@vitessce/vit-s 2.0.3 → 3.0.1

package/dist-tsc/data/AbstractLoader.js

@@ -0,0 +1,18 @@
+/**
+ * A loader ancestor class containing a default constructor
+ * and a stub for the required load() method.
+ */
+export default class AbstractLoader {
+    constructor({ type, fileType, url, requestInit, options, coordinationValues, }) {
+        this.fileType = fileType;
+        this.type = type;
+        this.url = url;
+        this.requestInit = requestInit;
+        this.options = options;
+        this.coordinationValues = coordinationValues;
+    }
+    // eslint-disable-next-line class-methods-use-this
+    load() {
+        return Promise.resolve(true);
+    }
+}

package/dist-tsc/data/AbstractTwoStepLoader.d.ts

@@ -0,0 +1,6 @@
+export default class AbstractTwoStepLoader extends AbstractLoader {
+    constructor(dataSource: any, params: any);
+    dataSource: any;
+}
+import AbstractLoader from "./AbstractLoader.js";
+//# sourceMappingURL=AbstractTwoStepLoader.d.ts.map

package/dist-tsc/data/AbstractTwoStepLoader.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AbstractTwoStepLoader.d.ts","sourceRoot":"","sources":["../../src/data/AbstractTwoStepLoader.js"],"names":[],"mappings":"AAEA;IACE,0CAGC;IADC,gBAA4B;CAE/B"}

package/dist-tsc/data/AbstractTwoStepLoader.js

@@ -0,0 +1,7 @@
+import AbstractLoader from './AbstractLoader.js';
+export default class AbstractTwoStepLoader extends AbstractLoader {
+    constructor(dataSource, params) {
+        super(params);
+        this.dataSource = dataSource;
+    }
+}

package/dist-tsc/data/LoaderResult.d.ts

@@ -0,0 +1,12 @@
+export default class LoaderResult {
+    /**
+     * @param {*} data
+     * @param {object[]|string|null} url Single URL or array of { url, name } objects.
+     * @param {object} coordinationValues
+     */
+    constructor(data: any, url: object[] | string | null, coordinationValues?: object);
+    data: any;
+    url: string | object[] | null;
+    coordinationValues: object;
+}
+//# sourceMappingURL=LoaderResult.d.ts.map

package/dist-tsc/data/LoaderResult.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoaderResult.d.ts","sourceRoot":"","sources":["../../src/data/LoaderResult.js"],"names":[],"mappings":"AACA;IACE;;;;OAIG;IACH,4BAHW,MAAM,EAAE,GAAC,MAAM,GAAC,IAAI,uBACpB,MAAM,EAMhB;IAHC,UAAgB;IAChB,8BAAc;IACd,2BAA4C;CAE/C"}

package/dist-tsc/data/LoaderResult.js

@@ -0,0 +1,12 @@
+export default class LoaderResult {
+    /**
+     * @param {*} data
+     * @param {object[]|string|null} url Single URL or array of { url, name } objects.
+     * @param {object} coordinationValues
+     */
+    constructor(data, url, coordinationValues = null) {
+        this.data = data;
+        this.url = url;
+        this.coordinationValues = coordinationValues;
+    }
+}

package/dist-tsc/data/index.d.ts

@@ -0,0 +1,4 @@
+export { default as AbstractLoader } from "./AbstractLoader.js";
+export { default as AbstractTwoStepLoader } from "./AbstractTwoStepLoader.js";
+export { default as LoaderResult } from "./LoaderResult.js";
+//# sourceMappingURL=index.d.ts.map

package/dist-tsc/data/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/data/index.js"],"names":[],"mappings":""}

package/dist-tsc/data/index.js

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+export { default as AbstractLoader } from './AbstractLoader.js';
+export { default as AbstractTwoStepLoader } from './AbstractTwoStepLoader.js';
+export { default as LoaderResult } from './LoaderResult.js';

package/dist-tsc/data/loader-registry.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Get the data source and data loader class.
+ * @param {string} type The fileType name.
+ * @param {PluginFileType[]} fileTypes The array of file types.
+ * @returns {array} [dataSourceClass, dataLoaderClass].
+ */
+export function getSourceAndLoaderFromFileType(type: string, fileTypes: PluginFileType[]): array;
+export function getDataTypeFromFileType(type: any, fileTypes: any): any;
+//# sourceMappingURL=loader-registry.d.ts.map

package/dist-tsc/data/loader-registry.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"loader-registry.d.ts","sourceRoot":"","sources":["../../src/data/loader-registry.js"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,qDAJW,MAAM,aACN,gBAAgB,SAc1B;AAED,wEAQC"}

package/dist-tsc/data/loader-registry.js

@@ -0,0 +1,27 @@
+/**
+ * Get the data source and data loader class.
+ * @param {string} type The fileType name.
+ * @param {PluginFileType[]} fileTypes The array of file types.
+ * @returns {array} [dataSourceClass, dataLoaderClass].
+ */
+export function getSourceAndLoaderFromFileType(type, fileTypes) {
+    if (Array.isArray(fileTypes)) {
+        const matchingFileType = fileTypes.find(ft => ft.name === type);
+        if (matchingFileType) {
+            return matchingFileType.getSourceAndLoader();
+        }
+    }
+    // Fallback to JSON.
+    // TODO(monorepo)
+    // return [JsonSource, JsonLoader];
+    return [null, null];
+}
+export function getDataTypeFromFileType(type, fileTypes) {
+    if (Array.isArray(fileTypes)) {
+        const matchingFileType = fileTypes.find(ft => ft.name === type);
+        if (matchingFileType) {
+            return matchingFileType.dataType;
+        }
+    }
+    return null;
+}

package/dist-tsc/data-hook-utils.d.ts

@@ -0,0 +1,65 @@
+/**
+ * Warn via publishing to the console
+ * and to the global warning store.
+ * @param {AbstractLoaderError} error An error instance.
+ */
+export function warn(error: AbstractLoaderError, setWarning: any): void;
+/**
+ * Initialize values in the coordination space.
+ * @param {object} values Object where
+ * keys are coordination type names,
+ * values are initial coordination values.
+ * @param {object} setters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialValues Object where
+ * keys are coordination type names and keys are values.
+ */
+export function initCoordinationSpace(values: object, setters: object, initialValues: object): void;
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [data, status, urls] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useDataType(dataType: any, loaders: object, dataset: string, isRequired: boolean, coordinationSetters: object, initialCoordinationValues: object, matchOn: any): array;
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [cells, cellsCount] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useDataTypeMulti(dataType: any, loaders: object, dataset: string, isRequired: boolean, coordinationSetters: object, initialCoordinationValues: object, matchOnObj: any): array;
+export function useHasLoader(loaders: any, dataset: any, dataType: any, matchOn: any): boolean;
+import { AbstractLoaderError } from "./errors/index.js";
+//# sourceMappingURL=data-hook-utils.d.ts.map

package/dist-tsc/data-hook-utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"data-hook-utils.d.ts","sourceRoot":"","sources":["../src/data-hook-utils.js"],"names":[],"mappings":"AAcA;;;;GAIG;AACH,4BAFW,mBAAmB,yBAS7B;AAED;;;;;;;;;;GAUG;AACH,8CATW,MAAM,WAGN,MAAM,iBAGN,MAAM,QAiBhB;AA4BD;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,oDAhBW,MAAM,WAEN,MAAM,cAEN,OAAO,uBAEP,MAAM,6BAGN,MAAM,uBA+ChB;AAED;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,yDAhBW,MAAM,WAEN,MAAM,cAEN,OAAO,uBAEP,MAAM,6BAGN,MAAM,0BAkEhB;AAED,+FAGC"}

package/dist-tsc/data-hook-utils.js

@@ -0,0 +1,191 @@
+import { useEffect, useMemo } from 'react';
+import { capitalize, fromEntries } from '@vitessce/utils';
+import { STATUS } from '@vitessce/constants-internal';
+import { useQuery, useQueries } from '@tanstack/react-query';
+import { getMatchingLoader, useMatchingLoader, useSetWarning, } from './state/hooks.js';
+import { AbstractLoaderError, LoaderNotFoundError, } from './errors/index.js';
+/**
+ * Warn via publishing to the console
+ * and to the global warning store.
+ * @param {AbstractLoaderError} error An error instance.
+ */
+export function warn(error, setWarning) {
+    setWarning(error.message);
+    console.warn(error.message);
+    console.error(error.stack);
+    if (error instanceof AbstractLoaderError) {
+        error.warnInConsole();
+    }
+}
+/**
+ * Initialize values in the coordination space.
+ * @param {object} values Object where
+ * keys are coordination type names,
+ * values are initial coordination values.
+ * @param {object} setters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialValues Object where
+ * keys are coordination type names and keys are values.
+ */
+export function initCoordinationSpace(values, setters, initialValues) {
+    if (!values || !setters) {
+        return;
+    }
+    Object.entries(values).forEach(([coordinationType, value]) => {
+        const setterName = `set${capitalize(coordinationType)}`;
+        const setterFunc = setters[setterName];
+        const initialValue = initialValues && initialValues[coordinationType];
+        // Interpret null as "uninitialized" and therefore needing initialization.
+        const shouldInit = initialValue === null;
+        if (shouldInit && setterFunc) {
+            setterFunc(value);
+        }
+    });
+}
+async function dataQueryFn(ctx) {
+    const { placeholderObject, loaders } = ctx.meta;
+    // This ordering of the queryKey must match.
+    const [dataset, dataType, matchOn, isRequired] = ctx.queryKey;
+    const loader = getMatchingLoader(loaders, dataset, dataType, matchOn);
+    if (loader) {
+        // TODO: can cacheing logic be removed from all loaders?
+        const payload = await loader.load();
+        if (!payload)
+            return placeholderObject; // TODO: throw error instead?
+        const { data, url, coordinationValues } = payload;
+        // Status: success
+        // Array of objects like  { url, name }.
+        const urls = Array.isArray(url) ? url : [{ url, name: dataType }];
+        return { data, coordinationValues, urls };
+    }
+    // No loader was found.
+    if (isRequired) {
+        // Status: error
+        throw new LoaderNotFoundError(loaders, dataset, dataType, matchOn);
+    }
+    else {
+        // Status: success
+        return { data: placeholderObject };
+    }
+}
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [data, status, urls] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useDataType(dataType, loaders, dataset, isRequired, coordinationSetters, initialCoordinationValues, matchOn) {
+    const setWarning = useSetWarning();
+    const placeholderObject = useMemo(() => ({}), []);
+    const dataQuery = useQuery({
+        // TODO: only enable when loaders has been initialized?
+        structuralSharing: false,
+        placeholderData: placeholderObject,
+        // Include the hook name in the queryKey to prevent the case in which an identical queryKey
+        // in a different hook would cause an accidental cache hit.
+        queryKey: [dataset, dataType, matchOn, isRequired, 'useDataType'],
+        // Query function should return an object
+        // { data, dataKey } where dataKey is the loaded gene selection.
+        queryFn: dataQueryFn,
+        meta: { loaders, placeholderObject },
+    });
+    const { data, status, isFetching, error } = dataQuery;
+    const loadedData = data?.data || placeholderObject;
+    const coordinationValues = data?.coordinationValues;
+    const urls = data?.urls;
+    useEffect(() => {
+        initCoordinationSpace(coordinationValues, coordinationSetters, initialCoordinationValues);
+    }, [coordinationValues]);
+    useEffect(() => {
+        if (error) {
+            warn(error, setWarning);
+        }
+    }, [error, setWarning]);
+    const dataStatus = isFetching ? STATUS.LOADING : status;
+    return [loadedData, dataStatus, urls];
+}
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [cells, cellsCount] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useDataTypeMulti(dataType, loaders, dataset, isRequired, coordinationSetters, initialCoordinationValues, matchOnObj) {
+    const placeholderObject = useMemo(() => ({}), []);
+    const setWarning = useSetWarning();
+    const matchOnEntries = matchOnObj ? Object.entries(matchOnObj) : [];
+    const dataQueries = useQueries({
+        // eslint-disable-next-line no-unused-vars
+        queries: matchOnEntries.map(([scopeKey, matchOn]) => ({
+            structuralSharing: false,
+            placeholderData: placeholderObject,
+            // Query key should match useDataType for shared cacheing
+            // and correctness of dataQueryFn.
+            queryKey: [dataset, dataType, matchOn, isRequired, 'useDataType'],
+            // Query function should return an object
+            // { data, dataKey } where dataKey is the loaded gene selection.
+            queryFn: dataQueryFn,
+            meta: { loaders, placeholderObject },
+        })),
+    });
+    const anyLoading = dataQueries.some(q => q.isFetching);
+    const anyError = dataQueries.some(q => q.isError);
+    // eslint-disable-next-line no-nested-ternary
+    const dataStatus = anyLoading ? STATUS.LOADING : (anyError ? STATUS.ERROR : STATUS.SUCCESS);
+    const isSuccess = dataStatus === STATUS.SUCCESS;
+    useEffect(() => {
+        dataQueries
+            .map(q => q.data?.coordinationValues)
+            .filter(v => Boolean(v))
+            .forEach((coordinationValues) => {
+            initCoordinationSpace(coordinationValues, coordinationSetters, initialCoordinationValues);
+        });
+        // Deliberate dependency omissions: use indirect dependencies for efficiency.
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [isSuccess]);
+    useEffect(() => {
+        dataQueries.map(q => q.error).filter(e => Boolean(e)).forEach((error) => {
+            warn(error, setWarning);
+        });
+        // Deliberate dependency omissions: use indirect dependencies for efficiency.
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [anyError, setWarning]);
+    // Convert data to object keyed by scopeKey.
+    const data = useMemo(() => fromEntries(matchOnEntries.map(([scopeKey], i) => ([scopeKey, dataQueries[i].data?.data]))), [dataQueries]);
+    return [data, dataStatus];
+}
+export function useHasLoader(loaders, dataset, dataType, matchOn) {
+    const loader = useMatchingLoader(loaders, dataset, dataType, matchOn);
+    return loader !== null;
+}

package/dist-tsc/data-hooks.d.ts

@@ -0,0 +1,73 @@
+/**
+ * Get the dataset description string.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @returns {array} [description] where
+ * description is a string.
+ */
+export function useDescription(loaders: object, dataset: string): array;
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [cells, cellsCount] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useObsEmbeddingData(loaders: object, dataset: string, isRequired: boolean, coordinationSetters: object, initialCoordinationValues: object, matchOn: any): array;
+export function useObsLocationsData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsLabelsData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsSegmentationsData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsSetsData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsFeatureMatrixData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useFeatureLabelsData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useImageData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useGenomicProfilesData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useNeighborhoodsData(loaders: any, dataset: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+/**
+ * Get data from the expression matrix data type loader for a given gene selection.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {boolean} selection A list of gene names to get expression data for.
+ * @returns {array} [geneData] where geneData is an array [Uint8Array, ..., Uint8Array]
+ * for however many genes are in the selection.
+ */
+export function useFeatureSelection(loaders: object, dataset: string, isRequired: boolean, selection: boolean, matchOn: any): array;
+/**
+ * Get the attributes for the expression matrix data type loader,
+ * i.e names of cells and genes.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.  Should not be used in conjunction (called in the same component)
+ * with useExpressionMatrixData.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @returns {object} [attrs] { rows, cols } object containing cell and gene names.
+ */
+export function useObsFeatureMatrixIndices(loaders: object, dataset: string, isRequired: boolean, matchOn: any): object;
+export function useMultiObsLabels(coordinationScopes: any, obsType: any, loaders: any, dataset: any): any[];
+//# sourceMappingURL=data-hooks.d.ts.map

package/dist-tsc/data-hooks.d.ts.map

@@ -0,0 +1 @@
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