@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

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

@@ -0,0 +1,412 @@
+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/src/joint-file-types.js

@@ -0,0 +1,171 @@
+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,
+};