@vitessce/all 2.0.3-beta.0 → 3.0.0

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

@@ -0,0 +1,266 @@
+import { FileType } from '@vitessce/constants-internal';
+export function expandMoleculesJson(fileDef) {
+    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) {
+    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) {
+    const baseFileDef = { ...fileDef };
+    delete baseFileDef.type;
+    return [
+        {
+            ...baseFileDef,
+            fileType: FileType.IMAGE_OME_ZARR,
+        },
+    ];
+}
+export function expandCellSetsJson(fileDef) {
+    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) {
+    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) {
+    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) {
+    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) {
+    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) {
+    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) {
+    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-tsc/joint-file-types-legacy.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=joint-file-types-legacy.test.d.ts.map

package/dist-tsc/joint-file-types-legacy.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"joint-file-types-legacy.test.d.ts","sourceRoot":"","sources":["../src/joint-file-types-legacy.test.ts"],"names":[],"mappings":""}

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

@@ -0,0 +1,401 @@
+import { describe, expect, it } from 'vitest';
+import { expandExpressionMatrixZarr, expandRasterJson, expandRasterOmeZarr, expandGenesJson, expandClustersJson, expandCellsJson, expandMoleculesJson, expandAnndataCellsZarr, expandAnndataCellSetsZarr, expandAnndataExpressionMatrixZarr, } from './joint-file-types-legacy.js';
+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',
+            })).toEqual([]);
+        });
+        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',
+                        },
+                    },
+                ]);
+            });
+        });
+    });
+});

package/dist-tsc/joint-file-types.d.ts

@@ -0,0 +1,4 @@
+import type { z } from 'zod';
+import type { latestFileDefSchema } from '@vitessce/schemas';
+export declare function expandAnndataZarr(fileDef: z.infer<typeof latestFileDefSchema>): any[];
+//# sourceMappingURL=joint-file-types.d.ts.map

package/dist-tsc/joint-file-types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"joint-file-types.d.ts","sourceRoot":"","sources":["../src/joint-file-types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAS7D,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,SAmI7E"}