@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

package/dist/errors/DatasetNotFoundError.js

@@ -1,17 +0,0 @@
-import AbstractLoaderError from './AbstractLoaderError';
-export default class DatasetNotFoundError extends AbstractLoaderError {
-    constructor(datasetUid) {
-        super(`Error finding dataset for ${datasetUid}. Please check that at least one dataset exists in the view config.`);
-        this.name = 'DatasetNotFoundError';
-        this.datasetUid = datasetUid;
-    }
-    warnInConsole() {
-        const { datasetUid, } = this;
-        if (datasetUid) {
-            console.warn(`Unable to find dataset for ${datasetUid}`);
-        }
-        else {
-            console.warn('No dataset uid specified.');
-        }
-    }
-}

package/dist/errors/LoaderNotFoundError.js

@@ -1,17 +0,0 @@
-import AbstractLoaderError from './AbstractLoaderError';
-export default class LoaderNotFoundError extends AbstractLoaderError {
-    constructor(loaders, dataset, fileType, viewCoordinationValues) {
-        super(`Error: unable to find matching ${fileType} file in dataset ${dataset}.`);
-        this.name = 'LoaderNotFoundError';
-        this.loaders = loaders;
-        this.dataset = dataset;
-        this.fileType = fileType;
-        this.viewCoordinationValues = viewCoordinationValues;
-    }
-    warnInConsole() {
-        const { loaders, viewCoordinationValues, } = this;
-        console.warn(
-        // eslint-disable-next-line prefer-template
-        `Expected to match on { ${Object.entries(viewCoordinationValues).map(([k, v]) => k + ': ' + v).join(', ')} }`, loaders);
-    }
-}

package/dist/errors/LoaderValidationError.js

@@ -1,15 +0,0 @@
-import AbstractLoaderError from './AbstractLoaderError';
-export default class LoaderValidationError extends AbstractLoaderError {
-    constructor(datasetType, datasetFileType, datasetUrl, reason) {
-        super(`Error while validating ${datasetType}.`);
-        this.name = 'LoaderValidationError';
-        this.datasetType = datasetType;
-        this.datasetFileType = datasetFileType;
-        this.datasetUrl = datasetUrl;
-        this.reason = reason;
-    }
-    warnInConsole() {
-        const { datasetType, datasetUrl, reason, } = this;
-        console.warn(`${datasetType} from ${datasetUrl}: validation failed`, JSON.stringify(reason, null, 2));
-    }
-}

package/dist/errors/OptionsValidationError.js

@@ -1,15 +0,0 @@
-import AbstractLoaderError from './AbstractLoaderError';
-export default class OptionsValidationError extends AbstractLoaderError {
-    constructor(fileType, url, options, reason) {
-        super(`Error while validating file definition options: ${fileType} from ${url}.`);
-        this.name = 'OptionsValidationError';
-        this.fileType = fileType;
-        this.url = url;
-        this.options = options;
-        this.reason = reason;
-    }
-    warnInConsole() {
-        const { options, reason, } = this;
-        console.warn('Received options\n', JSON.stringify(options, null, 2), 'JSON schema validation failure reason\n', JSON.stringify(reason, null, 2));
-    }
-}

package/dist/export-utils.js

@@ -1,70 +0,0 @@
-import Bowser from 'bowser';
-import { compressToEncodedURIComponent, decompressFromEncodedURIComponent } from 'lz-string';
-const CURRENT_VERSION = '0.0.1';
-const VITESSCE_CONF_QUERY_STRING = 'vitessce_conf';
-const VERSION_QUERY_STRING = 'vitessce_conf_version';
-const LENGTH_QUERY_STRING = 'vitessce_conf_length';
-function sniffBrowser() {
-    const { browser } = Bowser.parse(window.navigator.userAgent);
-    return browser.name;
-}
-// https://stackoverflow.com/questions/417142/what-is-the-maximum-length-of-a-url-in-different-browsers
-const MAX_BROWSER_URL_LENGTHS = {
-    Chrome: 32779,
-    'Internet Explorer': 2047,
-    Edge: 2047,
-    Safari: 65000,
-    Firefox: 65000,
-};
-export default class CompressedConfLengthError {
-    constructor(message) {
-        this.message = message;
-    }
-}
-/**
- * Encode a configuration as url params with a version and an lz-compressed conf.
- * @param {Object} params
- * @param {Object} params.conf Previous scope names.
- * @param {function} params.onOverMaximumUrlLength Callback for when new url
- * is over max length for your browser - takes two arguments: { message, willWorkOn }
- * for the error message and the browsers for which the url will work (optional).
- * @returns {string} The new params like
- * vitessce_conf_length=10&vitessce_conf_version=0.0.1&vitessce_conf=fksdfasdfjkl
- */
-export function encodeConfInUrl({ conf, onOverMaximumUrlLength = () => { }, }) {
-    const compressedConf = compressToEncodedURIComponent(JSON.stringify(conf));
-    const newParams = `${LENGTH_QUERY_STRING}=${compressedConf.length}&${VERSION_QUERY_STRING}=${CURRENT_VERSION}&${VITESSCE_CONF_QUERY_STRING}=${compressedConf}`;
-    const browser = sniffBrowser();
-    const maxLength = MAX_BROWSER_URL_LENGTHS[browser];
-    if (newParams.length > maxLength) {
-        const willWorkOn = Object.entries(MAX_BROWSER_URL_LENGTHS)
-            .filter(entry => entry[1] > newParams.length)
-            .map(entry => entry[0]);
-        const message = `Configuration is ${compressedConf.length} characters; max URL for ${browser} is ${maxLength}: it will work on ${willWorkOn.join(', ') || 'no browser'}.`;
-        console.error(message);
-        onOverMaximumUrlLength({ message, willWorkOn });
-    }
-    return newParams;
-}
-/**
- * Decode URL params to a Vitessce configuration.
- * The URL params must have version and vitessce_conf params,
- * like vitessce_conf_length=10&vitessce_conf_version=0.0.1&vitessce_conf=fksdfasdfjkl.
- * @param {Object} queryString The URL params,
- * like vitessce_conf_length=10&vitessce_conf_version=0.0.1&vitessce_conf=fksdfasdfjkl.
- * @returns {string} A vitessce configuration.
- */
-export function decodeURLParamsToConf(queryString) {
-    const params = new URLSearchParams(queryString.replace('#', '&'));
-    const compressedConfString = params.get(VITESSCE_CONF_QUERY_STRING);
-    const expectedConfLength = Number(params.get(LENGTH_QUERY_STRING));
-    if (expectedConfLength !== compressedConfString.length) {
-        throw new CompressedConfLengthError(`Compressed conf length (${compressedConfString.length}) != expected (${expectedConfLength}). URL truncated?`);
-    }
-    const version = params.get(VERSION_QUERY_STRING);
-    if (version === CURRENT_VERSION) {
-        const conf = JSON.parse(decompressFromEncodedURIComponent(compressedConfString));
-        return conf;
-    }
-    throw new Error('Unrecognized URL Param Version');
-}

package/dist/export-utils.test.js

@@ -1,66 +0,0 @@
-import expect from 'expect';
-import { encodeConfInUrl, decodeURLParamsToConf, } from './export-utils';
-const fakeConfig = {
-    version: '0.1.0',
-    public: false,
-    layers: [
-        {
-            name: 'cells',
-            type: 'CELLS',
-            fileType: 'cells.json',
-            url: 'http://example.com/cells.json',
-        },
-    ],
-    name: 'Just scatterplot',
-    staticLayout: [
-        {
-            component: 'scatterplot',
-            props: {
-                mapping: 't-SNE',
-                view: {
-                    zoom: 0.75,
-                    target: [0, 0, 0],
-                },
-            },
-            x: 0,
-            y: 0,
-            w: 12,
-            h: 2,
-        },
-    ],
-};
-function makeLongString(length) {
-    let result = '';
-    const characters = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789';
-    const charactersLength = characters.length;
-    // eslint-disable-next-line no-plusplus
-    for (let i = 0; i < length; i++) {
-        result += characters.charAt(Math.floor(Math.random() * charactersLength));
-    }
-    return result;
-}
-describe('src/app/export-utils.js', () => {
-    describe('encodeConfInUrl', () => {
-        it('encodes a view config for a URL', () => {
-            const urlParams1 = encodeConfInUrl({ conf: {} });
-            expect(urlParams1).toEqual('vitessce_conf_length=5&vitessce_conf_version=0.0.1&vitessce_conf=N4XyA');
-            const urlParams2 = encodeConfInUrl({ conf: fakeConfig });
-            expect(urlParams2).toEqual('vitessce_conf_length=327&vitessce_conf_version=0.0.1&vitessce_conf=N4IgbgpgTgzglgewHYgFwgAwDoCMWMgA0IADgK4BGANnAMZoBmAhlTBMVUwJ7QxoDaoJEwC2ENCFoQqrIiAAuXEuPQBhAKIAZTQGU5DOFQgAVJSsnTWWAFYxkcslCoSAFvPklUAei8QAHqIkRli0CCJeUjIwNnYoAL4AusTCYhIAUmQw8gAEMLRM7tBBCPJyWQV0mtwIZKWogpJhJMgQSHUgeQXyRVQlciRQCCR8qKAiTCQkcEgA5hLyALQ6AHLqcmBwEADuaKAAXghhaNgA7ACsxPJMUDMQdfwYhI8YCXFxxH7HxFxfIDuoOAATMQXGhAYk4kA');
-        });
-        it('Calls onOverMaximumUrlLength for conf too long', () => {
-            let browsers;
-            // eslint-disable-next-line no-return-assign
-            const onOverMaximumUrlLength = ({ willWorkOn }) => browsers = willWorkOn;
-            encodeConfInUrl({ conf: { foo: makeLongString(69000) }, onOverMaximumUrlLength });
-            expect(browsers).toEqual([]);
-            encodeConfInUrl({ conf: { foo: makeLongString(37000) }, onOverMaximumUrlLength });
-            expect(browsers).toEqual(['Safari', 'Firefox']);
-        });
-        it('decodes a view config for a URL', () => {
-            const viewConfig1 = decodeURLParamsToConf('vitessce_conf_length=5&vitessce_conf_version=0.0.1&vitessce_conf=N4XyA');
-            expect(viewConfig1).toEqual({});
-            const viewConfig2 = decodeURLParamsToConf('vitessce_conf_length=327&vitessce_conf_version=0.0.1&vitessce_conf=N4IgbgpgTgzglgewHYgFwgAwDoCMWMgA0IADgK4BGANnAMZoBmAhlTBMVUwJ7QxoDaoJEwC2ENCFoQqrIiAAuXEuPQBhAKIAZTQGU5DOFQgAVJSsnTWWAFYxkcslCoSAFvPklUAei8QAHqIkRli0CCJeUjIwNnYoAL4AusTCYhIAUmQw8gAEMLRM7tBBCPJyWQV0mtwIZKWogpJhJMgQSHUgeQXyRVQlciRQCCR8qKAiTCQkcEgA5hLyALQ6AHLqcmBwEADuaKAAXghhaNgA7ACsxPJMUDMQdfwYhI8YCXFxxH7HxFxfIDuoOAATMQXGhAYk4kA');
-            expect(viewConfig2).toEqual(fakeConfig);
-        });
-    });
-});

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

@@ -1,136 +0,0 @@
-export const cellsJsonSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#cells-json-options',
-    title: 'cells.json options',
-    oneOf: [
-        { type: 'null' },
-        {
-            type: 'object',
-            additionalProperties: false,
-            required: [],
-            properties: {
-                obsLabelsTypes: {
-                    type: 'array',
-                    items: { type: 'string' },
-                },
-                embeddingTypes: {
-                    type: 'array',
-                    items: { type: 'string' },
-                },
-            },
-        },
-    ],
-};
-export const anndataCellsZarrSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#anndata-cells-zarr-options',
-    title: 'anndata-cells.zarr options',
-    type: 'object',
-    minProperties: 1,
-    additionalProperties: false,
-    required: [],
-    properties: {
-        xy: {
-            type: 'string',
-            description: "The location in the AnnData store of cell centroids, like 'obsm/X_centroids.'",
-        },
-        poly: {
-            type: 'string',
-            description: "The location in the AnnData store of cell polygon outlines, like 'obsm/X_polygons.'",
-        },
-        factors: {
-            type: 'array',
-            description: "List of locations in the AnnData store of cell sets, like 'obs/louvain'",
-            items: {
-                type: 'string',
-            },
-        },
-        mappings: {
-            patternProperties: {
-                '.': {
-                    type: 'object',
-                    description: "An object containing key-values for mappings like { UMAP: { key: 'obsm/X_umap', dims: [0, 1] } }.",
-                    additionalProperties: false,
-                    required: ['key'],
-                    properties: {
-                        key: {
-                            type: 'string',
-                            description: "Where to look in the AnnData store for this mapping, like 'obsm/X_umap.'",
-                        },
-                        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',
-                            minItems: 2,
-                            maxItems: 2,
-                            items: { type: 'number' },
-                        },
-                    },
-                },
-            },
-        },
-    },
-};
-export const anndataCellSetsZarrSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#anndata-cell-sets-zarr-options',
-    title: 'anndata-cell-sets.zarr options',
-    type: 'array',
-    items: {
-        type: 'object',
-        additionalProperties: false,
-        required: ['groupName', 'setName'],
-        properties: {
-            groupName: {
-                type: 'string',
-                description: "The display name for the set, like 'Cell Type' or 'Louvain.'",
-            },
-            setName: {
-                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.',
-                    },
-                ],
-            },
-            scoreName: {
-                oneOf: [
-                    {
-                        type: 'string',
-                        description: "The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'",
-                    },
-                ],
-            },
-        },
-    },
-};
-export const anndataExpressionMatrixZarrSchema = {
-    $schema: 'http://json-schema.org/draft-07/schema#',
-    $id: 'https://github.com/vitessce/vitessce/#anndata-expression-matrix-zarr-options',
-    title: 'anndata-expression-matrix.zarr options',
-    type: 'object',
-    additionalProperties: false,
-    required: ['matrix'],
-    properties: {
-        matrix: {
-            type: 'string',
-            description: "The location in the AnnData store of the cell x gene matrix, like 'obsm/hvg_subset.' or 'X'",
-        },
-        geneFilter: {
-            type: 'string',
-            description: "The location in the AnnData store of a filter for the genes if using a subset of the data, like 'var.highly_variable.' if the matrix comes from 'obsm/hvg_subset.'",
-        },
-        matrixGeneFilter: {
-            type: 'string',
-            description: "The location in the AnnData store of a filter for the matrix data (used in heatmap and histogram), like 'var.highly_variable.''",
-        },
-        geneAlias: {
-            type: 'string',
-            description: 'The location in the AnnData store of a different list of names for gene list component, other than the `var` index',
-        },
-    },
-};

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

@@ -1,126 +0,0 @@
-import { expandExpressionMatrixZarr, expandRasterOmeZarr, expandGenesJson, expandCellsJson, expandCellSetsJson, expandMoleculesJson, expandAnndataCellsZarr, expandAnndataCellSetsZarr, expandAnndataExpressionMatrixZarr, expandClustersJson, } from './joint-file-types-legacy';
-describe('src/app/file-options-schemas-legacy.js', () => {
-    describe('Options validation for joint file type expansion functions', () => {
-        it('cells.json with extra options fails validation', () => {
-            expect(() => expandCellsJson({
-                fileType: 'cells.json',
-                url: 'http://localhost:8000/cells.json',
-                options: {
-                    badKey: 'test',
-                    embeddingTypes: ['UMAP', 't-SNE'],
-                    obsLabelsTypes: ['cluster', 'subcluster'],
-                },
-            })).toThrow();
-        });
-        it('molecules.json with any options fails validation', () => {
-            expect(() => expandMoleculesJson({
-                fileType: 'molecules.json',
-                url: 'http://localhost:8000/molecules.json',
-                options: {},
-            })).toThrow();
-        });
-        it('expression-matrix.zarr with any options fails validation', () => {
-            expect(() => expandExpressionMatrixZarr({
-                fileType: 'expression-matrix.zarr',
-                url: 'http://localhost:8000/expression-matrix.zarr',
-                options: {},
-            })).toThrow();
-        });
-        it('raster.ome-zarr with any options fails validation', () => {
-            expect(() => expandRasterOmeZarr({
-                fileType: 'raster.ome-zarr',
-                url: 'http://localhost:8000/raster.ome-zarr',
-                options: {},
-            })).toThrow();
-        });
-        it('cell-sets.json with any options fails validation', () => {
-            expect(() => expandCellSetsJson({
-                fileType: 'cell-sets.json',
-                url: 'http://localhost:8000/cell-sets.json',
-                options: {},
-            })).toThrow();
-        });
-        it('clusters.json with any options fails validation', () => {
-            expect(() => expandClustersJson({
-                fileType: 'clusters.json',
-                url: 'http://localhost:8000/clusters.json',
-                options: {},
-            })).toThrow();
-        });
-        it('genes.json with any options fails validation', () => {
-            expect(() => expandGenesJson({
-                fileType: 'genes.json',
-                url: 'http://localhost:8000/genes.json',
-                options: {},
-            })).toThrow();
-        });
-        it('anndata-cells.zarr with extra options fails validation', () => {
-            expect(() => expandAnndataCellsZarr({
-                fileType: 'anndata-cells.zarr',
-                url: 'http://localhost:8000/anndata-cells.zarr',
-                options: {
-                    poly: 'obsm/poly',
-                    xy: 'obsm/xy',
-                    bad: 'bad',
-                },
-            })).toThrow();
-        });
-        it('anndata-cells.zarr with invalid options fails validation', () => {
-            expect(() => expandAnndataCellsZarr({
-                fileType: 'anndata-cells.zarr',
-                url: 'http://localhost:8000/anndata-cells.zarr',
-                options: {
-                    poly: 'obsm/poly',
-                    xy: 'obsm/xy',
-                    mappings: {
-                        UMAP: ['bad'],
-                    },
-                },
-            })).toThrow();
-        });
-        it('anndata-cell-sets.zarr with invalid options fails validation', () => {
-            expect(() => expandAnndataCellSetsZarr({
-                fileType: 'anndata-cell-sets.zarr',
-                url: 'http://localhost:8000/anndata-cell-sets.zarr',
-                options: {},
-            })).toThrow();
-        });
-        it('anndata-cell-sets.zarr with extra options fails validation', () => {
-            expect(() => expandAnndataCellSetsZarr({
-                fileType: 'anndata-cell-sets.zarr',
-                url: 'http://localhost:8000/anndata-cell-sets.zarr',
-                options: [
-                    {
-                        groupName: 'Cell Type Annotations',
-                        setName: 'obs/cell_type',
-                        scoreName: 'obs/score',
-                        bad: 'bad',
-                    },
-                ],
-            })).toThrow();
-        });
-        it('anndata-expression-matrix.zarr with invalid options fails validation', () => {
-            expect(() => expandAnndataExpressionMatrixZarr({
-                fileType: 'anndata-expression-matrix.zarr',
-                url: 'http://localhost:8000/anndata-expression-matrix.zarr',
-                options: {
-                    matrix: 'good',
-                    geneAlias: 1,
-                },
-            })).toThrow();
-        });
-        it('anndata-expression-matrix.zarr with extra options fails validation', () => {
-            expect(() => expandAnndataExpressionMatrixZarr({
-                fileType: 'anndata-expression-matrix.zarr',
-                url: 'http://localhost:8000/anndata-expression-matrix.zarr',
-                options: {
-                    matrix: 'good',
-                    geneAlias: 'good',
-                    geneFilter: 'good',
-                    matrixGeneFilter: 'good',
-                    bad: 'bad',
-                },
-            })).toThrow();
-        });
-    });
-});