@vitessce/vit-s 2.0.0-beta.0

package/dist/joint-file-types.js

@@ -0,0 +1,148 @@
+import { FileType } from '@vitessce/constants-internal';
+import { validateOptions, anndataZarrSchema, } from './file-options-schemas';
+import { expandMoleculesJson, expandExpressionMatrixZarr, expandRasterJson, expandRasterOmeZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandGenesJson, expandAnndataCellsZarr, expandAnndataCellSetsZarr, expandAnndataExpressionMatrixZarr, } from './joint-file-types-legacy';
+export function expandAnndataZarr(fileDef) {
+    validateOptions(anndataZarrSchema, fileDef.options);
+    const baseFileDef = {
+        url: fileDef.url,
+        requestInit: fileDef.requestInit,
+        coordinationValues: {
+            ...fileDef.coordinationValues,
+            obsType: fileDef.coordinationValues?.obsType || 'cell',
+            featureType: fileDef.coordinationValues?.featureType || 'gene',
+            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
+        },
+    };
+    const { options = {} } = fileDef;
+    return [
+        // obsFeatureMatrix
+        ...(options.obsFeatureMatrix ? [{
+                ...baseFileDef,
+                fileType: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR,
+                options: options.obsFeatureMatrix,
+                coordinationValues: {
+                    obsType: baseFileDef.coordinationValues.obsType,
+                    featureType: baseFileDef.coordinationValues.featureType,
+                    featureValueType: baseFileDef.coordinationValues.featureValueType,
+                },
+            }] : []),
+        // obsSets
+        ...(options.obsSets ? [{
+                ...baseFileDef,
+                fileType: FileType.OBS_SETS_ANNDATA_ZARR,
+                options: options.obsSets,
+                coordinationValues: {
+                    obsType: baseFileDef.coordinationValues.obsType,
+                },
+            }] : []),
+        // obsLocations
+        ...(options.obsLocations ? [{
+                ...baseFileDef,
+                fileType: FileType.OBS_LOCATIONS_ANNDATA_ZARR,
+                options: options.obsLocations,
+                coordinationValues: {
+                    obsType: baseFileDef.coordinationValues.obsType,
+                },
+            }] : []),
+        // obsSegmentations
+        ...(options.obsSegmentations ? [{
+                ...baseFileDef,
+                fileType: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR,
+                options: options.obsSegmentations,
+                coordinationValues: {
+                    obsType: baseFileDef.coordinationValues.obsType,
+                },
+            }] : []),
+        // obsEmbedding
+        // eslint-disable-next-line no-nested-ternary
+        ...(options.obsEmbedding ? (Array.isArray(options.obsEmbedding) ? options.obsEmbedding.map(oe => ({
+            // obsEmbedding was an array, process each element.
+            ...baseFileDef,
+            fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
+            options: {
+                path: oe.path,
+                dims: oe.dims,
+            },
+            coordinationValues: {
+                obsType: baseFileDef.coordinationValues.obsType,
+                // Move embedding type property out of options and into coordinationValues.
+                embeddingType: oe.embeddingType,
+            },
+        })) : [{
+                // obsEmbedding was an object.
+                ...baseFileDef,
+                fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
+                options: options.obsEmbedding,
+                coordinationValues: {
+                    obsType: baseFileDef.coordinationValues.obsType,
+                    embeddingType: baseFileDef.coordinationValues.embeddingType,
+                },
+            }]) : []),
+        // obsLabels
+        // eslint-disable-next-line no-nested-ternary
+        ...(options.obsLabels ? (Array.isArray(options.obsLabels) ? options.obsLabels.map(ol => ({
+            // obsLabels was an array, process each element.
+            ...baseFileDef,
+            fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
+            options: {
+                path: ol.path,
+            },
+            coordinationValues: {
+                obsType: baseFileDef.coordinationValues.obsType,
+                // Move obsLabels type property out of options and into coordinationValues.
+                obsLabelsType: ol.obsLabelsType,
+            },
+        })) : [{
+                // obsLabels was an object.
+                ...baseFileDef,
+                fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
+                options: options.obsLabels,
+                coordinationValues: {
+                    obsType: baseFileDef.coordinationValues.obsType,
+                    obsLabelsType: baseFileDef.coordinationValues.obsLabelsType,
+                },
+            }]) : []),
+        // featureLabels
+        // eslint-disable-next-line no-nested-ternary
+        ...(options.featureLabels ? (Array.isArray(options.featureLabels) ? options.featureLabels.map(fl => ({
+            // featureLabels was an array, process each element.
+            ...baseFileDef,
+            fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
+            options: {
+                path: fl.path,
+            },
+            coordinationValues: {
+                featureType: baseFileDef.coordinationValues.featureType,
+                // Move featureLabels type property out of options and into coordinationValues.
+                featureLabelsType: fl.featureLabelsType,
+            },
+        })) : [{
+                // featureLabels was an object.
+                ...baseFileDef,
+                fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
+                options: options.featureLabels,
+                coordinationValues: {
+                    featureType: baseFileDef.coordinationValues.featureType,
+                    featureLabelsType: baseFileDef.coordinationValues.featureLabelsType,
+                },
+            }]) : []),
+    ];
+}
+/**
+ * Built-in joint file type
+ * expansion functions.
+ */
+export const JOINT_FILE_TYPES = {
+    [FileType.ANNDATA_ZARR]: expandAnndataZarr,
+    [FileType.ANNDATA_CELLS_ZARR]: expandAnndataCellsZarr,
+    [FileType.ANNDATA_CELL_SETS_ZARR]: expandAnndataCellSetsZarr,
+    [FileType.ANNDATA_EXPRESSION_MATRIX_ZARR]: expandAnndataExpressionMatrixZarr,
+    [FileType.EXPRESSION_MATRIX_ZARR]: expandExpressionMatrixZarr,
+    [FileType.RASTER_JSON]: expandRasterJson,
+    [FileType.RASTER_OME_ZARR]: expandRasterOmeZarr,
+    [FileType.CELL_SETS_JSON]: expandCellSetsJson,
+    [FileType.CLUSTERS_JSON]: expandClustersJson,
+    [FileType.GENES_JSON]: expandGenesJson,
+    [FileType.CELLS_JSON]: expandCellsJson,
+    [FileType.MOLECULES_JSON]: expandMoleculesJson,
+};

package/dist/joint-file-types.test.js

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+import { FileType, FILE_TYPE_DATA_TYPE_MAPPING } from '@vitessce/constants-internal';
+import { JOINT_FILE_TYPES, expandAnndataZarr, } from './joint-file-types';
+describe('src/app/joint-file-types.js', () => {
+    describe('FileType-to-DataType mappings', () => {
+        it('every file type is mapped to either a data type or a joint file type expansion function', () => {
+            const fileTypes = Object.values(FileType).sort();
+            const mappedFileTypes = [
+                ...Object.keys(FILE_TYPE_DATA_TYPE_MAPPING),
+                ...Object.keys(JOINT_FILE_TYPES),
+            ].sort();
+            expect(fileTypes.length).toEqual(mappedFileTypes.length);
+            expect(fileTypes).toEqual(mappedFileTypes);
+        });
+    });
+    describe('expandAnndataZarr', () => {
+        it('fails to expand when there are no options', () => {
+            expect(() => expandAnndataZarr({
+                fileType: 'anndata.zarr',
+                url: 'http://localhost:8000/anndata.zarr',
+            })).toThrow();
+        });
+        it('expands when there is an obsEmbedding object', () => {
+            expect(expandAnndataZarr({
+                fileType: 'anndata.zarr',
+                url: 'http://localhost:8000/anndata.zarr',
+                options: {
+                    obsLabels: {
+                        path: 'obs/spot_name',
+                    },
+                    featureLabels: {
+                        path: 'var/gene_symbol',
+                    },
+                    obsEmbedding: {
+                        path: 'obsm/pca',
+                        dims: [2, 4],
+                    },
+                },
+                coordinationValues: {
+                    obsType: 'spot',
+                    featureType: 'transcript',
+                    obsLabelsType: 'spotName',
+                    featureLabelsType: 'geneSymbol',
+                    embeddingType: 'PCA',
+                },
+            })).toEqual([
+                {
+                    fileType: 'obsEmbedding.anndata.zarr',
+                    url: 'http://localhost:8000/anndata.zarr',
+                    options: {
+                        path: 'obsm/pca',
+                        dims: [2, 4],
+                    },
+                    coordinationValues: {
+                        obsType: 'spot',
+                        embeddingType: 'PCA',
+                    },
+                },
+                {
+                    fileType: 'obsLabels.anndata.zarr',
+                    url: 'http://localhost:8000/anndata.zarr',
+                    options: {
+                        path: 'obs/spot_name',
+                    },
+                    coordinationValues: {
+                        obsType: 'spot',
+                        obsLabelsType: 'spotName',
+                    },
+                },
+                {
+                    fileType: 'featureLabels.anndata.zarr',
+                    url: 'http://localhost:8000/anndata.zarr',
+                    options: {
+                        path: 'var/gene_symbol',
+                    },
+                    coordinationValues: {
+                        featureType: 'transcript',
+                        featureLabelsType: 'geneSymbol',
+                    },
+                },
+            ]);
+        });
+        it('expands when there is an obsEmbedding array of objects', () => {
+            expect(expandAnndataZarr({
+                fileType: 'anndata.zarr',
+                url: 'http://localhost:8000/anndata.zarr',
+                options: {
+                    obsLocations: {
+                        path: 'obsm/xy',
+                    },
+                    obsEmbedding: [
+                        {
+                            path: 'obsm/pca',
+                            dims: [2, 4],
+                            embeddingType: 'PCA',
+                        },
+                        {
+                            path: 'obsm/umap',
+                            embeddingType: 'UMAP',
+                        },
+                    ],
+                },
+            })).toEqual([
+                {
+                    fileType: 'obsLocations.anndata.zarr',
+                    url: 'http://localhost:8000/anndata.zarr',
+                    options: {
+                        path: 'obsm/xy',
+                    },
+                    coordinationValues: {
+                        obsType: 'cell',
+                    },
+                },
+                {
+                    fileType: 'obsEmbedding.anndata.zarr',
+                    url: 'http://localhost:8000/anndata.zarr',
+                    options: {
+                        path: 'obsm/pca',
+                        dims: [2, 4],
+                    },
+                    coordinationValues: {
+                        obsType: 'cell',
+                        embeddingType: 'PCA',
+                    },
+                },
+                {
+                    fileType: 'obsEmbedding.anndata.zarr',
+                    url: 'http://localhost:8000/anndata.zarr',
+                    options: {
+                        path: 'obsm/umap',
+                    },
+                    coordinationValues: {
+                        obsType: 'cell',
+                        embeddingType: 'UMAP',
+                    },
+                },
+            ]);
+        });
+    });
+});

package/dist/loader-registry.js

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+import { getLoaderClassesForPluginFileType, } from './plugins';
+// TODO(monorepo)
+/*
+import {
+  AnnDataSource,
+  ZarrDataSource,
+  JsonSource,
+  CsvSource,
+} from './data-sources';
+import JsonLoader from './json-loaders/JsonLoader';
+import ObsSetsJsonLoader from './json-loaders/ObsSetsJson';
+import ObsSegmentationsJsonLoader from './json-loaders/ObsSegmentationsJson';
+import OmeZarrLoader from './OmeZarrLoader';
+import AnnDataLoaders from './anndata-loaders';
+import GenomicProfilesZarrLoader from './GenomicProfilesZarrLoader';
+import CellsJsonAsObsLabelsLoader from './legacy-loaders/CellsJsonAsObsLabels';
+import CellsJsonAsObsEmbeddingLoader from './legacy-loaders/CellsJsonAsObsEmbedding';
+import CellsJsonAsObsSegmentationsLoader from './legacy-loaders/CellsJsonAsObsSegmentations';
+import ClustersJsonAsObsFeatureMatrixLoader from './legacy-loaders/ClustersJsonAsObsFeatureMatrix';
+import GenesJsonAsObsFeatureMatrixLoader from './legacy-loaders/GenesJsonAsObsFeatureMatrix';
+import RasterJsonAsImageLoader from './raster-json-loaders/RasterJsonAsImageLoader';
+import RasterJsonAsObsSegmentationsLoader from './raster-json-loaders/RasterJsonAsObsSegmentationsLoader';
+import MatrixZarrAsObsFeatureMatrixLoader from './matrix-loaders/MatrixZarrAsObsFeatureMatrix';
+import MoleculesJsonAsObsLocationsLoader from './legacy-loaders/MoleculesJsonAsObsLocations';
+import MoleculesJsonAsObsLabelsLoader from './legacy-loaders/MoleculesJsonAsObsLabels';
+import CellsJsonAsObsLocationsLoader from './legacy-loaders/CellsJsonAsObsLocations';
+import ObsEmbeddingCsvLoader from './csv-loaders/ObsEmbeddingCsv';
+import ObsLocationsCsvLoader from './csv-loaders/ObsLocationsCsv';
+import ObsLabelsCsvLoader from './csv-loaders/ObsLabelsCsv';
+import FeatureLabelsCsvLoader from './csv-loaders/FeatureLabelsCsv';
+import ObsFeatureMatrixCsvLoader from './csv-loaders/ObsFeatureMatrixCsv';
+import ObsSetsCsvLoader from './csv-loaders/ObsSetsCsv';
+*/
+export const fileTypeToLoaderAndSource = {
+// TODO(monorepo)
+/*
+[FileType.OBS_EMBEDDING_CSV]: [CsvSource, ObsEmbeddingCsvLoader],
+[FileType.OBS_LOCATIONS_CSV]: [CsvSource, ObsLocationsCsvLoader],
+[FileType.OBS_LABELS_CSV]: [CsvSource, ObsLabelsCsvLoader],
+[FileType.FEATURE_LABELS_CSV]: [CsvSource, FeatureLabelsCsvLoader],
+[FileType.OBS_FEATURE_MATRIX_CSV]: [CsvSource, ObsFeatureMatrixCsvLoader],
+[FileType.OBS_SEGMENTATIONS_JSON]: [JsonSource, ObsSegmentationsJsonLoader],
+[FileType.OBS_SETS_CSV]: [CsvSource, ObsSetsCsvLoader],
+[FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsFeatureMatrixAnndataLoader,
+],
+[FileType.OBS_SETS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsSetsAnndataLoader,
+],
+[FileType.OBS_EMBEDDING_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsEmbeddingAnndataLoader,
+],
+[FileType.OBS_LOCATIONS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsLocationsAnndataLoader,
+],
+[FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsSegmentationsAnndataLoader,
+],
+[FileType.OBS_LABELS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.ObsLabelsAnndataLoader,
+],
+[FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR]: [
+  ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader,
+],
+[FileType.FEATURE_LABELS_ANNDATA_ZARR]: [
+  AnnDataSource, AnnDataLoaders.FeatureLabelsAnndataLoader,
+],
+[FileType.IMAGE_OME_ZARR]: [ZarrDataSource, OmeZarrLoader],
+[FileType.IMAGE_RASTER_JSON]: [JsonSource, RasterJsonAsImageLoader],
+[FileType.OBS_SEGMENTATIONS_RASTER_JSON]: [JsonSource, RasterJsonAsObsSegmentationsLoader],
+[FileType.OBS_SETS_JSON]: [JsonSource, ObsSetsJsonLoader],
+[FileType.OBS_SETS_CELL_SETS_JSON]: [JsonSource, ObsSetsJsonLoader],
+[FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON]: [JsonSource, ClustersJsonAsObsFeatureMatrixLoader],
+[FileType.OBS_FEATURE_MATRIX_GENES_JSON]: [JsonSource, GenesJsonAsObsFeatureMatrixLoader],
+[FileType.OBS_LABELS_CELLS_JSON]: [JsonSource, CellsJsonAsObsLabelsLoader],
+[FileType.OBS_EMBEDDING_CELLS_JSON]: [JsonSource, CellsJsonAsObsEmbeddingLoader],
+[FileType.OBS_LOCATIONS_CELLS_JSON]: [JsonSource, CellsJsonAsObsLocationsLoader],
+[FileType.OBS_SEGMENTATIONS_CELLS_JSON]: [JsonSource, CellsJsonAsObsSegmentationsLoader],
+[FileType.OBS_LOCATIONS_MOLECULES_JSON]: [JsonSource, MoleculesJsonAsObsLocationsLoader],
+[FileType.OBS_LABELS_MOLECULES_JSON]: [JsonSource, MoleculesJsonAsObsLabelsLoader],
+// Old mappings:
+[FileType.NEIGHBORHOODS_JSON]: [JsonSource, JsonLoader],
+[FileType.GENOMIC_PROFILES_ZARR]: [ZarrDataSource, GenomicProfilesZarrLoader],
+*/
+};
+export function getSourceAndLoaderFromFileType(type) {
+    if (fileTypeToLoaderAndSource[type]) {
+        return fileTypeToLoaderAndSource[type];
+    }
+    const pluginFileType = getLoaderClassesForPluginFileType(type);
+    if (pluginFileType) {
+        return pluginFileType;
+    }
+    // Fallback to JSON.
+    // TODO(monorepo)
+    // return [JsonSource, JsonLoader];
+    return [null, null];
+}

package/dist/plugins.js

@@ -0,0 +1,154 @@
+import { fromEntries } from '@vitessce/utils';
+import { FileType, CoordinationType, FILE_TYPE_DATA_TYPE_MAPPING, COMPONENT_COORDINATION_TYPES, DEFAULT_COORDINATION_VALUES, } from '@vitessce/constants-internal';
+import { JOINT_FILE_TYPES } from './joint-file-types';
+const PLUGINS_KEY = '__VITESSCE_PLUGINS__';
+const PLUGIN_VIEW_TYPES_KEY = 'viewTypes';
+const PLUGIN_COORDINATION_TYPES_KEY = 'coordinationTypes';
+const PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY = 'coordinationTypesPerView';
+const PLUGIN_FILE_TYPES_KEY = 'fileTypes';
+const PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY = 'fileTypeDataTypeMapping';
+const PLUGIN_JOINT_FILE_TYPES_KEY = 'jointFileTypes';
+window[PLUGINS_KEY] = {};
+const PLUGINS = window[PLUGINS_KEY];
+// Reference: https://github.com/higlass/higlass-register/blob/master/src/index.js
+PLUGINS[PLUGIN_VIEW_TYPES_KEY] = PLUGINS[PLUGIN_VIEW_TYPES_KEY] || {};
+PLUGINS[PLUGIN_COORDINATION_TYPES_KEY] = PLUGINS[PLUGIN_COORDINATION_TYPES_KEY] || {};
+PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY] = (PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY] || {});
+PLUGINS[PLUGIN_FILE_TYPES_KEY] = PLUGINS[PLUGIN_FILE_TYPES_KEY] || {};
+PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY] = (PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY] || {});
+PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY] = PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY] || {};
+/**
+ * Register a new coordination type.
+ * @param {string} typeName Name for the new coordination type.
+ * @param {*} defaultValue A default value for the coordination type.
+ */
+export function registerPluginCoordinationType(typeName, defaultValue) {
+    PLUGINS[PLUGIN_COORDINATION_TYPES_KEY][typeName] = defaultValue;
+}
+/**
+ * Register a new view type.
+ * @param {string} viewType A name
+ * @param {function} viewSubscriberReactComponent A react component.
+ * @param {string[]} coordinationTypes A list of coordination types that this view supports.
+ */
+export function registerPluginViewType(viewType, viewSubscriberReactComponent, coordinationTypes) {
+    PLUGINS[PLUGIN_VIEW_TYPES_KEY][viewType] = viewSubscriberReactComponent;
+    // Register the supported coordination types.
+    const pluginTypesPerView = PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY];
+    if (Array.isArray(pluginTypesPerView[viewType])) {
+        coordinationTypes.forEach((coordinationType) => {
+            if (!pluginTypesPerView[viewType].includes(coordinationType)) {
+                pluginTypesPerView[viewType].push(coordinationType);
+            }
+        });
+    }
+    else {
+        pluginTypesPerView[viewType] = coordinationTypes;
+    }
+}
+/**
+ * Register a new file type.
+ * @param {string} fileTypeName Name for the new file type.
+ * @param {string} dataTypeName Name for the data type associated with the file type.
+ * @param {class} dataSourceClass Data source class definition.
+ * @param {class} dataLoaderClass Data loader class definition.
+ */
+export function registerPluginFileType(
+// eslint-disable-next-line no-unused-vars
+fileTypeName, dataTypeName, dataLoaderClass, dataSourceClass) {
+    PLUGINS[PLUGIN_FILE_TYPES_KEY][fileTypeName] = [dataSourceClass, dataLoaderClass];
+    PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY][fileTypeName] = dataTypeName;
+}
+/**
+ * Register a new joint file type.
+ * @param {string} fileTypeName Name for the new file type.
+ * @param {function} expansionFunction The joint file type expansion function.
+ * Should take in a single file definition and return an array of
+ * file definitions with valid atomic fileType values.
+ */
+export function registerPluginJointFileType(
+// eslint-disable-next-line no-unused-vars
+fileTypeName, expansionFunction) {
+    PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY][fileTypeName] = expansionFunction;
+}
+// Plugin getter functions.
+export function getPluginViewTypes() {
+    return Object.keys(PLUGINS[PLUGIN_VIEW_TYPES_KEY]);
+}
+export function getPluginViewType(viewType) {
+    return PLUGINS[PLUGIN_VIEW_TYPES_KEY][viewType];
+}
+export function getPluginCoordinationTypes() {
+    return Object.keys(PLUGINS[PLUGIN_COORDINATION_TYPES_KEY]);
+}
+export function getPluginCoordinationTypeDefaults() {
+    return PLUGINS[PLUGIN_COORDINATION_TYPES_KEY];
+}
+export function getPluginCoordinationTypesForViewType(viewType) {
+    if (Array.isArray(PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY][viewType])) {
+        return PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY][viewType];
+    }
+    return [];
+}
+export function getPluginFileTypes() {
+    return Object.keys(PLUGINS[PLUGIN_FILE_TYPES_KEY]);
+}
+export function getPluginConvenienceFileTypes() {
+    return Object.keys(PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY]);
+}
+export function getDataTypeForPluginFileType(fileType) {
+    return PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY][fileType];
+}
+export function getLoaderClassesForPluginFileType(fileType) {
+    return PLUGINS[PLUGIN_FILE_TYPES_KEY][fileType];
+}
+export function getExpansionFunctionForPluginConvenienceFileType(fileType) {
+    return PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY][fileType];
+}
+// Getters that depend on plugins.
+export function getFileTypes() {
+    return [
+        ...Object.values(FileType),
+        ...getPluginFileTypes(),
+    ];
+}
+export function getCoordinationTypes() {
+    return [
+        ...Object.values(CoordinationType),
+        ...getPluginCoordinationTypes(),
+    ];
+}
+// Need to do this in a function since the plugin coordination
+// types are dynamic.
+export function getDefaultCoordinationValues() {
+    return {
+        ...DEFAULT_COORDINATION_VALUES,
+        ...getPluginCoordinationTypeDefaults(),
+    };
+}
+// Need to do this in a function since the plugin coordination
+// types are dynamic.
+export function getComponentCoordinationTypes() {
+    return {
+        ...COMPONENT_COORDINATION_TYPES,
+        ...fromEntries(getPluginViewTypes().map(viewType => ([
+            viewType,
+            getPluginCoordinationTypesForViewType(viewType),
+        ]))),
+    };
+}
+export function getFileTypeDataTypeMapping() {
+    return {
+        ...FILE_TYPE_DATA_TYPE_MAPPING,
+        ...fromEntries(getPluginFileTypes().map(fileType => ([
+            fileType,
+            getDataTypeForPluginFileType(fileType),
+        ]))),
+    };
+}
+export function getJointFileTypes() {
+    return {
+        ...JOINT_FILE_TYPES,
+        ...PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY],
+    };
+}

package/dist/plugins.test.fixtures.js

@@ -0,0 +1,76 @@
+export const convenienceFileDefsCollapsed = {
+    version: '1.0.15',
+    name: 'My config name',
+    description: 'My config description',
+    initStrategy: 'auto',
+    datasets: [
+        {
+            files: [
+                {
+                    fileType: 'anndata.convenience.zarr',
+                    url: 'http://localhost:8000/my_anndata.zarr',
+                    options: {
+                        cells: {
+                            xy: 'obsm/centroids',
+                        },
+                        cellSets: [
+                            {
+                                groupName: 'Leiden',
+                                setName: 'obs/leiden',
+                            },
+                        ],
+                    },
+                },
+            ],
+            name: 'A',
+            uid: 'A',
+        },
+    ],
+    layout: [],
+};
+export function pluginExpandAnnDataConvenience(fileDef) {
+    return [
+        {
+            fileType: 'anndata-cells.zarr',
+            url: fileDef.url,
+            options: fileDef.options.cells,
+        },
+        {
+            fileType: 'anndata-cell-sets.zarr',
+            url: fileDef.url,
+            options: fileDef.options.cellSets,
+        },
+    ];
+}
+export const convenienceFileDefsExpanded = {
+    version: '1.0.15',
+    name: 'My config name',
+    description: 'My config description',
+    initStrategy: 'auto',
+    datasets: [
+        {
+            files: [
+                {
+                    fileType: 'anndata-cells.zarr',
+                    url: 'http://localhost:8000/my_anndata.zarr',
+                    options: {
+                        xy: 'obsm/centroids',
+                    },
+                },
+                {
+                    fileType: 'anndata-cell-sets.zarr',
+                    url: 'http://localhost:8000/my_anndata.zarr',
+                    options: [
+                        {
+                            groupName: 'Leiden',
+                            setName: 'obs/leiden',
+                        },
+                    ],
+                },
+            ],
+            name: 'A',
+            uid: 'A',
+        },
+    ],
+    layout: [],
+};

package/dist/plugins.test.js

@@ -0,0 +1,30 @@
+/* eslint-disable camelcase */
+import { registerPluginFileType, registerPluginJointFileType, getFileTypeDataTypeMapping, getJointFileTypes, } from './plugins';
+import { convenienceFileDefsCollapsed, convenienceFileDefsExpanded, pluginExpandAnnDataConvenience, } from './plugins.test.fixtures';
+import { initialize, } from './view-config-utils';
+describe('src/app/plugins.js', () => {
+    describe('getFileTypeDataTypeMapping', () => {
+        it('returns the correct data type for built-in file types', () => {
+            const dataType = getFileTypeDataTypeMapping()['image.raster.json'];
+            expect(dataType).toEqual('image');
+        });
+        it('returns the correct data type for plugin file types', () => {
+            registerPluginFileType('plugin-cells.json', 'cells', null, null);
+            const dataType = getFileTypeDataTypeMapping()['plugin-cells.json'];
+            expect(dataType).toEqual('cells');
+        });
+    });
+    describe('convenience file types', () => {
+        it('registers plugin convenience file types', () => {
+            registerPluginJointFileType('anndata.convenience.zarr', pluginExpandAnnDataConvenience);
+            const expansionFuncs = getJointFileTypes();
+            expect(Object.keys(expansionFuncs).includes('anndata.convenience.zarr')).toBeTruthy();
+            expect(typeof expansionFuncs['anndata.convenience.zarr']).toEqual('function');
+        });
+        it('uses plugin convenience file types in view config initialization', () => {
+            registerPluginJointFileType('anndata.convenience.zarr', pluginExpandAnnDataConvenience);
+            expect(initialize(convenienceFileDefsCollapsed).datasets)
+                .toEqual(convenienceFileDefsExpanded.datasets);
+        });
+    });
+});

package/dist/schemas/PrettyJsonSchema.js

@@ -0,0 +1,34 @@
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import React from 'react';
+import yaml from 'js-yaml'; // eslint-disable-line import/no-extraneous-dependencies
+// This should only be used by docz, and should not be part of the app build.
+function abbreviateType(yamlString) {
+    return yamlString.replace(/:\s+type: (\w+)/g, ' ($1):');
+}
+function abbreviateRef(yamlString) {
+    return yamlString.replace(/:\s+\$ref: '#\/definitions\/(\w+)'/g, ' ($1)');
+}
+function stripAddProps(yamlString) {
+    // This should be the default in our schemas, but we don't need it in the docs.
+    return yamlString.replace(/\s+additionalProperties: false/g, '');
+}
+function valuesAre(yamlString) {
+    return yamlString.replace(/patternProperties:\s+\./g, 'Object values are');
+}
+function hasProperties(yamlString) {
+    return yamlString.replace(/\.:\s+properties:/g, 'Each value has these properties:');
+}
+function pretty(title, obj) {
+    // This is entirely ad-hoc:
+    // It woks well for our schema, but no assertion that it should work for anyone else.
+    if (!obj)
+        return '';
+    return (_jsxs(_Fragment, { children: [_jsx("h3", { children: title }), _jsx("pre", { children: hasProperties(valuesAre(stripAddProps(abbreviateRef(abbreviateType(yaml.safeDump(obj)))))) })] }));
+}
+export default function PrettyJsonSchema(props) {
+    const { children } = props;
+    const { definitions, patternProperties, properties } = children;
+    // We could grab the title as well, but when we output an <h2> it is not anchored;
+    // better to put the section headers in MD.
+    return (_jsxs("blockquote", { children: [pretty('Definitions', definitions), pretty('Properties', patternProperties), pretty('Properties', properties)] }));
+}