@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

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

@@ -1,278 +0,0 @@
-import { FileType } from '@vitessce/constants-internal';
-import { validateOptions, emptySchema, } from './file-options-schemas';
-import { cellsJsonSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, } from './file-options-schemas-legacy';
-export function expandMoleculesJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'molecule',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_LOCATIONS_MOLECULES_JSON,
-        },
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_LABELS_MOLECULES_JSON,
-        },
-    ];
-}
-export function expandExpressionMatrixZarr(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR,
-        },
-    ];
-}
-export function expandRasterJson(fileDef) {
-    // Validation already happens in the RasterJsonLoader.
-    const baseFileDef = { ...fileDef };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.IMAGE_RASTER_JSON,
-        },
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SEGMENTATIONS_RASTER_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues?.obsType || 'cell',
-            },
-        },
-    ];
-}
-export function expandRasterOmeZarr(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = { ...fileDef };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.IMAGE_OME_ZARR,
-        },
-    ];
-}
-export function expandCellSetsJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = { ...fileDef };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SETS_CELL_SETS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues?.obsType || 'cell',
-            },
-        },
-    ];
-}
-export function expandCellsJson(fileDef) {
-    validateOptions(cellsJsonSchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-        },
-    };
-    delete baseFileDef.type;
-    delete baseFileDef.options;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SEGMENTATIONS_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-            },
-        },
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_LOCATIONS_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-            },
-        },
-        ...(fileDef.options?.embeddingTypes ? fileDef.options.embeddingTypes.map(et => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_EMBEDDING_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                embeddingType: et,
-            },
-        })) : []),
-        ...(fileDef.options?.obsLabelsTypes ? fileDef.options.obsLabelsTypes.map(key => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_LABELS_CELLS_JSON,
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                obsLabelsType: key,
-            },
-        })) : []),
-    ];
-}
-export function expandClustersJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON,
-        },
-    ];
-}
-export function expandGenesJson(fileDef) {
-    validateOptions(emptySchema, fileDef.options);
-    const baseFileDef = {
-        ...fileDef,
-        coordinationValues: {
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-    delete baseFileDef.type;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_GENES_JSON,
-        },
-    ];
-}
-function getAnndataBaseFileDef(fileDef) {
-    return {
-        url: fileDef.url,
-        requestInit: fileDef.requestInit,
-        coordinationValues: {
-            ...fileDef.coordinationValues,
-            obsType: fileDef.coordinationValues?.obsType || 'cell',
-            featureType: fileDef.coordinationValues?.featureType || 'gene',
-            featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-        },
-    };
-}
-export function expandAnndataCellsZarr(fileDef) {
-    validateOptions(anndataCellsZarrSchema, fileDef.options);
-    const baseFileDef = getAnndataBaseFileDef(fileDef);
-    const { options = {} } = fileDef;
-    const embeddingTypes = options.mappings ? Object.keys(options.mappings) : [];
-    const obsLabelsTypes = options.factors ? options.factors : [];
-    return [
-        ...(options.poly ? [{
-                ...baseFileDef,
-                fileType: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR,
-                options: {
-                    path: options.poly,
-                },
-                coordinationValues: {
-                    obsType: baseFileDef.coordinationValues.obsType,
-                },
-            }] : []),
-        ...(options.xy ? [{
-                ...baseFileDef,
-                fileType: FileType.OBS_LOCATIONS_ANNDATA_ZARR,
-                options: {
-                    path: options.xy,
-                },
-                coordinationValues: {
-                    obsType: baseFileDef.coordinationValues.obsType,
-                },
-            }] : []),
-        ...embeddingTypes.map(et => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
-            options: {
-                path: options.mappings[et].key,
-                dims: options.mappings[et].dims,
-            },
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                embeddingType: et,
-            },
-        })),
-        ...obsLabelsTypes.map(olt => ({
-            ...baseFileDef,
-            fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
-            options: {
-                path: olt,
-            },
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                obsLabelsType: olt.split('/').at(-1),
-            },
-        })),
-    ];
-}
-export function expandAnndataCellSetsZarr(fileDef) {
-    validateOptions(anndataCellSetsZarrSchema, fileDef.options);
-    const baseFileDef = getAnndataBaseFileDef(fileDef);
-    const { options = [] } = fileDef;
-    return [
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_SETS_ANNDATA_ZARR,
-            options: options.map(option => ({
-                name: option.groupName,
-                path: option.setName,
-                scorePath: option.scoreName,
-            })),
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-            },
-        },
-    ];
-}
-export function expandAnndataExpressionMatrixZarr(fileDef) {
-    validateOptions(anndataExpressionMatrixZarrSchema, fileDef.options);
-    const baseFileDef = getAnndataBaseFileDef(fileDef);
-    const { options = {} } = fileDef;
-    return [
-        ...(options.geneAlias ? [{
-                ...baseFileDef,
-                fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
-                options: {
-                    path: options.geneAlias,
-                },
-                coordinationValues: {
-                    featureType: baseFileDef.coordinationValues.featureType,
-                },
-            }] : []),
-        {
-            ...baseFileDef,
-            fileType: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR,
-            options: {
-                path: options.matrix,
-                featureFilterPath: options.geneFilter,
-                initialFeatureFilterPath: options.matrixGeneFilter,
-            },
-            coordinationValues: {
-                obsType: baseFileDef.coordinationValues.obsType,
-                featureType: baseFileDef.coordinationValues.featureType,
-                featureValueType: baseFileDef.coordinationValues.featureValueType,
-            },
-        },
-    ];
-}

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

@@ -1,400 +0,0 @@
-import { expandExpressionMatrixZarr, expandRasterJson, expandRasterOmeZarr, expandGenesJson, expandClustersJson, expandCellsJson, expandMoleculesJson, expandAnndataCellsZarr, expandAnndataCellSetsZarr, expandAnndataExpressionMatrixZarr, } from './joint-file-types-legacy';
-describe('src/app/joint-file-types-legacy.js', () => {
-    describe('expandExpressionMatrixZarr', () => {
-        it('expands expression-matrix.zarr', () => {
-            expect(expandExpressionMatrixZarr({
-                fileType: 'expression-matrix.zarr',
-                url: 'http://localhost:8000/expression-matrix.zarr',
-            })).toEqual([
-                {
-                    fileType: 'obsFeatureMatrix.expression-matrix.zarr',
-                    url: 'http://localhost:8000/expression-matrix.zarr',
-                    coordinationValues: {
-                        obsType: 'cell',
-                        featureType: 'gene',
-                        featureValueType: 'expression',
-                    },
-                },
-            ]);
-        });
-    });
-    describe('expandRasterJson', () => {
-        it('expands raster.json', () => {
-            expect(expandRasterJson({
-                fileType: 'raster.json',
-                url: 'http://localhost:8000/raster.json',
-            })).toEqual([
-                {
-                    fileType: 'image.raster.json',
-                    url: 'http://localhost:8000/raster.json',
-                },
-                {
-                    fileType: 'obsSegmentations.raster.json',
-                    url: 'http://localhost:8000/raster.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-            ]);
-        });
-    });
-    describe('expandRasterOmeZarr', () => {
-        it('expands raster.ome-zarr', () => {
-            expect(expandRasterOmeZarr({
-                fileType: 'raster.ome-zarr',
-                url: 'http://localhost:8000/raster.zarr',
-            })).toEqual([
-                {
-                    fileType: 'image.ome-zarr',
-                    url: 'http://localhost:8000/raster.zarr',
-                },
-            ]);
-        });
-    });
-    describe('expandClustersJson', () => {
-        it('expands clusters.json', () => {
-            expect(expandClustersJson({
-                fileType: 'clusters.json',
-                url: 'http://localhost:8000/clusters.json',
-            })).toEqual([
-                {
-                    fileType: 'obsFeatureMatrix.clusters.json',
-                    url: 'http://localhost:8000/clusters.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                        featureType: 'gene',
-                        featureValueType: 'expression',
-                    },
-                },
-            ]);
-        });
-    });
-    describe('expandGenesJson', () => {
-        it('expands', () => {
-            expect(expandGenesJson({
-                fileType: 'genes.json',
-                url: 'http://localhost:8000/genes.json',
-            })).toEqual([
-                {
-                    fileType: 'obsFeatureMatrix.genes.json',
-                    url: 'http://localhost:8000/genes.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                        featureType: 'gene',
-                        featureValueType: 'expression',
-                    },
-                },
-            ]);
-        });
-    });
-    describe('expandMoleculesJson', () => {
-        it('expands when there are no options', () => {
-            expect(expandMoleculesJson({
-                fileType: 'molecules.json',
-                url: 'http://localhost:8000/molecules.json',
-            })).toEqual([
-                {
-                    fileType: 'obsLocations.molecules.json',
-                    url: 'http://localhost:8000/molecules.json',
-                    coordinationValues: {
-                        obsType: 'molecule',
-                    },
-                },
-                {
-                    fileType: 'obsLabels.molecules.json',
-                    url: 'http://localhost:8000/molecules.json',
-                    coordinationValues: {
-                        obsType: 'molecule',
-                    },
-                },
-            ]);
-        });
-    });
-    describe('expandCellsJson', () => {
-        it('expands when there are no options', () => {
-            expect(expandCellsJson({
-                fileType: 'cells.json',
-                url: 'http://localhost:8000/cells.json',
-            })).toEqual([
-                {
-                    fileType: 'obsSegmentations.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-                {
-                    fileType: 'obsLocations.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-            ]);
-        });
-        it('expands when there is an array of embedding types', () => {
-            expect(expandCellsJson({
-                fileType: 'cells.json',
-                url: 'http://localhost:8000/cells.json',
-                options: {
-                    embeddingTypes: ['UMAP', 't-SNE'],
-                    obsLabelsTypes: ['cluster', 'subcluster'],
-                },
-            })).toEqual([
-                {
-                    fileType: 'obsSegmentations.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-                {
-                    fileType: 'obsLocations.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-                {
-                    fileType: 'obsEmbedding.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                        embeddingType: 'UMAP',
-                    },
-                },
-                {
-                    fileType: 'obsEmbedding.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                        embeddingType: 't-SNE',
-                    },
-                },
-                {
-                    fileType: 'obsLabels.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                        obsLabelsType: 'cluster',
-                    },
-                },
-                {
-                    fileType: 'obsLabels.cells.json',
-                    url: 'http://localhost:8000/cells.json',
-                    coordinationValues: {
-                        obsType: 'cell',
-                        obsLabelsType: 'subcluster',
-                    },
-                },
-            ]);
-        });
-    });
-    // cells
-    describe('expandAnndataCellsZarr', () => {
-        it('fails to expand when there are no options', () => {
-            expect(() => expandAnndataCellsZarr({
-                fileType: 'anndata-cells.zarr',
-                url: 'http://localhost:8000/anndata.zarr',
-            })).toThrow();
-        });
-        it('expands when there are lots of options', () => {
-            expect(expandAnndataCellsZarr({
-                fileType: 'anndata-cells.zarr',
-                url: 'http://localhost:8000/anndata.zarr',
-                options: {
-                    mappings: {
-                        't-SNE': {
-                            key: 'obsm/tsne',
-                        },
-                        PCA: {
-                            dims: [2, 3],
-                            key: 'obsm/pca',
-                        },
-                    },
-                    xy: 'obsm/locations',
-                    poly: 'obsm/segmentations',
-                    factors: [
-                        'obs/cluster',
-                        'obs/subcluster',
-                    ],
-                },
-            })).toEqual([
-                {
-                    fileType: 'obsSegmentations.anndata.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        path: 'obsm/segmentations',
-                    },
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-                {
-                    fileType: 'obsLocations.anndata.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        path: 'obsm/locations',
-                    },
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-                {
-                    fileType: 'obsEmbedding.anndata.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        path: 'obsm/tsne',
-                    },
-                    coordinationValues: {
-                        obsType: 'cell',
-                        embeddingType: 't-SNE',
-                    },
-                },
-                {
-                    fileType: 'obsEmbedding.anndata.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        path: 'obsm/pca',
-                        dims: [2, 3],
-                    },
-                    coordinationValues: {
-                        obsType: 'cell',
-                        embeddingType: 'PCA',
-                    },
-                },
-                {
-                    fileType: 'obsLabels.anndata.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        path: 'obs/cluster',
-                    },
-                    coordinationValues: {
-                        obsType: 'cell',
-                        obsLabelsType: 'cluster',
-                    },
-                },
-                {
-                    fileType: 'obsLabels.anndata.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        path: 'obs/subcluster',
-                    },
-                    coordinationValues: {
-                        obsType: 'cell',
-                        obsLabelsType: 'subcluster',
-                    },
-                },
-            ]);
-        });
-    });
-    // cell sets
-    describe('expandAnndataCellSetsZarr', () => {
-        it('expands both flat and hierarchical cell sets', () => {
-            expect(expandAnndataCellSetsZarr({
-                fileType: 'anndata-cell-sets.zarr',
-                url: 'http://localhost:8000/anndata.zarr',
-                options: [
-                    {
-                        groupName: 'Leiden clustering',
-                        setName: 'obs/leiden',
-                    },
-                    {
-                        groupName: 'Predicted cell types',
-                        setName: 'obs/pred_types',
-                        scoreName: 'obs/pred_scores',
-                    },
-                    {
-                        groupName: 'Cell type annotations',
-                        setName: ['obs/l1', 'obs/l2', 'obs/l3'],
-                    },
-                ],
-            })).toEqual([
-                {
-                    fileType: 'obsSets.anndata.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: [
-                        {
-                            name: 'Leiden clustering',
-                            path: 'obs/leiden',
-                        },
-                        {
-                            name: 'Predicted cell types',
-                            path: 'obs/pred_types',
-                            scorePath: 'obs/pred_scores',
-                        },
-                        {
-                            name: 'Cell type annotations',
-                            path: ['obs/l1', 'obs/l2', 'obs/l3'],
-                        },
-                    ],
-                    coordinationValues: {
-                        obsType: 'cell',
-                    },
-                },
-            ]);
-        });
-        // expression-matrix
-        describe('expandAnndataExpressionMatrixZarr', () => {
-            it('expands when there are no options', () => {
-                expect(expandAnndataExpressionMatrixZarr({
-                    fileType: 'anndata-expression-matrix.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        matrix: 'X',
-                    },
-                })).toEqual([
-                    {
-                        fileType: 'obsFeatureMatrix.anndata.zarr',
-                        url: 'http://localhost:8000/anndata.zarr',
-                        options: {
-                            path: 'X',
-                        },
-                        coordinationValues: {
-                            obsType: 'cell',
-                            featureType: 'gene',
-                            featureValueType: 'expression',
-                        },
-                    },
-                ]);
-            });
-            it('expands when there are lots of options', () => {
-                expect(expandAnndataExpressionMatrixZarr({
-                    fileType: 'anndata-expression-matrix.zarr',
-                    url: 'http://localhost:8000/anndata.zarr',
-                    options: {
-                        matrix: 'obsm/hvg_subset',
-                        geneAlias: 'var/gene_symbol',
-                        geneFilter: 'var/in_hvg_subset',
-                        matrixGeneFilter: 'var/highly_variable',
-                    },
-                })).toEqual([
-                    {
-                        fileType: 'featureLabels.anndata.zarr',
-                        url: 'http://localhost:8000/anndata.zarr',
-                        options: {
-                            path: 'var/gene_symbol',
-                        },
-                        coordinationValues: {
-                            featureType: 'gene',
-                        },
-                    },
-                    {
-                        fileType: 'obsFeatureMatrix.anndata.zarr',
-                        url: 'http://localhost:8000/anndata.zarr',
-                        options: {
-                            path: 'obsm/hvg_subset',
-                            featureFilterPath: 'var/in_hvg_subset',
-                            initialFeatureFilterPath: 'var/highly_variable',
-                        },
-                        coordinationValues: {
-                            obsType: 'cell',
-                            featureType: 'gene',
-                            featureValueType: 'expression',
-                        },
-                    },
-                ]);
-            });
-        });
-    });
-});