+                '{indent}    {defi}"""'
+            ).format(
+                class_name=class_name,
+                indent=indent,
+                tier=tier,
+                defi=re.sub(
+                    r"`([^`]+)`.`([^`]+)`",
+                    replace,
+                    FreeTable(self.connection, table).describe(),
+                ).replace("\n", "\n    " + indent),
+            )
+
+        tables = self.connection.dependencies.topo_sort()
+        body = "\n\n".join(make_class_definition(table) for table in tables)
+        python_code = "\n\n".join(
+            (
+                '"""This module was auto-generated by datajoint from an existing schema"""',
+                "import datajoint as dj\n\nschema = dj.Schema('{db}')".format(db=db),
+                "\n".join(
+                    "{module} = dj.VirtualModule('{module}', '{schema_name}')".format(
+                        module=v, schema_name=k
+                    )
+                    for k, v in module_lookup.items()
+                ),
+                body,
+            )
+        )
+        if python_filename is None:
+            return python_code
+        with open(python_filename, "wt") as f:
+            f.write(python_code)
+
+    def list_tables(self):
+        """
+        Return a list of all tables in the schema except tables with ~ in first character such
+        as ~logs and ~job
+
+        :return: A list of table names from the database schema.
+        """
+        self.connection.dependencies.load()
+        return [
+            t
+            for d, t in (
+                table_name.replace("`", "").split(".")
+                for table_name in self.connection.dependencies.topo_sort()
+            )
+            if d == self.database
+        ]
+

+ + + +

+ + + + + + + +

+ + +

+ `activate(schema_name=None, *, connection=None, create_schema=None, create_tables=None, add_objects=None)` + +¶

+ + +

+ +

Associate database schema schema_name. If the schema does not exist, attempt to +create it on the server.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `schema_name` +	+	+ + the database schema to associate. +schema_name=None is used to assert that the schema has already been activated. + +	+ `None` +
+ `connection` +	+	+ + Connection object. Defaults to datajoint.conn(). + +	+ `None` +
+ `create_schema` +	+	+ + If False, do not create the schema and raise an error if missing. + +	+ `None` +
+ `create_tables` +	+	+ + If False, do not create tables and raise errors when attempting +to access missing tables. + +	+ `None` +
+ `add_objects` +	+	+ + a mapping with additional objects to make available to the context +in which table classes are declared. + +	+ `None` +

+ + +

Source code in datajoint/schemas.py

def activate(
+    self,
+    schema_name=None,
+    *,
+    connection=None,
+    create_schema=None,
+    create_tables=None,
+    add_objects=None,
+):
+    """
+    Associate database schema `schema_name`. If the schema does not exist, attempt to
+    create it on the server.
+
+    :param schema_name: the database schema to associate.
+        schema_name=None is used to assert that the schema has already been activated.
+    :param connection: Connection object. Defaults to datajoint.conn().
+    :param create_schema: If False, do not create the schema and raise an error if missing.
+    :param create_tables: If False, do not create tables and raise errors when attempting
+        to access missing tables.
+    :param add_objects: a mapping with additional objects to make available to the context
+        in which table classes are declared.
+    """
+    if schema_name is None:
+        if self.exists:
+            return
+        raise DataJointError("Please provide a schema_name to activate the schema.")
+    if self.database is not None and self.exists:
+        if self.database == schema_name:  # already activated
+            return
+        raise DataJointError(
+            "The schema is already activated for schema {db}.".format(
+                db=self.database
+            )
+        )
+    if connection is not None:
+        self.connection = connection
+    if self.connection is None:
+        self.connection = conn()
+    self.database = schema_name
+    if create_schema is not None:
+        self.create_schema = create_schema
+    if create_tables is not None:
+        self.create_tables = create_tables
+    if add_objects:
+        self.add_objects = add_objects
+    if not self.exists:
+        if not self.create_schema or not self.database:
+            raise DataJointError(
+                "Database `{name}` has not yet been declared. "
+                "Set argument create_schema=True to create it.".format(
+                    name=schema_name
+                )
+            )
+        # create database
+        logger.debug("Creating schema `{name}`.".format(name=schema_name))
+        try:
+            self.connection.query(
+                "CREATE DATABASE `{name}`".format(name=schema_name)
+            )
+        except AccessError:
+            raise DataJointError(
+                "Schema `{name}` does not exist and could not be created. "
+                "Check permissions.".format(name=schema_name)
+            )
+        else:
+            self.log("created")
+    self.connection.register(self)
+
+    # decorate all tables already decorated
+    for cls, context in self.declare_list:
+        if self.add_objects:
+            context = dict(context, **self.add_objects)
+        self._decorate_master(cls, context)
+

+ +

+ + + + + + +

+ + + +

+ `size_on_disk` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + size of the entire schema in bytes + +

+ +

+ + + + + + +

+ + +

+ `spawn_missing_classes(context=None)` + +¶

+ + +

+ +

Creates the appropriate python user table classes from tables in the schema and places them +in the context.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `context` +	+	+ + alternative context to place the missing classes into, e.g. locals() + +	+ `None` +

+ + +

Source code in datajoint/schemas.py

def spawn_missing_classes(self, context=None):
+    """
+    Creates the appropriate python user table classes from tables in the schema and places them
+    in the context.
+
+    :param context: alternative context to place the missing classes into, e.g. locals()
+    """
+    self._assert_exists()
+    if context is None:
+        if self.context is not None:
+            context = self.context
+        else:
+            # if context is missing, use the calling namespace
+            frame = inspect.currentframe().f_back
+            context = frame.f_locals
+            del frame
+    tables = [
+        row[0]
+        for row in self.connection.query("SHOW TABLES in `%s`" % self.database)
+        if lookup_class_name(
+            "`{db}`.`{tab}`".format(db=self.database, tab=row[0]), context, 0
+        )
+        is None
+    ]
+    master_classes = (Lookup, Manual, Imported, Computed)
+    part_tables = []
+    for table_name in tables:
+        class_name = to_camel_case(table_name)
+        if class_name not in context:
+            try:
+                cls = next(
+                    cls
+                    for cls in master_classes
+                    if re.fullmatch(cls.tier_regexp, table_name)
+                )
+            except StopIteration:
+                if re.fullmatch(Part.tier_regexp, table_name):
+                    part_tables.append(table_name)
+            else:
+                # declare and decorate master table classes
+                context[class_name] = self(
+                    type(class_name, (cls,), dict()), context=context
+                )
+
+    # attach parts to masters
+    for table_name in part_tables:
+        groups = re.fullmatch(Part.tier_regexp, table_name).groupdict()
+        class_name = to_camel_case(groups["part"])
+        try:
+            master_class = context[to_camel_case(groups["master"])]
+        except KeyError:
+            raise DataJointError(
+                "The table %s does not follow DataJoint naming conventions"
+                % table_name
+            )
+        part_class = type(class_name, (Part,), dict(definition=...))
+        part_class._master = master_class
+        self._decorate_table(part_class, context=context, assert_declared=True)
+        setattr(master_class, class_name, part_class)
+

+ +

+ + + + + + +

+ + +

+ `drop(force=False)` + +¶

+ + +

+ +

Drop the associated schema if it exists

+ + +

Source code in datajoint/schemas.py

def drop(self, force=False):
+    """
+    Drop the associated schema if it exists
+    """
+    if not self.exists:
+        logger.info(
+            "Schema named `{database}` does not exist. Doing nothing.".format(
+                database=self.database
+            )
+        )
+    elif (
+        not config["safemode"]
+        or force
+        or user_choice(
+            "Proceed to delete entire schema `%s`?" % self.database, default="no"
+        )
+        == "yes"
+    ):
+        logger.debug("Dropping `{database}`.".format(database=self.database))
+        try:
+            self.connection.query(
+                "DROP DATABASE `{database}`".format(database=self.database)
+            )
+            logger.debug(
+                "Schema `{database}` was dropped successfully.".format(
+                    database=self.database
+                )
+            )
+        except AccessError:
+            raise AccessError(
+                "An attempt to drop schema `{database}` "
+                "has failed. Check permissions.".format(database=self.database)
+            )
+

+ +

+ + + + + + +

+ + + +

+ `exists` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + true if the associated schema exists on the server + +

+ +

+ + + + + + +

+ + + +

+ `jobs` + + + `property` + + +¶

+ + +

+ +

schema.jobs provides a view of the job reservation table for the schema

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + jobs table + +

+ +

+ + + + + + +

+ + +

+ `save(python_filename=None)` + +¶

+ + +

+ +

Generate the code for a module that recreates the schema. +This method is in preparation for a future release and is not officially supported.

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a string containing the body of a complete Python module defining this schema. + +

+ + +

Source code in datajoint/schemas.py

def save(self, python_filename=None):
+    """
+    Generate the code for a module that recreates the schema.
+    This method is in preparation for a future release and is not officially supported.
+
+    :return: a string containing the body of a complete Python module defining this schema.
+    """
+    self.connection.dependencies.load()
+    self._assert_exists()
+    module_count = itertools.count()
+    # add virtual modules for referenced modules with names vmod0, vmod1, ...
+    module_lookup = collections.defaultdict(
+        lambda: "vmod" + str(next(module_count))
+    )
+    db = self.database
+
+    def make_class_definition(table):
+        tier = _get_tier(table).__name__
+        class_name = table.split(".")[1].strip("`")
+        indent = ""
+        if tier == "Part":
+            class_name = class_name.split("__")[-1]
+            indent += "    "
+        class_name = to_camel_case(class_name)
+
+        def replace(s):
+            d, tabs = s.group(1), s.group(2)
+            return ("" if d == db else (module_lookup[d] + ".")) + ".".join(
+                to_camel_case(tab) for tab in tabs.lstrip("__").split("__")
+            )
+
+        return ("" if tier == "Part" else "\n@schema\n") + (
+            "{indent}class {class_name}(dj.{tier}):\n"
+            '{indent}    definition = """\n'
+            '{indent}    {defi}"""'
+        ).format(
+            class_name=class_name,
+            indent=indent,
+            tier=tier,
+            defi=re.sub(
+                r"`([^`]+)`.`([^`]+)`",
+                replace,
+                FreeTable(self.connection, table).describe(),
+            ).replace("\n", "\n    " + indent),
+        )
+
+    tables = self.connection.dependencies.topo_sort()
+    body = "\n\n".join(make_class_definition(table) for table in tables)
+    python_code = "\n\n".join(
+        (
+            '"""This module was auto-generated by datajoint from an existing schema"""',
+            "import datajoint as dj\n\nschema = dj.Schema('{db}')".format(db=db),
+            "\n".join(
+                "{module} = dj.VirtualModule('{module}', '{schema_name}')".format(
+                    module=v, schema_name=k
+                )
+                for k, v in module_lookup.items()
+            ),
+            body,
+        )
+    )
+    if python_filename is None:
+        return python_code
+    with open(python_filename, "wt") as f:
+        f.write(python_code)
+

+ +

+ + + + + + +

+ + +

+ `list_tables()` + +¶

+ + +

+ +

Return a list of all tables in the schema except tables with ~ in first character such +as ~logs and ~job

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + A list of table names from the database schema. + +

+ + +

Source code in datajoint/schemas.py

def list_tables(self):
+    """
+    Return a list of all tables in the schema except tables with ~ in first character such
+    as ~logs and ~job
+
+    :return: A list of table names from the database schema.
+    """
+    self.connection.dependencies.load()
+    return [
+        t
+        for d, t in (
+            table_name.replace("`", "").split(".")
+            for table_name in self.connection.dependencies.topo_sort()
+        )
+        if d == self.database
+    ]
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `VirtualModule` + + +¶

+ + +

+ Bases: ModuleType

+ + + +

A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. +It declares the schema objects and a class for each table.

+ + + + + + + + +

Source code in datajoint/schemas.py

class VirtualModule(types.ModuleType):
+    """
+    A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database.
+    It declares the schema objects and a class for each table.
+    """
+
+    def __init__(
+        self,
+        module_name,
+        schema_name,
+        *,
+        create_schema=False,
+        create_tables=False,
+        connection=None,
+        add_objects=None,
+    ):
+        """
+        Creates a python module with the given name from the name of a schema on the server and
+        automatically adds classes to it corresponding to the tables in the schema.
+
+        :param module_name: displayed module name
+        :param schema_name: name of the database in mysql
+        :param create_schema: if True, create the schema on the database server
+        :param create_tables: if True, module.schema can be used as the decorator for declaring new
+        :param connection: a dj.Connection object to pass into the schema
+        :param add_objects: additional objects to add to the module
+        :return: the python module containing classes from the schema object and the table classes
+        """
+        super(VirtualModule, self).__init__(name=module_name)
+        _schema = Schema(
+            schema_name,
+            create_schema=create_schema,
+            create_tables=create_tables,
+            connection=connection,
+        )
+        if add_objects:
+            self.__dict__.update(add_objects)
+        self.__dict__["schema"] = _schema
+        _schema.spawn_missing_classes(context=self.__dict__)
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + +

+ `list_schemas(connection=None)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `connection` +	+	+ + a dj.Connection object + +	+ `None` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of all accessible schemas on the server + +

+ + +

Source code in datajoint/schemas.py

def list_schemas(connection=None):
+    """
+    :param connection: a dj.Connection object
+    :return: list of all accessible schemas on the server
+    """
+    return [
+        r[0]
+        for r in (connection or conn()).query(
+            "SELECT schema_name "
+            "FROM information_schema.schemata "
+            'WHERE schema_name <> "information_schema"'
+        )
+    ]
+

+ +

+ + + + + + +

+ + + +

+ `FreeTable` + + +¶

+ + +

+ Bases: Table

+ + + +

A base table without a dedicated class. Each instance is associated with a table +specified by full_table_name.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `conn` +	+	+ + a dj.Connection object + +	+ required +
+ `full_table_name` +	+	+ + in format `database`.`table_name` + +	+ required +

+ + + + + + + + +

Source code in datajoint/table.py

class FreeTable(Table):
+    """
+    A base table without a dedicated class. Each instance is associated with a table
+    specified by full_table_name.
+
+    :param conn:  a dj.Connection object
+    :param full_table_name: in format `database`.`table_name`
+    """
+
+    def __init__(self, conn, full_table_name):
+        self.database, self._table_name = (
+            s.strip("`") for s in full_table_name.split(".")
+        )
+        self._connection = conn
+        self._support = [full_table_name]
+        self._heading = Heading(
+            table_info=dict(
+                conn=conn,
+                database=self.database,
+                table_name=self.table_name,
+                context=None,
+            )
+        )
+
+    def __repr__(self):
+        return (
+            "FreeTable(`%s`.`%s`)\n" % (self.database, self._table_name)
+            + super().__repr__()
+        )
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Table` + + +¶

+ + +

+ Bases: QueryExpression

+ + + +

Table is an abstract class that represents a table in the schema. +It implements insert and delete methods and inherits query functionality. +To make it a concrete class, override the abstract properties specifying the connection, +table name, database, and definition.

+ + + + + + + + +

Source code in datajoint/table.py

class Table(QueryExpression):
+    """
+    Table is an abstract class that represents a table in the schema.
+    It implements insert and delete methods and inherits query functionality.
+    To make it a concrete class, override the abstract properties specifying the connection,
+    table name, database, and definition.
+    """
+
+    _table_name = None  # must be defined in subclass
+    _log_ = None  # placeholder for the Log table object
+
+    # These properties must be set by the schema decorator (schemas.py) at class level
+    # or by FreeTable at instance level
+    database = None
+    declaration_context = None
+
+    @property
+    def table_name(self):
+        return self._table_name
+
+    @property
+    def class_name(self):
+        return self.__class__.__name__
+
+    @property
+    def definition(self):
+        raise NotImplementedError(
+            "Subclasses of Table must implement the `definition` property"
+        )
+
+    def declare(self, context=None):
+        """
+        Declare the table in the schema based on self.definition.
+
+        :param context: the context for foreign key resolution. If None, foreign keys are
+            not allowed.
+        """
+        if self.connection.in_transaction:
+            raise DataJointError(
+                "Cannot declare new tables inside a transaction, "
+                "e.g. from inside a populate/make call"
+            )
+        # Enforce strict CamelCase #1150
+        if not is_camel_case(self.class_name):
+            raise DataJointError(
+                "Table class name `{name}` is invalid. Please use CamelCase. ".format(
+                    name=self.class_name
+                )
+                + "Classes defining tables should be formatted in strict CamelCase."
+            )
+        sql, external_stores = declare(self.full_table_name, self.definition, context)
+        sql = sql.format(database=self.database)
+        try:
+            # declare all external tables before declaring main table
+            for store in external_stores:
+                self.connection.schemas[self.database].external[store]
+            self.connection.query(sql)
+        except AccessError:
+            # skip if no create privilege
+            pass
+        else:
+            self._log("Declared " + self.full_table_name)
+
+    def alter(self, prompt=True, context=None):
+        """
+        Alter the table definition from self.definition
+        """
+        if self.connection.in_transaction:
+            raise DataJointError(
+                "Cannot update table declaration inside a transaction, "
+                "e.g. from inside a populate/make call"
+            )
+        if context is None:
+            frame = inspect.currentframe().f_back
+            context = dict(frame.f_globals, **frame.f_locals)
+            del frame
+        old_definition = self.describe(context=context)
+        sql, external_stores = alter(self.definition, old_definition, context)
+        if not sql:
+            if prompt:
+                logger.warning("Nothing to alter.")
+        else:
+            sql = "ALTER TABLE {tab}\n\t".format(
+                tab=self.full_table_name
+            ) + ",\n\t".join(sql)
+            if not prompt or user_choice(sql + "\n\nExecute?") == "yes":
+                try:
+                    # declare all external tables before declaring main table
+                    for store in external_stores:
+                        self.connection.schemas[self.database].external[store]
+                    self.connection.query(sql)
+                except AccessError:
+                    # skip if no create privilege
+                    pass
+                else:
+                    # reset heading
+                    self.__class__._heading = Heading(
+                        table_info=self.heading.table_info
+                    )
+                    if prompt:
+                        logger.info("Table altered")
+                    self._log("Altered " + self.full_table_name)
+
+    def from_clause(self):
+        """
+        :return: the FROM clause of SQL SELECT statements.
+        """
+        return self.full_table_name
+
+    def get_select_fields(self, select_fields=None):
+        """
+        :return: the selected attributes from the SQL SELECT statement.
+        """
+        return (
+            "*" if select_fields is None else self.heading.project(select_fields).as_sql
+        )
+
+    def parents(self, primary=None, as_objects=False, foreign_key_info=False):
+        """
+
+        :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
+            primary key attributes are considered.  If False, return foreign keys including at least one
+            secondary attribute.
+        :param as_objects: if False, return table names. If True, return table objects.
+        :param foreign_key_info: if True, each element in result also includes foreign key info.
+        :return: list of parents as table names or table objects
+            with (optional) foreign key information.
+        """
+        get_edge = self.connection.dependencies.parents
+        nodes = [
+            next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+            for name, props in get_edge(self.full_table_name, primary).items()
+        ]
+        if as_objects:
+            nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+        if not foreign_key_info:
+            nodes = [name for name, props in nodes]
+        return nodes
+
+    def children(self, primary=None, as_objects=False, foreign_key_info=False):
+        """
+        :param primary: if None, then all children are returned. If True, then only foreign keys composed of
+            primary key attributes are considered.  If False, return foreign keys including at least one
+            secondary attribute.
+        :param as_objects: if False, return table names. If True, return table objects.
+        :param foreign_key_info: if True, each element in result also includes foreign key info.
+        :return: list of children as table names or table objects
+            with (optional) foreign key information.
+        """
+        get_edge = self.connection.dependencies.children
+        nodes = [
+            next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+            for name, props in get_edge(self.full_table_name, primary).items()
+        ]
+        if as_objects:
+            nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+        if not foreign_key_info:
+            nodes = [name for name, props in nodes]
+        return nodes
+
+    def descendants(self, as_objects=False):
+        """
+        :param as_objects: False - a list of table names; True - a list of table objects.
+        :return: list of tables descendants in topological order.
+        """
+        return [
+            FreeTable(self.connection, node) if as_objects else node
+            for node in self.connection.dependencies.descendants(self.full_table_name)
+            if not node.isdigit()
+        ]
+
+    def ancestors(self, as_objects=False):
+        """
+        :param as_objects: False - a list of table names; True - a list of table objects.
+        :return: list of tables ancestors in topological order.
+        """
+        return [
+            FreeTable(self.connection, node) if as_objects else node
+            for node in self.connection.dependencies.ancestors(self.full_table_name)
+            if not node.isdigit()
+        ]
+
+    def parts(self, as_objects=False):
+        """
+        return part tables either as entries in a dict with foreign key information or a list of objects
+
+        :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects.
+        """
+        self.connection.dependencies.load(force=False)
+        nodes = [
+            node
+            for node in self.connection.dependencies.nodes
+            if not node.isdigit() and node.startswith(self.full_table_name[:-1] + "__")
+        ]
+        return [FreeTable(self.connection, c) for c in nodes] if as_objects else nodes
+
+    @property
+    def is_declared(self):
+        """
+        :return: True is the table is declared in the schema.
+        """
+        return (
+            self.connection.query(
+                'SHOW TABLES in `{database}` LIKE "{table_name}"'.format(
+                    database=self.database, table_name=self.table_name
+                )
+            ).rowcount
+            > 0
+        )
+
+    @property
+    def full_table_name(self):
+        """
+        :return: full table name in the schema
+        """
+        return r"`{0:s}`.`{1:s}`".format(self.database, self.table_name)
+
+    @property
+    def _log(self):
+        if self._log_ is None:
+            self._log_ = Log(
+                self.connection,
+                database=self.database,
+                skip_logging=self.table_name.startswith("~"),
+            )
+        return self._log_
+
+    @property
+    def external(self):
+        return self.connection.schemas[self.database].external
+
+    def update1(self, row):
+        """
+        ``update1`` updates one existing entry in the table.
+        Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and
+        ``delete`` entire records since referential integrity works on the level of records,
+        not fields. Therefore, updates are reserved for corrective operations outside of main
+        workflow. Use UPDATE methods sparingly with full awareness of potential violations of
+        assumptions.
+
+        :param row: a ``dict`` containing the primary key values and the attributes to update.
+            Setting an attribute value to None will reset it to the default value (if any).
+
+        The primary key attributes must always be provided.
+
+        Examples:
+
+        >>> table.update1({'id': 1, 'value': 3})  # update value in record with id=1
+        >>> table.update1({'id': 1, 'value': None})  # reset value to default
+        """
+        # argument validations
+        if not isinstance(row, collections.abc.Mapping):
+            raise DataJointError("The argument of update1 must be dict-like.")
+        if not set(row).issuperset(self.primary_key):
+            raise DataJointError(
+                "The argument of update1 must supply all primary key values."
+            )
+        try:
+            raise DataJointError(
+                "Attribute `%s` not found."
+                % next(k for k in row if k not in self.heading.names)
+            )
+        except StopIteration:
+            pass  # ok
+        if len(self.restriction):
+            raise DataJointError("Update cannot be applied to a restricted table.")
+        key = {k: row[k] for k in self.primary_key}
+        if len(self & key) != 1:
+            raise DataJointError("Update can only be applied to one existing entry.")
+        # UPDATE query
+        row = [
+            self.__make_placeholder(k, v)
+            for k, v in row.items()
+            if k not in self.primary_key
+        ]
+        query = "UPDATE {table} SET {assignments} WHERE {where}".format(
+            table=self.full_table_name,
+            assignments=",".join("`%s`=%s" % r[:2] for r in row),
+            where=make_condition(self, key, set()),
+        )
+        self.connection.query(query, args=list(r[2] for r in row if r[2] is not None))
+
+    def insert1(self, row, **kwargs):
+        """
+        Insert one data record into the table. For ``kwargs``, see ``insert()``.
+
+        :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted
+            as one row.
+        """
+        self.insert((row,), **kwargs)
+
+    def insert(
+        self,
+        rows,
+        replace=False,
+        skip_duplicates=False,
+        ignore_extra_fields=False,
+        allow_direct_insert=None,
+    ):
+        """
+        Insert a collection of rows.
+
+        :param rows: Either (a) an iterable where an element is a numpy record, a
+            dict-like object, a pandas.DataFrame, a sequence, or a query expression with
+            the same heading as self, or (b) a pathlib.Path object specifying a path
+            relative to the current directory with a CSV file, the contents of which
+            will be inserted.
+        :param replace: If True, replaces the existing tuple.
+        :param skip_duplicates: If True, silently skip duplicate inserts.
+        :param ignore_extra_fields: If False, fields that are not in the heading raise error.
+        :param allow_direct_insert: Only applies in auto-populated tables. If False (default),
+            insert may only be called from inside the make callback.
+
+        Example:
+
+            >>> Table.insert([
+            >>>     dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"),
+            >>>     dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")])
+        """
+        if isinstance(rows, pandas.DataFrame):
+            # drop 'extra' synthetic index for 1-field index case -
+            # frames with more advanced indices should be prepared by user.
+            rows = rows.reset_index(
+                drop=len(rows.index.names) == 1 and not rows.index.names[0]
+            ).to_records(index=False)
+
+        if isinstance(rows, Path):
+            with open(rows, newline="") as data_file:
+                rows = list(csv.DictReader(data_file, delimiter=","))
+
+        # prohibit direct inserts into auto-populated tables
+        if not allow_direct_insert and not getattr(self, "_allow_insert", True):
+            raise DataJointError(
+                "Inserts into an auto-populated table can only be done inside "
+                "its make method during a populate call."
+                " To override, set keyword argument allow_direct_insert=True."
+            )
+
+        if inspect.isclass(rows) and issubclass(rows, QueryExpression):
+            rows = rows()  # instantiate if a class
+        if isinstance(rows, QueryExpression):
+            # insert from select
+            if not ignore_extra_fields:
+                try:
+                    raise DataJointError(
+                        "Attribute %s not found. To ignore extra attributes in insert, "
+                        "set ignore_extra_fields=True."
+                        % next(
+                            name for name in rows.heading if name not in self.heading
+                        )
+                    )
+                except StopIteration:
+                    pass
+            fields = list(name for name in rows.heading if name in self.heading)
+            query = "{command} INTO {table} ({fields}) {select}{duplicate}".format(
+                command="REPLACE" if replace else "INSERT",
+                fields="`" + "`,`".join(fields) + "`",
+                table=self.full_table_name,
+                select=rows.make_sql(fields),
+                duplicate=(
+                    " ON DUPLICATE KEY UPDATE `{pk}`={table}.`{pk}`".format(
+                        table=self.full_table_name, pk=self.primary_key[0]
+                    )
+                    if skip_duplicates
+                    else ""
+                ),
+            )
+            self.connection.query(query)
+            return
+
+        # collects the field list from first row (passed by reference)
+        field_list = []
+        rows = list(
+            self.__make_row_to_insert(row, field_list, ignore_extra_fields)
+            for row in rows
+        )
+        if rows:
+            try:
+                query = "{command} INTO {destination}(`{fields}`) VALUES {placeholders}{duplicate}".format(
+                    command="REPLACE" if replace else "INSERT",
+                    destination=self.from_clause(),
+                    fields="`,`".join(field_list),
+                    placeholders=",".join(
+                        "(" + ",".join(row["placeholders"]) + ")" for row in rows
+                    ),
+                    duplicate=(
+                        " ON DUPLICATE KEY UPDATE `{pk}`=`{pk}`".format(
+                            pk=self.primary_key[0]
+                        )
+                        if skip_duplicates
+                        else ""
+                    ),
+                )
+                self.connection.query(
+                    query,
+                    args=list(
+                        itertools.chain.from_iterable(
+                            (v for v in r["values"] if v is not None) for r in rows
+                        )
+                    ),
+                )
+            except UnknownAttributeError as err:
+                raise err.suggest(
+                    "To ignore extra fields in insert, set ignore_extra_fields=True"
+                )
+            except DuplicateError as err:
+                raise err.suggest(
+                    "To ignore duplicate entries in insert, set skip_duplicates=True"
+                )
+
+    def delete_quick(self, get_count=False):
+        """
+        Deletes the table without cascading and without user prompt.
+        If this table has populated dependent tables, this will fail.
+        """
+        query = "DELETE FROM " + self.full_table_name + self.where_clause()
+        self.connection.query(query)
+        count = (
+            self.connection.query("SELECT ROW_COUNT()").fetchone()[0]
+            if get_count
+            else None
+        )
+        self._log(query[:255])
+        return count
+
+    def delete(
+        self,
+        transaction: bool = True,
+        safemode: Union[bool, None] = None,
+        force_parts: bool = False,
+        force_masters: bool = False,
+    ) -> int:
+        """
+        Deletes the contents of the table and its dependent tables, recursively.
+
+        Args:
+            transaction: If `True`, use of the entire delete becomes an atomic transaction.
+                This is the default and recommended behavior. Set to `False` if this delete is
+                nested within another transaction.
+            safemode: If `True`, prohibit nested transactions and prompt to confirm. Default
+                is `dj.config['safemode']`.
+            force_parts: Delete from parts even when not deleting from their masters.
+            force_masters: If `True`, include part/master pairs in the cascade.
+                Default is `False`.
+
+        Returns:
+            Number of deleted rows (excluding those from dependent tables).
+
+        Raises:
+            DataJointError: Delete exceeds maximum number of delete attempts.
+            DataJointError: When deleting within an existing transaction.
+            DataJointError: Deleting a part table before its master.
+        """
+        deleted = set()
+        visited_masters = set()
+
+        def cascade(table):
+            """service function to perform cascading deletes recursively."""
+            max_attempts = 50
+            for _ in range(max_attempts):
+                try:
+                    delete_count = table.delete_quick(get_count=True)
+                except IntegrityError as error:
+                    match = foreign_key_error_regexp.match(error.args[0])
+                    if match is None:
+                        raise DataJointError(
+                            "Cascading deletes failed because the error message is missing foreign key information."
+                            "Make sure you have REFERENCES privilege to all dependent tables."
+                        ) from None
+                    match = match.groupdict()
+                    # if schema name missing, use table
+                    if "`.`" not in match["child"]:
+                        match["child"] = "{}.{}".format(
+                            table.full_table_name.split(".")[0], match["child"]
+                        )
+                    if (
+                        match["pk_attrs"] is not None
+                    ):  # fully matched, adjusting the keys
+                        match["fk_attrs"] = [
+                            k.strip("`") for k in match["fk_attrs"].split(",")
+                        ]
+                        match["pk_attrs"] = [
+                            k.strip("`") for k in match["pk_attrs"].split(",")
+                        ]
+                    else:  # only partially matched, querying with constraint to determine keys
+                        match["fk_attrs"], match["parent"], match["pk_attrs"] = list(
+                            map(
+                                list,
+                                zip(
+                                    *table.connection.query(
+                                        constraint_info_query,
+                                        args=(
+                                            match["name"].strip("`"),
+                                            *[
+                                                _.strip("`")
+                                                for _ in match["child"].split("`.`")
+                                            ],
+                                        ),
+                                    ).fetchall()
+                                ),
+                            )
+                        )
+                        match["parent"] = match["parent"][0]
+
+                    # Restrict child by table if
+                    #   1. if table's restriction attributes are not in child's primary key
+                    #   2. if child renames any attributes
+                    # Otherwise restrict child by table's restriction.
+                    child = FreeTable(table.connection, match["child"])
+                    if (
+                        set(table.restriction_attributes) <= set(child.primary_key)
+                        and match["fk_attrs"] == match["pk_attrs"]
+                    ):
+                        child._restriction = table._restriction
+                        child._restriction_attributes = table.restriction_attributes
+                    elif match["fk_attrs"] != match["pk_attrs"]:
+                        child &= table.proj(
+                            **dict(zip(match["fk_attrs"], match["pk_attrs"]))
+                        )
+                    else:
+                        child &= table.proj()
+
+                    master_name = get_master(child.full_table_name)
+                    if (
+                        force_masters
+                        and master_name
+                        and master_name != table.full_table_name
+                        and master_name not in visited_masters
+                    ):
+                        master = FreeTable(table.connection, master_name)
+                        master._restriction_attributes = set()
+                        master._restriction = [
+                            make_condition(  # &= may cause in target tables in subquery
+                                master,
+                                (master.proj() & child.proj()).fetch(),
+                                master._restriction_attributes,
+                            )
+                        ]
+                        visited_masters.add(master_name)
+                        cascade(master)
+                    else:
+                        cascade(child)
+                else:
+                    deleted.add(table.full_table_name)
+                    logger.info(
+                        "Deleting {count} rows from {table}".format(
+                            count=delete_count, table=table.full_table_name
+                        )
+                    )
+                    break
+            else:
+                raise DataJointError("Exceeded maximum number of delete attempts.")
+            return delete_count
+
+        safemode = config["safemode"] if safemode is None else safemode
+
+        # Start transaction
+        if transaction:
+            if not self.connection.in_transaction:
+                self.connection.start_transaction()
+            else:
+                if not safemode:
+                    transaction = False
+                else:
+                    raise DataJointError(
+                        "Delete cannot use a transaction within an ongoing transaction. "
+                        "Set transaction=False or safemode=False)."
+                    )
+
+        # Cascading delete
+        try:
+            delete_count = cascade(self)
+        except:
+            if transaction:
+                self.connection.cancel_transaction()
+            raise
+
+        if not force_parts:
+            # Avoid deleting from child before master (See issue #151)
+            for part in deleted:
+                master = get_master(part)
+                if master and master not in deleted:
+                    if transaction:
+                        self.connection.cancel_transaction()
+                    raise DataJointError(
+                        "Attempt to delete part table {part} before deleting from "
+                        "its master {master} first.".format(part=part, master=master)
+                    )
+
+        # Confirm and commit
+        if delete_count == 0:
+            if safemode:
+                logger.warning("Nothing to delete.")
+            if transaction:
+                self.connection.cancel_transaction()
+        elif not transaction:
+            logger.info("Delete completed")
+        else:
+            if not safemode or user_choice("Commit deletes?", default="no") == "yes":
+                if transaction:
+                    self.connection.commit_transaction()
+                if safemode:
+                    logger.info("Delete committed.")
+            else:
+                if transaction:
+                    self.connection.cancel_transaction()
+                if safemode:
+                    logger.warning("Delete cancelled")
+        return delete_count
+
+    def drop_quick(self):
+        """
+        Drops the table without cascading to dependent tables and without user prompt.
+        """
+        if self.is_declared:
+            query = "DROP TABLE %s" % self.full_table_name
+            self.connection.query(query)
+            logger.info("Dropped table %s" % self.full_table_name)
+            self._log(query[:255])
+        else:
+            logger.info(
+                "Nothing to drop: table %s is not declared" % self.full_table_name
+            )
+
+    def drop(self):
+        """
+        Drop the table and all tables that reference it, recursively.
+        User is prompted for confirmation if config['safemode'] is set to True.
+        """
+        if self.restriction:
+            raise DataJointError(
+                "A table with an applied restriction cannot be dropped."
+                " Call drop() on the unrestricted Table."
+            )
+        self.connection.dependencies.load()
+        do_drop = True
+        tables = [
+            table
+            for table in self.connection.dependencies.descendants(self.full_table_name)
+            if not table.isdigit()
+        ]
+
+        # avoid dropping part tables without their masters: See issue #374
+        for part in tables:
+            master = get_master(part)
+            if master and master not in tables:
+                raise DataJointError(
+                    "Attempt to drop part table {part} before dropping "
+                    "its master. Drop {master} first.".format(part=part, master=master)
+                )
+
+        if config["safemode"]:
+            for table in tables:
+                logger.info(
+                    table + " (%d tuples)" % len(FreeTable(self.connection, table))
+                )
+            do_drop = user_choice("Proceed?", default="no") == "yes"
+        if do_drop:
+            for table in reversed(tables):
+                FreeTable(self.connection, table).drop_quick()
+            logger.info("Tables dropped. Restart kernel.")
+
+    @property
+    def size_on_disk(self):
+        """
+        :return: size of data and indices in bytes on the storage device
+        """
+        ret = self.connection.query(
+            'SHOW TABLE STATUS FROM `{database}` WHERE NAME="{table}"'.format(
+                database=self.database, table=self.table_name
+            ),
+            as_dict=True,
+        ).fetchone()
+        return ret["Data_length"] + ret["Index_length"]
+
+    def describe(self, context=None, printout=False):
+        """
+        :return:  the definition string for the query using DataJoint DDL.
+        """
+        if context is None:
+            frame = inspect.currentframe().f_back
+            context = dict(frame.f_globals, **frame.f_locals)
+            del frame
+        if self.full_table_name not in self.connection.dependencies:
+            self.connection.dependencies.load()
+        parents = self.parents(foreign_key_info=True)
+        in_key = True
+        definition = (
+            "# " + self.heading.table_status["comment"] + "\n"
+            if self.heading.table_status["comment"]
+            else ""
+        )
+        attributes_thus_far = set()
+        attributes_declared = set()
+        indexes = self.heading.indexes.copy()
+        for attr in self.heading.attributes.values():
+            if in_key and not attr.in_key:
+                definition += "---\n"
+                in_key = False
+            attributes_thus_far.add(attr.name)
+            do_include = True
+            for parent_name, fk_props in parents:
+                if attr.name in fk_props["attr_map"]:
+                    do_include = False
+                    if attributes_thus_far.issuperset(fk_props["attr_map"]):
+                        # foreign key properties
+                        try:
+                            index_props = indexes.pop(tuple(fk_props["attr_map"]))
+                        except KeyError:
+                            index_props = ""
+                        else:
+                            index_props = [k for k, v in index_props.items() if v]
+                            index_props = (
+                                " [{}]".format(", ".join(index_props))
+                                if index_props
+                                else ""
+                            )
+
+                        if not fk_props["aliased"]:
+                            # simple foreign key
+                            definition += "->{props} {class_name}\n".format(
+                                props=index_props,
+                                class_name=lookup_class_name(parent_name, context)
+                                or parent_name,
+                            )
+                        else:
+                            # projected foreign key
+                            definition += (
+                                "->{props} {class_name}.proj({proj_list})\n".format(
+                                    props=index_props,
+                                    class_name=lookup_class_name(parent_name, context)
+                                    or parent_name,
+                                    proj_list=",".join(
+                                        '{}="{}"'.format(attr, ref)
+                                        for attr, ref in fk_props["attr_map"].items()
+                                        if ref != attr
+                                    ),
+                                )
+                            )
+                            attributes_declared.update(fk_props["attr_map"])
+            if do_include:
+                attributes_declared.add(attr.name)
+                definition += "%-20s : %-28s %s\n" % (
+                    (
+                        attr.name
+                        if attr.default is None
+                        else "%s=%s" % (attr.name, attr.default)
+                    ),
+                    "%s%s"
+                    % (attr.type, " auto_increment" if attr.autoincrement else ""),
+                    "# " + attr.comment if attr.comment else "",
+                )
+        # add remaining indexes
+        for k, v in indexes.items():
+            definition += "{unique}INDEX ({attrs})\n".format(
+                unique="UNIQUE " if v["unique"] else "", attrs=", ".join(k)
+            )
+        if printout:
+            logger.info("\n" + definition)
+        return definition
+
+    # --- private helper functions ----
+    def __make_placeholder(self, name, value, ignore_extra_fields=False):
+        """
+        For a given attribute `name` with `value`, return its processed value or value placeholder
+        as a string to be included in the query and the value, if any, to be submitted for
+        processing by mysql API.
+
+        :param name:  name of attribute to be inserted
+        :param value: value of attribute to be inserted
+        """
+        if ignore_extra_fields and name not in self.heading:
+            return None
+        attr = self.heading[name]
+        if attr.adapter:
+            value = attr.adapter.put(value)
+        if value is None or (attr.numeric and (value == "" or np.isnan(float(value)))):
+            # set default value
+            placeholder, value = "DEFAULT", None
+        else:  # not NULL
+            placeholder = "%s"
+            if attr.uuid:
+                if not isinstance(value, uuid.UUID):
+                    try:
+                        value = uuid.UUID(value)
+                    except (AttributeError, ValueError):
+                        raise DataJointError(
+                            "badly formed UUID value {v} for attribute `{n}`".format(
+                                v=value, n=name
+                            )
+                        )
+                value = value.bytes
+            elif attr.is_blob:
+                value = blob.pack(value)
+                value = (
+                    self.external[attr.store].put(value).bytes
+                    if attr.is_external
+                    else value
+                )
+            elif attr.is_attachment:
+                attachment_path = Path(value)
+                if attr.is_external:
+                    # value is hash of contents
+                    value = (
+                        self.external[attr.store]
+                        .upload_attachment(attachment_path)
+                        .bytes
+                    )
+                else:
+                    # value is filename + contents
+                    value = (
+                        str.encode(attachment_path.name)
+                        + b"\0"
+                        + attachment_path.read_bytes()
+                    )
+            elif attr.is_filepath:
+                value = self.external[attr.store].upload_filepath(value).bytes
+            elif attr.numeric:
+                value = str(int(value) if isinstance(value, bool) else value)
+            elif attr.json:
+                value = json.dumps(value)
+        return name, placeholder, value
+
+    def __make_row_to_insert(self, row, field_list, ignore_extra_fields):
+        """
+        Helper function for insert and update
+
+        :param row:  A tuple to insert
+        :return: a dict with fields 'names', 'placeholders', 'values'
+        """
+
+        def check_fields(fields):
+            """
+            Validates that all items in `fields` are valid attributes in the heading
+
+            :param fields: field names of a tuple
+            """
+            if not field_list:
+                if not ignore_extra_fields:
+                    for field in fields:
+                        if field not in self.heading:
+                            raise KeyError(
+                                "`{0:s}` is not in the table heading".format(field)
+                            )
+            elif set(field_list) != set(fields).intersection(self.heading.names):
+                raise DataJointError("Attempt to insert rows with different fields.")
+
+        if isinstance(row, np.void):  # np.array
+            check_fields(row.dtype.fields)
+            attributes = [
+                self.__make_placeholder(name, row[name], ignore_extra_fields)
+                for name in self.heading
+                if name in row.dtype.fields
+            ]
+        elif isinstance(row, collections.abc.Mapping):  # dict-based
+            check_fields(row)
+            attributes = [
+                self.__make_placeholder(name, row[name], ignore_extra_fields)
+                for name in self.heading
+                if name in row
+            ]
+        else:  # positional
+            try:
+                if len(row) != len(self.heading):
+                    raise DataJointError(
+                        "Invalid insert argument. Incorrect number of attributes: "
+                        "{given} given; {expected} expected".format(
+                            given=len(row), expected=len(self.heading)
+                        )
+                    )
+            except TypeError:
+                raise DataJointError("Datatype %s cannot be inserted" % type(row))
+            else:
+                attributes = [
+                    self.__make_placeholder(name, value, ignore_extra_fields)
+                    for name, value in zip(self.heading, row)
+                ]
+        if ignore_extra_fields:
+            attributes = [a for a in attributes if a is not None]
+
+        assert len(attributes), "Empty tuple"
+        row_to_insert = dict(zip(("names", "placeholders", "values"), zip(*attributes)))
+        if not field_list:
+            # first row sets the composition of the field list
+            field_list.extend(row_to_insert["names"])
+        else:
+            #  reorder attributes in row_to_insert to match field_list
+            order = list(row_to_insert["names"].index(field) for field in field_list)
+            row_to_insert["names"] = list(row_to_insert["names"][i] for i in order)
+            row_to_insert["placeholders"] = list(
+                row_to_insert["placeholders"][i] for i in order
+            )
+            row_to_insert["values"] = list(row_to_insert["values"][i] for i in order)
+        return row_to_insert
+

+ + + +

+ + + + + + + +

+ + +

+ `declare(context=None)` + +¶

+ + +

+ +

Declare the table in the schema based on self.definition.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `context` +	+	+ + the context for foreign key resolution. If None, foreign keys are +not allowed. + +	+ `None` +

+ + +

Source code in datajoint/table.py

def declare(self, context=None):
+    """
+    Declare the table in the schema based on self.definition.
+
+    :param context: the context for foreign key resolution. If None, foreign keys are
+        not allowed.
+    """
+    if self.connection.in_transaction:
+        raise DataJointError(
+            "Cannot declare new tables inside a transaction, "
+            "e.g. from inside a populate/make call"
+        )
+    # Enforce strict CamelCase #1150
+    if not is_camel_case(self.class_name):
+        raise DataJointError(
+            "Table class name `{name}` is invalid. Please use CamelCase. ".format(
+                name=self.class_name
+            )
+            + "Classes defining tables should be formatted in strict CamelCase."
+        )
+    sql, external_stores = declare(self.full_table_name, self.definition, context)
+    sql = sql.format(database=self.database)
+    try:
+        # declare all external tables before declaring main table
+        for store in external_stores:
+            self.connection.schemas[self.database].external[store]
+        self.connection.query(sql)
+    except AccessError:
+        # skip if no create privilege
+        pass
+    else:
+        self._log("Declared " + self.full_table_name)
+

+ +

+ + + + + + +

+ + +

+ `alter(prompt=True, context=None)` + +¶

+ + +

+ +

Alter the table definition from self.definition

+ + +

Source code in datajoint/table.py

def alter(self, prompt=True, context=None):
+    """
+    Alter the table definition from self.definition
+    """
+    if self.connection.in_transaction:
+        raise DataJointError(
+            "Cannot update table declaration inside a transaction, "
+            "e.g. from inside a populate/make call"
+        )
+    if context is None:
+        frame = inspect.currentframe().f_back
+        context = dict(frame.f_globals, **frame.f_locals)
+        del frame
+    old_definition = self.describe(context=context)
+    sql, external_stores = alter(self.definition, old_definition, context)
+    if not sql:
+        if prompt:
+            logger.warning("Nothing to alter.")
+    else:
+        sql = "ALTER TABLE {tab}\n\t".format(
+            tab=self.full_table_name
+        ) + ",\n\t".join(sql)
+        if not prompt or user_choice(sql + "\n\nExecute?") == "yes":
+            try:
+                # declare all external tables before declaring main table
+                for store in external_stores:
+                    self.connection.schemas[self.database].external[store]
+                self.connection.query(sql)
+            except AccessError:
+                # skip if no create privilege
+                pass
+            else:
+                # reset heading
+                self.__class__._heading = Heading(
+                    table_info=self.heading.table_info
+                )
+                if prompt:
+                    logger.info("Table altered")
+                self._log("Altered " + self.full_table_name)
+

+ +

+ + + + + + +

+ + +

+ `from_clause()` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the FROM clause of SQL SELECT statements. + +

+ + +

Source code in datajoint/table.py

def from_clause(self):
+    """
+    :return: the FROM clause of SQL SELECT statements.
+    """
+    return self.full_table_name
+

+ +

+ + + + + + +

+ + +

+ `get_select_fields(select_fields=None)` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the selected attributes from the SQL SELECT statement. + +

+ + +

Source code in datajoint/table.py

def get_select_fields(self, select_fields=None):
+    """
+    :return: the selected attributes from the SQL SELECT statement.
+    """
+    return (
+        "*" if select_fields is None else self.heading.project(select_fields).as_sql
+    )
+

+ +

+ + + + + + +

+ + +

+ `parents(primary=None, as_objects=False, foreign_key_info=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `primary` +	+	+ + if None, then all parents are returned. If True, then only foreign keys composed of +primary key attributes are considered. If False, return foreign keys including at least one +secondary attribute. + +	+ `None` +
+ `as_objects` +	+	+ + if False, return table names. If True, return table objects. + +	+ `False` +
+ `foreign_key_info` +	+	+ + if True, each element in result also includes foreign key info. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of parents as table names or table objects +with (optional) foreign key information. + +

+ + +

Source code in datajoint/table.py

def parents(self, primary=None, as_objects=False, foreign_key_info=False):
+    """
+
+    :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
+        primary key attributes are considered.  If False, return foreign keys including at least one
+        secondary attribute.
+    :param as_objects: if False, return table names. If True, return table objects.
+    :param foreign_key_info: if True, each element in result also includes foreign key info.
+    :return: list of parents as table names or table objects
+        with (optional) foreign key information.
+    """
+    get_edge = self.connection.dependencies.parents
+    nodes = [
+        next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+        for name, props in get_edge(self.full_table_name, primary).items()
+    ]
+    if as_objects:
+        nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+    if not foreign_key_info:
+        nodes = [name for name, props in nodes]
+    return nodes
+

+ +

+ + + + + + +

+ + +

+ `children(primary=None, as_objects=False, foreign_key_info=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `primary` +	+	+ + if None, then all children are returned. If True, then only foreign keys composed of +primary key attributes are considered. If False, return foreign keys including at least one +secondary attribute. + +	+ `None` +
+ `as_objects` +	+	+ + if False, return table names. If True, return table objects. + +	+ `False` +
+ `foreign_key_info` +	+	+ + if True, each element in result also includes foreign key info. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of children as table names or table objects +with (optional) foreign key information. + +

+ + +

Source code in datajoint/table.py

def children(self, primary=None, as_objects=False, foreign_key_info=False):
+    """
+    :param primary: if None, then all children are returned. If True, then only foreign keys composed of
+        primary key attributes are considered.  If False, return foreign keys including at least one
+        secondary attribute.
+    :param as_objects: if False, return table names. If True, return table objects.
+    :param foreign_key_info: if True, each element in result also includes foreign key info.
+    :return: list of children as table names or table objects
+        with (optional) foreign key information.
+    """
+    get_edge = self.connection.dependencies.children
+    nodes = [
+        next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+        for name, props in get_edge(self.full_table_name, primary).items()
+    ]
+    if as_objects:
+        nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+    if not foreign_key_info:
+        nodes = [name for name, props in nodes]
+    return nodes
+

+ +

+ + + + + + +

+ + +

+ `descendants(as_objects=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `as_objects` +	+	+ + False - a list of table names; True - a list of table objects. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of tables descendants in topological order. + +

+ + +

Source code in datajoint/table.py

def descendants(self, as_objects=False):
+    """
+    :param as_objects: False - a list of table names; True - a list of table objects.
+    :return: list of tables descendants in topological order.
+    """
+    return [
+        FreeTable(self.connection, node) if as_objects else node
+        for node in self.connection.dependencies.descendants(self.full_table_name)
+        if not node.isdigit()
+    ]
+

+ +

+ + + + + + +

+ + +

+ `ancestors(as_objects=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `as_objects` +	+	+ + False - a list of table names; True - a list of table objects. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of tables ancestors in topological order. + +

+ + +

Source code in datajoint/table.py

def ancestors(self, as_objects=False):
+    """
+    :param as_objects: False - a list of table names; True - a list of table objects.
+    :return: list of tables ancestors in topological order.
+    """
+    return [
+        FreeTable(self.connection, node) if as_objects else node
+        for node in self.connection.dependencies.ancestors(self.full_table_name)
+        if not node.isdigit()
+    ]
+

+ +

+ + + + + + +

+ + +

+ `parts(as_objects=False)` + +¶

+ + +

+ +

return part tables either as entries in a dict with foreign key information or a list of objects

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `as_objects` +	+	+ + if False (default), the output is a dict describing the foreign keys. If True, return table objects. + +	+ `False` +

+ + +

Source code in datajoint/table.py

def parts(self, as_objects=False):
+    """
+    return part tables either as entries in a dict with foreign key information or a list of objects
+
+    :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects.
+    """
+    self.connection.dependencies.load(force=False)
+    nodes = [
+        node
+        for node in self.connection.dependencies.nodes
+        if not node.isdigit() and node.startswith(self.full_table_name[:-1] + "__")
+    ]
+    return [FreeTable(self.connection, c) for c in nodes] if as_objects else nodes
+

+ +

+ + + + + + +

+ + + +

+ `is_declared` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + True is the table is declared in the schema. + +

+ +

+ + + + + + +

+ + + +

+ `full_table_name` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + full table name in the schema + +

+ +

+ + + + + + +

+ + +

+ `update1(row)` + +¶

+ + +

+ +

update1 updates one existing entry in the table. +Caution: In DataJoint the primary modes for data manipulation is to insert and +delete entire records since referential integrity works on the level of records, +not fields. Therefore, updates are reserved for corrective operations outside of main +workflow. Use UPDATE methods sparingly with full awareness of potential violations of +assumptions.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `row` +	+	+ + a `dict` containing the primary key values and the attributes to update. + Setting an attribute value to None will reset it to the default value (if any). + The primary key attributes must always be provided. + Examples: + + + + table.update1({'id': 1, 'value': 3}) # update value in record with id=1 +table.update1({'id': 1, 'value': None}) # reset value to default + + + + +	+ required +

+ + +

Source code in datajoint/table.py

def update1(self, row):
+    """
+    ``update1`` updates one existing entry in the table.
+    Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and
+    ``delete`` entire records since referential integrity works on the level of records,
+    not fields. Therefore, updates are reserved for corrective operations outside of main
+    workflow. Use UPDATE methods sparingly with full awareness of potential violations of
+    assumptions.
+
+    :param row: a ``dict`` containing the primary key values and the attributes to update.
+        Setting an attribute value to None will reset it to the default value (if any).
+
+    The primary key attributes must always be provided.
+
+    Examples:
+
+    >>> table.update1({'id': 1, 'value': 3})  # update value in record with id=1
+    >>> table.update1({'id': 1, 'value': None})  # reset value to default
+    """
+    # argument validations
+    if not isinstance(row, collections.abc.Mapping):
+        raise DataJointError("The argument of update1 must be dict-like.")
+    if not set(row).issuperset(self.primary_key):
+        raise DataJointError(
+            "The argument of update1 must supply all primary key values."
+        )
+    try:
+        raise DataJointError(
+            "Attribute `%s` not found."
+            % next(k for k in row if k not in self.heading.names)
+        )
+    except StopIteration:
+        pass  # ok
+    if len(self.restriction):
+        raise DataJointError("Update cannot be applied to a restricted table.")
+    key = {k: row[k] for k in self.primary_key}
+    if len(self & key) != 1:
+        raise DataJointError("Update can only be applied to one existing entry.")
+    # UPDATE query
+    row = [
+        self.__make_placeholder(k, v)
+        for k, v in row.items()
+        if k not in self.primary_key
+    ]
+    query = "UPDATE {table} SET {assignments} WHERE {where}".format(
+        table=self.full_table_name,
+        assignments=",".join("`%s`=%s" % r[:2] for r in row),
+        where=make_condition(self, key, set()),
+    )
+    self.connection.query(query, args=list(r[2] for r in row if r[2] is not None))
+

+ +

+ + + + + + +

+ + +

+ `insert1(row, **kwargs)` + +¶

+ + +

+ +

Insert one data record into the table. For kwargs, see insert().

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `row` +	+	+ + a numpy record, a dict-like object, or an ordered sequence to be inserted +as one row. + +	+ required +

+ + +

Source code in datajoint/table.py

def insert1(self, row, **kwargs):
+    """
+    Insert one data record into the table. For ``kwargs``, see ``insert()``.
+
+    :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted
+        as one row.
+    """
+    self.insert((row,), **kwargs)
+

+ +

+ + + + + + +

+ + +

+ `insert(rows, replace=False, skip_duplicates=False, ignore_extra_fields=False, allow_direct_insert=None)` + +¶

+ + +

+ +

Insert a collection of rows.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `rows` +	+	+ + Either (a) an iterable where an element is a numpy record, a +dict-like object, a pandas.DataFrame, a sequence, or a query expression with +the same heading as self, or (b) a pathlib.Path object specifying a path +relative to the current directory with a CSV file, the contents of which +will be inserted. + +	+ required +
+ `replace` +	+	+ + If True, replaces the existing tuple. + +	+ `False` +
+ `skip_duplicates` +	+	+ + If True, silently skip duplicate inserts. + +	+ `False` +
+ `ignore_extra_fields` +	+	+ + If False, fields that are not in the heading raise error. + +	+ `False` +
+ `allow_direct_insert` +	+	+ + Only applies in auto-populated tables. If False (default), + insert may only be called from inside the make callback. + Example: + `>>> Table.insert([ +>>> dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"), +>>> dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")]) +` + +	+ `None` +

+ + +

Source code in datajoint/table.py

def insert(
+    self,
+    rows,
+    replace=False,
+    skip_duplicates=False,
+    ignore_extra_fields=False,
+    allow_direct_insert=None,
+):
+    """
+    Insert a collection of rows.
+
+    :param rows: Either (a) an iterable where an element is a numpy record, a
+        dict-like object, a pandas.DataFrame, a sequence, or a query expression with
+        the same heading as self, or (b) a pathlib.Path object specifying a path
+        relative to the current directory with a CSV file, the contents of which
+        will be inserted.
+    :param replace: If True, replaces the existing tuple.
+    :param skip_duplicates: If True, silently skip duplicate inserts.
+    :param ignore_extra_fields: If False, fields that are not in the heading raise error.
+    :param allow_direct_insert: Only applies in auto-populated tables. If False (default),
+        insert may only be called from inside the make callback.
+
+    Example:
+
+        >>> Table.insert([
+        >>>     dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"),
+        >>>     dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")])
+    """
+    if isinstance(rows, pandas.DataFrame):
+        # drop 'extra' synthetic index for 1-field index case -
+        # frames with more advanced indices should be prepared by user.
+        rows = rows.reset_index(
+            drop=len(rows.index.names) == 1 and not rows.index.names[0]
+        ).to_records(index=False)
+
+    if isinstance(rows, Path):
+        with open(rows, newline="") as data_file:
+            rows = list(csv.DictReader(data_file, delimiter=","))
+
+    # prohibit direct inserts into auto-populated tables
+    if not allow_direct_insert and not getattr(self, "_allow_insert", True):
+        raise DataJointError(
+            "Inserts into an auto-populated table can only be done inside "
+            "its make method during a populate call."
+            " To override, set keyword argument allow_direct_insert=True."
+        )
+
+    if inspect.isclass(rows) and issubclass(rows, QueryExpression):
+        rows = rows()  # instantiate if a class
+    if isinstance(rows, QueryExpression):
+        # insert from select
+        if not ignore_extra_fields:
+            try:
+                raise DataJointError(
+                    "Attribute %s not found. To ignore extra attributes in insert, "
+                    "set ignore_extra_fields=True."
+                    % next(
+                        name for name in rows.heading if name not in self.heading
+                    )
+                )
+            except StopIteration:
+                pass
+        fields = list(name for name in rows.heading if name in self.heading)
+        query = "{command} INTO {table} ({fields}) {select}{duplicate}".format(
+            command="REPLACE" if replace else "INSERT",
+            fields="`" + "`,`".join(fields) + "`",
+            table=self.full_table_name,
+            select=rows.make_sql(fields),
+            duplicate=(
+                " ON DUPLICATE KEY UPDATE `{pk}`={table}.`{pk}`".format(
+                    table=self.full_table_name, pk=self.primary_key[0]
+                )
+                if skip_duplicates
+                else ""
+            ),
+        )
+        self.connection.query(query)
+        return
+
+    # collects the field list from first row (passed by reference)
+    field_list = []
+    rows = list(
+        self.__make_row_to_insert(row, field_list, ignore_extra_fields)
+        for row in rows
+    )
+    if rows:
+        try:
+            query = "{command} INTO {destination}(`{fields}`) VALUES {placeholders}{duplicate}".format(
+                command="REPLACE" if replace else "INSERT",
+                destination=self.from_clause(),
+                fields="`,`".join(field_list),
+                placeholders=",".join(
+                    "(" + ",".join(row["placeholders"]) + ")" for row in rows
+                ),
+                duplicate=(
+                    " ON DUPLICATE KEY UPDATE `{pk}`=`{pk}`".format(
+                        pk=self.primary_key[0]
+                    )
+                    if skip_duplicates
+                    else ""
+                ),
+            )
+            self.connection.query(
+                query,
+                args=list(
+                    itertools.chain.from_iterable(
+                        (v for v in r["values"] if v is not None) for r in rows
+                    )
+                ),
+            )
+        except UnknownAttributeError as err:
+            raise err.suggest(
+                "To ignore extra fields in insert, set ignore_extra_fields=True"
+            )
+        except DuplicateError as err:
+            raise err.suggest(
+                "To ignore duplicate entries in insert, set skip_duplicates=True"
+            )
+

+ +

+ + + + + + +

+ + +

+ `delete_quick(get_count=False)` + +¶

+ + +

+ +

Deletes the table without cascading and without user prompt. +If this table has populated dependent tables, this will fail.

+ + +

Source code in datajoint/table.py

def delete_quick(self, get_count=False):
+    """
+    Deletes the table without cascading and without user prompt.
+    If this table has populated dependent tables, this will fail.
+    """
+    query = "DELETE FROM " + self.full_table_name + self.where_clause()
+    self.connection.query(query)
+    count = (
+        self.connection.query("SELECT ROW_COUNT()").fetchone()[0]
+        if get_count
+        else None
+    )
+    self._log(query[:255])
+    return count
+

+ +

+ + + + + + +

+ + +

+ `delete(transaction=True, safemode=None, force_parts=False, force_masters=False)` + +¶

+ + +

+ +

Deletes the contents of the table and its dependent tables, recursively.

Args: + transaction: If True, use of the entire delete becomes an atomic transaction. + This is the default and recommended behavior. Set to False if this delete is + nested within another transaction. + safemode: If True, prohibit nested transactions and prompt to confirm. Default + is dj.config['safemode']. + force_parts: Delete from parts even when not deleting from their masters. + force_masters: If True, include part/master pairs in the cascade. + Default is False.

Returns: + Number of deleted rows (excluding those from dependent tables).

Raises: + DataJointError: Delete exceeds maximum number of delete attempts. + DataJointError: When deleting within an existing transaction. + DataJointError: Deleting a part table before its master.

+ + +

Source code in datajoint/table.py

def delete(
+    self,
+    transaction: bool = True,
+    safemode: Union[bool, None] = None,
+    force_parts: bool = False,
+    force_masters: bool = False,
+) -> int:
+    """
+    Deletes the contents of the table and its dependent tables, recursively.
+
+    Args:
+        transaction: If `True`, use of the entire delete becomes an atomic transaction.
+            This is the default and recommended behavior. Set to `False` if this delete is
+            nested within another transaction.
+        safemode: If `True`, prohibit nested transactions and prompt to confirm. Default
+            is `dj.config['safemode']`.
+        force_parts: Delete from parts even when not deleting from their masters.
+        force_masters: If `True`, include part/master pairs in the cascade.
+            Default is `False`.
+
+    Returns:
+        Number of deleted rows (excluding those from dependent tables).
+
+    Raises:
+        DataJointError: Delete exceeds maximum number of delete attempts.
+        DataJointError: When deleting within an existing transaction.
+        DataJointError: Deleting a part table before its master.
+    """
+    deleted = set()
+    visited_masters = set()
+
+    def cascade(table):
+        """service function to perform cascading deletes recursively."""
+        max_attempts = 50
+        for _ in range(max_attempts):
+            try:
+                delete_count = table.delete_quick(get_count=True)
+            except IntegrityError as error:
+                match = foreign_key_error_regexp.match(error.args[0])
+                if match is None:
+                    raise DataJointError(
+                        "Cascading deletes failed because the error message is missing foreign key information."
+                        "Make sure you have REFERENCES privilege to all dependent tables."
+                    ) from None
+                match = match.groupdict()
+                # if schema name missing, use table
+                if "`.`" not in match["child"]:
+                    match["child"] = "{}.{}".format(
+                        table.full_table_name.split(".")[0], match["child"]
+                    )
+                if (
+                    match["pk_attrs"] is not None
+                ):  # fully matched, adjusting the keys
+                    match["fk_attrs"] = [
+                        k.strip("`") for k in match["fk_attrs"].split(",")
+                    ]
+                    match["pk_attrs"] = [
+                        k.strip("`") for k in match["pk_attrs"].split(",")
+                    ]
+                else:  # only partially matched, querying with constraint to determine keys
+                    match["fk_attrs"], match["parent"], match["pk_attrs"] = list(
+                        map(
+                            list,
+                            zip(
+                                *table.connection.query(
+                                    constraint_info_query,
+                                    args=(
+                                        match["name"].strip("`"),
+                                        *[
+                                            _.strip("`")
+                                            for _ in match["child"].split("`.`")
+                                        ],
+                                    ),
+                                ).fetchall()
+                            ),
+                        )
+                    )
+                    match["parent"] = match["parent"][0]
+
+                # Restrict child by table if
+                #   1. if table's restriction attributes are not in child's primary key
+                #   2. if child renames any attributes
+                # Otherwise restrict child by table's restriction.
+                child = FreeTable(table.connection, match["child"])
+                if (
+                    set(table.restriction_attributes) <= set(child.primary_key)
+                    and match["fk_attrs"] == match["pk_attrs"]
+                ):
+                    child._restriction = table._restriction
+                    child._restriction_attributes = table.restriction_attributes
+                elif match["fk_attrs"] != match["pk_attrs"]:
+                    child &= table.proj(
+                        **dict(zip(match["fk_attrs"], match["pk_attrs"]))
+                    )
+                else:
+                    child &= table.proj()
+
+                master_name = get_master(child.full_table_name)
+                if (
+                    force_masters
+                    and master_name
+                    and master_name != table.full_table_name
+                    and master_name not in visited_masters
+                ):
+                    master = FreeTable(table.connection, master_name)
+                    master._restriction_attributes = set()
+                    master._restriction = [
+                        make_condition(  # &= may cause in target tables in subquery
+                            master,
+                            (master.proj() & child.proj()).fetch(),
+                            master._restriction_attributes,
+                        )
+                    ]
+                    visited_masters.add(master_name)
+                    cascade(master)
+                else:
+                    cascade(child)
+            else:
+                deleted.add(table.full_table_name)
+                logger.info(
+                    "Deleting {count} rows from {table}".format(
+                        count=delete_count, table=table.full_table_name
+                    )
+                )
+                break
+        else:
+            raise DataJointError("Exceeded maximum number of delete attempts.")
+        return delete_count
+
+    safemode = config["safemode"] if safemode is None else safemode
+
+    # Start transaction
+    if transaction:
+        if not self.connection.in_transaction:
+            self.connection.start_transaction()
+        else:
+            if not safemode:
+                transaction = False
+            else:
+                raise DataJointError(
+                    "Delete cannot use a transaction within an ongoing transaction. "
+                    "Set transaction=False or safemode=False)."
+                )
+
+    # Cascading delete
+    try:
+        delete_count = cascade(self)
+    except:
+        if transaction:
+            self.connection.cancel_transaction()
+        raise
+
+    if not force_parts:
+        # Avoid deleting from child before master (See issue #151)
+        for part in deleted:
+            master = get_master(part)
+            if master and master not in deleted:
+                if transaction:
+                    self.connection.cancel_transaction()
+                raise DataJointError(
+                    "Attempt to delete part table {part} before deleting from "
+                    "its master {master} first.".format(part=part, master=master)
+                )
+
+    # Confirm and commit
+    if delete_count == 0:
+        if safemode:
+            logger.warning("Nothing to delete.")
+        if transaction:
+            self.connection.cancel_transaction()
+    elif not transaction:
+        logger.info("Delete completed")
+    else:
+        if not safemode or user_choice("Commit deletes?", default="no") == "yes":
+            if transaction:
+                self.connection.commit_transaction()
+            if safemode:
+                logger.info("Delete committed.")
+        else:
+            if transaction:
+                self.connection.cancel_transaction()
+            if safemode:
+                logger.warning("Delete cancelled")
+    return delete_count
+

+ +

+ + + + + + +

+ + +

+ `drop_quick()` + +¶

+ + +

+ +

Drops the table without cascading to dependent tables and without user prompt.

+ + +

Source code in datajoint/table.py

def drop_quick(self):
+    """
+    Drops the table without cascading to dependent tables and without user prompt.
+    """
+    if self.is_declared:
+        query = "DROP TABLE %s" % self.full_table_name
+        self.connection.query(query)
+        logger.info("Dropped table %s" % self.full_table_name)
+        self._log(query[:255])
+    else:
+        logger.info(
+            "Nothing to drop: table %s is not declared" % self.full_table_name
+        )
+

+ +

+ + + + + + +

+ + +

+ `drop()` + +¶

+ + +

+ +

Drop the table and all tables that reference it, recursively. +User is prompted for confirmation if config['safemode'] is set to True.

+ + +

Source code in datajoint/table.py

def drop(self):
+    """
+    Drop the table and all tables that reference it, recursively.
+    User is prompted for confirmation if config['safemode'] is set to True.
+    """
+    if self.restriction:
+        raise DataJointError(
+            "A table with an applied restriction cannot be dropped."
+            " Call drop() on the unrestricted Table."
+        )
+    self.connection.dependencies.load()
+    do_drop = True
+    tables = [
+        table
+        for table in self.connection.dependencies.descendants(self.full_table_name)
+        if not table.isdigit()
+    ]
+
+    # avoid dropping part tables without their masters: See issue #374
+    for part in tables:
+        master = get_master(part)
+        if master and master not in tables:
+            raise DataJointError(
+                "Attempt to drop part table {part} before dropping "
+                "its master. Drop {master} first.".format(part=part, master=master)
+            )
+
+    if config["safemode"]:
+        for table in tables:
+            logger.info(
+                table + " (%d tuples)" % len(FreeTable(self.connection, table))
+            )
+        do_drop = user_choice("Proceed?", default="no") == "yes"
+    if do_drop:
+        for table in reversed(tables):
+            FreeTable(self.connection, table).drop_quick()
+        logger.info("Tables dropped. Restart kernel.")
+

+ +

+ + + + + + +

+ + + +

+ `size_on_disk` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + size of data and indices in bytes on the storage device + +

+ +

+ + + + + + +

+ + +

+ `describe(context=None, printout=False)` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the definition string for the query using DataJoint DDL. + +

+ + +

Source code in datajoint/table.py

def describe(self, context=None, printout=False):
+    """
+    :return:  the definition string for the query using DataJoint DDL.
+    """
+    if context is None:
+        frame = inspect.currentframe().f_back
+        context = dict(frame.f_globals, **frame.f_locals)
+        del frame
+    if self.full_table_name not in self.connection.dependencies:
+        self.connection.dependencies.load()
+    parents = self.parents(foreign_key_info=True)
+    in_key = True
+    definition = (
+        "# " + self.heading.table_status["comment"] + "\n"
+        if self.heading.table_status["comment"]
+        else ""
+    )
+    attributes_thus_far = set()
+    attributes_declared = set()
+    indexes = self.heading.indexes.copy()
+    for attr in self.heading.attributes.values():
+        if in_key and not attr.in_key:
+            definition += "---\n"
+            in_key = False
+        attributes_thus_far.add(attr.name)
+        do_include = True
+        for parent_name, fk_props in parents:
+            if attr.name in fk_props["attr_map"]:
+                do_include = False
+                if attributes_thus_far.issuperset(fk_props["attr_map"]):
+                    # foreign key properties
+                    try:
+                        index_props = indexes.pop(tuple(fk_props["attr_map"]))
+                    except KeyError:
+                        index_props = ""
+                    else:
+                        index_props = [k for k, v in index_props.items() if v]
+                        index_props = (
+                            " [{}]".format(", ".join(index_props))
+                            if index_props
+                            else ""
+                        )
+
+                    if not fk_props["aliased"]:
+                        # simple foreign key
+                        definition += "->{props} {class_name}\n".format(
+                            props=index_props,
+                            class_name=lookup_class_name(parent_name, context)
+                            or parent_name,
+                        )
+                    else:
+                        # projected foreign key
+                        definition += (
+                            "->{props} {class_name}.proj({proj_list})\n".format(
+                                props=index_props,
+                                class_name=lookup_class_name(parent_name, context)
+                                or parent_name,
+                                proj_list=",".join(
+                                    '{}="{}"'.format(attr, ref)
+                                    for attr, ref in fk_props["attr_map"].items()
+                                    if ref != attr
+                                ),
+                            )
+                        )
+                        attributes_declared.update(fk_props["attr_map"])
+        if do_include:
+            attributes_declared.add(attr.name)
+            definition += "%-20s : %-28s %s\n" % (
+                (
+                    attr.name
+                    if attr.default is None
+                    else "%s=%s" % (attr.name, attr.default)
+                ),
+                "%s%s"
+                % (attr.type, " auto_increment" if attr.autoincrement else ""),
+                "# " + attr.comment if attr.comment else "",
+            )
+    # add remaining indexes
+    for k, v in indexes.items():
+        definition += "{unique}INDEX ({attrs})\n".format(
+            unique="UNIQUE " if v["unique"] else "", attrs=", ".join(k)
+        )
+    if printout:
+        logger.info("\n" + definition)
+    return definition
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `Computed` + + +¶

+ + +

+ Bases: UserTable, AutoPopulate

+ + + +

Inherit from this class if the table's values are computed from other tables in the schema. +The inherited class must at least provide the function _make_tuples.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Computed(UserTable, AutoPopulate):
+    """
+    Inherit from this class if the table's values are computed from other tables in the schema.
+    The inherited class must at least provide the function `_make_tuples`.
+    """
+
+    _prefix = "__"
+    tier_regexp = r"(?P<computed>" + _prefix + _base_regexp + ")"
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Imported` + + +¶

+ + +

+ Bases: UserTable, AutoPopulate

+ + + +

Inherit from this class if the table's values are imported from external data sources. +The inherited class must at least provide the function _make_tuples.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Imported(UserTable, AutoPopulate):
+    """
+    Inherit from this class if the table's values are imported from external data sources.
+    The inherited class must at least provide the function `_make_tuples`.
+    """
+
+    _prefix = "_"
+    tier_regexp = r"(?P<imported>" + _prefix + _base_regexp + ")"
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Lookup` + + +¶

+ + +

+ Bases: UserTable

+ + + +

Inherit from this class if the table's values are for lookup. This is +currently equivalent to defining the table as Manual and serves semantic +purposes only.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Lookup(UserTable):
+    """
+    Inherit from this class if the table's values are for lookup. This is
+    currently equivalent to defining the table as Manual and serves semantic
+    purposes only.
+    """
+
+    _prefix = "#"
+    tier_regexp = (
+        r"(?P<lookup>" + _prefix + _base_regexp.replace("TIER", "lookup") + ")"
+    )
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Manual` + + +¶

+ + +

+ Bases: UserTable

+ + + +

Inherit from this class if the table's values are entered manually.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Manual(UserTable):
+    """
+    Inherit from this class if the table's values are entered manually.
+    """
+
+    _prefix = r""
+    tier_regexp = r"(?P<manual>" + _prefix + _base_regexp + ")"
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Part` + + +¶

+ + +

+ Bases: UserTable

+ + + +

Inherit from this class if the table's values are details of an entry in another table +and if this table is populated by the other table. For example, the entries inheriting from +dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix. +Part tables are implemented as classes inside classes.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Part(UserTable):
+    """
+    Inherit from this class if the table's values are details of an entry in another table
+    and if this table is populated by the other table. For example, the entries inheriting from
+    dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix.
+    Part tables are implemented as classes inside classes.
+    """
+
+    _connection = None
+    _master = None
+
+    tier_regexp = (
+        r"(?P<master>"
+        + "|".join([c.tier_regexp for c in (Manual, Lookup, Imported, Computed)])
+        + r"){1,1}"
+        + "__"
+        + r"(?P<part>"
+        + _base_regexp
+        + ")"
+    )
+
+    @ClassProperty
+    def connection(cls):
+        return cls._connection
+
+    @ClassProperty
+    def full_table_name(cls):
+        return (
+            None
+            if cls.database is None or cls.table_name is None
+            else r"`{0:s}`.`{1:s}`".format(cls.database, cls.table_name)
+        )
+
+    @ClassProperty
+    def master(cls):
+        return cls._master
+
+    @ClassProperty
+    def table_name(cls):
+        return (
+            None
+            if cls.master is None
+            else cls.master.table_name + "__" + from_camel_case(cls.__name__)
+        )
+
+    def delete(self, force=False):
+        """
+        unless force is True, prohibits direct deletes from parts.
+        """
+        if force:
+            super().delete(force_parts=True)
+        else:
+            raise DataJointError(
+                "Cannot delete from a Part directly. Delete from master instead"
+            )
+
+    def drop(self, force=False):
+        """
+        unless force is True, prohibits direct deletes from parts.
+        """
+        if force:
+            super().drop()
+        else:
+            raise DataJointError(
+                "Cannot drop a Part directly.  Delete from master instead"
+            )
+
+    def alter(self, prompt=True, context=None):
+        # without context, use declaration context which maps master keyword to master table
+        super().alter(prompt=prompt, context=context or self.declaration_context)
+

+ + + +

+ + + + + + + +

+ + +

+ `delete(force=False)` + +¶

+ + +

+ +

unless force is True, prohibits direct deletes from parts.

+ + +

Source code in datajoint/user_tables.py

def delete(self, force=False):
+    """
+    unless force is True, prohibits direct deletes from parts.
+    """
+    if force:
+        super().delete(force_parts=True)
+    else:
+        raise DataJointError(
+            "Cannot delete from a Part directly. Delete from master instead"
+        )
+

+ +

+ + + + + + +

+ + +

+ `drop(force=False)` + +¶

+ + +

+ +

unless force is True, prohibits direct deletes from parts.

+ + +

Source code in datajoint/user_tables.py

def drop(self, force=False):
+    """
+    unless force is True, prohibits direct deletes from parts.
+    """
+    if force:
+        super().drop()
+    else:
+        raise DataJointError(
+            "Cannot drop a Part directly.  Delete from master instead"
+        )
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/admin/index.html b/0.14/api/datajoint/admin/index.html new file mode 100644 index 000000000..787ab7560 --- /dev/null +++ b/0.14/api/datajoint/admin/index.html @@ -0,0 +1,4062 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + admin.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + admin.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

admin.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + +

+ + +

+ `kill(restriction=None, connection=None, order_by=None)` + +¶

+ + +

+ +

view and kill database connections.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `restriction` +	+	+ + restriction to be applied to processlist + +	+ `None` +
+ `connection` +	+	+ + a datajoint.Connection object. Default calls datajoint.conn() + +	+ `None` +
+ `order_by` +	+	+ + order by a single attribute or the list of attributes. defaults to 'id'. + Restrictions are specified as strings and can involve any of the attributes of +information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. + Examples: + dj.kill('HOST LIKE "%compute%"') lists only connections from hosts containing "compute". + dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes + +	+ `None` +

+ + +

Source code in datajoint/admin.py

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def kill(restriction=None, connection=None, order_by=None):
+    """
+    view and kill database connections.
+
+    :param restriction: restriction to be applied to processlist
+    :param connection: a datajoint.Connection object. Default calls datajoint.conn()
+    :param order_by: order by a single attribute or the list of attributes. defaults to 'id'.
+
+    Restrictions are specified as strings and can involve any of the attributes of
+    information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO.
+
+    Examples:
+        dj.kill('HOST LIKE "%compute%"') lists only connections from hosts containing "compute".
+        dj.kill('TIME > 600') lists only connections in their current state for more than 10 minutes
+    """
+
+    if connection is None:
+        connection = conn()
+
+    if order_by is not None and not isinstance(order_by, str):
+        order_by = ",".join(order_by)
+
+    query = (
+        "SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()"
+        + ("" if restriction is None else " AND (%s)" % restriction)
+        + (" ORDER BY %s" % (order_by or "id"))
+    )
+
+    while True:
+        print("  ID USER         HOST          STATE         TIME    INFO")
+        print("+--+ +----------+ +-----------+ +-----------+ +-----+")
+        cur = (
+            {k.lower(): v for k, v in elem.items()}
+            for elem in connection.query(query, as_dict=True)
+        )
+        for process in cur:
+            try:
+                print(
+                    "{id:>4d} {user:<12s} {host:<12s} {state:<12s} {time:>7d}  {info}".format(
+                        **process
+                    )
+                )
+            except TypeError:
+                print(process)
+        response = input('process to kill or "q" to quit > ')
+        if response == "q":
+            break
+        if response:
+            try:
+                pid = int(response)
+            except ValueError:
+                pass  # ignore non-numeric input
+            else:
+                try:
+                    connection.query("kill %d" % pid)
+                except pymysql.err.InternalError:
+                    logger.warn("Process not found")
+

+ +

+ + + + + + +

+ + +

+ `kill_quick(restriction=None, connection=None)` + +¶

+ + +

+ +

Kill database connections without prompting. Returns number of terminated connections.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `restriction` +	+	+ + restriction to be applied to processlist + +	+ `None` +
+ `connection` +	+	+ + a datajoint.Connection object. Default calls datajoint.conn() + Restrictions are specified as strings and can involve any of the attributes of +information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO. + Examples: + dj.kill('HOST LIKE "%compute%"') terminates connections from hosts containing "compute". + +	+ `None` +

+ + +

Source code in datajoint/admin.py

def kill_quick(restriction=None, connection=None):
+    """
+    Kill database connections without prompting. Returns number of terminated connections.
+
+    :param restriction: restriction to be applied to processlist
+    :param connection: a datajoint.Connection object. Default calls datajoint.conn()
+
+    Restrictions are specified as strings and can involve any of the attributes of
+    information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO.
+
+    Examples:
+        dj.kill('HOST LIKE "%compute%"') terminates connections from hosts containing "compute".
+    """
+    if connection is None:
+        connection = conn()
+
+    query = (
+        "SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()"
+        + ("" if restriction is None else " AND (%s)" % restriction)
+    )
+
+    cur = (
+        {k.lower(): v for k, v in elem.items()}
+        for elem in connection.query(query, as_dict=True)
+    )
+    nkill = 0
+    for process in cur:
+        connection.query("kill %d" % process["id"])
+        nkill += 1
+    return nkill
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/attribute_adapter/index.html b/0.14/api/datajoint/attribute_adapter/index.html new file mode 100644 index 000000000..97aa78db1 --- /dev/null +++ b/0.14/api/datajoint/attribute_adapter/index.html @@ -0,0 +1,4197 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + attribute_adapter.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + attribute_adapter.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

attribute_adapter.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + +

+ + + +

+ `AttributeAdapter` + + +¶

+ + +

+ + + +

Base class for adapter objects for user-defined attribute types.

+ + + + + + + + +

Source code in datajoint/attribute_adapter.py

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class AttributeAdapter:
+    """
+    Base class for adapter objects for user-defined attribute types.
+    """
+
+    @property
+    def attribute_type(self):
+        """
+        :return: a supported DataJoint attribute type to use; e.g. "longblob", "blob@store"
+        """
+        raise NotImplementedError("Undefined attribute adapter")
+
+    def get(self, value):
+        """
+        convert value retrieved from the the attribute in a table into the adapted type
+
+        :param value: value from the database
+
+        :return: object of the adapted type
+        """
+        raise NotImplementedError("Undefined attribute adapter")
+
+    def put(self, obj):
+        """
+        convert an object of the adapted type into a value that DataJoint can store in a table attribute
+
+        :param obj: an object of the adapted type
+        :return: value to store in the database
+        """
+        raise NotImplementedError("Undefined attribute adapter")
+

+ + + +

+ + + + + + + +

+ + + +

+ `attribute_type` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a supported DataJoint attribute type to use; e.g. "longblob", "blob@store" + +

+ +

+ + + + + + +

+ + +

+ `get(value)` + +¶

+ + +

+ +

convert value retrieved from the the attribute in a table into the adapted type

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `value` +	+	+ + value from the database + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + object of the adapted type + +

+ + +

Source code in datajoint/attribute_adapter.py

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def get(self, value):
+    """
+    convert value retrieved from the the attribute in a table into the adapted type
+
+    :param value: value from the database
+
+    :return: object of the adapted type
+    """
+    raise NotImplementedError("Undefined attribute adapter")
+

+ +

+ + + + + + +

+ + +

+ `put(obj)` + +¶

+ + +

+ +

convert an object of the adapted type into a value that DataJoint can store in a table attribute

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `obj` +	+	+ + an object of the adapted type + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + value to store in the database + +

+ + +

Source code in datajoint/attribute_adapter.py

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def put(self, obj):
+    """
+    convert an object of the adapted type into a value that DataJoint can store in a table attribute
+
+    :param obj: an object of the adapted type
+    :return: value to store in the database
+    """
+    raise NotImplementedError("Undefined attribute adapter")
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + +

+ `get_adapter(context, adapter_name)` + +¶

+ + +

+ +

Extract the AttributeAdapter object by its name from the context and validate.

+ + +

Source code in datajoint/attribute_adapter.py

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def get_adapter(context, adapter_name):
+    """
+    Extract the AttributeAdapter object by its name from the context and validate.
+    """
+    if not _support_adapted_types():
+        raise DataJointError("Support for Adapted Attribute types is disabled.")
+    adapter_name = adapter_name.lstrip("<").rstrip(">")
+    try:
+        adapter = (
+            context[adapter_name]
+            if adapter_name in context
+            else type_plugins[adapter_name]["object"].load()
+        )
+    except KeyError:
+        raise DataJointError(
+            "Attribute adapter '{adapter_name}' is not defined.".format(
+                adapter_name=adapter_name
+            )
+        )
+    if not isinstance(adapter, AttributeAdapter):
+        raise DataJointError(
+            "Attribute adapter '{adapter_name}' must be an instance of datajoint.AttributeAdapter".format(
+                adapter_name=adapter_name
+            )
+        )
+    if not isinstance(adapter.attribute_type, str) or not re.match(
+        r"^\w", adapter.attribute_type
+    ):
+        raise DataJointError(
+            "Invalid attribute type {type} in attribute adapter '{adapter_name}'".format(
+                type=adapter.attribute_type, adapter_name=adapter_name
+            )
+        )
+    return adapter
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/autopopulate/index.html b/0.14/api/datajoint/autopopulate/index.html new file mode 100644 index 000000000..3ae756b16 --- /dev/null +++ b/0.14/api/datajoint/autopopulate/index.html @@ -0,0 +1,5685 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + autopopulate.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + autopopulate.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

autopopulate.py

+ +

+ + + + +

+ +

This module defines class dj.AutoPopulate

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ `AutoPopulate` + + +¶

+ + +

+ + + +

AutoPopulate is a mixin class that adds the method populate() to a Table class. +Auto-populated tables must inherit from both Table and AutoPopulate, +must define the property key_source, and must define the callback method make.

+ + + + + + + + +

Source code in datajoint/autopopulate.py

class AutoPopulate:
+    """
+    AutoPopulate is a mixin class that adds the method populate() to a Table class.
+    Auto-populated tables must inherit from both Table and AutoPopulate,
+    must define the property `key_source`, and must define the callback method `make`.
+    """
+
+    _key_source = None
+    _allow_insert = False
+
+    @property
+    def key_source(self):
+        """
+        :return: the query expression that yields primary key values to be passed,
+        sequentially, to the ``make`` method when populate() is called.
+        The default value is the join of the parent tables references from the primary key.
+        Subclasses may override they key_source to change the scope or the granularity
+        of the make calls.
+        """
+
+        def _rename_attributes(table, props):
+            return (
+                table.proj(
+                    **{
+                        attr: ref
+                        for attr, ref in props["attr_map"].items()
+                        if attr != ref
+                    }
+                )
+                if props["aliased"]
+                else table.proj()
+            )
+
+        if self._key_source is None:
+            parents = self.target.parents(
+                primary=True, as_objects=True, foreign_key_info=True
+            )
+            if not parents:
+                raise DataJointError(
+                    "A table must have dependencies "
+                    "from its primary key for auto-populate to work"
+                )
+            self._key_source = _rename_attributes(*parents[0])
+            for q in parents[1:]:
+                self._key_source *= _rename_attributes(*q)
+        return self._key_source
+
+    def make(self, key, **kwargs):
+        """
+        This method must be implemented by derived classes to perform automated computation.
+        The method must implement the following three steps:
+
+        1. Fetch data from tables above in the dependency hierarchy, restricted by the given key.
+        2. Compute secondary attributes based on the fetched data.
+        3. Insert the new tuple(s) into the current table.
+
+        The method can be implemented either as:
+        (a) Regular method: All three steps are performed in a single database transaction.
+            The method must return None.
+        (b) Generator method:
+            The make method is split into three functions:
+            - `make_fetch`: Fetches data from the parent tables.
+            - `make_compute`: Computes secondary attributes based on the fetched data.
+            - `make_insert`: Inserts the computed data into the current table.
+
+            Then populate logic is executes as follows:
+
+            <pseudocode>
+            fetched_data1 = self.make_fetch(key)
+            computed_result = self.make_compute(key, *fetched_data1)
+            begin transaction:
+                fetched_data2 = self.make_fetch(key)
+                if fetched_data1 != fetched_data2:
+                    cancel transaction
+                else:
+                    self.make_insert(key, *computed_result)
+                    commit_transaction
+            <pseudocode>
+
+        Importantly, the output of make_fetch is a tuple that serves as the input into `make_compute`.
+        The output of `make_compute` is a tuple that serves as the input into `make_insert`.
+
+        The functionality must be strictly divided between these three methods:
+        - All database queries must be completed in `make_fetch`.
+        - All computation must be completed in `make_compute`.
+        - All database inserts must be completed in `make_insert`.
+
+        DataJoint may programmatically enforce this separation in the future.
+
+        :param key: The primary key value used to restrict the data fetching.
+        :param kwargs: Keyword arguments passed from populate(make_kwargs=...).
+            These are passed to make_fetch for the tripartite pattern.
+        :raises NotImplementedError: If the derived class does not implement the required methods.
+        """
+
+        if not (
+            hasattr(self, "make_fetch")
+            and hasattr(self, "make_insert")
+            and hasattr(self, "make_compute")
+        ):
+            # user must implement `make`
+            raise NotImplementedError(
+                "Subclasses of AutoPopulate must implement the method `make` "
+                "or (`make_fetch` + `make_compute` + `make_insert`)"
+            )
+
+        # User has implemented `_fetch`, `_compute`, and `_insert` methods instead
+
+        # Step 1: Fetch data from parent tables
+        fetched_data = self.make_fetch(key, **kwargs)  # fetched_data is a tuple
+        computed_result = yield fetched_data  # passed as input into make_compute
+
+        # Step 2: If computed result is not passed in, compute the result
+        if computed_result is None:
+            # this is only executed in the first invocation
+            computed_result = self.make_compute(key, *fetched_data)
+            yield computed_result  # this is passed to the second invocation of make
+
+        # Step 3: Insert the computed result into the current table.
+        self.make_insert(key, *computed_result)
+        yield
+
+    @property
+    def target(self):
+        """
+        :return: table to be populated.
+        In the typical case, dj.AutoPopulate is mixed into a dj.Table class by
+        inheritance and the target is self.
+        """
+        return self
+
+    def _job_key(self, key):
+        """
+        :param key:  they key returned for the job from the key source
+        :return: the dict to use to generate the job reservation hash
+        This method allows subclasses to control the job reservation granularity.
+        """
+        return key
+
+    def _jobs_to_do(self, restrictions):
+        """
+        :return: the query yielding the keys to be computed (derived from self.key_source)
+        """
+        if self.restriction:
+            raise DataJointError(
+                "Cannot call populate on a restricted table. "
+                "Instead, pass conditions to populate() as arguments."
+            )
+        todo = self.key_source
+
+        # key_source is a QueryExpression subclass -- trigger instantiation
+        if inspect.isclass(todo) and issubclass(todo, QueryExpression):
+            todo = todo()
+
+        if not isinstance(todo, QueryExpression):
+            raise DataJointError("Invalid key_source value")
+
+        try:
+            # check if target lacks any attributes from the primary key of key_source
+            raise DataJointError(
+                "The populate target lacks attribute %s "
+                "from the primary key of key_source"
+                % next(
+                    name
+                    for name in todo.heading.primary_key
+                    if name not in self.target.heading
+                )
+            )
+        except StopIteration:
+            pass
+        return (todo & AndList(restrictions)).proj()
+
+    def populate(
+        self,
+        *restrictions,
+        keys=None,
+        suppress_errors=False,
+        return_exception_objects=False,
+        reserve_jobs=False,
+        order="original",
+        limit=None,
+        max_calls=None,
+        display_progress=False,
+        processes=1,
+        make_kwargs=None,
+    ):
+        """
+        ``table.populate()`` calls ``table.make(key)`` for every primary key in
+        ``self.key_source`` for which there is not already a tuple in table.
+
+        :param restrictions: a list of restrictions each restrict
+            (table.key_source - target.proj())
+        :param keys: The list of keys (dicts) to send to self.make().
+            If None (default), then use self.key_source to query they keys.
+        :param suppress_errors: if True, do not terminate execution.
+        :param return_exception_objects: return error objects instead of just error messages
+        :param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion
+        :param order: "original"|"reverse"|"random"  - the order of execution
+        :param limit: if not None, check at most this many keys
+        :param max_calls: if not None, populate at most this many keys
+        :param display_progress: if True, report progress_bar
+        :param processes: number of processes to use. Set to None to use all cores
+        :param make_kwargs: Keyword arguments which do not affect the result of computation
+            to be passed down to each ``make()`` call. Computation arguments should be
+            specified within the pipeline e.g. using a `dj.Lookup` table.
+        :type make_kwargs: dict, optional
+        :return: a dict with two keys
+            "success_count": the count of successful ``make()`` calls in this ``populate()`` call
+            "error_list": the error list that is filled if `suppress_errors` is True
+        """
+        if self.connection.in_transaction:
+            raise DataJointError("Populate cannot be called during a transaction.")
+
+        valid_order = ["original", "reverse", "random"]
+        if order not in valid_order:
+            raise DataJointError(
+                "The order argument must be one of %s" % str(valid_order)
+            )
+        jobs = (
+            self.connection.schemas[self.target.database].jobs if reserve_jobs else None
+        )
+
+        if reserve_jobs:
+            # Define a signal handler for SIGTERM
+            def handler(signum, frame):
+                logger.info("Populate terminated by SIGTERM")
+                raise SystemExit("SIGTERM received")
+
+            old_handler = signal.signal(signal.SIGTERM, handler)
+
+        if keys is None:
+            keys = (self._jobs_to_do(restrictions) - self.target).fetch(
+                "KEY", limit=limit
+            )
+
+        # exclude "error", "ignore" or "reserved" jobs
+        if reserve_jobs:
+            exclude_key_hashes = (
+                jobs
+                & {"table_name": self.target.table_name}
+                & 'status in ("error", "ignore", "reserved")'
+            ).fetch("key_hash")
+            keys = [key for key in keys if key_hash(key) not in exclude_key_hashes]
+
+        if order == "reverse":
+            keys.reverse()
+        elif order == "random":
+            random.shuffle(keys)
+
+        logger.debug("Found %d keys to populate" % len(keys))
+
+        keys = keys[:max_calls]
+        nkeys = len(keys)
+
+        error_list = []
+        success_list = []
+
+        if nkeys:
+            processes = min(_ for _ in (processes, nkeys, mp.cpu_count()) if _)
+
+            populate_kwargs = dict(
+                suppress_errors=suppress_errors,
+                return_exception_objects=return_exception_objects,
+                make_kwargs=make_kwargs,
+            )
+
+            if processes == 1:
+                for key in (
+                    tqdm(keys, desc=self.__class__.__name__)
+                    if display_progress
+                    else keys
+                ):
+                    status = self._populate1(key, jobs, **populate_kwargs)
+                    if status is True:
+                        success_list.append(1)
+                    elif isinstance(status, tuple):
+                        error_list.append(status)
+                    else:
+                        assert status is False
+            else:
+                # spawn multiple processes
+                self.connection.close()  # disconnect parent process from MySQL server
+                del self.connection._conn.ctx  # SSLContext is not pickleable
+                with (
+                    mp.Pool(
+                        processes, _initialize_populate, (self, jobs, populate_kwargs)
+                    ) as pool,
+                    (
+                        tqdm(desc="Processes: ", total=nkeys)
+                        if display_progress
+                        else contextlib.nullcontext()
+                    ) as progress_bar,
+                ):
+                    for status in pool.imap(_call_populate1, keys, chunksize=1):
+                        if status is True:
+                            success_list.append(1)
+                        elif isinstance(status, tuple):
+                            error_list.append(status)
+                        else:
+                            assert status is False
+                        if display_progress:
+                            progress_bar.update()
+                self.connection.connect()  # reconnect parent process to MySQL server
+
+        # restore original signal handler:
+        if reserve_jobs:
+            signal.signal(signal.SIGTERM, old_handler)
+
+        return {
+            "success_count": sum(success_list),
+            "error_list": error_list,
+        }
+
+    def _populate1(
+        self, key, jobs, suppress_errors, return_exception_objects, make_kwargs=None
+    ):
+        """
+        populates table for one source key, calling self.make inside a transaction.
+        :param jobs: the jobs table or None if not reserve_jobs
+        :param key: dict specifying job to populate
+        :param suppress_errors: bool if errors should be suppressed and returned
+        :param return_exception_objects: if True, errors must be returned as objects
+        :return: (key, error) when suppress_errors=True,
+            True if successfully invoke one `make()` call, otherwise False
+        """
+        # use the legacy `_make_tuples` callback.
+        make = self._make_tuples if hasattr(self, "_make_tuples") else self.make
+
+        if jobs is not None and not jobs.reserve(
+            self.target.table_name, self._job_key(key)
+        ):
+            return False
+
+        # if make is a generator, it transaction can be delayed until the final stage
+        is_generator = inspect.isgeneratorfunction(make)
+        if not is_generator:
+            self.connection.start_transaction()
+
+        if key in self.target:  # already populated
+            if not is_generator:
+                self.connection.cancel_transaction()
+            if jobs is not None:
+                jobs.complete(self.target.table_name, self._job_key(key))
+            return False
+
+        logger.debug(f"Making {key} -> {self.target.full_table_name}")
+        self.__class__._allow_insert = True
+
+        try:
+            if not is_generator:
+                make(dict(key), **(make_kwargs or {}))
+            else:
+                # tripartite make - transaction is delayed until the final stage
+                gen = make(dict(key), **(make_kwargs or {}))
+                fetched_data = next(gen)
+                fetch_hash = deepdiff.DeepHash(
+                    fetched_data, ignore_iterable_order=False
+                )[fetched_data]
+                computed_result = next(gen)  # perform the computation
+                # fetch and insert inside a transaction
+                self.connection.start_transaction()
+                gen = make(dict(key), **(make_kwargs or {}))  # restart make
+                fetched_data = next(gen)
+                if (
+                    fetch_hash
+                    != deepdiff.DeepHash(fetched_data, ignore_iterable_order=False)[
+                        fetched_data
+                    ]
+                ):  # raise error if fetched data has changed
+                    raise DataJointError(
+                        "Referential integrity failed! The `make_fetch` data has changed"
+                    )
+                gen.send(computed_result)  # insert
+
+        except (KeyboardInterrupt, SystemExit, Exception) as error:
+            try:
+                self.connection.cancel_transaction()
+            except LostConnectionError:
+                pass
+            error_message = "{exception}{msg}".format(
+                exception=error.__class__.__name__,
+                msg=": " + str(error) if str(error) else "",
+            )
+            logger.debug(
+                f"Error making {key} -> {self.target.full_table_name} - {error_message}"
+            )
+            if jobs is not None:
+                # show error name and error message (if any)
+                jobs.error(
+                    self.target.table_name,
+                    self._job_key(key),
+                    error_message=error_message,
+                    error_stack=traceback.format_exc(),
+                )
+            if not suppress_errors or isinstance(error, SystemExit):
+                raise
+            else:
+                logger.error(error)
+                return key, error if return_exception_objects else error_message
+        else:
+            self.connection.commit_transaction()
+            logger.debug(f"Success making {key} -> {self.target.full_table_name}")
+            if jobs is not None:
+                jobs.complete(self.target.table_name, self._job_key(key))
+            return True
+        finally:
+            self.__class__._allow_insert = False
+
+    def progress(self, *restrictions, display=False):
+        """
+        Report the progress of populating the table.
+        :return: (remaining, total) -- numbers of tuples to be populated
+        """
+        todo = self._jobs_to_do(restrictions)
+        total = len(todo)
+        remaining = len(todo - self.target)
+        if display:
+            logger.info(
+                "%-20s" % self.__class__.__name__
+                + " Completed %d of %d (%2.1f%%)   %s"
+                % (
+                    total - remaining,
+                    total,
+                    100 - 100 * remaining / (total + 1e-12),
+                    datetime.datetime.strftime(
+                        datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"
+                    ),
+                ),
+            )
+        return remaining, total
+

+ + + +

+ + + + + + + +

+ + + +

+ `key_source` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the query expression that yields primary key values to be passed, +sequentially, to the `make` method when populate() is called. +The default value is the join of the parent tables references from the primary key. +Subclasses may override they key_source to change the scope or the granularity +of the make calls. + +

+ +

+ + + + + + +

+ + +

+ `make(key, **kwargs)` + +¶

+ + +

+ +

This method must be implemented by derived classes to perform automated computation. +The method must implement the following three steps:

Fetch data from tables above in the dependency hierarchy, restricted by the given key.
Compute secondary attributes based on the fetched data.
Insert the new tuple(s) into the current table.

The method can be implemented either as: +(a) Regular method: All three steps are performed in a single database transaction. + The method must return None. +(b) Generator method: + The make method is split into three functions: + - make_fetch: Fetches data from the parent tables. + - make_compute: Computes secondary attributes based on the fetched data. + - make_insert: Inserts the computed data into the current table.

Then populate logic is executes as follows:
+
+<pseudocode>
+fetched_data1 = self.make_fetch(key)
+computed_result = self.make_compute(key, *fetched_data1)
+begin transaction:
+    fetched_data2 = self.make_fetch(key)
+    if fetched_data1 != fetched_data2:
+        cancel transaction
+    else:
+        self.make_insert(key, *computed_result)
+        commit_transaction
+<pseudocode>
+

Importantly, the output of make_fetch is a tuple that serves as the input into make_compute. +The output of make_compute is a tuple that serves as the input into make_insert.

The functionality must be strictly divided between these three methods: +- All database queries must be completed in make_fetch. +- All computation must be completed in make_compute. +- All database inserts must be completed in make_insert.

DataJoint may programmatically enforce this separation in the future.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `key` +	+	+ + The primary key value used to restrict the data fetching. + +	+ required +
+ `kwargs` +	+	+ + Keyword arguments passed from populate(make_kwargs=...). +These are passed to make_fetch for the tripartite pattern. + +	+ `{}` +

+ + +

Raises:

+ + + + + + + + + + + + + +

Type	Description
+ `NotImplementedError` +	+ + If the derived class does not implement the required methods. + +

+ + +

Source code in datajoint/autopopulate.py

def make(self, key, **kwargs):
+    """
+    This method must be implemented by derived classes to perform automated computation.
+    The method must implement the following three steps:
+
+    1. Fetch data from tables above in the dependency hierarchy, restricted by the given key.
+    2. Compute secondary attributes based on the fetched data.
+    3. Insert the new tuple(s) into the current table.
+
+    The method can be implemented either as:
+    (a) Regular method: All three steps are performed in a single database transaction.
+        The method must return None.
+    (b) Generator method:
+        The make method is split into three functions:
+        - `make_fetch`: Fetches data from the parent tables.
+        - `make_compute`: Computes secondary attributes based on the fetched data.
+        - `make_insert`: Inserts the computed data into the current table.
+
+        Then populate logic is executes as follows:
+
+        <pseudocode>
+        fetched_data1 = self.make_fetch(key)
+        computed_result = self.make_compute(key, *fetched_data1)
+        begin transaction:
+            fetched_data2 = self.make_fetch(key)
+            if fetched_data1 != fetched_data2:
+                cancel transaction
+            else:
+                self.make_insert(key, *computed_result)
+                commit_transaction
+        <pseudocode>
+
+    Importantly, the output of make_fetch is a tuple that serves as the input into `make_compute`.
+    The output of `make_compute` is a tuple that serves as the input into `make_insert`.
+
+    The functionality must be strictly divided between these three methods:
+    - All database queries must be completed in `make_fetch`.
+    - All computation must be completed in `make_compute`.
+    - All database inserts must be completed in `make_insert`.
+
+    DataJoint may programmatically enforce this separation in the future.
+
+    :param key: The primary key value used to restrict the data fetching.
+    :param kwargs: Keyword arguments passed from populate(make_kwargs=...).
+        These are passed to make_fetch for the tripartite pattern.
+    :raises NotImplementedError: If the derived class does not implement the required methods.
+    """
+
+    if not (
+        hasattr(self, "make_fetch")
+        and hasattr(self, "make_insert")
+        and hasattr(self, "make_compute")
+    ):
+        # user must implement `make`
+        raise NotImplementedError(
+            "Subclasses of AutoPopulate must implement the method `make` "
+            "or (`make_fetch` + `make_compute` + `make_insert`)"
+        )
+
+    # User has implemented `_fetch`, `_compute`, and `_insert` methods instead
+
+    # Step 1: Fetch data from parent tables
+    fetched_data = self.make_fetch(key, **kwargs)  # fetched_data is a tuple
+    computed_result = yield fetched_data  # passed as input into make_compute
+
+    # Step 2: If computed result is not passed in, compute the result
+    if computed_result is None:
+        # this is only executed in the first invocation
+        computed_result = self.make_compute(key, *fetched_data)
+        yield computed_result  # this is passed to the second invocation of make
+
+    # Step 3: Insert the computed result into the current table.
+    self.make_insert(key, *computed_result)
+    yield
+

+ +

+ + + + + + +

+ + + +

+ `target` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + table to be populated. +In the typical case, dj.AutoPopulate is mixed into a dj.Table class by +inheritance and the target is self. + +

+ +

+ + + + + + +

+ + +

+ `populate(*restrictions, keys=None, suppress_errors=False, return_exception_objects=False, reserve_jobs=False, order='original', limit=None, max_calls=None, display_progress=False, processes=1, make_kwargs=None)` + +¶

+ + +

+ +

table.populate() calls table.make(key) for every primary key in +self.key_source for which there is not already a tuple in table.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `restrictions` +	+	+ + a list of restrictions each restrict +(table.key_source - target.proj()) + +	+ `()` +
+ `keys` +	+	+ + The list of keys (dicts) to send to self.make(). +If None (default), then use self.key_source to query they keys. + +	+ `None` +
+ `suppress_errors` +	+	+ + if True, do not terminate execution. + +	+ `False` +
+ `return_exception_objects` +	+	+ + return error objects instead of just error messages + +	+ `False` +
+ `reserve_jobs` +	+	+ + if True, reserve jobs to populate in asynchronous fashion + +	+ `False` +
+ `order` +	+	+ + "original"\|"reverse"\|"random" - the order of execution + +	+ `'original'` +
+ `limit` +	+	+ + if not None, check at most this many keys + +	+ `None` +
+ `max_calls` +	+	+ + if not None, populate at most this many keys + +	+ `None` +
+ `display_progress` +	+	+ + if True, report progress_bar + +	+ `False` +
+ `processes` +	+	+ + number of processes to use. Set to None to use all cores + +	+ `1` +
+ `make_kwargs` +	+ `(dict, optional)` +	+ + Keyword arguments which do not affect the result of computation +to be passed down to each `make()` call. Computation arguments should be +specified within the pipeline e.g. using a `dj.Lookup` table. + +	+ `None` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a dict with two keys +"success_count": the count of successful `make()` calls in this `populate()` call +"error_list": the error list that is filled if `suppress_errors` is True + +

+ + +

Source code in datajoint/autopopulate.py

def populate(
+    self,
+    *restrictions,
+    keys=None,
+    suppress_errors=False,
+    return_exception_objects=False,
+    reserve_jobs=False,
+    order="original",
+    limit=None,
+    max_calls=None,
+    display_progress=False,
+    processes=1,
+    make_kwargs=None,
+):
+    """
+    ``table.populate()`` calls ``table.make(key)`` for every primary key in
+    ``self.key_source`` for which there is not already a tuple in table.
+
+    :param restrictions: a list of restrictions each restrict
+        (table.key_source - target.proj())
+    :param keys: The list of keys (dicts) to send to self.make().
+        If None (default), then use self.key_source to query they keys.
+    :param suppress_errors: if True, do not terminate execution.
+    :param return_exception_objects: return error objects instead of just error messages
+    :param reserve_jobs: if True, reserve jobs to populate in asynchronous fashion
+    :param order: "original"|"reverse"|"random"  - the order of execution
+    :param limit: if not None, check at most this many keys
+    :param max_calls: if not None, populate at most this many keys
+    :param display_progress: if True, report progress_bar
+    :param processes: number of processes to use. Set to None to use all cores
+    :param make_kwargs: Keyword arguments which do not affect the result of computation
+        to be passed down to each ``make()`` call. Computation arguments should be
+        specified within the pipeline e.g. using a `dj.Lookup` table.
+    :type make_kwargs: dict, optional
+    :return: a dict with two keys
+        "success_count": the count of successful ``make()`` calls in this ``populate()`` call
+        "error_list": the error list that is filled if `suppress_errors` is True
+    """
+    if self.connection.in_transaction:
+        raise DataJointError("Populate cannot be called during a transaction.")
+
+    valid_order = ["original", "reverse", "random"]
+    if order not in valid_order:
+        raise DataJointError(
+            "The order argument must be one of %s" % str(valid_order)
+        )
+    jobs = (
+        self.connection.schemas[self.target.database].jobs if reserve_jobs else None
+    )
+
+    if reserve_jobs:
+        # Define a signal handler for SIGTERM
+        def handler(signum, frame):
+            logger.info("Populate terminated by SIGTERM")
+            raise SystemExit("SIGTERM received")
+
+        old_handler = signal.signal(signal.SIGTERM, handler)
+
+    if keys is None:
+        keys = (self._jobs_to_do(restrictions) - self.target).fetch(
+            "KEY", limit=limit
+        )
+
+    # exclude "error", "ignore" or "reserved" jobs
+    if reserve_jobs:
+        exclude_key_hashes = (
+            jobs
+            & {"table_name": self.target.table_name}
+            & 'status in ("error", "ignore", "reserved")'
+        ).fetch("key_hash")
+        keys = [key for key in keys if key_hash(key) not in exclude_key_hashes]
+
+    if order == "reverse":
+        keys.reverse()
+    elif order == "random":
+        random.shuffle(keys)
+
+    logger.debug("Found %d keys to populate" % len(keys))
+
+    keys = keys[:max_calls]
+    nkeys = len(keys)
+
+    error_list = []
+    success_list = []
+
+    if nkeys:
+        processes = min(_ for _ in (processes, nkeys, mp.cpu_count()) if _)
+
+        populate_kwargs = dict(
+            suppress_errors=suppress_errors,
+            return_exception_objects=return_exception_objects,
+            make_kwargs=make_kwargs,
+        )
+
+        if processes == 1:
+            for key in (
+                tqdm(keys, desc=self.__class__.__name__)
+                if display_progress
+                else keys
+            ):
+                status = self._populate1(key, jobs, **populate_kwargs)
+                if status is True:
+                    success_list.append(1)
+                elif isinstance(status, tuple):
+                    error_list.append(status)
+                else:
+                    assert status is False
+        else:
+            # spawn multiple processes
+            self.connection.close()  # disconnect parent process from MySQL server
+            del self.connection._conn.ctx  # SSLContext is not pickleable
+            with (
+                mp.Pool(
+                    processes, _initialize_populate, (self, jobs, populate_kwargs)
+                ) as pool,
+                (
+                    tqdm(desc="Processes: ", total=nkeys)
+                    if display_progress
+                    else contextlib.nullcontext()
+                ) as progress_bar,
+            ):
+                for status in pool.imap(_call_populate1, keys, chunksize=1):
+                    if status is True:
+                        success_list.append(1)
+                    elif isinstance(status, tuple):
+                        error_list.append(status)
+                    else:
+                        assert status is False
+                    if display_progress:
+                        progress_bar.update()
+            self.connection.connect()  # reconnect parent process to MySQL server
+
+    # restore original signal handler:
+    if reserve_jobs:
+        signal.signal(signal.SIGTERM, old_handler)
+
+    return {
+        "success_count": sum(success_list),
+        "error_list": error_list,
+    }
+

+ +

+ + + + + + +

+ + +

+ `progress(*restrictions, display=False)` + +¶

+ + +

+ +

Report the progress of populating the table.

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + (remaining, total) -- numbers of tuples to be populated + +

+ + +

Source code in datajoint/autopopulate.py

def progress(self, *restrictions, display=False):
+    """
+    Report the progress of populating the table.
+    :return: (remaining, total) -- numbers of tuples to be populated
+    """
+    todo = self._jobs_to_do(restrictions)
+    total = len(todo)
+    remaining = len(todo - self.target)
+    if display:
+        logger.info(
+            "%-20s" % self.__class__.__name__
+            + " Completed %d of %d (%2.1f%%)   %s"
+            % (
+                total - remaining,
+                total,
+                100 - 100 * remaining / (total + 1e-12),
+                datetime.datetime.strftime(
+                    datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"
+                ),
+            ),
+        )
+    return remaining, total
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/blob/index.html b/0.14/api/datajoint/blob/index.html new file mode 100644 index 000000000..a26c71719 --- /dev/null +++ b/0.14/api/datajoint/blob/index.html @@ -0,0 +1,5476 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + blob.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + blob.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

blob.py

+ +

+ + + + +

+ +

(De)serialization methods for basic datatypes and numpy.ndarrays with provisions for mutual +compatibility with Matlab-based serialization implemented by mYm.

+ + + + + + + + + + +

+ + + + + + + + + + + +

+ + + +

+ `MatCell` + + +¶

+ + +

+ Bases: ndarray

+ + + +

a numpy ndarray representing a Matlab cell array

+ + + + + + + + +

Source code in datajoint/blob.py

74
+75
+76
+77
class MatCell(np.ndarray):
+    """a numpy ndarray representing a Matlab cell array"""
+
+    pass
+

+ +

+ + + + + + +

+ + + +

+ `MatStruct` + + +¶

+ + +

+ Bases: recarray

+ + + +

numpy.recarray representing a Matlab struct array

+ + + + + + + + +

Source code in datajoint/blob.py

80
+81
+82
+83
class MatStruct(np.recarray):
+    """numpy.recarray representing a Matlab struct array"""
+
+    pass
+

+ +

+ + + + + + +

+ + + +

+ `Blob` + + +¶

+ + +

+ + + + + + + + + + +

Source code in datajoint/blob.py

class Blob:
+    def __init__(self, squeeze=False):
+        self._squeeze = squeeze
+        self._blob = None
+        self._pos = 0
+        self.protocol = None
+
+    def set_dj0(self):
+        if not config.get("enable_python_native_blobs"):
+            raise DataJointError(
+                """v0.12+ python native blobs disabled.
+                See also: https://github.com/datajoint/datajoint-python#python-native-blobs"""
+            )
+
+        self.protocol = b"dj0\0"  # when using new blob features
+
+    def squeeze(self, array, convert_to_scalar=True):
+        """
+        Simplify the input array - squeeze out all singleton dimensions.
+        If convert_to_scalar, then convert zero-dimensional arrays to scalars
+        """
+        if not self._squeeze:
+            return array
+        array = array.squeeze()
+        return array.item() if array.ndim == 0 and convert_to_scalar else array
+
+    def unpack(self, blob):
+        self._blob = blob
+        try:
+            # decompress
+            prefix = next(
+                p for p in compression if self._blob[self._pos :].startswith(p)
+            )
+        except StopIteration:
+            pass  # assume uncompressed but could be unrecognized compression
+        else:
+            self._pos += len(prefix)
+            blob_size = self.read_value()
+            blob = compression[prefix](self._blob[self._pos :])
+            assert len(blob) == blob_size
+            self._blob = blob
+            self._pos = 0
+        blob_format = self.read_zero_terminated_string()
+        if blob_format in ("mYm", "dj0"):
+            return self.read_blob(n_bytes=len(self._blob) - self._pos)
+
+    def read_blob(self, n_bytes=None):
+        start = self._pos
+        data_structure_code = chr(self.read_value("uint8"))
+        try:
+            call = {
+                # MATLAB-compatible, inherited from original mYm
+                "A": self.read_array,  # matlab-compatible numeric arrays and scalars with ndim==0
+                "P": self.read_sparse_array,  # matlab sparse array -- not supported yet
+                "S": self.read_struct,  # matlab struct array
+                "C": self.read_cell_array,  # matlab cell array
+                # basic data types
+                "\xff": self.read_none,  # None
+                "\x01": self.read_tuple,  # a Sequence (e.g. tuple)
+                "\x02": self.read_list,  # a MutableSequence (e.g. list)
+                "\x03": self.read_set,  # a Set
+                "\x04": self.read_dict,  # a Mapping (e.g. dict)
+                "\x05": self.read_string,  # a UTF8-encoded string
+                "\x06": self.read_bytes,  # a ByteString
+                "\x0a": self.read_int,  # unbounded scalar int
+                "\x0b": self.read_bool,  # scalar boolean
+                "\x0c": self.read_complex,  # scalar 128-bit complex number
+                "\x0d": self.read_float,  # scalar 64-bit float
+                "F": self.read_recarray,  # numpy array with fields, including recarrays
+                "d": self.read_decimal,  # a decimal
+                "t": self.read_datetime,  # date, time, or datetime
+                "u": self.read_uuid,  # UUID
+            }[data_structure_code]
+        except KeyError:
+            raise DataJointError(
+                'Unknown data structure code "%s". Upgrade datajoint.'
+                % data_structure_code
+            )
+        v = call()
+        if n_bytes is not None and self._pos - start != n_bytes:
+            raise DataJointError("Blob length check failed! Invalid blob")
+        return v
+
+    def pack_blob(self, obj):
+        # original mYm-based serialization from datajoint-matlab
+        if isinstance(obj, MatCell):
+            return self.pack_cell_array(obj)
+        if isinstance(obj, MatStruct):
+            return self.pack_struct(obj)
+        if isinstance(obj, np.ndarray) and obj.dtype.fields is None:
+            return self.pack_array(obj)
+
+        # blob types in the expanded dj0 blob format
+        self.set_dj0()
+        if not isinstance(obj, (np.ndarray, np.number)):
+            # python built-in data types
+            if isinstance(obj, bool):
+                return self.pack_bool(obj)
+            if isinstance(obj, int):
+                return self.pack_int(obj)
+            if isinstance(obj, complex):
+                return self.pack_complex(obj)
+            if isinstance(obj, float):
+                return self.pack_float(obj)
+        if isinstance(obj, np.ndarray) and obj.dtype.fields:
+            return self.pack_recarray(np.array(obj))
+        if isinstance(obj, (np.number, np.datetime64)):
+            return self.pack_array(np.array(obj))
+        if isinstance(obj, (bool, np.bool_)):
+            return self.pack_array(np.array(obj))
+        if isinstance(obj, (float, int, complex)):
+            return self.pack_array(np.array(obj))
+        if isinstance(obj, (datetime.datetime, datetime.date, datetime.time)):
+            return self.pack_datetime(obj)
+        if isinstance(obj, Decimal):
+            return self.pack_decimal(obj)
+        if isinstance(obj, uuid.UUID):
+            return self.pack_uuid(obj)
+        if isinstance(obj, collections.abc.Mapping):
+            return self.pack_dict(obj)
+        if isinstance(obj, str):
+            return self.pack_string(obj)
+        if isinstance(obj, (bytes, bytearray)):
+            return self.pack_bytes(obj)
+        if isinstance(obj, collections.abc.MutableSequence):
+            return self.pack_list(obj)
+        if isinstance(obj, collections.abc.Sequence):
+            return self.pack_tuple(obj)
+        if isinstance(obj, collections.abc.Set):
+            return self.pack_set(obj)
+        if obj is None:
+            return self.pack_none()
+        raise DataJointError(
+            "Packing object of type %s currently not supported!" % type(obj)
+        )
+
+    def read_array(self):
+        n_dims = int(self.read_value())
+        shape = self.read_value(count=n_dims)
+        n_elem = np.prod(shape, dtype=int)
+        dtype_id, is_complex = self.read_value("uint32", 2)
+
+        # Get dtype from type id
+        dtype = deserialize_lookup[dtype_id]["dtype"]
+
+        # Check if name is void
+        if deserialize_lookup[dtype_id]["scalar_type"] == "VOID":
+            data = np.array(
+                list(self.read_blob(self.read_value()) for _ in range(n_elem)),
+                dtype=np.dtype("O"),
+            )
+        # Check if name is char
+        elif deserialize_lookup[dtype_id]["scalar_type"] == "CHAR":
+            # compensate for MATLAB packing of char arrays
+            data = self.read_value(dtype, count=2 * n_elem)
+            data = data[::2].astype("U1")
+            if n_dims == 2 and shape[0] == 1 or n_dims == 1:
+                compact = data.squeeze()
+                data = (
+                    compact
+                    if compact.shape == ()
+                    else np.array("".join(data.squeeze()))
+                )
+                shape = (1,)
+        else:
+            data = self.read_value(dtype, count=n_elem)
+            if is_complex:
+                data = data + 1j * self.read_value(dtype, count=n_elem)
+        return self.squeeze(data.reshape(shape, order="F"))
+
+    def pack_array(self, array):
+        """
+        Serialize an np.ndarray into bytes.  Scalars are encoded with ndim=0.
+        """
+        if "datetime64" in array.dtype.name:
+            self.set_dj0()
+        blob = (
+            b"A"
+            + np.uint64(array.ndim).tobytes()
+            + np.array(array.shape, dtype=np.uint64).tobytes()
+        )
+        is_complex = np.iscomplexobj(array)
+        if is_complex:
+            array, imaginary = np.real(array), np.imag(array)
+        try:
+            type_id = serialize_lookup[array.dtype]["type_id"]
+        except KeyError:
+            # U is for unicode string
+            if array.dtype.char == "U":
+                type_id = serialize_lookup[np.dtype("O")]["type_id"]
+            else:
+                raise DataJointError(f"Type {array.dtype} is ambiguous or unknown")
+
+        blob += np.array([type_id, is_complex], dtype=np.uint32).tobytes()
+        if (
+            array.dtype.char == "U"
+            or serialize_lookup[array.dtype]["scalar_type"] == "VOID"
+        ):
+            blob += b"".join(
+                len_u64(it) + it
+                for it in (self.pack_blob(e) for e in array.flatten(order="F"))
+            )
+            self.set_dj0()  # not supported by original mym
+        elif serialize_lookup[array.dtype]["scalar_type"] == "CHAR":
+            blob += (
+                array.view(np.uint8).astype(np.uint16).tobytes()
+            )  # convert to 16-bit chars for MATLAB
+        else:  # numeric arrays
+            if array.ndim == 0:  # not supported by original mym
+                self.set_dj0()
+            blob += array.tobytes(order="F")
+            if is_complex:
+                blob += imaginary.tobytes(order="F")
+        return blob
+
+    def read_recarray(self):
+        """
+        Serialize an np.ndarray with fields, including recarrays
+        """
+        n_fields = self.read_value("uint32")
+        if not n_fields:
+            return np.array(None)  # empty array
+        field_names = [self.read_zero_terminated_string() for _ in range(n_fields)]
+        arrays = [self.read_blob() for _ in range(n_fields)]
+        rec = np.empty(
+            arrays[0].shape,
+            np.dtype([(f, t.dtype) for f, t in zip(field_names, arrays)]),
+        )
+        for f, t in zip(field_names, arrays):
+            rec[f] = t
+        return rec.view(np.recarray)
+
+    def pack_recarray(self, array):
+        """Serialize a Matlab struct array"""
+        return (
+            b"F"
+            + len_u32(array.dtype)
+            + "\0".join(array.dtype.names).encode()  # number of fields
+            + b"\0"
+            + b"".join(  # field names
+                (
+                    self.pack_recarray(array[f])
+                    if array[f].dtype.fields
+                    else self.pack_array(array[f])
+                )
+                for f in array.dtype.names
+            )
+        )
+
+    def read_sparse_array(self):
+        raise DataJointError(
+            "datajoint-python does not yet support sparse arrays. Issue (#590)"
+        )
+
+    def read_int(self):
+        return int.from_bytes(
+            self.read_binary(self.read_value("uint16")), byteorder="little", signed=True
+        )
+
+    @staticmethod
+    def pack_int(v):
+        n_bytes = v.bit_length() // 8 + 1
+        assert 0 < n_bytes <= 0xFFFF, "Integers are limited to 65535 bytes"
+        return (
+            b"\x0a"
+            + np.uint16(n_bytes).tobytes()
+            + v.to_bytes(n_bytes, byteorder="little", signed=True)
+        )
+
+    def read_bool(self):
+        return bool(self.read_value("bool"))
+
+    @staticmethod
+    def pack_bool(v):
+        return b"\x0b" + np.array(v, dtype="bool").tobytes()
+
+    def read_complex(self):
+        return complex(self.read_value("complex128"))
+
+    @staticmethod
+    def pack_complex(v):
+        return b"\x0c" + np.array(v, dtype="complex128").tobytes()
+
+    def read_float(self):
+        return float(self.read_value("float64"))
+
+    @staticmethod
+    def pack_float(v):
+        return b"\x0d" + np.array(v, dtype="float64").tobytes()
+
+    def read_decimal(self):
+        return Decimal(self.read_string())
+
+    @staticmethod
+    def pack_decimal(d):
+        s = str(d)
+        return b"d" + len_u64(s) + s.encode()
+
+    def read_string(self):
+        return self.read_binary(self.read_value()).decode()
+
+    @staticmethod
+    def pack_string(s):
+        blob = s.encode()
+        return b"\5" + len_u64(blob) + blob
+
+    def read_bytes(self):
+        return self.read_binary(self.read_value())
+
+    @staticmethod
+    def pack_bytes(s):
+        return b"\6" + len_u64(s) + s
+
+    def read_none(self):
+        pass
+
+    @staticmethod
+    def pack_none():
+        return b"\xff"
+
+    def read_tuple(self):
+        return tuple(
+            self.read_blob(self.read_value()) for _ in range(self.read_value())
+        )
+
+    def pack_tuple(self, t):
+        return (
+            b"\1"
+            + len_u64(t)
+            + b"".join(len_u64(it) + it for it in (self.pack_blob(i) for i in t))
+        )
+
+    def read_list(self):
+        return list(self.read_blob(self.read_value()) for _ in range(self.read_value()))
+
+    def pack_list(self, t):
+        return (
+            b"\2"
+            + len_u64(t)
+            + b"".join(len_u64(it) + it for it in (self.pack_blob(i) for i in t))
+        )
+
+    def read_set(self):
+        return set(self.read_blob(self.read_value()) for _ in range(self.read_value()))
+
+    def pack_set(self, t):
+        return (
+            b"\3"
+            + len_u64(t)
+            + b"".join(len_u64(it) + it for it in (self.pack_blob(i) for i in t))
+        )
+
+    def read_dict(self):
+        return dict(
+            (self.read_blob(self.read_value()), self.read_blob(self.read_value()))
+            for _ in range(self.read_value())
+        )
+
+    def pack_dict(self, d):
+        return (
+            b"\4"
+            + len_u64(d)
+            + b"".join(
+                b"".join((len_u64(it) + it) for it in packed)
+                for packed in (map(self.pack_blob, pair) for pair in d.items())
+            )
+        )
+
+    def read_struct(self):
+        """deserialize matlab struct"""
+        n_dims = self.read_value()
+        shape = self.read_value(count=n_dims)
+        n_elem = np.prod(shape, dtype=int)
+        n_fields = self.read_value("uint32")
+        if not n_fields:
+            return np.array(None)  # empty array
+        field_names = [self.read_zero_terminated_string() for _ in range(n_fields)]
+        raw_data = [
+            tuple(
+                self.read_blob(n_bytes=int(self.read_value())) for _ in range(n_fields)
+            )
+            for __ in range(n_elem)
+        ]
+        data = np.array(raw_data, dtype=list(zip(field_names, repeat(object))))
+        return self.squeeze(
+            data.reshape(shape, order="F"), convert_to_scalar=False
+        ).view(MatStruct)
+
+    def pack_struct(self, array):
+        """Serialize a Matlab struct array"""
+        return (
+            b"S"
+            + np.array((array.ndim,) + array.shape, dtype=np.uint64).tobytes()
+            + len_u32(array.dtype.names)  # dimensionality
+            + "\0".join(array.dtype.names).encode()  # number of fields
+            + b"\0"
+            + b"".join(  # field names
+                len_u64(it) + it
+                for it in (
+                    self.pack_blob(e) for rec in array.flatten(order="F") for e in rec
+                )
+            )
+        )  # values
+
+    def read_cell_array(self):
+        """deserialize MATLAB cell array"""
+        n_dims = self.read_value()
+        shape = self.read_value(count=n_dims)
+        n_elem = int(np.prod(shape))
+        result = [self.read_blob(n_bytes=self.read_value()) for _ in range(n_elem)]
+        return (
+            self.squeeze(
+                np.array(result).reshape(shape, order="F"), convert_to_scalar=False
+            )
+        ).view(MatCell)
+
+    def pack_cell_array(self, array):
+        return (
+            b"C"
+            + np.array((array.ndim,) + array.shape, dtype=np.uint64).tobytes()
+            + b"".join(
+                len_u64(it) + it
+                for it in (self.pack_blob(e) for e in array.flatten(order="F"))
+            )
+        )
+
+    def read_datetime(self):
+        """deserialize datetime.date, .time, or .datetime"""
+        date, time = self.read_value("int32"), self.read_value("int64")
+        date = (
+            datetime.date(year=date // 10000, month=(date // 100) % 100, day=date % 100)
+            if date >= 0
+            else None
+        )
+        time = (
+            datetime.time(
+                hour=(time // 10000000000) % 100,
+                minute=(time // 100000000) % 100,
+                second=(time // 1000000) % 100,
+                microsecond=time % 1000000,
+            )
+            if time >= 0
+            else None
+        )
+        return time and date and datetime.datetime.combine(date, time) or time or date
+
+    @staticmethod
+    def pack_datetime(d):
+        if isinstance(d, datetime.datetime):
+            date, time = d.date(), d.time()
+        elif isinstance(d, datetime.date):
+            date, time = d, None
+        else:
+            date, time = None, d
+        return b"t" + (
+            np.int32(
+                -1 if date is None else (date.year * 100 + date.month) * 100 + date.day
+            ).tobytes()
+            + np.int64(
+                -1
+                if time is None
+                else ((time.hour * 100 + time.minute) * 100 + time.second) * 1000000
+                + time.microsecond
+            ).tobytes()
+        )
+
+    def read_uuid(self):
+        q = self.read_binary(16)
+        return uuid.UUID(bytes=q)
+
+    @staticmethod
+    def pack_uuid(obj):
+        return b"u" + obj.bytes
+
+    def read_zero_terminated_string(self):
+        target = self._blob.find(b"\0", self._pos)
+        data = self._blob[self._pos : target].decode()
+        self._pos = target + 1
+        return data
+
+    def read_value(self, dtype=None, count=1):
+        if dtype is None:
+            dtype = "uint32" if use_32bit_dims else "uint64"
+        data = np.frombuffer(self._blob, dtype=dtype, count=count, offset=self._pos)
+        self._pos += data.dtype.itemsize * data.size
+        return data[0] if count == 1 else data
+
+    def read_binary(self, size):
+        self._pos += int(size)
+        return self._blob[self._pos - int(size) : self._pos]
+
+    def pack(self, obj, compress):
+        self.protocol = b"mYm\0"  # will be replaced with dj0 if new features are used
+        blob = self.pack_blob(
+            obj
+        )  # this may reset the protocol and must precede protocol evaluation
+        blob = self.protocol + blob
+        if compress and len(blob) > 1000:
+            compressed = b"ZL123\0" + len_u64(blob) + zlib.compress(blob)
+            if len(compressed) < len(blob):
+                blob = compressed
+        return blob
+

+ + + +

+ + + + + + + +

+ + +

+ `squeeze(array, convert_to_scalar=True)` + +¶

+ + +

+ +

Simplify the input array - squeeze out all singleton dimensions. +If convert_to_scalar, then convert zero-dimensional arrays to scalars

+ + +

Source code in datajoint/blob.py

def squeeze(self, array, convert_to_scalar=True):
+    """
+    Simplify the input array - squeeze out all singleton dimensions.
+    If convert_to_scalar, then convert zero-dimensional arrays to scalars
+    """
+    if not self._squeeze:
+        return array
+    array = array.squeeze()
+    return array.item() if array.ndim == 0 and convert_to_scalar else array
+

+ +

+ + + + + + +

+ + +

+ `pack_array(array)` + +¶

+ + +

+ +

Serialize an np.ndarray into bytes. Scalars are encoded with ndim=0.

+ + +

Source code in datajoint/blob.py

def pack_array(self, array):
+    """
+    Serialize an np.ndarray into bytes.  Scalars are encoded with ndim=0.
+    """
+    if "datetime64" in array.dtype.name:
+        self.set_dj0()
+    blob = (
+        b"A"
+        + np.uint64(array.ndim).tobytes()
+        + np.array(array.shape, dtype=np.uint64).tobytes()
+    )
+    is_complex = np.iscomplexobj(array)
+    if is_complex:
+        array, imaginary = np.real(array), np.imag(array)
+    try:
+        type_id = serialize_lookup[array.dtype]["type_id"]
+    except KeyError:
+        # U is for unicode string
+        if array.dtype.char == "U":
+            type_id = serialize_lookup[np.dtype("O")]["type_id"]
+        else:
+            raise DataJointError(f"Type {array.dtype} is ambiguous or unknown")
+
+    blob += np.array([type_id, is_complex], dtype=np.uint32).tobytes()
+    if (
+        array.dtype.char == "U"
+        or serialize_lookup[array.dtype]["scalar_type"] == "VOID"
+    ):
+        blob += b"".join(
+            len_u64(it) + it
+            for it in (self.pack_blob(e) for e in array.flatten(order="F"))
+        )
+        self.set_dj0()  # not supported by original mym
+    elif serialize_lookup[array.dtype]["scalar_type"] == "CHAR":
+        blob += (
+            array.view(np.uint8).astype(np.uint16).tobytes()
+        )  # convert to 16-bit chars for MATLAB
+    else:  # numeric arrays
+        if array.ndim == 0:  # not supported by original mym
+            self.set_dj0()
+        blob += array.tobytes(order="F")
+        if is_complex:
+            blob += imaginary.tobytes(order="F")
+    return blob
+

+ +

+ + + + + + +

+ + +

+ `read_recarray()` + +¶

+ + +

+ +

Serialize an np.ndarray with fields, including recarrays

+ + +

Source code in datajoint/blob.py

def read_recarray(self):
+    """
+    Serialize an np.ndarray with fields, including recarrays
+    """
+    n_fields = self.read_value("uint32")
+    if not n_fields:
+        return np.array(None)  # empty array
+    field_names = [self.read_zero_terminated_string() for _ in range(n_fields)]
+    arrays = [self.read_blob() for _ in range(n_fields)]
+    rec = np.empty(
+        arrays[0].shape,
+        np.dtype([(f, t.dtype) for f, t in zip(field_names, arrays)]),
+    )
+    for f, t in zip(field_names, arrays):
+        rec[f] = t
+    return rec.view(np.recarray)
+

+ +

+ + + + + + +

+ + +

+ `pack_recarray(array)` + +¶

+ + +

+ +

Serialize a Matlab struct array

+ + +

Source code in datajoint/blob.py

def pack_recarray(self, array):
+    """Serialize a Matlab struct array"""
+    return (
+        b"F"
+        + len_u32(array.dtype)
+        + "\0".join(array.dtype.names).encode()  # number of fields
+        + b"\0"
+        + b"".join(  # field names
+            (
+                self.pack_recarray(array[f])
+                if array[f].dtype.fields
+                else self.pack_array(array[f])
+            )
+            for f in array.dtype.names
+        )
+    )
+

+ +

+ + + + + + +

+ + +

+ `read_struct()` + +¶

+ + +

+ +

deserialize matlab struct

+ + +

Source code in datajoint/blob.py

def read_struct(self):
+    """deserialize matlab struct"""
+    n_dims = self.read_value()
+    shape = self.read_value(count=n_dims)
+    n_elem = np.prod(shape, dtype=int)
+    n_fields = self.read_value("uint32")
+    if not n_fields:
+        return np.array(None)  # empty array
+    field_names = [self.read_zero_terminated_string() for _ in range(n_fields)]
+    raw_data = [
+        tuple(
+            self.read_blob(n_bytes=int(self.read_value())) for _ in range(n_fields)
+        )
+        for __ in range(n_elem)
+    ]
+    data = np.array(raw_data, dtype=list(zip(field_names, repeat(object))))
+    return self.squeeze(
+        data.reshape(shape, order="F"), convert_to_scalar=False
+    ).view(MatStruct)
+

+ +

+ + + + + + +

+ + +

+ `pack_struct(array)` + +¶

+ + +

+ +

Serialize a Matlab struct array

+ + +

Source code in datajoint/blob.py

def pack_struct(self, array):
+    """Serialize a Matlab struct array"""
+    return (
+        b"S"
+        + np.array((array.ndim,) + array.shape, dtype=np.uint64).tobytes()
+        + len_u32(array.dtype.names)  # dimensionality
+        + "\0".join(array.dtype.names).encode()  # number of fields
+        + b"\0"
+        + b"".join(  # field names
+            len_u64(it) + it
+            for it in (
+                self.pack_blob(e) for rec in array.flatten(order="F") for e in rec
+            )
+        )
+    )  # values
+

+ +

+ + + + + + +

+ + +

+ `read_cell_array()` + +¶

+ + +

+ +

deserialize MATLAB cell array

+ + +

Source code in datajoint/blob.py

def read_cell_array(self):
+    """deserialize MATLAB cell array"""
+    n_dims = self.read_value()
+    shape = self.read_value(count=n_dims)
+    n_elem = int(np.prod(shape))
+    result = [self.read_blob(n_bytes=self.read_value()) for _ in range(n_elem)]
+    return (
+        self.squeeze(
+            np.array(result).reshape(shape, order="F"), convert_to_scalar=False
+        )
+    ).view(MatCell)
+

+ +

+ + + + + + +

+ + +

+ `read_datetime()` + +¶

+ + +

+ +

deserialize datetime.date, .time, or .datetime

+ + +

Source code in datajoint/blob.py

def read_datetime(self):
+    """deserialize datetime.date, .time, or .datetime"""
+    date, time = self.read_value("int32"), self.read_value("int64")
+    date = (
+        datetime.date(year=date // 10000, month=(date // 100) % 100, day=date % 100)
+        if date >= 0
+        else None
+    )
+    time = (
+        datetime.time(
+            hour=(time // 10000000000) % 100,
+            minute=(time // 100000000) % 100,
+            second=(time // 1000000) % 100,
+            microsecond=time % 1000000,
+        )
+        if time >= 0
+        else None
+    )
+    return time and date and datetime.datetime.combine(date, time) or time or date
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/cli/index.html b/0.14/api/datajoint/cli/index.html new file mode 100644 index 000000000..6bb8cd9dd --- /dev/null +++ b/0.14/api/datajoint/cli/index.html @@ -0,0 +1,3894 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + cli.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + cli.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

cli.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + +

+ + +

+ `cli(args=None)` + +¶

+ + +

+ +

Console interface for DataJoint Python

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `args` +	+ `list` +	+ + List of arguments to be passed in, defaults to reading stdin + +	+ `None` +

+ + +

Source code in datajoint/cli.py

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def cli(args: list = None):
+    """
+    Console interface for DataJoint Python
+
+    :param args: List of arguments to be passed in, defaults to reading stdin
+    :type args: list, optional
+    """
+    parser = argparse.ArgumentParser(
+        prog="datajoint",
+        description="DataJoint console interface.",
+        conflict_handler="resolve",
+    )
+    parser.add_argument(
+        "-V", "--version", action="version", version=f"{dj.__name__} {dj.__version__}"
+    )
+    parser.add_argument(
+        "-u",
+        "--user",
+        type=str,
+        default=dj.config["database.user"],
+        required=False,
+        help="Datajoint username",
+    )
+    parser.add_argument(
+        "-p",
+        "--password",
+        type=str,
+        default=dj.config["database.password"],
+        required=False,
+        help="Datajoint password",
+    )
+    parser.add_argument(
+        "-h",
+        "--host",
+        type=str,
+        default=dj.config["database.host"],
+        required=False,
+        help="Datajoint host",
+    )
+    parser.add_argument(
+        "-s",
+        "--schemas",
+        nargs="+",
+        type=str,
+        required=False,
+        help="A list of virtual module mappings in `db:schema ...` format",
+    )
+    kwargs = vars(parser.parse_args(args))
+    mods = {}
+    if kwargs["user"]:
+        dj.config["database.user"] = kwargs["user"]
+    if kwargs["password"]:
+        dj.config["database.password"] = kwargs["password"]
+    if kwargs["host"]:
+        dj.config["database.host"] = kwargs["host"]
+    if kwargs["schemas"]:
+        for vm in kwargs["schemas"]:
+            d, m = vm.split(":")
+            mods[m] = dj.create_virtual_module(m, d)
+
+    banner = "dj repl\n"
+    if mods:
+        modstr = "\n".join("  - {}".format(m) for m in mods)
+        banner += "\nschema modules:\n\n" + modstr + "\n"
+    interact(banner, local=dict(ChainMap(mods, locals(), globals())))
+
+    raise SystemExit
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/condition/index.html b/0.14/api/datajoint/condition/index.html new file mode 100644 index 000000000..a14a8ffb7 --- /dev/null +++ b/0.14/api/datajoint/condition/index.html @@ -0,0 +1,4851 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + condition.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + condition.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

condition.py

+ +

+ + + + +

+ +

methods for generating SQL WHERE clauses from datajoint restriction conditions

+ + + + + + + + + + +

+ + + + + + + + + + + +

+ + + +

+ `PromiscuousOperand` + + +¶

+ + +

+ + + +

A container for an operand to ignore join compatibility

+ + + + + + + + +

Source code in datajoint/condition.py

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class PromiscuousOperand:
+    """
+    A container for an operand to ignore join compatibility
+    """
+
+    def __init__(self, operand):
+        self.operand = operand
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `AndList` + + +¶

+ + +

+ Bases: list

+ + + +

Example: +expr2 = expr & dj.AndList((cond1, cond2, cond3)) +is equivalent to +expr2 = expr & cond1 & cond2 & cond3

+ + + + + + + + +

Source code in datajoint/condition.py

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class AndList(list):
+    """
+    A list of conditions to by applied to a query expression by logical conjunction: the
+    conditions are AND-ed. All other collections (lists, sets, other entity sets, etc) are
+    applied by logical disjunction (OR).
+
+    Example:
+    expr2 = expr & dj.AndList((cond1, cond2, cond3))
+    is equivalent to
+    expr2 = expr & cond1 & cond2 & cond3
+    """
+
+    def append(self, restriction):
+        if isinstance(restriction, AndList):
+            # extend to reduce nesting
+            self.extend(restriction)
+        else:
+            super().append(restriction)
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Top` + + + + `dataclass` + + +¶

+ + +

+ + + +

A restriction to the top entities of a query. +In SQL, this corresponds to ORDER BY ... LIMIT ... OFFSET

+ + + + + + + + +

Source code in datajoint/condition.py

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@dataclass
+class Top:
+    """
+    A restriction to the top entities of a query.
+    In SQL, this corresponds to ORDER BY ... LIMIT ... OFFSET
+    """
+
+    limit: Union[int, None] = 1
+    order_by: Union[str, List[str]] = "KEY"
+    offset: int = 0
+
+    def __post_init__(self):
+        self.order_by = self.order_by or ["KEY"]
+        self.offset = self.offset or 0
+
+        if self.limit is not None and not isinstance(self.limit, int):
+            raise TypeError("Top limit must be an integer")
+        if not isinstance(self.order_by, (str, collections.abc.Sequence)) or not all(
+            isinstance(r, str) for r in self.order_by
+        ):
+            raise TypeError("Top order_by attributes must all be strings")
+        if not isinstance(self.offset, int):
+            raise TypeError("The offset argument must be an integer")
+        if self.offset and self.limit is None:
+            self.limit = 999999999999  # arbitrary large number to allow query
+        if isinstance(self.order_by, str):
+            self.order_by = [self.order_by]
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Not` + + +¶

+ + +

+ + + +

invert restriction

+ + + + + + + + +

Source code in datajoint/condition.py

class Not:
+    """invert restriction"""
+
+    def __init__(self, restriction):
+        self.restriction = restriction
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + +

+ `assert_join_compatibility(expr1, expr2)` + +¶

+ + +

+ +

Determine if expressions expr1 and expr2 are join-compatible. To be join-compatible, +the matching attributes in the two expressions must be in the primary key of one or the +other expression. +Raises an exception if not compatible.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `expr1` +	+	+ + A QueryExpression object + +	+ required +
+ `expr2` +	+	+ + A QueryExpression object + +	+ required +

+ + +

Source code in datajoint/condition.py

def assert_join_compatibility(expr1, expr2):
+    """
+    Determine if expressions expr1 and expr2 are join-compatible.  To be join-compatible,
+    the matching attributes in the two expressions must be in the primary key of one or the
+    other expression.
+    Raises an exception if not compatible.
+
+    :param expr1: A QueryExpression object
+    :param expr2: A QueryExpression object
+    """
+    from .expression import QueryExpression, U
+
+    for rel in (expr1, expr2):
+        if not isinstance(rel, (U, QueryExpression)):
+            raise DataJointError(
+                "Object %r is not a QueryExpression and cannot be joined." % rel
+            )
+    if not isinstance(expr1, U) and not isinstance(
+        expr2, U
+    ):  # dj.U is always compatible
+        try:
+            raise DataJointError(
+                "Cannot join query expressions on dependent attribute `%s`"
+                % next(
+                    r
+                    for r in set(expr1.heading.secondary_attributes).intersection(
+                        expr2.heading.secondary_attributes
+                    )
+                )
+            )
+        except StopIteration:
+            pass  # all ok
+

+ +

+ + + + + + +

+ + +

+ `make_condition(query_expression, condition, columns)` + +¶

+ + +

+ +

Translate the input condition into the equivalent SQL condition (a string)

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `query_expression` +	+	+ + a dj.QueryExpression object to apply condition + +	+ required +
+ `condition` +	+	+ + any valid restriction object. + +	+ required +
+ `columns` +	+	+ + a set passed by reference to collect all column names used in the +condition. + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + an SQL condition string or a boolean value. + +

+ + +

Source code in datajoint/condition.py

def make_condition(query_expression, condition, columns):
+    """
+    Translate the input condition into the equivalent SQL condition (a string)
+
+    :param query_expression: a dj.QueryExpression object to apply condition
+    :param condition: any valid restriction object.
+    :param columns: a set passed by reference to collect all column names used in the
+        condition.
+    :return: an SQL condition string or a boolean value.
+    """
+    from .expression import Aggregation, QueryExpression, U
+
+    def prep_value(k, v):
+        """prepare SQL condition"""
+        key_match, k = translate_attribute(k)
+        if key_match["path"] is None:
+            k = f"`{k}`"
+        if (
+            query_expression.heading[key_match["attr"]].json
+            and key_match["path"] is not None
+            and isinstance(v, dict)
+        ):
+            return f"{k}='{json.dumps(v)}'"
+        if v is None:
+            return f"{k} IS NULL"
+        if query_expression.heading[key_match["attr"]].uuid:
+            if not isinstance(v, uuid.UUID):
+                try:
+                    v = uuid.UUID(v)
+                except (AttributeError, ValueError):
+                    raise DataJointError(
+                        "Badly formed UUID {v} in restriction by `{k}`".format(k=k, v=v)
+                    )
+            return f"{k}=X'{v.bytes.hex()}'"
+        if isinstance(
+            v,
+            (
+                datetime.date,
+                datetime.datetime,
+                datetime.time,
+                decimal.Decimal,
+                list,
+            ),
+        ):
+            return f'{k}="{v}"'
+        if isinstance(v, str):
+            v = v.replace("%", "%%").replace("\\", "\\\\")
+            return f'{k}="{v}"'
+        return f"{k}={v}"
+
+    def combine_conditions(negate, conditions):
+        return f"{'NOT ' if negate else ''} ({')AND('.join(conditions)})"
+
+    negate = False
+    while isinstance(condition, Not):
+        negate = not negate
+        condition = condition.restriction
+
+    # restrict by string
+    if isinstance(condition, str):
+        columns.update(extract_column_names(condition))
+        return combine_conditions(
+            negate, conditions=[condition.strip().replace("%", "%%")]
+        )  # escape %, see issue #376
+
+    # restrict by AndList
+    if isinstance(condition, AndList):
+        # omit all conditions that evaluate to True
+        items = [
+            item
+            for item in (
+                make_condition(query_expression, cond, columns) for cond in condition
+            )
+            if item is not True
+        ]
+        if any(item is False for item in items):
+            return negate  # if any item is False, the whole thing is False
+        if not items:
+            return not negate  # and empty AndList is True
+        return combine_conditions(negate, conditions=items)
+
+    # restriction by dj.U evaluates to True
+    if isinstance(condition, U):
+        return not negate
+
+    # restrict by boolean
+    if isinstance(condition, bool):
+        return negate != condition
+
+    # restrict by a mapping/dict -- convert to an AndList of string equality conditions
+    if isinstance(condition, collections.abc.Mapping):
+        common_attributes = set(c.split(".", 1)[0] for c in condition).intersection(
+            query_expression.heading.names
+        )
+        if not common_attributes:
+            return not negate  # no matching attributes -> evaluates to True
+        columns.update(common_attributes)
+        return combine_conditions(
+            negate,
+            conditions=[
+                prep_value(k, v)
+                for k, v in condition.items()
+                if k.split(".", 1)[0] in common_attributes  # handle json indexing
+            ],
+        )
+
+    # restrict by a numpy record -- convert to an AndList of string equality conditions
+    if isinstance(condition, numpy.void):
+        common_attributes = set(condition.dtype.fields).intersection(
+            query_expression.heading.names
+        )
+        if not common_attributes:
+            return not negate  # no matching attributes -> evaluate to True
+        columns.update(common_attributes)
+        return combine_conditions(
+            negate,
+            conditions=[prep_value(k, condition[k]) for k in common_attributes],
+        )
+
+    # restrict by a QueryExpression subclass -- trigger instantiation and move on
+    if inspect.isclass(condition) and issubclass(condition, QueryExpression):
+        condition = condition()
+
+    # restrict by another expression (aka semijoin and antijoin)
+    check_compatibility = True
+    if isinstance(condition, PromiscuousOperand):
+        condition = condition.operand
+        check_compatibility = False
+
+    if isinstance(condition, QueryExpression):
+        if check_compatibility:
+            assert_join_compatibility(query_expression, condition)
+        common_attributes = [
+            q for q in condition.heading.names if q in query_expression.heading.names
+        ]
+        columns.update(common_attributes)
+        if isinstance(condition, Aggregation):
+            condition = condition.make_subquery()
+        return (
+            # without common attributes, any non-empty set matches everything
+            (not negate if condition else negate)
+            if not common_attributes
+            else "({fields}) {not_}in ({subquery})".format(
+                fields="`" + "`,`".join(common_attributes) + "`",
+                not_="not " if negate else "",
+                subquery=condition.make_sql(common_attributes),
+            )
+        )
+
+    # restrict by pandas.DataFrames
+    if isinstance(condition, pandas.DataFrame):
+        condition = condition.to_records()  # convert to numpy.recarray and move on
+
+    # if iterable (but not a string, a QueryExpression, or an AndList), treat as an OrList
+    try:
+        or_list = [make_condition(query_expression, q, columns) for q in condition]
+    except TypeError:
+        raise DataJointError("Invalid restriction type %r" % condition)
+    else:
+        or_list = [
+            item for item in or_list if item is not False
+        ]  # ignore False conditions
+        if any(item is True for item in or_list):  # if any item is True, entirely True
+            return not negate
+        return (
+            f"{'NOT ' if negate else ''} ({' OR '.join(or_list)})"
+            if or_list
+            else negate
+        )
+

+ +

+ + + + + + +

+ + +

+ `extract_column_names(sql_expression)` + +¶

+ + +

+ +

extract all presumed column names from an sql expression such as the WHERE clause, +for example.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `sql_expression` +	+	+ + a string containing an SQL expression + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + set of extracted column names +This may be MySQL-specific for now. + +

+ + +

Source code in datajoint/condition.py

def extract_column_names(sql_expression):
+    """
+    extract all presumed column names from an sql expression such as the WHERE clause,
+    for example.
+
+    :param sql_expression: a string containing an SQL expression
+    :return: set of extracted column names
+    This may be MySQL-specific for now.
+    """
+    assert isinstance(sql_expression, str)
+    result = set()
+    s = sql_expression  # for terseness
+    # remove escaped quotes
+    s = re.sub(r"(\\\")|(\\\')", "", s)
+    # remove quoted text
+    s = re.sub(r"'[^']*'", "", s)
+    s = re.sub(r'"[^"]*"', "", s)
+    # find all tokens in back quotes and remove them
+    result.update(re.findall(r"`([a-z][a-z_0-9]*)`", s))
+    s = re.sub(r"`[a-z][a-z_0-9]*`", "", s)
+    # remove space before parentheses
+    s = re.sub(r"\s*\(", "(", s)
+    # remove tokens followed by ( since they must be functions
+    s = re.sub(r"(\b[a-z][a-z_0-9]*)\(", "(", s)
+    remaining_tokens = set(re.findall(r"\b[a-z][a-z_0-9]*\b", s))
+    # update result removing reserved words
+    result.update(
+        remaining_tokens
+        - {
+            "is",
+            "in",
+            "between",
+            "like",
+            "and",
+            "or",
+            "null",
+            "not",
+            "interval",
+            "second",
+            "minute",
+            "hour",
+            "day",
+            "month",
+            "week",
+            "year",
+        }
+    )
+    return result
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/connection/index.html b/0.14/api/datajoint/connection/index.html new file mode 100644 index 000000000..db9390569 --- /dev/null +++ b/0.14/api/datajoint/connection/index.html @@ -0,0 +1,5849 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + connection.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + connection.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

connection.py

+ +

+ + + + +

+ +

This module contains the Connection class that manages the connection to the database, and +the conn function that provides access to a persistent connection in datajoint.

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + +

+ + +

+ `translate_query_error(client_error, query)` + +¶

+ + +

+ +

Take client error and original query and return the corresponding DataJoint exception.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `client_error` +	+	+ + the exception raised by the client interface + +	+ required +
+ `query` +	+	+ + sql query with placeholders + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + an instance of the corresponding subclass of datajoint.errors.DataJointError + +

+ + +

Source code in datajoint/connection.py

def translate_query_error(client_error, query):
+    """
+    Take client error and original query and return the corresponding DataJoint exception.
+
+    :param client_error: the exception raised by the client interface
+    :param query: sql query with placeholders
+    :return: an instance of the corresponding subclass of datajoint.errors.DataJointError
+    """
+    logger.debug("type: {}, args: {}".format(type(client_error), client_error.args))
+
+    err, *args = client_error.args
+
+    # Loss of connection errors
+    if err in (0, "(0, '')"):
+        return errors.LostConnectionError(
+            "Server connection lost due to an interface error.", *args
+        )
+    if err == 2006:
+        return errors.LostConnectionError("Connection timed out", *args)
+    if err == 2013:
+        return errors.LostConnectionError("Server connection lost", *args)
+    # Access errors
+    if err in (1044, 1142):
+        return errors.AccessError("Insufficient privileges.", args[0], query)
+    # Integrity errors
+    if err == 1062:
+        return errors.DuplicateError(*args)
+    if err == 1217:  # MySQL 8 error code
+        return errors.IntegrityError(*args)
+    if err == 1451:
+        return errors.IntegrityError(*args)
+    if err == 1452:
+        return errors.IntegrityError(*args)
+    # Syntax errors
+    if err == 1064:
+        return errors.QuerySyntaxError(args[0], query)
+    # Existence errors
+    if err == 1146:
+        return errors.MissingTableError(args[0], query)
+    if err == 1364:
+        return errors.MissingAttributeError(*args)
+    if err == 1054:
+        return errors.UnknownAttributeError(*args)
+    # all the other errors are re-raised in original form
+    return client_error
+

+ +

+ + + + + + +

+ + +

+ `conn(host=None, user=None, password=None, *, init_fun=None, reset=False, use_tls=None)` + +¶

+ + +

+ +

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `host` +	+	+ + hostname + +	+ `None` +
+ `user` +	+	+ + mysql user + +	+ `None` +
+ `password` +	+	+ + mysql password + +	+ `None` +
+ `init_fun` +	+	+ + initialization function + +	+ `None` +
+ `reset` +	+	+ + whether the connection should be reset or not + +	+ `False` +
+ `use_tls` +	+	+ + TLS encryption option. Valid options are: True (required), False +(required no TLS), None (TLS preferred, default), dict (Manually specify values per +https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options). + +	+ `None` +

+ + +

Source code in datajoint/connection.py

def conn(
+    host=None, user=None, password=None, *, init_fun=None, reset=False, use_tls=None
+):
+    """
+    Returns a persistent connection object to be shared by multiple modules.
+    If the connection is not yet established or reset=True, a new connection is set up.
+    If connection information is not provided, it is taken from config which takes the
+    information from dj_local_conf.json. If the password is not specified in that file
+    datajoint prompts for the password.
+
+    :param host: hostname
+    :param user: mysql user
+    :param password: mysql password
+    :param init_fun: initialization function
+    :param reset: whether the connection should be reset or not
+    :param use_tls: TLS encryption option. Valid options are: True (required), False
+        (required no TLS), None (TLS preferred, default), dict (Manually specify values per
+        https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options).
+    """
+    if not hasattr(conn, "connection") or reset:
+        host = host if host is not None else config["database.host"]
+        user = user if user is not None else config["database.user"]
+        password = password if password is not None else config["database.password"]
+        if user is None:
+            user = input("Please enter DataJoint username: ")
+        if password is None:
+            password = getpass(prompt="Please enter DataJoint password: ")
+        init_fun = (
+            init_fun if init_fun is not None else config["connection.init_function"]
+        )
+        use_tls = use_tls if use_tls is not None else config["database.use_tls"]
+        conn.connection = Connection(host, user, password, None, init_fun, use_tls)
+    return conn.connection
+

+ +

+ + + + + + +

+ + + +

+ `EmulatedCursor` + + +¶

+ + +

+ + + +

acts like a cursor

+ + + + + + + + +

Source code in datajoint/connection.py

class EmulatedCursor:
+    """acts like a cursor"""
+
+    def __init__(self, data):
+        self._data = data
+        self._iter = iter(self._data)
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        return next(self._iter)
+
+    def fetchall(self):
+        return self._data
+
+    def fetchone(self):
+        return next(self._iter)
+
+    @property
+    def rowcount(self):
+        return len(self._data)
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Connection` + + +¶

+ + +

+ + + +

A dj.Connection object manages a connection to a database server. +It also catalogues modules, schemas, tables, and their dependencies (foreign keys).

Most of the parameters below should be set in the local configuration file.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `host` +	+	+ + host name, may include port number as hostname:port, in which case it overrides the value in port + +	+ required +
+ `user` +	+	+ + user name + +	+ required +
+ `password` +	+	+ + password + +	+ required +
+ `port` +	+	+ + port number + +	+ `None` +
+ `init_fun` +	+	+ + connection initialization function (SQL) + +	+ `None` +
+ `use_tls` +	+	+ + TLS encryption option + +	+ `None` +

+ + + + + + + + +

Source code in datajoint/connection.py

class Connection:
+    """
+    A dj.Connection object manages a connection to a database server.
+    It also catalogues modules, schemas, tables, and their dependencies (foreign keys).
+
+    Most of the parameters below should be set in the local configuration file.
+
+    :param host: host name, may include port number as hostname:port, in which case it overrides the value in port
+    :param user: user name
+    :param password: password
+    :param port: port number
+    :param init_fun: connection initialization function (SQL)
+    :param use_tls: TLS encryption option
+    """
+
+    def __init__(self, host, user, password, port=None, init_fun=None, use_tls=None):
+        host_input, host = (host, get_host_hook(host))
+        if ":" in host:
+            # the port in the hostname overrides the port argument
+            host, port = host.split(":")
+            port = int(port)
+        elif port is None:
+            port = config["database.port"]
+        self.conn_info = dict(host=host, port=port, user=user, passwd=password)
+        if use_tls is not False:
+            self.conn_info["ssl"] = (
+                use_tls if isinstance(use_tls, dict) else {"ssl": {}}
+            )
+        self.conn_info["ssl_input"] = use_tls
+        self.conn_info["host_input"] = host_input
+        self.init_fun = init_fun
+        self._conn = None
+        self._query_cache = None
+        connect_host_hook(self)
+        if self.is_connected:
+            logger.info(
+                "DataJoint {version} connected to {user}@{host}:{port}".format(
+                    version=__version__, **self.conn_info
+                )
+            )
+            self.connection_id = self.query("SELECT connection_id()").fetchone()[0]
+        else:
+            raise errors.LostConnectionError(
+                "Connection failed {user}@{host}:{port}".format(**self.conn_info)
+            )
+        self._in_transaction = False
+        self.schemas = dict()
+        self.dependencies = Dependencies(self)
+
+    def __eq__(self, other):
+        return self.conn_info == other.conn_info
+
+    def __repr__(self):
+        connected = "connected" if self.is_connected else "disconnected"
+        return "DataJoint connection ({connected}) {user}@{host}:{port}".format(
+            connected=connected, **self.conn_info
+        )
+
+    def connect(self):
+        """Connect to the database server."""
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", ".*deprecated.*")
+            try:
+                self._conn = client.connect(
+                    init_command=self.init_fun,
+                    sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                    "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                    charset=config["connection.charset"],
+                    **{
+                        k: v
+                        for k, v in self.conn_info.items()
+                        if k not in ["ssl_input", "host_input"]
+                    },
+                )
+            except client.err.InternalError:
+                self._conn = client.connect(
+                    init_command=self.init_fun,
+                    sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                    "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                    charset=config["connection.charset"],
+                    **{
+                        k: v
+                        for k, v in self.conn_info.items()
+                        if not (
+                            k in ["ssl_input", "host_input"]
+                            or k == "ssl"
+                            and self.conn_info["ssl_input"] is None
+                        )
+                    },
+                )
+        self._conn.autocommit(True)
+
+    def set_query_cache(self, query_cache=None):
+        """
+        When query_cache is not None, the connection switches into the query caching mode, which entails:
+        1. Only SELECT queries are allowed.
+        2. The results of queries are cached under the path indicated by dj.config['query_cache']
+        3. query_cache is a string that differentiates different cache states.
+
+        :param query_cache: a string to initialize the hash for query results
+        """
+        self._query_cache = query_cache
+
+    def purge_query_cache(self):
+        """Purges all query cache."""
+        if (
+            isinstance(config.get(cache_key), str)
+            and pathlib.Path(config[cache_key]).is_dir()
+        ):
+            for path in pathlib.Path(config[cache_key]).iterdir():
+                if not path.is_dir():
+                    path.unlink()
+
+    def close(self):
+        self._conn.close()
+
+    def register(self, schema):
+        self.schemas[schema.database] = schema
+        self.dependencies.clear()
+
+    def ping(self):
+        """Ping the connection or raises an exception if the connection is closed."""
+        self._conn.ping(reconnect=False)
+
+    @property
+    def is_connected(self):
+        """Return true if the object is connected to the database server."""
+        try:
+            self.ping()
+        except:
+            return False
+        return True
+
+    @staticmethod
+    def _execute_query(cursor, query, args, suppress_warnings):
+        try:
+            with warnings.catch_warnings():
+                if suppress_warnings:
+                    # suppress all warnings arising from underlying SQL library
+                    warnings.simplefilter("ignore")
+                cursor.execute(query, args)
+        except client.err.Error as err:
+            raise translate_query_error(err, query)
+
+    def query(
+        self, query, args=(), *, as_dict=False, suppress_warnings=True, reconnect=None
+    ):
+        """
+        Execute the specified query and return the tuple generator (cursor).
+
+        :param query: SQL query
+        :param args: additional arguments for the client.cursor
+        :param as_dict: If as_dict is set to True, the returned cursor objects returns
+                        query results as dictionary.
+        :param suppress_warnings: If True, suppress all warnings arising from underlying query library
+        :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected
+        """
+        # check cache first:
+        use_query_cache = bool(self._query_cache)
+        if use_query_cache and not re.match(r"\s*(SELECT|SHOW)", query):
+            raise errors.DataJointError(
+                "Only SELECT queries are allowed when query caching is on."
+            )
+        if use_query_cache:
+            if not config[cache_key]:
+                raise errors.DataJointError(
+                    f"Provide filepath dj.config['{cache_key}'] when using query caching."
+                )
+            hash_ = uuid_from_buffer(
+                (str(self._query_cache) + re.sub(r"`\$\w+`", "", query)).encode()
+                + pack(args)
+            )
+            cache_path = pathlib.Path(config[cache_key]) / str(hash_)
+            try:
+                buffer = cache_path.read_bytes()
+            except FileNotFoundError:
+                pass  # proceed to query the database
+            else:
+                return EmulatedCursor(unpack(buffer))
+
+        if reconnect is None:
+            reconnect = config["database.reconnect"]
+        logger.debug("Executing SQL:" + query[:query_log_max_length])
+        cursor_class = client.cursors.DictCursor if as_dict else client.cursors.Cursor
+        cursor = self._conn.cursor(cursor=cursor_class)
+        try:
+            self._execute_query(cursor, query, args, suppress_warnings)
+        except errors.LostConnectionError:
+            if not reconnect:
+                raise
+            logger.warning("Reconnecting to MySQL server.")
+            connect_host_hook(self)
+            if self._in_transaction:
+                self.cancel_transaction()
+                raise errors.LostConnectionError(
+                    "Connection was lost during a transaction."
+                )
+            logger.debug("Re-executing")
+            cursor = self._conn.cursor(cursor=cursor_class)
+            self._execute_query(cursor, query, args, suppress_warnings)
+
+        if use_query_cache:
+            data = cursor.fetchall()
+            cache_path.write_bytes(pack(data))
+            return EmulatedCursor(data)
+
+        return cursor
+
+    def get_user(self):
+        """
+        :return: the user name and host name provided by the client to the server.
+        """
+        return self.query("SELECT user()").fetchone()[0]
+
+    # ---------- transaction processing
+    @property
+    def in_transaction(self):
+        """
+        :return: True if there is an open transaction.
+        """
+        self._in_transaction = self._in_transaction and self.is_connected
+        return self._in_transaction
+
+    def start_transaction(self):
+        """
+        Starts a transaction error.
+        """
+        if self.in_transaction:
+            raise errors.DataJointError("Nested connections are not supported.")
+        self.query("START TRANSACTION WITH CONSISTENT SNAPSHOT")
+        self._in_transaction = True
+        logger.debug("Transaction started")
+
+    def cancel_transaction(self):
+        """
+        Cancels the current transaction and rolls back all changes made during the transaction.
+        """
+        self.query("ROLLBACK")
+        self._in_transaction = False
+        logger.debug("Transaction cancelled. Rolling back ...")
+
+    def commit_transaction(self):
+        """
+        Commit all changes made during the transaction and close it.
+
+        """
+        self.query("COMMIT")
+        self._in_transaction = False
+        logger.debug("Transaction committed and closed.")
+
+    # -------- context manager for transactions
+    @property
+    @contextmanager
+    def transaction(self):
+        """
+        Context manager for transactions. Opens an transaction and closes it after the with statement.
+        If an error is caught during the transaction, the commits are automatically rolled back.
+        All errors are raised again.
+
+        Example:
+        >>> import datajoint as dj
+        >>> with dj.conn().transaction as conn:
+        >>>     # transaction is open here
+        """
+        try:
+            self.start_transaction()
+            yield self
+        except:
+            self.cancel_transaction()
+            raise
+        else:
+            self.commit_transaction()
+

+ + + +

+ + + + + + + +

+ + +

+ `connect()` + +¶

+ + +

+ +

Connect to the database server.

+ + +

Source code in datajoint/connection.py

def connect(self):
+    """Connect to the database server."""
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", ".*deprecated.*")
+        try:
+            self._conn = client.connect(
+                init_command=self.init_fun,
+                sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                charset=config["connection.charset"],
+                **{
+                    k: v
+                    for k, v in self.conn_info.items()
+                    if k not in ["ssl_input", "host_input"]
+                },
+            )
+        except client.err.InternalError:
+            self._conn = client.connect(
+                init_command=self.init_fun,
+                sql_mode="NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+                "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+                charset=config["connection.charset"],
+                **{
+                    k: v
+                    for k, v in self.conn_info.items()
+                    if not (
+                        k in ["ssl_input", "host_input"]
+                        or k == "ssl"
+                        and self.conn_info["ssl_input"] is None
+                    )
+                },
+            )
+    self._conn.autocommit(True)
+

+ +

+ + + + + + +

+ + +

+ `set_query_cache(query_cache=None)` + +¶

+ + +

+ +

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `query_cache` +	+	+ + a string to initialize the hash for query results + +	+ `None` +

+ + +

Source code in datajoint/connection.py

def set_query_cache(self, query_cache=None):
+    """
+    When query_cache is not None, the connection switches into the query caching mode, which entails:
+    1. Only SELECT queries are allowed.
+    2. The results of queries are cached under the path indicated by dj.config['query_cache']
+    3. query_cache is a string that differentiates different cache states.
+
+    :param query_cache: a string to initialize the hash for query results
+    """
+    self._query_cache = query_cache
+

+ +

+ + + + + + +

+ + +

+ `purge_query_cache()` + +¶

+ + +

+ +

Purges all query cache.

+ + +

Source code in datajoint/connection.py

def purge_query_cache(self):
+    """Purges all query cache."""
+    if (
+        isinstance(config.get(cache_key), str)
+        and pathlib.Path(config[cache_key]).is_dir()
+    ):
+        for path in pathlib.Path(config[cache_key]).iterdir():
+            if not path.is_dir():
+                path.unlink()
+

+ +

+ + + + + + +

+ + +

+ `ping()` + +¶

+ + +

+ +

Ping the connection or raises an exception if the connection is closed.

+ + +

Source code in datajoint/connection.py

def ping(self):
+    """Ping the connection or raises an exception if the connection is closed."""
+    self._conn.ping(reconnect=False)
+

+ +

+ + + + + + +

+ + + +

+ `is_connected` + + + `property` + + +¶

+ + +

+ +

Return true if the object is connected to the database server.

+ +

+ + + + + + +

+ + +

+ `query(query, args=(), *, as_dict=False, suppress_warnings=True, reconnect=None)` + +¶

+ + +

+ +

Execute the specified query and return the tuple generator (cursor).

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `query` +	+	+ + SQL query + +	+ required +
+ `args` +	+	+ + additional arguments for the client.cursor + +	+ `()` +
+ `as_dict` +	+	+ + If as_dict is set to True, the returned cursor objects returns +query results as dictionary. + +	+ `False` +
+ `suppress_warnings` +	+	+ + If True, suppress all warnings arising from underlying query library + +	+ `True` +
+ `reconnect` +	+	+ + when None, get from config, when True, attempt to reconnect if disconnected + +	+ `None` +

+ + +

Source code in datajoint/connection.py

def query(
+    self, query, args=(), *, as_dict=False, suppress_warnings=True, reconnect=None
+):
+    """
+    Execute the specified query and return the tuple generator (cursor).
+
+    :param query: SQL query
+    :param args: additional arguments for the client.cursor
+    :param as_dict: If as_dict is set to True, the returned cursor objects returns
+                    query results as dictionary.
+    :param suppress_warnings: If True, suppress all warnings arising from underlying query library
+    :param reconnect: when None, get from config, when True, attempt to reconnect if disconnected
+    """
+    # check cache first:
+    use_query_cache = bool(self._query_cache)
+    if use_query_cache and not re.match(r"\s*(SELECT|SHOW)", query):
+        raise errors.DataJointError(
+            "Only SELECT queries are allowed when query caching is on."
+        )
+    if use_query_cache:
+        if not config[cache_key]:
+            raise errors.DataJointError(
+                f"Provide filepath dj.config['{cache_key}'] when using query caching."
+            )
+        hash_ = uuid_from_buffer(
+            (str(self._query_cache) + re.sub(r"`\$\w+`", "", query)).encode()
+            + pack(args)
+        )
+        cache_path = pathlib.Path(config[cache_key]) / str(hash_)
+        try:
+            buffer = cache_path.read_bytes()
+        except FileNotFoundError:
+            pass  # proceed to query the database
+        else:
+            return EmulatedCursor(unpack(buffer))
+
+    if reconnect is None:
+        reconnect = config["database.reconnect"]
+    logger.debug("Executing SQL:" + query[:query_log_max_length])
+    cursor_class = client.cursors.DictCursor if as_dict else client.cursors.Cursor
+    cursor = self._conn.cursor(cursor=cursor_class)
+    try:
+        self._execute_query(cursor, query, args, suppress_warnings)
+    except errors.LostConnectionError:
+        if not reconnect:
+            raise
+        logger.warning("Reconnecting to MySQL server.")
+        connect_host_hook(self)
+        if self._in_transaction:
+            self.cancel_transaction()
+            raise errors.LostConnectionError(
+                "Connection was lost during a transaction."
+            )
+        logger.debug("Re-executing")
+        cursor = self._conn.cursor(cursor=cursor_class)
+        self._execute_query(cursor, query, args, suppress_warnings)
+
+    if use_query_cache:
+        data = cursor.fetchall()
+        cache_path.write_bytes(pack(data))
+        return EmulatedCursor(data)
+
+    return cursor
+

+ +

+ + + + + + +

+ + +

+ `get_user()` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the user name and host name provided by the client to the server. + +

+ + +

Source code in datajoint/connection.py

def get_user(self):
+    """
+    :return: the user name and host name provided by the client to the server.
+    """
+    return self.query("SELECT user()").fetchone()[0]
+

+ +

+ + + + + + +

+ + + +

+ `in_transaction` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + True if there is an open transaction. + +

+ +

+ + + + + + +

+ + +

+ `start_transaction()` + +¶

+ + +

+ +

Starts a transaction error.

+ + +

Source code in datajoint/connection.py

def start_transaction(self):
+    """
+    Starts a transaction error.
+    """
+    if self.in_transaction:
+        raise errors.DataJointError("Nested connections are not supported.")
+    self.query("START TRANSACTION WITH CONSISTENT SNAPSHOT")
+    self._in_transaction = True
+    logger.debug("Transaction started")
+

+ +

+ + + + + + +

+ + +

+ `cancel_transaction()` + +¶

+ + +

+ +

Cancels the current transaction and rolls back all changes made during the transaction.

+ + +

Source code in datajoint/connection.py

def cancel_transaction(self):
+    """
+    Cancels the current transaction and rolls back all changes made during the transaction.
+    """
+    self.query("ROLLBACK")
+    self._in_transaction = False
+    logger.debug("Transaction cancelled. Rolling back ...")
+

+ +

+ + + + + + +

+ + +

+ `commit_transaction()` + +¶

+ + +

+ +

Commit all changes made during the transaction and close it.

+ + +

Source code in datajoint/connection.py

def commit_transaction(self):
+    """
+    Commit all changes made during the transaction and close it.
+
+    """
+    self.query("COMMIT")
+    self._in_transaction = False
+    logger.debug("Transaction committed and closed.")
+

+ +

+ + + + + + +

+ + + +

+ `transaction` + + + `property` + + +¶

+ + +

+ +

Example:

+
+
+
import datajoint as dj +with dj.conn().transaction as conn: + # transaction is open here
+
+
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/declare/index.html b/0.14/api/datajoint/declare/index.html new file mode 100644 index 000000000..f340c1aca --- /dev/null +++ b/0.14/api/datajoint/declare/index.html @@ -0,0 +1,5018 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + declare.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + declare.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

declare.py

+ +

+ + + + +

+ +

This module hosts functions to convert DataJoint table definitions into mysql table definitions, and to +declare the corresponding mysql tables.

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + +

+ + +

+ `is_foreign_key(line)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `line` +	+	+ + a line from the table definition + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + true if the line appears to be a foreign key definition + +

+ + +

Source code in datajoint/declare.py

def is_foreign_key(line):
+    """
+
+    :param line: a line from the table definition
+    :return: true if the line appears to be a foreign key definition
+    """
+    arrow_position = line.find("->")
+    return arrow_position >= 0 and not any(c in line[:arrow_position] for c in "\"#'")
+

+ +

+ + + + + + +

+ + +

+ `compile_foreign_key(line, context, attributes, primary_key, attr_sql, foreign_key_sql, index_sql)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `line` +	+	+ + a line from a table definition + +	+ required +
+ `context` +	+	+ + namespace containing referenced objects + +	+ required +
+ `attributes` +	+	+ + list of attribute names already in the declaration -- to be updated by this function + +	+ required +
+ `primary_key` +	+	+ + None if the current foreign key is made from the dependent section. Otherwise it is the list +of primary key attributes thus far -- to be updated by the function + +	+ required +
+ `attr_sql` +	+	+ + list of sql statements defining attributes -- to be updated by this function. + +	+ required +
+ `foreign_key_sql` +	+	+ + list of sql statements specifying foreign key constraints -- to be updated by this function. + +	+ required +
+ `index_sql` +	+	+ + list of INDEX declaration statements, duplicate or redundant indexes are ok. + +	+ required +

+ + +

Source code in datajoint/declare.py

def compile_foreign_key(
+    line, context, attributes, primary_key, attr_sql, foreign_key_sql, index_sql
+):
+    """
+    :param line: a line from a table definition
+    :param context: namespace containing referenced objects
+    :param attributes: list of attribute names already in the declaration -- to be updated by this function
+    :param primary_key: None if the current foreign key is made from the dependent section. Otherwise it is the list
+        of primary key attributes thus far -- to be updated by the function
+    :param attr_sql: list of sql statements defining attributes -- to be updated by this function.
+    :param foreign_key_sql: list of sql statements specifying foreign key constraints -- to be updated by this function.
+    :param index_sql: list of INDEX declaration statements, duplicate or redundant indexes are ok.
+    """
+    # Parse and validate
+    from .expression import QueryExpression
+    from .table import Table
+
+    try:
+        result = foreign_key_parser.parseString(line)
+    except pp.ParseException as err:
+        raise DataJointError('Parsing error in line "%s". %s.' % (line, err))
+
+    try:
+        ref = eval(result.ref_table, context)
+    except Exception:
+        raise DataJointError(
+            "Foreign key reference %s could not be resolved" % result.ref_table
+        )
+
+    options = [opt.upper() for opt in result.options]
+    for opt in options:  # check for invalid options
+        if opt not in {"NULLABLE", "UNIQUE"}:
+            raise DataJointError('Invalid foreign key option "{opt}"'.format(opt=opt))
+    is_nullable = "NULLABLE" in options
+    is_unique = "UNIQUE" in options
+    if is_nullable and primary_key is not None:
+        raise DataJointError(
+            'Primary dependencies cannot be nullable in line "{line}"'.format(line=line)
+        )
+
+    if isinstance(ref, type) and issubclass(ref, Table):
+        ref = ref()
+
+    # check that dependency is of a supported type
+    if (
+        not isinstance(ref, QueryExpression)
+        or len(ref.restriction)
+        or len(ref.support) != 1
+        or not isinstance(ref.support[0], str)
+    ):
+        raise DataJointError(
+            'Dependency "%s" is not supported (yet). Use a base table or its projection.'
+            % result.ref_table
+        )
+
+    # declare new foreign key attributes
+    for attr in ref.primary_key:
+        if attr not in attributes:
+            attributes.append(attr)
+            if primary_key is not None:
+                primary_key.append(attr)
+            attr_sql.append(
+                ref.heading[attr].sql.replace("NOT NULL ", "", int(is_nullable))
+            )
+
+    # declare the foreign key
+    foreign_key_sql.append(
+        "FOREIGN KEY (`{fk}`) REFERENCES {ref} (`{pk}`) ON UPDATE CASCADE ON DELETE RESTRICT".format(
+            fk="`,`".join(ref.primary_key),
+            pk="`,`".join(ref.heading[name].original_name for name in ref.primary_key),
+            ref=ref.support[0],
+        )
+    )
+
+    # declare unique index
+    if is_unique:
+        index_sql.append(
+            "UNIQUE INDEX ({attrs})".format(
+                attrs=",".join("`%s`" % attr for attr in ref.primary_key)
+            )
+        )
+

+ +

+ + + + + + +

+ + +

+ `declare(full_table_name, definition, context)` + +¶

+ + +

+ +

Parse declaration and generate the SQL CREATE TABLE code

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `full_table_name` +	+	+ + full name of the table + +	+ required +
+ `definition` +	+	+ + DataJoint table definition + +	+ required +
+ `context` +	+	+ + dictionary of objects that might be referred to in the table + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + SQL CREATE TABLE statement, list of external stores used + +

+ + +

Source code in datajoint/declare.py

def declare(full_table_name, definition, context):
+    """
+    Parse declaration and generate the SQL CREATE TABLE code
+
+    :param full_table_name: full name of the table
+    :param definition: DataJoint table definition
+    :param context: dictionary of objects that might be referred to in the table
+    :return: SQL CREATE TABLE statement, list of external stores used
+    """
+    table_name = full_table_name.strip("`").split(".")[1]
+    if len(table_name) > MAX_TABLE_NAME_LENGTH:
+        raise DataJointError(
+            "Table name `{name}` exceeds the max length of {max_length}".format(
+                name=table_name, max_length=MAX_TABLE_NAME_LENGTH
+            )
+        )
+
+    (
+        table_comment,
+        primary_key,
+        attribute_sql,
+        foreign_key_sql,
+        index_sql,
+        external_stores,
+    ) = prepare_declare(definition, context)
+
+    if config.get("add_hidden_timestamp", False):
+        metadata_attr_sql = [
+            "`_{full_table_name}_timestamp` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP"
+        ]
+        attribute_sql.extend(
+            attr.format(
+                full_table_name=sha1(
+                    full_table_name.replace("`", "").encode("utf-8")
+                ).hexdigest()
+            )
+            for attr in metadata_attr_sql
+        )
+
+    if not primary_key:
+        raise DataJointError("Table must have a primary key")
+
+    return (
+        "CREATE TABLE IF NOT EXISTS %s (\n" % full_table_name
+        + ",\n".join(
+            attribute_sql
+            + ["PRIMARY KEY (`" + "`,`".join(primary_key) + "`)"]
+            + foreign_key_sql
+            + index_sql
+        )
+        + '\n) ENGINE=InnoDB, COMMENT "%s"' % table_comment
+    ), external_stores
+

+ +

+ + + + + + +

+ + +

+ `alter(definition, old_definition, context)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `definition` +	+	+ + new table definition + +	+ required +
+ `old_definition` +	+	+ + current table definition + +	+ required +
+ `context` +	+	+ + the context in which to evaluate foreign key definitions + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + string SQL ALTER command, list of new stores used for external storage + +

+ + +

Source code in datajoint/declare.py

def alter(definition, old_definition, context):
+    """
+    :param definition: new table definition
+    :param old_definition: current table definition
+    :param context: the context in which to evaluate foreign key definitions
+    :return: string SQL ALTER command, list of new stores used for external storage
+    """
+    (
+        table_comment,
+        primary_key,
+        attribute_sql,
+        foreign_key_sql,
+        index_sql,
+        external_stores,
+    ) = prepare_declare(definition, context)
+    (
+        table_comment_,
+        primary_key_,
+        attribute_sql_,
+        foreign_key_sql_,
+        index_sql_,
+        external_stores_,
+    ) = prepare_declare(old_definition, context)
+
+    # analyze differences between declarations
+    sql = list()
+    if primary_key != primary_key_:
+        raise NotImplementedError("table.alter cannot alter the primary key (yet).")
+    if foreign_key_sql != foreign_key_sql_:
+        raise NotImplementedError("table.alter cannot alter foreign keys (yet).")
+    if index_sql != index_sql_:
+        raise NotImplementedError("table.alter cannot alter indexes (yet)")
+    if attribute_sql != attribute_sql_:
+        sql.extend(_make_attribute_alter(attribute_sql, attribute_sql_, primary_key))
+    if table_comment != table_comment_:
+        sql.append('COMMENT="%s"' % table_comment)
+    return sql, [e for e in external_stores if e not in external_stores_]
+

+ +

+ + + + + + +

+ + +

+ `substitute_special_type(match, category, foreign_key_sql, context)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `match` +	+	+ + dict containing with keys "type" and "comment" -- will be modified in place + +	+ required +
+ `category` +	+	+ + attribute type category from TYPE_PATTERN + +	+ required +
+ `foreign_key_sql` +	+	+ + list of foreign key declarations to add to + +	+ required +
+ `context` +	+	+ + context for looking up user-defined attribute_type adapters + +	+ required +

+ + +

Source code in datajoint/declare.py

def substitute_special_type(match, category, foreign_key_sql, context):
+    """
+    :param match: dict containing with keys "type" and "comment" -- will be modified in place
+    :param category: attribute type category from TYPE_PATTERN
+    :param foreign_key_sql: list of foreign key declarations to add to
+    :param context: context for looking up user-defined attribute_type adapters
+    """
+    if category == "UUID":
+        match["type"] = UUID_DATA_TYPE
+    elif category == "INTERNAL_ATTACH":
+        match["type"] = "LONGBLOB"
+    elif category in EXTERNAL_TYPES:
+        if category == "FILEPATH" and not _support_filepath_types():
+            raise DataJointError(
+                """
+            The filepath data type is disabled until complete validation.
+            To turn it on as experimental feature, set the environment variable
+            {env} = TRUE or upgrade datajoint.
+            """.format(
+                    env=FILEPATH_FEATURE_SWITCH
+                )
+            )
+        match["store"] = match["type"].split("@", 1)[1]
+        match["type"] = UUID_DATA_TYPE
+        foreign_key_sql.append(
+            "FOREIGN KEY (`{name}`) REFERENCES `{{database}}`.`{external_table_root}_{store}` (`hash`) "
+            "ON UPDATE RESTRICT ON DELETE RESTRICT".format(
+                external_table_root=EXTERNAL_TABLE_ROOT, **match
+            )
+        )
+    elif category == "ADAPTED":
+        adapter = get_adapter(context, match["type"])
+        match["type"] = adapter.attribute_type
+        category = match_type(match["type"])
+        if category in SPECIAL_TYPES:
+            # recursive redefinition from user-defined datatypes.
+            substitute_special_type(match, category, foreign_key_sql, context)
+    else:
+        assert False, "Unknown special type"
+

+ +

+ + + + + + +

+ + +

+ `compile_attribute(line, in_key, foreign_key_sql, context)` + +¶

+ + +

+ +

Convert attribute definition from DataJoint format to SQL

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `line` +	+	+ + attribution line + +	+ required +
+ `in_key` +	+	+ + set to True if attribute is in primary key set + +	+ required +
+ `foreign_key_sql` +	+	+ + the list of foreign key declarations to add to + +	+ required +
+ `context` +	+	+ + context in which to look up user-defined attribute type adapterss + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + (name, sql, is_external) -- attribute name and sql code for its declaration + +

+ + +

Source code in datajoint/declare.py

def compile_attribute(line, in_key, foreign_key_sql, context):
+    """
+    Convert attribute definition from DataJoint format to SQL
+
+    :param line: attribution line
+    :param in_key: set to True if attribute is in primary key set
+    :param foreign_key_sql: the list of foreign key declarations to add to
+    :param context: context in which to look up user-defined attribute type adapterss
+    :returns: (name, sql, is_external) -- attribute name and sql code for its declaration
+    """
+    try:
+        match = attribute_parser.parseString(line + "#", parseAll=True)
+    except pp.ParseException as err:
+        raise DataJointError(
+            "Declaration error in position {pos} in line:\n  {line}\n{msg}".format(
+                line=err.args[0], pos=err.args[1], msg=err.args[2]
+            )
+        )
+    match["comment"] = match["comment"].rstrip("#")
+    if "default" not in match:
+        match["default"] = ""
+    match = {k: v.strip() for k, v in match.items()}
+    match["nullable"] = match["default"].lower() == "null"
+
+    if match["nullable"]:
+        if in_key:
+            raise DataJointError(
+                'Primary key attributes cannot be nullable in line "%s"' % line
+            )
+        match["default"] = "DEFAULT NULL"  # nullable attributes default to null
+    else:
+        if match["default"]:
+            quote = (
+                match["default"].split("(")[0].upper() not in CONSTANT_LITERALS
+                and match["default"][0] not in "\"'"
+            )
+            match["default"] = (
+                "NOT NULL DEFAULT " + ('"%s"' if quote else "%s") % match["default"]
+            )
+        else:
+            match["default"] = "NOT NULL"
+
+    match["comment"] = match["comment"].replace(
+        '"', '\\"'
+    )  # escape double quotes in comment
+
+    if match["comment"].startswith(":"):
+        raise DataJointError(
+            'An attribute comment must not start with a colon in comment "{comment}"'.format(
+                **match
+            )
+        )
+
+    category = match_type(match["type"])
+    if category in SPECIAL_TYPES:
+        match["comment"] = ":{type}:{comment}".format(
+            **match
+        )  # insert custom type into comment
+        substitute_special_type(match, category, foreign_key_sql, context)
+
+    if category in SERIALIZED_TYPES and match["default"] not in {
+        "DEFAULT NULL",
+        "NOT NULL",
+    }:
+        raise DataJointError(
+            "The default value for a blob or attachment attributes can only be NULL in:\n{line}".format(
+                line=line
+            )
+        )
+
+    sql = (
+        "`{name}` {type} {default}"
+        + (' COMMENT "{comment}"' if match["comment"] else "")
+    ).format(**match)
+    return match["name"], sql, match.get("store")
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/dependencies/index.html b/0.14/api/datajoint/dependencies/index.html new file mode 100644 index 000000000..54237b8d8 --- /dev/null +++ b/0.14/api/datajoint/dependencies/index.html @@ -0,0 +1,5023 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + dependencies.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + dependencies.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

dependencies.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + +

+ + +

+ `extract_master(part_table)` + +¶

+ + +

+ +

given a part table name, return master part. None if not a part table

+ + +

Source code in datajoint/dependencies.py

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+13
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def extract_master(part_table):
+    """
+    given a part table name, return master part. None if not a part table
+    """
+    match = re.match(r"(?P<master>`\w+`.`#?\w+)__\w+`", part_table)
+    return match["master"] + "`" if match else None
+

+ +

+ + + + + + +

+ + +

+ `topo_sort(graph)` + +¶

+ + +

+ +

topological sort of a dependency graph that keeps part tables together with their masters

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of table names in topological order + +

+ + +

Source code in datajoint/dependencies.py

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def topo_sort(graph):
+    """
+    topological sort of a dependency graph that keeps part tables together with their masters
+    :return: list of table names in topological order
+    """
+
+    graph = nx.DiGraph(graph)  # make a copy
+
+    # collapse alias nodes
+    alias_nodes = [node for node in graph if node.isdigit()]
+    for node in alias_nodes:
+        try:
+            direct_edge = (
+                next(x for x in graph.in_edges(node))[0],
+                next(x for x in graph.out_edges(node))[1],
+            )
+        except StopIteration:
+            pass  # a disconnected alias node
+        else:
+            graph.add_edge(*direct_edge)
+    graph.remove_nodes_from(alias_nodes)
+
+    # Add parts' dependencies to their masters' dependencies
+    # to ensure correct topological ordering of the masters.
+    for part in graph:
+        # find the part's master
+        if (master := extract_master(part)) in graph:
+            for edge in graph.in_edges(part):
+                parent = edge[0]
+                if master not in (parent, extract_master(parent)):
+                    # if parent is neither master nor part of master
+                    graph.add_edge(parent, master)
+    sorted_nodes = list(nx.topological_sort(graph))
+
+    # bring parts up to their masters
+    pos = len(sorted_nodes) - 1
+    placed = set()
+    while pos > 1:
+        part = sorted_nodes[pos]
+        if (master := extract_master(part)) not in graph or part in placed:
+            pos -= 1
+        else:
+            placed.add(part)
+            insert_pos = sorted_nodes.index(master) + 1
+            if pos > insert_pos:
+                # move the part to the position immediately after its master
+                del sorted_nodes[pos]
+                sorted_nodes.insert(insert_pos, part)
+
+    return sorted_nodes
+

+ +

+ + + + + + +

+ + + +

+ `Dependencies` + + +¶

+ + +

+ Bases: DiGraph

+ + + +

The graph of dependencies (foreign keys) between loaded tables.

Note: the 'connection' argument should normally be supplied; +Empty use is permitted to facilitate use of networkx algorithms which +internally create objects with the expectation of empty constructors. +See also: https://github.com/datajoint/datajoint-python/pull/443

+ + + + + + + + +

Source code in datajoint/dependencies.py

class Dependencies(nx.DiGraph):
+    """
+    The graph of dependencies (foreign keys) between loaded tables.
+
+    Note: the 'connection' argument should normally be supplied;
+    Empty use is permitted to facilitate use of networkx algorithms which
+    internally create objects with the expectation of empty constructors.
+    See also: https://github.com/datajoint/datajoint-python/pull/443
+    """
+
+    def __init__(self, connection=None):
+        self._conn = connection
+        self._node_alias_count = itertools.count()
+        self._loaded = False
+        super().__init__(self)
+
+    def clear(self):
+        self._loaded = False
+        super().clear()
+
+    def load(self, force=True):
+        """
+        Load dependencies for all loaded schemas.
+        This method gets called before any operation that requires dependencies: delete, drop, populate, progress.
+        """
+        # reload from scratch to prevent duplication of renamed edges
+        if self._loaded and not force:
+            return
+
+        self.clear()
+
+        # load primary key info
+        keys = self._conn.query(
+            """
+                SELECT
+                    concat('`', table_schema, '`.`', table_name, '`') as tab, column_name
+                FROM information_schema.key_column_usage
+                WHERE table_name not LIKE "~%%" AND table_schema in ('{schemas}') AND constraint_name="PRIMARY"
+                """.format(
+                schemas="','".join(self._conn.schemas)
+            )
+        )
+        pks = defaultdict(set)
+        for key in keys:
+            pks[key[0]].add(key[1])
+
+        # add nodes to the graph
+        for n, pk in pks.items():
+            self.add_node(n, primary_key=pk)
+
+        # load foreign keys
+        keys = (
+            {k.lower(): v for k, v in elem.items()}
+            for elem in self._conn.query(
+                """
+        SELECT constraint_name,
+            concat('`', table_schema, '`.`', table_name, '`') as referencing_table,
+            concat('`', referenced_table_schema, '`.`',  referenced_table_name, '`') as referenced_table,
+            column_name, referenced_column_name
+        FROM information_schema.key_column_usage
+        WHERE referenced_table_name NOT LIKE "~%%" AND (referenced_table_schema in ('{schemas}') OR
+            referenced_table_schema is not NULL AND table_schema in ('{schemas}'))
+        """.format(
+                    schemas="','".join(self._conn.schemas)
+                ),
+                as_dict=True,
+            )
+        )
+        fks = defaultdict(lambda: dict(attr_map=dict()))
+        for key in keys:
+            d = fks[
+                (
+                    key["constraint_name"],
+                    key["referencing_table"],
+                    key["referenced_table"],
+                )
+            ]
+            d["referencing_table"] = key["referencing_table"]
+            d["referenced_table"] = key["referenced_table"]
+            d["attr_map"][key["column_name"]] = key["referenced_column_name"]
+
+        # add edges to the graph
+        for fk in fks.values():
+            props = dict(
+                primary=set(fk["attr_map"]) <= set(pks[fk["referencing_table"]]),
+                attr_map=fk["attr_map"],
+                aliased=any(k != v for k, v in fk["attr_map"].items()),
+                multi=set(fk["attr_map"]) != set(pks[fk["referencing_table"]]),
+            )
+            if not props["aliased"]:
+                self.add_edge(fk["referenced_table"], fk["referencing_table"], **props)
+            else:
+                # for aliased dependencies, add an extra node in the format '1', '2', etc
+                alias_node = "%d" % next(self._node_alias_count)
+                self.add_node(alias_node)
+                self.add_edge(fk["referenced_table"], alias_node, **props)
+                self.add_edge(alias_node, fk["referencing_table"], **props)
+
+        if not nx.is_directed_acyclic_graph(self):
+            raise DataJointError("DataJoint can only work with acyclic dependencies")
+        self._loaded = True
+
+    def topo_sort(self):
+        """:return: list of tables names in topological order"""
+        return topo_sort(self)
+
+    def parents(self, table_name, primary=None):
+        """
+        :param table_name: `schema`.`table`
+        :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
+            primary key attributes are considered.  If False, the only foreign keys including at least one non-primary
+            attribute are considered.
+        :return: dict of tables referenced by the foreign keys of table
+        """
+        self.load(force=False)
+        return {
+            p[0]: p[2]
+            for p in self.in_edges(table_name, data=True)
+            if primary is None or p[2]["primary"] == primary
+        }
+
+    def children(self, table_name, primary=None):
+        """
+        :param table_name: `schema`.`table`
+        :param primary: if None, then all children are returned. If True, then only foreign keys composed of
+            primary key attributes are considered.  If False, the only foreign keys including at least one non-primary
+            attribute are considered.
+        :return: dict of tables referencing the table through foreign keys
+        """
+        self.load(force=False)
+        return {
+            p[1]: p[2]
+            for p in self.out_edges(table_name, data=True)
+            if primary is None or p[2]["primary"] == primary
+        }
+
+    def descendants(self, full_table_name):
+        """
+        :param full_table_name:  In form `schema`.`table_name`
+        :return: all dependent tables sorted in topological order.  Self is included.
+        """
+        self.load(force=False)
+        nodes = self.subgraph(nx.descendants(self, full_table_name))
+        return [full_table_name] + nodes.topo_sort()
+
+    def ancestors(self, full_table_name):
+        """
+        :param full_table_name:  In form `schema`.`table_name`
+        :return: all dependent tables sorted in topological order.  Self is included.
+        """
+        self.load(force=False)
+        nodes = self.subgraph(nx.ancestors(self, full_table_name))
+        return reversed(nodes.topo_sort() + [full_table_name])
+

+ + + +

+ + + + + + + +

+ + +

+ `load(force=True)` + +¶

+ + +

+ +

Load dependencies for all loaded schemas. +This method gets called before any operation that requires dependencies: delete, drop, populate, progress.

+ + +

Source code in datajoint/dependencies.py

def load(self, force=True):
+    """
+    Load dependencies for all loaded schemas.
+    This method gets called before any operation that requires dependencies: delete, drop, populate, progress.
+    """
+    # reload from scratch to prevent duplication of renamed edges
+    if self._loaded and not force:
+        return
+
+    self.clear()
+
+    # load primary key info
+    keys = self._conn.query(
+        """
+            SELECT
+                concat('`', table_schema, '`.`', table_name, '`') as tab, column_name
+            FROM information_schema.key_column_usage
+            WHERE table_name not LIKE "~%%" AND table_schema in ('{schemas}') AND constraint_name="PRIMARY"
+            """.format(
+            schemas="','".join(self._conn.schemas)
+        )
+    )
+    pks = defaultdict(set)
+    for key in keys:
+        pks[key[0]].add(key[1])
+
+    # add nodes to the graph
+    for n, pk in pks.items():
+        self.add_node(n, primary_key=pk)
+
+    # load foreign keys
+    keys = (
+        {k.lower(): v for k, v in elem.items()}
+        for elem in self._conn.query(
+            """
+    SELECT constraint_name,
+        concat('`', table_schema, '`.`', table_name, '`') as referencing_table,
+        concat('`', referenced_table_schema, '`.`',  referenced_table_name, '`') as referenced_table,
+        column_name, referenced_column_name
+    FROM information_schema.key_column_usage
+    WHERE referenced_table_name NOT LIKE "~%%" AND (referenced_table_schema in ('{schemas}') OR
+        referenced_table_schema is not NULL AND table_schema in ('{schemas}'))
+    """.format(
+                schemas="','".join(self._conn.schemas)
+            ),
+            as_dict=True,
+        )
+    )
+    fks = defaultdict(lambda: dict(attr_map=dict()))
+    for key in keys:
+        d = fks[
+            (
+                key["constraint_name"],
+                key["referencing_table"],
+                key["referenced_table"],
+            )
+        ]
+        d["referencing_table"] = key["referencing_table"]
+        d["referenced_table"] = key["referenced_table"]
+        d["attr_map"][key["column_name"]] = key["referenced_column_name"]
+
+    # add edges to the graph
+    for fk in fks.values():
+        props = dict(
+            primary=set(fk["attr_map"]) <= set(pks[fk["referencing_table"]]),
+            attr_map=fk["attr_map"],
+            aliased=any(k != v for k, v in fk["attr_map"].items()),
+            multi=set(fk["attr_map"]) != set(pks[fk["referencing_table"]]),
+        )
+        if not props["aliased"]:
+            self.add_edge(fk["referenced_table"], fk["referencing_table"], **props)
+        else:
+            # for aliased dependencies, add an extra node in the format '1', '2', etc
+            alias_node = "%d" % next(self._node_alias_count)
+            self.add_node(alias_node)
+            self.add_edge(fk["referenced_table"], alias_node, **props)
+            self.add_edge(alias_node, fk["referencing_table"], **props)
+
+    if not nx.is_directed_acyclic_graph(self):
+        raise DataJointError("DataJoint can only work with acyclic dependencies")
+    self._loaded = True
+

+ +

+ + + + + + +

+ + +

+ `topo_sort()` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of tables names in topological order + +

+ + +

Source code in datajoint/dependencies.py

def topo_sort(self):
+    """:return: list of tables names in topological order"""
+    return topo_sort(self)
+

+ +

+ + + + + + +

+ + +

+ `parents(table_name, primary=None)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `table_name` +	+	+ + `schema`.`table` + +	+ required +
+ `primary` +	+	+ + if None, then all parents are returned. If True, then only foreign keys composed of +primary key attributes are considered. If False, the only foreign keys including at least one non-primary +attribute are considered. + +	+ `None` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + dict of tables referenced by the foreign keys of table + +

+ + +

Source code in datajoint/dependencies.py

def parents(self, table_name, primary=None):
+    """
+    :param table_name: `schema`.`table`
+    :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
+        primary key attributes are considered.  If False, the only foreign keys including at least one non-primary
+        attribute are considered.
+    :return: dict of tables referenced by the foreign keys of table
+    """
+    self.load(force=False)
+    return {
+        p[0]: p[2]
+        for p in self.in_edges(table_name, data=True)
+        if primary is None or p[2]["primary"] == primary
+    }
+

+ +

+ + + + + + +

+ + +

+ `children(table_name, primary=None)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `table_name` +	+	+ + `schema`.`table` + +	+ required +
+ `primary` +	+	+ + if None, then all children are returned. If True, then only foreign keys composed of +primary key attributes are considered. If False, the only foreign keys including at least one non-primary +attribute are considered. + +	+ `None` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + dict of tables referencing the table through foreign keys + +

+ + +

Source code in datajoint/dependencies.py

def children(self, table_name, primary=None):
+    """
+    :param table_name: `schema`.`table`
+    :param primary: if None, then all children are returned. If True, then only foreign keys composed of
+        primary key attributes are considered.  If False, the only foreign keys including at least one non-primary
+        attribute are considered.
+    :return: dict of tables referencing the table through foreign keys
+    """
+    self.load(force=False)
+    return {
+        p[1]: p[2]
+        for p in self.out_edges(table_name, data=True)
+        if primary is None or p[2]["primary"] == primary
+    }
+

+ +

+ + + + + + +

+ + +

+ `descendants(full_table_name)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `full_table_name` +	+	+ + In form `schema`.`table_name` + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + all dependent tables sorted in topological order. Self is included. + +

+ + +

Source code in datajoint/dependencies.py

def descendants(self, full_table_name):
+    """
+    :param full_table_name:  In form `schema`.`table_name`
+    :return: all dependent tables sorted in topological order.  Self is included.
+    """
+    self.load(force=False)
+    nodes = self.subgraph(nx.descendants(self, full_table_name))
+    return [full_table_name] + nodes.topo_sort()
+

+ +

+ + + + + + +

+ + +

+ `ancestors(full_table_name)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `full_table_name` +	+	+ + In form `schema`.`table_name` + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + all dependent tables sorted in topological order. Self is included. + +

+ + +

Source code in datajoint/dependencies.py

def ancestors(self, full_table_name):
+    """
+    :param full_table_name:  In form `schema`.`table_name`
+    :return: all dependent tables sorted in topological order.  Self is included.
+    """
+    self.load(force=False)
+    nodes = self.subgraph(nx.ancestors(self, full_table_name))
+    return reversed(nodes.topo_sort() + [full_table_name])
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/diagram/index.html b/0.14/api/datajoint/diagram/index.html new file mode 100644 index 000000000..062efe674 --- /dev/null +++ b/0.14/api/datajoint/diagram/index.html @@ -0,0 +1,4945 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + diagram.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + diagram.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

diagram.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ `Diagram` + + +¶

+ + +

+ Bases: DiGraph

+ + + +

Schema diagram showing tables and foreign keys between in the form of a directed +acyclic graph (DAG). The diagram is derived from the connection.dependencies object.

Usage:

+
+
+
diag = Diagram(source)
+
+
+

source can be a table object, a table class, a schema, or a module that has a schema.

+
+
+
diag.draw()
+
+
+

draws the diagram using pyplot

Note that diagram + 1 - 1 may differ from diagram - 1 + 1 and so forth. +Only those tables that are loaded in the connection object are displayed

+ + + + + + + + +

Source code in datajoint/diagram.py

class Diagram(nx.DiGraph):
+    """
+    Schema diagram showing tables and foreign keys between in the form of a directed
+    acyclic graph (DAG).  The diagram is derived from the connection.dependencies object.
+
+    Usage:
+
+    >>>  diag = Diagram(source)
+
+    source can be a table object, a table class, a schema, or a module that has a schema.
+
+    >>> diag.draw()
+
+    draws the diagram using pyplot
+
+    diag1 + diag2  - combines the two diagrams.
+    diag1 - diag2  - difference between diagrams
+    diag1 * diag2  - intersection of diagrams
+    diag + n   - expands n levels of successors
+    diag - n   - expands n levels of predecessors
+    Thus dj.Diagram(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table
+
+    Note that diagram + 1 - 1  may differ from diagram - 1 + 1 and so forth.
+    Only those tables that are loaded in the connection object are displayed
+    """
+
+    def __init__(self, source, context=None):
+
+        if isinstance(source, Diagram):
+            # copy constructor
+            self.nodes_to_show = set(source.nodes_to_show)
+            self.context = source.context
+            super().__init__(source)
+            return
+
+        # get the caller's context
+        if context is None:
+            frame = inspect.currentframe().f_back
+            self.context = dict(frame.f_globals, **frame.f_locals)
+            del frame
+        else:
+            self.context = context
+
+        # find connection in the source
+        try:
+            connection = source.connection
+        except AttributeError:
+            try:
+                connection = source.schema.connection
+            except AttributeError:
+                raise DataJointError(
+                    "Could not find database connection in %s" % repr(source[0])
+                )
+
+        # initialize graph from dependencies
+        connection.dependencies.load()
+        super().__init__(connection.dependencies)
+
+        # Enumerate nodes from all the items in the list
+        self.nodes_to_show = set()
+        try:
+            self.nodes_to_show.add(source.full_table_name)
+        except AttributeError:
+            try:
+                database = source.database
+            except AttributeError:
+                try:
+                    database = source.schema.database
+                except AttributeError:
+                    raise DataJointError(
+                        "Cannot plot Diagram for %s" % repr(source)
+                    )
+            for node in self:
+                if node.startswith("`%s`" % database):
+                    self.nodes_to_show.add(node)
+
+    @classmethod
+    def from_sequence(cls, sequence):
+        """
+        The join Diagram for all objects in sequence
+
+        :param sequence: a sequence (e.g. list, tuple)
+        :return: Diagram(arg1) + ... + Diagram(argn)
+        """
+        return functools.reduce(lambda x, y: x + y, map(Diagram, sequence))
+
+    def add_parts(self):
+        """
+        Adds to the diagram the part tables of all master tables already in the diagram
+        :return:
+        """
+
+        def is_part(part, master):
+            """
+            :param part:  `database`.`table_name`
+            :param master:   `database`.`table_name`
+            :return: True if part is part of master.
+            """
+            part = [s.strip("`") for s in part.split(".")]
+            master = [s.strip("`") for s in master.split(".")]
+            return (
+                master[0] == part[0]
+                and master[1] + "__" == part[1][: len(master[1]) + 2]
+            )
+
+        self = Diagram(self)  # copy
+        self.nodes_to_show.update(
+            n
+            for n in self.nodes()
+            if any(is_part(n, m) for m in self.nodes_to_show)
+        )
+        return self
+
+    def __add__(self, arg):
+        """
+        :param arg: either another Diagram or a positive integer.
+        :return: Union of the diagrams when arg is another Diagram
+                 or an expansion downstream when arg is a positive integer.
+        """
+        self = Diagram(self)  # copy
+        try:
+            self.nodes_to_show.update(arg.nodes_to_show)
+        except AttributeError:
+            try:
+                self.nodes_to_show.add(arg.full_table_name)
+            except AttributeError:
+                for i in range(arg):
+                    new = nx.algorithms.boundary.node_boundary(
+                        self, self.nodes_to_show
+                    )
+                    if not new:
+                        break
+                    # add nodes referenced by aliased nodes
+                    new.update(
+                        nx.algorithms.boundary.node_boundary(
+                            self, (a for a in new if a.isdigit())
+                        )
+                    )
+                    self.nodes_to_show.update(new)
+        return self
+
+    def __sub__(self, arg):
+        """
+        :param arg: either another Diagram or a positive integer.
+        :return: Difference of the diagrams when arg is another Diagram or
+                 an expansion upstream when arg is a positive integer.
+        """
+        self = Diagram(self)  # copy
+        try:
+            self.nodes_to_show.difference_update(arg.nodes_to_show)
+        except AttributeError:
+            try:
+                self.nodes_to_show.remove(arg.full_table_name)
+            except AttributeError:
+                for i in range(arg):
+                    graph = nx.DiGraph(self).reverse()
+                    new = nx.algorithms.boundary.node_boundary(
+                        graph, self.nodes_to_show
+                    )
+                    if not new:
+                        break
+                    # add nodes referenced by aliased nodes
+                    new.update(
+                        nx.algorithms.boundary.node_boundary(
+                            graph, (a for a in new if a.isdigit())
+                        )
+                    )
+                    self.nodes_to_show.update(new)
+        return self
+
+    def __mul__(self, arg):
+        """
+        Intersection of two diagrams
+        :param arg: another Diagram
+        :return: a new Diagram comprising nodes that are present in both operands.
+        """
+        self = Diagram(self)  # copy
+        self.nodes_to_show.intersection_update(arg.nodes_to_show)
+        return self
+
+    def topo_sort(self):
+        """return nodes in lexicographical topological order"""
+        return topo_sort(self)
+
+    def _make_graph(self):
+        """
+        Make the self.graph - a graph object ready for drawing
+        """
+        # mark "distinguished" tables, i.e. those that introduce new primary key
+        # attributes
+        for name in self.nodes_to_show:
+            foreign_attributes = set(
+                attr
+                for p in self.in_edges(name, data=True)
+                for attr in p[2]["attr_map"]
+                if p[2]["primary"]
+            )
+            self.nodes[name]["distinguished"] = (
+                "primary_key" in self.nodes[name]
+                and foreign_attributes < self.nodes[name]["primary_key"]
+            )
+        # include aliased nodes that are sandwiched between two displayed nodes
+        gaps = set(
+            nx.algorithms.boundary.node_boundary(self, self.nodes_to_show)
+        ).intersection(
+            nx.algorithms.boundary.node_boundary(
+                nx.DiGraph(self).reverse(), self.nodes_to_show
+            )
+        )
+        nodes = self.nodes_to_show.union(a for a in gaps if a.isdigit)
+        # construct subgraph and rename nodes to class names
+        graph = nx.DiGraph(nx.DiGraph(self).subgraph(nodes))
+        nx.set_node_attributes(
+            graph, name="node_type", values={n: _get_tier(n) for n in graph}
+        )
+        # relabel nodes to class names
+        mapping = {
+            node: lookup_class_name(node, self.context) or node
+            for node in graph.nodes()
+        }
+        new_names = [mapping.values()]
+        if len(new_names) > len(set(new_names)):
+            raise DataJointError(
+                "Some classes have identical names. The Diagram cannot be plotted."
+            )
+        nx.relabel_nodes(graph, mapping, copy=False)
+        return graph
+
+    @staticmethod
+    def _encapsulate_edge_attributes(graph):
+        """
+        Modifies the `nx.Graph`'s edge attribute `attr_map` to be a string representation
+        of the attribute map, and encapsulates the string in double quotes.
+        Changes the graph in place.
+
+        Implements workaround described in
+        https://github.com/pydot/pydot/issues/258#issuecomment-795798099
+        """
+        for u, v, *_, edgedata in graph.edges(data=True):
+            if "attr_map" in edgedata:
+                graph.edges[u, v]["attr_map"] = '"{0}"'.format(edgedata["attr_map"])
+
+    @staticmethod
+    def _encapsulate_node_names(graph):
+        """
+        Modifies the `nx.Graph`'s node names string representations encapsulated in
+        double quotes.
+        Changes the graph in place.
+
+        Implements workaround described in
+        https://github.com/datajoint/datajoint-python/pull/1176
+        """
+        nx.relabel_nodes(
+            graph,
+            {node: '"{0}"'.format(node) for node in graph.nodes()},
+            copy=False,
+        )
+
+    def make_dot(self):
+        graph = self._make_graph()
+        graph.nodes()
+
+        scale = 1.2  # scaling factor for fonts and boxes
+        label_props = {  # http://matplotlib.org/examples/color/named_colors.html
+            None: dict(
+                shape="circle",
+                color="#FFFF0040",
+                fontcolor="yellow",
+                fontsize=round(scale * 8),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            _AliasNode: dict(
+                shape="circle",
+                color="#FF880080",
+                fontcolor="#FF880080",
+                fontsize=round(scale * 0),
+                size=0.05 * scale,
+                fixed=True,
+            ),
+            Manual: dict(
+                shape="box",
+                color="#00FF0030",
+                fontcolor="darkgreen",
+                fontsize=round(scale * 10),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            Lookup: dict(
+                shape="plaintext",
+                color="#00000020",
+                fontcolor="black",
+                fontsize=round(scale * 8),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            Computed: dict(
+                shape="ellipse",
+                color="#FF000020",
+                fontcolor="#7F0000A0",
+                fontsize=round(scale * 10),
+                size=0.3 * scale,
+                fixed=True,
+            ),
+            Imported: dict(
+                shape="ellipse",
+                color="#00007F40",
+                fontcolor="#00007FA0",
+                fontsize=round(scale * 10),
+                size=0.4 * scale,
+                fixed=False,
+            ),
+            Part: dict(
+                shape="plaintext",
+                color="#0000000",
+                fontcolor="black",
+                fontsize=round(scale * 8),
+                size=0.1 * scale,
+                fixed=False,
+            ),
+        }
+        node_props = {
+            node: label_props[d["node_type"]]
+            for node, d in dict(graph.nodes(data=True)).items()
+        }
+
+        self._encapsulate_node_names(graph)
+        self._encapsulate_edge_attributes(graph)
+        dot = nx.drawing.nx_pydot.to_pydot(graph)
+        for node in dot.get_nodes():
+            node.set_shape("circle")
+            name = node.get_name().strip('"')
+            props = node_props[name]
+            node.set_fontsize(props["fontsize"])
+            node.set_fontcolor(props["fontcolor"])
+            node.set_shape(props["shape"])
+            node.set_fontname("arial")
+            node.set_fixedsize("shape" if props["fixed"] else False)
+            node.set_width(props["size"])
+            node.set_height(props["size"])
+            if name.split(".")[0] in self.context:
+                cls = eval(name, self.context)
+                assert issubclass(cls, Table)
+                description = cls().describe(context=self.context).split("\n")
+                description = (
+                    (
+                        "-" * 30
+                        if q.startswith("---")
+                        else (
+                            q.replace("->", "&#8594;")
+                            if "->" in q
+                            else q.split(":")[0]
+                        )
+                    )
+                    for q in description
+                    if not q.startswith("#")
+                )
+                node.set_tooltip("&#13;".join(description))
+            node.set_label(
+                "<<u>" + name + "</u>>"
+                if node.get("distinguished") == "True"
+                else name
+            )
+            node.set_color(props["color"])
+            node.set_style("filled")
+
+        for edge in dot.get_edges():
+            # see https://graphviz.org/doc/info/attrs.html
+            src = edge.get_source()
+            dest = edge.get_destination()
+            props = graph.get_edge_data(src, dest)
+            if props is None:
+                raise DataJointError(
+                    "Could not find edge with source "
+                    "'{}' and destination '{}'".format(src, dest)
+                )
+            edge.set_color("#00000040")
+            edge.set_style("solid" if props["primary"] else "dashed")
+            master_part = graph.nodes[dest][
+                "node_type"
+            ] is Part and dest.startswith(src + ".")
+            edge.set_weight(3 if master_part else 1)
+            edge.set_arrowhead("none")
+            edge.set_penwidth(0.75 if props["multi"] else 2)
+
+        return dot
+
+    def make_svg(self):
+        from IPython.display import SVG
+
+        return SVG(self.make_dot().create_svg())
+
+    def make_png(self):
+        return io.BytesIO(self.make_dot().create_png())
+
+    def make_image(self):
+        if plot_active:
+            return plt.imread(self.make_png())
+        else:
+            raise DataJointError("pyplot was not imported")
+
+    def _repr_svg_(self):
+        return self.make_svg()._repr_svg_()
+
+    def draw(self):
+        if plot_active:
+            plt.imshow(self.make_image())
+            plt.gca().axis("off")
+            plt.show()
+        else:
+            raise DataJointError("pyplot was not imported")
+
+    def save(self, filename, format=None):
+        if format is None:
+            if filename.lower().endswith(".png"):
+                format = "png"
+            elif filename.lower().endswith(".svg"):
+                format = "svg"
+        if format.lower() == "png":
+            with open(filename, "wb") as f:
+                f.write(self.make_png().getbuffer().tobytes())
+        elif format.lower() == "svg":
+            with open(filename, "w") as f:
+                f.write(self.make_svg().data)
+        else:
+            raise DataJointError("Unsupported file format")
+
+    @staticmethod
+    def _layout(graph, **kwargs):
+        return pydot_layout(graph, prog="dot", **kwargs)
+

+ + + +

+ + + + + + + +

+ + +

+ `from_sequence(sequence)` + + + `classmethod` + + +¶

+ + +

+ +

The join Diagram for all objects in sequence

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `sequence` +	+	+ + a sequence (e.g. list, tuple) + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + Diagram(arg1) + ... + Diagram(argn) + +

+ + +

Source code in datajoint/diagram.py

@classmethod
+def from_sequence(cls, sequence):
+    """
+    The join Diagram for all objects in sequence
+
+    :param sequence: a sequence (e.g. list, tuple)
+    :return: Diagram(arg1) + ... + Diagram(argn)
+    """
+    return functools.reduce(lambda x, y: x + y, map(Diagram, sequence))
+

+ +

+ + + + + + +

+ + +

+ `add_parts()` + +¶

+ + +

+ +

Adds to the diagram the part tables of all master tables already in the diagram

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + + +

+ + +

Source code in datajoint/diagram.py

def add_parts(self):
+    """
+    Adds to the diagram the part tables of all master tables already in the diagram
+    :return:
+    """
+
+    def is_part(part, master):
+        """
+        :param part:  `database`.`table_name`
+        :param master:   `database`.`table_name`
+        :return: True if part is part of master.
+        """
+        part = [s.strip("`") for s in part.split(".")]
+        master = [s.strip("`") for s in master.split(".")]
+        return (
+            master[0] == part[0]
+            and master[1] + "__" == part[1][: len(master[1]) + 2]
+        )
+
+    self = Diagram(self)  # copy
+    self.nodes_to_show.update(
+        n
+        for n in self.nodes()
+        if any(is_part(n, m) for m in self.nodes_to_show)
+    )
+    return self
+

+ +

+ + + + + + +

+ + +

+ `topo_sort()` + +¶

+ + +

+ +

return nodes in lexicographical topological order

+ + +

Source code in datajoint/diagram.py

def topo_sort(self):
+    """return nodes in lexicographical topological order"""
+    return topo_sort(self)
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/errors/index.html b/0.14/api/datajoint/errors/index.html new file mode 100644 index 000000000..3ee793afb --- /dev/null +++ b/0.14/api/datajoint/errors/index.html @@ -0,0 +1,4669 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + errors.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + errors.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

errors.py

+ +

+ + + + +

+ +

Exception classes for the DataJoint library

+ + + + + + + + + + +

+ + + + + + + +

+ + + +

+ `DataJointError` + + +¶

+ + +

+ Bases: Exception

+ + + +

Base class for errors specific to DataJoint internal operation.

+ + + + + + + + +

Source code in datajoint/errors.py

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+39
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class DataJointError(Exception):
+    """
+    Base class for errors specific to DataJoint internal operation.
+    """
+
+    def __init__(self, *args):
+        from .plugin import connection_plugins, type_plugins
+
+        self.__cause__ = (
+            PluginWarning("Unverified DataJoint plugin detected.")
+            if any(
+                [
+                    any([not plugins[k]["verified"] for k in plugins])
+                    for plugins in [connection_plugins, type_plugins]
+                    if plugins
+                ]
+            )
+            else None
+        )
+
+    def suggest(self, *args):
+        """
+        regenerate the exception with additional arguments
+
+        :param args: addition arguments
+        :return: a new exception of the same type with the additional arguments
+        """
+        return self.__class__(*(self.args + args))
+

+ + + +

+ + + + + + + +

+ + +

+ `suggest(*args)` + +¶

+ + +

+ +

regenerate the exception with additional arguments

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `args` +	+	+ + addition arguments + +	+ `()` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a new exception of the same type with the additional arguments + +

+ + +

Source code in datajoint/errors.py

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+35
+36
+37
+38
+39
+40
+41
def suggest(self, *args):
+    """
+    regenerate the exception with additional arguments
+
+    :param args: addition arguments
+    :return: a new exception of the same type with the additional arguments
+    """
+    return self.__class__(*(self.args + args))
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `LostConnectionError` + + +¶

+ + +

+ Bases: DataJointError

+ + + +

Loss of server connection

+ + + + + + + + +

Source code in datajoint/errors.py

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+46
+47
+48
class LostConnectionError(DataJointError):
+    """
+    Loss of server connection
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `QueryError` + + +¶

+ + +

+ Bases: DataJointError

+ + + +

Errors arising from queries to the database

+ + + + + + + + +

Source code in datajoint/errors.py

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+52
+53
+54
class QueryError(DataJointError):
+    """
+    Errors arising from queries to the database
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `QuerySyntaxError` + + +¶

+ + +

+ Bases: QueryError

+ + + +

Errors arising from incorrect query syntax

+ + + + + + + + +

Source code in datajoint/errors.py

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+59
+60
+61
class QuerySyntaxError(QueryError):
+    """
+    Errors arising from incorrect query syntax
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `AccessError` + + +¶

+ + +

+ Bases: QueryError

+ + + +

User access error: insufficient privileges.

+ + + + + + + + +

Source code in datajoint/errors.py

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+65
+66
+67
class AccessError(QueryError):
+    """
+    User access error: insufficient privileges.
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `MissingTableError` + + +¶

+ + +

+ Bases: DataJointError

+ + + +

Query on a table that has not been declared

+ + + + + + + + +

Source code in datajoint/errors.py

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+71
+72
+73
class MissingTableError(DataJointError):
+    """
+    Query on a table that has not been declared
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `DuplicateError` + + +¶

+ + +

+ Bases: QueryError

+ + + +

An integrity error caused by a duplicate entry into a unique key

+ + + + + + + + +

Source code in datajoint/errors.py

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+77
+78
+79
class DuplicateError(QueryError):
+    """
+    An integrity error caused by a duplicate entry into a unique key
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `IntegrityError` + + +¶

+ + +

+ Bases: QueryError

+ + + +

An integrity error triggered by foreign key constraints

+ + + + + + + + +

Source code in datajoint/errors.py

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+83
+84
+85
class IntegrityError(QueryError):
+    """
+    An integrity error triggered by foreign key constraints
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `UnknownAttributeError` + + +¶

+ + +

+ Bases: QueryError

+ + + +

User requests an attribute name not found in query heading

+ + + + + + + + +

Source code in datajoint/errors.py

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+89
+90
+91
class UnknownAttributeError(QueryError):
+    """
+    User requests an attribute name not found in query heading
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `MissingAttributeError` + + +¶

+ + +

+ Bases: QueryError

+ + + +

An error arising when a required attribute value is not provided in INSERT

+ + + + + + + + +

Source code in datajoint/errors.py

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+95
+96
+97
class MissingAttributeError(QueryError):
+    """
+    An error arising when a required attribute value is not provided in INSERT
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `MissingExternalFile` + + +¶

+ + +

+ Bases: DataJointError

+ + + +

Error raised when an external file managed by DataJoint is no longer accessible

+ + + + + + + + +

Source code in datajoint/errors.py

class MissingExternalFile(DataJointError):
+    """
+    Error raised when an external file managed by DataJoint is no longer accessible
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `BucketInaccessible` + + +¶

+ + +

+ Bases: DataJointError

+ + + +

Error raised when a S3 bucket is inaccessible

+ + + + + + + + +

Source code in datajoint/errors.py

class BucketInaccessible(DataJointError):
+    """
+    Error raised when a S3 bucket is inaccessible
+    """
+

+ + + +

+ + + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/expression/index.html b/0.14/api/datajoint/expression/index.html new file mode 100644 index 000000000..0da584823 --- /dev/null +++ b/0.14/api/datajoint/expression/index.html @@ -0,0 +1,8079 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + expression.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + expression.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

expression.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ `QueryExpression` + + +¶

+ + +

+ + + +

QueryExpression implements query operators to derive new entity set from its input. +A QueryExpression object generates a SELECT statement in SQL. +QueryExpression operators are restrict, join, proj, aggr, and union.

A QueryExpression object has a support, a restriction (an AndList), and heading. +Property heading (type dj.Heading) contains information about the attributes. +It is loaded from the database and updated by proj.

Property support is the list of table names or other QueryExpressions to be joined.

The restriction is applied first without having access to the attributes generated by the projection. +Then projection is applied by selecting modifying the heading attribute.

Application of operators does not always lead to the creation of a subquery. +A subquery is generated when: + 1. A restriction is applied on any computed or renamed attributes + 2. A projection is applied remapping remapped attributes + 3. Subclasses: Join, Aggregation, and Union have additional specific rules.

+ + + + + + + + +

Source code in datajoint/expression.py

class QueryExpression:
+    """
+    QueryExpression implements query operators to derive new entity set from its input.
+    A QueryExpression object generates a SELECT statement in SQL.
+    QueryExpression operators are restrict, join, proj, aggr, and union.
+
+    A QueryExpression object has a support, a restriction (an AndList), and heading.
+    Property `heading` (type dj.Heading) contains information about the attributes.
+    It is loaded from the database and updated by proj.
+
+    Property `support` is the list of table names or other QueryExpressions to be joined.
+
+    The restriction is applied first without having access to the attributes generated by the projection.
+    Then projection is applied by selecting modifying the heading attribute.
+
+    Application of operators does not always lead to the creation of a subquery.
+    A subquery is generated when:
+        1. A restriction is applied on any computed or renamed attributes
+        2. A projection is applied remapping remapped attributes
+        3. Subclasses: Join, Aggregation, and Union have additional specific rules.
+    """
+
+    _restriction = None
+    _restriction_attributes = None
+    _left = []  # list of booleans True for left joins, False for inner joins
+    _original_heading = None  # heading before projections
+
+    # subclasses or instantiators must provide values
+    _connection = None
+    _heading = None
+    _support = None
+    _top = None
+
+    # If the query will be using distinct
+    _distinct = False
+
+    @property
+    def connection(self):
+        """a dj.Connection object"""
+        assert self._connection is not None
+        return self._connection
+
+    @property
+    def support(self):
+        """A list of table names or subqueries to from the FROM clause"""
+        assert self._support is not None
+        return self._support
+
+    @property
+    def heading(self):
+        """a dj.Heading object, reflects the effects of the projection operator .proj"""
+        return self._heading
+
+    @property
+    def original_heading(self):
+        """a dj.Heading object reflecting the attributes before projection"""
+        return self._original_heading or self.heading
+
+    @property
+    def restriction(self):
+        """a AndList object of restrictions applied to input to produce the result"""
+        if self._restriction is None:
+            self._restriction = AndList()
+        return self._restriction
+
+    @property
+    def restriction_attributes(self):
+        """the set of attribute names invoked in the WHERE clause"""
+        if self._restriction_attributes is None:
+            self._restriction_attributes = set()
+        return self._restriction_attributes
+
+    @property
+    def primary_key(self):
+        return self.heading.primary_key
+
+    _subquery_alias_count = count()  # count for alias names used in the FROM clause
+
+    def from_clause(self):
+        support = (
+            (
+                "(" + src.make_sql() + ") as `$%x`" % next(self._subquery_alias_count)
+                if isinstance(src, QueryExpression)
+                else src
+            )
+            for src in self.support
+        )
+        clause = next(support)
+        for s, left in zip(support, self._left):
+            clause += " NATURAL{left} JOIN {clause}".format(
+                left=" LEFT" if left else "", clause=s
+            )
+        return clause
+
+    def where_clause(self):
+        return (
+            ""
+            if not self.restriction
+            else " WHERE (%s)" % ")AND(".join(str(s) for s in self.restriction)
+        )
+
+    def sorting_clauses(self):
+        if not self._top:
+            return ""
+        clause = ", ".join(
+            _wrap_attributes(
+                _flatten_attribute_list(self.primary_key, self._top.order_by)
+            )
+        )
+        if clause:
+            clause = f" ORDER BY {clause}"
+        if self._top.limit is not None:
+            clause += f" LIMIT {self._top.limit}{f' OFFSET {self._top.offset}' if self._top.offset else ''}"
+
+        return clause
+
+    def make_sql(self, fields=None):
+        """
+        Make the SQL SELECT statement.
+
+        :param fields: used to explicitly set the select attributes
+        """
+        return "SELECT {distinct}{fields} FROM {from_}{where}{sorting}".format(
+            distinct="DISTINCT " if self._distinct else "",
+            fields=self.heading.as_sql(fields or self.heading.names),
+            from_=self.from_clause(),
+            where=self.where_clause(),
+            sorting=self.sorting_clauses(),
+        )
+
+    # --------- query operators -----------
+    def make_subquery(self):
+        """create a new SELECT statement where self is the FROM clause"""
+        result = QueryExpression()
+        result._connection = self.connection
+        result._support = [self]
+        result._heading = self.heading.make_subquery_heading()
+        return result
+
+    def restrict(self, restriction):
+        """
+        Produces a new expression with the new restriction applied.
+        rel.restrict(restriction)  is equivalent to  rel & restriction.
+        rel.restrict(Not(restriction))  is equivalent to  rel - restriction
+        The primary key of the result is unaffected.
+        Successive restrictions are combined as logical AND:   r & a & b  is equivalent to r & AndList((a, b))
+        Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists
+        (logical disjunction of conditions)
+        Inverse restriction is accomplished by either using the subtraction operator or the Not class.
+
+        The expressions in each row equivalent:
+
+        rel & True                          rel
+        rel & False                         the empty entity set
+        rel & 'TRUE'                        rel
+        rel & 'FALSE'                       the empty entity set
+        rel - cond                          rel & Not(cond)
+        rel - 'TRUE'                        rel & False
+        rel - 'FALSE'                       rel
+        rel & AndList((cond1,cond2))        rel & cond1 & cond2
+        rel & AndList()                     rel
+        rel & [cond1, cond2]                rel & OrList((cond1, cond2))
+        rel & []                            rel & False
+        rel & None                          rel & False
+        rel & any_empty_entity_set          rel & False
+        rel - AndList((cond1,cond2))        rel & [Not(cond1), Not(cond2)]
+        rel - [cond1, cond2]                rel & Not(cond1) & Not(cond2)
+        rel - AndList()                     rel & False
+        rel - []                            rel
+        rel - None                          rel
+        rel - any_empty_entity_set          rel
+
+        When arg is another QueryExpression, the restriction  rel & arg  restricts rel to elements that match at least
+        one element in arg (hence arg is treated as an OrList).
+        Conversely,  rel - arg  restricts rel to elements that do not match any elements in arg.
+        Two elements match when their common attributes have equal values or when they have no common attributes.
+        All shared attributes must be in the primary key of either rel or arg or both or an error will be raised.
+
+        QueryExpression.restrict is the only access point that modifies restrictions. All other operators must
+        ultimately call restrict()
+
+        :param restriction: a sequence or an array (treated as OR list), another QueryExpression, an SQL condition
+        string, or an AndList.
+        """
+        attributes = set()
+        if isinstance(restriction, Top):
+            result = (
+                self.make_subquery()
+                if self._top and not self._top.__eq__(restriction)
+                else copy.copy(self)
+            )  # make subquery to avoid overwriting existing Top
+            result._top = restriction
+            return result
+        new_condition = make_condition(self, restriction, attributes)
+        if new_condition is True:
+            return self  # restriction has no effect, return the same object
+        # check that all attributes in condition are present in the query
+        try:
+            raise DataJointError(
+                "Attribute `%s` is not found in query."
+                % next(attr for attr in attributes if attr not in self.heading.names)
+            )
+        except StopIteration:
+            pass  # all ok
+        # If the new condition uses any new attributes, a subquery is required.
+        # However, Aggregation's HAVING statement works fine with aliased attributes.
+        need_subquery = (
+            isinstance(self, Union)
+            or (not isinstance(self, Aggregation) and self.heading.new_attributes)
+            or self._top
+        )
+        if need_subquery:
+            result = self.make_subquery()
+        else:
+            result = copy.copy(self)
+            result._restriction = AndList(
+                self.restriction
+            )  # copy to preserve the original
+        result.restriction.append(new_condition)
+        result.restriction_attributes.update(attributes)
+        return result
+
+    def restrict_in_place(self, restriction):
+        self.__dict__.update(self.restrict(restriction).__dict__)
+
+    def __and__(self, restriction):
+        """
+        Restriction operator e.g. ``q1 & q2``.
+        :return: a restricted copy of the input argument
+        See QueryExpression.restrict for more detail.
+        """
+        return self.restrict(restriction)
+
+    def __xor__(self, restriction):
+        """
+        Permissive restriction operator ignoring compatibility check  e.g. ``q1 ^ q2``.
+        """
+        if inspect.isclass(restriction) and issubclass(restriction, QueryExpression):
+            restriction = restriction()
+        if isinstance(restriction, Not):
+            return self.restrict(Not(PromiscuousOperand(restriction.restriction)))
+        return self.restrict(PromiscuousOperand(restriction))
+
+    def __sub__(self, restriction):
+        """
+        Inverted restriction e.g. ``q1 - q2``.
+        :return: a restricted copy of the input argument
+        See QueryExpression.restrict for more detail.
+        """
+        return self.restrict(Not(restriction))
+
+    def __neg__(self):
+        """
+        Convert between restriction and inverted restriction e.g. ``-q1``.
+        :return: target restriction
+        See QueryExpression.restrict for more detail.
+        """
+        if isinstance(self, Not):
+            return self.restriction
+        return Not(self)
+
+    def __mul__(self, other):
+        """
+        join of query expressions `self` and `other` e.g. ``q1 * q2``.
+        """
+        return self.join(other)
+
+    def __matmul__(self, other):
+        """
+        Permissive join of query expressions `self` and `other` ignoring compatibility check
+            e.g. ``q1 @ q2``.
+        """
+        if inspect.isclass(other) and issubclass(other, QueryExpression):
+            other = other()  # instantiate
+        return self.join(other, semantic_check=False)
+
+    def join(self, other, semantic_check=True, left=False):
+        """
+        create the joined QueryExpression.
+        a * b  is short for A.join(B)
+        a @ b  is short for A.join(B, semantic_check=False)
+        Additionally, left=True will retain the rows of self, effectively performing a left join.
+        """
+        # trigger subqueries if joining on renamed attributes
+        if isinstance(other, U):
+            return other * self
+        if inspect.isclass(other) and issubclass(other, QueryExpression):
+            other = other()  # instantiate
+        if not isinstance(other, QueryExpression):
+            raise DataJointError("The argument of join must be a QueryExpression")
+        if semantic_check:
+            assert_join_compatibility(self, other)
+        join_attributes = set(n for n in self.heading.names if n in other.heading.names)
+        # needs subquery if self's FROM clause has common attributes with other's FROM clause
+        need_subquery1 = need_subquery2 = bool(
+            (set(self.original_heading.names) & set(other.original_heading.names))
+            - join_attributes
+        )
+        # need subquery if any of the join attributes are derived
+        need_subquery1 = (
+            need_subquery1
+            or isinstance(self, Aggregation)
+            or any(n in self.heading.new_attributes for n in join_attributes)
+            or isinstance(self, Union)
+        )
+        need_subquery2 = (
+            need_subquery2
+            or isinstance(other, Aggregation)
+            or any(n in other.heading.new_attributes for n in join_attributes)
+            or isinstance(self, Union)
+        )
+        if need_subquery1:
+            self = self.make_subquery()
+        if need_subquery2:
+            other = other.make_subquery()
+        result = QueryExpression()
+        result._connection = self.connection
+        result._support = self.support + other.support
+        result._left = self._left + [left] + other._left
+        result._heading = self.heading.join(other.heading)
+        result._restriction = AndList(self.restriction)
+        result._restriction.append(other.restriction)
+        result._original_heading = self.original_heading.join(other.original_heading)
+        assert len(result.support) == len(result._left) + 1
+        return result
+
+    def __add__(self, other):
+        """union e.g. ``q1 + q2``."""
+        return Union.create(self, other)
+
+    def proj(self, *attributes, **named_attributes):
+        """
+        Projection operator.
+
+        :param attributes:  attributes to be included in the result. (The primary key is already included).
+        :param named_attributes: new attributes computed or renamed from existing attributes.
+        :return: the projected expression.
+        Primary key attributes cannot be excluded but may be renamed.
+        If the attribute list contains an Ellipsis ..., then all secondary attributes are included too
+        Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present.
+        Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or
+        self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self)
+        self.proj() -- include only primary key
+        self.proj('attr1', 'attr2')  -- include primary key and attributes attr1 and attr2
+        self.proj(..., '-attr1', '-attr2')  -- include all attributes except attr1 and attr2
+        self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1
+        self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup'
+        self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax)
+        from other attributes available before the projection.
+        Each attribute name can only be used once.
+        """
+        named_attributes = {
+            k: translate_attribute(v)[1] for k, v in named_attributes.items()
+        }
+        # new attributes in parentheses are included again with the new name without removing original
+        duplication_pattern = re.compile(
+            rf'^\s*\(\s*(?!{"|".join(CONSTANT_LITERALS)})(?P<name>[a-zA-Z_]\w*)\s*\)\s*$'
+        )
+        # attributes without parentheses renamed
+        rename_pattern = re.compile(
+            rf'^\s*(?!{"|".join(CONSTANT_LITERALS)})(?P<name>[a-zA-Z_]\w*)\s*$'
+        )
+        replicate_map = {
+            k: m.group("name")
+            for k, m in (
+                (k, duplication_pattern.match(v)) for k, v in named_attributes.items()
+            )
+            if m
+        }
+        rename_map = {
+            k: m.group("name")
+            for k, m in (
+                (k, rename_pattern.match(v)) for k, v in named_attributes.items()
+            )
+            if m
+        }
+        compute_map = {
+            k: v
+            for k, v in named_attributes.items()
+            if not duplication_pattern.match(v) and not rename_pattern.match(v)
+        }
+        attributes = set(attributes)
+        # include primary key
+        attributes.update((k for k in self.primary_key if k not in rename_map.values()))
+        # include all secondary attributes with Ellipsis
+        if Ellipsis in attributes:
+            attributes.discard(Ellipsis)
+            attributes.update(
+                (
+                    a
+                    for a in self.heading.secondary_attributes
+                    if a not in attributes and a not in rename_map.values()
+                )
+            )
+        try:
+            raise DataJointError(
+                "%s is not a valid data type for an attribute in .proj"
+                % next(a for a in attributes if not isinstance(a, str))
+            )
+        except StopIteration:
+            pass  # normal case
+        # remove excluded attributes, specified as `-attr'
+        excluded = set(a for a in attributes if a.strip().startswith("-"))
+        attributes.difference_update(excluded)
+        excluded = set(a.lstrip("-").strip() for a in excluded)
+        attributes.difference_update(excluded)
+        try:
+            raise DataJointError(
+                "Cannot exclude primary key attribute %s",
+                next(a for a in excluded if a in self.primary_key),
+            )
+        except StopIteration:
+            pass  # all ok
+        # check that all attributes exist in heading
+        try:
+            raise DataJointError(
+                "Attribute `%s` not found."
+                % next(a for a in attributes if a not in self.heading.names)
+            )
+        except StopIteration:
+            pass  # all ok
+
+        # check that all mentioned names are present in heading
+        mentions = attributes.union(replicate_map.values()).union(rename_map.values())
+        try:
+            raise DataJointError(
+                "Attribute '%s' not found."
+                % next(a for a in mentions if not self.heading.names)
+            )
+        except StopIteration:
+            pass  # all ok
+
+        # check that newly created attributes do not clash with any other selected attributes
+        try:
+            raise DataJointError(
+                "Attribute `%s` already exists"
+                % next(
+                    a
+                    for a in rename_map
+                    if a in attributes.union(compute_map).union(replicate_map)
+                )
+            )
+        except StopIteration:
+            pass  # all ok
+        try:
+            raise DataJointError(
+                "Attribute `%s` already exists"
+                % next(
+                    a
+                    for a in compute_map
+                    if a in attributes.union(rename_map).union(replicate_map)
+                )
+            )
+        except StopIteration:
+            pass  # all ok
+        try:
+            raise DataJointError(
+                "Attribute `%s` already exists"
+                % next(
+                    a
+                    for a in replicate_map
+                    if a in attributes.union(rename_map).union(compute_map)
+                )
+            )
+        except StopIteration:
+            pass  # all ok
+
+        # need a subquery if the projection remaps any remapped attributes
+        used = set(q for v in compute_map.values() for q in extract_column_names(v))
+        used.update(rename_map.values())
+        used.update(replicate_map.values())
+        used.intersection_update(self.heading.names)
+        need_subquery = isinstance(self, Union) or any(
+            self.heading[name].attribute_expression is not None for name in used
+        )
+        if not need_subquery and self.restriction:
+            # need a subquery if the restriction applies to attributes that have been renamed
+            need_subquery = any(
+                name in self.restriction_attributes
+                for name in self.heading.new_attributes
+            )
+
+        result = self.make_subquery() if need_subquery else copy.copy(self)
+        result._original_heading = result.original_heading
+        result._heading = result.heading.select(
+            attributes,
+            rename_map=dict(**rename_map, **replicate_map),
+            compute_map=compute_map,
+        )
+        return result
+
+    def aggr(self, group, *attributes, keep_all_rows=False, **named_attributes):
+        """
+        Aggregation of the type U('attr1','attr2').aggr(group, computation="QueryExpression")
+        has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`.
+
+        :param group:  The query expression to be aggregated.
+        :param keep_all_rows: True=keep all the rows from self. False=keep only rows that match entries in group.
+        :param named_attributes: computations of the form new_attribute="sql expression on attributes of group"
+        :return: The derived query expression
+        """
+        if Ellipsis in attributes:
+            # expand ellipsis to include only attributes from the left table
+            attributes = set(attributes)
+            attributes.discard(Ellipsis)
+            attributes.update(self.heading.secondary_attributes)
+        return Aggregation.create(self, group=group, keep_all_rows=keep_all_rows).proj(
+            *attributes, **named_attributes
+        )
+
+    aggregate = aggr  # alias for aggr
+
+    # ---------- Fetch operators --------------------
+    @property
+    def fetch1(self):
+        return Fetch1(self)
+
+    @property
+    def fetch(self):
+        return Fetch(self)
+
+    def head(self, limit=25, **fetch_kwargs):
+        """
+        shortcut to fetch the first few entries from query expression.
+        Equivalent to fetch(order_by="KEY", limit=25)
+
+        :param limit:  number of entries
+        :param fetch_kwargs: kwargs for fetch
+        :return: query result
+        """
+        return self.fetch(order_by="KEY", limit=limit, **fetch_kwargs)
+
+    def tail(self, limit=25, **fetch_kwargs):
+        """
+        shortcut to fetch the last few entries from query expression.
+        Equivalent to fetch(order_by="KEY DESC", limit=25)[::-1]
+
+        :param limit:  number of entries
+        :param fetch_kwargs: kwargs for fetch
+        :return: query result
+        """
+        return self.fetch(order_by="KEY DESC", limit=limit, **fetch_kwargs)[::-1]
+
+    def __len__(self):
+        """:return: number of elements in the result set e.g. ``len(q1)``."""
+        result = self.make_subquery() if self._top else copy.copy(self)
+        return result.connection.query(
+            "SELECT {select_} FROM {from_}{where}".format(
+                select_=(
+                    "count(*)"
+                    if any(result._left)
+                    else "count(DISTINCT {fields})".format(
+                        fields=result.heading.as_sql(
+                            result.primary_key, include_aliases=False
+                        )
+                    )
+                ),
+                from_=result.from_clause(),
+                where=result.where_clause(),
+            )
+        ).fetchone()[0]
+
+    def __bool__(self):
+        """
+        :return: True if the result is not empty. Equivalent to len(self) > 0 but often
+            faster e.g. ``bool(q1)``.
+        """
+        return bool(
+            self.connection.query(
+                "SELECT EXISTS(SELECT 1 FROM {from_}{where})".format(
+                    from_=self.from_clause(), where=self.where_clause()
+                )
+            ).fetchone()[0]
+        )
+
+    def __contains__(self, item):
+        """
+        returns True if the restriction in item matches any entries in self
+            e.g. ``restriction in q1``.
+
+        :param item: any restriction
+        (item in query_expression) is equivalent to bool(query_expression & item) but may be
+        executed more efficiently.
+        """
+        return bool(self & item)  # May be optimized e.g. using an EXISTS query
+
+    def __iter__(self):
+        """
+        returns an iterator-compatible QueryExpression object e.g. ``iter(q1)``.
+
+        :param self: iterator-compatible QueryExpression object
+        """
+        self._iter_only_key = all(v.in_key for v in self.heading.attributes.values())
+        self._iter_keys = self.fetch("KEY")
+        return self
+
+    def __next__(self):
+        """
+        returns the next record on an iterator-compatible QueryExpression object
+            e.g. ``next(q1)``.
+
+        :param self: A query expression
+        :type self: :class:`QueryExpression`
+        :rtype: dict
+        """
+        try:
+            key = self._iter_keys.pop(0)
+        except AttributeError:
+            # self._iter_keys is missing because __iter__ has not been called.
+            raise TypeError(
+                "A QueryExpression object is not an iterator. "
+                "Use iter(obj) to create an iterator."
+            )
+        except IndexError:
+            raise StopIteration
+        else:
+            if self._iter_only_key:
+                return key
+            else:
+                try:
+                    return (self & key).fetch1()
+                except DataJointError:
+                    # The data may have been deleted since the moment the keys were fetched
+                    # -- move on to next entry.
+                    return next(self)
+
+    def cursor(self, as_dict=False):
+        """
+        See expression.fetch() for input description.
+        :return: query cursor
+        """
+        sql = self.make_sql()
+        logger.debug(sql)
+        return self.connection.query(sql, as_dict=as_dict)
+
+    def __repr__(self):
+        """
+        returns the string representation of a QueryExpression object e.g. ``str(q1)``.
+
+        :param self: A query expression
+        :type self: :class:`QueryExpression`
+        :rtype: str
+        """
+        return (
+            super().__repr__()
+            if config["loglevel"].lower() == "debug"
+            else self.preview()
+        )
+
+    def preview(self, limit=None, width=None):
+        """:return: a string of preview of the contents of the query."""
+        return preview(self, limit, width)
+
+    def _repr_html_(self):
+        """:return: HTML to display table in Jupyter notebook."""
+        return repr_html(self)
+

+ + + +

+ + + + + + + +

+ + + +

+ `connection` + + + `property` + + +¶

+ + +

+ +

a dj.Connection object

+ +

+ + + + + + +

+ + + +

+ `support` + + + `property` + + +¶

+ + +

+ +

A list of table names or subqueries to from the FROM clause

+ +

+ + + + + + +

+ + + +

+ `heading` + + + `property` + + +¶

+ + +

+ +

a dj.Heading object, reflects the effects of the projection operator .proj

+ +

+ + + + + + +

+ + + +

+ `original_heading` + + + `property` + + +¶

+ + +

+ +

a dj.Heading object reflecting the attributes before projection

+ +

+ + + + + + +

+ + + +

+ `restriction` + + + `property` + + +¶

+ + +

+ +

a AndList object of restrictions applied to input to produce the result

+ +

+ + + + + + +

+ + + +

+ `restriction_attributes` + + + `property` + + +¶

+ + +

+ +

the set of attribute names invoked in the WHERE clause

+ +

+ + + + + + +

+ + +

+ `make_sql(fields=None)` + +¶

+ + +

+ +

Make the SQL SELECT statement.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `fields` +	+	+ + used to explicitly set the select attributes + +	+ `None` +

+ + +

Source code in datajoint/expression.py

def make_sql(self, fields=None):
+    """
+    Make the SQL SELECT statement.
+
+    :param fields: used to explicitly set the select attributes
+    """
+    return "SELECT {distinct}{fields} FROM {from_}{where}{sorting}".format(
+        distinct="DISTINCT " if self._distinct else "",
+        fields=self.heading.as_sql(fields or self.heading.names),
+        from_=self.from_clause(),
+        where=self.where_clause(),
+        sorting=self.sorting_clauses(),
+    )
+

+ +

+ + + + + + +

+ + +

+ `make_subquery()` + +¶

+ + +

+ +

create a new SELECT statement where self is the FROM clause

+ + +

Source code in datajoint/expression.py

def make_subquery(self):
+    """create a new SELECT statement where self is the FROM clause"""
+    result = QueryExpression()
+    result._connection = self.connection
+    result._support = [self]
+    result._heading = self.heading.make_subquery_heading()
+    return result
+

+ +

+ + + + + + +

+ + +

+ `restrict(restriction)` + +¶

+ + +

+ +

Produces a new expression with the new restriction applied. +rel.restrict(restriction) is equivalent to rel & restriction. +rel.restrict(Not(restriction)) is equivalent to rel - restriction +The primary key of the result is unaffected. +Successive restrictions are combined as logical AND: r & a & b is equivalent to r & AndList((a, b)) +Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists +(logical disjunction of conditions) +Inverse restriction is accomplished by either using the subtraction operator or the Not class.

The expressions in each row equivalent:

rel & True rel +rel & False the empty entity set +rel & 'TRUE' rel +rel & 'FALSE' the empty entity set +rel - cond rel & Not(cond) +rel - 'TRUE' rel & False +rel - 'FALSE' rel +rel & AndList((cond1,cond2)) rel & cond1 & cond2 +rel & AndList() rel +rel & [cond1, cond2] rel & OrList((cond1, cond2)) +rel & [] rel & False +rel & None rel & False +rel & any_empty_entity_set rel & False +rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)] +rel - [cond1, cond2] rel & Not(cond1) & Not(cond2) +rel - AndList() rel & False +rel - [] rel +rel - None rel +rel - any_empty_entity_set rel

When arg is another QueryExpression, the restriction rel & arg restricts rel to elements that match at least +one element in arg (hence arg is treated as an OrList). +Conversely, rel - arg restricts rel to elements that do not match any elements in arg. +Two elements match when their common attributes have equal values or when they have no common attributes. +All shared attributes must be in the primary key of either rel or arg or both or an error will be raised.

QueryExpression.restrict is the only access point that modifies restrictions. All other operators must +ultimately call restrict()

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `restriction` +	+	+ + a sequence or an array (treated as OR list), another QueryExpression, an SQL condition +string, or an AndList. + +	+ required +

+ + +

Source code in datajoint/expression.py

def restrict(self, restriction):
+    """
+    Produces a new expression with the new restriction applied.
+    rel.restrict(restriction)  is equivalent to  rel & restriction.
+    rel.restrict(Not(restriction))  is equivalent to  rel - restriction
+    The primary key of the result is unaffected.
+    Successive restrictions are combined as logical AND:   r & a & b  is equivalent to r & AndList((a, b))
+    Any QueryExpression, collection, or sequence other than an AndList are treated as OrLists
+    (logical disjunction of conditions)
+    Inverse restriction is accomplished by either using the subtraction operator or the Not class.
+
+    The expressions in each row equivalent:
+
+    rel & True                          rel
+    rel & False                         the empty entity set
+    rel & 'TRUE'                        rel
+    rel & 'FALSE'                       the empty entity set
+    rel - cond                          rel & Not(cond)
+    rel - 'TRUE'                        rel & False
+    rel - 'FALSE'                       rel
+    rel & AndList((cond1,cond2))        rel & cond1 & cond2
+    rel & AndList()                     rel
+    rel & [cond1, cond2]                rel & OrList((cond1, cond2))
+    rel & []                            rel & False
+    rel & None                          rel & False
+    rel & any_empty_entity_set          rel & False
+    rel - AndList((cond1,cond2))        rel & [Not(cond1), Not(cond2)]
+    rel - [cond1, cond2]                rel & Not(cond1) & Not(cond2)
+    rel - AndList()                     rel & False
+    rel - []                            rel
+    rel - None                          rel
+    rel - any_empty_entity_set          rel
+
+    When arg is another QueryExpression, the restriction  rel & arg  restricts rel to elements that match at least
+    one element in arg (hence arg is treated as an OrList).
+    Conversely,  rel - arg  restricts rel to elements that do not match any elements in arg.
+    Two elements match when their common attributes have equal values or when they have no common attributes.
+    All shared attributes must be in the primary key of either rel or arg or both or an error will be raised.
+
+    QueryExpression.restrict is the only access point that modifies restrictions. All other operators must
+    ultimately call restrict()
+
+    :param restriction: a sequence or an array (treated as OR list), another QueryExpression, an SQL condition
+    string, or an AndList.
+    """
+    attributes = set()
+    if isinstance(restriction, Top):
+        result = (
+            self.make_subquery()
+            if self._top and not self._top.__eq__(restriction)
+            else copy.copy(self)
+        )  # make subquery to avoid overwriting existing Top
+        result._top = restriction
+        return result
+    new_condition = make_condition(self, restriction, attributes)
+    if new_condition is True:
+        return self  # restriction has no effect, return the same object
+    # check that all attributes in condition are present in the query
+    try:
+        raise DataJointError(
+            "Attribute `%s` is not found in query."
+            % next(attr for attr in attributes if attr not in self.heading.names)
+        )
+    except StopIteration:
+        pass  # all ok
+    # If the new condition uses any new attributes, a subquery is required.
+    # However, Aggregation's HAVING statement works fine with aliased attributes.
+    need_subquery = (
+        isinstance(self, Union)
+        or (not isinstance(self, Aggregation) and self.heading.new_attributes)
+        or self._top
+    )
+    if need_subquery:
+        result = self.make_subquery()
+    else:
+        result = copy.copy(self)
+        result._restriction = AndList(
+            self.restriction
+        )  # copy to preserve the original
+    result.restriction.append(new_condition)
+    result.restriction_attributes.update(attributes)
+    return result
+

+ +

+ + + + + + +

+ + +

+ `join(other, semantic_check=True, left=False)` + +¶

+ + +

+ +

create the joined QueryExpression. +a * b is short for A.join(B) +a @ b is short for A.join(B, semantic_check=False) +Additionally, left=True will retain the rows of self, effectively performing a left join.

+ + +

Source code in datajoint/expression.py

def join(self, other, semantic_check=True, left=False):
+    """
+    create the joined QueryExpression.
+    a * b  is short for A.join(B)
+    a @ b  is short for A.join(B, semantic_check=False)
+    Additionally, left=True will retain the rows of self, effectively performing a left join.
+    """
+    # trigger subqueries if joining on renamed attributes
+    if isinstance(other, U):
+        return other * self
+    if inspect.isclass(other) and issubclass(other, QueryExpression):
+        other = other()  # instantiate
+    if not isinstance(other, QueryExpression):
+        raise DataJointError("The argument of join must be a QueryExpression")
+    if semantic_check:
+        assert_join_compatibility(self, other)
+    join_attributes = set(n for n in self.heading.names if n in other.heading.names)
+    # needs subquery if self's FROM clause has common attributes with other's FROM clause
+    need_subquery1 = need_subquery2 = bool(
+        (set(self.original_heading.names) & set(other.original_heading.names))
+        - join_attributes
+    )
+    # need subquery if any of the join attributes are derived
+    need_subquery1 = (
+        need_subquery1
+        or isinstance(self, Aggregation)
+        or any(n in self.heading.new_attributes for n in join_attributes)
+        or isinstance(self, Union)
+    )
+    need_subquery2 = (
+        need_subquery2
+        or isinstance(other, Aggregation)
+        or any(n in other.heading.new_attributes for n in join_attributes)
+        or isinstance(self, Union)
+    )
+    if need_subquery1:
+        self = self.make_subquery()
+    if need_subquery2:
+        other = other.make_subquery()
+    result = QueryExpression()
+    result._connection = self.connection
+    result._support = self.support + other.support
+    result._left = self._left + [left] + other._left
+    result._heading = self.heading.join(other.heading)
+    result._restriction = AndList(self.restriction)
+    result._restriction.append(other.restriction)
+    result._original_heading = self.original_heading.join(other.original_heading)
+    assert len(result.support) == len(result._left) + 1
+    return result
+

+ +

+ + + + + + +

+ + +

+ `proj(*attributes, **named_attributes)` + +¶

+ + +

+ +

Projection operator.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `attributes` +	+	+ + attributes to be included in the result. (The primary key is already included). + +	+ `()` +
+ `named_attributes` +	+	+ + new attributes computed or renamed from existing attributes. + +	+ `{}` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type

Description

the projected expression. +Primary key attributes cannot be excluded but may be renamed. +If the attribute list contains an Ellipsis ..., then all secondary attributes are included too +Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present. +Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or +self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self) +self.proj() -- include only primary key +self.proj('attr1', 'attr2') -- include primary key and attributes attr1 and attr2 +self.proj(..., '-attr1', '-attr2') -- include all attributes except attr1 and attr2 +self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1 +self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup' +self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax) +from other attributes available before the projection. +Each attribute name can only be used once.

+ + +

Source code in datajoint/expression.py

def proj(self, *attributes, **named_attributes):
+    """
+    Projection operator.
+
+    :param attributes:  attributes to be included in the result. (The primary key is already included).
+    :param named_attributes: new attributes computed or renamed from existing attributes.
+    :return: the projected expression.
+    Primary key attributes cannot be excluded but may be renamed.
+    If the attribute list contains an Ellipsis ..., then all secondary attributes are included too
+    Prefixing an attribute name with a dash '-attr' removes the attribute from the list if present.
+    Keyword arguments can be used to rename attributes as in name='attr', duplicate them as in name='(attr)', or
+    self.proj(...) or self.proj(Ellipsis) -- include all attributes (return self)
+    self.proj() -- include only primary key
+    self.proj('attr1', 'attr2')  -- include primary key and attributes attr1 and attr2
+    self.proj(..., '-attr1', '-attr2')  -- include all attributes except attr1 and attr2
+    self.proj(name1='attr1') -- include primary key and 'attr1' renamed as name1
+    self.proj('attr1', dup='(attr1)') -- include primary key and attribute attr1 twice, with the duplicate 'dup'
+    self.proj(k='abs(attr1)') adds the new attribute k with the value computed as an expression (SQL syntax)
+    from other attributes available before the projection.
+    Each attribute name can only be used once.
+    """
+    named_attributes = {
+        k: translate_attribute(v)[1] for k, v in named_attributes.items()
+    }
+    # new attributes in parentheses are included again with the new name without removing original
+    duplication_pattern = re.compile(
+        rf'^\s*\(\s*(?!{"|".join(CONSTANT_LITERALS)})(?P<name>[a-zA-Z_]\w*)\s*\)\s*$'
+    )
+    # attributes without parentheses renamed
+    rename_pattern = re.compile(
+        rf'^\s*(?!{"|".join(CONSTANT_LITERALS)})(?P<name>[a-zA-Z_]\w*)\s*$'
+    )
+    replicate_map = {
+        k: m.group("name")
+        for k, m in (
+            (k, duplication_pattern.match(v)) for k, v in named_attributes.items()
+        )
+        if m
+    }
+    rename_map = {
+        k: m.group("name")
+        for k, m in (
+            (k, rename_pattern.match(v)) for k, v in named_attributes.items()
+        )
+        if m
+    }
+    compute_map = {
+        k: v
+        for k, v in named_attributes.items()
+        if not duplication_pattern.match(v) and not rename_pattern.match(v)
+    }
+    attributes = set(attributes)
+    # include primary key
+    attributes.update((k for k in self.primary_key if k not in rename_map.values()))
+    # include all secondary attributes with Ellipsis
+    if Ellipsis in attributes:
+        attributes.discard(Ellipsis)
+        attributes.update(
+            (
+                a
+                for a in self.heading.secondary_attributes
+                if a not in attributes and a not in rename_map.values()
+            )
+        )
+    try:
+        raise DataJointError(
+            "%s is not a valid data type for an attribute in .proj"
+            % next(a for a in attributes if not isinstance(a, str))
+        )
+    except StopIteration:
+        pass  # normal case
+    # remove excluded attributes, specified as `-attr'
+    excluded = set(a for a in attributes if a.strip().startswith("-"))
+    attributes.difference_update(excluded)
+    excluded = set(a.lstrip("-").strip() for a in excluded)
+    attributes.difference_update(excluded)
+    try:
+        raise DataJointError(
+            "Cannot exclude primary key attribute %s",
+            next(a for a in excluded if a in self.primary_key),
+        )
+    except StopIteration:
+        pass  # all ok
+    # check that all attributes exist in heading
+    try:
+        raise DataJointError(
+            "Attribute `%s` not found."
+            % next(a for a in attributes if a not in self.heading.names)
+        )
+    except StopIteration:
+        pass  # all ok
+
+    # check that all mentioned names are present in heading
+    mentions = attributes.union(replicate_map.values()).union(rename_map.values())
+    try:
+        raise DataJointError(
+            "Attribute '%s' not found."
+            % next(a for a in mentions if not self.heading.names)
+        )
+    except StopIteration:
+        pass  # all ok
+
+    # check that newly created attributes do not clash with any other selected attributes
+    try:
+        raise DataJointError(
+            "Attribute `%s` already exists"
+            % next(
+                a
+                for a in rename_map
+                if a in attributes.union(compute_map).union(replicate_map)
+            )
+        )
+    except StopIteration:
+        pass  # all ok
+    try:
+        raise DataJointError(
+            "Attribute `%s` already exists"
+            % next(
+                a
+                for a in compute_map
+                if a in attributes.union(rename_map).union(replicate_map)
+            )
+        )
+    except StopIteration:
+        pass  # all ok
+    try:
+        raise DataJointError(
+            "Attribute `%s` already exists"
+            % next(
+                a
+                for a in replicate_map
+                if a in attributes.union(rename_map).union(compute_map)
+            )
+        )
+    except StopIteration:
+        pass  # all ok
+
+    # need a subquery if the projection remaps any remapped attributes
+    used = set(q for v in compute_map.values() for q in extract_column_names(v))
+    used.update(rename_map.values())
+    used.update(replicate_map.values())
+    used.intersection_update(self.heading.names)
+    need_subquery = isinstance(self, Union) or any(
+        self.heading[name].attribute_expression is not None for name in used
+    )
+    if not need_subquery and self.restriction:
+        # need a subquery if the restriction applies to attributes that have been renamed
+        need_subquery = any(
+            name in self.restriction_attributes
+            for name in self.heading.new_attributes
+        )
+
+    result = self.make_subquery() if need_subquery else copy.copy(self)
+    result._original_heading = result.original_heading
+    result._heading = result.heading.select(
+        attributes,
+        rename_map=dict(**rename_map, **replicate_map),
+        compute_map=compute_map,
+    )
+    return result
+

+ +

+ + + + + + +

+ + +

+ `aggr(group, *attributes, keep_all_rows=False, **named_attributes)` + +¶

+ + +

+ +

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `group` +	+	+ + The query expression to be aggregated. + +	+ required +
+ `keep_all_rows` +	+	+ + True=keep all the rows from self. False=keep only rows that match entries in group. + +	+ `False` +
+ `named_attributes` +	+	+ + computations of the form new_attribute="sql expression on attributes of group" + +	+ `{}` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + The derived query expression + +

+ + +

Source code in datajoint/expression.py

def aggr(self, group, *attributes, keep_all_rows=False, **named_attributes):
+    """
+    Aggregation of the type U('attr1','attr2').aggr(group, computation="QueryExpression")
+    has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`.
+
+    :param group:  The query expression to be aggregated.
+    :param keep_all_rows: True=keep all the rows from self. False=keep only rows that match entries in group.
+    :param named_attributes: computations of the form new_attribute="sql expression on attributes of group"
+    :return: The derived query expression
+    """
+    if Ellipsis in attributes:
+        # expand ellipsis to include only attributes from the left table
+        attributes = set(attributes)
+        attributes.discard(Ellipsis)
+        attributes.update(self.heading.secondary_attributes)
+    return Aggregation.create(self, group=group, keep_all_rows=keep_all_rows).proj(
+        *attributes, **named_attributes
+    )
+

+ +

+ + + + + + +

+ + +

+ `head(limit=25, **fetch_kwargs)` + +¶

+ + +

+ +

shortcut to fetch the first few entries from query expression. +Equivalent to fetch(order_by="KEY", limit=25)

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `limit` +	+	+ + number of entries + +	+ `25` +
+ `fetch_kwargs` +	+	+ + kwargs for fetch + +	+ `{}` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + query result + +

+ + +

Source code in datajoint/expression.py

def head(self, limit=25, **fetch_kwargs):
+    """
+    shortcut to fetch the first few entries from query expression.
+    Equivalent to fetch(order_by="KEY", limit=25)
+
+    :param limit:  number of entries
+    :param fetch_kwargs: kwargs for fetch
+    :return: query result
+    """
+    return self.fetch(order_by="KEY", limit=limit, **fetch_kwargs)
+

+ +

+ + + + + + +

+ + +

+ `tail(limit=25, **fetch_kwargs)` + +¶

+ + +

+ +

shortcut to fetch the last few entries from query expression. +Equivalent to fetch(order_by="KEY DESC", limit=25)[::-1]

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `limit` +	+	+ + number of entries + +	+ `25` +
+ `fetch_kwargs` +	+	+ + kwargs for fetch + +	+ `{}` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + query result + +

+ + +

Source code in datajoint/expression.py

def tail(self, limit=25, **fetch_kwargs):
+    """
+    shortcut to fetch the last few entries from query expression.
+    Equivalent to fetch(order_by="KEY DESC", limit=25)[::-1]
+
+    :param limit:  number of entries
+    :param fetch_kwargs: kwargs for fetch
+    :return: query result
+    """
+    return self.fetch(order_by="KEY DESC", limit=limit, **fetch_kwargs)[::-1]
+

+ +

+ + + + + + +

+ + +

+ `cursor(as_dict=False)` + +¶

+ + +

+ +

See expression.fetch() for input description.

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + query cursor + +

+ + +

Source code in datajoint/expression.py

def cursor(self, as_dict=False):
+    """
+    See expression.fetch() for input description.
+    :return: query cursor
+    """
+    sql = self.make_sql()
+    logger.debug(sql)
+    return self.connection.query(sql, as_dict=as_dict)
+

+ +

+ + + + + + +

+ + +

+ `preview(limit=None, width=None)` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a string of preview of the contents of the query. + +

+ + +

Source code in datajoint/expression.py

def preview(self, limit=None, width=None):
+    """:return: a string of preview of the contents of the query."""
+    return preview(self, limit, width)
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `Aggregation` + + +¶

+ + +

+ Bases: QueryExpression

+ + + +

Aggregation.create(arg, group, comp1='calc1', ..., compn='calcn') yields an entity set +with primary key from arg. +The computed arguments comp1, ..., compn use aggregation calculations on the attributes of +group or simple projections and calculations on the attributes of arg. +Aggregation is used QueryExpression.aggr and U.aggr. +Aggregation is a private class in DataJoint, not exposed to users.

+ + + + + + + + +

Source code in datajoint/expression.py

class Aggregation(QueryExpression):
+    """
+    Aggregation.create(arg, group, comp1='calc1', ..., compn='calcn')  yields an entity set
+    with primary key from arg.
+    The computed arguments comp1, ..., compn use aggregation calculations on the attributes of
+    group or simple projections and calculations on the attributes of arg.
+    Aggregation is used QueryExpression.aggr and U.aggr.
+    Aggregation is a private class in DataJoint, not exposed to users.
+    """
+
+    _left_restrict = None  # the pre-GROUP BY conditions for the WHERE clause
+    _subquery_alias_count = count()
+
+    @classmethod
+    def create(cls, arg, group, keep_all_rows=False):
+        if inspect.isclass(group) and issubclass(group, QueryExpression):
+            group = group()  # instantiate if a class
+        assert isinstance(group, QueryExpression)
+        if keep_all_rows and len(group.support) > 1 or group.heading.new_attributes:
+            group = group.make_subquery()  # subquery if left joining a join
+        join = arg.join(group, left=keep_all_rows)  # reuse the join logic
+        result = cls()
+        result._connection = join.connection
+        result._heading = join.heading.set_primary_key(
+            arg.primary_key
+        )  # use left operand's primary key
+        result._support = join.support
+        result._left = join._left
+        result._left_restrict = join.restriction  # WHERE clause applied before GROUP BY
+        result._grouping_attributes = result.primary_key
+
+        return result
+
+    def where_clause(self):
+        return (
+            ""
+            if not self._left_restrict
+            else " WHERE (%s)" % ")AND(".join(str(s) for s in self._left_restrict)
+        )
+
+    def make_sql(self, fields=None):
+        fields = self.heading.as_sql(fields or self.heading.names)
+        assert self._grouping_attributes or not self.restriction
+        distinct = set(self.heading.names) == set(self.primary_key)
+        return (
+            "SELECT {distinct}{fields} FROM {from_}{where}{group_by}{sorting}".format(
+                distinct="DISTINCT " if distinct else "",
+                fields=fields,
+                from_=self.from_clause(),
+                where=self.where_clause(),
+                group_by=(
+                    ""
+                    if not self.primary_key
+                    else (
+                        " GROUP BY `%s`" % "`,`".join(self._grouping_attributes)
+                        + (
+                            ""
+                            if not self.restriction
+                            else " HAVING (%s)" % ")AND(".join(self.restriction)
+                        )
+                    )
+                ),
+                sorting=self.sorting_clauses(),
+            )
+        )
+
+    def __len__(self):
+        return self.connection.query(
+            "SELECT count(1) FROM ({subquery}) `${alias:x}`".format(
+                subquery=self.make_sql(), alias=next(self._subquery_alias_count)
+            )
+        ).fetchone()[0]
+
+    def __bool__(self):
+        return bool(
+            self.connection.query("SELECT EXISTS({sql})".format(sql=self.make_sql()))
+        )
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Union` + + +¶

+ + +

+ Bases: QueryExpression

+ + + +

Union is the private DataJoint class that implements the union operator.

+ + + + + + + + +

Source code in datajoint/expression.py

class Union(QueryExpression):
+    """
+    Union is the private DataJoint class that implements the union operator.
+    """
+
+    __count = count()
+
+    @classmethod
+    def create(cls, arg1, arg2):
+        if inspect.isclass(arg2) and issubclass(arg2, QueryExpression):
+            arg2 = arg2()  # instantiate if a class
+        if not isinstance(arg2, QueryExpression):
+            raise DataJointError(
+                "A QueryExpression can only be unioned with another QueryExpression"
+            )
+        if arg1.connection != arg2.connection:
+            raise DataJointError(
+                "Cannot operate on QueryExpressions originating from different connections."
+            )
+        if set(arg1.primary_key) != set(arg2.primary_key):
+            raise DataJointError(
+                "The operands of a union must share the same primary key."
+            )
+        if set(arg1.heading.secondary_attributes) & set(
+            arg2.heading.secondary_attributes
+        ):
+            raise DataJointError(
+                "The operands of a union must not share any secondary attributes."
+            )
+        result = cls()
+        result._connection = arg1.connection
+        result._heading = arg1.heading.join(arg2.heading)
+        result._support = [arg1, arg2]
+        return result
+
+    def make_sql(self):
+        arg1, arg2 = self._support
+        if (
+            not arg1.heading.secondary_attributes
+            and not arg2.heading.secondary_attributes
+        ):
+            # no secondary attributes: use UNION DISTINCT
+            fields = arg1.primary_key
+            return "SELECT * FROM (({sql1}) UNION ({sql2})) as `_u{alias}{sorting}`".format(
+                sql1=(
+                    arg1.make_sql()
+                    if isinstance(arg1, Union)
+                    else arg1.make_sql(fields)
+                ),
+                sql2=(
+                    arg2.make_sql()
+                    if isinstance(arg2, Union)
+                    else arg2.make_sql(fields)
+                ),
+                alias=next(self.__count),
+                sorting=self.sorting_clauses(),
+            )
+        # with secondary attributes, use union of left join with antijoin
+        fields = self.heading.names
+        sql1 = arg1.join(arg2, left=True).make_sql(fields)
+        sql2 = (
+            (arg2 - arg1)
+            .proj(..., **{k: "NULL" for k in arg1.heading.secondary_attributes})
+            .make_sql(fields)
+        )
+        return "({sql1})  UNION ({sql2})".format(sql1=sql1, sql2=sql2)
+
+    def from_clause(self):
+        """The union does not use a FROM clause"""
+        assert False
+
+    def where_clause(self):
+        """The union does not use a WHERE clause"""
+        assert False
+
+    def __len__(self):
+        return self.connection.query(
+            "SELECT count(1) FROM ({subquery}) `${alias:x}`".format(
+                subquery=self.make_sql(),
+                alias=next(QueryExpression._subquery_alias_count),
+            )
+        ).fetchone()[0]
+
+    def __bool__(self):
+        return bool(
+            self.connection.query("SELECT EXISTS({sql})".format(sql=self.make_sql()))
+        )
+

+ + + +

+ + + + + + + +

+ + +

+ `from_clause()` + +¶

+ + +

+ +

The union does not use a FROM clause

+ + +

Source code in datajoint/expression.py

def from_clause(self):
+    """The union does not use a FROM clause"""
+    assert False
+

+ +

+ + + + + + +

+ + +

+ `where_clause()` + +¶

+ + +

+ +

The union does not use a WHERE clause

+ + +

Source code in datajoint/expression.py

def where_clause(self):
+    """The union does not use a WHERE clause"""
+    assert False
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `U` + + +¶

+ + +

+ + + +

Restriction:

dj.U can be used to enumerate unique combinations of values of attributes from other expressions.

The following expression yields all unique combinations of contrast and brightness found in the stimulus set:

+
+
+
dj.U('contrast', 'brightness') & stimulus
+
+
+

Aggregation:

In aggregation, dj.U is used for summary calculation over an entire set:

The following expression yields one element with one attribute s containing the total number of elements in +query expression expr:

+
+
+
dj.U().aggr(expr, n='count(*)')
+
+
+

The following expressions both yield one element containing the number n of distinct values of attribute attr in +query expression expr.

+
+
+
dj.U().aggr(expr, n='count(distinct attr)') +dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)')
+
+
+

The following expression yields one element and one attribute s containing the sum of values of attribute attr +over entire result set of expression expr:

+
+
+
dj.U().aggr(expr, s='sum(attr)')
+
+
+

The following expression yields the set of all unique combinations of attributes attr1, attr2 and the number of +their occurrences in the result set of query expression expr.

+
+
+
dj.U(attr1,attr2).aggr(expr, n='count(*)')
+
+
+

Joins:

+ + + + + + + + +

Source code in datajoint/expression.py

class U:
+    """
+    dj.U objects are the universal sets representing all possible values of their attributes.
+    dj.U objects cannot be queried on their own but are useful for forming some queries.
+    dj.U('attr1', ..., 'attrn') represents the universal set with the primary key attributes attr1 ... attrn.
+    The universal set is the set of all possible combinations of values of the attributes.
+    Without any attributes, dj.U() represents the set with one element that has no attributes.
+
+    Restriction:
+
+    dj.U can be used to enumerate unique combinations of values of attributes from other expressions.
+
+    The following expression yields all unique combinations of contrast and brightness found in the `stimulus` set:
+
+    >>> dj.U('contrast', 'brightness') & stimulus
+
+    Aggregation:
+
+    In aggregation, dj.U is used for summary calculation over an entire set:
+
+    The following expression yields one element with one attribute `s` containing the total number of elements in
+    query expression `expr`:
+
+    >>> dj.U().aggr(expr, n='count(*)')
+
+    The following expressions both yield one element containing the number `n` of distinct values of attribute `attr` in
+    query expression `expr`.
+
+    >>> dj.U().aggr(expr, n='count(distinct attr)')
+    >>> dj.U().aggr(dj.U('attr').aggr(expr), 'n=count(*)')
+
+    The following expression yields one element and one attribute `s` containing the sum of values of attribute `attr`
+    over entire result set of expression `expr`:
+
+    >>> dj.U().aggr(expr, s='sum(attr)')
+
+    The following expression yields the set of all unique combinations of attributes `attr1`, `attr2` and the number of
+    their occurrences in the result set of query expression `expr`.
+
+    >>> dj.U(attr1,attr2).aggr(expr, n='count(*)')
+
+    Joins:
+
+    If expression `expr` has attributes 'attr1' and 'attr2', then expr * dj.U('attr1','attr2') yields the same result
+    as `expr` but `attr1` and `attr2` are promoted to the the primary key.  This is useful for producing a join on
+    non-primary key attributes.
+    For example, if `attr` is in both expr1 and expr2 but not in their primary keys, then expr1 * expr2 will throw
+    an error because in most cases, it does not make sense to join on non-primary key attributes and users must first
+    rename `attr` in one of the operands.  The expression dj.U('attr') * rel1 * rel2 overrides this constraint.
+    """
+
+    def __init__(self, *primary_key):
+        self._primary_key = primary_key
+
+    @property
+    def primary_key(self):
+        return self._primary_key
+
+    def __and__(self, other):
+        if inspect.isclass(other) and issubclass(other, QueryExpression):
+            other = other()  # instantiate if a class
+        if not isinstance(other, QueryExpression):
+            raise DataJointError("Set U can only be restricted with a QueryExpression.")
+        result = copy.copy(other)
+        result._distinct = True
+        result._heading = result.heading.set_primary_key(self.primary_key)
+        result = result.proj()
+        return result
+
+    def join(self, other, left=False):
+        """
+        Joining U with a query expression has the effect of promoting the attributes of U to
+        the primary key of the other query expression.
+
+        :param other: the other query expression to join with.
+        :param left: ignored. dj.U always acts as if left=False
+        :return: a copy of the other query expression with the primary key extended.
+        """
+        if inspect.isclass(other) and issubclass(other, QueryExpression):
+            other = other()  # instantiate if a class
+        if not isinstance(other, QueryExpression):
+            raise DataJointError("Set U can only be joined with a QueryExpression.")
+        try:
+            raise DataJointError(
+                "Attribute `%s` not found"
+                % next(k for k in self.primary_key if k not in other.heading.names)
+            )
+        except StopIteration:
+            pass  # all ok
+        result = copy.copy(other)
+        result._heading = result.heading.set_primary_key(
+            other.primary_key
+            + [k for k in self.primary_key if k not in other.primary_key]
+        )
+        return result
+
+    def __mul__(self, other):
+        """shorthand for join"""
+        return self.join(other)
+
+    def aggr(self, group, **named_attributes):
+        """
+        Aggregation of the type U('attr1','attr2').aggr(group, computation="QueryExpression")
+        has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`.
+
+        :param group:  The query expression to be aggregated.
+        :param named_attributes: computations of the form new_attribute="sql expression on attributes of group"
+        :return: The derived query expression
+        """
+        if named_attributes.get("keep_all_rows", False):
+            raise DataJointError(
+                "Cannot set keep_all_rows=True when aggregating on a universal set."
+            )
+        return Aggregation.create(self, group=group, keep_all_rows=False).proj(
+            **named_attributes
+        )
+
+    aggregate = aggr  # alias for aggr
+

+ + + +

+ + + + + + + +

+ + +

+ `join(other, left=False)` + +¶

+ + +

+ +

Joining U with a query expression has the effect of promoting the attributes of U to +the primary key of the other query expression.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `other` +	+	+ + the other query expression to join with. + +	+ required +
+ `left` +	+	+ + ignored. dj.U always acts as if left=False + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a copy of the other query expression with the primary key extended. + +

+ + +

Source code in datajoint/expression.py

def join(self, other, left=False):
+    """
+    Joining U with a query expression has the effect of promoting the attributes of U to
+    the primary key of the other query expression.
+
+    :param other: the other query expression to join with.
+    :param left: ignored. dj.U always acts as if left=False
+    :return: a copy of the other query expression with the primary key extended.
+    """
+    if inspect.isclass(other) and issubclass(other, QueryExpression):
+        other = other()  # instantiate if a class
+    if not isinstance(other, QueryExpression):
+        raise DataJointError("Set U can only be joined with a QueryExpression.")
+    try:
+        raise DataJointError(
+            "Attribute `%s` not found"
+            % next(k for k in self.primary_key if k not in other.heading.names)
+        )
+    except StopIteration:
+        pass  # all ok
+    result = copy.copy(other)
+    result._heading = result.heading.set_primary_key(
+        other.primary_key
+        + [k for k in self.primary_key if k not in other.primary_key]
+    )
+    return result
+

+ +

+ + + + + + +

+ + +

+ `aggr(group, **named_attributes)` + +¶

+ + +

+ +

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `group` +	+	+ + The query expression to be aggregated. + +	+ required +
+ `named_attributes` +	+	+ + computations of the form new_attribute="sql expression on attributes of group" + +	+ `{}` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + The derived query expression + +

+ + +

Source code in datajoint/expression.py

def aggr(self, group, **named_attributes):
+    """
+    Aggregation of the type U('attr1','attr2').aggr(group, computation="QueryExpression")
+    has the primary key ('attr1','attr2') and performs aggregation computations for all matching elements of `group`.
+
+    :param group:  The query expression to be aggregated.
+    :param named_attributes: computations of the form new_attribute="sql expression on attributes of group"
+    :return: The derived query expression
+    """
+    if named_attributes.get("keep_all_rows", False):
+        raise DataJointError(
+            "Cannot set keep_all_rows=True when aggregating on a universal set."
+        )
+    return Aggregation.create(self, group=group, keep_all_rows=False).proj(
+        **named_attributes
+    )
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/external/index.html b/0.14/api/datajoint/external/index.html new file mode 100644 index 000000000..2bae20d9c --- /dev/null +++ b/0.14/api/datajoint/external/index.html @@ -0,0 +1,6200 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + external.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + external.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

external.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + +

+ `subfold(name, folds)` + +¶

+ + +

+ +

subfolding for external storage: e.g. subfold('aBCdefg', (2, 3)) --> ['ab','cde']

+ + +

Source code in datajoint/external.py

25
+26
+27
+28
+29
+30
+31
+32
+33
def subfold(name, folds):
+    """
+    subfolding for external storage: e.g.  subfold('aBCdefg', (2, 3))  -->  ['ab','cde']
+    """
+    return (
+        (name[: folds[0]].lower(),) + subfold(name[folds[0] :], folds[1:])
+        if folds
+        else ()
+    )
+

+ +

+ + + + + + +

+ + + +

+ `ExternalTable` + + +¶

+ + +

+ Bases: Table

+ + + +

The table tracking externally stored objects. +Declare as ExternalTable(connection, database)

+ + + + + + + + +

Source code in datajoint/external.py

class ExternalTable(Table):
+    """
+    The table tracking externally stored objects.
+    Declare as ExternalTable(connection, database)
+    """
+
+    def __init__(self, connection, store, database):
+        self.store = store
+        self.spec = config.get_store_spec(store)
+        self._s3 = None
+        self.database = database
+        self._connection = connection
+        self._heading = Heading(
+            table_info=dict(
+                conn=connection,
+                database=database,
+                table_name=self.table_name,
+                context=None,
+            )
+        )
+        self._support = [self.full_table_name]
+        if not self.is_declared:
+            self.declare()
+        self._s3 = None
+        if self.spec["protocol"] == "file" and not Path(self.spec["location"]).is_dir():
+            raise FileNotFoundError(
+                "Inaccessible local directory %s" % self.spec["location"]
+            ) from None
+
+    @property
+    def definition(self):
+        return """
+        # external storage tracking
+        hash  : uuid    #  hash of contents (blob), of filename + contents (attach), or relative filepath (filepath)
+        ---
+        size      :bigint unsigned     # size of object in bytes
+        attachment_name=null : varchar(255)  # the filename of an attachment
+        filepath=null : varchar(1000)  # relative filepath or attachment filename
+        contents_hash=null : uuid      # used for the filepath datatype
+        timestamp=CURRENT_TIMESTAMP  :timestamp   # automatic timestamp
+        """
+
+    @property
+    def table_name(self):
+        return f"{EXTERNAL_TABLE_ROOT}_{self.store}"
+
+    @property
+    def s3(self):
+        if self._s3 is None:
+            self._s3 = s3.Folder(**self.spec)
+        return self._s3
+
+    # - low-level operations - private
+
+    def _make_external_filepath(self, relative_filepath):
+        """resolve the complete external path based on the relative path"""
+        # Strip root
+        if self.spec["protocol"] == "s3":
+            posix_path = PurePosixPath(PureWindowsPath(self.spec["location"]))
+            location_path = (
+                Path(*posix_path.parts[1:])
+                if len(self.spec["location"]) > 0
+                and any(case in posix_path.parts[0] for case in ("\\", ":"))
+                else Path(posix_path)
+            )
+            return PurePosixPath(location_path, relative_filepath)
+        # Preserve root
+        elif self.spec["protocol"] == "file":
+            return PurePosixPath(Path(self.spec["location"]), relative_filepath)
+        else:
+            assert False
+
+    def _make_uuid_path(self, uuid, suffix=""):
+        """create external path based on the uuid hash"""
+        return self._make_external_filepath(
+            PurePosixPath(
+                self.database,
+                "/".join(subfold(uuid.hex, self.spec["subfolding"])),
+                uuid.hex,
+            ).with_suffix(suffix)
+        )
+
+    def _upload_file(self, local_path, external_path, metadata=None):
+        if self.spec["protocol"] == "s3":
+            self.s3.fput(local_path, external_path, metadata)
+        elif self.spec["protocol"] == "file":
+            safe_copy(local_path, external_path, overwrite=True)
+        else:
+            assert False
+
+    def _download_file(self, external_path, download_path):
+        if self.spec["protocol"] == "s3":
+            self.s3.fget(external_path, download_path)
+        elif self.spec["protocol"] == "file":
+            safe_copy(external_path, download_path)
+        else:
+            assert False
+
+    def _upload_buffer(self, buffer, external_path):
+        if self.spec["protocol"] == "s3":
+            self.s3.put(external_path, buffer)
+        elif self.spec["protocol"] == "file":
+            safe_write(external_path, buffer)
+        else:
+            assert False
+
+    def _download_buffer(self, external_path):
+        if self.spec["protocol"] == "s3":
+            return self.s3.get(external_path)
+        if self.spec["protocol"] == "file":
+            try:
+                return Path(external_path).read_bytes()
+            except FileNotFoundError:
+                raise errors.MissingExternalFile(
+                    f"Missing external file {external_path}"
+                ) from None
+        assert False
+
+    def _remove_external_file(self, external_path):
+        if self.spec["protocol"] == "s3":
+            self.s3.remove_object(external_path)
+        elif self.spec["protocol"] == "file":
+            try:
+                Path(external_path).unlink()
+            except FileNotFoundError:
+                pass
+
+    def exists(self, external_filepath):
+        """
+        :return: True if the external file is accessible
+        """
+        if self.spec["protocol"] == "s3":
+            return self.s3.exists(external_filepath)
+        if self.spec["protocol"] == "file":
+            return Path(external_filepath).is_file()
+        assert False
+
+    # --- BLOBS ----
+
+    def put(self, blob):
+        """
+        put a binary string (blob) in external store
+        """
+        uuid = uuid_from_buffer(blob)
+        self._upload_buffer(blob, self._make_uuid_path(uuid))
+        # insert tracking info
+        self.connection.query(
+            "INSERT INTO {tab} (hash, size) VALUES (%s, {size}) ON DUPLICATE KEY "
+            "UPDATE timestamp=CURRENT_TIMESTAMP".format(
+                tab=self.full_table_name, size=len(blob)
+            ),
+            args=(uuid.bytes,),
+        )
+        return uuid
+
+    def get(self, uuid):
+        """
+        get an object from external store.
+        """
+        if uuid is None:
+            return None
+        # attempt to get object from cache
+        blob = None
+        cache_folder = config.get("cache", None)
+        if cache_folder:
+            try:
+                cache_path = Path(cache_folder, *subfold(uuid.hex, CACHE_SUBFOLDING))
+                cache_file = Path(cache_path, uuid.hex)
+                blob = cache_file.read_bytes()
+            except FileNotFoundError:
+                pass  # not cached
+        # download blob from external store
+        if blob is None:
+            try:
+                blob = self._download_buffer(self._make_uuid_path(uuid))
+            except MissingExternalFile:
+                if not SUPPORT_MIGRATED_BLOBS:
+                    raise
+                # blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths
+                relative_filepath, contents_hash = (self & {"hash": uuid}).fetch1(
+                    "filepath", "contents_hash"
+                )
+                if relative_filepath is None:
+                    raise
+                blob = self._download_buffer(
+                    self._make_external_filepath(relative_filepath)
+                )
+            if cache_folder:
+                cache_path.mkdir(parents=True, exist_ok=True)
+                safe_write(cache_path / uuid.hex, blob)
+        return blob
+
+    # --- ATTACHMENTS ---
+
+    def upload_attachment(self, local_path):
+        attachment_name = Path(local_path).name
+        uuid = uuid_from_file(local_path, init_string=attachment_name + "\0")
+        external_path = self._make_uuid_path(uuid, "." + attachment_name)
+        self._upload_file(local_path, external_path)
+        # insert tracking info
+        self.connection.query(
+            """
+        INSERT INTO {tab} (hash, size, attachment_name)
+        VALUES (%s, {size}, "{attachment_name}")
+        ON DUPLICATE KEY UPDATE timestamp=CURRENT_TIMESTAMP""".format(
+                tab=self.full_table_name,
+                size=Path(local_path).stat().st_size,
+                attachment_name=attachment_name,
+            ),
+            args=[uuid.bytes],
+        )
+        return uuid
+
+    def get_attachment_name(self, uuid):
+        return (self & {"hash": uuid}).fetch1("attachment_name")
+
+    def download_attachment(self, uuid, attachment_name, download_path):
+        """save attachment from memory buffer into the save_path"""
+        external_path = self._make_uuid_path(uuid, "." + attachment_name)
+        self._download_file(external_path, download_path)
+
+    # --- FILEPATH ---
+
+    def upload_filepath(self, local_filepath):
+        """
+        Raise exception if an external entry already exists with a different contents checksum.
+        Otherwise, copy (with overwrite) file to remote and
+        If an external entry exists with the same checksum, then no copying should occur
+        """
+        local_filepath = Path(local_filepath)
+        try:
+            relative_filepath = str(
+                local_filepath.relative_to(self.spec["stage"]).as_posix()
+            )
+        except ValueError:
+            raise DataJointError(
+                "The path {path} is not in stage {stage}".format(
+                    path=local_filepath.parent, **self.spec
+                )
+            )
+        uuid = uuid_from_buffer(
+            init_string=relative_filepath
+        )  # hash relative path, not contents
+
+        # Check if checksum should be skipped based on file size limit
+        file_size = Path(local_filepath).stat().st_size
+        size_limit = config.get("filepath_checksum_size_limit_insert")
+        skip_checksum = size_limit is not None and file_size > size_limit
+
+        if skip_checksum:
+            contents_hash = None
+            logger.warning(
+                f"Skipping checksum for '{relative_filepath}' ({file_size} bytes > {size_limit} byte limit)"
+            )
+        else:
+            contents_hash = uuid_from_file(local_filepath)
+
+        # check if the remote file already exists and verify that it matches
+        check_hash = (self & {"hash": uuid}).fetch("contents_hash")
+        if check_hash.size:
+            # the tracking entry exists, check that it's the same file as before
+            if not skip_checksum and contents_hash != check_hash[0]:
+                raise DataJointError(
+                    f"A different version of '{relative_filepath}' has already been placed."
+                )
+        else:
+            # upload the file and create its tracking entry
+            external_path = self._make_external_filepath(relative_filepath)
+            already_uploaded = False
+            if self.spec["protocol"] == "s3":
+                stat = self.s3.stat(str(external_path))
+                if stat is not None and stat.size == file_size:
+                    # Verify contents_hash from S3 metadata when available
+                    if skip_checksum:
+                        already_uploaded = True
+                    else:
+                        remote_meta = {
+                            k.lower().lstrip("x-amz-meta-"): v
+                            for k, v in (stat.metadata or {}).items()
+                        }
+                        remote_hash = remote_meta.get("contents_hash", "")
+                        if remote_hash == str(contents_hash):
+                            already_uploaded = True
+                    if already_uploaded:
+                        logger.info(
+                            f"File already exists on S3 with matching size"
+                            f"{'' if skip_checksum else ' and checksum'}"
+                            f", skipping upload: '{relative_filepath}'"
+                        )
+            if not already_uploaded:
+                self._upload_file(
+                    local_filepath,
+                    external_path,
+                    metadata={
+                        "contents_hash": str(contents_hash) if contents_hash else ""
+                    },
+                )
+            self.connection.query(
+                "INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES (%s, {size}, '{filepath}', %s)".format(
+                    tab=self.full_table_name,
+                    size=file_size,
+                    filepath=relative_filepath,
+                ),
+                args=(uuid.bytes, contents_hash.bytes if contents_hash else None),
+            )
+        return uuid
+
+    def download_filepath(self, filepath_hash):
+        """
+        sync a file from external store to the local stage
+
+        :param filepath_hash: The hash (UUID) of the relative_path
+        :return: hash (UUID) of the contents of the downloaded file or Nones
+        """
+
+        def _need_checksum(local_filepath, expected_size):
+            limit = config.get("filepath_checksum_size_limit")
+            actual_size = Path(local_filepath).stat().st_size
+            if expected_size != actual_size:
+                # this should never happen without outside interference
+                raise DataJointError(
+                    f"'{local_filepath}' downloaded but size did not match."
+                )
+            return limit is None or actual_size < limit
+
+        if filepath_hash is not None:
+            relative_filepath, contents_hash, size = (
+                self & {"hash": filepath_hash}
+            ).fetch1("filepath", "contents_hash", "size")
+            external_path = self._make_external_filepath(relative_filepath)
+            local_filepath = Path(self.spec["stage"]).absolute() / relative_filepath
+
+            file_exists = Path(local_filepath).is_file() and (
+                not _need_checksum(local_filepath, size)
+                or uuid_from_file(local_filepath) == contents_hash
+            )
+
+            if not file_exists:
+                self._download_file(external_path, local_filepath)
+                if (
+                    _need_checksum(local_filepath, size)
+                    and uuid_from_file(local_filepath) != contents_hash
+                ):
+                    # this should never happen without outside interference
+                    raise DataJointError(
+                        f"'{local_filepath}' downloaded but did not pass checksum."
+                    )
+            if not _need_checksum(local_filepath, size):
+                logger.warning(
+                    f"Skipped checksum for file with hash: {contents_hash}, and path: {local_filepath}"
+                )
+            return str(local_filepath), contents_hash
+
+    # --- UTILITIES ---
+
+    @property
+    def references(self):
+        """
+        :return: generator of referencing table names and their referencing columns
+        """
+        return (
+            {k.lower(): v for k, v in elem.items()}
+            for elem in self.connection.query(
+                """
+        SELECT concat('`', table_schema, '`.`', table_name, '`') as referencing_table, column_name
+        FROM information_schema.key_column_usage
+        WHERE referenced_table_name="{tab}" and referenced_table_schema="{db}"
+        """.format(
+                    tab=self.table_name, db=self.database
+                ),
+                as_dict=True,
+            )
+        )
+
+    def fetch_external_paths(self, **fetch_kwargs):
+        """
+        generate complete external filepaths from the query.
+        Each element is a tuple: (uuid, path)
+
+        :param fetch_kwargs: keyword arguments to pass to fetch
+        """
+        fetch_kwargs.update(as_dict=True)
+        paths = []
+        for item in self.fetch("hash", "attachment_name", "filepath", **fetch_kwargs):
+            if item["attachment_name"]:
+                # attachments
+                path = self._make_uuid_path(item["hash"], "." + item["attachment_name"])
+            elif item["filepath"]:
+                # external filepaths
+                path = self._make_external_filepath(item["filepath"])
+            else:
+                # blobs
+                path = self._make_uuid_path(item["hash"])
+            paths.append((item["hash"], path))
+        return paths
+
+    def unused(self):
+        """
+        query expression for unused hashes
+
+        :return: self restricted to elements that are not in use by any tables in the schema
+        """
+        return self - [
+            FreeTable(self.connection, ref["referencing_table"]).proj(
+                hash=ref["column_name"]
+            )
+            for ref in self.references
+        ]
+
+    def used(self):
+        """
+        query expression for used hashes
+
+        :return: self restricted to elements that in use by tables in the schema
+        """
+        return self & [
+            FreeTable(self.connection, ref["referencing_table"]).proj(
+                hash=ref["column_name"]
+            )
+            for ref in self.references
+        ]
+
+    def delete(
+        self,
+        *,
+        delete_external_files=None,
+        limit=None,
+        display_progress=True,
+        errors_as_string=True,
+    ):
+        """
+
+        :param delete_external_files: True or False. If False, only the tracking info is removed from the external
+                store table but the external files remain intact. If True, then the external files themselves are deleted too.
+        :param errors_as_string: If True any errors returned when deleting from external files will be strings
+        :param limit: (integer) limit the number of items to delete
+        :param display_progress: if True, display progress as files are cleaned up
+        :return: if deleting external files, returns errors
+        """
+        if delete_external_files not in (True, False):
+            raise DataJointError(
+                "The delete_external_files argument must be set to either "
+                "True or False in delete()"
+            )
+
+        if not delete_external_files:
+            self.unused().delete_quick()
+        else:
+            items = self.unused().fetch_external_paths(limit=limit)
+            if display_progress:
+                items = tqdm(items)
+            # delete items one by one, close to transaction-safe
+            error_list = []
+            for uuid, external_path in items:
+                row = (self & {"hash": uuid}).fetch()
+                if row.size:
+                    try:
+                        (self & {"hash": uuid}).delete_quick()
+                    except Exception:
+                        pass  # if delete failed, do not remove the external file
+                    else:
+                        try:
+                            self._remove_external_file(external_path)
+                        except Exception as error:
+                            # adding row back into table after failed delete
+                            self.insert1(row[0], skip_duplicates=True)
+                            error_list.append(
+                                (
+                                    uuid,
+                                    external_path,
+                                    str(error) if errors_as_string else error,
+                                )
+                            )
+            return error_list
+

+ + + +

+ + + + + + + +

+ + +

+ `exists(external_filepath)` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + True if the external file is accessible + +

+ + +

Source code in datajoint/external.py

def exists(self, external_filepath):
+    """
+    :return: True if the external file is accessible
+    """
+    if self.spec["protocol"] == "s3":
+        return self.s3.exists(external_filepath)
+    if self.spec["protocol"] == "file":
+        return Path(external_filepath).is_file()
+    assert False
+

+ +

+ + + + + + +

+ + +

+ `put(blob)` + +¶

+ + +

+ +

put a binary string (blob) in external store

+ + +

Source code in datajoint/external.py

def put(self, blob):
+    """
+    put a binary string (blob) in external store
+    """
+    uuid = uuid_from_buffer(blob)
+    self._upload_buffer(blob, self._make_uuid_path(uuid))
+    # insert tracking info
+    self.connection.query(
+        "INSERT INTO {tab} (hash, size) VALUES (%s, {size}) ON DUPLICATE KEY "
+        "UPDATE timestamp=CURRENT_TIMESTAMP".format(
+            tab=self.full_table_name, size=len(blob)
+        ),
+        args=(uuid.bytes,),
+    )
+    return uuid
+

+ +

+ + + + + + +

+ + +

+ `get(uuid)` + +¶

+ + +

+ +

get an object from external store.

+ + +

Source code in datajoint/external.py

def get(self, uuid):
+    """
+    get an object from external store.
+    """
+    if uuid is None:
+        return None
+    # attempt to get object from cache
+    blob = None
+    cache_folder = config.get("cache", None)
+    if cache_folder:
+        try:
+            cache_path = Path(cache_folder, *subfold(uuid.hex, CACHE_SUBFOLDING))
+            cache_file = Path(cache_path, uuid.hex)
+            blob = cache_file.read_bytes()
+        except FileNotFoundError:
+            pass  # not cached
+    # download blob from external store
+    if blob is None:
+        try:
+            blob = self._download_buffer(self._make_uuid_path(uuid))
+        except MissingExternalFile:
+            if not SUPPORT_MIGRATED_BLOBS:
+                raise
+            # blobs migrated from datajoint 0.11 are stored at explicitly defined filepaths
+            relative_filepath, contents_hash = (self & {"hash": uuid}).fetch1(
+                "filepath", "contents_hash"
+            )
+            if relative_filepath is None:
+                raise
+            blob = self._download_buffer(
+                self._make_external_filepath(relative_filepath)
+            )
+        if cache_folder:
+            cache_path.mkdir(parents=True, exist_ok=True)
+            safe_write(cache_path / uuid.hex, blob)
+    return blob
+

+ +

+ + + + + + +

+ + +

+ `download_attachment(uuid, attachment_name, download_path)` + +¶

+ + +

+ +

save attachment from memory buffer into the save_path

+ + +

Source code in datajoint/external.py

def download_attachment(self, uuid, attachment_name, download_path):
+    """save attachment from memory buffer into the save_path"""
+    external_path = self._make_uuid_path(uuid, "." + attachment_name)
+    self._download_file(external_path, download_path)
+

+ +

+ + + + + + +

+ + +

+ `upload_filepath(local_filepath)` + +¶

+ + +

+ +

Raise exception if an external entry already exists with a different contents checksum. +Otherwise, copy (with overwrite) file to remote and +If an external entry exists with the same checksum, then no copying should occur

+ + +

Source code in datajoint/external.py

def upload_filepath(self, local_filepath):
+    """
+    Raise exception if an external entry already exists with a different contents checksum.
+    Otherwise, copy (with overwrite) file to remote and
+    If an external entry exists with the same checksum, then no copying should occur
+    """
+    local_filepath = Path(local_filepath)
+    try:
+        relative_filepath = str(
+            local_filepath.relative_to(self.spec["stage"]).as_posix()
+        )
+    except ValueError:
+        raise DataJointError(
+            "The path {path} is not in stage {stage}".format(
+                path=local_filepath.parent, **self.spec
+            )
+        )
+    uuid = uuid_from_buffer(
+        init_string=relative_filepath
+    )  # hash relative path, not contents
+
+    # Check if checksum should be skipped based on file size limit
+    file_size = Path(local_filepath).stat().st_size
+    size_limit = config.get("filepath_checksum_size_limit_insert")
+    skip_checksum = size_limit is not None and file_size > size_limit
+
+    if skip_checksum:
+        contents_hash = None
+        logger.warning(
+            f"Skipping checksum for '{relative_filepath}' ({file_size} bytes > {size_limit} byte limit)"
+        )
+    else:
+        contents_hash = uuid_from_file(local_filepath)
+
+    # check if the remote file already exists and verify that it matches
+    check_hash = (self & {"hash": uuid}).fetch("contents_hash")
+    if check_hash.size:
+        # the tracking entry exists, check that it's the same file as before
+        if not skip_checksum and contents_hash != check_hash[0]:
+            raise DataJointError(
+                f"A different version of '{relative_filepath}' has already been placed."
+            )
+    else:
+        # upload the file and create its tracking entry
+        external_path = self._make_external_filepath(relative_filepath)
+        already_uploaded = False
+        if self.spec["protocol"] == "s3":
+            stat = self.s3.stat(str(external_path))
+            if stat is not None and stat.size == file_size:
+                # Verify contents_hash from S3 metadata when available
+                if skip_checksum:
+                    already_uploaded = True
+                else:
+                    remote_meta = {
+                        k.lower().lstrip("x-amz-meta-"): v
+                        for k, v in (stat.metadata or {}).items()
+                    }
+                    remote_hash = remote_meta.get("contents_hash", "")
+                    if remote_hash == str(contents_hash):
+                        already_uploaded = True
+                if already_uploaded:
+                    logger.info(
+                        f"File already exists on S3 with matching size"
+                        f"{'' if skip_checksum else ' and checksum'}"
+                        f", skipping upload: '{relative_filepath}'"
+                    )
+        if not already_uploaded:
+            self._upload_file(
+                local_filepath,
+                external_path,
+                metadata={
+                    "contents_hash": str(contents_hash) if contents_hash else ""
+                },
+            )
+        self.connection.query(
+            "INSERT INTO {tab} (hash, size, filepath, contents_hash) VALUES (%s, {size}, '{filepath}', %s)".format(
+                tab=self.full_table_name,
+                size=file_size,
+                filepath=relative_filepath,
+            ),
+            args=(uuid.bytes, contents_hash.bytes if contents_hash else None),
+        )
+    return uuid
+

+ +

+ + + + + + +

+ + +

+ `download_filepath(filepath_hash)` + +¶

+ + +

+ +

sync a file from external store to the local stage

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `filepath_hash` +	+	+ + The hash (UUID) of the relative_path + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + hash (UUID) of the contents of the downloaded file or Nones + +

+ + +

Source code in datajoint/external.py

def download_filepath(self, filepath_hash):
+    """
+    sync a file from external store to the local stage
+
+    :param filepath_hash: The hash (UUID) of the relative_path
+    :return: hash (UUID) of the contents of the downloaded file or Nones
+    """
+
+    def _need_checksum(local_filepath, expected_size):
+        limit = config.get("filepath_checksum_size_limit")
+        actual_size = Path(local_filepath).stat().st_size
+        if expected_size != actual_size:
+            # this should never happen without outside interference
+            raise DataJointError(
+                f"'{local_filepath}' downloaded but size did not match."
+            )
+        return limit is None or actual_size < limit
+
+    if filepath_hash is not None:
+        relative_filepath, contents_hash, size = (
+            self & {"hash": filepath_hash}
+        ).fetch1("filepath", "contents_hash", "size")
+        external_path = self._make_external_filepath(relative_filepath)
+        local_filepath = Path(self.spec["stage"]).absolute() / relative_filepath
+
+        file_exists = Path(local_filepath).is_file() and (
+            not _need_checksum(local_filepath, size)
+            or uuid_from_file(local_filepath) == contents_hash
+        )
+
+        if not file_exists:
+            self._download_file(external_path, local_filepath)
+            if (
+                _need_checksum(local_filepath, size)
+                and uuid_from_file(local_filepath) != contents_hash
+            ):
+                # this should never happen without outside interference
+                raise DataJointError(
+                    f"'{local_filepath}' downloaded but did not pass checksum."
+                )
+        if not _need_checksum(local_filepath, size):
+            logger.warning(
+                f"Skipped checksum for file with hash: {contents_hash}, and path: {local_filepath}"
+            )
+        return str(local_filepath), contents_hash
+

+ +

+ + + + + + +

+ + + +

+ `references` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + generator of referencing table names and their referencing columns + +

+ +

+ + + + + + +

+ + +

+ `fetch_external_paths(**fetch_kwargs)` + +¶

+ + +

+ +

generate complete external filepaths from the query. +Each element is a tuple: (uuid, path)

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `fetch_kwargs` +	+	+ + keyword arguments to pass to fetch + +	+ `{}` +

+ + +

Source code in datajoint/external.py

def fetch_external_paths(self, **fetch_kwargs):
+    """
+    generate complete external filepaths from the query.
+    Each element is a tuple: (uuid, path)
+
+    :param fetch_kwargs: keyword arguments to pass to fetch
+    """
+    fetch_kwargs.update(as_dict=True)
+    paths = []
+    for item in self.fetch("hash", "attachment_name", "filepath", **fetch_kwargs):
+        if item["attachment_name"]:
+            # attachments
+            path = self._make_uuid_path(item["hash"], "." + item["attachment_name"])
+        elif item["filepath"]:
+            # external filepaths
+            path = self._make_external_filepath(item["filepath"])
+        else:
+            # blobs
+            path = self._make_uuid_path(item["hash"])
+        paths.append((item["hash"], path))
+    return paths
+

+ +

+ + + + + + +

+ + +

+ `unused()` + +¶

+ + +

+ +

query expression for unused hashes

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + self restricted to elements that are not in use by any tables in the schema + +

+ + +

Source code in datajoint/external.py

def unused(self):
+    """
+    query expression for unused hashes
+
+    :return: self restricted to elements that are not in use by any tables in the schema
+    """
+    return self - [
+        FreeTable(self.connection, ref["referencing_table"]).proj(
+            hash=ref["column_name"]
+        )
+        for ref in self.references
+    ]
+

+ +

+ + + + + + +

+ + +

+ `used()` + +¶

+ + +

+ +

query expression for used hashes

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + self restricted to elements that in use by tables in the schema + +

+ + +

Source code in datajoint/external.py

def used(self):
+    """
+    query expression for used hashes
+
+    :return: self restricted to elements that in use by tables in the schema
+    """
+    return self & [
+        FreeTable(self.connection, ref["referencing_table"]).proj(
+            hash=ref["column_name"]
+        )
+        for ref in self.references
+    ]
+

+ +

+ + + + + + +

+ + +

+ `delete(*, delete_external_files=None, limit=None, display_progress=True, errors_as_string=True)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `delete_external_files` +	+	+ + True or False. If False, only the tracking info is removed from the external +store table but the external files remain intact. If True, then the external files themselves are deleted too. + +	+ `None` +
+ `errors_as_string` +	+	+ + If True any errors returned when deleting from external files will be strings + +	+ `True` +
+ `limit` +	+	+ + (integer) limit the number of items to delete + +	+ `None` +
+ `display_progress` +	+	+ + if True, display progress as files are cleaned up + +	+ `True` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + if deleting external files, returns errors + +

+ + +

Source code in datajoint/external.py

def delete(
+    self,
+    *,
+    delete_external_files=None,
+    limit=None,
+    display_progress=True,
+    errors_as_string=True,
+):
+    """
+
+    :param delete_external_files: True or False. If False, only the tracking info is removed from the external
+            store table but the external files remain intact. If True, then the external files themselves are deleted too.
+    :param errors_as_string: If True any errors returned when deleting from external files will be strings
+    :param limit: (integer) limit the number of items to delete
+    :param display_progress: if True, display progress as files are cleaned up
+    :return: if deleting external files, returns errors
+    """
+    if delete_external_files not in (True, False):
+        raise DataJointError(
+            "The delete_external_files argument must be set to either "
+            "True or False in delete()"
+        )
+
+    if not delete_external_files:
+        self.unused().delete_quick()
+    else:
+        items = self.unused().fetch_external_paths(limit=limit)
+        if display_progress:
+            items = tqdm(items)
+        # delete items one by one, close to transaction-safe
+        error_list = []
+        for uuid, external_path in items:
+            row = (self & {"hash": uuid}).fetch()
+            if row.size:
+                try:
+                    (self & {"hash": uuid}).delete_quick()
+                except Exception:
+                    pass  # if delete failed, do not remove the external file
+                else:
+                    try:
+                        self._remove_external_file(external_path)
+                    except Exception as error:
+                        # adding row back into table after failed delete
+                        self.insert1(row[0], skip_duplicates=True)
+                        error_list.append(
+                            (
+                                uuid,
+                                external_path,
+                                str(error) if errors_as_string else error,
+                            )
+                        )
+        return error_list
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `ExternalMapping` + + +¶

+ + +

+ Bases: Mapping

+ + + +

The external manager contains all the tables for all external stores for a given schema +:Example: + e = ExternalMapping(schema) + external_table = e[store]

+ + + + + + + + +

Source code in datajoint/external.py

class ExternalMapping(Mapping):
+    """
+    The external manager contains all the tables for all external stores for a given schema
+    :Example:
+        e = ExternalMapping(schema)
+        external_table = e[store]
+    """
+
+    def __init__(self, schema):
+        self.schema = schema
+        self._tables = {}
+
+    def __repr__(self):
+        return "External file tables for schema `{schema}`:\n    ".format(
+            schema=self.schema.database
+        ) + "\n    ".join(
+            '"{store}" {protocol}:{location}'.format(store=k, **v.spec)
+            for k, v in self.items()
+        )
+
+    def __getitem__(self, store):
+        """
+        Triggers the creation of an external table.
+        Should only be used when ready to save or read from external storage.
+
+        :param store: the name of the store
+        :return: the ExternalTable object for the store
+        """
+        if store not in self._tables:
+            self._tables[store] = ExternalTable(
+                connection=self.schema.connection,
+                store=store,
+                database=self.schema.database,
+            )
+        return self._tables[store]
+
+    def __len__(self):
+        return len(self._tables)
+
+    def __iter__(self):
+        return iter(self._tables)
+

+ + + +

+ + + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/fetch/index.html b/0.14/api/datajoint/fetch/index.html new file mode 100644 index 000000000..d1ced35ca --- /dev/null +++ b/0.14/api/datajoint/fetch/index.html @@ -0,0 +1,4438 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + fetch.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + fetch.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

fetch.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ `key` + + +¶

+ + +

+ + + +

object that allows requesting the primary key as an argument in expression.fetch() +The string "KEY" can be used instead of the class key

+ + + + + + + + +

Source code in datajoint/fetch.py

19
+20
+21
+22
+23
+24
+25
class key:
+    """
+    object that allows requesting the primary key as an argument in expression.fetch()
+    The string "KEY" can be used instead of the class key
+    """
+
+    pass
+

+ +

+ + + + + + +

+ + +

+ `to_dicts(recarray)` + +¶

+ + +

+ +

convert record array to a dictionaries

+ + +

Source code in datajoint/fetch.py

32
+33
+34
+35
def to_dicts(recarray):
+    """convert record array to a dictionaries"""
+    for rec in recarray:
+        yield dict(zip(recarray.dtype.names, rec.tolist()))
+

+ +

+ + + + + + +

+ + + +

+ `Fetch` + + +¶

+ + +

+ + + +

A fetch object that handles retrieving elements from the table expression.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `expression` +	+	+ + the QueryExpression object to fetch from. + +	+ required +

+ + + + + + + + +

Source code in datajoint/fetch.py

class Fetch:
+    """
+    A fetch object that handles retrieving elements from the table expression.
+
+    :param expression: the QueryExpression object to fetch from.
+    """
+
+    def __init__(self, expression):
+        self._expression = expression
+
+    def __call__(
+        self,
+        *attrs,
+        offset=None,
+        limit=None,
+        order_by=None,
+        format=None,
+        as_dict=None,
+        squeeze=False,
+        download_path=".",
+    ):
+        """
+        Fetches the expression results from the database into an np.array or list of dictionaries and
+        unpacks blob attributes.
+
+        :param attrs: zero or more attributes to fetch. If not provided, the call will return all attributes of this
+                        table. If provided, returns tuples with an entry for each attribute.
+        :param offset: the number of tuples to skip in the returned result
+        :param limit: the maximum number of tuples to return
+        :param order_by: a single attribute or the list of attributes to order the results. No ordering should be assumed
+                        if order_by=None. To reverse the order, add DESC to the attribute name or names: e.g. ("age DESC",
+                        "frequency") To order by primary key, use "KEY" or "KEY DESC"
+        :param format: Effective when as_dict=None and when attrs is empty None: default from config['fetch_format'] or
+                        'array' if not configured "array": use numpy.key_array "frame": output pandas.DataFrame. .
+        :param as_dict: returns a list of dictionaries instead of a record array. Defaults to False for .fetch() and to
+                        True for .fetch('KEY')
+        :param squeeze:  if True, remove extra dimensions from arrays
+        :param download_path: for fetches that download data, e.g. attachments
+        :return: the contents of the table in the form of a structured numpy.array or a dict list
+        """
+        if offset or order_by or limit:
+            self._expression = self._expression.restrict(
+                Top(
+                    limit,
+                    order_by,
+                    offset,
+                )
+            )
+
+        attrs_as_dict = as_dict and attrs
+        if attrs_as_dict:
+            # absorb KEY into attrs and prepare to return attributes as dict (issue #595)
+            if any(is_key(k) for k in attrs):
+                attrs = list(self._expression.primary_key) + [
+                    a for a in attrs if a not in self._expression.primary_key
+                ]
+        if as_dict is None:
+            as_dict = bool(attrs)  # default to True for "KEY" and False otherwise
+        # format should not be specified with attrs or is_dict=True
+        if format is not None and (as_dict or attrs):
+            raise DataJointError(
+                "Cannot specify output format when as_dict=True or "
+                "when attributes are selected to be fetched separately."
+            )
+        if format not in {None, "array", "frame"}:
+            raise DataJointError(
+                "Fetch output format must be in "
+                '{{"array", "frame"}} but "{}" was given'.format(format)
+            )
+
+        if not (attrs or as_dict) and format is None:
+            format = config["fetch_format"]  # default to array
+            if format not in {"array", "frame"}:
+                raise DataJointError(
+                    'Invalid entry "{}" in datajoint.config["fetch_format"]: '
+                    'use "array" or "frame"'.format(format)
+                )
+
+        get = partial(
+            _get,
+            self._expression.connection,
+            squeeze=squeeze,
+            download_path=download_path,
+        )
+        if attrs:  # a list of attributes provided
+            attributes = [a for a in attrs if not is_key(a)]
+            ret = self._expression.proj(*attributes)
+            ret = ret.fetch(
+                offset=offset,
+                limit=limit,
+                order_by=order_by,
+                as_dict=False,
+                squeeze=squeeze,
+                download_path=download_path,
+                format="array",
+            )
+            if attrs_as_dict:
+                ret = [
+                    {k: v for k, v in zip(ret.dtype.names, x) if k in attrs}
+                    for x in ret
+                ]
+            else:
+                return_values = [
+                    (
+                        list(
+                            (to_dicts if as_dict else lambda x: x)(
+                                ret[self._expression.primary_key]
+                            )
+                        )
+                        if is_key(attribute)
+                        else ret[attribute]
+                    )
+                    for attribute in attrs
+                ]
+                ret = return_values[0] if len(attrs) == 1 else return_values
+        else:  # fetch all attributes as a numpy.record_array or pandas.DataFrame
+            cur = self._expression.cursor(as_dict=as_dict)
+            heading = self._expression.heading
+            if as_dict:
+                ret = [
+                    dict((name, get(heading[name], d[name])) for name in heading.names)
+                    for d in cur
+                ]
+            else:
+                ret = list(cur.fetchall())
+                record_type = (
+                    heading.as_dtype
+                    if not ret
+                    else np.dtype(
+                        [
+                            (
+                                (
+                                    name,
+                                    type(value),
+                                )  # use the first element to determine blob type
+                                if heading[name].is_blob
+                                and isinstance(value, numbers.Number)
+                                else (name, heading.as_dtype[name])
+                            )
+                            for value, name in zip(ret[0], heading.as_dtype.names)
+                        ]
+                    )
+                )
+                try:
+                    ret = np.array(ret, dtype=record_type)
+                except Exception as e:
+                    raise e
+                for name in heading:
+                    # unpack blobs and externals
+                    ret[name] = list(map(partial(get, heading[name]), ret[name]))
+                if format == "frame":
+                    ret = pandas.DataFrame(ret).set_index(heading.primary_key)
+        return ret
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Fetch1` + + +¶

+ + +

+ + + +

Fetch object for fetching the result of a query yielding one row.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `expression` +	+	+ + a query expression to fetch from. + +	+ required +

+ + + + + + + + +

Source code in datajoint/fetch.py

class Fetch1:
+    """
+    Fetch object for fetching the result of a query yielding one row.
+
+    :param expression: a query expression to fetch from.
+    """
+
+    def __init__(self, expression):
+        self._expression = expression
+
+    def __call__(self, *attrs, squeeze=False, download_path="."):
+        """
+        Fetches the result of a query expression that yields one entry.
+
+        If no attributes are specified, returns the result as a dict.
+        If attributes are specified returns the corresponding results as a tuple.
+
+        Examples:
+        d = rel.fetch1()   # as a dictionary
+        a, b = rel.fetch1('a', 'b')   # as a tuple
+
+        :params *attrs: attributes to return when expanding into a tuple.
+                 If attrs is empty, the return result is a dict
+        :param squeeze:  When true, remove extra dimensions from arrays in attributes
+        :param download_path: for fetches that download data, e.g. attachments
+        :return: the one tuple in the table in the form of a dict
+        """
+        heading = self._expression.heading
+
+        if not attrs:  # fetch all attributes, return as ordered dict
+            cur = self._expression.cursor(as_dict=True)
+            ret = cur.fetchone()
+            if not ret or cur.fetchone():
+                raise DataJointError(
+                    "fetch1 requires exactly one tuple in the input set."
+                )
+            ret = dict(
+                (
+                    name,
+                    _get(
+                        self._expression.connection,
+                        heading[name],
+                        ret[name],
+                        squeeze=squeeze,
+                        download_path=download_path,
+                    ),
+                )
+                for name in heading.names
+            )
+        else:  # fetch some attributes, return as tuple
+            attributes = [a for a in attrs if not is_key(a)]
+            result = self._expression.proj(*attributes).fetch(
+                squeeze=squeeze, download_path=download_path, format="array"
+            )
+            if len(result) != 1:
+                raise DataJointError(
+                    "fetch1 should only return one tuple. %d tuples found" % len(result)
+                )
+            return_values = tuple(
+                (
+                    next(to_dicts(result[self._expression.primary_key]))
+                    if is_key(attribute)
+                    else result[attribute][0]
+                )
+                for attribute in attrs
+            )
+            ret = return_values[0] if len(attrs) == 1 else return_values
+        return ret
+

+ + + +

+ + + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/hash/index.html b/0.14/api/datajoint/hash/index.html new file mode 100644 index 000000000..0f1d68750 --- /dev/null +++ b/0.14/api/datajoint/hash/index.html @@ -0,0 +1,3837 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + hash.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + hash.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

hash.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + +

+ + +

+ `key_hash(mapping)` + +¶

+ + +

+ +

+ + +

Source code in datajoint/hash.py

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+ 8
+ 9
+10
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+12
+13
+14
+15
+16
def key_hash(mapping):
+    """
+    32-byte hash of the mapping's key values sorted by the key name.
+    This is often used to convert a long primary key value into a shorter hash.
+    For example, the JobTable in datajoint.jobs uses this function to hash the primary key of autopopulated tables.
+    """
+    hashed = hashlib.md5()
+    for k, v in sorted(mapping.items()):
+        hashed.update(str(v).encode())
+    return hashed.hexdigest()
+

+ +

+ + + + + + +

+ + +

+ `uuid_from_stream(stream, *, init_string='')` + +¶

+ + +

+ +

:stream: stream object or open file handle +:init_string: string to initialize the checksum

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + 16-byte digest of stream data + +

+ + +

Source code in datajoint/hash.py

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def uuid_from_stream(stream, *, init_string=""):
+    """
+    :return: 16-byte digest of stream data
+    :stream: stream object or open file handle
+    :init_string: string to initialize the checksum
+    """
+    hashed = hashlib.md5(init_string.encode())
+    chunk = True
+    chunk_size = 1 << 14
+    while chunk:
+        chunk = stream.read(chunk_size)
+        hashed.update(chunk)
+    return uuid.UUID(bytes=hashed.digest())
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/heading/index.html b/0.14/api/datajoint/heading/index.html new file mode 100644 index 000000000..cdf90f1f7 --- /dev/null +++ b/0.14/api/datajoint/heading/index.html @@ -0,0 +1,5507 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + heading.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + heading.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

heading.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + +

+ + + +

+ `Attribute` + + +¶

+ + +

+ Bases: namedtuple('_Attribute', default_attribute_properties)

+ + + +

Properties of a table column (attribute)

+ + + + + + + + +

Source code in datajoint/heading.py

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class Attribute(namedtuple("_Attribute", default_attribute_properties)):
+    """
+    Properties of a table column (attribute)
+    """
+
+    def todict(self):
+        """Convert namedtuple to dict."""
+        return dict((name, self[i]) for i, name in enumerate(self._fields))
+
+    @property
+    def sql_type(self):
+        """:return: datatype (as string) in database. In most cases, it is the same as self.type"""
+        return UUID_DATA_TYPE if self.uuid else self.type
+
+    @property
+    def sql_comment(self):
+        """:return: full comment for the SQL declaration. Includes custom type specification"""
+        return (":uuid:" if self.uuid else "") + self.comment
+
+    @property
+    def sql(self):
+        """
+        Convert primary key attribute tuple into its SQL CREATE TABLE clause.
+        Default values are not reflected.
+        This is used for declaring foreign keys in referencing tables
+
+        :return: SQL code for attribute declaration
+        """
+        return '`{name}` {type} NOT NULL COMMENT "{comment}"'.format(
+            name=self.name, type=self.sql_type, comment=self.sql_comment
+        )
+
+    @property
+    def original_name(self):
+        if self.attribute_expression is None:
+            return self.name
+        assert self.attribute_expression.startswith("`")
+        return self.attribute_expression.strip("`")
+

+ + + +

+ + + + + + + +

+ + +

+ `todict()` + +¶

+ + +

+ +

Convert namedtuple to dict.

+ + +

Source code in datajoint/heading.py

def todict(self):
+    """Convert namedtuple to dict."""
+    return dict((name, self[i]) for i, name in enumerate(self._fields))
+

+ +

+ + + + + + +

+ + + +

+ `sql_type` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + datatype (as string) in database. In most cases, it is the same as self.type + +

+ +

+ + + + + + +

+ + + +

+ `sql_comment` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + full comment for the SQL declaration. Includes custom type specification + +

+ +

+ + + + + + +

+ + + +

+ `sql` + + + `property` + + +¶

+ + +

+ +

Convert primary key attribute tuple into its SQL CREATE TABLE clause. +Default values are not reflected. +This is used for declaring foreign keys in referencing tables

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + SQL code for attribute declaration + +

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `Heading` + + +¶

+ + +

+ + + +

Local class for table headings. +Heading contains the property attributes, which is an dict in which the keys are +the attribute names and the values are Attributes.

+ + + + + + + + +

Source code in datajoint/heading.py

class Heading:
+    """
+    Local class for table headings.
+    Heading contains the property attributes, which is an dict in which the keys are
+    the attribute names and the values are Attributes.
+    """
+
+    def __init__(self, attribute_specs=None, table_info=None):
+        """
+
+        :param attribute_specs: a list of dicts with the same keys as Attribute
+        :param table_info: a dict with information to load the heading from the database
+        """
+        self.indexes = None
+        self.table_info = table_info
+        self._table_status = None
+        self._attributes = (
+            None
+            if attribute_specs is None
+            else dict((q["name"], Attribute(**q)) for q in attribute_specs)
+        )
+
+    def __len__(self):
+        return 0 if self.attributes is None else len(self.attributes)
+
+    @property
+    def table_status(self):
+        if self.table_info is None:
+            return None
+        if self._table_status is None:
+            self._init_from_database()
+        return self._table_status
+
+    @property
+    def attributes(self):
+        if self._attributes is None:
+            self._init_from_database()  # lazy loading from database
+        return {k: v for k, v in self._attributes.items() if not v.is_hidden}
+
+    @property
+    def names(self):
+        return [k for k in self.attributes]
+
+    @property
+    def primary_key(self):
+        return [k for k, v in self.attributes.items() if v.in_key]
+
+    @property
+    def secondary_attributes(self):
+        return [k for k, v in self.attributes.items() if not v.in_key]
+
+    @property
+    def blobs(self):
+        return [k for k, v in self.attributes.items() if v.is_blob]
+
+    @property
+    def non_blobs(self):
+        return [
+            k
+            for k, v in self.attributes.items()
+            if not (v.is_blob or v.is_attachment or v.is_filepath or v.json)
+        ]
+
+    @property
+    def new_attributes(self):
+        return [
+            k for k, v in self.attributes.items() if v.attribute_expression is not None
+        ]
+
+    def __getitem__(self, name):
+        """shortcut to the attribute"""
+        return self.attributes[name]
+
+    def __repr__(self):
+        """
+        :return:  heading representation in DataJoint declaration format but without foreign key expansion
+        """
+        in_key = True
+        ret = ""
+        if self._table_status is not None:
+            ret += "# " + self.table_status["comment"] + "\n"
+        for v in self.attributes.values():
+            if in_key and not v.in_key:
+                ret += "---\n"
+                in_key = False
+            ret += "%-20s : %-28s # %s\n" % (
+                v.name if v.default is None else "%s=%s" % (v.name, v.default),
+                "%s%s" % (v.type, "auto_increment" if v.autoincrement else ""),
+                v.comment,
+            )
+        return ret
+
+    @property
+    def has_autoincrement(self):
+        return any(e.autoincrement for e in self.attributes.values())
+
+    @property
+    def as_dtype(self):
+        """
+        represent the heading as a numpy dtype
+        """
+        return np.dtype(
+            dict(names=self.names, formats=[v.dtype for v in self.attributes.values()])
+        )
+
+    def as_sql(self, fields, include_aliases=True):
+        """
+        represent heading as the SQL SELECT clause.
+        """
+        return ",".join(
+            (
+                "`%s`" % name
+                if self.attributes[name].attribute_expression is None
+                else self.attributes[name].attribute_expression
+                + (" as `%s`" % name if include_aliases else "")
+            )
+            for name in fields
+        )
+
+    def __iter__(self):
+        return iter(self.attributes)
+
+    def _init_from_database(self):
+        """initialize heading from an existing database table."""
+        conn, database, table_name, context = (
+            self.table_info[k] for k in ("conn", "database", "table_name", "context")
+        )
+        info = conn.query(
+            'SHOW TABLE STATUS FROM `{database}` WHERE name="{table_name}"'.format(
+                table_name=table_name, database=database
+            ),
+            as_dict=True,
+        ).fetchone()
+        if info is None:
+            if table_name == "~log":
+                logger.warning("Could not create the ~log table")
+                return
+            raise DataJointError(
+                "The table `{database}`.`{table_name}` is not defined.".format(
+                    table_name=table_name, database=database
+                )
+            )
+        self._table_status = {k.lower(): v for k, v in info.items()}
+        cur = conn.query(
+            "SHOW FULL COLUMNS FROM `{table_name}` IN `{database}`".format(
+                table_name=table_name, database=database
+            ),
+            as_dict=True,
+        )
+
+        attributes = cur.fetchall()
+
+        rename_map = {
+            "Field": "name",
+            "Type": "type",
+            "Null": "nullable",
+            "Default": "default",
+            "Key": "in_key",
+            "Comment": "comment",
+        }
+
+        fields_to_drop = ("Privileges", "Collation")
+
+        # rename and drop attributes
+        attributes = [
+            {
+                rename_map[k] if k in rename_map else k: v
+                for k, v in x.items()
+                if k not in fields_to_drop
+            }
+            for x in attributes
+        ]
+        numeric_types = {
+            ("float", False): np.float64,
+            ("float", True): np.float64,
+            ("double", False): np.float64,
+            ("double", True): np.float64,
+            ("tinyint", False): np.int64,
+            ("tinyint", True): np.int64,
+            ("smallint", False): np.int64,
+            ("smallint", True): np.int64,
+            ("mediumint", False): np.int64,
+            ("mediumint", True): np.int64,
+            ("int", False): np.int64,
+            ("int", True): np.int64,
+            ("bigint", False): np.int64,
+            ("bigint", True): np.uint64,
+        }
+
+        sql_literals = ["CURRENT_TIMESTAMP"]
+
+        # additional attribute properties
+        for attr in attributes:
+            attr.update(
+                in_key=(attr["in_key"] == "PRI"),
+                database=database,
+                nullable=attr["nullable"] == "YES",
+                autoincrement=bool(
+                    re.search(r"auto_increment", attr["Extra"], flags=re.I)
+                ),
+                numeric=any(
+                    TYPE_PATTERN[t].match(attr["type"])
+                    for t in ("DECIMAL", "INTEGER", "FLOAT")
+                ),
+                string=any(
+                    TYPE_PATTERN[t].match(attr["type"])
+                    for t in ("ENUM", "TEMPORAL", "STRING")
+                ),
+                is_blob=bool(TYPE_PATTERN["INTERNAL_BLOB"].match(attr["type"])),
+                uuid=False,
+                json=bool(TYPE_PATTERN["JSON"].match(attr["type"])),
+                is_attachment=False,
+                is_filepath=False,
+                adapter=None,
+                store=None,
+                is_external=False,
+                attribute_expression=None,
+                is_hidden=attr["name"].startswith("_"),
+            )
+
+            if any(TYPE_PATTERN[t].match(attr["type"]) for t in ("INTEGER", "FLOAT")):
+                attr["type"] = re.sub(
+                    r"\(\d+\)", "", attr["type"], count=1
+                )  # strip size off integers and floats
+            attr["unsupported"] = not any(
+                (attr["is_blob"], attr["numeric"], attr["numeric"])
+            )
+            attr.pop("Extra")
+
+            # process custom DataJoint types
+            special = re.match(r":(?P<type>[^:]+):(?P<comment>.*)", attr["comment"])
+            if special:
+                special = special.groupdict()
+                attr.update(special)
+            # process adapted attribute types
+            if special and TYPE_PATTERN["ADAPTED"].match(attr["type"]):
+                assert context is not None, "Declaration context is not set"
+                adapter_name = special["type"]
+                try:
+                    attr.update(adapter=get_adapter(context, adapter_name))
+                except DataJointError:
+                    # if no adapter, then delay the error until the first invocation
+                    attr.update(adapter=AttributeAdapter())
+                else:
+                    attr.update(type=attr["adapter"].attribute_type)
+                    if not any(r.match(attr["type"]) for r in TYPE_PATTERN.values()):
+                        raise DataJointError(
+                            "Invalid attribute type '{type}' in adapter object <{adapter_name}>.".format(
+                                adapter_name=adapter_name, **attr
+                            )
+                        )
+                    special = not any(
+                        TYPE_PATTERN[c].match(attr["type"]) for c in NATIVE_TYPES
+                    )
+
+            if special:
+                try:
+                    category = next(
+                        c for c in SPECIAL_TYPES if TYPE_PATTERN[c].match(attr["type"])
+                    )
+                except StopIteration:
+                    if attr["type"].startswith("external"):
+                        url = (
+                            "https://docs.datajoint.io/python/admin/5-blob-config.html"
+                            "#migration-between-datajoint-v0-11-and-v0-12"
+                        )
+                        raise DataJointError(
+                            "Legacy datatype `{type}`. Migrate your external stores to "
+                            "datajoint 0.12: {url}".format(url=url, **attr)
+                        )
+                    raise DataJointError(
+                        "Unknown attribute type `{type}`".format(**attr)
+                    )
+                if category == "FILEPATH" and not _support_filepath_types():
+                    raise DataJointError(
+                        """
+                        The filepath data type is disabled until complete validation.
+                        To turn it on as experimental feature, set the environment variable
+                        {env} = TRUE or upgrade datajoint.
+                        """.format(
+                            env=FILEPATH_FEATURE_SWITCH
+                        )
+                    )
+                attr.update(
+                    unsupported=False,
+                    is_attachment=category in ("INTERNAL_ATTACH", "EXTERNAL_ATTACH"),
+                    is_filepath=category == "FILEPATH",
+                    # INTERNAL_BLOB is not a custom type but is included for completeness
+                    is_blob=category in ("INTERNAL_BLOB", "EXTERNAL_BLOB"),
+                    uuid=category == "UUID",
+                    is_external=category in EXTERNAL_TYPES,
+                    store=(
+                        attr["type"].split("@")[1]
+                        if category in EXTERNAL_TYPES
+                        else None
+                    ),
+                )
+
+            if attr["in_key"] and any(
+                (
+                    attr["is_blob"],
+                    attr["is_attachment"],
+                    attr["is_filepath"],
+                    attr["json"],
+                )
+            ):
+                raise DataJointError(
+                    "Json, Blob, attachment, or filepath attributes are not allowed in the primary key"
+                )
+
+            if (
+                attr["string"]
+                and attr["default"] is not None
+                and attr["default"] not in sql_literals
+            ):
+                attr["default"] = '"%s"' % attr["default"]
+
+            if attr["nullable"]:  # nullable fields always default to null
+                attr["default"] = "null"
+
+            # fill out dtype. All floats and non-nullable integers are turned into specific dtypes
+            attr["dtype"] = object
+            if attr["numeric"] and not attr["adapter"]:
+                is_integer = TYPE_PATTERN["INTEGER"].match(attr["type"])
+                is_float = TYPE_PATTERN["FLOAT"].match(attr["type"])
+                if is_integer and not attr["nullable"] or is_float:
+                    is_unsigned = bool(re.match("sunsigned", attr["type"], flags=re.I))
+                    t = re.sub(r"\(.*\)", "", attr["type"])  # remove parentheses
+                    t = re.sub(r" unsigned$", "", t)  # remove unsigned
+                    assert (t, is_unsigned) in numeric_types, (
+                        "dtype not found for type %s" % t
+                    )
+                    attr["dtype"] = numeric_types[(t, is_unsigned)]
+
+            if attr["adapter"]:
+                # restore adapted type name
+                attr["type"] = adapter_name
+
+        self._attributes = dict(((q["name"], Attribute(**q)) for q in attributes))
+
+        # Read and tabulate secondary indexes
+        keys = defaultdict(dict)
+        for item in conn.query(
+            "SHOW KEYS FROM `{db}`.`{tab}`".format(db=database, tab=table_name),
+            as_dict=True,
+        ):
+            if item["Key_name"] != "PRIMARY":
+                keys[item["Key_name"]][item["Seq_in_index"]] = dict(
+                    column=item["Column_name"]
+                    or f"({item['Expression']})".replace(r"\'", "'"),
+                    unique=(item["Non_unique"] == 0),
+                    nullable=item["Null"].lower() == "yes",
+                )
+        self.indexes = {
+            tuple(item[k]["column"] for k in sorted(item.keys())): dict(
+                unique=item[1]["unique"],
+                nullable=any(v["nullable"] for v in item.values()),
+            )
+            for item in keys.values()
+        }
+
+    def select(self, select_list, rename_map=None, compute_map=None):
+        """
+        derive a new heading by selecting, renaming, or computing attributes.
+        In relational algebra these operators are known as project, rename, and extend.
+
+        :param select_list:  the full list of existing attributes to include
+        :param rename_map:  dictionary of renamed attributes: keys=new names, values=old names
+        :param compute_map: a direction of computed attributes
+        This low-level method performs no error checking.
+        """
+        rename_map = rename_map or {}
+        compute_map = compute_map or {}
+        copy_attrs = list()
+        for name in self.attributes:
+            if name in select_list:
+                copy_attrs.append(self.attributes[name].todict())
+            copy_attrs.extend(
+                (
+                    dict(
+                        self.attributes[old_name].todict(),
+                        name=new_name,
+                        attribute_expression="`%s`" % old_name,
+                    )
+                    for new_name, old_name in rename_map.items()
+                    if old_name == name
+                )
+            )
+        compute_attrs = (
+            dict(default_attribute_properties, name=new_name, attribute_expression=expr)
+            for new_name, expr in compute_map.items()
+        )
+        return Heading(chain(copy_attrs, compute_attrs))
+
+    def join(self, other):
+        """
+        Join two headings into a new one.
+        It assumes that self and other are headings that share no common dependent attributes.
+        """
+        return Heading(
+            [self.attributes[name].todict() for name in self.primary_key]
+            + [
+                other.attributes[name].todict()
+                for name in other.primary_key
+                if name not in self.primary_key
+            ]
+            + [
+                self.attributes[name].todict()
+                for name in self.secondary_attributes
+                if name not in other.primary_key
+            ]
+            + [
+                other.attributes[name].todict()
+                for name in other.secondary_attributes
+                if name not in self.primary_key
+            ]
+        )
+
+    def set_primary_key(self, primary_key):
+        """
+        Create a new heading with the specified primary key.
+        This low-level method performs no error checking.
+        """
+        return Heading(
+            chain(
+                (
+                    dict(self.attributes[name].todict(), in_key=True)
+                    for name in primary_key
+                ),
+                (
+                    dict(self.attributes[name].todict(), in_key=False)
+                    for name in self.names
+                    if name not in primary_key
+                ),
+            )
+        )
+
+    def make_subquery_heading(self):
+        """
+        Create a new heading with removed attribute sql_expressions.
+        Used by subqueries, which resolve the sql_expressions.
+        """
+        return Heading(
+            dict(v.todict(), attribute_expression=None)
+            for v in self.attributes.values()
+        )
+

+ + + +

+ + + + + + + +

+ + + +

+ `as_dtype` + + + `property` + + +¶

+ + +

+ +

represent the heading as a numpy dtype

+ +

+ + + + + + +

+ + +

+ `as_sql(fields, include_aliases=True)` + +¶

+ + +

+ +

represent heading as the SQL SELECT clause.

+ + +

Source code in datajoint/heading.py

def as_sql(self, fields, include_aliases=True):
+    """
+    represent heading as the SQL SELECT clause.
+    """
+    return ",".join(
+        (
+            "`%s`" % name
+            if self.attributes[name].attribute_expression is None
+            else self.attributes[name].attribute_expression
+            + (" as `%s`" % name if include_aliases else "")
+        )
+        for name in fields
+    )
+

+ +

+ + + + + + +

+ + +

+ `select(select_list, rename_map=None, compute_map=None)` + +¶

+ + +

+ +

derive a new heading by selecting, renaming, or computing attributes. +In relational algebra these operators are known as project, rename, and extend.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `select_list` +	+	+ + the full list of existing attributes to include + +	+ required +
+ `rename_map` +	+	+ + dictionary of renamed attributes: keys=new names, values=old names + +	+ `None` +
+ `compute_map` +	+	+ + a direction of computed attributes +This low-level method performs no error checking. + +	+ `None` +

+ + +

Source code in datajoint/heading.py

def select(self, select_list, rename_map=None, compute_map=None):
+    """
+    derive a new heading by selecting, renaming, or computing attributes.
+    In relational algebra these operators are known as project, rename, and extend.
+
+    :param select_list:  the full list of existing attributes to include
+    :param rename_map:  dictionary of renamed attributes: keys=new names, values=old names
+    :param compute_map: a direction of computed attributes
+    This low-level method performs no error checking.
+    """
+    rename_map = rename_map or {}
+    compute_map = compute_map or {}
+    copy_attrs = list()
+    for name in self.attributes:
+        if name in select_list:
+            copy_attrs.append(self.attributes[name].todict())
+        copy_attrs.extend(
+            (
+                dict(
+                    self.attributes[old_name].todict(),
+                    name=new_name,
+                    attribute_expression="`%s`" % old_name,
+                )
+                for new_name, old_name in rename_map.items()
+                if old_name == name
+            )
+        )
+    compute_attrs = (
+        dict(default_attribute_properties, name=new_name, attribute_expression=expr)
+        for new_name, expr in compute_map.items()
+    )
+    return Heading(chain(copy_attrs, compute_attrs))
+

+ +

+ + + + + + +

+ + +

+ `join(other)` + +¶

+ + +

+ +

Join two headings into a new one. +It assumes that self and other are headings that share no common dependent attributes.

+ + +

Source code in datajoint/heading.py

def join(self, other):
+    """
+    Join two headings into a new one.
+    It assumes that self and other are headings that share no common dependent attributes.
+    """
+    return Heading(
+        [self.attributes[name].todict() for name in self.primary_key]
+        + [
+            other.attributes[name].todict()
+            for name in other.primary_key
+            if name not in self.primary_key
+        ]
+        + [
+            self.attributes[name].todict()
+            for name in self.secondary_attributes
+            if name not in other.primary_key
+        ]
+        + [
+            other.attributes[name].todict()
+            for name in other.secondary_attributes
+            if name not in self.primary_key
+        ]
+    )
+

+ +

+ + + + + + +

+ + +

+ `set_primary_key(primary_key)` + +¶

+ + +

+ +

Create a new heading with the specified primary key. +This low-level method performs no error checking.

+ + +

Source code in datajoint/heading.py

def set_primary_key(self, primary_key):
+    """
+    Create a new heading with the specified primary key.
+    This low-level method performs no error checking.
+    """
+    return Heading(
+        chain(
+            (
+                dict(self.attributes[name].todict(), in_key=True)
+                for name in primary_key
+            ),
+            (
+                dict(self.attributes[name].todict(), in_key=False)
+                for name in self.names
+                if name not in primary_key
+            ),
+        )
+    )
+

+ +

+ + + + + + +

+ + +

+ `make_subquery_heading()` + +¶

+ + +

+ +

Create a new heading with removed attribute sql_expressions. +Used by subqueries, which resolve the sql_expressions.

+ + +

Source code in datajoint/heading.py

def make_subquery_heading(self):
+    """
+    Create a new heading with removed attribute sql_expressions.
+    Used by subqueries, which resolve the sql_expressions.
+    """
+    return Heading(
+        dict(v.todict(), attribute_expression=None)
+        for v in self.attributes.values()
+    )
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/jobs/index.html b/0.14/api/datajoint/jobs/index.html new file mode 100644 index 000000000..a2e5f1d75 --- /dev/null +++ b/0.14/api/datajoint/jobs/index.html @@ -0,0 +1,4697 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + jobs.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + jobs.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

jobs.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ `JobTable` + + +¶

+ + +

+ Bases: Table

+ + + +

A base table with no definition. Allows reserving jobs

+ + + + + + + + +

Source code in datajoint/jobs.py

class JobTable(Table):
+    """
+    A base table with no definition. Allows reserving jobs
+    """
+
+    def __init__(self, conn, database):
+        self.database = database
+        self._connection = conn
+        self._heading = Heading(
+            table_info=dict(
+                conn=conn, database=database, table_name=self.table_name, context=None
+            )
+        )
+        self._support = [self.full_table_name]
+
+        self._definition = """    # job reservation table for `{database}`
+        table_name  :varchar(255)  # className of the table
+        key_hash  :char(32)  # key hash
+        ---
+        status  :enum('reserved','error','ignore')  # if tuple is missing, the job is available
+        key=null  :blob  # structure containing the key
+        error_message=""  :varchar({error_message_length})  # error message returned if failed
+        error_stack=null  :mediumblob  # error stack if failed
+        user="" :varchar(255) # database user
+        host=""  :varchar(255)  # system hostname
+        pid=0  :int unsigned  # system process id
+        connection_id = 0  : bigint unsigned          # connection_id()
+        timestamp=CURRENT_TIMESTAMP  :timestamp   # automatic timestamp
+        """.format(
+            database=database, error_message_length=ERROR_MESSAGE_LENGTH
+        )
+        if not self.is_declared:
+            self.declare()
+        self._user = self.connection.get_user()
+
+    @property
+    def definition(self):
+        return self._definition
+
+    @property
+    def table_name(self):
+        return "~jobs"
+
+    def delete(self):
+        """bypass interactive prompts and dependencies"""
+        self.delete_quick()
+
+    def drop(self):
+        """bypass interactive prompts and dependencies"""
+        self.drop_quick()
+
+    def reserve(self, table_name, key):
+        """
+        Reserve a job for computation.  When a job is reserved, the job table contains an entry for the
+        job key, identified by its hash. When jobs are completed, the entry is removed.
+
+        :param table_name: `database`.`table_name`
+        :param key: the dict of the job's primary key
+        :return: True if reserved job successfully. False = the jobs is already taken
+        """
+        job = dict(
+            table_name=table_name,
+            key_hash=key_hash(key),
+            status="reserved",
+            host=platform.node(),
+            pid=os.getpid(),
+            connection_id=self.connection.connection_id,
+            key=key,
+            user=self._user,
+        )
+        try:
+            with config(enable_python_native_blobs=True):
+                self.insert1(job, ignore_extra_fields=True)
+        except DuplicateError:
+            return False
+        return True
+
+    def ignore(self, table_name, key):
+        """
+        Set a job to be ignored for computation.  When a job is ignored, the job table contains an entry for the
+        job key, identified by its hash, with status "ignore".
+
+        Args:
+        table_name:
+            Table name (str) - `database`.`table_name`
+        key:
+            The dict of the job's primary key
+
+        Returns:
+            True if ignore job successfully. False = the jobs is already taken
+        """
+        job = dict(
+            table_name=table_name,
+            key_hash=key_hash(key),
+            status="ignore",
+            host=platform.node(),
+            pid=os.getpid(),
+            connection_id=self.connection.connection_id,
+            key=key,
+            user=self._user,
+        )
+        try:
+            with config(enable_python_native_blobs=True):
+                self.insert1(job, ignore_extra_fields=True)
+        except DuplicateError:
+            return False
+        return True
+
+    def complete(self, table_name, key):
+        """
+        Log a completed job.  When a job is completed, its reservation entry is deleted.
+
+        :param table_name: `database`.`table_name`
+        :param key: the dict of the job's primary key
+        """
+        job_key = dict(table_name=table_name, key_hash=key_hash(key))
+        (self & job_key).delete_quick()
+
+    def error(self, table_name, key, error_message, error_stack=None):
+        """
+        Log an error message.  The job reservation is replaced with an error entry.
+        if an error occurs, leave an entry describing the problem
+
+        :param table_name: `database`.`table_name`
+        :param key: the dict of the job's primary key
+        :param error_message: string error message
+        :param error_stack: stack trace
+        """
+        if len(error_message) > ERROR_MESSAGE_LENGTH:
+            error_message = (
+                error_message[: ERROR_MESSAGE_LENGTH - len(TRUNCATION_APPENDIX)]
+                + TRUNCATION_APPENDIX
+            )
+        with config(enable_python_native_blobs=True):
+            self.insert1(
+                dict(
+                    table_name=table_name,
+                    key_hash=key_hash(key),
+                    status="error",
+                    host=platform.node(),
+                    pid=os.getpid(),
+                    connection_id=self.connection.connection_id,
+                    user=self._user,
+                    key=key,
+                    error_message=error_message,
+                    error_stack=error_stack,
+                ),
+                replace=True,
+                ignore_extra_fields=True,
+            )
+

+ + + +

+ + + + + + + +

+ + +

+ `delete()` + +¶

+ + +

+ +

bypass interactive prompts and dependencies

+ + +

Source code in datajoint/jobs.py

def delete(self):
+    """bypass interactive prompts and dependencies"""
+    self.delete_quick()
+

+ +

+ + + + + + +

+ + +

+ `drop()` + +¶

+ + +

+ +

bypass interactive prompts and dependencies

+ + +

Source code in datajoint/jobs.py

def drop(self):
+    """bypass interactive prompts and dependencies"""
+    self.drop_quick()
+

+ +

+ + + + + + +

+ + +

+ `reserve(table_name, key)` + +¶

+ + +

+ +

Reserve a job for computation. When a job is reserved, the job table contains an entry for the +job key, identified by its hash. When jobs are completed, the entry is removed.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `table_name` +	+	+ + `database`.`table_name` + +	+ required +
+ `key` +	+	+ + the dict of the job's primary key + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + True if reserved job successfully. False = the jobs is already taken + +

+ + +

Source code in datajoint/jobs.py

65
+66
+67
+68
+69
+70
+71
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+73
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+79
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+87
+88
+89
def reserve(self, table_name, key):
+    """
+    Reserve a job for computation.  When a job is reserved, the job table contains an entry for the
+    job key, identified by its hash. When jobs are completed, the entry is removed.
+
+    :param table_name: `database`.`table_name`
+    :param key: the dict of the job's primary key
+    :return: True if reserved job successfully. False = the jobs is already taken
+    """
+    job = dict(
+        table_name=table_name,
+        key_hash=key_hash(key),
+        status="reserved",
+        host=platform.node(),
+        pid=os.getpid(),
+        connection_id=self.connection.connection_id,
+        key=key,
+        user=self._user,
+    )
+    try:
+        with config(enable_python_native_blobs=True):
+            self.insert1(job, ignore_extra_fields=True)
+    except DuplicateError:
+        return False
+    return True
+

+ +

+ + + + + + +

+ + +

+ `ignore(table_name, key)` + +¶

+ + +

+ +

Set a job to be ignored for computation. When a job is ignored, the job table contains an entry for the +job key, identified by its hash, with status "ignore".

Args: +table_name: + Table name (str) - database.table_name +key: + The dict of the job's primary key

Returns: + True if ignore job successfully. False = the jobs is already taken

+ + +

Source code in datajoint/jobs.py

def ignore(self, table_name, key):
+    """
+    Set a job to be ignored for computation.  When a job is ignored, the job table contains an entry for the
+    job key, identified by its hash, with status "ignore".
+
+    Args:
+    table_name:
+        Table name (str) - `database`.`table_name`
+    key:
+        The dict of the job's primary key
+
+    Returns:
+        True if ignore job successfully. False = the jobs is already taken
+    """
+    job = dict(
+        table_name=table_name,
+        key_hash=key_hash(key),
+        status="ignore",
+        host=platform.node(),
+        pid=os.getpid(),
+        connection_id=self.connection.connection_id,
+        key=key,
+        user=self._user,
+    )
+    try:
+        with config(enable_python_native_blobs=True):
+            self.insert1(job, ignore_extra_fields=True)
+    except DuplicateError:
+        return False
+    return True
+

+ +

+ + + + + + +

+ + +

+ `complete(table_name, key)` + +¶

+ + +

+ +

Log a completed job. When a job is completed, its reservation entry is deleted.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `table_name` +	+	+ + `database`.`table_name` + +	+ required +
+ `key` +	+	+ + the dict of the job's primary key + +	+ required +

+ + +

Source code in datajoint/jobs.py

def complete(self, table_name, key):
+    """
+    Log a completed job.  When a job is completed, its reservation entry is deleted.
+
+    :param table_name: `database`.`table_name`
+    :param key: the dict of the job's primary key
+    """
+    job_key = dict(table_name=table_name, key_hash=key_hash(key))
+    (self & job_key).delete_quick()
+

+ +

+ + + + + + +

+ + +

+ `error(table_name, key, error_message, error_stack=None)` + +¶

+ + +

+ +

Log an error message. The job reservation is replaced with an error entry. +if an error occurs, leave an entry describing the problem

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `table_name` +	+	+ + `database`.`table_name` + +	+ required +
+ `key` +	+	+ + the dict of the job's primary key + +	+ required +
+ `error_message` +	+	+ + string error message + +	+ required +
+ `error_stack` +	+	+ + stack trace + +	+ `None` +

+ + +

Source code in datajoint/jobs.py

def error(self, table_name, key, error_message, error_stack=None):
+    """
+    Log an error message.  The job reservation is replaced with an error entry.
+    if an error occurs, leave an entry describing the problem
+
+    :param table_name: `database`.`table_name`
+    :param key: the dict of the job's primary key
+    :param error_message: string error message
+    :param error_stack: stack trace
+    """
+    if len(error_message) > ERROR_MESSAGE_LENGTH:
+        error_message = (
+            error_message[: ERROR_MESSAGE_LENGTH - len(TRUNCATION_APPENDIX)]
+            + TRUNCATION_APPENDIX
+        )
+    with config(enable_python_native_blobs=True):
+        self.insert1(
+            dict(
+                table_name=table_name,
+                key_hash=key_hash(key),
+                status="error",
+                host=platform.node(),
+                pid=os.getpid(),
+                connection_id=self.connection.connection_id,
+                user=self._user,
+                key=key,
+                error_message=error_message,
+                error_stack=error_stack,
+            ),
+            replace=True,
+            ignore_extra_fields=True,
+        )
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/logging/index.html b/0.14/api/datajoint/logging/index.html new file mode 100644 index 000000000..1b995cb16 --- /dev/null +++ b/0.14/api/datajoint/logging/index.html @@ -0,0 +1,3692 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + logging.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + logging.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/plugin/index.html b/0.14/api/datajoint/plugin/index.html new file mode 100644 index 000000000..2be5b921b --- /dev/null +++ b/0.14/api/datajoint/plugin/index.html @@ -0,0 +1,3692 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + plugin.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + plugin.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/preview/index.html b/0.14/api/datajoint/preview/index.html new file mode 100644 index 000000000..0c7f40c83 --- /dev/null +++ b/0.14/api/datajoint/preview/index.html @@ -0,0 +1,3694 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + preview.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + preview.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/s3/index.html b/0.14/api/datajoint/s3/index.html new file mode 100644 index 000000000..50cf85ec5 --- /dev/null +++ b/0.14/api/datajoint/s3/index.html @@ -0,0 +1,4100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + s3.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + s3.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

s3.py

+ +

+ + + + +

+ +

AWS S3 operations

+ + + + + + + + + + +

+ + + + + + + + + + + +

+ + + +

+ `Folder` + + +¶

+ + +

+ + + +

A Folder instance manipulates a flat folder of objects within an S3-compatible object store

+ + + + + + + + +

Source code in datajoint/s3.py

class Folder:
+    """
+    A Folder instance manipulates a flat folder of objects within an S3-compatible object store
+    """
+
+    def __init__(
+        self,
+        endpoint,
+        bucket,
+        access_key,
+        secret_key,
+        *,
+        secure=False,
+        proxy_server=None,
+        **_,
+    ):
+        # from https://docs.min.io/docs/python-client-api-reference
+        self.client = minio.Minio(
+            endpoint,
+            access_key=access_key,
+            secret_key=secret_key,
+            secure=secure,
+            http_client=(
+                urllib3.ProxyManager(
+                    proxy_server,
+                    timeout=urllib3.Timeout.DEFAULT_TIMEOUT,
+                    cert_reqs="CERT_REQUIRED",
+                    retries=urllib3.Retry(
+                        total=5,
+                        backoff_factor=0.2,
+                        status_forcelist=[500, 502, 503, 504],
+                    ),
+                )
+                if proxy_server
+                else None
+            ),
+        )
+        self.bucket = bucket
+        if not self.client.bucket_exists(bucket):
+            raise errors.BucketInaccessible("Inaccessible s3 bucket %s" % bucket)
+
+    def put(self, name, buffer):
+        logger.debug("put: {}:{}".format(self.bucket, name))
+        return self.client.put_object(
+            self.bucket, str(name), BytesIO(buffer), length=len(buffer)
+        )
+
+    def fput(self, local_file, name, metadata=None):
+        logger.debug("fput: {} -> {}:{}".format(self.bucket, local_file, name))
+        return self.client.fput_object(
+            self.bucket, str(name), str(local_file), metadata=metadata
+        )
+
+    def get(self, name):
+        logger.debug("get: {}:{}".format(self.bucket, name))
+        try:
+            with self.client.get_object(self.bucket, str(name)) as result:
+                data = [d for d in result.stream()]
+            return b"".join(data)
+        except minio.error.S3Error as e:
+            if e.code == "NoSuchKey":
+                raise errors.MissingExternalFile("Missing s3 key %s" % name)
+            else:
+                raise e
+
+    def fget(self, name, local_filepath):
+        """get file from object name to local filepath"""
+        logger.debug("fget: {}:{}".format(self.bucket, name))
+        name = str(name)
+        stat = self.client.stat_object(self.bucket, name)
+        meta = {k.lower().lstrip("x-amz-meta"): v for k, v in stat.metadata.items()}
+        data = self.client.get_object(self.bucket, name)
+        local_filepath = Path(local_filepath)
+        local_filepath.parent.mkdir(parents=True, exist_ok=True)
+        with local_filepath.open("wb") as f:
+            for d in data.stream(1 << 16):
+                f.write(d)
+        if "contents_hash" in meta:
+            return uuid.UUID(meta["contents_hash"])
+
+    def stat(self, name):
+        """Return stat result for an object, or None if it does not exist."""
+        logger.debug("stat: {}:{}".format(self.bucket, name))
+        try:
+            return self.client.stat_object(self.bucket, str(name))
+        except minio.error.S3Error as e:
+            if e.code == "NoSuchKey":
+                return None
+            raise e
+
+    def exists(self, name):
+        logger.debug("exists: {}:{}".format(self.bucket, name))
+        return self.stat(name) is not None
+
+    def get_size(self, name):
+        logger.debug("get_size: {}:{}".format(self.bucket, name))
+        try:
+            return self.client.stat_object(self.bucket, str(name)).size
+        except minio.error.S3Error as e:
+            if e.code == "NoSuchKey":
+                raise errors.MissingExternalFile
+            raise e
+
+    def remove_object(self, name):
+        logger.debug("remove_object: {}:{}".format(self.bucket, name))
+        try:
+            self.client.remove_object(self.bucket, str(name))
+        except minio.error.MinioException:
+            raise errors.DataJointError("Failed to delete %s from s3 storage" % name)
+

+ + + +

+ + + + + + + +

+ + +

+ `fget(name, local_filepath)` + +¶

+ + +

+ +

get file from object name to local filepath

+ + +

Source code in datajoint/s3.py

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def fget(self, name, local_filepath):
+    """get file from object name to local filepath"""
+    logger.debug("fget: {}:{}".format(self.bucket, name))
+    name = str(name)
+    stat = self.client.stat_object(self.bucket, name)
+    meta = {k.lower().lstrip("x-amz-meta"): v for k, v in stat.metadata.items()}
+    data = self.client.get_object(self.bucket, name)
+    local_filepath = Path(local_filepath)
+    local_filepath.parent.mkdir(parents=True, exist_ok=True)
+    with local_filepath.open("wb") as f:
+        for d in data.stream(1 << 16):
+            f.write(d)
+    if "contents_hash" in meta:
+        return uuid.UUID(meta["contents_hash"])
+

+ +

+ + + + + + +

+ + +

+ `stat(name)` + +¶

+ + +

+ +

Return stat result for an object, or None if it does not exist.

+ + +

Source code in datajoint/s3.py

def stat(self, name):
+    """Return stat result for an object, or None if it does not exist."""
+    logger.debug("stat: {}:{}".format(self.bucket, name))
+    try:
+        return self.client.stat_object(self.bucket, str(name))
+    except minio.error.S3Error as e:
+        if e.code == "NoSuchKey":
+            return None
+        raise e
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/schemas/index.html b/0.14/api/datajoint/schemas/index.html new file mode 100644 index 000000000..410af0b94 --- /dev/null +++ b/0.14/api/datajoint/schemas/index.html @@ -0,0 +1,6127 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + schemas.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + schemas.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

schemas.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + +

+ `ordered_dir(class_)` + +¶

+ + +

+ +

List (most) attributes of the class including inherited ones, similar to dir built-in function, +but respects order of attribute declaration as much as possible.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `class_` +	+	+ + class to list members for + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a list of attributes declared in class_ and its superclasses + +

+ + +

Source code in datajoint/schemas.py

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def ordered_dir(class_):
+    """
+    List (most) attributes of the class including inherited ones, similar to `dir` built-in function,
+    but respects order of attribute declaration as much as possible.
+
+    :param class_: class to list members for
+    :return: a list of attributes declared in class_ and its superclasses
+    """
+    attr_list = list()
+    for c in reversed(class_.mro()):
+        attr_list.extend(e for e in c.__dict__ if e not in attr_list)
+    return attr_list
+

+ +

+ + + + + + +

+ + + +

+ `Schema` + + +¶

+ + +

+ + + +

A schema object is a decorator for UserTable classes that binds them to their database. +It also specifies the namespace context in which other UserTable classes are defined.

+ + + + + + + + +

Source code in datajoint/schemas.py

class Schema:
+    """
+    A schema object is a decorator for UserTable classes that binds them to their database.
+    It also specifies the namespace `context` in which other UserTable classes are defined.
+    """
+
+    def __init__(
+        self,
+        schema_name=None,
+        context=None,
+        *,
+        connection=None,
+        create_schema=True,
+        create_tables=True,
+        add_objects=None,
+    ):
+        """
+        Associate database schema `schema_name`. If the schema does not exist, attempt to
+        create it on the server.
+
+        If the schema_name is omitted, then schema.activate(..) must be called later
+        to associate with the database.
+
+        :param schema_name: the database schema to associate.
+        :param context: dictionary for looking up foreign key references, leave None to use local context.
+        :param connection: Connection object. Defaults to datajoint.conn().
+        :param create_schema: When False, do not create the schema and raise an error if missing.
+        :param create_tables: When False, do not create tables and raise errors when accessing missing tables.
+        :param add_objects: a mapping with additional objects to make available to the context in which table classes
+        are declared.
+        """
+        self._log = None
+        self.connection = connection
+        self.database = None
+        self.context = context
+        self.create_schema = create_schema
+        self.create_tables = create_tables
+        self._jobs = None
+        self.external = ExternalMapping(self)
+        self.add_objects = add_objects
+        self.declare_list = []
+        if schema_name:
+            self.activate(schema_name)
+
+    def is_activated(self):
+        return self.database is not None
+
+    def activate(
+        self,
+        schema_name=None,
+        *,
+        connection=None,
+        create_schema=None,
+        create_tables=None,
+        add_objects=None,
+    ):
+        """
+        Associate database schema `schema_name`. If the schema does not exist, attempt to
+        create it on the server.
+
+        :param schema_name: the database schema to associate.
+            schema_name=None is used to assert that the schema has already been activated.
+        :param connection: Connection object. Defaults to datajoint.conn().
+        :param create_schema: If False, do not create the schema and raise an error if missing.
+        :param create_tables: If False, do not create tables and raise errors when attempting
+            to access missing tables.
+        :param add_objects: a mapping with additional objects to make available to the context
+            in which table classes are declared.
+        """
+        if schema_name is None:
+            if self.exists:
+                return
+            raise DataJointError("Please provide a schema_name to activate the schema.")
+        if self.database is not None and self.exists:
+            if self.database == schema_name:  # already activated
+                return
+            raise DataJointError(
+                "The schema is already activated for schema {db}.".format(
+                    db=self.database
+                )
+            )
+        if connection is not None:
+            self.connection = connection
+        if self.connection is None:
+            self.connection = conn()
+        self.database = schema_name
+        if create_schema is not None:
+            self.create_schema = create_schema
+        if create_tables is not None:
+            self.create_tables = create_tables
+        if add_objects:
+            self.add_objects = add_objects
+        if not self.exists:
+            if not self.create_schema or not self.database:
+                raise DataJointError(
+                    "Database `{name}` has not yet been declared. "
+                    "Set argument create_schema=True to create it.".format(
+                        name=schema_name
+                    )
+                )
+            # create database
+            logger.debug("Creating schema `{name}`.".format(name=schema_name))
+            try:
+                self.connection.query(
+                    "CREATE DATABASE `{name}`".format(name=schema_name)
+                )
+            except AccessError:
+                raise DataJointError(
+                    "Schema `{name}` does not exist and could not be created. "
+                    "Check permissions.".format(name=schema_name)
+                )
+            else:
+                self.log("created")
+        self.connection.register(self)
+
+        # decorate all tables already decorated
+        for cls, context in self.declare_list:
+            if self.add_objects:
+                context = dict(context, **self.add_objects)
+            self._decorate_master(cls, context)
+
+    def _assert_exists(self, message=None):
+        if not self.exists:
+            raise DataJointError(
+                message
+                or "Schema `{db}` has not been created.".format(db=self.database)
+            )
+
+    def __call__(self, cls, *, context=None):
+        """
+        Binds the supplied class to a schema. This is intended to be used as a decorator.
+
+        :param cls: class to decorate.
+        :param context: supplied when called from spawn_missing_classes
+        """
+        context = context or self.context or inspect.currentframe().f_back.f_locals
+        if issubclass(cls, Part):
+            raise DataJointError(
+                "The schema decorator should not be applied to Part tables."
+            )
+        if self.is_activated():
+            self._decorate_master(cls, context)
+        else:
+            self.declare_list.append((cls, context))
+        return cls
+
+    def _decorate_master(self, cls, context):
+        """
+
+        :param cls: the master class to process
+        :param context: the class' declaration context
+        """
+        self._decorate_table(
+            cls, context=dict(context, self=cls, **{cls.__name__: cls})
+        )
+        # Process part tables
+        for part in ordered_dir(cls):
+            if part[0].isupper():
+                part = getattr(cls, part)
+                if inspect.isclass(part) and issubclass(part, Part):
+                    part._master = cls
+                    # allow addressing master by name or keyword 'master'
+                    self._decorate_table(
+                        part,
+                        context=dict(
+                            context, master=cls, self=part, **{cls.__name__: cls}
+                        ),
+                    )
+
+    def _decorate_table(self, table_class, context, assert_declared=False):
+        """
+        assign schema properties to the table class and declare the table
+        """
+        table_class.database = self.database
+        table_class._connection = self.connection
+        table_class._heading = Heading(
+            table_info=dict(
+                conn=self.connection,
+                database=self.database,
+                table_name=table_class.table_name,
+                context=context,
+            )
+        )
+        table_class._support = [table_class.full_table_name]
+        table_class.declaration_context = context
+
+        # instantiate the class, declare the table if not already
+        instance = table_class()
+        is_declared = instance.is_declared
+        if not is_declared and not assert_declared and self.create_tables:
+            instance.declare(context)
+            self.connection.dependencies.clear()
+        is_declared = is_declared or instance.is_declared
+
+        # add table definition to the doc string
+        if isinstance(table_class.definition, str):
+            table_class.__doc__ = (
+                (table_class.__doc__ or "")
+                + "\nTable definition:\n\n"
+                + table_class.definition
+            )
+
+        # fill values in Lookup tables from their contents property
+        if (
+            isinstance(instance, Lookup)
+            and hasattr(instance, "contents")
+            and is_declared
+        ):
+            contents = list(instance.contents)
+            if len(contents) > len(instance):
+                if instance.heading.has_autoincrement:
+                    warnings.warn(
+                        (
+                            "Contents has changed but cannot be inserted because "
+                            "{table} has autoincrement."
+                        ).format(table=instance.__class__.__name__)
+                    )
+                else:
+                    instance.insert(contents, skip_duplicates=True)
+
+    @property
+    def log(self):
+        self._assert_exists()
+        if self._log is None:
+            self._log = Log(self.connection, self.database)
+        return self._log
+
+    def __repr__(self):
+        return "Schema `{name}`\n".format(name=self.database)
+
+    @property
+    def size_on_disk(self):
+        """
+        :return: size of the entire schema in bytes
+        """
+        self._assert_exists()
+        return int(
+            self.connection.query(
+                """
+            SELECT SUM(data_length + index_length)
+            FROM information_schema.tables WHERE table_schema='{db}'
+            """.format(
+                    db=self.database
+                )
+            ).fetchone()[0]
+        )
+
+    def spawn_missing_classes(self, context=None):
+        """
+        Creates the appropriate python user table classes from tables in the schema and places them
+        in the context.
+
+        :param context: alternative context to place the missing classes into, e.g. locals()
+        """
+        self._assert_exists()
+        if context is None:
+            if self.context is not None:
+                context = self.context
+            else:
+                # if context is missing, use the calling namespace
+                frame = inspect.currentframe().f_back
+                context = frame.f_locals
+                del frame
+        tables = [
+            row[0]
+            for row in self.connection.query("SHOW TABLES in `%s`" % self.database)
+            if lookup_class_name(
+                "`{db}`.`{tab}`".format(db=self.database, tab=row[0]), context, 0
+            )
+            is None
+        ]
+        master_classes = (Lookup, Manual, Imported, Computed)
+        part_tables = []
+        for table_name in tables:
+            class_name = to_camel_case(table_name)
+            if class_name not in context:
+                try:
+                    cls = next(
+                        cls
+                        for cls in master_classes
+                        if re.fullmatch(cls.tier_regexp, table_name)
+                    )
+                except StopIteration:
+                    if re.fullmatch(Part.tier_regexp, table_name):
+                        part_tables.append(table_name)
+                else:
+                    # declare and decorate master table classes
+                    context[class_name] = self(
+                        type(class_name, (cls,), dict()), context=context
+                    )
+
+        # attach parts to masters
+        for table_name in part_tables:
+            groups = re.fullmatch(Part.tier_regexp, table_name).groupdict()
+            class_name = to_camel_case(groups["part"])
+            try:
+                master_class = context[to_camel_case(groups["master"])]
+            except KeyError:
+                raise DataJointError(
+                    "The table %s does not follow DataJoint naming conventions"
+                    % table_name
+                )
+            part_class = type(class_name, (Part,), dict(definition=...))
+            part_class._master = master_class
+            self._decorate_table(part_class, context=context, assert_declared=True)
+            setattr(master_class, class_name, part_class)
+
+    def drop(self, force=False):
+        """
+        Drop the associated schema if it exists
+        """
+        if not self.exists:
+            logger.info(
+                "Schema named `{database}` does not exist. Doing nothing.".format(
+                    database=self.database
+                )
+            )
+        elif (
+            not config["safemode"]
+            or force
+            or user_choice(
+                "Proceed to delete entire schema `%s`?" % self.database, default="no"
+            )
+            == "yes"
+        ):
+            logger.debug("Dropping `{database}`.".format(database=self.database))
+            try:
+                self.connection.query(
+                    "DROP DATABASE `{database}`".format(database=self.database)
+                )
+                logger.debug(
+                    "Schema `{database}` was dropped successfully.".format(
+                        database=self.database
+                    )
+                )
+            except AccessError:
+                raise AccessError(
+                    "An attempt to drop schema `{database}` "
+                    "has failed. Check permissions.".format(database=self.database)
+                )
+
+    @property
+    def exists(self):
+        """
+        :return: true if the associated schema exists on the server
+        """
+        if self.database is None:
+            raise DataJointError("Schema must be activated first.")
+        return bool(
+            self.connection.query(
+                "SELECT schema_name "
+                "FROM information_schema.schemata "
+                "WHERE schema_name = '{database}'".format(database=self.database)
+            ).rowcount
+        )
+
+    @property
+    def jobs(self):
+        """
+        schema.jobs provides a view of the job reservation table for the schema
+
+        :return: jobs table
+        """
+        self._assert_exists()
+        if self._jobs is None:
+            self._jobs = JobTable(self.connection, self.database)
+        return self._jobs
+
+    @property
+    def code(self):
+        self._assert_exists()
+        return self.save()
+
+    def save(self, python_filename=None):
+        """
+        Generate the code for a module that recreates the schema.
+        This method is in preparation for a future release and is not officially supported.
+
+        :return: a string containing the body of a complete Python module defining this schema.
+        """
+        self.connection.dependencies.load()
+        self._assert_exists()
+        module_count = itertools.count()
+        # add virtual modules for referenced modules with names vmod0, vmod1, ...
+        module_lookup = collections.defaultdict(
+            lambda: "vmod" + str(next(module_count))
+        )
+        db = self.database
+
+        def make_class_definition(table):
+            tier = _get_tier(table).__name__
+            class_name = table.split(".")[1].strip("`")
+            indent = ""
+            if tier == "Part":
+                class_name = class_name.split("__")[-1]
+                indent += "    "
+            class_name = to_camel_case(class_name)
+
+            def replace(s):
+                d, tabs = s.group(1), s.group(2)
+                return ("" if d == db else (module_lookup[d] + ".")) + ".".join(
+                    to_camel_case(tab) for tab in tabs.lstrip("__").split("__")
+                )
+
+            return ("" if tier == "Part" else "\n@schema\n") + (
+                "{indent}class {class_name}(dj.{tier}):\n"
+                '{indent}    definition = """\n'
+                '{indent}    {defi}"""'
+            ).format(
+                class_name=class_name,
+                indent=indent,
+                tier=tier,
+                defi=re.sub(
+                    r"`([^`]+)`.`([^`]+)`",
+                    replace,
+                    FreeTable(self.connection, table).describe(),
+                ).replace("\n", "\n    " + indent),
+            )
+
+        tables = self.connection.dependencies.topo_sort()
+        body = "\n\n".join(make_class_definition(table) for table in tables)
+        python_code = "\n\n".join(
+            (
+                '"""This module was auto-generated by datajoint from an existing schema"""',
+                "import datajoint as dj\n\nschema = dj.Schema('{db}')".format(db=db),
+                "\n".join(
+                    "{module} = dj.VirtualModule('{module}', '{schema_name}')".format(
+                        module=v, schema_name=k
+                    )
+                    for k, v in module_lookup.items()
+                ),
+                body,
+            )
+        )
+        if python_filename is None:
+            return python_code
+        with open(python_filename, "wt") as f:
+            f.write(python_code)
+
+    def list_tables(self):
+        """
+        Return a list of all tables in the schema except tables with ~ in first character such
+        as ~logs and ~job
+
+        :return: A list of table names from the database schema.
+        """
+        self.connection.dependencies.load()
+        return [
+            t
+            for d, t in (
+                table_name.replace("`", "").split(".")
+                for table_name in self.connection.dependencies.topo_sort()
+            )
+            if d == self.database
+        ]
+

+ + + +

+ + + + + + + +

+ + +

+ `activate(schema_name=None, *, connection=None, create_schema=None, create_tables=None, add_objects=None)` + +¶

+ + +

+ +

Associate database schema schema_name. If the schema does not exist, attempt to +create it on the server.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `schema_name` +	+	+ + the database schema to associate. +schema_name=None is used to assert that the schema has already been activated. + +	+ `None` +
+ `connection` +	+	+ + Connection object. Defaults to datajoint.conn(). + +	+ `None` +
+ `create_schema` +	+	+ + If False, do not create the schema and raise an error if missing. + +	+ `None` +
+ `create_tables` +	+	+ + If False, do not create tables and raise errors when attempting +to access missing tables. + +	+ `None` +
+ `add_objects` +	+	+ + a mapping with additional objects to make available to the context +in which table classes are declared. + +	+ `None` +

+ + +

Source code in datajoint/schemas.py

def activate(
+    self,
+    schema_name=None,
+    *,
+    connection=None,
+    create_schema=None,
+    create_tables=None,
+    add_objects=None,
+):
+    """
+    Associate database schema `schema_name`. If the schema does not exist, attempt to
+    create it on the server.
+
+    :param schema_name: the database schema to associate.
+        schema_name=None is used to assert that the schema has already been activated.
+    :param connection: Connection object. Defaults to datajoint.conn().
+    :param create_schema: If False, do not create the schema and raise an error if missing.
+    :param create_tables: If False, do not create tables and raise errors when attempting
+        to access missing tables.
+    :param add_objects: a mapping with additional objects to make available to the context
+        in which table classes are declared.
+    """
+    if schema_name is None:
+        if self.exists:
+            return
+        raise DataJointError("Please provide a schema_name to activate the schema.")
+    if self.database is not None and self.exists:
+        if self.database == schema_name:  # already activated
+            return
+        raise DataJointError(
+            "The schema is already activated for schema {db}.".format(
+                db=self.database
+            )
+        )
+    if connection is not None:
+        self.connection = connection
+    if self.connection is None:
+        self.connection = conn()
+    self.database = schema_name
+    if create_schema is not None:
+        self.create_schema = create_schema
+    if create_tables is not None:
+        self.create_tables = create_tables
+    if add_objects:
+        self.add_objects = add_objects
+    if not self.exists:
+        if not self.create_schema or not self.database:
+            raise DataJointError(
+                "Database `{name}` has not yet been declared. "
+                "Set argument create_schema=True to create it.".format(
+                    name=schema_name
+                )
+            )
+        # create database
+        logger.debug("Creating schema `{name}`.".format(name=schema_name))
+        try:
+            self.connection.query(
+                "CREATE DATABASE `{name}`".format(name=schema_name)
+            )
+        except AccessError:
+            raise DataJointError(
+                "Schema `{name}` does not exist and could not be created. "
+                "Check permissions.".format(name=schema_name)
+            )
+        else:
+            self.log("created")
+    self.connection.register(self)
+
+    # decorate all tables already decorated
+    for cls, context in self.declare_list:
+        if self.add_objects:
+            context = dict(context, **self.add_objects)
+        self._decorate_master(cls, context)
+

+ +

+ + + + + + +

+ + + +

+ `size_on_disk` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + size of the entire schema in bytes + +

+ +

+ + + + + + +

+ + +

+ `spawn_missing_classes(context=None)` + +¶

+ + +

+ +

Creates the appropriate python user table classes from tables in the schema and places them +in the context.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `context` +	+	+ + alternative context to place the missing classes into, e.g. locals() + +	+ `None` +

+ + +

Source code in datajoint/schemas.py

def spawn_missing_classes(self, context=None):
+    """
+    Creates the appropriate python user table classes from tables in the schema and places them
+    in the context.
+
+    :param context: alternative context to place the missing classes into, e.g. locals()
+    """
+    self._assert_exists()
+    if context is None:
+        if self.context is not None:
+            context = self.context
+        else:
+            # if context is missing, use the calling namespace
+            frame = inspect.currentframe().f_back
+            context = frame.f_locals
+            del frame
+    tables = [
+        row[0]
+        for row in self.connection.query("SHOW TABLES in `%s`" % self.database)
+        if lookup_class_name(
+            "`{db}`.`{tab}`".format(db=self.database, tab=row[0]), context, 0
+        )
+        is None
+    ]
+    master_classes = (Lookup, Manual, Imported, Computed)
+    part_tables = []
+    for table_name in tables:
+        class_name = to_camel_case(table_name)
+        if class_name not in context:
+            try:
+                cls = next(
+                    cls
+                    for cls in master_classes
+                    if re.fullmatch(cls.tier_regexp, table_name)
+                )
+            except StopIteration:
+                if re.fullmatch(Part.tier_regexp, table_name):
+                    part_tables.append(table_name)
+            else:
+                # declare and decorate master table classes
+                context[class_name] = self(
+                    type(class_name, (cls,), dict()), context=context
+                )
+
+    # attach parts to masters
+    for table_name in part_tables:
+        groups = re.fullmatch(Part.tier_regexp, table_name).groupdict()
+        class_name = to_camel_case(groups["part"])
+        try:
+            master_class = context[to_camel_case(groups["master"])]
+        except KeyError:
+            raise DataJointError(
+                "The table %s does not follow DataJoint naming conventions"
+                % table_name
+            )
+        part_class = type(class_name, (Part,), dict(definition=...))
+        part_class._master = master_class
+        self._decorate_table(part_class, context=context, assert_declared=True)
+        setattr(master_class, class_name, part_class)
+

+ +

+ + + + + + +

+ + +

+ `drop(force=False)` + +¶

+ + +

+ +

Drop the associated schema if it exists

+ + +

Source code in datajoint/schemas.py

def drop(self, force=False):
+    """
+    Drop the associated schema if it exists
+    """
+    if not self.exists:
+        logger.info(
+            "Schema named `{database}` does not exist. Doing nothing.".format(
+                database=self.database
+            )
+        )
+    elif (
+        not config["safemode"]
+        or force
+        or user_choice(
+            "Proceed to delete entire schema `%s`?" % self.database, default="no"
+        )
+        == "yes"
+    ):
+        logger.debug("Dropping `{database}`.".format(database=self.database))
+        try:
+            self.connection.query(
+                "DROP DATABASE `{database}`".format(database=self.database)
+            )
+            logger.debug(
+                "Schema `{database}` was dropped successfully.".format(
+                    database=self.database
+                )
+            )
+        except AccessError:
+            raise AccessError(
+                "An attempt to drop schema `{database}` "
+                "has failed. Check permissions.".format(database=self.database)
+            )
+

+ +

+ + + + + + +

+ + + +

+ `exists` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + true if the associated schema exists on the server + +

+ +

+ + + + + + +

+ + + +

+ `jobs` + + + `property` + + +¶

+ + +

+ +

schema.jobs provides a view of the job reservation table for the schema

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + jobs table + +

+ +

+ + + + + + +

+ + +

+ `save(python_filename=None)` + +¶

+ + +

+ +

Generate the code for a module that recreates the schema. +This method is in preparation for a future release and is not officially supported.

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a string containing the body of a complete Python module defining this schema. + +

+ + +

Source code in datajoint/schemas.py

def save(self, python_filename=None):
+    """
+    Generate the code for a module that recreates the schema.
+    This method is in preparation for a future release and is not officially supported.
+
+    :return: a string containing the body of a complete Python module defining this schema.
+    """
+    self.connection.dependencies.load()
+    self._assert_exists()
+    module_count = itertools.count()
+    # add virtual modules for referenced modules with names vmod0, vmod1, ...
+    module_lookup = collections.defaultdict(
+        lambda: "vmod" + str(next(module_count))
+    )
+    db = self.database
+
+    def make_class_definition(table):
+        tier = _get_tier(table).__name__
+        class_name = table.split(".")[1].strip("`")
+        indent = ""
+        if tier == "Part":
+            class_name = class_name.split("__")[-1]
+            indent += "    "
+        class_name = to_camel_case(class_name)
+
+        def replace(s):
+            d, tabs = s.group(1), s.group(2)
+            return ("" if d == db else (module_lookup[d] + ".")) + ".".join(
+                to_camel_case(tab) for tab in tabs.lstrip("__").split("__")
+            )
+
+        return ("" if tier == "Part" else "\n@schema\n") + (
+            "{indent}class {class_name}(dj.{tier}):\n"
+            '{indent}    definition = """\n'
+            '{indent}    {defi}"""'
+        ).format(
+            class_name=class_name,
+            indent=indent,
+            tier=tier,
+            defi=re.sub(
+                r"`([^`]+)`.`([^`]+)`",
+                replace,
+                FreeTable(self.connection, table).describe(),
+            ).replace("\n", "\n    " + indent),
+        )
+
+    tables = self.connection.dependencies.topo_sort()
+    body = "\n\n".join(make_class_definition(table) for table in tables)
+    python_code = "\n\n".join(
+        (
+            '"""This module was auto-generated by datajoint from an existing schema"""',
+            "import datajoint as dj\n\nschema = dj.Schema('{db}')".format(db=db),
+            "\n".join(
+                "{module} = dj.VirtualModule('{module}', '{schema_name}')".format(
+                    module=v, schema_name=k
+                )
+                for k, v in module_lookup.items()
+            ),
+            body,
+        )
+    )
+    if python_filename is None:
+        return python_code
+    with open(python_filename, "wt") as f:
+        f.write(python_code)
+

+ +

+ + + + + + +

+ + +

+ `list_tables()` + +¶

+ + +

+ +

Return a list of all tables in the schema except tables with ~ in first character such +as ~logs and ~job

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + A list of table names from the database schema. + +

+ + +

Source code in datajoint/schemas.py

def list_tables(self):
+    """
+    Return a list of all tables in the schema except tables with ~ in first character such
+    as ~logs and ~job
+
+    :return: A list of table names from the database schema.
+    """
+    self.connection.dependencies.load()
+    return [
+        t
+        for d, t in (
+            table_name.replace("`", "").split(".")
+            for table_name in self.connection.dependencies.topo_sort()
+        )
+        if d == self.database
+    ]
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `VirtualModule` + + +¶

+ + +

+ Bases: ModuleType

+ + + +

A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database. +It declares the schema objects and a class for each table.

+ + + + + + + + +

Source code in datajoint/schemas.py

class VirtualModule(types.ModuleType):
+    """
+    A virtual module imitates a Python module representing a DataJoint schema from table definitions in the database.
+    It declares the schema objects and a class for each table.
+    """
+
+    def __init__(
+        self,
+        module_name,
+        schema_name,
+        *,
+        create_schema=False,
+        create_tables=False,
+        connection=None,
+        add_objects=None,
+    ):
+        """
+        Creates a python module with the given name from the name of a schema on the server and
+        automatically adds classes to it corresponding to the tables in the schema.
+
+        :param module_name: displayed module name
+        :param schema_name: name of the database in mysql
+        :param create_schema: if True, create the schema on the database server
+        :param create_tables: if True, module.schema can be used as the decorator for declaring new
+        :param connection: a dj.Connection object to pass into the schema
+        :param add_objects: additional objects to add to the module
+        :return: the python module containing classes from the schema object and the table classes
+        """
+        super(VirtualModule, self).__init__(name=module_name)
+        _schema = Schema(
+            schema_name,
+            create_schema=create_schema,
+            create_tables=create_tables,
+            connection=connection,
+        )
+        if add_objects:
+            self.__dict__.update(add_objects)
+        self.__dict__["schema"] = _schema
+        _schema.spawn_missing_classes(context=self.__dict__)
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + +

+ `list_schemas(connection=None)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `connection` +	+	+ + a dj.Connection object + +	+ `None` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of all accessible schemas on the server + +

+ + +

Source code in datajoint/schemas.py

def list_schemas(connection=None):
+    """
+    :param connection: a dj.Connection object
+    :return: list of all accessible schemas on the server
+    """
+    return [
+        r[0]
+        for r in (connection or conn()).query(
+            "SELECT schema_name "
+            "FROM information_schema.schemata "
+            'WHERE schema_name <> "information_schema"'
+        )
+    ]
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/settings/index.html b/0.14/api/datajoint/settings/index.html new file mode 100644 index 000000000..92bfe225b --- /dev/null +++ b/0.14/api/datajoint/settings/index.html @@ -0,0 +1,4608 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + settings.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + settings.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

settings.py

+ +

+ + + + +

+ +

Settings for DataJoint

+ + + + + + + + + + +

+ + + + + + + + + + + +

+ + + +

+ `Config` + + +¶

+ + +

+ Bases: MutableMapping

+ + + + + + + + + + +

Source code in datajoint/settings.py

class Config(collections.abc.MutableMapping):
+    instance = None
+
+    def __init__(self, *args, **kwargs):
+        if not Config.instance:
+            Config.instance = Config.__Config(*args, **kwargs)
+        else:
+            Config.instance._conf.update(dict(*args, **kwargs))
+
+    def __getattr__(self, name):
+        return getattr(self.instance, name)
+
+    def __getitem__(self, item):
+        return self.instance.__getitem__(item)
+
+    def __setitem__(self, item, value):
+        self.instance.__setitem__(item, value)
+
+    def __str__(self):
+        return pprint.pformat(self.instance._conf, indent=4)
+
+    def __repr__(self):
+        return self.__str__()
+
+    def __delitem__(self, key):
+        del self.instance._conf[key]
+
+    def __iter__(self):
+        return iter(self.instance._conf)
+
+    def __len__(self):
+        return len(self.instance._conf)
+
+    def save(self, filename, verbose=False):
+        """
+        Saves the settings in JSON format to the given file path.
+
+        :param filename: filename of the local JSON settings file.
+        :param verbose: report having saved the settings file
+        """
+        with open(filename, "w") as fid:
+            json.dump(self._conf, fid, indent=4)
+        if verbose:
+            logger.info("Saved settings in " + filename)
+
+    def load(self, filename):
+        """
+        Updates the setting from config file in JSON format.
+
+        :param filename: filename of the local JSON settings file. If None, the local config file is used.
+        """
+        if filename is None:
+            filename = LOCALCONFIG
+        with open(filename, "r") as fid:
+            logger.info(f"DataJoint is configured from {os.path.abspath(filename)}")
+            self._conf.update(json.load(fid))
+
+    def save_local(self, verbose=False):
+        """
+        saves the settings in the local config file
+        """
+        self.save(LOCALCONFIG, verbose)
+
+    def save_global(self, verbose=False):
+        """
+        saves the settings in the global config file
+        """
+        self.save(os.path.expanduser(os.path.join("~", GLOBALCONFIG)), verbose)
+
+    def get_store_spec(self, store):
+        """
+        find configuration of external stores for blobs and attachments
+        """
+        try:
+            spec = self["stores"][store]
+        except KeyError:
+            raise DataJointError(
+                "Storage {store} is requested but not configured".format(store=store)
+            )
+
+        spec["subfolding"] = spec.get("subfolding", DEFAULT_SUBFOLDING)
+        spec_keys = {  # REQUIRED in uppercase and allowed in lowercase
+            "file": ("PROTOCOL", "LOCATION", "subfolding", "stage"),
+            "s3": (
+                "PROTOCOL",
+                "ENDPOINT",
+                "BUCKET",
+                "ACCESS_KEY",
+                "SECRET_KEY",
+                "LOCATION",
+                "secure",
+                "subfolding",
+                "stage",
+                "proxy_server",
+            ),
+        }
+
+        try:
+            spec_keys = spec_keys[spec.get("protocol", "").lower()]
+        except KeyError:
+            raise DataJointError(
+                'Missing or invalid protocol in dj.config["stores"]["{store}"]'.format(
+                    store=store
+                )
+            )
+
+        # check that all required keys are present in spec
+        try:
+            raise DataJointError(
+                'dj.config["stores"]["{store}"] is missing "{k}"'.format(
+                    store=store,
+                    k=next(
+                        k.lower()
+                        for k in spec_keys
+                        if k.isupper() and k.lower() not in spec
+                    ),
+                )
+            )
+        except StopIteration:
+            pass
+
+        # check that only allowed keys are present in spec
+        try:
+            raise DataJointError(
+                'Invalid key "{k}" in dj.config["stores"]["{store}"]'.format(
+                    store=store,
+                    k=next(
+                        k
+                        for k in spec
+                        if k.upper() not in spec_keys and k.lower() not in spec_keys
+                    ),
+                )
+            )
+        except StopIteration:
+            pass  # no invalid keys
+
+        return spec
+
+    @contextmanager
+    def __call__(self, **kwargs):
+        """
+        The config object can also be used in a with statement to change the state of the configuration
+        temporarily. kwargs to the context manager are the keys into config, where '.' is replaced by a
+        double underscore '__'. The context manager yields the changed config object.
+
+        Example:
+        >>> import datajoint as dj
+        >>> with dj.config(safemode=False, database__host="localhost") as cfg:
+        >>>     # do dangerous stuff here
+        """
+
+        try:
+            backup = self.instance
+            self.instance = Config.__Config(self.instance._conf)
+            new = {k.replace("__", "."): v for k, v in kwargs.items()}
+            self.instance._conf.update(new)
+            yield self
+        except:
+            self.instance = backup
+            raise
+        else:
+            self.instance = backup
+
+    class __Config:
+        """
+        Stores datajoint settings. Behaves like a dictionary, but applies validator functions
+        when certain keys are set.
+
+        The default parameters are stored in datajoint.settings.default . If a local config file
+        exists, the settings specified in this file override the default settings.
+        """
+
+        def __init__(self, *args, **kwargs):
+            self._conf = dict(default)
+            # use the free update to set keys
+            self._conf.update(dict(*args, **kwargs))
+
+        def __getitem__(self, key):
+            return self._conf[key]
+
+        def __setitem__(self, key, value):
+            logger.debug("Setting {0:s} to {1:s}".format(str(key), str(value)))
+            if validators[key](value):
+                self._conf[key] = value
+            else:
+                raise DataJointError("Validator for {0:s} did not pass".format(key))
+            valid_logging_levels = {"DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"}
+            if key == "loglevel":
+                if value not in valid_logging_levels:
+                    raise ValueError(
+                        f"'{value}' is not a valid logging value {tuple(valid_logging_levels)}"
+                    )
+                logger.setLevel(value)
+

+ + + +

+ + + + + + + +

+ + +

+ `save(filename, verbose=False)` + +¶

+ + +

+ +

Saves the settings in JSON format to the given file path.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `filename` +	+	+ + filename of the local JSON settings file. + +	+ required +
+ `verbose` +	+	+ + report having saved the settings file + +	+ `False` +

+ + +

Source code in datajoint/settings.py

def save(self, filename, verbose=False):
+    """
+    Saves the settings in JSON format to the given file path.
+
+    :param filename: filename of the local JSON settings file.
+    :param verbose: report having saved the settings file
+    """
+    with open(filename, "w") as fid:
+        json.dump(self._conf, fid, indent=4)
+    if verbose:
+        logger.info("Saved settings in " + filename)
+

+ +

+ + + + + + +

+ + +

+ `load(filename)` + +¶

+ + +

+ +

Updates the setting from config file in JSON format.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `filename` +	+	+ + filename of the local JSON settings file. If None, the local config file is used. + +	+ required +

+ + +

Source code in datajoint/settings.py

def load(self, filename):
+    """
+    Updates the setting from config file in JSON format.
+
+    :param filename: filename of the local JSON settings file. If None, the local config file is used.
+    """
+    if filename is None:
+        filename = LOCALCONFIG
+    with open(filename, "r") as fid:
+        logger.info(f"DataJoint is configured from {os.path.abspath(filename)}")
+        self._conf.update(json.load(fid))
+

+ +

+ + + + + + +

+ + +

+ `save_local(verbose=False)` + +¶

+ + +

+ +

saves the settings in the local config file

+ + +

Source code in datajoint/settings.py

def save_local(self, verbose=False):
+    """
+    saves the settings in the local config file
+    """
+    self.save(LOCALCONFIG, verbose)
+

+ +

+ + + + + + +

+ + +

+ `save_global(verbose=False)` + +¶

+ + +

+ +

saves the settings in the global config file

+ + +

Source code in datajoint/settings.py

def save_global(self, verbose=False):
+    """
+    saves the settings in the global config file
+    """
+    self.save(os.path.expanduser(os.path.join("~", GLOBALCONFIG)), verbose)
+

+ +

+ + + + + + +

+ + +

+ `get_store_spec(store)` + +¶

+ + +

+ +

find configuration of external stores for blobs and attachments

+ + +

Source code in datajoint/settings.py

def get_store_spec(self, store):
+    """
+    find configuration of external stores for blobs and attachments
+    """
+    try:
+        spec = self["stores"][store]
+    except KeyError:
+        raise DataJointError(
+            "Storage {store} is requested but not configured".format(store=store)
+        )
+
+    spec["subfolding"] = spec.get("subfolding", DEFAULT_SUBFOLDING)
+    spec_keys = {  # REQUIRED in uppercase and allowed in lowercase
+        "file": ("PROTOCOL", "LOCATION", "subfolding", "stage"),
+        "s3": (
+            "PROTOCOL",
+            "ENDPOINT",
+            "BUCKET",
+            "ACCESS_KEY",
+            "SECRET_KEY",
+            "LOCATION",
+            "secure",
+            "subfolding",
+            "stage",
+            "proxy_server",
+        ),
+    }
+
+    try:
+        spec_keys = spec_keys[spec.get("protocol", "").lower()]
+    except KeyError:
+        raise DataJointError(
+            'Missing or invalid protocol in dj.config["stores"]["{store}"]'.format(
+                store=store
+            )
+        )
+
+    # check that all required keys are present in spec
+    try:
+        raise DataJointError(
+            'dj.config["stores"]["{store}"] is missing "{k}"'.format(
+                store=store,
+                k=next(
+                    k.lower()
+                    for k in spec_keys
+                    if k.isupper() and k.lower() not in spec
+                ),
+            )
+        )
+    except StopIteration:
+        pass
+
+    # check that only allowed keys are present in spec
+    try:
+        raise DataJointError(
+            'Invalid key "{k}" in dj.config["stores"]["{store}"]'.format(
+                store=store,
+                k=next(
+                    k
+                    for k in spec
+                    if k.upper() not in spec_keys and k.lower() not in spec_keys
+                ),
+            )
+        )
+    except StopIteration:
+        pass  # no invalid keys
+
+    return spec
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/table/index.html b/0.14/api/datajoint/table/index.html new file mode 100644 index 000000000..2d846bdb0 --- /dev/null +++ b/0.14/api/datajoint/table/index.html @@ -0,0 +1,9097 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + table.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + table.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

table.py

+ +

+ + + + +

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ `Table` + + +¶

+ + +

+ Bases: QueryExpression

+ + + +

+ + + + + + + + +

Source code in datajoint/table.py

class Table(QueryExpression):
+    """
+    Table is an abstract class that represents a table in the schema.
+    It implements insert and delete methods and inherits query functionality.
+    To make it a concrete class, override the abstract properties specifying the connection,
+    table name, database, and definition.
+    """
+
+    _table_name = None  # must be defined in subclass
+    _log_ = None  # placeholder for the Log table object
+
+    # These properties must be set by the schema decorator (schemas.py) at class level
+    # or by FreeTable at instance level
+    database = None
+    declaration_context = None
+
+    @property
+    def table_name(self):
+        return self._table_name
+
+    @property
+    def class_name(self):
+        return self.__class__.__name__
+
+    @property
+    def definition(self):
+        raise NotImplementedError(
+            "Subclasses of Table must implement the `definition` property"
+        )
+
+    def declare(self, context=None):
+        """
+        Declare the table in the schema based on self.definition.
+
+        :param context: the context for foreign key resolution. If None, foreign keys are
+            not allowed.
+        """
+        if self.connection.in_transaction:
+            raise DataJointError(
+                "Cannot declare new tables inside a transaction, "
+                "e.g. from inside a populate/make call"
+            )
+        # Enforce strict CamelCase #1150
+        if not is_camel_case(self.class_name):
+            raise DataJointError(
+                "Table class name `{name}` is invalid. Please use CamelCase. ".format(
+                    name=self.class_name
+                )
+                + "Classes defining tables should be formatted in strict CamelCase."
+            )
+        sql, external_stores = declare(self.full_table_name, self.definition, context)
+        sql = sql.format(database=self.database)
+        try:
+            # declare all external tables before declaring main table
+            for store in external_stores:
+                self.connection.schemas[self.database].external[store]
+            self.connection.query(sql)
+        except AccessError:
+            # skip if no create privilege
+            pass
+        else:
+            self._log("Declared " + self.full_table_name)
+
+    def alter(self, prompt=True, context=None):
+        """
+        Alter the table definition from self.definition
+        """
+        if self.connection.in_transaction:
+            raise DataJointError(
+                "Cannot update table declaration inside a transaction, "
+                "e.g. from inside a populate/make call"
+            )
+        if context is None:
+            frame = inspect.currentframe().f_back
+            context = dict(frame.f_globals, **frame.f_locals)
+            del frame
+        old_definition = self.describe(context=context)
+        sql, external_stores = alter(self.definition, old_definition, context)
+        if not sql:
+            if prompt:
+                logger.warning("Nothing to alter.")
+        else:
+            sql = "ALTER TABLE {tab}\n\t".format(
+                tab=self.full_table_name
+            ) + ",\n\t".join(sql)
+            if not prompt or user_choice(sql + "\n\nExecute?") == "yes":
+                try:
+                    # declare all external tables before declaring main table
+                    for store in external_stores:
+                        self.connection.schemas[self.database].external[store]
+                    self.connection.query(sql)
+                except AccessError:
+                    # skip if no create privilege
+                    pass
+                else:
+                    # reset heading
+                    self.__class__._heading = Heading(
+                        table_info=self.heading.table_info
+                    )
+                    if prompt:
+                        logger.info("Table altered")
+                    self._log("Altered " + self.full_table_name)
+
+    def from_clause(self):
+        """
+        :return: the FROM clause of SQL SELECT statements.
+        """
+        return self.full_table_name
+
+    def get_select_fields(self, select_fields=None):
+        """
+        :return: the selected attributes from the SQL SELECT statement.
+        """
+        return (
+            "*" if select_fields is None else self.heading.project(select_fields).as_sql
+        )
+
+    def parents(self, primary=None, as_objects=False, foreign_key_info=False):
+        """
+
+        :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
+            primary key attributes are considered.  If False, return foreign keys including at least one
+            secondary attribute.
+        :param as_objects: if False, return table names. If True, return table objects.
+        :param foreign_key_info: if True, each element in result also includes foreign key info.
+        :return: list of parents as table names or table objects
+            with (optional) foreign key information.
+        """
+        get_edge = self.connection.dependencies.parents
+        nodes = [
+            next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+            for name, props in get_edge(self.full_table_name, primary).items()
+        ]
+        if as_objects:
+            nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+        if not foreign_key_info:
+            nodes = [name for name, props in nodes]
+        return nodes
+
+    def children(self, primary=None, as_objects=False, foreign_key_info=False):
+        """
+        :param primary: if None, then all children are returned. If True, then only foreign keys composed of
+            primary key attributes are considered.  If False, return foreign keys including at least one
+            secondary attribute.
+        :param as_objects: if False, return table names. If True, return table objects.
+        :param foreign_key_info: if True, each element in result also includes foreign key info.
+        :return: list of children as table names or table objects
+            with (optional) foreign key information.
+        """
+        get_edge = self.connection.dependencies.children
+        nodes = [
+            next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+            for name, props in get_edge(self.full_table_name, primary).items()
+        ]
+        if as_objects:
+            nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+        if not foreign_key_info:
+            nodes = [name for name, props in nodes]
+        return nodes
+
+    def descendants(self, as_objects=False):
+        """
+        :param as_objects: False - a list of table names; True - a list of table objects.
+        :return: list of tables descendants in topological order.
+        """
+        return [
+            FreeTable(self.connection, node) if as_objects else node
+            for node in self.connection.dependencies.descendants(self.full_table_name)
+            if not node.isdigit()
+        ]
+
+    def ancestors(self, as_objects=False):
+        """
+        :param as_objects: False - a list of table names; True - a list of table objects.
+        :return: list of tables ancestors in topological order.
+        """
+        return [
+            FreeTable(self.connection, node) if as_objects else node
+            for node in self.connection.dependencies.ancestors(self.full_table_name)
+            if not node.isdigit()
+        ]
+
+    def parts(self, as_objects=False):
+        """
+        return part tables either as entries in a dict with foreign key information or a list of objects
+
+        :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects.
+        """
+        self.connection.dependencies.load(force=False)
+        nodes = [
+            node
+            for node in self.connection.dependencies.nodes
+            if not node.isdigit() and node.startswith(self.full_table_name[:-1] + "__")
+        ]
+        return [FreeTable(self.connection, c) for c in nodes] if as_objects else nodes
+
+    @property
+    def is_declared(self):
+        """
+        :return: True is the table is declared in the schema.
+        """
+        return (
+            self.connection.query(
+                'SHOW TABLES in `{database}` LIKE "{table_name}"'.format(
+                    database=self.database, table_name=self.table_name
+                )
+            ).rowcount
+            > 0
+        )
+
+    @property
+    def full_table_name(self):
+        """
+        :return: full table name in the schema
+        """
+        return r"`{0:s}`.`{1:s}`".format(self.database, self.table_name)
+
+    @property
+    def _log(self):
+        if self._log_ is None:
+            self._log_ = Log(
+                self.connection,
+                database=self.database,
+                skip_logging=self.table_name.startswith("~"),
+            )
+        return self._log_
+
+    @property
+    def external(self):
+        return self.connection.schemas[self.database].external
+
+    def update1(self, row):
+        """
+        ``update1`` updates one existing entry in the table.
+        Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and
+        ``delete`` entire records since referential integrity works on the level of records,
+        not fields. Therefore, updates are reserved for corrective operations outside of main
+        workflow. Use UPDATE methods sparingly with full awareness of potential violations of
+        assumptions.
+
+        :param row: a ``dict`` containing the primary key values and the attributes to update.
+            Setting an attribute value to None will reset it to the default value (if any).
+
+        The primary key attributes must always be provided.
+
+        Examples:
+
+        >>> table.update1({'id': 1, 'value': 3})  # update value in record with id=1
+        >>> table.update1({'id': 1, 'value': None})  # reset value to default
+        """
+        # argument validations
+        if not isinstance(row, collections.abc.Mapping):
+            raise DataJointError("The argument of update1 must be dict-like.")
+        if not set(row).issuperset(self.primary_key):
+            raise DataJointError(
+                "The argument of update1 must supply all primary key values."
+            )
+        try:
+            raise DataJointError(
+                "Attribute `%s` not found."
+                % next(k for k in row if k not in self.heading.names)
+            )
+        except StopIteration:
+            pass  # ok
+        if len(self.restriction):
+            raise DataJointError("Update cannot be applied to a restricted table.")
+        key = {k: row[k] for k in self.primary_key}
+        if len(self & key) != 1:
+            raise DataJointError("Update can only be applied to one existing entry.")
+        # UPDATE query
+        row = [
+            self.__make_placeholder(k, v)
+            for k, v in row.items()
+            if k not in self.primary_key
+        ]
+        query = "UPDATE {table} SET {assignments} WHERE {where}".format(
+            table=self.full_table_name,
+            assignments=",".join("`%s`=%s" % r[:2] for r in row),
+            where=make_condition(self, key, set()),
+        )
+        self.connection.query(query, args=list(r[2] for r in row if r[2] is not None))
+
+    def insert1(self, row, **kwargs):
+        """
+        Insert one data record into the table. For ``kwargs``, see ``insert()``.
+
+        :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted
+            as one row.
+        """
+        self.insert((row,), **kwargs)
+
+    def insert(
+        self,
+        rows,
+        replace=False,
+        skip_duplicates=False,
+        ignore_extra_fields=False,
+        allow_direct_insert=None,
+    ):
+        """
+        Insert a collection of rows.
+
+        :param rows: Either (a) an iterable where an element is a numpy record, a
+            dict-like object, a pandas.DataFrame, a sequence, or a query expression with
+            the same heading as self, or (b) a pathlib.Path object specifying a path
+            relative to the current directory with a CSV file, the contents of which
+            will be inserted.
+        :param replace: If True, replaces the existing tuple.
+        :param skip_duplicates: If True, silently skip duplicate inserts.
+        :param ignore_extra_fields: If False, fields that are not in the heading raise error.
+        :param allow_direct_insert: Only applies in auto-populated tables. If False (default),
+            insert may only be called from inside the make callback.
+
+        Example:
+
+            >>> Table.insert([
+            >>>     dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"),
+            >>>     dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")])
+        """
+        if isinstance(rows, pandas.DataFrame):
+            # drop 'extra' synthetic index for 1-field index case -
+            # frames with more advanced indices should be prepared by user.
+            rows = rows.reset_index(
+                drop=len(rows.index.names) == 1 and not rows.index.names[0]
+            ).to_records(index=False)
+
+        if isinstance(rows, Path):
+            with open(rows, newline="") as data_file:
+                rows = list(csv.DictReader(data_file, delimiter=","))
+
+        # prohibit direct inserts into auto-populated tables
+        if not allow_direct_insert and not getattr(self, "_allow_insert", True):
+            raise DataJointError(
+                "Inserts into an auto-populated table can only be done inside "
+                "its make method during a populate call."
+                " To override, set keyword argument allow_direct_insert=True."
+            )
+
+        if inspect.isclass(rows) and issubclass(rows, QueryExpression):
+            rows = rows()  # instantiate if a class
+        if isinstance(rows, QueryExpression):
+            # insert from select
+            if not ignore_extra_fields:
+                try:
+                    raise DataJointError(
+                        "Attribute %s not found. To ignore extra attributes in insert, "
+                        "set ignore_extra_fields=True."
+                        % next(
+                            name for name in rows.heading if name not in self.heading
+                        )
+                    )
+                except StopIteration:
+                    pass
+            fields = list(name for name in rows.heading if name in self.heading)
+            query = "{command} INTO {table} ({fields}) {select}{duplicate}".format(
+                command="REPLACE" if replace else "INSERT",
+                fields="`" + "`,`".join(fields) + "`",
+                table=self.full_table_name,
+                select=rows.make_sql(fields),
+                duplicate=(
+                    " ON DUPLICATE KEY UPDATE `{pk}`={table}.`{pk}`".format(
+                        table=self.full_table_name, pk=self.primary_key[0]
+                    )
+                    if skip_duplicates
+                    else ""
+                ),
+            )
+            self.connection.query(query)
+            return
+
+        # collects the field list from first row (passed by reference)
+        field_list = []
+        rows = list(
+            self.__make_row_to_insert(row, field_list, ignore_extra_fields)
+            for row in rows
+        )
+        if rows:
+            try:
+                query = "{command} INTO {destination}(`{fields}`) VALUES {placeholders}{duplicate}".format(
+                    command="REPLACE" if replace else "INSERT",
+                    destination=self.from_clause(),
+                    fields="`,`".join(field_list),
+                    placeholders=",".join(
+                        "(" + ",".join(row["placeholders"]) + ")" for row in rows
+                    ),
+                    duplicate=(
+                        " ON DUPLICATE KEY UPDATE `{pk}`=`{pk}`".format(
+                            pk=self.primary_key[0]
+                        )
+                        if skip_duplicates
+                        else ""
+                    ),
+                )
+                self.connection.query(
+                    query,
+                    args=list(
+                        itertools.chain.from_iterable(
+                            (v for v in r["values"] if v is not None) for r in rows
+                        )
+                    ),
+                )
+            except UnknownAttributeError as err:
+                raise err.suggest(
+                    "To ignore extra fields in insert, set ignore_extra_fields=True"
+                )
+            except DuplicateError as err:
+                raise err.suggest(
+                    "To ignore duplicate entries in insert, set skip_duplicates=True"
+                )
+
+    def delete_quick(self, get_count=False):
+        """
+        Deletes the table without cascading and without user prompt.
+        If this table has populated dependent tables, this will fail.
+        """
+        query = "DELETE FROM " + self.full_table_name + self.where_clause()
+        self.connection.query(query)
+        count = (
+            self.connection.query("SELECT ROW_COUNT()").fetchone()[0]
+            if get_count
+            else None
+        )
+        self._log(query[:255])
+        return count
+
+    def delete(
+        self,
+        transaction: bool = True,
+        safemode: Union[bool, None] = None,
+        force_parts: bool = False,
+        force_masters: bool = False,
+    ) -> int:
+        """
+        Deletes the contents of the table and its dependent tables, recursively.
+
+        Args:
+            transaction: If `True`, use of the entire delete becomes an atomic transaction.
+                This is the default and recommended behavior. Set to `False` if this delete is
+                nested within another transaction.
+            safemode: If `True`, prohibit nested transactions and prompt to confirm. Default
+                is `dj.config['safemode']`.
+            force_parts: Delete from parts even when not deleting from their masters.
+            force_masters: If `True`, include part/master pairs in the cascade.
+                Default is `False`.
+
+        Returns:
+            Number of deleted rows (excluding those from dependent tables).
+
+        Raises:
+            DataJointError: Delete exceeds maximum number of delete attempts.
+            DataJointError: When deleting within an existing transaction.
+            DataJointError: Deleting a part table before its master.
+        """
+        deleted = set()
+        visited_masters = set()
+
+        def cascade(table):
+            """service function to perform cascading deletes recursively."""
+            max_attempts = 50
+            for _ in range(max_attempts):
+                try:
+                    delete_count = table.delete_quick(get_count=True)
+                except IntegrityError as error:
+                    match = foreign_key_error_regexp.match(error.args[0])
+                    if match is None:
+                        raise DataJointError(
+                            "Cascading deletes failed because the error message is missing foreign key information."
+                            "Make sure you have REFERENCES privilege to all dependent tables."
+                        ) from None
+                    match = match.groupdict()
+                    # if schema name missing, use table
+                    if "`.`" not in match["child"]:
+                        match["child"] = "{}.{}".format(
+                            table.full_table_name.split(".")[0], match["child"]
+                        )
+                    if (
+                        match["pk_attrs"] is not None
+                    ):  # fully matched, adjusting the keys
+                        match["fk_attrs"] = [
+                            k.strip("`") for k in match["fk_attrs"].split(",")
+                        ]
+                        match["pk_attrs"] = [
+                            k.strip("`") for k in match["pk_attrs"].split(",")
+                        ]
+                    else:  # only partially matched, querying with constraint to determine keys
+                        match["fk_attrs"], match["parent"], match["pk_attrs"] = list(
+                            map(
+                                list,
+                                zip(
+                                    *table.connection.query(
+                                        constraint_info_query,
+                                        args=(
+                                            match["name"].strip("`"),
+                                            *[
+                                                _.strip("`")
+                                                for _ in match["child"].split("`.`")
+                                            ],
+                                        ),
+                                    ).fetchall()
+                                ),
+                            )
+                        )
+                        match["parent"] = match["parent"][0]
+
+                    # Restrict child by table if
+                    #   1. if table's restriction attributes are not in child's primary key
+                    #   2. if child renames any attributes
+                    # Otherwise restrict child by table's restriction.
+                    child = FreeTable(table.connection, match["child"])
+                    if (
+                        set(table.restriction_attributes) <= set(child.primary_key)
+                        and match["fk_attrs"] == match["pk_attrs"]
+                    ):
+                        child._restriction = table._restriction
+                        child._restriction_attributes = table.restriction_attributes
+                    elif match["fk_attrs"] != match["pk_attrs"]:
+                        child &= table.proj(
+                            **dict(zip(match["fk_attrs"], match["pk_attrs"]))
+                        )
+                    else:
+                        child &= table.proj()
+
+                    master_name = get_master(child.full_table_name)
+                    if (
+                        force_masters
+                        and master_name
+                        and master_name != table.full_table_name
+                        and master_name not in visited_masters
+                    ):
+                        master = FreeTable(table.connection, master_name)
+                        master._restriction_attributes = set()
+                        master._restriction = [
+                            make_condition(  # &= may cause in target tables in subquery
+                                master,
+                                (master.proj() & child.proj()).fetch(),
+                                master._restriction_attributes,
+                            )
+                        ]
+                        visited_masters.add(master_name)
+                        cascade(master)
+                    else:
+                        cascade(child)
+                else:
+                    deleted.add(table.full_table_name)
+                    logger.info(
+                        "Deleting {count} rows from {table}".format(
+                            count=delete_count, table=table.full_table_name
+                        )
+                    )
+                    break
+            else:
+                raise DataJointError("Exceeded maximum number of delete attempts.")
+            return delete_count
+
+        safemode = config["safemode"] if safemode is None else safemode
+
+        # Start transaction
+        if transaction:
+            if not self.connection.in_transaction:
+                self.connection.start_transaction()
+            else:
+                if not safemode:
+                    transaction = False
+                else:
+                    raise DataJointError(
+                        "Delete cannot use a transaction within an ongoing transaction. "
+                        "Set transaction=False or safemode=False)."
+                    )
+
+        # Cascading delete
+        try:
+            delete_count = cascade(self)
+        except:
+            if transaction:
+                self.connection.cancel_transaction()
+            raise
+
+        if not force_parts:
+            # Avoid deleting from child before master (See issue #151)
+            for part in deleted:
+                master = get_master(part)
+                if master and master not in deleted:
+                    if transaction:
+                        self.connection.cancel_transaction()
+                    raise DataJointError(
+                        "Attempt to delete part table {part} before deleting from "
+                        "its master {master} first.".format(part=part, master=master)
+                    )
+
+        # Confirm and commit
+        if delete_count == 0:
+            if safemode:
+                logger.warning("Nothing to delete.")
+            if transaction:
+                self.connection.cancel_transaction()
+        elif not transaction:
+            logger.info("Delete completed")
+        else:
+            if not safemode or user_choice("Commit deletes?", default="no") == "yes":
+                if transaction:
+                    self.connection.commit_transaction()
+                if safemode:
+                    logger.info("Delete committed.")
+            else:
+                if transaction:
+                    self.connection.cancel_transaction()
+                if safemode:
+                    logger.warning("Delete cancelled")
+        return delete_count
+
+    def drop_quick(self):
+        """
+        Drops the table without cascading to dependent tables and without user prompt.
+        """
+        if self.is_declared:
+            query = "DROP TABLE %s" % self.full_table_name
+            self.connection.query(query)
+            logger.info("Dropped table %s" % self.full_table_name)
+            self._log(query[:255])
+        else:
+            logger.info(
+                "Nothing to drop: table %s is not declared" % self.full_table_name
+            )
+
+    def drop(self):
+        """
+        Drop the table and all tables that reference it, recursively.
+        User is prompted for confirmation if config['safemode'] is set to True.
+        """
+        if self.restriction:
+            raise DataJointError(
+                "A table with an applied restriction cannot be dropped."
+                " Call drop() on the unrestricted Table."
+            )
+        self.connection.dependencies.load()
+        do_drop = True
+        tables = [
+            table
+            for table in self.connection.dependencies.descendants(self.full_table_name)
+            if not table.isdigit()
+        ]
+
+        # avoid dropping part tables without their masters: See issue #374
+        for part in tables:
+            master = get_master(part)
+            if master and master not in tables:
+                raise DataJointError(
+                    "Attempt to drop part table {part} before dropping "
+                    "its master. Drop {master} first.".format(part=part, master=master)
+                )
+
+        if config["safemode"]:
+            for table in tables:
+                logger.info(
+                    table + " (%d tuples)" % len(FreeTable(self.connection, table))
+                )
+            do_drop = user_choice("Proceed?", default="no") == "yes"
+        if do_drop:
+            for table in reversed(tables):
+                FreeTable(self.connection, table).drop_quick()
+            logger.info("Tables dropped. Restart kernel.")
+
+    @property
+    def size_on_disk(self):
+        """
+        :return: size of data and indices in bytes on the storage device
+        """
+        ret = self.connection.query(
+            'SHOW TABLE STATUS FROM `{database}` WHERE NAME="{table}"'.format(
+                database=self.database, table=self.table_name
+            ),
+            as_dict=True,
+        ).fetchone()
+        return ret["Data_length"] + ret["Index_length"]
+
+    def describe(self, context=None, printout=False):
+        """
+        :return:  the definition string for the query using DataJoint DDL.
+        """
+        if context is None:
+            frame = inspect.currentframe().f_back
+            context = dict(frame.f_globals, **frame.f_locals)
+            del frame
+        if self.full_table_name not in self.connection.dependencies:
+            self.connection.dependencies.load()
+        parents = self.parents(foreign_key_info=True)
+        in_key = True
+        definition = (
+            "# " + self.heading.table_status["comment"] + "\n"
+            if self.heading.table_status["comment"]
+            else ""
+        )
+        attributes_thus_far = set()
+        attributes_declared = set()
+        indexes = self.heading.indexes.copy()
+        for attr in self.heading.attributes.values():
+            if in_key and not attr.in_key:
+                definition += "---\n"
+                in_key = False
+            attributes_thus_far.add(attr.name)
+            do_include = True
+            for parent_name, fk_props in parents:
+                if attr.name in fk_props["attr_map"]:
+                    do_include = False
+                    if attributes_thus_far.issuperset(fk_props["attr_map"]):
+                        # foreign key properties
+                        try:
+                            index_props = indexes.pop(tuple(fk_props["attr_map"]))
+                        except KeyError:
+                            index_props = ""
+                        else:
+                            index_props = [k for k, v in index_props.items() if v]
+                            index_props = (
+                                " [{}]".format(", ".join(index_props))
+                                if index_props
+                                else ""
+                            )
+
+                        if not fk_props["aliased"]:
+                            # simple foreign key
+                            definition += "->{props} {class_name}\n".format(
+                                props=index_props,
+                                class_name=lookup_class_name(parent_name, context)
+                                or parent_name,
+                            )
+                        else:
+                            # projected foreign key
+                            definition += (
+                                "->{props} {class_name}.proj({proj_list})\n".format(
+                                    props=index_props,
+                                    class_name=lookup_class_name(parent_name, context)
+                                    or parent_name,
+                                    proj_list=",".join(
+                                        '{}="{}"'.format(attr, ref)
+                                        for attr, ref in fk_props["attr_map"].items()
+                                        if ref != attr
+                                    ),
+                                )
+                            )
+                            attributes_declared.update(fk_props["attr_map"])
+            if do_include:
+                attributes_declared.add(attr.name)
+                definition += "%-20s : %-28s %s\n" % (
+                    (
+                        attr.name
+                        if attr.default is None
+                        else "%s=%s" % (attr.name, attr.default)
+                    ),
+                    "%s%s"
+                    % (attr.type, " auto_increment" if attr.autoincrement else ""),
+                    "# " + attr.comment if attr.comment else "",
+                )
+        # add remaining indexes
+        for k, v in indexes.items():
+            definition += "{unique}INDEX ({attrs})\n".format(
+                unique="UNIQUE " if v["unique"] else "", attrs=", ".join(k)
+            )
+        if printout:
+            logger.info("\n" + definition)
+        return definition
+
+    # --- private helper functions ----
+    def __make_placeholder(self, name, value, ignore_extra_fields=False):
+        """
+        For a given attribute `name` with `value`, return its processed value or value placeholder
+        as a string to be included in the query and the value, if any, to be submitted for
+        processing by mysql API.
+
+        :param name:  name of attribute to be inserted
+        :param value: value of attribute to be inserted
+        """
+        if ignore_extra_fields and name not in self.heading:
+            return None
+        attr = self.heading[name]
+        if attr.adapter:
+            value = attr.adapter.put(value)
+        if value is None or (attr.numeric and (value == "" or np.isnan(float(value)))):
+            # set default value
+            placeholder, value = "DEFAULT", None
+        else:  # not NULL
+            placeholder = "%s"
+            if attr.uuid:
+                if not isinstance(value, uuid.UUID):
+                    try:
+                        value = uuid.UUID(value)
+                    except (AttributeError, ValueError):
+                        raise DataJointError(
+                            "badly formed UUID value {v} for attribute `{n}`".format(
+                                v=value, n=name
+                            )
+                        )
+                value = value.bytes
+            elif attr.is_blob:
+                value = blob.pack(value)
+                value = (
+                    self.external[attr.store].put(value).bytes
+                    if attr.is_external
+                    else value
+                )
+            elif attr.is_attachment:
+                attachment_path = Path(value)
+                if attr.is_external:
+                    # value is hash of contents
+                    value = (
+                        self.external[attr.store]
+                        .upload_attachment(attachment_path)
+                        .bytes
+                    )
+                else:
+                    # value is filename + contents
+                    value = (
+                        str.encode(attachment_path.name)
+                        + b"\0"
+                        + attachment_path.read_bytes()
+                    )
+            elif attr.is_filepath:
+                value = self.external[attr.store].upload_filepath(value).bytes
+            elif attr.numeric:
+                value = str(int(value) if isinstance(value, bool) else value)
+            elif attr.json:
+                value = json.dumps(value)
+        return name, placeholder, value
+
+    def __make_row_to_insert(self, row, field_list, ignore_extra_fields):
+        """
+        Helper function for insert and update
+
+        :param row:  A tuple to insert
+        :return: a dict with fields 'names', 'placeholders', 'values'
+        """
+
+        def check_fields(fields):
+            """
+            Validates that all items in `fields` are valid attributes in the heading
+
+            :param fields: field names of a tuple
+            """
+            if not field_list:
+                if not ignore_extra_fields:
+                    for field in fields:
+                        if field not in self.heading:
+                            raise KeyError(
+                                "`{0:s}` is not in the table heading".format(field)
+                            )
+            elif set(field_list) != set(fields).intersection(self.heading.names):
+                raise DataJointError("Attempt to insert rows with different fields.")
+
+        if isinstance(row, np.void):  # np.array
+            check_fields(row.dtype.fields)
+            attributes = [
+                self.__make_placeholder(name, row[name], ignore_extra_fields)
+                for name in self.heading
+                if name in row.dtype.fields
+            ]
+        elif isinstance(row, collections.abc.Mapping):  # dict-based
+            check_fields(row)
+            attributes = [
+                self.__make_placeholder(name, row[name], ignore_extra_fields)
+                for name in self.heading
+                if name in row
+            ]
+        else:  # positional
+            try:
+                if len(row) != len(self.heading):
+                    raise DataJointError(
+                        "Invalid insert argument. Incorrect number of attributes: "
+                        "{given} given; {expected} expected".format(
+                            given=len(row), expected=len(self.heading)
+                        )
+                    )
+            except TypeError:
+                raise DataJointError("Datatype %s cannot be inserted" % type(row))
+            else:
+                attributes = [
+                    self.__make_placeholder(name, value, ignore_extra_fields)
+                    for name, value in zip(self.heading, row)
+                ]
+        if ignore_extra_fields:
+            attributes = [a for a in attributes if a is not None]
+
+        assert len(attributes), "Empty tuple"
+        row_to_insert = dict(zip(("names", "placeholders", "values"), zip(*attributes)))
+        if not field_list:
+            # first row sets the composition of the field list
+            field_list.extend(row_to_insert["names"])
+        else:
+            #  reorder attributes in row_to_insert to match field_list
+            order = list(row_to_insert["names"].index(field) for field in field_list)
+            row_to_insert["names"] = list(row_to_insert["names"][i] for i in order)
+            row_to_insert["placeholders"] = list(
+                row_to_insert["placeholders"][i] for i in order
+            )
+            row_to_insert["values"] = list(row_to_insert["values"][i] for i in order)
+        return row_to_insert
+

+ + + +

+ + + + + + + +

+ + +

+ `declare(context=None)` + +¶

+ + +

+ +

Declare the table in the schema based on self.definition.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `context` +	+	+ + the context for foreign key resolution. If None, foreign keys are +not allowed. + +	+ `None` +

+ + +

Source code in datajoint/table.py

def declare(self, context=None):
+    """
+    Declare the table in the schema based on self.definition.
+
+    :param context: the context for foreign key resolution. If None, foreign keys are
+        not allowed.
+    """
+    if self.connection.in_transaction:
+        raise DataJointError(
+            "Cannot declare new tables inside a transaction, "
+            "e.g. from inside a populate/make call"
+        )
+    # Enforce strict CamelCase #1150
+    if not is_camel_case(self.class_name):
+        raise DataJointError(
+            "Table class name `{name}` is invalid. Please use CamelCase. ".format(
+                name=self.class_name
+            )
+            + "Classes defining tables should be formatted in strict CamelCase."
+        )
+    sql, external_stores = declare(self.full_table_name, self.definition, context)
+    sql = sql.format(database=self.database)
+    try:
+        # declare all external tables before declaring main table
+        for store in external_stores:
+            self.connection.schemas[self.database].external[store]
+        self.connection.query(sql)
+    except AccessError:
+        # skip if no create privilege
+        pass
+    else:
+        self._log("Declared " + self.full_table_name)
+

+ +

+ + + + + + +

+ + +

+ `alter(prompt=True, context=None)` + +¶

+ + +

+ +

Alter the table definition from self.definition

+ + +

Source code in datajoint/table.py

def alter(self, prompt=True, context=None):
+    """
+    Alter the table definition from self.definition
+    """
+    if self.connection.in_transaction:
+        raise DataJointError(
+            "Cannot update table declaration inside a transaction, "
+            "e.g. from inside a populate/make call"
+        )
+    if context is None:
+        frame = inspect.currentframe().f_back
+        context = dict(frame.f_globals, **frame.f_locals)
+        del frame
+    old_definition = self.describe(context=context)
+    sql, external_stores = alter(self.definition, old_definition, context)
+    if not sql:
+        if prompt:
+            logger.warning("Nothing to alter.")
+    else:
+        sql = "ALTER TABLE {tab}\n\t".format(
+            tab=self.full_table_name
+        ) + ",\n\t".join(sql)
+        if not prompt or user_choice(sql + "\n\nExecute?") == "yes":
+            try:
+                # declare all external tables before declaring main table
+                for store in external_stores:
+                    self.connection.schemas[self.database].external[store]
+                self.connection.query(sql)
+            except AccessError:
+                # skip if no create privilege
+                pass
+            else:
+                # reset heading
+                self.__class__._heading = Heading(
+                    table_info=self.heading.table_info
+                )
+                if prompt:
+                    logger.info("Table altered")
+                self._log("Altered " + self.full_table_name)
+

+ +

+ + + + + + +

+ + +

+ `from_clause()` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the FROM clause of SQL SELECT statements. + +

+ + +

Source code in datajoint/table.py

def from_clause(self):
+    """
+    :return: the FROM clause of SQL SELECT statements.
+    """
+    return self.full_table_name
+

+ +

+ + + + + + +

+ + +

+ `get_select_fields(select_fields=None)` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the selected attributes from the SQL SELECT statement. + +

+ + +

Source code in datajoint/table.py

def get_select_fields(self, select_fields=None):
+    """
+    :return: the selected attributes from the SQL SELECT statement.
+    """
+    return (
+        "*" if select_fields is None else self.heading.project(select_fields).as_sql
+    )
+

+ +

+ + + + + + +

+ + +

+ `parents(primary=None, as_objects=False, foreign_key_info=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `primary` +	+	+ + if None, then all parents are returned. If True, then only foreign keys composed of +primary key attributes are considered. If False, return foreign keys including at least one +secondary attribute. + +	+ `None` +
+ `as_objects` +	+	+ + if False, return table names. If True, return table objects. + +	+ `False` +
+ `foreign_key_info` +	+	+ + if True, each element in result also includes foreign key info. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of parents as table names or table objects +with (optional) foreign key information. + +

+ + +

Source code in datajoint/table.py

def parents(self, primary=None, as_objects=False, foreign_key_info=False):
+    """
+
+    :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
+        primary key attributes are considered.  If False, return foreign keys including at least one
+        secondary attribute.
+    :param as_objects: if False, return table names. If True, return table objects.
+    :param foreign_key_info: if True, each element in result also includes foreign key info.
+    :return: list of parents as table names or table objects
+        with (optional) foreign key information.
+    """
+    get_edge = self.connection.dependencies.parents
+    nodes = [
+        next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+        for name, props in get_edge(self.full_table_name, primary).items()
+    ]
+    if as_objects:
+        nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+    if not foreign_key_info:
+        nodes = [name for name, props in nodes]
+    return nodes
+

+ +

+ + + + + + +

+ + +

+ `children(primary=None, as_objects=False, foreign_key_info=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `primary` +	+	+ + if None, then all children are returned. If True, then only foreign keys composed of +primary key attributes are considered. If False, return foreign keys including at least one +secondary attribute. + +	+ `None` +
+ `as_objects` +	+	+ + if False, return table names. If True, return table objects. + +	+ `False` +
+ `foreign_key_info` +	+	+ + if True, each element in result also includes foreign key info. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of children as table names or table objects +with (optional) foreign key information. + +

+ + +

Source code in datajoint/table.py

def children(self, primary=None, as_objects=False, foreign_key_info=False):
+    """
+    :param primary: if None, then all children are returned. If True, then only foreign keys composed of
+        primary key attributes are considered.  If False, return foreign keys including at least one
+        secondary attribute.
+    :param as_objects: if False, return table names. If True, return table objects.
+    :param foreign_key_info: if True, each element in result also includes foreign key info.
+    :return: list of children as table names or table objects
+        with (optional) foreign key information.
+    """
+    get_edge = self.connection.dependencies.children
+    nodes = [
+        next(iter(get_edge(name).items())) if name.isdigit() else (name, props)
+        for name, props in get_edge(self.full_table_name, primary).items()
+    ]
+    if as_objects:
+        nodes = [(FreeTable(self.connection, name), props) for name, props in nodes]
+    if not foreign_key_info:
+        nodes = [name for name, props in nodes]
+    return nodes
+

+ +

+ + + + + + +

+ + +

+ `descendants(as_objects=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `as_objects` +	+	+ + False - a list of table names; True - a list of table objects. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of tables descendants in topological order. + +

+ + +

Source code in datajoint/table.py

def descendants(self, as_objects=False):
+    """
+    :param as_objects: False - a list of table names; True - a list of table objects.
+    :return: list of tables descendants in topological order.
+    """
+    return [
+        FreeTable(self.connection, node) if as_objects else node
+        for node in self.connection.dependencies.descendants(self.full_table_name)
+        if not node.isdigit()
+    ]
+

+ +

+ + + + + + +

+ + +

+ `ancestors(as_objects=False)` + +¶

+ + +

+ + + + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `as_objects` +	+	+ + False - a list of table names; True - a list of table objects. + +	+ `False` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + list of tables ancestors in topological order. + +

+ + +

Source code in datajoint/table.py

def ancestors(self, as_objects=False):
+    """
+    :param as_objects: False - a list of table names; True - a list of table objects.
+    :return: list of tables ancestors in topological order.
+    """
+    return [
+        FreeTable(self.connection, node) if as_objects else node
+        for node in self.connection.dependencies.ancestors(self.full_table_name)
+        if not node.isdigit()
+    ]
+

+ +

+ + + + + + +

+ + +

+ `parts(as_objects=False)` + +¶

+ + +

+ +

return part tables either as entries in a dict with foreign key information or a list of objects

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `as_objects` +	+	+ + if False (default), the output is a dict describing the foreign keys. If True, return table objects. + +	+ `False` +

+ + +

Source code in datajoint/table.py

def parts(self, as_objects=False):
+    """
+    return part tables either as entries in a dict with foreign key information or a list of objects
+
+    :param as_objects: if False (default), the output is a dict describing the foreign keys. If True, return table objects.
+    """
+    self.connection.dependencies.load(force=False)
+    nodes = [
+        node
+        for node in self.connection.dependencies.nodes
+        if not node.isdigit() and node.startswith(self.full_table_name[:-1] + "__")
+    ]
+    return [FreeTable(self.connection, c) for c in nodes] if as_objects else nodes
+

+ +

+ + + + + + +

+ + + +

+ `is_declared` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + True is the table is declared in the schema. + +

+ +

+ + + + + + +

+ + + +

+ `full_table_name` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + full table name in the schema + +

+ +

+ + + + + + +

+ + +

+ `update1(row)` + +¶

+ + +

+ +

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `row` +	+	+ + a `dict` containing the primary key values and the attributes to update. + Setting an attribute value to None will reset it to the default value (if any). + The primary key attributes must always be provided. + Examples: + + + + table.update1({'id': 1, 'value': 3}) # update value in record with id=1 +table.update1({'id': 1, 'value': None}) # reset value to default + + + + +	+ required +

+ + +

Source code in datajoint/table.py

def update1(self, row):
+    """
+    ``update1`` updates one existing entry in the table.
+    Caution: In DataJoint the primary modes for data manipulation is to ``insert`` and
+    ``delete`` entire records since referential integrity works on the level of records,
+    not fields. Therefore, updates are reserved for corrective operations outside of main
+    workflow. Use UPDATE methods sparingly with full awareness of potential violations of
+    assumptions.
+
+    :param row: a ``dict`` containing the primary key values and the attributes to update.
+        Setting an attribute value to None will reset it to the default value (if any).
+
+    The primary key attributes must always be provided.
+
+    Examples:
+
+    >>> table.update1({'id': 1, 'value': 3})  # update value in record with id=1
+    >>> table.update1({'id': 1, 'value': None})  # reset value to default
+    """
+    # argument validations
+    if not isinstance(row, collections.abc.Mapping):
+        raise DataJointError("The argument of update1 must be dict-like.")
+    if not set(row).issuperset(self.primary_key):
+        raise DataJointError(
+            "The argument of update1 must supply all primary key values."
+        )
+    try:
+        raise DataJointError(
+            "Attribute `%s` not found."
+            % next(k for k in row if k not in self.heading.names)
+        )
+    except StopIteration:
+        pass  # ok
+    if len(self.restriction):
+        raise DataJointError("Update cannot be applied to a restricted table.")
+    key = {k: row[k] for k in self.primary_key}
+    if len(self & key) != 1:
+        raise DataJointError("Update can only be applied to one existing entry.")
+    # UPDATE query
+    row = [
+        self.__make_placeholder(k, v)
+        for k, v in row.items()
+        if k not in self.primary_key
+    ]
+    query = "UPDATE {table} SET {assignments} WHERE {where}".format(
+        table=self.full_table_name,
+        assignments=",".join("`%s`=%s" % r[:2] for r in row),
+        where=make_condition(self, key, set()),
+    )
+    self.connection.query(query, args=list(r[2] for r in row if r[2] is not None))
+

+ +

+ + + + + + +

+ + +

+ `insert1(row, **kwargs)` + +¶

+ + +

+ +

Insert one data record into the table. For kwargs, see insert().

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `row` +	+	+ + a numpy record, a dict-like object, or an ordered sequence to be inserted +as one row. + +	+ required +

+ + +

Source code in datajoint/table.py

def insert1(self, row, **kwargs):
+    """
+    Insert one data record into the table. For ``kwargs``, see ``insert()``.
+
+    :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted
+        as one row.
+    """
+    self.insert((row,), **kwargs)
+

+ +

+ + + + + + +

+ + +

+ `insert(rows, replace=False, skip_duplicates=False, ignore_extra_fields=False, allow_direct_insert=None)` + +¶

+ + +

+ +

Insert a collection of rows.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `rows` +	+	+ + Either (a) an iterable where an element is a numpy record, a +dict-like object, a pandas.DataFrame, a sequence, or a query expression with +the same heading as self, or (b) a pathlib.Path object specifying a path +relative to the current directory with a CSV file, the contents of which +will be inserted. + +	+ required +
+ `replace` +	+	+ + If True, replaces the existing tuple. + +	+ `False` +
+ `skip_duplicates` +	+	+ + If True, silently skip duplicate inserts. + +	+ `False` +
+ `ignore_extra_fields` +	+	+ + If False, fields that are not in the heading raise error. + +	+ `False` +
+ `allow_direct_insert` +	+	+ + Only applies in auto-populated tables. If False (default), + insert may only be called from inside the make callback. + Example: + `>>> Table.insert([ +>>> dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"), +>>> dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")]) +` + +	+ `None` +

+ + +

Source code in datajoint/table.py

def insert(
+    self,
+    rows,
+    replace=False,
+    skip_duplicates=False,
+    ignore_extra_fields=False,
+    allow_direct_insert=None,
+):
+    """
+    Insert a collection of rows.
+
+    :param rows: Either (a) an iterable where an element is a numpy record, a
+        dict-like object, a pandas.DataFrame, a sequence, or a query expression with
+        the same heading as self, or (b) a pathlib.Path object specifying a path
+        relative to the current directory with a CSV file, the contents of which
+        will be inserted.
+    :param replace: If True, replaces the existing tuple.
+    :param skip_duplicates: If True, silently skip duplicate inserts.
+    :param ignore_extra_fields: If False, fields that are not in the heading raise error.
+    :param allow_direct_insert: Only applies in auto-populated tables. If False (default),
+        insert may only be called from inside the make callback.
+
+    Example:
+
+        >>> Table.insert([
+        >>>     dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"),
+        >>>     dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")])
+    """
+    if isinstance(rows, pandas.DataFrame):
+        # drop 'extra' synthetic index for 1-field index case -
+        # frames with more advanced indices should be prepared by user.
+        rows = rows.reset_index(
+            drop=len(rows.index.names) == 1 and not rows.index.names[0]
+        ).to_records(index=False)
+
+    if isinstance(rows, Path):
+        with open(rows, newline="") as data_file:
+            rows = list(csv.DictReader(data_file, delimiter=","))
+
+    # prohibit direct inserts into auto-populated tables
+    if not allow_direct_insert and not getattr(self, "_allow_insert", True):
+        raise DataJointError(
+            "Inserts into an auto-populated table can only be done inside "
+            "its make method during a populate call."
+            " To override, set keyword argument allow_direct_insert=True."
+        )
+
+    if inspect.isclass(rows) and issubclass(rows, QueryExpression):
+        rows = rows()  # instantiate if a class
+    if isinstance(rows, QueryExpression):
+        # insert from select
+        if not ignore_extra_fields:
+            try:
+                raise DataJointError(
+                    "Attribute %s not found. To ignore extra attributes in insert, "
+                    "set ignore_extra_fields=True."
+                    % next(
+                        name for name in rows.heading if name not in self.heading
+                    )
+                )
+            except StopIteration:
+                pass
+        fields = list(name for name in rows.heading if name in self.heading)
+        query = "{command} INTO {table} ({fields}) {select}{duplicate}".format(
+            command="REPLACE" if replace else "INSERT",
+            fields="`" + "`,`".join(fields) + "`",
+            table=self.full_table_name,
+            select=rows.make_sql(fields),
+            duplicate=(
+                " ON DUPLICATE KEY UPDATE `{pk}`={table}.`{pk}`".format(
+                    table=self.full_table_name, pk=self.primary_key[0]
+                )
+                if skip_duplicates
+                else ""
+            ),
+        )
+        self.connection.query(query)
+        return
+
+    # collects the field list from first row (passed by reference)
+    field_list = []
+    rows = list(
+        self.__make_row_to_insert(row, field_list, ignore_extra_fields)
+        for row in rows
+    )
+    if rows:
+        try:
+            query = "{command} INTO {destination}(`{fields}`) VALUES {placeholders}{duplicate}".format(
+                command="REPLACE" if replace else "INSERT",
+                destination=self.from_clause(),
+                fields="`,`".join(field_list),
+                placeholders=",".join(
+                    "(" + ",".join(row["placeholders"]) + ")" for row in rows
+                ),
+                duplicate=(
+                    " ON DUPLICATE KEY UPDATE `{pk}`=`{pk}`".format(
+                        pk=self.primary_key[0]
+                    )
+                    if skip_duplicates
+                    else ""
+                ),
+            )
+            self.connection.query(
+                query,
+                args=list(
+                    itertools.chain.from_iterable(
+                        (v for v in r["values"] if v is not None) for r in rows
+                    )
+                ),
+            )
+        except UnknownAttributeError as err:
+            raise err.suggest(
+                "To ignore extra fields in insert, set ignore_extra_fields=True"
+            )
+        except DuplicateError as err:
+            raise err.suggest(
+                "To ignore duplicate entries in insert, set skip_duplicates=True"
+            )
+

+ +

+ + + + + + +

+ + +

+ `delete_quick(get_count=False)` + +¶

+ + +

+ +

Deletes the table without cascading and without user prompt. +If this table has populated dependent tables, this will fail.

+ + +

Source code in datajoint/table.py

def delete_quick(self, get_count=False):
+    """
+    Deletes the table without cascading and without user prompt.
+    If this table has populated dependent tables, this will fail.
+    """
+    query = "DELETE FROM " + self.full_table_name + self.where_clause()
+    self.connection.query(query)
+    count = (
+        self.connection.query("SELECT ROW_COUNT()").fetchone()[0]
+        if get_count
+        else None
+    )
+    self._log(query[:255])
+    return count
+

+ +

+ + + + + + +

+ + +

+ `delete(transaction=True, safemode=None, force_parts=False, force_masters=False)` + +¶

+ + +

+ +

Deletes the contents of the table and its dependent tables, recursively.

Returns: + Number of deleted rows (excluding those from dependent tables).

Raises: + DataJointError: Delete exceeds maximum number of delete attempts. + DataJointError: When deleting within an existing transaction. + DataJointError: Deleting a part table before its master.

+ + +

Source code in datajoint/table.py

def delete(
+    self,
+    transaction: bool = True,
+    safemode: Union[bool, None] = None,
+    force_parts: bool = False,
+    force_masters: bool = False,
+) -> int:
+    """
+    Deletes the contents of the table and its dependent tables, recursively.
+
+    Args:
+        transaction: If `True`, use of the entire delete becomes an atomic transaction.
+            This is the default and recommended behavior. Set to `False` if this delete is
+            nested within another transaction.
+        safemode: If `True`, prohibit nested transactions and prompt to confirm. Default
+            is `dj.config['safemode']`.
+        force_parts: Delete from parts even when not deleting from their masters.
+        force_masters: If `True`, include part/master pairs in the cascade.
+            Default is `False`.
+
+    Returns:
+        Number of deleted rows (excluding those from dependent tables).
+
+    Raises:
+        DataJointError: Delete exceeds maximum number of delete attempts.
+        DataJointError: When deleting within an existing transaction.
+        DataJointError: Deleting a part table before its master.
+    """
+    deleted = set()
+    visited_masters = set()
+
+    def cascade(table):
+        """service function to perform cascading deletes recursively."""
+        max_attempts = 50
+        for _ in range(max_attempts):
+            try:
+                delete_count = table.delete_quick(get_count=True)
+            except IntegrityError as error:
+                match = foreign_key_error_regexp.match(error.args[0])
+                if match is None:
+                    raise DataJointError(
+                        "Cascading deletes failed because the error message is missing foreign key information."
+                        "Make sure you have REFERENCES privilege to all dependent tables."
+                    ) from None
+                match = match.groupdict()
+                # if schema name missing, use table
+                if "`.`" not in match["child"]:
+                    match["child"] = "{}.{}".format(
+                        table.full_table_name.split(".")[0], match["child"]
+                    )
+                if (
+                    match["pk_attrs"] is not None
+                ):  # fully matched, adjusting the keys
+                    match["fk_attrs"] = [
+                        k.strip("`") for k in match["fk_attrs"].split(",")
+                    ]
+                    match["pk_attrs"] = [
+                        k.strip("`") for k in match["pk_attrs"].split(",")
+                    ]
+                else:  # only partially matched, querying with constraint to determine keys
+                    match["fk_attrs"], match["parent"], match["pk_attrs"] = list(
+                        map(
+                            list,
+                            zip(
+                                *table.connection.query(
+                                    constraint_info_query,
+                                    args=(
+                                        match["name"].strip("`"),
+                                        *[
+                                            _.strip("`")
+                                            for _ in match["child"].split("`.`")
+                                        ],
+                                    ),
+                                ).fetchall()
+                            ),
+                        )
+                    )
+                    match["parent"] = match["parent"][0]
+
+                # Restrict child by table if
+                #   1. if table's restriction attributes are not in child's primary key
+                #   2. if child renames any attributes
+                # Otherwise restrict child by table's restriction.
+                child = FreeTable(table.connection, match["child"])
+                if (
+                    set(table.restriction_attributes) <= set(child.primary_key)
+                    and match["fk_attrs"] == match["pk_attrs"]
+                ):
+                    child._restriction = table._restriction
+                    child._restriction_attributes = table.restriction_attributes
+                elif match["fk_attrs"] != match["pk_attrs"]:
+                    child &= table.proj(
+                        **dict(zip(match["fk_attrs"], match["pk_attrs"]))
+                    )
+                else:
+                    child &= table.proj()
+
+                master_name = get_master(child.full_table_name)
+                if (
+                    force_masters
+                    and master_name
+                    and master_name != table.full_table_name
+                    and master_name not in visited_masters
+                ):
+                    master = FreeTable(table.connection, master_name)
+                    master._restriction_attributes = set()
+                    master._restriction = [
+                        make_condition(  # &= may cause in target tables in subquery
+                            master,
+                            (master.proj() & child.proj()).fetch(),
+                            master._restriction_attributes,
+                        )
+                    ]
+                    visited_masters.add(master_name)
+                    cascade(master)
+                else:
+                    cascade(child)
+            else:
+                deleted.add(table.full_table_name)
+                logger.info(
+                    "Deleting {count} rows from {table}".format(
+                        count=delete_count, table=table.full_table_name
+                    )
+                )
+                break
+        else:
+            raise DataJointError("Exceeded maximum number of delete attempts.")
+        return delete_count
+
+    safemode = config["safemode"] if safemode is None else safemode
+
+    # Start transaction
+    if transaction:
+        if not self.connection.in_transaction:
+            self.connection.start_transaction()
+        else:
+            if not safemode:
+                transaction = False
+            else:
+                raise DataJointError(
+                    "Delete cannot use a transaction within an ongoing transaction. "
+                    "Set transaction=False or safemode=False)."
+                )
+
+    # Cascading delete
+    try:
+        delete_count = cascade(self)
+    except:
+        if transaction:
+            self.connection.cancel_transaction()
+        raise
+
+    if not force_parts:
+        # Avoid deleting from child before master (See issue #151)
+        for part in deleted:
+            master = get_master(part)
+            if master and master not in deleted:
+                if transaction:
+                    self.connection.cancel_transaction()
+                raise DataJointError(
+                    "Attempt to delete part table {part} before deleting from "
+                    "its master {master} first.".format(part=part, master=master)
+                )
+
+    # Confirm and commit
+    if delete_count == 0:
+        if safemode:
+            logger.warning("Nothing to delete.")
+        if transaction:
+            self.connection.cancel_transaction()
+    elif not transaction:
+        logger.info("Delete completed")
+    else:
+        if not safemode or user_choice("Commit deletes?", default="no") == "yes":
+            if transaction:
+                self.connection.commit_transaction()
+            if safemode:
+                logger.info("Delete committed.")
+        else:
+            if transaction:
+                self.connection.cancel_transaction()
+            if safemode:
+                logger.warning("Delete cancelled")
+    return delete_count
+

+ +

+ + + + + + +

+ + +

+ `drop_quick()` + +¶

+ + +

+ +

Drops the table without cascading to dependent tables and without user prompt.

+ + +

Source code in datajoint/table.py

def drop_quick(self):
+    """
+    Drops the table without cascading to dependent tables and without user prompt.
+    """
+    if self.is_declared:
+        query = "DROP TABLE %s" % self.full_table_name
+        self.connection.query(query)
+        logger.info("Dropped table %s" % self.full_table_name)
+        self._log(query[:255])
+    else:
+        logger.info(
+            "Nothing to drop: table %s is not declared" % self.full_table_name
+        )
+

+ +

+ + + + + + +

+ + +

+ `drop()` + +¶

+ + +

+ +

Drop the table and all tables that reference it, recursively. +User is prompted for confirmation if config['safemode'] is set to True.

+ + +

Source code in datajoint/table.py

def drop(self):
+    """
+    Drop the table and all tables that reference it, recursively.
+    User is prompted for confirmation if config['safemode'] is set to True.
+    """
+    if self.restriction:
+        raise DataJointError(
+            "A table with an applied restriction cannot be dropped."
+            " Call drop() on the unrestricted Table."
+        )
+    self.connection.dependencies.load()
+    do_drop = True
+    tables = [
+        table
+        for table in self.connection.dependencies.descendants(self.full_table_name)
+        if not table.isdigit()
+    ]
+
+    # avoid dropping part tables without their masters: See issue #374
+    for part in tables:
+        master = get_master(part)
+        if master and master not in tables:
+            raise DataJointError(
+                "Attempt to drop part table {part} before dropping "
+                "its master. Drop {master} first.".format(part=part, master=master)
+            )
+
+    if config["safemode"]:
+        for table in tables:
+            logger.info(
+                table + " (%d tuples)" % len(FreeTable(self.connection, table))
+            )
+        do_drop = user_choice("Proceed?", default="no") == "yes"
+    if do_drop:
+        for table in reversed(tables):
+            FreeTable(self.connection, table).drop_quick()
+        logger.info("Tables dropped. Restart kernel.")
+

+ +

+ + + + + + +

+ + + +

+ `size_on_disk` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + size of data and indices in bytes on the storage device + +

+ +

+ + + + + + +

+ + +

+ `describe(context=None, printout=False)` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the definition string for the query using DataJoint DDL. + +

+ + +

Source code in datajoint/table.py

def describe(self, context=None, printout=False):
+    """
+    :return:  the definition string for the query using DataJoint DDL.
+    """
+    if context is None:
+        frame = inspect.currentframe().f_back
+        context = dict(frame.f_globals, **frame.f_locals)
+        del frame
+    if self.full_table_name not in self.connection.dependencies:
+        self.connection.dependencies.load()
+    parents = self.parents(foreign_key_info=True)
+    in_key = True
+    definition = (
+        "# " + self.heading.table_status["comment"] + "\n"
+        if self.heading.table_status["comment"]
+        else ""
+    )
+    attributes_thus_far = set()
+    attributes_declared = set()
+    indexes = self.heading.indexes.copy()
+    for attr in self.heading.attributes.values():
+        if in_key and not attr.in_key:
+            definition += "---\n"
+            in_key = False
+        attributes_thus_far.add(attr.name)
+        do_include = True
+        for parent_name, fk_props in parents:
+            if attr.name in fk_props["attr_map"]:
+                do_include = False
+                if attributes_thus_far.issuperset(fk_props["attr_map"]):
+                    # foreign key properties
+                    try:
+                        index_props = indexes.pop(tuple(fk_props["attr_map"]))
+                    except KeyError:
+                        index_props = ""
+                    else:
+                        index_props = [k for k, v in index_props.items() if v]
+                        index_props = (
+                            " [{}]".format(", ".join(index_props))
+                            if index_props
+                            else ""
+                        )
+
+                    if not fk_props["aliased"]:
+                        # simple foreign key
+                        definition += "->{props} {class_name}\n".format(
+                            props=index_props,
+                            class_name=lookup_class_name(parent_name, context)
+                            or parent_name,
+                        )
+                    else:
+                        # projected foreign key
+                        definition += (
+                            "->{props} {class_name}.proj({proj_list})\n".format(
+                                props=index_props,
+                                class_name=lookup_class_name(parent_name, context)
+                                or parent_name,
+                                proj_list=",".join(
+                                    '{}="{}"'.format(attr, ref)
+                                    for attr, ref in fk_props["attr_map"].items()
+                                    if ref != attr
+                                ),
+                            )
+                        )
+                        attributes_declared.update(fk_props["attr_map"])
+        if do_include:
+            attributes_declared.add(attr.name)
+            definition += "%-20s : %-28s %s\n" % (
+                (
+                    attr.name
+                    if attr.default is None
+                    else "%s=%s" % (attr.name, attr.default)
+                ),
+                "%s%s"
+                % (attr.type, " auto_increment" if attr.autoincrement else ""),
+                "# " + attr.comment if attr.comment else "",
+            )
+    # add remaining indexes
+    for k, v in indexes.items():
+        definition += "{unique}INDEX ({attrs})\n".format(
+            unique="UNIQUE " if v["unique"] else "", attrs=", ".join(k)
+        )
+    if printout:
+        logger.info("\n" + definition)
+    return definition
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + +

+ `lookup_class_name(name, context, depth=3)` + +¶

+ + +

+ +

given a table name in the form schema_name.table_name, find its class in the context.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `name` +	+	+ + `schema_name`.`table_name` + +	+ required +
+ `context` +	+	+ + dictionary representing the namespace + +	+ required +
+ `depth` +	+	+ + search depth into imported modules, helps avoid infinite recursion. + +	+ `3` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + class name found in the context or None if not found + +

+ + +

Source code in datajoint/table.py

def lookup_class_name(name, context, depth=3):
+    """
+    given a table name in the form `schema_name`.`table_name`, find its class in the context.
+
+    :param name: `schema_name`.`table_name`
+    :param context: dictionary representing the namespace
+    :param depth: search depth into imported modules, helps avoid infinite recursion.
+    :return: class name found in the context or None if not found
+    """
+    # breadth-first search
+    nodes = [dict(context=context, context_name="", depth=depth)]
+    while nodes:
+        node = nodes.pop(0)
+        for member_name, member in node["context"].items():
+            # skip IPython's implicit variables
+            if not member_name.startswith("_"):
+                if inspect.isclass(member) and issubclass(member, Table):
+                    if member.full_table_name == name:  # found it!
+                        return ".".join([node["context_name"], member_name]).lstrip(".")
+                    try:  # look for part tables
+                        parts = member.__dict__
+                    except AttributeError:
+                        pass  # not a UserTable -- cannot have part tables.
+                    else:
+                        for part in (
+                            getattr(member, p)
+                            for p in parts
+                            if p[0].isupper() and hasattr(member, p)
+                        ):
+                            if (
+                                inspect.isclass(part)
+                                and issubclass(part, Table)
+                                and part.full_table_name == name
+                            ):
+                                return ".".join(
+                                    [node["context_name"], member_name, part.__name__]
+                                ).lstrip(".")
+                elif (
+                    node["depth"] > 0
+                    and inspect.ismodule(member)
+                    and member.__name__ != "datajoint"
+                ):
+                    try:
+                        nodes.append(
+                            dict(
+                                context=dict(inspect.getmembers(member)),
+                                context_name=node["context_name"] + "." + member_name,
+                                depth=node["depth"] - 1,
+                            )
+                        )
+                    except ImportError:
+                        pass  # could not import, so do not attempt
+    return None
+

+ +

+ + + + + + +

+ + + +

+ `FreeTable` + + +¶

+ + +

+ Bases: Table

+ + + +

A base table without a dedicated class. Each instance is associated with a table +specified by full_table_name.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `conn` +	+	+ + a dj.Connection object + +	+ required +
+ `full_table_name` +	+	+ + in format `database`.`table_name` + +	+ required +

+ + + + + + + + +

Source code in datajoint/table.py

class FreeTable(Table):
+    """
+    A base table without a dedicated class. Each instance is associated with a table
+    specified by full_table_name.
+
+    :param conn:  a dj.Connection object
+    :param full_table_name: in format `database`.`table_name`
+    """
+
+    def __init__(self, conn, full_table_name):
+        self.database, self._table_name = (
+            s.strip("`") for s in full_table_name.split(".")
+        )
+        self._connection = conn
+        self._support = [full_table_name]
+        self._heading = Heading(
+            table_info=dict(
+                conn=conn,
+                database=self.database,
+                table_name=self.table_name,
+                context=None,
+            )
+        )
+
+    def __repr__(self):
+        return (
+            "FreeTable(`%s`.`%s`)\n" % (self.database, self._table_name)
+            + super().__repr__()
+        )
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Log` + + +¶

+ + +

+ Bases: Table

+ + + +

The log table for each schema. +Instances are callable. Calls log the time and identifying information along with the event.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `skip_logging` +	+	+ + if True, then log entry is skipped by default. See call + +	+ `False` +

+ + + + + + + + +

Source code in datajoint/table.py

class Log(Table):
+    """
+    The log table for each schema.
+    Instances are callable.  Calls log the time and identifying information along with the event.
+
+    :param skip_logging: if True, then log entry is skipped by default. See __call__
+    """
+
+    _table_name = "~log"
+
+    def __init__(self, conn, database, skip_logging=False):
+        self.database = database
+        self.skip_logging = skip_logging
+        self._connection = conn
+        self._heading = Heading(
+            table_info=dict(
+                conn=conn, database=database, table_name=self.table_name, context=None
+            )
+        )
+        self._support = [self.full_table_name]
+
+        self._definition = """    # event logging table for `{database}`
+        id       :int unsigned auto_increment     # event order id
+        ---
+        timestamp = CURRENT_TIMESTAMP : timestamp # event timestamp
+        version  :varchar(12)                     # datajoint version
+        user     :varchar(255)                    # user@host
+        host=""  :varchar(255)                    # system hostname
+        event="" :varchar(255)                    # event message
+        """.format(
+            database=database
+        )
+
+        super().__init__()
+
+        if not self.is_declared:
+            self.declare()
+            self.connection.dependencies.clear()
+        self._user = self.connection.get_user()
+
+    @property
+    def definition(self):
+        return self._definition
+
+    def __call__(self, event, skip_logging=None):
+        """
+
+        :param event: string to write into the log table
+        :param skip_logging: If True then do not log. If None, then use self.skip_logging
+        """
+        skip_logging = self.skip_logging if skip_logging is None else skip_logging
+        if not skip_logging:
+            try:
+                self.insert1(
+                    dict(
+                        user=self._user,
+                        version=version + "py",
+                        host=platform.uname().node,
+                        event=event,
+                    ),
+                    skip_duplicates=True,
+                    ignore_extra_fields=True,
+                )
+            except DataJointError:
+                logger.info("could not log event in table ~log")
+
+    def delete(self):
+        """
+        bypass interactive prompts and cascading dependencies
+
+        :return: number of deleted items
+        """
+        return self.delete_quick(get_count=True)
+
+    def drop(self):
+        """bypass interactive prompts and cascading dependencies"""
+        self.drop_quick()
+

+ + + +

+ + + + + + + +

+ + +

+ `delete()` + +¶

+ + +

+ +

bypass interactive prompts and cascading dependencies

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + number of deleted items + +

+ + +

Source code in datajoint/table.py

def delete(self):
+    """
+    bypass interactive prompts and cascading dependencies
+
+    :return: number of deleted items
+    """
+    return self.delete_quick(get_count=True)
+

+ +

+ + + + + + +

+ + +

+ `drop()` + +¶

+ + +

+ +

bypass interactive prompts and cascading dependencies

+ + +

Source code in datajoint/table.py

def drop(self):
+    """bypass interactive prompts and cascading dependencies"""
+    self.drop_quick()
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/user_tables/index.html b/0.14/api/datajoint/user_tables/index.html new file mode 100644 index 000000000..4db5148c2 --- /dev/null +++ b/0.14/api/datajoint/user_tables/index.html @@ -0,0 +1,4776 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + user_tables.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + user_tables.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

user_tables.py

+ +

+ + + + +

+ +

Hosts the table tiers, user tables should be derived from.

+ + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ `TableMeta` + + +¶

+ + +

+ Bases: type

+ + + +

TableMeta subclasses allow applying some instance methods and properties directly +at class level. For example, this allows Table.fetch() instead of Table().fetch().

+ + + + + + + + +

Source code in datajoint/user_tables.py

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class TableMeta(type):
+    """
+    TableMeta subclasses allow applying some instance methods and properties directly
+    at class level. For example, this allows Table.fetch() instead of Table().fetch().
+    """
+
+    def __getattribute__(cls, name):
+        # trigger instantiation for supported class attrs
+        return (
+            cls().__getattribute__(name)
+            if name in supported_class_attrs
+            else super().__getattribute__(name)
+        )
+
+    def __and__(cls, arg):
+        return cls() & arg
+
+    def __xor__(cls, arg):
+        return cls() ^ arg
+
+    def __sub__(cls, arg):
+        return cls() - arg
+
+    def __neg__(cls):
+        return -cls()
+
+    def __mul__(cls, arg):
+        return cls() * arg
+
+    def __matmul__(cls, arg):
+        return cls() @ arg
+
+    def __add__(cls, arg):
+        return cls() + arg
+
+    def __iter__(cls):
+        return iter(cls())
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `UserTable` + + +¶

+ + +

+ Bases: Table

+ + + +

A subclass of UserTable is a dedicated class interfacing a base table. +UserTable is initialized by the decorator generated by schema().

+ + + + + + + + +

Source code in datajoint/user_tables.py

class UserTable(Table, metaclass=TableMeta):
+    """
+    A subclass of UserTable is a dedicated class interfacing a base table.
+    UserTable is initialized by the decorator generated by schema().
+    """
+
+    # set by @schema
+    _connection = None
+    _heading = None
+    _support = None
+
+    # set by subclass
+    tier_regexp = None
+    _prefix = None
+
+    @property
+    def definition(self):
+        """
+        :return: a string containing the table definition using the DataJoint DDL.
+        """
+        raise NotImplementedError(
+            'Subclasses of Table must implement the property "definition"'
+        )
+
+    @ClassProperty
+    def connection(cls):
+        return cls._connection
+
+    @ClassProperty
+    def table_name(cls):
+        """
+        :return: the table name of the table formatted for mysql.
+        """
+        if cls._prefix is None:
+            raise AttributeError("Class prefix is not defined!")
+        return cls._prefix + from_camel_case(cls.__name__)
+
+    @ClassProperty
+    def full_table_name(cls):
+        if cls not in {Manual, Imported, Lookup, Computed, Part, UserTable}:
+            # for derived classes only
+            if cls.database is None:
+                raise DataJointError(
+                    "Class %s is not properly declared (schema decorator not applied?)"
+                    % cls.__name__
+                )
+            return r"`{0:s}`.`{1:s}`".format(cls.database, cls.table_name)
+

+ + + +

+ + + + + + + +

+ + + +

+ `definition` + + + `property` + + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + a string containing the table definition using the DataJoint DDL. + +

+ +

+ + + + + + +

+ + +

+ `table_name()` + +¶

+ + +

+ + + + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the table name of the table formatted for mysql. + +

+ + +

Source code in datajoint/user_tables.py

@ClassProperty
+def table_name(cls):
+    """
+    :return: the table name of the table formatted for mysql.
+    """
+    if cls._prefix is None:
+        raise AttributeError("Class prefix is not defined!")
+    return cls._prefix + from_camel_case(cls.__name__)
+

+ +

+ + + + +

+ +

+ + + + + + +

+ + + +

+ `Manual` + + +¶

+ + +

+ Bases: UserTable

+ + + +

Inherit from this class if the table's values are entered manually.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Manual(UserTable):
+    """
+    Inherit from this class if the table's values are entered manually.
+    """
+
+    _prefix = r""
+    tier_regexp = r"(?P<manual>" + _prefix + _base_regexp + ")"
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Lookup` + + +¶

+ + +

+ Bases: UserTable

+ + + +

Inherit from this class if the table's values are for lookup. This is +currently equivalent to defining the table as Manual and serves semantic +purposes only.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Lookup(UserTable):
+    """
+    Inherit from this class if the table's values are for lookup. This is
+    currently equivalent to defining the table as Manual and serves semantic
+    purposes only.
+    """
+
+    _prefix = "#"
+    tier_regexp = (
+        r"(?P<lookup>" + _prefix + _base_regexp.replace("TIER", "lookup") + ")"
+    )
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Imported` + + +¶

+ + +

+ Bases: UserTable, AutoPopulate

+ + + +

Inherit from this class if the table's values are imported from external data sources. +The inherited class must at least provide the function _make_tuples.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Imported(UserTable, AutoPopulate):
+    """
+    Inherit from this class if the table's values are imported from external data sources.
+    The inherited class must at least provide the function `_make_tuples`.
+    """
+
+    _prefix = "_"
+    tier_regexp = r"(?P<imported>" + _prefix + _base_regexp + ")"
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Computed` + + +¶

+ + +

+ Bases: UserTable, AutoPopulate

+ + + +

Inherit from this class if the table's values are computed from other tables in the schema. +The inherited class must at least provide the function _make_tuples.

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Computed(UserTable, AutoPopulate):
+    """
+    Inherit from this class if the table's values are computed from other tables in the schema.
+    The inherited class must at least provide the function `_make_tuples`.
+    """
+
+    _prefix = "__"
+    tier_regexp = r"(?P<computed>" + _prefix + _base_regexp + ")"
+

+ + + +

+ + + + + +

+ +

+ + + + + + +

+ + + +

+ `Part` + + +¶

+ + +

+ Bases: UserTable

+ + + +

+ + + + + + + + +

Source code in datajoint/user_tables.py

class Part(UserTable):
+    """
+    Inherit from this class if the table's values are details of an entry in another table
+    and if this table is populated by the other table. For example, the entries inheriting from
+    dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix.
+    Part tables are implemented as classes inside classes.
+    """
+
+    _connection = None
+    _master = None
+
+    tier_regexp = (
+        r"(?P<master>"
+        + "|".join([c.tier_regexp for c in (Manual, Lookup, Imported, Computed)])
+        + r"){1,1}"
+        + "__"
+        + r"(?P<part>"
+        + _base_regexp
+        + ")"
+    )
+
+    @ClassProperty
+    def connection(cls):
+        return cls._connection
+
+    @ClassProperty
+    def full_table_name(cls):
+        return (
+            None
+            if cls.database is None or cls.table_name is None
+            else r"`{0:s}`.`{1:s}`".format(cls.database, cls.table_name)
+        )
+
+    @ClassProperty
+    def master(cls):
+        return cls._master
+
+    @ClassProperty
+    def table_name(cls):
+        return (
+            None
+            if cls.master is None
+            else cls.master.table_name + "__" + from_camel_case(cls.__name__)
+        )
+
+    def delete(self, force=False):
+        """
+        unless force is True, prohibits direct deletes from parts.
+        """
+        if force:
+            super().delete(force_parts=True)
+        else:
+            raise DataJointError(
+                "Cannot delete from a Part directly. Delete from master instead"
+            )
+
+    def drop(self, force=False):
+        """
+        unless force is True, prohibits direct deletes from parts.
+        """
+        if force:
+            super().drop()
+        else:
+            raise DataJointError(
+                "Cannot drop a Part directly.  Delete from master instead"
+            )
+
+    def alter(self, prompt=True, context=None):
+        # without context, use declaration context which maps master keyword to master table
+        super().alter(prompt=prompt, context=context or self.declaration_context)
+

+ + + +

+ + + + + + + +

+ + +

+ `delete(force=False)` + +¶

+ + +

+ +

unless force is True, prohibits direct deletes from parts.

+ + +

Source code in datajoint/user_tables.py

def delete(self, force=False):
+    """
+    unless force is True, prohibits direct deletes from parts.
+    """
+    if force:
+        super().delete(force_parts=True)
+    else:
+        raise DataJointError(
+            "Cannot delete from a Part directly. Delete from master instead"
+        )
+

+ +

+ + + + + + +

+ + +

+ `drop(force=False)` + +¶

+ + +

+ +

unless force is True, prohibits direct deletes from parts.

+ + +

Source code in datajoint/user_tables.py

def drop(self, force=False):
+    """
+    unless force is True, prohibits direct deletes from parts.
+    """
+    if force:
+        super().drop()
+    else:
+        raise DataJointError(
+            "Cannot drop a Part directly.  Delete from master instead"
+        )
+

+ +

+ + + + +

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/utils/index.html b/0.14/api/datajoint/utils/index.html new file mode 100644 index 000000000..359b082ac --- /dev/null +++ b/0.14/api/datajoint/utils/index.html @@ -0,0 +1,4601 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + utils.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + utils.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + + + + + +

+ + + +

+ +

+ + + + +

+ +

+ + + + + +

utils.py

+ +

+ + + + +

+ +

General-purpose utilities

+ + + + + + + + + + +

+ + + + + + + + + + + +

+ + +

+ `user_choice(prompt, choices=('yes', 'no'), default=None)` + +¶

+ + +

+ +

Prompts the user for confirmation. The default value, if any, is capitalized.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `prompt` +	+	+ + Information to display to the user. + +	+ required +
+ `choices` +	+	+ + an iterable of possible choices. + +	+ `('yes', 'no')` +
+ `default` +	+	+ + default choice + +	+ `None` +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + the user's choice + +

+ + +

Source code in datajoint/utils.py

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def user_choice(prompt, choices=("yes", "no"), default=None):
+    """
+    Prompts the user for confirmation.  The default value, if any, is capitalized.
+
+    :param prompt: Information to display to the user.
+    :param choices: an iterable of possible choices.
+    :param default: default choice
+    :return: the user's choice
+    """
+    assert default is None or default in choices
+    choice_list = ", ".join(
+        (choice.title() if choice == default else choice for choice in choices)
+    )
+    response = None
+    while response not in choices:
+        response = input(prompt + " [" + choice_list + "]: ")
+        response = response.lower() if response else default
+    return response
+

+ +

+ + + + + + +

+ + +

+ `get_master(full_table_name)` + +¶

+ + +

+ +

If the table name is that of a part table, then return what the master table name would be. +This follows DataJoint's table naming convention where a master and a part must be in the +same schema and the part table is prefixed with the master table name + __.

Example: + ephys.session -- master + ephys.session__recording -- part

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `full_table_name` +	+ `str` +	+ + Full table name including part. + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+ `str` +	+ + Supposed master full table name or empty string if not a part table name. + +

+ + +

Source code in datajoint/utils.py

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def get_master(full_table_name: str) -> str:
+    """
+    If the table name is that of a part table, then return what the master table name would be.
+    This follows DataJoint's table naming convention where a master and a part must be in the
+    same schema and the part table is prefixed with the master table name + ``__``.
+
+    Example:
+       `ephys`.`session`    -- master
+       `ephys`.`session__recording`  -- part
+
+    :param full_table_name: Full table name including part.
+    :type full_table_name: str
+    :return: Supposed master full table name or empty string if not a part table name.
+    :rtype: str
+    """
+    match = re.match(r"(?P<master>`\w+`.`\w+)__(?P<part>\w+)`", full_table_name)
+    return match["master"] + "`" if match else ""
+

+ +

+ + + + + + +

+ + +

+ `is_camel_case(s)` + +¶

+ + +

+ +

Check if a string is in CamelCase notation.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `s` +	+	+ + string to check + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + True if the string is in CamelCase notation, False otherwise +Example: + + + + is_camel_case("TableName") # returns True +is_camel_case("table_name") # returns False + + + + +

+ + +

Source code in datajoint/utils.py

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def is_camel_case(s):
+    """
+    Check if a string is in CamelCase notation.
+
+    :param s: string to check
+    :returns: True if the string is in CamelCase notation, False otherwise
+    Example:
+    >>> is_camel_case("TableName")  # returns True
+    >>> is_camel_case("table_name")  # returns False
+    """
+    return bool(re.match(r"^[A-Z][A-Za-z0-9]*$", s))
+

+ +

+ + + + + + +

+ + +

+ `to_camel_case(s)` + +¶

+ + +

+ +

Convert names with under score (_) separation into camel case names.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `s` +	+	+ + string in under_score notation + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + string in CamelCase notation +Example: + + + + to_camel_case("table_name") # returns "TableName" + + + + +

+ + +

Source code in datajoint/utils.py

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def to_camel_case(s):
+    """
+    Convert names with under score (_) separation into camel case names.
+
+    :param s: string in under_score notation
+    :returns: string in CamelCase notation
+    Example:
+    >>> to_camel_case("table_name")  # returns "TableName"
+    """
+
+    def to_upper(match):
+        return match.group(0)[-1].upper()
+
+    return re.sub(r"(^|[_\W])+[a-zA-Z]", to_upper, s)
+

+ +

+ + + + + + +

+ + +

+ `from_camel_case(s)` + +¶

+ + +

+ +

Convert names in camel case into underscore (_) separated names

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `s` +	+	+ + string in CamelCase notation + +	+ required +

+ + +

Returns:

+ + + + + + + + + + + + + +

Type	Description
+	+ + string in under_score notation +Example: + + + + from_camel_case("TableName") # yields "table_name" + + + + +

+ + +

Source code in datajoint/utils.py

def from_camel_case(s):
+    """
+    Convert names in camel case into underscore (_) separated names
+
+    :param s: string in CamelCase notation
+    :returns: string in under_score notation
+    Example:
+    >>> from_camel_case("TableName") # yields "table_name"
+    """
+
+    def convert(match):
+        return ("_" if match.groups()[0] else "") + match.group(0).lower()
+
+    if not is_camel_case(s):
+        raise DataJointError(
+            "ClassName must be alphanumeric in CamelCase, begin with a capital letter"
+        )
+    return re.sub(r"(\B[A-Z])|(\b[A-Z])", convert, s)
+

+ +

+ + + + + + +

+ + +

+ `safe_write(filepath, blob)` + +¶

+ + +

+ +

A two-step write.

+ + +

Parameters:

+ + + + + + + + + + + + + + + + + + + + + + + +

Name	Type	Description	Default
+ `filename` +	+	+ + full path + +	+ required +
+ `blob` +	+	+ + binary data + +	+ required +

+ + +

Source code in datajoint/utils.py

def safe_write(filepath, blob):
+    """
+    A two-step write.
+
+    :param filename: full path
+    :param blob: binary data
+    """
+    filepath = Path(filepath)
+    if not filepath.is_file():
+        filepath.parent.mkdir(parents=True, exist_ok=True)
+        temp_file = filepath.with_suffix(filepath.suffix + ".saving")
+        temp_file.write_bytes(blob)
+        temp_file.rename(filepath)
+

+ +

+ + + + + + +

+ + +

+ `safe_copy(src, dest, overwrite=False)` + +¶

+ + +

+ +

Copy the contents of src file into dest file as a two-step process. Skip if dest exists already

+ + +

Source code in datajoint/utils.py

def safe_copy(src, dest, overwrite=False):
+    """
+    Copy the contents of src file into dest file as a two-step process. Skip if dest exists already
+    """
+    src, dest = Path(src), Path(dest)
+    if not (dest.exists() and src.samefile(dest)) and (overwrite or not dest.is_file()):
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        temp_file = dest.with_suffix(dest.suffix + ".copying")
+        shutil.copyfile(str(src), str(temp_file))
+        temp_file.rename(dest)
+

+ +

+ + + + + + +

+ + +

+ `parse_sql(filepath)` + +¶

+ + +

+ +

yield SQL statements from an SQL file

+ + +

Source code in datajoint/utils.py

def parse_sql(filepath):
+    """
+    yield SQL statements from an SQL file
+    """
+    delimiter = ";"
+    statement = []
+    with Path(filepath).open("rt") as f:
+        for line in f:
+            line = line.strip()
+            if not line.startswith("--") and len(line) > 1:
+                if line.startswith("delimiter"):
+                    delimiter = line.split()[1]
+                else:
+                    statement.append(line)
+                    if line.endswith(delimiter):
+                        yield " ".join(statement)
+                        statement = []
+        if statement:
+            yield " ".join(statement)
+

+ +

+ + + + +

+ +

+ + + + + + + + + + + + + +

+ + + +

+ +

+ + + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/datajoint/version/index.html b/0.14/api/datajoint/version/index.html new file mode 100644 index 000000000..2017db7cd --- /dev/null +++ b/0.14/api/datajoint/version/index.html @@ -0,0 +1,3690 @@ + + + + + + + + + + + + + + + + + + + + + + + + version.py - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + Skip to content + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + version.py + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/api/make_pages.py b/0.14/api/make_pages.py new file mode 100644 index 000000000..3072cb46a --- /dev/null +++ b/0.14/api/make_pages.py @@ -0,0 +1,19 @@ +"""Generate the api pages and navigation.""" + +import os +from pathlib import Path + +import mkdocs_gen_files + +package = os.getenv("PACKAGE", "datajoint") +nav = mkdocs_gen_files.Nav() +for path in sorted(Path(package).glob("**/*.py")): + with mkdocs_gen_files.open(f"api/{path.with_suffix('')}.md", "w") as f: + module_path = ".".join( + [p for p in path.with_suffix("").parts if p != "__init__"] + ) + print(f"::: {module_path}", file=f) + nav[path.parts] = f"{path.with_suffix('')}.md" + +with mkdocs_gen_files.open("api/navigation.md", "w") as nav_file: + nav_file.writelines(nav.build_literate_nav()) diff --git a/0.14/api/navigation/index.html b/0.14/api/navigation/index.html new file mode 100644 index 000000000..f594f55ae --- /dev/null +++ b/0.14/api/navigation/index.html @@ -0,0 +1,3629 @@ + + + + + + + + + + + + + + + + + + + + + + Navigation - DataJoint Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ +

+ + + + + + + + +

+ + + + + + + + + + + + + +

+ + DataJoint Documentation + +

+ + + Navigation + + +

+ + + + + + + + + + + + + + + + + + + + +

+ +

+ + +

+ datajoint/datajoint-python +

+ +

+ + +

+ + + + + + + + + + + + + \ No newline at end of file diff --git a/0.14/assets/_mkdocstrings.css b/0.14/assets/_mkdocstrings.css new file mode 100644 index 000000000..854048ca1 --- /dev/null +++ b/0.14/assets/_mkdocstrings.css @@ -0,0 +1,237 @@ + +/* Avoid breaking parameter names, etc. in table cells. */ +.doc-contents td code { + word-break: normal !important; +} + +/* No line break before first paragraph of descriptions. */ +.doc-md-description, +.doc-md-description>p:first-child { + display: inline; +} + +/* No text transformation from Material for MkDocs for H5 headings. */ +.md-typeset h5 .doc-object-name { + text-transform: none; +} + +/* Max width for docstring sections tables. */ +.doc .md-typeset__table, +.doc .md-typeset__table table { + display: table !important; + width: 100%; +} + +.doc .md-typeset__table tr { + display: table-row; +} + +/* Defaults in Spacy table style. */ +.doc-param-default, +.doc-type_param-default { + float: right; +} + +/* Parameter headings must be inline, not blocks. */ +.doc-heading-parameter, +.doc-heading-type_parameter { + display: inline; +} + +/* Default font size for parameter headings. */ +.md-typeset .doc-heading-parameter { + font-size: inherit; +} + +/* Prefer space on the right, not the left of parameter permalinks. */ +.doc-heading-parameter .headerlink, +.doc-heading-type_parameter .headerlink { + margin-left: 0 !important; + margin-right: 0.2rem; +} + +/* Backward-compatibility: docstring section titles in bold. */ +.doc-section-title { + font-weight: bold; +} + +/* Backlinks crumb separator. */ +.doc-backlink-crumb { + display: inline-flex; + gap: .2rem; + white-space: nowrap; + align-items: center; + vertical-align: middle; +} +.doc-backlink-crumb:not(:first-child)::before { + background-color: var(--md-default-fg-color--lighter); + content: ""; + display: inline; + height: 1rem; + --md-path-icon: url('data:image/svg+xml;charset=utf-8,'); + -webkit-mask-image: var(--md-path-icon); + mask-image: var(--md-path-icon); + width: 1rem; +} +.doc-backlink-crumb.last { + font-weight: bold; +} + +/* Symbols in Navigation and ToC. */ +:root, :host, +[data-md-color-scheme="default"] { + --doc-symbol-parameter-fg-color: #df50af; + --doc-symbol-type_parameter-fg-color: #df50af; + --doc-symbol-attribute-fg-color: #953800; + --doc-symbol-function-fg-color: #8250df; + --doc-symbol-method-fg-color: #8250df; + --doc-symbol-class-fg-color: #0550ae; + --doc-symbol-type_alias-fg-color: #0550ae; + --doc-symbol-module-fg-color: #5cad0f; + + --doc-symbol-parameter-bg-color: #df50af1a; + --doc-symbol-type_parameter-bg-color: #df50af1a; + --doc-symbol-attribute-bg-color: #9538001a; + --doc-symbol-function-bg-color: #8250df1a; + --doc-symbol-method-bg-color: #8250df1a; + --doc-symbol-class-bg-color: #0550ae1a; + --doc-symbol-type_alias-bg-color: #0550ae1a; + --doc-symbol-module-bg-color: #5cad0f1a; +} + +[data-md-color-scheme="slate"] { + --doc-symbol-parameter-fg-color: #ffa8cc; + --doc-symbol-type_parameter-fg-color: #ffa8cc; + --doc-symbol-attribute-fg-color: #ffa657; + --doc-symbol-function-fg-color: #d2a8ff; + --doc-symbol-method-fg-color: #d2a8ff; + --doc-symbol-class-fg-color: #79c0ff; + --doc-symbol-type_alias-fg-color: #79c0ff; + --doc-symbol-module-fg-color: #baff79; + + --doc-symbol-parameter-bg-color: #ffa8cc1a; + --doc-symbol-type_parameter-bg-color: #ffa8cc1a; + --doc-symbol-attribute-bg-color: #ffa6571a; + --doc-symbol-function-bg-color: #d2a8ff1a; + --doc-symbol-method-bg-color: #d2a8ff1a; + --doc-symbol-class-bg-color: #79c0ff1a; + --doc-symbol-type_alias-bg-color: #79c0ff1a; + --doc-symbol-module-bg-color: #baff791a; +} + +code.doc-symbol { + border-radius: .1rem; + font-size: .85em; + padding: 0 .3em; + font-weight: bold; +} + +code.doc-symbol-parameter, +a code.doc-symbol-parameter { + color: var(--doc-symbol-parameter-fg-color); + background-color: var(--doc-symbol-parameter-bg-color); +} + +code.doc-symbol-parameter::after { + content: "param"; +} + +code.doc-symbol-type_parameter, +a code.doc-symbol-type_parameter { + color: var(--doc-symbol-type_parameter-fg-color); + background-color: var(--doc-symbol-type_parameter-bg-color); +} + +code.doc-symbol-type_parameter::after { + content: "type-param"; +} + +code.doc-symbol-attribute, +a code.doc-symbol-attribute { + color: var(--doc-symbol-attribute-fg-color); + background-color: var(--doc-symbol-attribute-bg-color); +} + +code.doc-symbol-attribute::after { + content: "attr"; +} + +code.doc-symbol-function, +a code.doc-symbol-function { + color: var(--doc-symbol-function-fg-color); + background-color: var(--doc-symbol-function-bg-color); +} + +code.doc-symbol-function::after { + content: "func"; +} + +code.doc-symbol-method, +a code.doc-symbol-method { + color: var(--doc-symbol-method-fg-color); + background-color: var(--doc-symbol-method-bg-color); +} + +code.doc-symbol-method::after { + content: "meth"; +} + +code.doc-symbol-class, +a code.doc-symbol-class { + color: var(--doc-symbol-class-fg-color); + background-color: var(--doc-symbol-class-bg-color); +} + +code.doc-symbol-class::after { + content: "class"; +} + + +code.doc-symbol-type_alias, +a code.doc-symbol-type_alias { + color: var(--doc-symbol-type_alias-fg-color); + background-color: var(--doc-symbol-type_alias-bg-color); +} + +code.doc-symbol-type_alias::after { + content: "type"; +} + +code.doc-symbol-module, +a code.doc-symbol-module { + color: var(--doc-symbol-module-fg-color); + background-color: var(--doc-symbol-module-bg-color); +} + +code.doc-symbol-module::after { + content: "mod"; +} + +.doc-signature .autorefs { + color: inherit; + border-bottom: 1px dotted currentcolor; +} + +/* Source code blocks (admonitions). */ +:root { + --md-admonition-icon--mkdocstrings-source: url('data:image/svg+xml;charset=utf-8,') +} +.md-typeset .admonition.mkdocstrings-source, +.md-typeset details.mkdocstrings-source { + border: none; + padding: 0; +} +.md-typeset .admonition.mkdocstrings-source:focus-within, +.md-typeset details.mkdocstrings-source:focus-within { + box-shadow: none; +} +.md-typeset .mkdocstrings-source > .admonition-title, +.md-typeset .mkdocstrings-source > summary { + background-color: inherit; +} +.md-typeset .mkdocstrings-source > .admonition-title::before, +.md-typeset .mkdocstrings-source > summary::before { + background-color: var(--md-default-fg-color); + -webkit-mask-image: var(--md-admonition-icon--mkdocstrings-source); + mask-image: var(--md-admonition-icon--mkdocstrings-source); +} diff --git a/0.14/assets/images/company-logo-blue.png b/0.14/assets/images/company-logo-blue.png new file mode 100644 index 000000000..d15194b8d Binary files /dev/null and b/0.14/assets/images/company-logo-blue.png differ diff --git a/0.14/assets/images/favicon.png b/0.14/assets/images/favicon.png new file mode 100644 index 000000000..1cf13b9f9 Binary files /dev/null and b/0.14/assets/images/favicon.png differ diff --git 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foreignObject{line-height:normal;overflow:visible}.label div .edgeLabel{color:var(--md-mermaid-label-fg-color)}.edgeLabel,.edgeLabel p,.label div .edgeLabel{background-color:var(--md-mermaid-label-bg-color)}.edgeLabel,.edgeLabel p{fill:var(--md-mermaid-label-bg-color);color:var(--md-mermaid-edge-color)}.edgePath .path,.flowchart-link{stroke:var(--md-mermaid-edge-color)}.edgePath .arrowheadPath{fill:var(--md-mermaid-edge-color);stroke:none}.cluster rect{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}.cluster span{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}g #flowchart-circleEnd,g #flowchart-circleStart,g #flowchart-crossEnd,g #flowchart-crossStart,g #flowchart-pointEnd,g #flowchart-pointStart{stroke:none}.classDiagramTitleText{fill:var(--md-mermaid-label-fg-color)}g.classGroup line,g.classGroup rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}g.classGroup text{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.classLabel .box{fill:var(--md-mermaid-label-bg-color);background-color:var(--md-mermaid-label-bg-color);opacity:1}.classLabel .label{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.node .divider{stroke:var(--md-mermaid-node-fg-color)}.relation{stroke:var(--md-mermaid-edge-color)}.cardinality{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.cardinality text{fill:inherit!important}defs marker.marker.composition.class path,defs marker.marker.dependency.class path,defs marker.marker.extension.class path{fill:var(--md-mermaid-edge-color)!important;stroke:var(--md-mermaid-edge-color)!important}defs marker.marker.aggregation.class path{fill:var(--md-mermaid-label-bg-color)!important;stroke:var(--md-mermaid-edge-color)!important}.statediagramTitleText{fill:var(--md-mermaid-label-fg-color)}g.stateGroup rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}g.stateGroup .state-title{fill:var(--md-mermaid-label-fg-color)!important;font-family:var(--md-mermaid-font-family)}g.stateGroup .composit{fill:var(--md-mermaid-label-bg-color)}.nodeLabel,.nodeLabel p{color:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}a .nodeLabel{text-decoration:underline}.node circle.state-end,.node circle.state-start,.start-state{fill:var(--md-mermaid-edge-color);stroke:none}.end-state-inner,.end-state-outer{fill:var(--md-mermaid-edge-color)}.end-state-inner,.node circle.state-end{stroke:var(--md-mermaid-label-bg-color)}.transition{stroke:var(--md-mermaid-edge-color)}[id^=state-fork] rect,[id^=state-join] rect{fill:var(--md-mermaid-edge-color)!important;stroke:none!important}.statediagram-cluster.statediagram-cluster .inner{fill:var(--md-default-bg-color)}.statediagram-cluster rect{fill:var(--md-mermaid-node-bg-color);stroke:var(--md-mermaid-node-fg-color)}.statediagram-state rect.divider{fill:var(--md-default-fg-color--lightest);stroke:var(--md-default-fg-color--lighter)}defs #statediagram-barbEnd{stroke:var(--md-mermaid-edge-color)}[id^=entity] path,[id^=entity] rect{fill:var(--md-default-bg-color)}.relationshipLine{stroke:var(--md-mermaid-edge-color)}defs .marker.oneOrMore.er *,defs .marker.onlyOne.er *,defs .marker.zeroOrMore.er *,defs .marker.zeroOrOne.er *{stroke:var(--md-mermaid-edge-color)!important}text:not([class]):last-child{fill:var(--md-mermaid-label-fg-color)}.actor{fill:var(--md-mermaid-sequence-actor-bg-color);stroke:var(--md-mermaid-sequence-actor-border-color)}text.actor>tspan{fill:var(--md-mermaid-sequence-actor-fg-color);font-family:var(--md-mermaid-font-family)}line{stroke:var(--md-mermaid-sequence-actor-line-color)}.actor-man circle,.actor-man line{fill:var(--md-mermaid-sequence-actorman-bg-color);stroke:var(--md-mermaid-sequence-actorman-line-color)}.messageLine0,.messageLine1{stroke:var(--md-mermaid-sequence-message-line-color)}.note{fill:var(--md-mermaid-sequence-note-bg-color);stroke:var(--md-mermaid-sequence-note-border-color)}.loopText,.loopText>tspan,.messageText,.noteText>tspan{stroke:none;font-family:var(--md-mermaid-font-family)!important}.messageText{fill:var(--md-mermaid-sequence-message-fg-color)}.loopText,.loopText>tspan{fill:var(--md-mermaid-sequence-loop-fg-color)}.noteText>tspan{fill:var(--md-mermaid-sequence-note-fg-color)}#arrowhead path{fill:var(--md-mermaid-sequence-message-line-color);stroke:none}.loopLine{fill:var(--md-mermaid-sequence-loop-bg-color);stroke:var(--md-mermaid-sequence-loop-border-color)}.labelBox{fill:var(--md-mermaid-sequence-label-bg-color);stroke:none}.labelText,.labelText>span{fill:var(--md-mermaid-sequence-label-fg-color);font-family:var(--md-mermaid-font-family)}.sequenceNumber{fill:var(--md-mermaid-sequence-number-fg-color)}rect.rect{fill:var(--md-mermaid-sequence-box-bg-color);stroke:none}rect.rect+text.text{fill:var(--md-mermaid-sequence-box-fg-color)}defs #sequencenumber{fill:var(--md-mermaid-sequence-number-bg-color)!important}";var so,is=0;function as(){return typeof mermaid=="undefined"||mermaid instanceof Element?_t("https://unpkg.com/mermaid@11/dist/mermaid.min.js"):$(void 0)}function Zn(e){return 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T,c=a.pipe(oe(),ae(!0));z([a,Le(e),mt(e)]).pipe(W(c),$e(1,ye)).subscribe({next([{active:p},l]){let f=Be(p),{width:u}=de(p);e.style.setProperty("--md-indicator-x",`${f.x}px`),e.style.setProperty("--md-indicator-width",`${u}px`);let d=gr(o);(f.xd.x+l.width)&&o.scrollTo({left:Math.max(0,f.x-16),behavior:"smooth"})},complete(){e.style.removeProperty("--md-indicator-x"),e.style.removeProperty("--md-indicator-width")}}),z([Ge(o),Le(o)]).pipe(W(c)).subscribe(([p,l])=>{let f=At(o);i.hidden=p.x<16,s.hidden=p.x>f.width-l.width-16}),L(h(i,"click").pipe(m(()=>-1)),h(s,"click").pipe(m(()=>1))).pipe(W(c)).subscribe(p=>{let{width:l}=de(o);o.scrollBy({left:l*p,behavior:"smooth"})}),r.pipe(W(c),g(p=>n.includes(p))).subscribe(p=>p.click()),o.classList.add("tabbed-labels--linked");for(let p of n){let 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t.pipe(b(r=>L($(!0),$(!1).pipe(nt(2e3))).pipe(m(o=>({message:r,active:o})))))}function ni(e,t){let r=j(".md-typeset",e);return H(()=>{let o=new T;return o.subscribe(({message:n,active:i})=>{e.classList.toggle("md-dialog--active",i),r.textContent=n}),cs(e,t).pipe(O(n=>o.next(n)),A(()=>o.complete()),m(n=>P({ref:e},n)))})}var ps=0;function ls(e,t){document.body.append(e);let{width:r}=de(e);e.style.setProperty("--md-tooltip-width",`${r}px`),e.remove();let o=vr(t),n=typeof o!="undefined"?Ge(o):$({x:0,y:0}),i=L(Ye(t),it(t)).pipe(Y());return z([i,n]).pipe(m(([s,a])=>{let{x:c,y:p}=Be(t),l=de(t),f=t.closest("table");return f&&t.parentElement&&(c+=f.offsetLeft+t.parentElement.offsetLeft,p+=f.offsetTop+t.parentElement.offsetTop),{active:s,offset:{x:c-a.x+l.width/2-r/2,y:p-a.y+l.height+8}}}))}function ii(e){let t=e.title;if(!t.length)return y;let r=`__tooltip_${ps++}`,o=Dt(r,"inline"),n=j(".md-typeset",o);return n.innerHTML=t,H(()=>{let i=new T;return 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ms({viewport$:e}){if(!V("header.autohide"))return $(!1);let t=e.pipe(m(({offset:{y:n}})=>n),ot(2,1),m(([n,i])=>[nMath.abs(i-n.y)>100),m(([,[n]])=>n),Y()),o=Je("search");return z([e,o]).pipe(m(([{offset:n},i])=>n.y>400&&!i),Y(),b(n=>n?r:$(!1)),Q(!1))}function ai(e,t){return H(()=>z([Le(e),ms(t)])).pipe(m(([{height:r},o])=>({height:r,hidden:o})),Y((r,o)=>r.height===o.height&&r.hidden===o.hidden),Z(1))}function si(e,{header$:t,main$:r}){return H(()=>{let o=new T,n=o.pipe(oe(),ae(!0));o.pipe(ne("active"),Pe(t)).subscribe(([{active:s},{hidden:a}])=>{e.classList.toggle("md-header--shadow",s&&!a),e.hidden=a});let i=fe(M("[title]",e)).pipe(g(()=>V("content.tooltips")),J(s=>ii(s)));return r.subscribe(o),t.pipe(W(n),m(s=>P({ref:e},s)),Ve(i.pipe(W(n))))})}function fs(e,{viewport$:t,header$:r}){return Er(e,{viewport$:t,header$:r}).pipe(m(({offset:{y:o}})=>{let{height:n}=de(e);return{active:n>0&&o>=n}}),ne("active"))}function ci(e,t){return H(()=>{let r=new T;r.subscribe({next({active:n}){e.classList.toggle("md-header__title--active",n)},complete(){e.classList.remove("md-header__title--active")}});let o=ue(".md-content h1");return typeof o=="undefined"?y:fs(o,t).pipe(O(n=>r.next(n)),A(()=>r.complete()),m(n=>P({ref:e},n)))})}function pi(e,{viewport$:t,header$:r}){let o=r.pipe(m(({height:i})=>i),Y()),n=o.pipe(b(()=>Le(e).pipe(m(({height:i})=>({top:e.offsetTop,bottom:e.offsetTop+i})),ne("bottom"))));return z([o,n,t]).pipe(m(([i,{top:s,bottom:a},{offset:{y:c},size:{height:p}}])=>(p=Math.max(0,p-Math.max(0,s-c,i)-Math.max(0,p+c-a)),{offset:s-i,height:p,active:s-i<=c})),Y((i,s)=>i.offset===s.offset&&i.height===s.height&&i.active===s.active))}function us(e){let t=__md_get("__palette")||{index:e.findIndex(o=>matchMedia(o.getAttribute("data-md-color-media")).matches)},r=Math.max(0,Math.min(t.index,e.length-1));return $(...e).pipe(J(o=>h(o,"change").pipe(m(()=>o))),Q(e[r]),m(o=>({index:e.indexOf(o),color:{media:o.getAttribute("data-md-color-media"),scheme:o.getAttribute("data-md-color-scheme"),primary:o.getAttribute("data-md-color-primary"),accent:o.getAttribute("data-md-color-accent")}})),Z(1))}function li(e){let t=M("input",e),r=x("meta",{name:"theme-color"});document.head.appendChild(r);let o=x("meta",{name:"color-scheme"});document.head.appendChild(o);let n=Wt("(prefers-color-scheme: light)");return H(()=>{let i=new T;return i.subscribe(s=>{if(document.body.setAttribute("data-md-color-switching",""),s.color.media==="(prefers-color-scheme)"){let a=matchMedia("(prefers-color-scheme: light)"),c=document.querySelector(a.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: 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Ii(e,{viewport$:t,header$:r,main$:o,target$:n}){let i=new T,s=i.pipe(oe(),ae(!0));return i.subscribe({next({hidden:a}){e.hidden=a,a?(e.setAttribute("tabindex","-1"),e.blur()):e.removeAttribute("tabindex")},complete(){e.style.top="",e.hidden=!0,e.removeAttribute("tabindex")}}),r.pipe(W(s),ne("height")).subscribe(({height:a})=>{e.style.top=`${a+16}px`}),h(e,"click").subscribe(a=>{a.preventDefault(),window.scrollTo({top:0})}),As(e,{viewport$:t,main$:o,target$:n}).pipe(O(a=>i.next(a)),A(()=>i.complete()),m(a=>P({ref:e},a)))}function Fi({document$:e,viewport$:t}){e.pipe(b(()=>M(".md-ellipsis")),J(r=>mt(r).pipe(W(e.pipe(Ie(1))),g(o=>o),m(()=>r),Ee(1))),g(r=>r.offsetWidth{let o=r.innerText,n=r.closest("a")||r;return n.title=o,V("content.tooltips")?Xe(n,{viewport$:t}).pipe(W(e.pipe(Ie(1))),A(()=>n.removeAttribute("title"))):y})).subscribe(),V("content.tooltips")&&e.pipe(b(()=>M(".md-status")),J(r=>Xe(r,{viewport$:t}))).subscribe()}function ji({document$:e,tablet$:t}){e.pipe(b(()=>M(".md-toggle--indeterminate")),O(r=>{r.indeterminate=!0,r.checked=!1}),J(r=>h(r,"change").pipe(Jr(()=>r.classList.contains("md-toggle--indeterminate")),m(()=>r))),te(t)).subscribe(([r,o])=>{r.classList.remove("md-toggle--indeterminate"),o&&(r.checked=!1)})}function Cs(){return/(iPad|iPhone|iPod)/.test(navigator.userAgent)}function Ui({document$:e}){e.pipe(b(()=>M("[data-md-scrollfix]")),O(t=>t.removeAttribute("data-md-scrollfix")),g(Cs),J(t=>h(t,"touchstart").pipe(m(()=>t)))).subscribe(t=>{let r=t.scrollTop;r===0?t.scrollTop=1:r+t.offsetHeight===t.scrollHeight&&(t.scrollTop=r-1)})}function Wi({viewport$:e,tablet$:t}){z([Je("search"),t]).pipe(m(([r,o])=>r&&!o),b(r=>$(r).pipe(nt(r?400:100))),te(e)).subscribe(([r,{offset:{y:o}}])=>{if(r)document.body.setAttribute("data-md-scrolllock",""),document.body.style.top=`-${o}px`;else{let 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URL("search/search_index.js",Or.base)}`).pipe(m(()=>__index),Z(1)):ze(new URL("search/search_index.json",Or.base))}document.documentElement.classList.remove("no-js");document.documentElement.classList.add("js");var ct=an(),Kt=bn(),Ht=yn(Kt),mo=hn(),ke=Ln(),Lr=Wt("(min-width: 60em)"),Vi=Wt("(min-width: 76.25em)"),Ni=xn(),Or=Te(),zi=document.forms.namedItem("search")?ks():tt,fo=new T;di({alert$:fo});ui({document$:ct});var uo=new T,qi=kt(Or.base);V("navigation.instant")&&gi({sitemap$:qi,location$:Kt,viewport$:ke,progress$:uo}).subscribe(ct);var Di;((Di=Or.version)==null?void 0:Di.provider)==="mike"&&Ti({document$:ct});L(Kt,Ht).pipe(nt(125)).subscribe(()=>{at("drawer",!1),at("search",!1)});mo.pipe(g(({mode:e})=>e==="global")).subscribe(e=>{switch(e.type){case"p":case",":let t=ue("link[rel=prev]");typeof t!="undefined"&&st(t);break;case"n":case".":let r=ue("link[rel=next]");typeof r!="undefined"&&st(r);break;case"Enter":let o=Ne();o instanceof 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ft=ai(Ce("header"),{viewport$:ke}),qt=ct.pipe(m(()=>Ce("main")),b(e=>pi(e,{viewport$:ke,header$:ft})),Z(1)),Hs=L(...me("consent").map(e=>An(e,{target$:Ht})),...me("dialog").map(e=>ni(e,{alert$:fo})),...me("palette").map(e=>li(e)),...me("progress").map(e=>mi(e,{progress$:uo})),...me("search").map(e=>_i(e,{index$:zi,keyboard$:mo})),...me("source").map(e=>$i(e))),$s=H(()=>L(...me("announce").map(e=>_n(e)),...me("content").map(e=>oi(e,{sitemap$:qi,viewport$:ke,target$:Ht,print$:Ni})),...me("content").map(e=>V("search.highlight")?Ai(e,{index$:zi,location$:Kt}):y),...me("header").map(e=>si(e,{viewport$:ke,header$:ft,main$:qt})),...me("header-title").map(e=>ci(e,{viewport$:ke,header$:ft})),...me("sidebar").map(e=>e.getAttribute("data-md-type")==="navigation"?eo(Vi,()=>lo(e,{viewport$:ke,header$:ft,main$:qt})):eo(Lr,()=>lo(e,{viewport$:ke,header$:ft,main$:qt}))),...me("tabs").map(e=>Pi(e,{viewport$:ke,header$:ft})),...me("toc").map(e=>Ri(e,{viewport$:ke,header$:ft,main$:qt,target$:Ht})),...me("top").map(e=>Ii(e,{viewport$:ke,header$:ft,main$:qt,target$:Ht})))),Ki=ct.pipe(b(()=>$s),Ve(Hs),Z(1));Ki.subscribe();window.document$=ct;window.location$=Kt;window.target$=Ht;window.keyboard$=mo;window.viewport$=ke;window.tablet$=Lr;window.screen$=Vi;window.print$=Ni;window.alert$=fo;window.progress$=uo;window.component$=Ki;})(); 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"src/templates/assets/javascripts/browser/viewport/offset/index.ts", "src/templates/assets/javascripts/browser/viewport/size/index.ts", "src/templates/assets/javascripts/browser/viewport/_/index.ts", "src/templates/assets/javascripts/browser/viewport/at/index.ts", "src/templates/assets/javascripts/browser/worker/index.ts", "src/templates/assets/javascripts/_/index.ts", "src/templates/assets/javascripts/components/_/index.ts", "src/templates/assets/javascripts/components/announce/index.ts", "src/templates/assets/javascripts/components/consent/index.ts", "src/templates/assets/javascripts/templates/tooltip/index.tsx", "src/templates/assets/javascripts/templates/annotation/index.tsx", "src/templates/assets/javascripts/templates/clipboard/index.tsx", "src/templates/assets/javascripts/templates/search/index.tsx", "src/templates/assets/javascripts/templates/source/index.tsx", "src/templates/assets/javascripts/templates/tabbed/index.tsx", "src/templates/assets/javascripts/templates/table/index.tsx", "src/templates/assets/javascripts/templates/version/index.tsx", "src/templates/assets/javascripts/components/tooltip2/index.ts", "src/templates/assets/javascripts/components/content/annotation/_/index.ts", "src/templates/assets/javascripts/components/content/annotation/list/index.ts", "src/templates/assets/javascripts/components/content/annotation/block/index.ts", "src/templates/assets/javascripts/components/content/code/_/index.ts", "src/templates/assets/javascripts/components/content/details/index.ts", "src/templates/assets/javascripts/components/content/link/index.ts", "src/templates/assets/javascripts/components/content/mermaid/index.css", "src/templates/assets/javascripts/components/content/mermaid/index.ts", "src/templates/assets/javascripts/components/content/table/index.ts", "src/templates/assets/javascripts/components/content/tabs/index.ts", "src/templates/assets/javascripts/components/content/_/index.ts", "src/templates/assets/javascripts/components/dialog/index.ts", "src/templates/assets/javascripts/components/tooltip/index.ts", "src/templates/assets/javascripts/components/header/_/index.ts", "src/templates/assets/javascripts/components/header/title/index.ts", "src/templates/assets/javascripts/components/main/index.ts", "src/templates/assets/javascripts/components/palette/index.ts", "src/templates/assets/javascripts/components/progress/index.ts", "src/templates/assets/javascripts/integrations/sitemap/index.ts", "src/templates/assets/javascripts/integrations/alternate/index.ts", "src/templates/assets/javascripts/integrations/clipboard/index.ts", "src/templates/assets/javascripts/integrations/instant/index.ts", "src/templates/assets/javascripts/integrations/search/highlighter/index.ts", "src/templates/assets/javascripts/integrations/search/worker/message/index.ts", "src/templates/assets/javascripts/integrations/search/worker/_/index.ts", "src/templates/assets/javascripts/integrations/version/findurl/index.ts", "src/templates/assets/javascripts/integrations/version/index.ts", "src/templates/assets/javascripts/components/search/query/index.ts", "src/templates/assets/javascripts/components/search/result/index.ts", "src/templates/assets/javascripts/components/search/share/index.ts", "src/templates/assets/javascripts/components/search/suggest/index.ts", "src/templates/assets/javascripts/components/search/_/index.ts", "src/templates/assets/javascripts/components/search/highlight/index.ts", "src/templates/assets/javascripts/components/sidebar/index.ts", "src/templates/assets/javascripts/components/source/facts/github/index.ts", "src/templates/assets/javascripts/components/source/facts/gitlab/index.ts", "src/templates/assets/javascripts/components/source/facts/_/index.ts", "src/templates/assets/javascripts/components/source/_/index.ts", "src/templates/assets/javascripts/components/tabs/index.ts", "src/templates/assets/javascripts/components/toc/index.ts", "src/templates/assets/javascripts/components/top/index.ts", "src/templates/assets/javascripts/patches/ellipsis/index.ts", "src/templates/assets/javascripts/patches/indeterminate/index.ts", "src/templates/assets/javascripts/patches/scrollfix/index.ts", "src/templates/assets/javascripts/patches/scrolllock/index.ts", "src/templates/assets/javascripts/polyfills/index.ts"], + "sourcesContent": ["(function (global, factory) {\n typeof exports === 'object' && typeof module !== 'undefined' ? factory() :\n typeof define === 'function' && define.amd ? define(factory) :\n (factory());\n}(this, (function () { 'use strict';\n\n /**\n * Applies the :focus-visible polyfill at the given scope.\n * A scope in this case is either the top-level Document or a Shadow Root.\n *\n * @param {(Document|ShadowRoot)} scope\n * @see https://github.com/WICG/focus-visible\n */\n function applyFocusVisiblePolyfill(scope) {\n var hadKeyboardEvent = true;\n var hadFocusVisibleRecently = false;\n var hadFocusVisibleRecentlyTimeout = null;\n\n var inputTypesAllowlist = {\n text: true,\n search: true,\n url: true,\n tel: true,\n email: true,\n password: true,\n number: true,\n date: true,\n month: true,\n week: true,\n time: true,\n datetime: true,\n 'datetime-local': true\n };\n\n /**\n * Helper function for legacy browsers and iframes which sometimes focus\n * elements like document, body, and non-interactive SVG.\n * @param {Element} el\n */\n function isValidFocusTarget(el) {\n if (\n el &&\n el !== document &&\n el.nodeName !== 'HTML' &&\n el.nodeName !== 'BODY' &&\n 'classList' in el &&\n 'contains' in el.classList\n ) {\n return true;\n }\n return false;\n }\n\n /**\n * Computes whether the given element should automatically trigger the\n * `focus-visible` class being added, i.e. whether it should always match\n * `:focus-visible` when focused.\n * @param {Element} el\n * @return {boolean}\n */\n function focusTriggersKeyboardModality(el) {\n var type = el.type;\n var tagName = el.tagName;\n\n if (tagName === 'INPUT' && inputTypesAllowlist[type] && !el.readOnly) {\n return true;\n }\n\n if (tagName === 'TEXTAREA' && !el.readOnly) {\n return true;\n }\n\n if (el.isContentEditable) {\n return true;\n }\n\n return false;\n }\n\n /**\n * Add the `focus-visible` class to the given element if it was not added by\n * the author.\n * @param {Element} el\n */\n function addFocusVisibleClass(el) {\n if (el.classList.contains('focus-visible')) {\n return;\n }\n el.classList.add('focus-visible');\n el.setAttribute('data-focus-visible-added', '');\n }\n\n /**\n * Remove the `focus-visible` class from the given element if it was not\n * originally added by the author.\n * @param {Element} el\n */\n function removeFocusVisibleClass(el) {\n if (!el.hasAttribute('data-focus-visible-added')) {\n return;\n }\n el.classList.remove('focus-visible');\n el.removeAttribute('data-focus-visible-added');\n }\n\n /**\n * If the most recent user interaction was via the keyboard;\n * and the key press did not include a meta, alt/option, or control key;\n * then the modality is keyboard. Otherwise, the modality is not keyboard.\n * Apply `focus-visible` to any current active element and keep track\n * of our keyboard modality state with `hadKeyboardEvent`.\n * @param {KeyboardEvent} e\n */\n function onKeyDown(e) {\n if (e.metaKey || e.altKey || e.ctrlKey) {\n return;\n }\n\n if (isValidFocusTarget(scope.activeElement)) {\n addFocusVisibleClass(scope.activeElement);\n }\n\n hadKeyboardEvent = true;\n }\n\n /**\n * If at any point a user clicks with a pointing device, ensure that we change\n * the modality away from keyboard.\n * This avoids the situation where a user presses a key on an already focused\n * element, and then clicks on a different element, focusing it with a\n * pointing device, while we still think we're in keyboard modality.\n * @param {Event} e\n */\n function onPointerDown(e) {\n hadKeyboardEvent = false;\n }\n\n /**\n * On `focus`, add the `focus-visible` class to the target if:\n * - the target received focus as a result of keyboard navigation, or\n * - the event target is an element that will likely require interaction\n * via the keyboard (e.g. a text box)\n * @param {Event} e\n */\n function onFocus(e) {\n // Prevent IE from focusing the document or HTML element.\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (hadKeyboardEvent || focusTriggersKeyboardModality(e.target)) {\n addFocusVisibleClass(e.target);\n }\n }\n\n /**\n * On `blur`, remove the `focus-visible` class from the target.\n * @param {Event} e\n */\n function onBlur(e) {\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (\n e.target.classList.contains('focus-visible') ||\n e.target.hasAttribute('data-focus-visible-added')\n ) {\n // To detect a tab/window switch, we look for a blur event followed\n // rapidly by a visibility change.\n // If we don't see a visibility change within 100ms, it's probably a\n // regular focus change.\n hadFocusVisibleRecently = true;\n window.clearTimeout(hadFocusVisibleRecentlyTimeout);\n hadFocusVisibleRecentlyTimeout = window.setTimeout(function() {\n hadFocusVisibleRecently = false;\n }, 100);\n removeFocusVisibleClass(e.target);\n }\n }\n\n /**\n * If the user changes tabs, keep track of whether or not the previously\n * focused element had .focus-visible.\n * @param {Event} e\n */\n function onVisibilityChange(e) {\n if (document.visibilityState === 'hidden') {\n // If the tab becomes active again, the browser will handle calling focus\n // on the element (Safari actually calls it twice).\n // If this tab change caused a blur on an element with focus-visible,\n // re-apply the class when the user switches back to the tab.\n if (hadFocusVisibleRecently) {\n hadKeyboardEvent = true;\n }\n addInitialPointerMoveListeners();\n }\n }\n\n /**\n * Add a group of listeners to detect usage of any pointing devices.\n * These listeners will be added when the polyfill first loads, and anytime\n * the window is blurred, so that they are active when the window regains\n * focus.\n */\n function addInitialPointerMoveListeners() {\n document.addEventListener('mousemove', onInitialPointerMove);\n document.addEventListener('mousedown', onInitialPointerMove);\n document.addEventListener('mouseup', onInitialPointerMove);\n document.addEventListener('pointermove', onInitialPointerMove);\n document.addEventListener('pointerdown', onInitialPointerMove);\n document.addEventListener('pointerup', onInitialPointerMove);\n document.addEventListener('touchmove', onInitialPointerMove);\n document.addEventListener('touchstart', onInitialPointerMove);\n document.addEventListener('touchend', onInitialPointerMove);\n }\n\n function removeInitialPointerMoveListeners() {\n document.removeEventListener('mousemove', onInitialPointerMove);\n document.removeEventListener('mousedown', onInitialPointerMove);\n document.removeEventListener('mouseup', onInitialPointerMove);\n document.removeEventListener('pointermove', onInitialPointerMove);\n document.removeEventListener('pointerdown', onInitialPointerMove);\n document.removeEventListener('pointerup', onInitialPointerMove);\n document.removeEventListener('touchmove', onInitialPointerMove);\n document.removeEventListener('touchstart', onInitialPointerMove);\n document.removeEventListener('touchend', onInitialPointerMove);\n }\n\n /**\n * When the polfyill first loads, assume the user is in keyboard modality.\n * If any event is received from a pointing device (e.g. mouse, pointer,\n * touch), turn off keyboard modality.\n * This accounts for situations where focus enters the page from the URL bar.\n * @param {Event} e\n */\n function onInitialPointerMove(e) {\n // Work around a Safari quirk that fires a mousemove on whenever the\n // window blurs, even if you're tabbing out of the page. \u00AF\\_(\u30C4)_/\u00AF\n if (e.target.nodeName && e.target.nodeName.toLowerCase() === 'html') {\n return;\n }\n\n hadKeyboardEvent = false;\n removeInitialPointerMoveListeners();\n }\n\n // For some kinds of state, we are interested in changes at the global scope\n // only. For example, global pointer input, global key presses and global\n // visibility change should affect the state at every scope:\n document.addEventListener('keydown', onKeyDown, true);\n document.addEventListener('mousedown', onPointerDown, true);\n document.addEventListener('pointerdown', onPointerDown, true);\n document.addEventListener('touchstart', onPointerDown, true);\n document.addEventListener('visibilitychange', onVisibilityChange, true);\n\n addInitialPointerMoveListeners();\n\n // For focus and blur, we specifically care about state changes in the local\n // scope. This is because focus / blur events that originate from within a\n // shadow root are not re-dispatched from the host element if it was already\n // the active element in its own scope:\n scope.addEventListener('focus', onFocus, true);\n scope.addEventListener('blur', onBlur, true);\n\n // We detect that a node is a ShadowRoot by ensuring that it is a\n // DocumentFragment and also has a host property. This check covers native\n // implementation and polyfill implementation transparently. If we only cared\n // about the native implementation, we could just check if the scope was\n // an instance of a ShadowRoot.\n if (scope.nodeType === Node.DOCUMENT_FRAGMENT_NODE && scope.host) {\n // Since a ShadowRoot is a special kind of DocumentFragment, it does not\n // have a root element to add a class to. So, we add this attribute to the\n // host element instead:\n scope.host.setAttribute('data-js-focus-visible', '');\n } else if (scope.nodeType === Node.DOCUMENT_NODE) {\n document.documentElement.classList.add('js-focus-visible');\n document.documentElement.setAttribute('data-js-focus-visible', '');\n }\n }\n\n // It is important to wrap all references to global window and document in\n // these checks to support server-side rendering use cases\n // @see https://github.com/WICG/focus-visible/issues/199\n if (typeof window !== 'undefined' && typeof document !== 'undefined') {\n // Make the polyfill helper globally available. This can be used as a signal\n // to interested libraries that wish to coordinate with the polyfill for e.g.,\n // applying the polyfill to a shadow root:\n window.applyFocusVisiblePolyfill = applyFocusVisiblePolyfill;\n\n // Notify interested libraries of the polyfill's presence, in case the\n // polyfill was loaded lazily:\n var event;\n\n try {\n event = new CustomEvent('focus-visible-polyfill-ready');\n } catch (error) {\n // IE11 does not support using CustomEvent as a constructor directly:\n event = document.createEvent('CustomEvent');\n event.initCustomEvent('focus-visible-polyfill-ready', false, false, {});\n }\n\n window.dispatchEvent(event);\n }\n\n if (typeof document !== 'undefined') {\n // Apply the polyfill to the global document, so that no JavaScript\n // coordination is required to use the polyfill in the top-level document:\n applyFocusVisiblePolyfill(document);\n }\n\n})));\n", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "/*!\n * clipboard.js v2.0.11\n * https://clipboardjs.com/\n *\n * Licensed MIT \u00A9 Zeno Rocha\n */\n(function webpackUniversalModuleDefinition(root, factory) {\n\tif(typeof exports === 'object' && typeof module === 'object')\n\t\tmodule.exports = factory();\n\telse if(typeof define === 'function' && define.amd)\n\t\tdefine([], factory);\n\telse if(typeof exports === 'object')\n\t\texports[\"ClipboardJS\"] = factory();\n\telse\n\t\troot[\"ClipboardJS\"] = factory();\n})(this, function() {\nreturn /******/ (function() { // webpackBootstrap\n/******/ \tvar __webpack_modules__ = ({\n\n/***/ 686:\n/***/ (function(__unused_webpack_module, __webpack_exports__, __webpack_require__) {\n\n\"use strict\";\n\n// EXPORTS\n__webpack_require__.d(__webpack_exports__, {\n \"default\": function() { return /* binding */ clipboard; }\n});\n\n// EXTERNAL MODULE: ./node_modules/tiny-emitter/index.js\nvar tiny_emitter = __webpack_require__(279);\nvar tiny_emitter_default = /*#__PURE__*/__webpack_require__.n(tiny_emitter);\n// EXTERNAL MODULE: ./node_modules/good-listener/src/listen.js\nvar listen = __webpack_require__(370);\nvar listen_default = /*#__PURE__*/__webpack_require__.n(listen);\n// EXTERNAL MODULE: ./node_modules/select/src/select.js\nvar src_select = __webpack_require__(817);\nvar select_default = /*#__PURE__*/__webpack_require__.n(src_select);\n;// CONCATENATED MODULE: ./src/common/command.js\n/**\n * Executes a given operation type.\n * @param {String} type\n * @return {Boolean}\n */\nfunction command(type) {\n try {\n return document.execCommand(type);\n } catch (err) {\n return false;\n }\n}\n;// CONCATENATED MODULE: ./src/actions/cut.js\n\n\n/**\n * Cut action wrapper.\n * @param {String|HTMLElement} target\n * @return {String}\n */\n\nvar ClipboardActionCut = function ClipboardActionCut(target) {\n var selectedText = select_default()(target);\n command('cut');\n return selectedText;\n};\n\n/* harmony default export */ var actions_cut = (ClipboardActionCut);\n;// CONCATENATED MODULE: ./src/common/create-fake-element.js\n/**\n * Creates a fake textarea element with a value.\n * @param {String} value\n * @return {HTMLElement}\n */\nfunction createFakeElement(value) {\n var isRTL = document.documentElement.getAttribute('dir') === 'rtl';\n var fakeElement = document.createElement('textarea'); // Prevent zooming on iOS\n\n fakeElement.style.fontSize = '12pt'; // Reset box model\n\n fakeElement.style.border = '0';\n fakeElement.style.padding = '0';\n fakeElement.style.margin = '0'; // Move element out of screen horizontally\n\n fakeElement.style.position = 'absolute';\n fakeElement.style[isRTL ? 'right' : 'left'] = '-9999px'; // Move element to the same position vertically\n\n var yPosition = window.pageYOffset || document.documentElement.scrollTop;\n fakeElement.style.top = \"\".concat(yPosition, \"px\");\n fakeElement.setAttribute('readonly', '');\n fakeElement.value = value;\n return fakeElement;\n}\n;// CONCATENATED MODULE: ./src/actions/copy.js\n\n\n\n/**\n * Create fake copy action wrapper using a fake element.\n * @param {String} target\n * @param {Object} options\n * @return {String}\n */\n\nvar fakeCopyAction = function fakeCopyAction(value, options) {\n var fakeElement = createFakeElement(value);\n options.container.appendChild(fakeElement);\n var selectedText = select_default()(fakeElement);\n command('copy');\n fakeElement.remove();\n return selectedText;\n};\n/**\n * Copy action wrapper.\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @return {String}\n */\n\n\nvar ClipboardActionCopy = function ClipboardActionCopy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n var selectedText = '';\n\n if (typeof target === 'string') {\n selectedText = fakeCopyAction(target, options);\n } else if (target instanceof HTMLInputElement && !['text', 'search', 'url', 'tel', 'password'].includes(target === null || target === void 0 ? void 0 : target.type)) {\n // If input type doesn't support `setSelectionRange`. Simulate it. https://developer.mozilla.org/en-US/docs/Web/API/HTMLInputElement/setSelectionRange\n selectedText = fakeCopyAction(target.value, options);\n } else {\n selectedText = select_default()(target);\n command('copy');\n }\n\n return selectedText;\n};\n\n/* harmony default export */ var actions_copy = (ClipboardActionCopy);\n;// CONCATENATED MODULE: ./src/actions/default.js\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return _typeof(obj); }\n\n\n\n/**\n * Inner function which performs selection from either `text` or `target`\n * properties and then executes copy or cut operations.\n * @param {Object} options\n */\n\nvar ClipboardActionDefault = function ClipboardActionDefault() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n // Defines base properties passed from constructor.\n var _options$action = options.action,\n action = _options$action === void 0 ? 'copy' : _options$action,\n container = options.container,\n target = options.target,\n text = options.text; // Sets the `action` to be performed which can be either 'copy' or 'cut'.\n\n if (action !== 'copy' && action !== 'cut') {\n throw new Error('Invalid \"action\" value, use either \"copy\" or \"cut\"');\n } // Sets the `target` property using an element that will be have its content copied.\n\n\n if (target !== undefined) {\n if (target && _typeof(target) === 'object' && target.nodeType === 1) {\n if (action === 'copy' && target.hasAttribute('disabled')) {\n throw new Error('Invalid \"target\" attribute. Please use \"readonly\" instead of \"disabled\" attribute');\n }\n\n if (action === 'cut' && (target.hasAttribute('readonly') || target.hasAttribute('disabled'))) {\n throw new Error('Invalid \"target\" attribute. You can\\'t cut text from elements with \"readonly\" or \"disabled\" attributes');\n }\n } else {\n throw new Error('Invalid \"target\" value, use a valid Element');\n }\n } // Define selection strategy based on `text` property.\n\n\n if (text) {\n return actions_copy(text, {\n container: container\n });\n } // Defines which selection strategy based on `target` property.\n\n\n if (target) {\n return action === 'cut' ? actions_cut(target) : actions_copy(target, {\n container: container\n });\n }\n};\n\n/* harmony default export */ var actions_default = (ClipboardActionDefault);\n;// CONCATENATED MODULE: ./src/clipboard.js\nfunction clipboard_typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { clipboard_typeof = function _typeof(obj) { return typeof obj; }; } else { clipboard_typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return clipboard_typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (clipboard_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n/**\n * Helper function to retrieve attribute value.\n * @param {String} suffix\n * @param {Element} element\n */\n\nfunction getAttributeValue(suffix, element) {\n var attribute = \"data-clipboard-\".concat(suffix);\n\n if (!element.hasAttribute(attribute)) {\n return;\n }\n\n return element.getAttribute(attribute);\n}\n/**\n * Base class which takes one or more elements, adds event listeners to them,\n * and instantiates a new `ClipboardAction` on each click.\n */\n\n\nvar Clipboard = /*#__PURE__*/function (_Emitter) {\n _inherits(Clipboard, _Emitter);\n\n var _super = _createSuper(Clipboard);\n\n /**\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n * @param {Object} options\n */\n function Clipboard(trigger, options) {\n var _this;\n\n _classCallCheck(this, Clipboard);\n\n _this = _super.call(this);\n\n _this.resolveOptions(options);\n\n _this.listenClick(trigger);\n\n return _this;\n }\n /**\n * Defines if attributes would be resolved using internal setter functions\n * or custom functions that were passed in the constructor.\n * @param {Object} options\n */\n\n\n _createClass(Clipboard, [{\n key: \"resolveOptions\",\n value: function resolveOptions() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n this.action = typeof options.action === 'function' ? options.action : this.defaultAction;\n this.target = typeof options.target === 'function' ? options.target : this.defaultTarget;\n this.text = typeof options.text === 'function' ? options.text : this.defaultText;\n this.container = clipboard_typeof(options.container) === 'object' ? options.container : document.body;\n }\n /**\n * Adds a click event listener to the passed trigger.\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n */\n\n }, {\n key: \"listenClick\",\n value: function listenClick(trigger) {\n var _this2 = this;\n\n this.listener = listen_default()(trigger, 'click', function (e) {\n return _this2.onClick(e);\n });\n }\n /**\n * Defines a new `ClipboardAction` on each click event.\n * @param {Event} e\n */\n\n }, {\n key: \"onClick\",\n value: function onClick(e) {\n var trigger = e.delegateTarget || e.currentTarget;\n var action = this.action(trigger) || 'copy';\n var text = actions_default({\n action: action,\n container: this.container,\n target: this.target(trigger),\n text: this.text(trigger)\n }); // Fires an event based on the copy operation result.\n\n this.emit(text ? 'success' : 'error', {\n action: action,\n text: text,\n trigger: trigger,\n clearSelection: function clearSelection() {\n if (trigger) {\n trigger.focus();\n }\n\n window.getSelection().removeAllRanges();\n }\n });\n }\n /**\n * Default `action` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultAction\",\n value: function defaultAction(trigger) {\n return getAttributeValue('action', trigger);\n }\n /**\n * Default `target` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultTarget\",\n value: function defaultTarget(trigger) {\n var selector = getAttributeValue('target', trigger);\n\n if (selector) {\n return document.querySelector(selector);\n }\n }\n /**\n * Allow fire programmatically a copy action\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @returns Text copied.\n */\n\n }, {\n key: \"defaultText\",\n\n /**\n * Default `text` lookup function.\n * @param {Element} trigger\n */\n value: function defaultText(trigger) {\n return getAttributeValue('text', trigger);\n }\n /**\n * Destroy lifecycle.\n */\n\n }, {\n key: \"destroy\",\n value: function destroy() {\n this.listener.destroy();\n }\n }], [{\n key: \"copy\",\n value: function copy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n return actions_copy(target, options);\n }\n /**\n * Allow fire programmatically a cut action\n * @param {String|HTMLElement} target\n * @returns Text cutted.\n */\n\n }, {\n key: \"cut\",\n value: function cut(target) {\n return actions_cut(target);\n }\n /**\n * Returns the support of the given action, or all actions if no action is\n * given.\n * @param {String} [action]\n */\n\n }, {\n key: \"isSupported\",\n value: function isSupported() {\n var action = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : ['copy', 'cut'];\n var actions = typeof action === 'string' ? [action] : action;\n var support = !!document.queryCommandSupported;\n actions.forEach(function (action) {\n support = support && !!document.queryCommandSupported(action);\n });\n return support;\n }\n }]);\n\n return Clipboard;\n}((tiny_emitter_default()));\n\n/* harmony default export */ var clipboard = (Clipboard);\n\n/***/ }),\n\n/***/ 828:\n/***/ (function(module) {\n\nvar DOCUMENT_NODE_TYPE = 9;\n\n/**\n * A polyfill for Element.matches()\n */\nif (typeof Element !== 'undefined' && !Element.prototype.matches) {\n var proto = Element.prototype;\n\n proto.matches = proto.matchesSelector ||\n proto.mozMatchesSelector ||\n proto.msMatchesSelector ||\n proto.oMatchesSelector ||\n proto.webkitMatchesSelector;\n}\n\n/**\n * Finds the closest parent that matches a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @return {Function}\n */\nfunction closest (element, selector) {\n while (element && element.nodeType !== DOCUMENT_NODE_TYPE) {\n if (typeof element.matches === 'function' &&\n element.matches(selector)) {\n return element;\n }\n element = element.parentNode;\n }\n}\n\nmodule.exports = closest;\n\n\n/***/ }),\n\n/***/ 438:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar closest = __webpack_require__(828);\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction _delegate(element, selector, type, callback, useCapture) {\n var listenerFn = listener.apply(this, arguments);\n\n element.addEventListener(type, listenerFn, useCapture);\n\n return {\n destroy: function() {\n element.removeEventListener(type, listenerFn, useCapture);\n }\n }\n}\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element|String|Array} [elements]\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction delegate(elements, selector, type, callback, useCapture) {\n // Handle the regular Element usage\n if (typeof elements.addEventListener === 'function') {\n return _delegate.apply(null, arguments);\n }\n\n // Handle Element-less usage, it defaults to global delegation\n if (typeof type === 'function') {\n // Use `document` as the first parameter, then apply arguments\n // This is a short way to .unshift `arguments` without running into deoptimizations\n return _delegate.bind(null, document).apply(null, arguments);\n }\n\n // Handle Selector-based usage\n if (typeof elements === 'string') {\n elements = document.querySelectorAll(elements);\n }\n\n // Handle Array-like based usage\n return Array.prototype.map.call(elements, function (element) {\n return _delegate(element, selector, type, callback, useCapture);\n });\n}\n\n/**\n * Finds closest match and invokes callback.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Function}\n */\nfunction listener(element, selector, type, callback) {\n return function(e) {\n e.delegateTarget = closest(e.target, selector);\n\n if (e.delegateTarget) {\n callback.call(element, e);\n }\n }\n}\n\nmodule.exports = delegate;\n\n\n/***/ }),\n\n/***/ 879:\n/***/ (function(__unused_webpack_module, exports) {\n\n/**\n * Check if argument is a HTML element.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.node = function(value) {\n return value !== undefined\n && value instanceof HTMLElement\n && value.nodeType === 1;\n};\n\n/**\n * Check if argument is a list of HTML elements.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.nodeList = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return value !== undefined\n && (type === '[object NodeList]' || type === '[object HTMLCollection]')\n && ('length' in value)\n && (value.length === 0 || exports.node(value[0]));\n};\n\n/**\n * Check if argument is a string.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.string = function(value) {\n return typeof value === 'string'\n || value instanceof String;\n};\n\n/**\n * Check if argument is a function.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.fn = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return type === '[object Function]';\n};\n\n\n/***/ }),\n\n/***/ 370:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar is = __webpack_require__(879);\nvar delegate = __webpack_require__(438);\n\n/**\n * Validates all params and calls the right\n * listener function based on its target type.\n *\n * @param {String|HTMLElement|HTMLCollection|NodeList} target\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listen(target, type, callback) {\n if (!target && !type && !callback) {\n throw new Error('Missing required arguments');\n }\n\n if (!is.string(type)) {\n throw new TypeError('Second argument must be a String');\n }\n\n if (!is.fn(callback)) {\n throw new TypeError('Third argument must be a Function');\n }\n\n if (is.node(target)) {\n return listenNode(target, type, callback);\n }\n else if (is.nodeList(target)) {\n return listenNodeList(target, type, callback);\n }\n else if (is.string(target)) {\n return listenSelector(target, type, callback);\n }\n else {\n throw new TypeError('First argument must be a String, HTMLElement, HTMLCollection, or NodeList');\n }\n}\n\n/**\n * Adds an event listener to a HTML element\n * and returns a remove listener function.\n *\n * @param {HTMLElement} node\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNode(node, type, callback) {\n node.addEventListener(type, callback);\n\n return {\n destroy: function() {\n node.removeEventListener(type, callback);\n }\n }\n}\n\n/**\n * Add an event listener to a list of HTML elements\n * and returns a remove listener function.\n *\n * @param {NodeList|HTMLCollection} nodeList\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNodeList(nodeList, type, callback) {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.addEventListener(type, callback);\n });\n\n return {\n destroy: function() {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.removeEventListener(type, callback);\n });\n }\n }\n}\n\n/**\n * Add an event listener to a selector\n * and returns a remove listener function.\n *\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenSelector(selector, type, callback) {\n return delegate(document.body, selector, type, callback);\n}\n\nmodule.exports = listen;\n\n\n/***/ }),\n\n/***/ 817:\n/***/ (function(module) {\n\nfunction select(element) {\n var selectedText;\n\n if (element.nodeName === 'SELECT') {\n element.focus();\n\n selectedText = element.value;\n }\n else if (element.nodeName === 'INPUT' || element.nodeName === 'TEXTAREA') {\n var isReadOnly = element.hasAttribute('readonly');\n\n if (!isReadOnly) {\n element.setAttribute('readonly', '');\n }\n\n element.select();\n element.setSelectionRange(0, element.value.length);\n\n if (!isReadOnly) {\n element.removeAttribute('readonly');\n }\n\n selectedText = element.value;\n }\n else {\n if (element.hasAttribute('contenteditable')) {\n element.focus();\n }\n\n var selection = window.getSelection();\n var range = document.createRange();\n\n range.selectNodeContents(element);\n selection.removeAllRanges();\n selection.addRange(range);\n\n selectedText = selection.toString();\n }\n\n return selectedText;\n}\n\nmodule.exports = select;\n\n\n/***/ }),\n\n/***/ 279:\n/***/ (function(module) {\n\nfunction E () {\n // Keep this empty so it's easier to inherit from\n // (via https://github.com/lipsmack from https://github.com/scottcorgan/tiny-emitter/issues/3)\n}\n\nE.prototype = {\n on: function (name, callback, ctx) {\n var e = this.e || (this.e = {});\n\n (e[name] || (e[name] = [])).push({\n fn: callback,\n ctx: ctx\n });\n\n return this;\n },\n\n once: function (name, callback, ctx) {\n var self = this;\n function listener () {\n self.off(name, listener);\n callback.apply(ctx, arguments);\n };\n\n listener._ = callback\n return this.on(name, listener, ctx);\n },\n\n emit: function (name) {\n var data = [].slice.call(arguments, 1);\n var evtArr = ((this.e || (this.e = {}))[name] || []).slice();\n var i = 0;\n var len = evtArr.length;\n\n for (i; i < len; i++) {\n evtArr[i].fn.apply(evtArr[i].ctx, data);\n }\n\n return this;\n },\n\n off: function (name, callback) {\n var e = this.e || (this.e = {});\n var evts = e[name];\n var liveEvents = [];\n\n if (evts && callback) {\n for (var i = 0, len = evts.length; i < len; i++) {\n if (evts[i].fn !== callback && evts[i].fn._ !== callback)\n liveEvents.push(evts[i]);\n }\n }\n\n // Remove event from queue to prevent memory leak\n // Suggested by https://github.com/lazd\n // Ref: https://github.com/scottcorgan/tiny-emitter/commit/c6ebfaa9bc973b33d110a84a307742b7cf94c953#commitcomment-5024910\n\n (liveEvents.length)\n ? e[name] = liveEvents\n : delete e[name];\n\n return this;\n }\n};\n\nmodule.exports = E;\nmodule.exports.TinyEmitter = E;\n\n\n/***/ })\n\n/******/ \t});\n/************************************************************************/\n/******/ \t// The module cache\n/******/ \tvar __webpack_module_cache__ = {};\n/******/ \t\n/******/ \t// The require function\n/******/ \tfunction __webpack_require__(moduleId) {\n/******/ \t\t// Check if module is in cache\n/******/ \t\tif(__webpack_module_cache__[moduleId]) {\n/******/ \t\t\treturn __webpack_module_cache__[moduleId].exports;\n/******/ \t\t}\n/******/ \t\t// Create a new module (and put it into the cache)\n/******/ \t\tvar module = __webpack_module_cache__[moduleId] = {\n/******/ \t\t\t// no module.id needed\n/******/ \t\t\t// no module.loaded needed\n/******/ \t\t\texports: {}\n/******/ \t\t};\n/******/ \t\n/******/ \t\t// Execute the module function\n/******/ \t\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n/******/ \t\n/******/ \t\t// Return the exports of the module\n/******/ \t\treturn module.exports;\n/******/ \t}\n/******/ \t\n/************************************************************************/\n/******/ \t/* webpack/runtime/compat get default export */\n/******/ \t!function() {\n/******/ \t\t// getDefaultExport function for compatibility with non-harmony modules\n/******/ \t\t__webpack_require__.n = function(module) {\n/******/ \t\t\tvar getter = module && module.__esModule ?\n/******/ \t\t\t\tfunction() { return module['default']; } :\n/******/ \t\t\t\tfunction() { return module; };\n/******/ \t\t\t__webpack_require__.d(getter, { a: getter });\n/******/ \t\t\treturn getter;\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/define property getters */\n/******/ \t!function() {\n/******/ \t\t// define getter functions for harmony exports\n/******/ \t\t__webpack_require__.d = function(exports, definition) {\n/******/ \t\t\tfor(var key in definition) {\n/******/ \t\t\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n/******/ \t\t\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n/******/ \t\t\t\t}\n/******/ \t\t\t}\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/hasOwnProperty shorthand */\n/******/ \t!function() {\n/******/ \t\t__webpack_require__.o = function(obj, prop) { return Object.prototype.hasOwnProperty.call(obj, prop); }\n/******/ \t}();\n/******/ \t\n/************************************************************************/\n/******/ \t// module exports must be returned from runtime so entry inlining is disabled\n/******/ \t// startup\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(686);\n/******/ })()\n.default;\n});", "/*\n * Copyright (c) 2016-2025 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport \"focus-visible\"\n\nimport {\n EMPTY,\n NEVER,\n Observable,\n Subject,\n defer,\n delay,\n filter,\n map,\n merge,\n mergeWith,\n shareReplay,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"./_\"\nimport {\n at,\n getActiveElement,\n getOptionalElement,\n requestJSON,\n setLocation,\n setToggle,\n watchDocument,\n watchKeyboard,\n watchLocation,\n watchLocationTarget,\n watchMedia,\n watchPrint,\n watchScript,\n watchViewport\n} from \"./browser\"\nimport {\n getComponentElement,\n getComponentElements,\n mountAnnounce,\n mountBackToTop,\n mountConsent,\n mountContent,\n mountDialog,\n mountHeader,\n mountHeaderTitle,\n mountPalette,\n mountProgress,\n mountSearch,\n mountSearchHiglight,\n mountSidebar,\n mountSource,\n mountTableOfContents,\n mountTabs,\n watchHeader,\n watchMain\n} from \"./components\"\nimport {\n SearchIndex,\n fetchSitemap,\n setupAlternate,\n setupClipboardJS,\n setupInstantNavigation,\n setupVersionSelector\n} from \"./integrations\"\nimport {\n patchEllipsis,\n patchIndeterminate,\n patchScrollfix,\n patchScrolllock\n} from \"./patches\"\nimport \"./polyfills\"\n\n/* ----------------------------------------------------------------------------\n * Functions - @todo refactor\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch search index\n *\n * @returns Search index observable\n */\nfunction fetchSearchIndex(): Observable {\n if (location.protocol === \"file:\") {\n return watchScript(\n `${new URL(\"search/search_index.js\", config.base)}`\n )\n .pipe(\n // @ts-ignore - @todo fix typings\n map(() => __index),\n shareReplay(1)\n )\n } else {\n return requestJSON(\n new URL(\"search/search_index.json\", config.base)\n )\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Application\n * ------------------------------------------------------------------------- */\n\n/* Yay, JavaScript is available */\ndocument.documentElement.classList.remove(\"no-js\")\ndocument.documentElement.classList.add(\"js\")\n\n/* Set up navigation observables and subjects */\nconst document$ = watchDocument()\nconst location$ = watchLocation()\nconst target$ = watchLocationTarget(location$)\nconst keyboard$ = watchKeyboard()\n\n/* Set up media observables */\nconst viewport$ = watchViewport()\nconst tablet$ = watchMedia(\"(min-width: 60em)\")\nconst screen$ = watchMedia(\"(min-width: 76.25em)\")\nconst print$ = watchPrint()\n\n/* Retrieve search index, if search is enabled */\nconst config = configuration()\nconst index$ = document.forms.namedItem(\"search\")\n ? fetchSearchIndex()\n : NEVER\n\n/* Set up Clipboard.js integration */\nconst alert$ = new Subject()\nsetupClipboardJS({ alert$ })\n\n/* Set up language selector */\nsetupAlternate({ document$ })\n\n/* Set up progress indicator */\nconst progress$ = new Subject()\n\n/* Set up sitemap for instant navigation and previews */\nconst sitemap$ = fetchSitemap(config.base)\n\n/* Set up instant navigation, if enabled */\nif (feature(\"navigation.instant\"))\n setupInstantNavigation({ sitemap$, location$, viewport$, progress$ })\n .subscribe(document$)\n\n/* Set up version selector */\nif (config.version?.provider === \"mike\")\n setupVersionSelector({ document$ })\n\n/* Always close drawer and search on navigation */\nmerge(location$, target$)\n .pipe(\n delay(125)\n )\n .subscribe(() => {\n setToggle(\"drawer\", false)\n setToggle(\"search\", false)\n })\n\n/* Set up global keyboard handlers */\nkeyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Go to previous page */\n case \"p\":\n case \",\":\n const prev = getOptionalElement(\"link[rel=prev]\")\n if (typeof prev !== \"undefined\")\n setLocation(prev)\n break\n\n /* Go to next page */\n case \"n\":\n case \".\":\n const next = getOptionalElement(\"link[rel=next]\")\n if (typeof next !== \"undefined\")\n setLocation(next)\n break\n\n /* Expand navigation, see https://bit.ly/3ZjG5io */\n case \"Enter\":\n const active = getActiveElement()\n if (active instanceof HTMLLabelElement)\n active.click()\n }\n })\n\n/* Set up patches */\npatchEllipsis({ viewport$, document$ })\npatchIndeterminate({ document$, tablet$ })\npatchScrollfix({ document$ })\npatchScrolllock({ viewport$, tablet$ })\n\n/* Set up header and main area observable */\nconst header$ = watchHeader(getComponentElement(\"header\"), { viewport$ })\nconst main$ = document$\n .pipe(\n map(() => getComponentElement(\"main\")),\n switchMap(el => watchMain(el, { viewport$, header$ })),\n shareReplay(1)\n )\n\n/* Set up control component observables */\nconst control$ = merge(\n\n /* Consent */\n ...getComponentElements(\"consent\")\n .map(el => mountConsent(el, { target$ })),\n\n /* Dialog */\n ...getComponentElements(\"dialog\")\n .map(el => mountDialog(el, { alert$ })),\n\n /* Color palette */\n ...getComponentElements(\"palette\")\n .map(el => mountPalette(el)),\n\n /* Progress bar */\n ...getComponentElements(\"progress\")\n .map(el => mountProgress(el, { progress$ })),\n\n /* Search */\n ...getComponentElements(\"search\")\n .map(el => mountSearch(el, { index$, keyboard$ })),\n\n /* Repository information */\n ...getComponentElements(\"source\")\n .map(el => mountSource(el))\n)\n\n/* Set up content component observables */\nconst content$ = defer(() => merge(\n\n /* Announcement bar */\n ...getComponentElements(\"announce\")\n .map(el => mountAnnounce(el)),\n\n /* Content */\n ...getComponentElements(\"content\")\n .map(el => mountContent(el, { sitemap$, viewport$, target$, print$ })),\n\n /* Search highlighting */\n ...getComponentElements(\"content\")\n .map(el => feature(\"search.highlight\")\n ? mountSearchHiglight(el, { index$, location$ })\n : EMPTY\n ),\n\n /* Header */\n ...getComponentElements(\"header\")\n .map(el => mountHeader(el, { viewport$, header$, main$ })),\n\n /* Header title */\n ...getComponentElements(\"header-title\")\n .map(el => mountHeaderTitle(el, { viewport$, header$ })),\n\n /* Sidebar */\n ...getComponentElements(\"sidebar\")\n .map(el => el.getAttribute(\"data-md-type\") === \"navigation\"\n ? at(screen$, () => mountSidebar(el, { viewport$, header$, main$ }))\n : at(tablet$, () => mountSidebar(el, { viewport$, header$, main$ }))\n ),\n\n /* Navigation tabs */\n ...getComponentElements(\"tabs\")\n .map(el => mountTabs(el, { viewport$, header$ })),\n\n /* Table of contents */\n ...getComponentElements(\"toc\")\n .map(el => mountTableOfContents(el, {\n viewport$, header$, main$, target$\n })),\n\n /* Back-to-top button */\n ...getComponentElements(\"top\")\n .map(el => mountBackToTop(el, { viewport$, header$, main$, target$ }))\n))\n\n/* Set up component observables */\nconst component$ = document$\n .pipe(\n switchMap(() => content$),\n mergeWith(control$),\n shareReplay(1)\n )\n\n/* Subscribe to all components */\ncomponent$.subscribe()\n\n/* ----------------------------------------------------------------------------\n * Exports\n * ------------------------------------------------------------------------- */\n\nwindow.document$ = document$ /* Document observable */\nwindow.location$ = location$ /* Location subject */\nwindow.target$ = target$ /* Location target observable */\nwindow.keyboard$ = keyboard$ /* Keyboard observable */\nwindow.viewport$ = viewport$ /* Viewport observable */\nwindow.tablet$ = tablet$ /* Media tablet observable */\nwindow.screen$ = screen$ /* Media screen observable */\nwindow.print$ = print$ /* Media print observable */\nwindow.alert$ = alert$ /* Alert subject */\nwindow.progress$ = progress$ /* Progress indicator subject */\nwindow.component$ = component$ /* Component observable */\n", "/******************************************************************************\nCopyright (c) Microsoft Corporation.\n\nPermission to use, copy, modify, and/or distribute this software for any\npurpose with or without fee is hereby granted.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH\nREGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY\nAND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\nPERFORMANCE OF THIS SOFTWARE.\n***************************************************************************** */\n/* global Reflect, Promise, SuppressedError, Symbol, Iterator */\n\nvar extendStatics = function(d, b) {\n extendStatics = Object.setPrototypeOf ||\n ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\n function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\n return extendStatics(d, b);\n};\n\nexport function __extends(d, b) {\n if (typeof b !== \"function\" && b !== null)\n throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\n extendStatics(d, b);\n function __() { this.constructor = d; }\n d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());\n}\n\nexport var __assign = function() {\n __assign = Object.assign || function __assign(t) {\n for (var s, i = 1, n = arguments.length; i < n; i++) {\n s = arguments[i];\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p)) t[p] = s[p];\n }\n return t;\n }\n return __assign.apply(this, arguments);\n}\n\nexport function __rest(s, e) {\n var t = {};\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)\n t[p] = s[p];\n if (s != null && typeof Object.getOwnPropertySymbols === \"function\")\n for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {\n if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))\n t[p[i]] = s[p[i]];\n }\n return t;\n}\n\nexport function __decorate(decorators, target, key, desc) {\n var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;\n if (typeof Reflect === \"object\" && typeof Reflect.decorate === \"function\") r = Reflect.decorate(decorators, target, key, desc);\n else for (var i = decorators.length - 1; i >= 0; i--) if (d = decorators[i]) r = (c < 3 ? d(r) : c > 3 ? d(target, key, r) : d(target, key)) || r;\n return c > 3 && r && Object.defineProperty(target, key, r), r;\n}\n\nexport function __param(paramIndex, decorator) {\n return function (target, key) { decorator(target, key, paramIndex); }\n}\n\nexport function __esDecorate(ctor, descriptorIn, decorators, contextIn, initializers, extraInitializers) {\n function accept(f) { if (f !== void 0 && typeof f !== \"function\") throw new TypeError(\"Function expected\"); return f; }\n var kind = contextIn.kind, key = kind === \"getter\" ? \"get\" : kind === \"setter\" ? \"set\" : \"value\";\n var target = !descriptorIn && ctor ? contextIn[\"static\"] ? ctor : ctor.prototype : null;\n var descriptor = descriptorIn || (target ? Object.getOwnPropertyDescriptor(target, contextIn.name) : {});\n var _, done = false;\n for (var i = decorators.length - 1; i >= 0; i--) {\n var context = {};\n for (var p in contextIn) context[p] = p === \"access\" ? {} : contextIn[p];\n for (var p in contextIn.access) context.access[p] = contextIn.access[p];\n context.addInitializer = function (f) { if (done) throw new TypeError(\"Cannot add initializers after decoration has completed\"); extraInitializers.push(accept(f || null)); };\n var result = (0, decorators[i])(kind === \"accessor\" ? { get: descriptor.get, set: descriptor.set } : descriptor[key], context);\n if (kind === \"accessor\") {\n if (result === void 0) continue;\n if (result === null || typeof result !== \"object\") throw new TypeError(\"Object expected\");\n if (_ = accept(result.get)) descriptor.get = _;\n if (_ = accept(result.set)) descriptor.set = _;\n if (_ = accept(result.init)) initializers.unshift(_);\n }\n else if (_ = accept(result)) {\n if (kind === \"field\") initializers.unshift(_);\n else descriptor[key] = _;\n }\n }\n if (target) Object.defineProperty(target, contextIn.name, descriptor);\n done = true;\n};\n\nexport function __runInitializers(thisArg, initializers, value) {\n var useValue = arguments.length > 2;\n for (var i = 0; i < initializers.length; i++) {\n value = useValue ? initializers[i].call(thisArg, value) : initializers[i].call(thisArg);\n }\n return useValue ? value : void 0;\n};\n\nexport function __propKey(x) {\n return typeof x === \"symbol\" ? x : \"\".concat(x);\n};\n\nexport function __setFunctionName(f, name, prefix) {\n if (typeof name === \"symbol\") name = name.description ? \"[\".concat(name.description, \"]\") : \"\";\n return Object.defineProperty(f, \"name\", { configurable: true, value: prefix ? \"\".concat(prefix, \" \", name) : name });\n};\n\nexport function __metadata(metadataKey, metadataValue) {\n if (typeof Reflect === \"object\" && typeof Reflect.metadata === \"function\") return Reflect.metadata(metadataKey, metadataValue);\n}\n\nexport function __awaiter(thisArg, _arguments, P, generator) {\n function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }\n return new (P || (P = Promise))(function (resolve, reject) {\n function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }\n function rejected(value) { try { step(generator[\"throw\"](value)); } catch (e) { reject(e); } }\n function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }\n step((generator = generator.apply(thisArg, _arguments || [])).next());\n });\n}\n\nexport function __generator(thisArg, body) {\n var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g = Object.create((typeof Iterator === \"function\" ? Iterator : Object).prototype);\n return g.next = verb(0), g[\"throw\"] = verb(1), g[\"return\"] = verb(2), typeof Symbol === \"function\" && (g[Symbol.iterator] = function() { return this; }), g;\n function verb(n) { return function (v) { return step([n, v]); }; }\n function step(op) {\n if (f) throw new TypeError(\"Generator is already executing.\");\n while (g && (g = 0, op[0] && (_ = 0)), _) try {\n if (f = 1, y && (t = op[0] & 2 ? y[\"return\"] : op[0] ? y[\"throw\"] || ((t = y[\"return\"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;\n if (y = 0, t) op = [op[0] & 2, t.value];\n switch (op[0]) {\n case 0: case 1: t = op; break;\n case 4: _.label++; return { value: op[1], done: false };\n case 5: _.label++; y = op[1]; op = [0]; continue;\n case 7: op = _.ops.pop(); _.trys.pop(); continue;\n default:\n if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }\n if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }\n if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }\n if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }\n if (t[2]) _.ops.pop();\n _.trys.pop(); continue;\n }\n op = body.call(thisArg, _);\n } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }\n if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };\n }\n}\n\nexport var __createBinding = Object.create ? (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n var desc = Object.getOwnPropertyDescriptor(m, k);\n if (!desc || (\"get\" in desc ? !m.__esModule : desc.writable || desc.configurable)) {\n desc = { enumerable: true, get: function() { return m[k]; } };\n }\n Object.defineProperty(o, k2, desc);\n}) : (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n o[k2] = m[k];\n});\n\nexport function __exportStar(m, o) {\n for (var p in m) if (p !== \"default\" && !Object.prototype.hasOwnProperty.call(o, p)) __createBinding(o, m, p);\n}\n\nexport function __values(o) {\n var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\n if (m) return m.call(o);\n if (o && typeof o.length === \"number\") return {\n next: function () {\n if (o && i >= o.length) o = void 0;\n return { value: o && o[i++], done: !o };\n }\n };\n throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n}\n\nexport function __read(o, n) {\n var m = typeof Symbol === \"function\" && o[Symbol.iterator];\n if (!m) return o;\n var i = m.call(o), r, ar = [], e;\n try {\n while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);\n }\n catch (error) { e = { error: error }; }\n finally {\n try {\n if (r && !r.done && (m = i[\"return\"])) m.call(i);\n }\n finally { if (e) throw e.error; }\n }\n return ar;\n}\n\n/** @deprecated */\nexport function __spread() {\n for (var ar = [], i = 0; i < arguments.length; i++)\n ar = ar.concat(__read(arguments[i]));\n return ar;\n}\n\n/** @deprecated */\nexport function __spreadArrays() {\n for (var s = 0, i = 0, il = arguments.length; i < il; i++) s += arguments[i].length;\n for (var r = Array(s), k = 0, i = 0; i < il; i++)\n for (var a = arguments[i], j = 0, jl = a.length; j < jl; j++, k++)\n r[k] = a[j];\n return r;\n}\n\nexport function __spreadArray(to, from, pack) {\n if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {\n if (ar || !(i in from)) {\n if (!ar) ar = Array.prototype.slice.call(from, 0, i);\n ar[i] = from[i];\n }\n }\n return to.concat(ar || Array.prototype.slice.call(from));\n}\n\nexport function __await(v) {\n return this instanceof __await ? (this.v = v, this) : new __await(v);\n}\n\nexport function __asyncGenerator(thisArg, _arguments, generator) {\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n var g = generator.apply(thisArg, _arguments || []), i, q = [];\n return i = Object.create((typeof AsyncIterator === \"function\" ? AsyncIterator : Object).prototype), verb(\"next\"), verb(\"throw\"), verb(\"return\", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;\n function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }\n function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }\n function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }\n function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }\n function fulfill(value) { resume(\"next\", value); }\n function reject(value) { resume(\"throw\", value); }\n function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }\n}\n\nexport function __asyncDelegator(o) {\n var i, p;\n return i = {}, verb(\"next\"), verb(\"throw\", function (e) { throw e; }), verb(\"return\"), i[Symbol.iterator] = function () { return this; }, i;\n function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }\n}\n\nexport function __asyncValues(o) {\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n var m = o[Symbol.asyncIterator], i;\n return m ? m.call(o) : (o = typeof __values === \"function\" ? __values(o) : o[Symbol.iterator](), i = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i);\n function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }\n function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }\n}\n\nexport function __makeTemplateObject(cooked, raw) {\n if (Object.defineProperty) { Object.defineProperty(cooked, \"raw\", { value: raw }); } else { cooked.raw = raw; }\n return cooked;\n};\n\nvar __setModuleDefault = Object.create ? (function(o, v) {\n Object.defineProperty(o, \"default\", { enumerable: true, value: v });\n}) : function(o, v) {\n o[\"default\"] = v;\n};\n\nexport function __importStar(mod) {\n if (mod && mod.__esModule) return mod;\n var result = {};\n if (mod != null) for (var k in mod) if (k !== \"default\" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\n __setModuleDefault(result, mod);\n return result;\n}\n\nexport function __importDefault(mod) {\n return (mod && mod.__esModule) ? mod : { default: mod };\n}\n\nexport function __classPrivateFieldGet(receiver, state, kind, f) {\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a getter\");\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot read private member from an object whose class did not declare it\");\n return kind === \"m\" ? f : kind === \"a\" ? f.call(receiver) : f ? f.value : state.get(receiver);\n}\n\nexport function __classPrivateFieldSet(receiver, state, value, kind, f) {\n if (kind === \"m\") throw new TypeError(\"Private method is not writable\");\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a setter\");\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot write private member to an object whose class did not declare it\");\n return (kind === \"a\" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;\n}\n\nexport function __classPrivateFieldIn(state, receiver) {\n if (receiver === null || (typeof receiver !== \"object\" && typeof receiver !== \"function\")) throw new TypeError(\"Cannot use 'in' operator on non-object\");\n return typeof state === \"function\" ? receiver === state : state.has(receiver);\n}\n\nexport function __addDisposableResource(env, value, async) {\n if (value !== null && value !== void 0) {\n if (typeof value !== \"object\" && typeof value !== \"function\") throw new TypeError(\"Object expected.\");\n var dispose, inner;\n if (async) {\n if (!Symbol.asyncDispose) throw new TypeError(\"Symbol.asyncDispose is not defined.\");\n dispose = value[Symbol.asyncDispose];\n }\n if (dispose === void 0) {\n if (!Symbol.dispose) throw new TypeError(\"Symbol.dispose is not defined.\");\n dispose = value[Symbol.dispose];\n if (async) inner = dispose;\n }\n if (typeof dispose !== \"function\") throw new TypeError(\"Object not disposable.\");\n if (inner) dispose = function() { try { inner.call(this); } catch (e) { return Promise.reject(e); } };\n env.stack.push({ value: value, dispose: dispose, async: async });\n }\n else if (async) {\n env.stack.push({ async: true });\n }\n return value;\n}\n\nvar _SuppressedError = typeof SuppressedError === \"function\" ? SuppressedError : function (error, suppressed, message) {\n var e = new Error(message);\n return e.name = \"SuppressedError\", e.error = error, e.suppressed = suppressed, e;\n};\n\nexport function __disposeResources(env) {\n function fail(e) {\n env.error = env.hasError ? new _SuppressedError(e, env.error, \"An error was suppressed during disposal.\") : e;\n env.hasError = true;\n }\n var r, s = 0;\n function next() {\n while (r = env.stack.pop()) {\n try {\n if (!r.async && s === 1) return s = 0, env.stack.push(r), Promise.resolve().then(next);\n if (r.dispose) {\n var result = r.dispose.call(r.value);\n if (r.async) return s |= 2, Promise.resolve(result).then(next, function(e) { fail(e); return next(); });\n }\n else s |= 1;\n }\n catch (e) {\n fail(e);\n }\n }\n if (s === 1) return env.hasError ? Promise.reject(env.error) : Promise.resolve();\n if (env.hasError) throw env.error;\n }\n return next();\n}\n\nexport default {\n __extends,\n __assign,\n __rest,\n __decorate,\n __param,\n __metadata,\n __awaiter,\n __generator,\n __createBinding,\n __exportStar,\n __values,\n __read,\n __spread,\n __spreadArrays,\n __spreadArray,\n __await,\n __asyncGenerator,\n __asyncDelegator,\n __asyncValues,\n __makeTemplateObject,\n __importStar,\n __importDefault,\n __classPrivateFieldGet,\n __classPrivateFieldSet,\n __classPrivateFieldIn,\n __addDisposableResource,\n __disposeResources,\n};\n", "/**\n * Returns true if the object is a function.\n * @param value The value to check\n */\nexport function isFunction(value: any): value is (...args: any[]) => any {\n return typeof value === 'function';\n}\n", "/**\n * Used to create Error subclasses until the community moves away from ES5.\n *\n * This is because compiling from TypeScript down to ES5 has issues with subclassing Errors\n * as well as other built-in types: https://github.com/Microsoft/TypeScript/issues/12123\n *\n * @param createImpl A factory function to create the actual constructor implementation. The returned\n * function should be a named function that calls `_super` internally.\n */\nexport function createErrorClass(createImpl: (_super: any) => any): T {\n const _super = (instance: any) => {\n Error.call(instance);\n instance.stack = new Error().stack;\n };\n\n const ctorFunc = createImpl(_super);\n ctorFunc.prototype = Object.create(Error.prototype);\n ctorFunc.prototype.constructor = ctorFunc;\n return ctorFunc;\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface UnsubscriptionError extends Error {\n readonly errors: any[];\n}\n\nexport interface UnsubscriptionErrorCtor {\n /**\n * @deprecated Internal implementation detail. Do not construct error instances.\n * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n */\n new (errors: any[]): UnsubscriptionError;\n}\n\n/**\n * An error thrown when one or more errors have occurred during the\n * `unsubscribe` of a {@link Subscription}.\n */\nexport const UnsubscriptionError: UnsubscriptionErrorCtor = createErrorClass(\n (_super) =>\n function UnsubscriptionErrorImpl(this: any, errors: (Error | string)[]) {\n _super(this);\n this.message = errors\n ? `${errors.length} errors occurred during unsubscription:\n${errors.map((err, i) => `${i + 1}) ${err.toString()}`).join('\\n ')}`\n : '';\n this.name = 'UnsubscriptionError';\n this.errors = errors;\n }\n);\n", "/**\n * Removes an item from an array, mutating it.\n * @param arr The array to remove the item from\n * @param item The item to remove\n */\nexport function arrRemove(arr: T[] | undefined | null, item: T) {\n if (arr) {\n const index = arr.indexOf(item);\n 0 <= index && arr.splice(index, 1);\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { UnsubscriptionError } from './util/UnsubscriptionError';\nimport { SubscriptionLike, TeardownLogic, Unsubscribable } from './types';\nimport { arrRemove } from './util/arrRemove';\n\n/**\n * Represents a disposable resource, such as the execution of an Observable. A\n * Subscription has one important method, `unsubscribe`, that takes no argument\n * and just disposes the resource held by the subscription.\n *\n * Additionally, subscriptions may be grouped together through the `add()`\n * method, which will attach a child Subscription to the current Subscription.\n * When a Subscription is unsubscribed, all its children (and its grandchildren)\n * will be unsubscribed as well.\n */\nexport class Subscription implements SubscriptionLike {\n public static EMPTY = (() => {\n const empty = new Subscription();\n empty.closed = true;\n return empty;\n })();\n\n /**\n * A flag to indicate whether this Subscription has already been unsubscribed.\n */\n public closed = false;\n\n private _parentage: Subscription[] | Subscription | null = null;\n\n /**\n * The list of registered finalizers to execute upon unsubscription. Adding and removing from this\n * list occurs in the {@link #add} and {@link #remove} methods.\n */\n private _finalizers: Exclude[] | null = null;\n\n /**\n * @param initialTeardown A function executed first as part of the finalization\n * process that is kicked off when {@link #unsubscribe} is called.\n */\n constructor(private initialTeardown?: () => void) {}\n\n /**\n * Disposes the resources held by the subscription. May, for instance, cancel\n * an ongoing Observable execution or cancel any other type of work that\n * started when the Subscription was created.\n */\n unsubscribe(): void {\n let errors: any[] | undefined;\n\n if (!this.closed) {\n this.closed = true;\n\n // Remove this from it's parents.\n const { _parentage } = this;\n if (_parentage) {\n this._parentage = null;\n if (Array.isArray(_parentage)) {\n for (const parent of _parentage) {\n parent.remove(this);\n }\n } else {\n _parentage.remove(this);\n }\n }\n\n const { initialTeardown: initialFinalizer } = this;\n if (isFunction(initialFinalizer)) {\n try {\n initialFinalizer();\n } catch (e) {\n errors = e instanceof UnsubscriptionError ? e.errors : [e];\n }\n }\n\n const { _finalizers } = this;\n if (_finalizers) {\n this._finalizers = null;\n for (const finalizer of _finalizers) {\n try {\n execFinalizer(finalizer);\n } catch (err) {\n errors = errors ?? [];\n if (err instanceof UnsubscriptionError) {\n errors = [...errors, ...err.errors];\n } else {\n errors.push(err);\n }\n }\n }\n }\n\n if (errors) {\n throw new UnsubscriptionError(errors);\n }\n }\n }\n\n /**\n * Adds a finalizer to this subscription, so that finalization will be unsubscribed/called\n * when this subscription is unsubscribed. If this subscription is already {@link #closed},\n * because it has already been unsubscribed, then whatever finalizer is passed to it\n * will automatically be executed (unless the finalizer itself is also a closed subscription).\n *\n * Closed Subscriptions cannot be added as finalizers to any subscription. Adding a closed\n * subscription to a any subscription will result in no operation. (A noop).\n *\n * Adding a subscription to itself, or adding `null` or `undefined` will not perform any\n * operation at all. (A noop).\n *\n * `Subscription` instances that are added to this instance will automatically remove themselves\n * if they are unsubscribed. Functions and {@link Unsubscribable} objects that you wish to remove\n * will need to be removed manually with {@link #remove}\n *\n * @param teardown The finalization logic to add to this subscription.\n */\n add(teardown: TeardownLogic): void {\n // Only add the finalizer if it's not undefined\n // and don't add a subscription to itself.\n if (teardown && teardown !== this) {\n if (this.closed) {\n // If this subscription is already closed,\n // execute whatever finalizer is handed to it automatically.\n execFinalizer(teardown);\n } else {\n if (teardown instanceof Subscription) {\n // We don't add closed subscriptions, and we don't add the same subscription\n // twice. Subscription unsubscribe is idempotent.\n if (teardown.closed || teardown._hasParent(this)) {\n return;\n }\n teardown._addParent(this);\n }\n (this._finalizers = this._finalizers ?? []).push(teardown);\n }\n }\n }\n\n /**\n * Checks to see if a this subscription already has a particular parent.\n * This will signal that this subscription has already been added to the parent in question.\n * @param parent the parent to check for\n */\n private _hasParent(parent: Subscription) {\n const { _parentage } = this;\n return _parentage === parent || (Array.isArray(_parentage) && _parentage.includes(parent));\n }\n\n /**\n * Adds a parent to this subscription so it can be removed from the parent if it\n * unsubscribes on it's own.\n *\n * NOTE: THIS ASSUMES THAT {@link _hasParent} HAS ALREADY BEEN CHECKED.\n * @param parent The parent subscription to add\n */\n private _addParent(parent: Subscription) {\n const { _parentage } = this;\n this._parentage = Array.isArray(_parentage) ? (_parentage.push(parent), _parentage) : _parentage ? [_parentage, parent] : parent;\n }\n\n /**\n * Called on a child when it is removed via {@link #remove}.\n * @param parent The parent to remove\n */\n private _removeParent(parent: Subscription) {\n const { _parentage } = this;\n if (_parentage === parent) {\n this._parentage = null;\n } else if (Array.isArray(_parentage)) {\n arrRemove(_parentage, parent);\n }\n }\n\n /**\n * Removes a finalizer from this subscription that was previously added with the {@link #add} method.\n *\n * Note that `Subscription` instances, when unsubscribed, will automatically remove themselves\n * from every other `Subscription` they have been added to. This means that using the `remove` method\n * is not a common thing and should be used thoughtfully.\n *\n * If you add the same finalizer instance of a function or an unsubscribable object to a `Subscription` instance\n * more than once, you will need to call `remove` the same number of times to remove all instances.\n *\n * All finalizer instances are removed to free up memory upon unsubscription.\n *\n * @param teardown The finalizer to remove from this subscription\n */\n remove(teardown: Exclude): void {\n const { _finalizers } = this;\n _finalizers && arrRemove(_finalizers, teardown);\n\n if (teardown instanceof Subscription) {\n teardown._removeParent(this);\n }\n }\n}\n\nexport const EMPTY_SUBSCRIPTION = Subscription.EMPTY;\n\nexport function isSubscription(value: any): value is Subscription {\n return (\n value instanceof Subscription ||\n (value && 'closed' in value && isFunction(value.remove) && isFunction(value.add) && isFunction(value.unsubscribe))\n );\n}\n\nfunction execFinalizer(finalizer: Unsubscribable | (() => void)) {\n if (isFunction(finalizer)) {\n finalizer();\n } else {\n finalizer.unsubscribe();\n }\n}\n", "import { Subscriber } from './Subscriber';\nimport { ObservableNotification } from './types';\n\n/**\n * The {@link GlobalConfig} object for RxJS. It is used to configure things\n * like how to react on unhandled errors.\n */\nexport const config: GlobalConfig = {\n onUnhandledError: null,\n onStoppedNotification: null,\n Promise: undefined,\n useDeprecatedSynchronousErrorHandling: false,\n useDeprecatedNextContext: false,\n};\n\n/**\n * The global configuration object for RxJS, used to configure things\n * like how to react on unhandled errors. Accessible via {@link config}\n * object.\n */\nexport interface GlobalConfig {\n /**\n * A registration point for unhandled errors from RxJS. These are errors that\n * cannot were not handled by consuming code in the usual subscription path. For\n * example, if you have this configured, and you subscribe to an observable without\n * providing an error handler, errors from that subscription will end up here. This\n * will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onUnhandledError: ((err: any) => void) | null;\n\n /**\n * A registration point for notifications that cannot be sent to subscribers because they\n * have completed, errored or have been explicitly unsubscribed. By default, next, complete\n * and error notifications sent to stopped subscribers are noops. However, sometimes callers\n * might want a different behavior. For example, with sources that attempt to report errors\n * to stopped subscribers, a caller can configure RxJS to throw an unhandled error instead.\n * This will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onStoppedNotification: ((notification: ObservableNotification, subscriber: Subscriber) => void) | null;\n\n /**\n * The promise constructor used by default for {@link Observable#toPromise toPromise} and {@link Observable#forEach forEach}\n * methods.\n *\n * @deprecated As of version 8, RxJS will no longer support this sort of injection of a\n * Promise constructor. If you need a Promise implementation other than native promises,\n * please polyfill/patch Promise as you see appropriate. Will be removed in v8.\n */\n Promise?: PromiseConstructorLike;\n\n /**\n * If true, turns on synchronous error rethrowing, which is a deprecated behavior\n * in v6 and higher. This behavior enables bad patterns like wrapping a subscribe\n * call in a try/catch block. It also enables producer interference, a nasty bug\n * where a multicast can be broken for all observers by a downstream consumer with\n * an unhandled error. DO NOT USE THIS FLAG UNLESS IT'S NEEDED TO BUY TIME\n * FOR MIGRATION REASONS.\n *\n * @deprecated As of version 8, RxJS will no longer support synchronous throwing\n * of unhandled errors. All errors will be thrown on a separate call stack to prevent bad\n * behaviors described above. Will be removed in v8.\n */\n useDeprecatedSynchronousErrorHandling: boolean;\n\n /**\n * If true, enables an as-of-yet undocumented feature from v5: The ability to access\n * `unsubscribe()` via `this` context in `next` functions created in observers passed\n * to `subscribe`.\n *\n * This is being removed because the performance was severely problematic, and it could also cause\n * issues when types other than POJOs are passed to subscribe as subscribers, as they will likely have\n * their `this` context overwritten.\n *\n * @deprecated As of version 8, RxJS will no longer support altering the\n * context of next functions provided as part of an observer to Subscribe. Instead,\n * you will have access to a subscription or a signal or token that will allow you to do things like\n * unsubscribe and test closed status. Will be removed in v8.\n */\n useDeprecatedNextContext: boolean;\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetTimeoutFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearTimeoutFunction = (handle: TimerHandle) => void;\n\ninterface TimeoutProvider {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n delegate:\n | {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n }\n | undefined;\n}\n\nexport const timeoutProvider: TimeoutProvider = {\n // When accessing the delegate, use the variable rather than `this` so that\n // the functions can be called without being bound to the provider.\n setTimeout(handler: () => void, timeout?: number, ...args) {\n const { delegate } = timeoutProvider;\n if (delegate?.setTimeout) {\n return delegate.setTimeout(handler, timeout, ...args);\n }\n return setTimeout(handler, timeout, ...args);\n },\n clearTimeout(handle) {\n const { delegate } = timeoutProvider;\n return (delegate?.clearTimeout || clearTimeout)(handle as any);\n },\n delegate: undefined,\n};\n", "import { config } from '../config';\nimport { timeoutProvider } from '../scheduler/timeoutProvider';\n\n/**\n * Handles an error on another job either with the user-configured {@link onUnhandledError},\n * or by throwing it on that new job so it can be picked up by `window.onerror`, `process.on('error')`, etc.\n *\n * This should be called whenever there is an error that is out-of-band with the subscription\n * or when an error hits a terminal boundary of the subscription and no error handler was provided.\n *\n * @param err the error to report\n */\nexport function reportUnhandledError(err: any) {\n timeoutProvider.setTimeout(() => {\n const { onUnhandledError } = config;\n if (onUnhandledError) {\n // Execute the user-configured error handler.\n onUnhandledError(err);\n } else {\n // Throw so it is picked up by the runtime's uncaught error mechanism.\n throw err;\n }\n });\n}\n", "/* tslint:disable:no-empty */\nexport function noop() { }\n", "import { CompleteNotification, NextNotification, ErrorNotification } from './types';\n\n/**\n * A completion object optimized for memory use and created to be the\n * same \"shape\" as other notifications in v8.\n * @internal\n */\nexport const COMPLETE_NOTIFICATION = (() => createNotification('C', undefined, undefined) as CompleteNotification)();\n\n/**\n * Internal use only. Creates an optimized error notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function errorNotification(error: any): ErrorNotification {\n return createNotification('E', undefined, error) as any;\n}\n\n/**\n * Internal use only. Creates an optimized next notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function nextNotification(value: T) {\n return createNotification('N', value, undefined) as NextNotification;\n}\n\n/**\n * Ensures that all notifications created internally have the same \"shape\" in v8.\n *\n * TODO: This is only exported to support a crazy legacy test in `groupBy`.\n * @internal\n */\nexport function createNotification(kind: 'N' | 'E' | 'C', value: any, error: any) {\n return {\n kind,\n value,\n error,\n };\n}\n", "import { config } from '../config';\n\nlet context: { errorThrown: boolean; error: any } | null = null;\n\n/**\n * Handles dealing with errors for super-gross mode. Creates a context, in which\n * any synchronously thrown errors will be passed to {@link captureError}. Which\n * will record the error such that it will be rethrown after the call back is complete.\n * TODO: Remove in v8\n * @param cb An immediately executed function.\n */\nexport function errorContext(cb: () => void) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n const isRoot = !context;\n if (isRoot) {\n context = { errorThrown: false, error: null };\n }\n cb();\n if (isRoot) {\n const { errorThrown, error } = context!;\n context = null;\n if (errorThrown) {\n throw error;\n }\n }\n } else {\n // This is the general non-deprecated path for everyone that\n // isn't crazy enough to use super-gross mode (useDeprecatedSynchronousErrorHandling)\n cb();\n }\n}\n\n/**\n * Captures errors only in super-gross mode.\n * @param err the error to capture\n */\nexport function captureError(err: any) {\n if (config.useDeprecatedSynchronousErrorHandling && context) {\n context.errorThrown = true;\n context.error = err;\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { Observer, ObservableNotification } from './types';\nimport { isSubscription, Subscription } from './Subscription';\nimport { config } from './config';\nimport { reportUnhandledError } from './util/reportUnhandledError';\nimport { noop } from './util/noop';\nimport { nextNotification, errorNotification, COMPLETE_NOTIFICATION } from './NotificationFactories';\nimport { timeoutProvider } from './scheduler/timeoutProvider';\nimport { captureError } from './util/errorContext';\n\n/**\n * Implements the {@link Observer} interface and extends the\n * {@link Subscription} class. While the {@link Observer} is the public API for\n * consuming the values of an {@link Observable}, all Observers get converted to\n * a Subscriber, in order to provide Subscription-like capabilities such as\n * `unsubscribe`. Subscriber is a common type in RxJS, and crucial for\n * implementing operators, but it is rarely used as a public API.\n */\nexport class Subscriber extends Subscription implements Observer {\n /**\n * A static factory for a Subscriber, given a (potentially partial) definition\n * of an Observer.\n * @param next The `next` callback of an Observer.\n * @param error The `error` callback of an\n * Observer.\n * @param complete The `complete` callback of an\n * Observer.\n * @return A Subscriber wrapping the (partially defined)\n * Observer represented by the given arguments.\n * @deprecated Do not use. Will be removed in v8. There is no replacement for this\n * method, and there is no reason to be creating instances of `Subscriber` directly.\n * If you have a specific use case, please file an issue.\n */\n static create(next?: (x?: T) => void, error?: (e?: any) => void, complete?: () => void): Subscriber {\n return new SafeSubscriber(next, error, complete);\n }\n\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected isStopped: boolean = false;\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected destination: Subscriber | Observer; // this `any` is the escape hatch to erase extra type param (e.g. R)\n\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n * There is no reason to directly create an instance of Subscriber. This type is exported for typings reasons.\n */\n constructor(destination?: Subscriber | Observer) {\n super();\n if (destination) {\n this.destination = destination;\n // Automatically chain subscriptions together here.\n // if destination is a Subscription, then it is a Subscriber.\n if (isSubscription(destination)) {\n destination.add(this);\n }\n } else {\n this.destination = EMPTY_OBSERVER;\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `next` from\n * the Observable, with a value. The Observable may call this method 0 or more\n * times.\n * @param value The `next` value.\n */\n next(value: T): void {\n if (this.isStopped) {\n handleStoppedNotification(nextNotification(value), this);\n } else {\n this._next(value!);\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `error` from\n * the Observable, with an attached `Error`. Notifies the Observer that\n * the Observable has experienced an error condition.\n * @param err The `error` exception.\n */\n error(err?: any): void {\n if (this.isStopped) {\n handleStoppedNotification(errorNotification(err), this);\n } else {\n this.isStopped = true;\n this._error(err);\n }\n }\n\n /**\n * The {@link Observer} callback to receive a valueless notification of type\n * `complete` from the Observable. Notifies the Observer that the Observable\n * has finished sending push-based notifications.\n */\n complete(): void {\n if (this.isStopped) {\n handleStoppedNotification(COMPLETE_NOTIFICATION, this);\n } else {\n this.isStopped = true;\n this._complete();\n }\n }\n\n unsubscribe(): void {\n if (!this.closed) {\n this.isStopped = true;\n super.unsubscribe();\n this.destination = null!;\n }\n }\n\n protected _next(value: T): void {\n this.destination.next(value);\n }\n\n protected _error(err: any): void {\n try {\n this.destination.error(err);\n } finally {\n this.unsubscribe();\n }\n }\n\n protected _complete(): void {\n try {\n this.destination.complete();\n } finally {\n this.unsubscribe();\n }\n }\n}\n\n/**\n * This bind is captured here because we want to be able to have\n * compatibility with monoid libraries that tend to use a method named\n * `bind`. In particular, a library called Monio requires this.\n */\nconst _bind = Function.prototype.bind;\n\nfunction bind any>(fn: Fn, thisArg: any): Fn {\n return _bind.call(fn, thisArg);\n}\n\n/**\n * Internal optimization only, DO NOT EXPOSE.\n * @internal\n */\nclass ConsumerObserver implements Observer {\n constructor(private partialObserver: Partial>) {}\n\n next(value: T): void {\n const { partialObserver } = this;\n if (partialObserver.next) {\n try {\n partialObserver.next(value);\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n\n error(err: any): void {\n const { partialObserver } = this;\n if (partialObserver.error) {\n try {\n partialObserver.error(err);\n } catch (error) {\n handleUnhandledError(error);\n }\n } else {\n handleUnhandledError(err);\n }\n }\n\n complete(): void {\n const { partialObserver } = this;\n if (partialObserver.complete) {\n try {\n partialObserver.complete();\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n}\n\nexport class SafeSubscriber extends Subscriber {\n constructor(\n observerOrNext?: Partial> | ((value: T) => void) | null,\n error?: ((e?: any) => void) | null,\n complete?: (() => void) | null\n ) {\n super();\n\n let partialObserver: Partial>;\n if (isFunction(observerOrNext) || !observerOrNext) {\n // The first argument is a function, not an observer. The next\n // two arguments *could* be observers, or they could be empty.\n partialObserver = {\n next: (observerOrNext ?? undefined) as ((value: T) => void) | undefined,\n error: error ?? undefined,\n complete: complete ?? undefined,\n };\n } else {\n // The first argument is a partial observer.\n let context: any;\n if (this && config.useDeprecatedNextContext) {\n // This is a deprecated path that made `this.unsubscribe()` available in\n // next handler functions passed to subscribe. This only exists behind a flag\n // now, as it is *very* slow.\n context = Object.create(observerOrNext);\n context.unsubscribe = () => this.unsubscribe();\n partialObserver = {\n next: observerOrNext.next && bind(observerOrNext.next, context),\n error: observerOrNext.error && bind(observerOrNext.error, context),\n complete: observerOrNext.complete && bind(observerOrNext.complete, context),\n };\n } else {\n // The \"normal\" path. Just use the partial observer directly.\n partialObserver = observerOrNext;\n }\n }\n\n // Wrap the partial observer to ensure it's a full observer, and\n // make sure proper error handling is accounted for.\n this.destination = new ConsumerObserver(partialObserver);\n }\n}\n\nfunction handleUnhandledError(error: any) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n captureError(error);\n } else {\n // Ideal path, we report this as an unhandled error,\n // which is thrown on a new call stack.\n reportUnhandledError(error);\n }\n}\n\n/**\n * An error handler used when no error handler was supplied\n * to the SafeSubscriber -- meaning no error handler was supplied\n * do the `subscribe` call on our observable.\n * @param err The error to handle\n */\nfunction defaultErrorHandler(err: any) {\n throw err;\n}\n\n/**\n * A handler for notifications that cannot be sent to a stopped subscriber.\n * @param notification The notification being sent.\n * @param subscriber The stopped subscriber.\n */\nfunction handleStoppedNotification(notification: ObservableNotification, subscriber: Subscriber) {\n const { onStoppedNotification } = config;\n onStoppedNotification && timeoutProvider.setTimeout(() => onStoppedNotification(notification, subscriber));\n}\n\n/**\n * The observer used as a stub for subscriptions where the user did not\n * pass any arguments to `subscribe`. Comes with the default error handling\n * behavior.\n */\nexport const EMPTY_OBSERVER: Readonly> & { closed: true } = {\n closed: true,\n next: noop,\n error: defaultErrorHandler,\n complete: noop,\n};\n", "/**\n * Symbol.observable or a string \"@@observable\". Used for interop\n *\n * @deprecated We will no longer be exporting this symbol in upcoming versions of RxJS.\n * Instead polyfill and use Symbol.observable directly *or* use https://www.npmjs.com/package/symbol-observable\n */\nexport const observable: string | symbol = (() => (typeof Symbol === 'function' && Symbol.observable) || '@@observable')();\n", "/**\n * This function takes one parameter and just returns it. Simply put,\n * this is like `(x: T): T => x`.\n *\n * ## Examples\n *\n * This is useful in some cases when using things like `mergeMap`\n *\n * ```ts\n * import { interval, take, map, range, mergeMap, identity } from 'rxjs';\n *\n * const source$ = interval(1000).pipe(take(5));\n *\n * const result$ = source$.pipe(\n * map(i => range(i)),\n * mergeMap(identity) // same as mergeMap(x => x)\n * );\n *\n * result$.subscribe({\n * next: console.log\n * });\n * ```\n *\n * Or when you want to selectively apply an operator\n *\n * ```ts\n * import { interval, take, identity } from 'rxjs';\n *\n * const shouldLimit = () => Math.random() < 0.5;\n *\n * const source$ = interval(1000);\n *\n * const result$ = source$.pipe(shouldLimit() ? take(5) : identity);\n *\n * result$.subscribe({\n * next: console.log\n * });\n * ```\n *\n * @param x Any value that is returned by this function\n * @returns The value passed as the first parameter to this function\n */\nexport function identity(x: T): T {\n return x;\n}\n", "import { identity } from './identity';\nimport { UnaryFunction } from '../types';\n\nexport function pipe(): typeof identity;\nexport function pipe(fn1: UnaryFunction): UnaryFunction;\nexport function pipe(fn1: UnaryFunction, fn2: UnaryFunction): UnaryFunction;\nexport function pipe(fn1: UnaryFunction, fn2: UnaryFunction, fn3: UnaryFunction): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction,\n fn9: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction,\n fn9: UnaryFunction,\n ...fns: UnaryFunction[]\n): UnaryFunction;\n\n/**\n * pipe() can be called on one or more functions, each of which can take one argument (\"UnaryFunction\")\n * and uses it to return a value.\n * It returns a function that takes one argument, passes it to the first UnaryFunction, and then\n * passes the result to the next one, passes that result to the next one, and so on. \n */\nexport function pipe(...fns: Array>): UnaryFunction {\n return pipeFromArray(fns);\n}\n\n/** @internal */\nexport function pipeFromArray(fns: Array>): UnaryFunction {\n if (fns.length === 0) {\n return identity as UnaryFunction;\n }\n\n if (fns.length === 1) {\n return fns[0];\n }\n\n return function piped(input: T): R {\n return fns.reduce((prev: any, fn: UnaryFunction) => fn(prev), input as any);\n };\n}\n", "import { Operator } from './Operator';\nimport { SafeSubscriber, Subscriber } from './Subscriber';\nimport { isSubscription, Subscription } from './Subscription';\nimport { TeardownLogic, OperatorFunction, Subscribable, Observer } from './types';\nimport { observable as Symbol_observable } from './symbol/observable';\nimport { pipeFromArray } from './util/pipe';\nimport { config } from './config';\nimport { isFunction } from './util/isFunction';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A representation of any set of values over any amount of time. This is the most basic building block\n * of RxJS.\n */\nexport class Observable implements Subscribable {\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n */\n source: Observable | undefined;\n\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n */\n operator: Operator | undefined;\n\n /**\n * @param subscribe The function that is called when the Observable is\n * initially subscribed to. This function is given a Subscriber, to which new values\n * can be `next`ed, or an `error` method can be called to raise an error, or\n * `complete` can be called to notify of a successful completion.\n */\n constructor(subscribe?: (this: Observable, subscriber: Subscriber) => TeardownLogic) {\n if (subscribe) {\n this._subscribe = subscribe;\n }\n }\n\n // HACK: Since TypeScript inherits static properties too, we have to\n // fight against TypeScript here so Subject can have a different static create signature\n /**\n * Creates a new Observable by calling the Observable constructor\n * @param subscribe the subscriber function to be passed to the Observable constructor\n * @return A new observable.\n * @deprecated Use `new Observable()` instead. Will be removed in v8.\n */\n static create: (...args: any[]) => any = (subscribe?: (subscriber: Subscriber) => TeardownLogic) => {\n return new Observable(subscribe);\n };\n\n /**\n * Creates a new Observable, with this Observable instance as the source, and the passed\n * operator defined as the new observable's operator.\n * @param operator the operator defining the operation to take on the observable\n * @return A new observable with the Operator applied.\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n * If you have implemented an operator using `lift`, it is recommended that you create an\n * operator by simply returning `new Observable()` directly. See \"Creating new operators from\n * scratch\" section here: https://rxjs.dev/guide/operators\n */\n lift(operator?: Operator): Observable {\n const observable = new Observable();\n observable.source = this;\n observable.operator = operator;\n return observable;\n }\n\n subscribe(observerOrNext?: Partial

Name	Type	Description	Default
`rows`	+	An iterable where an element is a numpy record, a dict-like object, a pandas.DataFrame, a sequence, or a query expression with the same heading as self.	+ required +
`replace`	+	If True, replaces the existing tuple.	+ `False` +
`skip_duplicates`	+	If True, silently skip duplicate inserts.	+ `False` +
`ignore_extra_fields`	+	If False, fields that are not in the heading raise error.	+ `False` +
`allow_direct_insert`	+	applies only in auto-populated tables. If False (default), insert are allowed only from inside the make callback. Example: >>> Table.insert([ >>> dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"), >>> dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")])	+ `None` +

Name	Type	Description	Default
`host`	+	hostname	+ `None` +
`user`	+	mysql user	+ `None` +
`password`	+	mysql password	+ `None` +
`init_fun`	+	initialization function	+ `None` +
`reset`	+	whether the connection should be reset or not	+ `False` +
`use_tls`	+	TLS encryption option. Valid options are: True (required), False (required no TLS), None (TLS prefered, default), dict (Manually specify values per https://dev.mysql.com/doc/refman/5.7/en/connection-options.html#encrypted-connection-options).	+ `None` +

Name	Type	Description	Default
`host`	+	host name, may include port number as hostname:port, in which case it overrides the value in port	+ required +
`user`	+	user name	+ required +
`password`	+	password	+ required +
`port`	+	port number	+ `None` +
`init_fun`	+	connection initialization function (SQL)	+ `None` +
`use_tls`	+	TLS encryption option	+ `None` +

Name	Type	Description	Default
`query`	+	SQL query	+ required +
`args`	+	additional arguments for the client.cursor	+ `()` +
`as_dict`	+	If as_dict is set to True, the returned cursor objects returns query results as dictionary.	+ `False` +
`suppress_warnings`	+	If True, suppress all warnings arising from underlying query library	+ `True` +
`reconnect`	+	when None, get from config, when True, attempt to reconnect if disconnected	+ `None` +

Name	Type	Description	Default
`other`	+	the other query expression to join with.	+ required +
`left`	+	ignored. dj.U always acts as if left=False	+ `False` +

Name	Type	Description	Default
`group`	+	The query expression to be aggregated.	+ required +
`named_attributes`	+	computations of the form new_attribute="sql expression on attributes of group"	+ required +

Name	Type	Description	Default
`conn`	+	a dj.Connection object	+ required +
`full_table_name`	+	in format `database`.`table_name`	+ required +

Name	Type	Description	Default
`restrictions`	+	a list of restrictions each restrict (table.key_source - target.proj())	+ required +
`suppress_errors`	+	if True, do not terminate execution.	+ `False` +
`return_exception_objects`	+	return error objects instead of just error messages	+ `False` +
`reserve_jobs`	+	if True, reserve jobs to populate in asynchronous fashion	+ `False` +
`order`	+	"original"\|"reverse"\|"random" - the order of execution	+ `'original'` +
`limit`	+	if not None, check at most this many keys	+ `None` +
`max_calls`	+	if not None, populate at most this many keys	+ `None` +
`display_progress`	+	if True, report progress_bar	+ `False` +
`processes`	+	number of processes to use. Set to None to use all cores	+ `1` +
`make_kwargs`	+ `dict, optional` +	Keyword arguments which do not affect the result of computation to be passed down to each `make()` call. Computation arguments should be specified within the pipeline e.g. using a `dj.Lookup` table.	+ `None` +

Name	Type	Description	Default
`expr1`	+	A QueryExpression object	+ required +
`expr2`	+	A QueryExpression object	+ required +

Name	Type	Description	Default
`query_expression`	+	a dj.QueryExpression object to apply condition	+ required +
`condition`	+	any valid restriction object.	+ required +
`columns`	+	a set passed by reference to collect all column names used in the condition.	+ required +

Name	Type	Description	Default
`client_error`	+	the exception raised by the client interface	+ required +
`query`	+	sql query with placeholders	+ required +

Name	Type	Description	Default
`line`	+	a line from a table definition	+ required +
`context`	+	namespace containing referenced objects	+ required +
`attributes`	+	list of attribute names already in the declaration -- to be updated by this function	+ required +
`primary_key`	+	None if the current foreign key is made from the dependent section. Otherwise it is the list of primary key attributes thus far -- to be updated by the function	+ required +
`attr_sql`	+	list of sql statements defining attributes -- to be updated by this function.	+ required +
`foreign_key_sql`	+	list of sql statements specifying foreign key constraints -- to be updated by this function.	+ required +
`index_sql`	+	list of INDEX declaration statements, duplicate or redundant indexes are ok.	+ required +

Name	Type	Description	Default
`full_table_name`	+	full name of the table	+ required +
`definition`	+	DataJoint table definition	+ required +
`context`	+	dictionary of objects that might be referred to in the table	+ required +

Name	Type	Description	Default
`definition`	+	new table definition	+ required +
`old_definition`	+	current table definition	+ required +
`context`	+	the context in which to evaluate foreign key definitions	+ required +

Name	Type	Description	Default
`match`	+	dict containing with keys "type" and "comment" -- will be modified in place	+ required +
`category`	+	attribute type category from TYPE_PATTERN	+ required +
`foreign_key_sql`	+	list of foreign key declarations to add to	+ required +
`context`	+	context for looking up user-defined attribute_type adapters	+ required +

Name	Type	Description	Default
`line`	+	attribution line	+ required +
`in_key`	+	set to True if attribute is in primary key set	+ required +
`foreign_key_sql`	+	the list of foreign key declarations to add to	+ required +
`context`	+	context in which to look up user-defined attribute type adapterss	+ required +

Name	Type	Description	Default
`table_name`	+	`schema`.`table`	+ required +
`primary`	+	if None, then all parents are returned. If True, then only foreign keys composed of primary key attributes are considered. If False, the only foreign keys including at least one non-primary attribute are considered.	+ `None` +

Name	Type	Description	Default
`attributes`	+	attributes to be included in the result. (The primary key is already included).	+ required +
`named_attributes`	+	new attributes computed or renamed from existing attributes.	+ required +

Name	Type	Description	Default
`limit`	+	number of entries	+ `25` +
`fetch_kwargs`	+	kwargs for fetch	+ required +

Name	Type	Description	Default
`delete_external_files`	+	True or False. If False, only the tracking info is removed from the external store table but the external files remain intact. If True, then the external files themselves are deleted too.	+ `None` +
`errors_as_string`	+	If True any errors returned when deleting from external files will be strings	+ `True` +
`limit`	+	(integer) limit the number of items to delete	+ `None` +
`display_progress`	+	if True, display progress as files are cleaned up	+ `True` +

404 - Not found

Changelog

Release notes¶

0.13.8 -- Sep 21, 2022¶

0.13.7 -- Jul 13, 2022¶

0.13.6 -- Jun 13, 2022¶

0.13.5 -- May 19, 2022¶

0.13.4 -- Mar, 28 2022¶

0.13.3 -- Feb 9, 2022¶

0.13.2 -- May 7, 2021¶

0.13.1 -- Apr 16, 2021¶

0.13.0 -- Mar 24, 2021¶

0.12.9 -- Mar 12, 2021¶

0.12.8 -- Jan 12, 2021¶

0.12.7 -- Oct 27, 2020¶

0.12.6 -- May 15, 2020¶

0.12.5 -- Feb 24, 2020¶

0.12.4 -- Jan 14, 2020¶

0.12.3 -- Nov 22, 2019¶

0.12.2 -- Nov 11, 2019¶

0.12.1 -- Nov 2, 2019¶

0.12.0 -- Oct 31, 2019¶

0.11.3 -- Jul 26, 2019¶

0.11.2 -- Jul 25, 2019¶

0.11.1 -- Nov 15, 2018¶

0.11.0 -- Oct 25, 2018¶

0.10.1 -- Aug 28, 2018¶

0.10.0 -- Jan 10, 2018¶

0.9.0 -- Nov 17, 2017¶

0.8.0 -- Jul 26, 2017¶

0.5.0 (#298) -- Mar 8, 2017¶

0.4.10 (#286) -- Feb 6, 2017¶

0.4.9 (#285) -- Feb 2, 2017¶

0.4.7 (#281) -- Jan 24, 2017¶

0.4.6 (#277) -- Dec 22, 2016¶

0.4.5 (#274) -- Dec 20, 2016¶

0.4.3 (#271) -- Dec 6, 2016¶

0.4.2 (#267) -- Dec 6, 2016¶

0.4.1 (#266) -- Oct 28, 2016¶

0.3.9 -- Sep 27, 2016¶

0.3.8 -- Aug 2, 2016¶

0.3.7 -- Jul 31, 2016¶

0.3.6 -- Jul 30, 2016¶

0.3.5¶

0.3.4¶

0.3.3¶

0.3.2.¶

__init__.py

+ AttributeAdapter + + +¶

+attribute_type() + + + property + + +¶

+get(value) + +¶

+put(obj) + +¶

+key_hash(mapping) + +¶

+migrate_dj011_external_blob_storage_to_dj012(migration_schema, store) + +¶

+ DataJointError + + +¶

+suggest(*args) + +¶

+ key + + +¶

+ AndList + + +¶

+kill(restriction=None, connection=None, order_by=None) + +¶

+ Schema + + +¶

+activate(schema_name=None, *, connection=None, create_schema=None, create_tables=None, add_objects=None) + +¶

+size_on_disk() + + + property + + +¶

+spawn_missing_classes(context=None) + +¶

+drop(force=False) + +¶

+exists() + + + property + + +¶

+jobs() + + + property + + +¶

+save(python_filename=None) + +¶

+list_tables() + +¶

+ Not + + +¶

+ Table + + +¶

+declare(context=None) + +¶

+alter(prompt=True, context=None) + +¶

+from_clause() + +¶

+get_select_fields(select_fields=None) + +¶

+parents(primary=None, as_objects=False, foreign_key_info=False) + +¶

+children(primary=None, as_objects=False, foreign_key_info=False) + +¶

+descendants(as_objects=False) + +¶

+ancestors(as_objects=False) + +¶

+parts(as_objects=False) + +¶

+is_declared() + + + property + + +¶

init.py

+ `AttributeAdapter` + + +¶

+`attribute_type()` + + + `property` + + +¶

+`get(value)` + +¶

+`put(obj)` + +¶

+`key_hash(mapping)` + +¶

+`migrate_dj011_external_blob_storage_to_dj012(migration_schema, store)` + +¶

+ `DataJointError` + + +¶

+`suggest(*args)` + +¶

+ `key` + + +¶

+ `AndList` + + +¶

+`kill(restriction=None, connection=None, order_by=None)` + +¶

+ `Schema` + + +¶

+`activate(schema_name=None, *, connection=None, create_schema=None, create_tables=None, add_objects=None)` + +¶

+`size_on_disk()` + + + `property` + + +¶

+`spawn_missing_classes(context=None)` + +¶

+`drop(force=False)` + +¶

+`exists()` + + + `property` + + +¶

+`jobs()` + + + `property` + + +¶

+`save(python_filename=None)` + +¶

+`list_tables()` + +¶

+ `Not` + + +¶

+ `Table` + + +¶

+`declare(context=None)` + +¶

+`alter(prompt=True, context=None)` + +¶

+`from_clause()` + +¶

+`get_select_fields(select_fields=None)` + +¶

+`parents(primary=None, as_objects=False, foreign_key_info=False)` + +¶

+`children(primary=None, as_objects=False, foreign_key_info=False)` + +¶

+`descendants(as_objects=False)` + +¶

+`ancestors(as_objects=False)` + +¶

+`parts(as_objects=False)` + +¶

+`is_declared()` + + + `property` + + +¶

+`full_table_name()` + + + `property` + + +¶

+`update1(row)` + +¶

+`insert1(row, **kwargs)` + +¶

+`insert(rows, replace=False, skip_duplicates=False, ignore_extra_fields=False, allow_direct_insert=None)` + +¶

+`delete_quick(get_count=False)` + +¶

+`delete(transaction=True, safemode=None, force_parts=False)` + +¶

+`drop_quick()` + +¶

+`drop()` + +¶

+`size_on_disk()` + + + `property` + + +¶

+`describe(context=None, printout=True)` + +¶

+ `Diagram` + + +¶

+`from_sequence(sequence)` + + + `classmethod` + + +¶

+`add_parts()` + +¶

+`topological_sort()` + +¶

+ `MatCell` + + +¶

+ `MatStruct` + + +¶

+`conn(host=None, user=None, password=None, *, init_fun=None, reset=False, use_tls=None)` + +¶

+ `Manual` + + +¶

+ `Lookup` + + +¶

+ `Imported` + + +¶

+ `Connection` + + +¶

+`connect()` + +¶

+`set_query_cache(query_cache=None)` + +¶

+`purge_query_cache()` + +¶

+`ping()` + +¶

+`is_connected()` + + + `property` + + +¶

+`query(query, args=(), *, as_dict=False, suppress_warnings=True, reconnect=None)` + +¶

+`get_user()` + +¶

+`in_transaction()` + + + `property` + + +¶

+`start_transaction()` + +¶

+`cancel_transaction()` + +¶

+`commit_transaction()` + +¶

+`transaction()` + + + `property` + + +¶

+ `Computed` + + +¶

+ `Part` + + +¶

+`delete(force=False)` + +¶

+`drop(force=False)` + +¶

+ `VirtualModule` + + +¶

+`list_schemas(connection=None)` + +¶

+ `U` + + +¶

+`join(other, left=False)` + +¶

+`aggr(group, **named_attributes)` + +¶

+ `FreeTable` + + +¶

+`kill(restriction=None, connection=None, order_by=None)` + +¶

+`kill_quick(restriction=None, connection=None)` + +¶

+ `AttributeAdapter` + + +¶

+`attribute_type()` + + + `property` + + +¶

Name	Type	Description	Default
`select_list`	+	the full list of existing attributes to include	+ required +
`rename_map`	+	dictionary of renamed attributes: keys=new names, values=old names	+ `None` +
`compute_map`	+	a direction of computed attributes This low-level method performs no error checking.	+ `None` +

Name	Type	Description	Default
`table_name`	+	`database`.`table_name`	+ required +
`key`	+	the dict of the job's primary key	+ required +

Name	Type	Description	Default
`filename`	+	filename of the local JSON settings file.	+ required +
`verbose`	+	report having saved the settings file	+ `False` +

Name	Type	Description	Default
`name`	+	`schema_name`.`table_name`	+ required +
`context`	+	dictionary representing the namespace	+ required +
`depth`	+	search depth into imported modules, helps avoid infinite recursion.	+ `3` +

Name	Type	Description	Default
`prompt`	+	Information to display to the user.	+ required +
`choices`	+	an iterable of possible choices.	+ `('yes', 'no')` +
`default`	+	default choice	+ `None` +

Name	Type	Description	Default
`filename`	+	full path	+ required +
`blob`	+	binary data	+ required +