@vitessce/vit-s 2.0.2 → 2.0.3

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',
-                        },
-                    },
-                ]);
-            });
-        });
-    });
-});

package/dist/joint-file-types.js

@@ -1,148 +0,0 @@
-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

@@ -1,139 +0,0 @@
-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',
-                    },
-                },
-            ]);
-        });
-    });
-});