@vitessce/all 2.0.3 → 3.0.1

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

@@ -0,0 +1,413 @@
+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/src/joint-file-types-legacy.ts

@@ -0,0 +1,284 @@
+import type { z } from 'zod';
+import type { latestFileDefSchema } from '@vitessce/schemas';
+import { FileType } from '@vitessce/constants-internal';
+
+type legacyFileDefSchema = z.infer<typeof latestFileDefSchema> & {
+  type?: string;
+};
+
+export function expandMoleculesJson(fileDef: legacyFileDefSchema) {
+  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: legacyFileDefSchema) {
+  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: legacyFileDefSchema) {
+  // 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: legacyFileDefSchema) {
+  const baseFileDef = { ...fileDef };
+  delete baseFileDef.type;
+  return [
+    {
+      ...baseFileDef,
+      fileType: FileType.IMAGE_OME_ZARR,
+    },
+  ];
+}
+
+export function expandCellSetsJson(fileDef: legacyFileDefSchema) {
+  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: legacyFileDefSchema) {
+  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: string) => ({
+      ...baseFileDef,
+      fileType: FileType.OBS_EMBEDDING_CELLS_JSON,
+      coordinationValues: {
+        obsType: baseFileDef.coordinationValues.obsType,
+        embeddingType: et,
+      },
+    })) : []),
+    ...(fileDef.options?.obsLabelsTypes ? fileDef.options.obsLabelsTypes.map((key: string) => ({
+      ...baseFileDef,
+      fileType: FileType.OBS_LABELS_CELLS_JSON,
+      coordinationValues: {
+        obsType: baseFileDef.coordinationValues.obsType,
+        obsLabelsType: key,
+      },
+    })) : []),
+  ];
+}
+
+export function expandClustersJson(fileDef: legacyFileDefSchema) {
+  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: legacyFileDefSchema) {
+  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: legacyFileDefSchema) {
+  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: legacyFileDefSchema) {
+  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: string) => ({
+      ...baseFileDef,
+      fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
+      options: {
+        path: olt,
+      },
+      coordinationValues: {
+        obsType: baseFileDef.coordinationValues.obsType,
+        obsLabelsType: olt.split('/').at(-1),
+      },
+    })),
+  ];
+}
+
+export function expandAnndataCellSetsZarr(fileDef: legacyFileDefSchema) {
+  const baseFileDef = getAnndataBaseFileDef(fileDef);
+  const { options = [] } = fileDef;
+  return [
+    {
+      ...baseFileDef,
+      fileType: FileType.OBS_SETS_ANNDATA_ZARR,
+      options: options.map((option: any) => ({
+        name: option.groupName,
+        path: option.setName,
+        scorePath: option.scoreName,
+      })),
+      coordinationValues: {
+        obsType: baseFileDef.coordinationValues.obsType,
+      },
+    },
+  ];
+}
+
+export function expandAnndataExpressionMatrixZarr(fileDef: legacyFileDefSchema) {
+  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,
+      },
+    },
+  ];
+}