@vitessce/vit-s 2.0.3 → 3.0.0

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

@@ -1,298 +0,0 @@
-import { FileType } from '@vitessce/constants-internal';
-import {
-  validateOptions,
-  emptySchema,
-} from './file-options-schemas';
-import {
-  cellsJsonSchema,
-  anndataCellsZarrSchema,
-  anndataCellSetsZarrSchema,
-  anndataExpressionMatrixZarrSchema,
-} from './file-options-schemas-legacy';
-
-export function expandMoleculesJson(fileDef) {
-  validateOptions(emptySchema, fileDef.options);
-  const baseFileDef = {
-    ...fileDef,
-    coordinationValues: {
-      obsType: fileDef.coordinationValues?.obsType || 'molecule',
-    },
-  };
-  delete baseFileDef.type;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_LOCATIONS_MOLECULES_JSON,
-    },
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_LABELS_MOLECULES_JSON,
-    },
-  ];
-}
-
-export function expandExpressionMatrixZarr(fileDef) {
-  validateOptions(emptySchema, fileDef.options);
-  const baseFileDef = {
-    ...fileDef,
-    coordinationValues: {
-      obsType: fileDef.coordinationValues?.obsType || 'cell',
-      featureType: fileDef.coordinationValues?.featureType || 'gene',
-      featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-    },
-  };
-  delete baseFileDef.type;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR,
-    },
-  ];
-}
-
-export function expandRasterJson(fileDef) {
-  // Validation already happens in the RasterJsonLoader.
-  const baseFileDef = { ...fileDef };
-  delete baseFileDef.type;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.IMAGE_RASTER_JSON,
-    },
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_SEGMENTATIONS_RASTER_JSON,
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues?.obsType || 'cell',
-      },
-    },
-  ];
-}
-
-export function expandRasterOmeZarr(fileDef) {
-  validateOptions(emptySchema, fileDef.options);
-  const baseFileDef = { ...fileDef };
-  delete baseFileDef.type;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.IMAGE_OME_ZARR,
-    },
-  ];
-}
-
-export function expandCellSetsJson(fileDef) {
-  validateOptions(emptySchema, fileDef.options);
-  const baseFileDef = { ...fileDef };
-  delete baseFileDef.type;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_SETS_CELL_SETS_JSON,
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues?.obsType || 'cell',
-      },
-    },
-  ];
-}
-
-export function expandCellsJson(fileDef) {
-  validateOptions(cellsJsonSchema, fileDef.options);
-  const baseFileDef = {
-    ...fileDef,
-    coordinationValues: {
-      obsType: fileDef.coordinationValues?.obsType || 'cell',
-      featureType: fileDef.coordinationValues?.featureType || 'gene',
-    },
-  };
-  delete baseFileDef.type;
-  delete baseFileDef.options;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_SEGMENTATIONS_CELLS_JSON,
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-      },
-    },
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_LOCATIONS_CELLS_JSON,
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-      },
-    },
-    ...(fileDef.options?.embeddingTypes ? fileDef.options.embeddingTypes.map(et => ({
-      ...baseFileDef,
-      fileType: FileType.OBS_EMBEDDING_CELLS_JSON,
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-        embeddingType: et,
-      },
-    })) : []),
-    ...(fileDef.options?.obsLabelsTypes ? fileDef.options.obsLabelsTypes.map(key => ({
-      ...baseFileDef,
-      fileType: FileType.OBS_LABELS_CELLS_JSON,
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-        obsLabelsType: key,
-      },
-    })) : []),
-  ];
-}
-
-export function expandClustersJson(fileDef) {
-  validateOptions(emptySchema, fileDef.options);
-  const baseFileDef = {
-    ...fileDef,
-    coordinationValues: {
-      obsType: fileDef.coordinationValues?.obsType || 'cell',
-      featureType: fileDef.coordinationValues?.featureType || 'gene',
-      featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-    },
-  };
-  delete baseFileDef.type;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON,
-    },
-  ];
-}
-
-export function expandGenesJson(fileDef) {
-  validateOptions(emptySchema, fileDef.options);
-  const baseFileDef = {
-    ...fileDef,
-    coordinationValues: {
-      obsType: fileDef.coordinationValues?.obsType || 'cell',
-      featureType: fileDef.coordinationValues?.featureType || 'gene',
-      featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-    },
-  };
-  delete baseFileDef.type;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_FEATURE_MATRIX_GENES_JSON,
-    },
-  ];
-}
-
-function getAnndataBaseFileDef(fileDef) {
-  return {
-    url: fileDef.url,
-    requestInit: fileDef.requestInit,
-    coordinationValues: {
-      ...fileDef.coordinationValues,
-      obsType: fileDef.coordinationValues?.obsType || 'cell',
-      featureType: fileDef.coordinationValues?.featureType || 'gene',
-      featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
-    },
-  };
-}
-
-export function expandAnndataCellsZarr(fileDef) {
-  validateOptions(anndataCellsZarrSchema, fileDef.options);
-  const baseFileDef = getAnndataBaseFileDef(fileDef);
-  const { options = {} } = fileDef;
-  const embeddingTypes = options.mappings ? Object.keys(options.mappings) : [];
-  const obsLabelsTypes = options.factors ? options.factors : [];
-  return [
-    ...(options.poly ? [{
-      ...baseFileDef,
-      fileType: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR,
-      options: {
-        path: options.poly,
-      },
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-      },
-    }] : []),
-    ...(options.xy ? [{
-      ...baseFileDef,
-      fileType: FileType.OBS_LOCATIONS_ANNDATA_ZARR,
-      options: {
-        path: options.xy,
-      },
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-      },
-    }] : []),
-    ...embeddingTypes.map(et => ({
-      ...baseFileDef,
-      fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
-      options: {
-        path: options.mappings[et].key,
-        dims: options.mappings[et].dims,
-      },
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-        embeddingType: et,
-      },
-    })),
-    ...obsLabelsTypes.map(olt => ({
-      ...baseFileDef,
-      fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
-      options: {
-        path: olt,
-      },
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-        obsLabelsType: olt.split('/').at(-1),
-      },
-    })),
-  ];
-}
-
-export function expandAnndataCellSetsZarr(fileDef) {
-  validateOptions(anndataCellSetsZarrSchema, fileDef.options);
-  const baseFileDef = getAnndataBaseFileDef(fileDef);
-  const { options = [] } = fileDef;
-  return [
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_SETS_ANNDATA_ZARR,
-      options: options.map(option => ({
-        name: option.groupName,
-        path: option.setName,
-        scorePath: option.scoreName,
-      })),
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-      },
-    },
-  ];
-}
-
-export function expandAnndataExpressionMatrixZarr(fileDef) {
-  validateOptions(anndataExpressionMatrixZarrSchema, fileDef.options);
-  const baseFileDef = getAnndataBaseFileDef(fileDef);
-  const { options = {} } = fileDef;
-  return [
-    ...(options.geneAlias ? [{
-      ...baseFileDef,
-      fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
-      options: {
-        path: options.geneAlias,
-      },
-      coordinationValues: {
-        featureType: baseFileDef.coordinationValues.featureType,
-      },
-    }] : []),
-    {
-      ...baseFileDef,
-      fileType: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR,
-      options: {
-        path: options.matrix,
-        featureFilterPath: options.geneFilter,
-        initialFeatureFilterPath: options.matrixGeneFilter,
-      },
-      coordinationValues: {
-        obsType: baseFileDef.coordinationValues.obsType,
-        featureType: baseFileDef.coordinationValues.featureType,
-        featureValueType: baseFileDef.coordinationValues.featureValueType,
-      },
-    },
-  ];
-}

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

@@ -1,412 +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',
-            },
-          },
-        ]);
-      });
-    });
-  });
-});