@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

package/dist/file-options-schemas.js

@@ -1,322 +0,0 @@
-import Ajv from 'ajv';
-export function validateOptions(optionsSchema, options) {
-    const validate = new Ajv().compile(optionsSchema);
-    const valid = validate(options || null);
-    if (!valid) {
-        console.warn(JSON.stringify(validate.errors, null, 2));
-        throw new Error(`File definition options failed schema validation (${optionsSchema.title})`);
-    }
-    return true;
-}
-export const emptySchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#empty-options',
-    title: 'Empty options',
-    oneOf: [
-        { type: 'null' },
-    ],
-};
-const sharedDefinitions = {
-    annDataObs: {
-        type: 'object',
-        additionalProperties: false,
-        required: ['path'],
-        properties: {
-            path: { type: 'string' },
-        },
-    },
-    annDataObsm: {
-        type: 'object',
-        additionalProperties: false,
-        required: ['path'],
-        properties: {
-            path: { type: 'string' },
-            dims: {
-                type: 'array',
-                description: 'Which indices of the obsm object to take for a scatterplot, allowing for, for example, different PCs from obsm/X_pca',
-                items: { type: 'number' },
-            },
-        },
-    },
-    annDataConvenienceObsLabelsItem: {
-        type: 'object',
-        additionalProperties: false,
-        required: ['path', 'obsLabelsType'],
-        properties: {
-            path: { type: 'string' },
-            obsLabelsType: { type: 'string' },
-        },
-    },
-    annDataConvenienceFeatureLabelsItem: {
-        type: 'object',
-        additionalProperties: false,
-        required: ['path', 'featureLabelsType'],
-        properties: {
-            path: { type: 'string' },
-            featureLabelsType: { type: 'string' },
-        },
-    },
-    annDataConvenienceObsEmbeddingItem: {
-        type: 'object',
-        additionalProperties: false,
-        required: ['path', 'embeddingType'],
-        properties: {
-            path: { type: 'string' },
-            dims: {
-                type: 'array',
-                description: 'Which indices of the obsm object to take for a scatterplot, allowing for, for example, different PCs from obsm/X_pca',
-                items: { type: 'number' },
-            },
-            embeddingType: { type: 'string' },
-        },
-    },
-    annDataObsLabels: { $ref: '#/definitions/annDataObs' },
-    annDataFeatureLabels: { $ref: '#/definitions/annDataObs' },
-    annDataObsFeatureMatrix: {
-        type: 'object',
-        description: 'Options for the obsFeatureMatrix.anndata.zarr file type.',
-        additionalProperties: false,
-        required: ['path'],
-        properties: {
-            path: { type: 'string' },
-            featureFilterPath: {
-                type: 'string',
-                description: 'If the feature index should be filtered, put a boolean column here (analogous to the previous geneFilter option). e.g., var/in_obsm_X_small_matrix',
-            },
-            initialFeatureFilterPath: {
-                type: 'string',
-                description: 'If only a subset of the matrix should be loaded initially, put a boolean column along the feature axis here (analogous to the previous matrixGeneFilter option). e.g., var/highly_variable',
-            },
-        },
-    },
-    annDataObsSets: {
-        type: 'array',
-        description: 'Options for the obsSets.anndata.zarr file type.',
-        items: {
-            type: 'object',
-            additionalProperties: false,
-            required: ['name', 'path'],
-            properties: {
-                name: {
-                    type: 'string',
-                    description: "The display name for the set, like 'Cell Type' or 'Louvain.'",
-                },
-                path: {
-                    oneOf: [
-                        {
-                            type: 'string',
-                            description: "The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'",
-                        },
-                        {
-                            type: 'array',
-                            items: { type: 'string' },
-                            description: 'An array of locations in the AnnData store for a hierarchy of set names, from coarse to fine levels.',
-                        },
-                    ],
-                },
-                scorePath: {
-                    oneOf: [
-                        {
-                            type: 'string',
-                            description: "The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'",
-                        },
-                    ],
-                },
-            },
-        },
-    },
-    annDataObsLocations: { $ref: '#/definitions/annDataObsm' },
-    annDataObsEmbedding: { $ref: '#/definitions/annDataObsm' },
-    annDataObsSegmentations: { $ref: '#/definitions/annDataObs' },
-};
-/**
- * Options schemas for atomic file types.
- */
-// AnnData
-export const obsEmbeddingAnndataSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsEmbedding-anndata-zarr-options',
-    title: 'obsEmbedding.anndata.zarr options',
-    definitions: sharedDefinitions,
-    $ref: '#/definitions/annDataObsEmbedding',
-};
-export const obsLocationsAnndataSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsLocations-anndata-zarr-options',
-    title: 'obsLocations.anndata.zarr options',
-    definitions: sharedDefinitions,
-    $ref: '#/definitions/annDataObsLocations',
-};
-export const obsSegmentationsAnndataSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsSegmentations-anndata-zarr-options',
-    title: 'obsSegmentations.anndata.zarr options',
-    definitions: sharedDefinitions,
-    $ref: '#/definitions/annDataObsSegmentations',
-};
-export const obsSetsAnndataSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsSets-anndata-zarr-options',
-    title: 'obsSets.anndata.zarr options',
-    definitions: sharedDefinitions,
-    $ref: '#/definitions/annDataObsSets',
-};
-export const obsFeatureMatrixAnndataSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsFeatureMatrix-anndata-zarr-options',
-    title: 'obsFeatureMatrix.anndata.zarr options',
-    definitions: sharedDefinitions,
-    $ref: '#/definitions/annDataObsFeatureMatrix',
-};
-export const obsLabelsAnndataSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsLabels-anndata-zarr-options',
-    title: 'obsLabels.anndata.zarr options',
-    definitions: sharedDefinitions,
-    $ref: '#/definitions/annDataObsLabels',
-};
-export const featureLabelsAnndataSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#featureLabels-anndata-zarr-options',
-    title: 'featureLabels.anndata.zarr options',
-    definitions: sharedDefinitions,
-    $ref: '#/definitions/annDataFeatureLabels',
-};
-// CSV
-export const obsEmbeddingCsvSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsEmbedding-csv-options',
-    title: 'obsEmbedding.csv options',
-    type: 'object',
-    required: ['obsIndex', 'obsEmbedding'],
-    properties: {
-        obsIndex: { type: 'string' },
-        obsEmbedding: {
-            type: 'array',
-            items: { type: 'string' },
-            minItems: 2,
-            maxItems: 2,
-        },
-    },
-};
-export const obsLocationsCsvSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsLocations-csv-options',
-    title: 'obsLocations.csv options',
-    type: 'object',
-    required: ['obsIndex', 'obsLocations'],
-    properties: {
-        obsIndex: { type: 'string' },
-        obsLocations: {
-            type: 'array',
-            items: { type: 'string' },
-            minItems: 2,
-            maxItems: 2,
-        },
-    },
-};
-export const obsLabelsCsvSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsLabels-csv-options',
-    title: 'obsLabels.csv options',
-    type: 'object',
-    required: ['obsIndex', 'obsLabels'],
-    properties: {
-        obsIndex: { type: 'string' },
-        obsLabels: { type: 'string' },
-    },
-};
-export const featureLabelsCsvSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#featureLabels-csv-options',
-    title: 'featureLabels.csv options',
-    type: 'object',
-    required: ['featureIndex', 'featureLabels'],
-    properties: {
-        featureIndex: { type: 'string' },
-        featureLabels: { type: 'string' },
-    },
-};
-export const obsSetsCsvSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#obsLabels-csv-options',
-    title: 'obsLabels.csv options',
-    type: 'object',
-    additionalProperties: false,
-    required: ['obsIndex', 'obsSets'],
-    properties: {
-        obsIndex: { type: 'string' },
-        obsSets: {
-            type: 'array',
-            items: {
-                type: 'object',
-                additionalProperties: false,
-                required: ['name', 'column'],
-                properties: {
-                    name: {
-                        type: 'string',
-                        description: "The display name for the set, like 'Cell Type' or 'Louvain'",
-                    },
-                    column: {
-                        oneOf: [
-                            {
-                                type: 'string',
-                                description: "The column for the set, like 'cell_type'",
-                            },
-                            {
-                                type: 'array',
-                                items: { type: 'string' },
-                                description: 'An array of columns for a hierarchy of set names, from coarse to fine levels.',
-                            },
-                        ],
-                    },
-                    scoreColumn: {
-                        oneOf: [
-                            {
-                                type: 'string',
-                                description: "The column for the set confidence scores, like 'celltype_prediction_score'",
-                            },
-                        ],
-                    },
-                },
-            },
-        },
-    },
-};
-/**
- * Options schemas for joint file types.
- */
-export const anndataZarrSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#anndata-zarr-options',
-    title: 'anndata.zarr options',
-    definitions: sharedDefinitions,
-    type: 'object',
-    minProperties: 1,
-    additionalProperties: false,
-    required: [],
-    properties: {
-        obsLabels: {
-            oneOf: [
-                { $ref: '#/definitions/annDataObsLabels' },
-                { type: 'array', items: { $ref: '#/definitions/annDataConvenienceObsLabelsItem' } },
-            ],
-        },
-        featureLabels: {
-            oneOf: [
-                { $ref: '#/definitions/annDataFeatureLabels' },
-                { type: 'array', items: { $ref: '#/definitions/annDataConvenienceFeatureLabelsItem' } },
-            ],
-        },
-        obsFeatureMatrix: { $ref: '#/definitions/annDataObsFeatureMatrix' },
-        obsSets: { $ref: '#/definitions/annDataObsSets' },
-        obsLocations: { $ref: '#/definitions/annDataObsLocations' },
-        obsSegmentations: { $ref: '#/definitions/annDataObsSegmentations' },
-        obsEmbedding: {
-            oneOf: [
-                { $ref: '#/definitions/annDataObsEmbedding' },
-                { type: 'array', items: { $ref: '#/definitions/annDataConvenienceObsEmbeddingItem' } },
-            ],
-        },
-    },
-};

package/dist/file-options-schemas.test.js

@@ -1,23 +0,0 @@
-import { expandAnndataZarr, } from './joint-file-types';
-describe('src/app/file-options-schemas.js', () => {
-    describe('Options validation for joint file type expansion functions', () => {
-        it('anndata.zarr with invalid options fails validation', () => {
-            expect(() => expandAnndataZarr({
-                fileType: 'anndata.zarr',
-                url: 'http://localhost:8000/anndata.zarr',
-                options: {
-                    obsFeatureMatrix: 1,
-                },
-            })).toThrow();
-        });
-        it('anndata.zarr with extra options fails validation', () => {
-            expect(() => expandAnndataZarr({
-                fileType: 'anndata.zarr',
-                url: 'http://localhost:8000/anndata.zarr',
-                options: {
-                    bad: 'bad',
-                },
-            })).toThrow();
-        });
-    });
-});

package/dist/hooks.js

@@ -1,215 +0,0 @@
-import { useRef, useState, useEffect, useCallback, useMemo, } from 'react';
-import debounce from 'lodash/debounce';
-import every from 'lodash/every';
-import { capitalize, fromEntries } from '@vitessce/utils';
-import { useGridResize, useEmitGridResize } from './state/hooks';
-import { VITESSCE_CONTAINER } from './classNames';
-function getWindowDimensions() {
-    const { innerWidth: width, innerHeight: height } = window;
-    return {
-        width,
-        height,
-    };
-}
-export function useVitessceContainer(ref) {
-    return useCallback(() => {
-        if (ref.current) {
-            return ref.current.closest(`.${VITESSCE_CONTAINER}`);
-        }
-        return null;
-    }, [ref]);
-}
-/**
- * Custom hook, gets the full window dimensions.
- * @returns {array} `[width, height]` where width and height
- * are numbers.
- */
-export function useWindowDimensions() {
-    const [windowDimensions, setWindowDimensions] = useState(getWindowDimensions());
-    useEffect(() => {
-        function handleResize() {
-            setWindowDimensions(getWindowDimensions());
-        }
-        const onResizeDebounced = debounce(handleResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        return () => window.removeEventListener('resize', onResizeDebounced);
-    }, []);
-    return windowDimensions;
-}
-/**
- * Custom hook, subscribes to GRID_RESIZE and window resize events.
- * @returns {array} `[width, height, containerRef]` where width and height
- * are numbers and containerRef is a React ref.
- */
-export function useGridItemSize() {
-    const containerRef = useRef();
-    const [height, setHeight] = useState();
-    const [width, setWidth] = useState();
-    const resizeCount = useGridResize();
-    const incrementResizeCount = useEmitGridResize();
-    // On window resize events, increment the grid resize count.
-    useEffect(() => {
-        function onWindowResize() {
-            incrementResizeCount();
-        }
-        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        onWindowResize();
-        return () => {
-            window.removeEventListener('resize', onResizeDebounced);
-        };
-    }, [incrementResizeCount]);
-    // On new grid resize counts, re-compute the component
-    // width/height.
-    useEffect(() => {
-        if (!containerRef.current)
-            return;
-        const container = containerRef.current;
-        const containerRect = container.getBoundingClientRect();
-        setHeight(containerRect.height);
-        setWidth(containerRect.width);
-    }, [resizeCount]);
-    return [width, height, containerRef];
-}
-/**
- * Custom hook, subscribes to GRID_RESIZE and window resize events.
- * @returns {array} `[width, height, deckRef]` where width and height
- * are numbers and deckRef is a React ref to be used with
- * a <DeckGL/> element (or a forwardRef to one).
- */
-export function useDeckCanvasSize() {
-    const deckRef = useRef();
-    const [height, setHeight] = useState();
-    const [width, setWidth] = useState();
-    const resizeCount = useGridResize();
-    const incrementResizeCount = useEmitGridResize();
-    // On window resize events, increment the grid resize count.
-    useEffect(() => {
-        function onWindowResize() {
-            incrementResizeCount();
-        }
-        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        onWindowResize();
-        return () => {
-            window.removeEventListener('resize', onResizeDebounced);
-        };
-    }, [incrementResizeCount]);
-    // On new grid resize counts, re-compute the DeckGL canvas
-    // width/height.
-    useEffect(() => {
-        if (!deckRef.current)
-            return;
-        const { canvas } = deckRef.current.deck;
-        const canvasRect = canvas.getBoundingClientRect();
-        setHeight(canvasRect.height);
-        setWidth(canvasRect.width);
-    }, [resizeCount]);
-    return [width, height, deckRef];
-}
-/**
- * This hook handles a boolean isReady value,
- * which only returns true once every item in the
- * input list has been marked as "ready".
- * @param {string[]} statusValues The items to wait on.
- * @returns {boolean} Whether the status values are all success.
- */
-export function useReady(statusValues) {
-    return useMemo(() => every(statusValues, val => val === 'success'), statusValues);
-}
-/**
- * This hook helps manage a list of URLs.
- * @param {object} loaders The loaders dependency.
- * @param {string} dataset The dataset UID dependency.
- * @returns {array} An array
- * [urls, addUrl]
- * where urls is the array of URL objects,
- * and addUrl is a function for adding a URL to the array.
- */
-export function useUrls(loaders, dataset) {
-    const [urls, setUrls] = useState([]);
-    const addUrl = useCallback((url, name) => {
-        if (url) {
-            setUrls(prev => ([...prev, { url, name }]));
-        }
-    }, [setUrls]);
-    useEffect(() => {
-        setUrls([]);
-    }, [loaders, dataset]);
-    return [urls, addUrl];
-}
-/**
- * Custom hook, subscribes to the width and height of the closest .vitessce-container
- * element and updates upon window resize events.
- * @param {Ref} ref A React ref object within the `.vitessce-container`.
- * @returns {array} `[width, height]` where width and height
- * are numbers.
- */
-export function useClosestVitessceContainerSize(ref) {
-    const [height, setHeight] = useState();
-    const [width, setWidth] = useState();
-    useEffect(() => {
-        function onWindowResize() {
-            if (ref.current) {
-                const { clientHeight: componentHeight, clientWidth: componentWidth, } = ref.current.closest(`.${VITESSCE_CONTAINER}`);
-                setWidth(componentWidth);
-                setHeight(componentHeight);
-            }
-        }
-        const onResizeDebounced = debounce(onWindowResize, 100, { trailing: true });
-        window.addEventListener('resize', onResizeDebounced);
-        onWindowResize();
-        return () => {
-            window.removeEventListener('resize', onResizeDebounced);
-        };
-    }, [ref]);
-    return [width, height];
-}
-export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, expressionData }) {
-    // Get a mapping from cell ID to row index in the gene expression matrix.
-    // Since the two obsIndices (instanceObsIndex = the obsIndex from obsEmbedding)
-    // may be ordered differently (matrixObsIndex = the obsIndex from obsFeatureMatrix),
-    // we need a way to look up an obsFeatureMatrix obsIndex index
-    // given an obsEmbedding obsIndex index.
-    const toMatrixIndexMap = useMemo(() => {
-        if (instanceObsIndex && matrixObsIndex) {
-            const matrixIndexMap = new Map(matrixObsIndex.map((key, i) => ([key, i])));
-            return instanceObsIndex.map(key => matrixIndexMap.get(key));
-        }
-        return null;
-    }, [instanceObsIndex, matrixObsIndex]);
-    // Set up a getter function for gene expression values, to be used
-    // by the DeckGL layer to obtain values for instanced attributes.
-    const getExpressionValue = useCallback((entry, { index: instanceIndex }) => {
-        if (toMatrixIndexMap && expressionData && expressionData[0]) {
-            const rowIndex = toMatrixIndexMap[instanceIndex];
-            const val = expressionData[0][rowIndex];
-            return val;
-        }
-        return 0;
-    }, [toMatrixIndexMap, expressionData]);
-    return getExpressionValue;
-}
-export function useGetObsInfo(obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership) {
-    return useCallback((obsId) => {
-        if (obsId) {
-            const obsMembership = obsSetsMembership?.get(obsId) || [];
-            return {
-                [`${capitalize(obsType)} ID`]: obsId,
-                ...fromEntries(obsMembership.flatMap(path => path.slice(1).map((pathEl, elLevel) => ([
-                    `${path[0]}${path.length > 2 ? ` L${elLevel + 1}` : ''}`,
-                    pathEl,
-                ])))),
-                ...fromEntries(Object.entries(obsLabelsTypes).map(([scopeKey, obsLabelsType]) => ([
-                    obsLabelsType,
-                    obsLabelsData?.[scopeKey]?.obsLabels?.[
-                    // TODO: Maybe all loaders that return obsIndex should also return an obsIndexMap
-                    // with keys: obsId, values: obsIdx
-                    // which would avoid the indexOf calls.
-                    obsLabelsData?.[scopeKey]?.obsIndex?.indexOf(obsId)],
-                ])).filter(([obsLabelsType]) => Boolean(obsLabelsType))),
-            };
-        }
-        return null;
-    }, [obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership]);
-}