@vitessce/all 2.0.3-beta.0 → 3.0.0

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

@@ -0,0 +1,132 @@
+import { describe, expect, it } from 'vitest';
+import {
+  expandAnndataZarr,
+} from './joint-file-types.js';
+
+
+describe('src/app/joint-file-types.js', () => {
+  describe('expandAnndataZarr', () => {
+    it('fails to expand when there are no options', () => {
+      expect(expandAnndataZarr({
+        fileType: 'anndata.zarr',
+        url: 'http://localhost:8000/anndata.zarr',
+      })).toEqual([]);
+    });
+    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',
+          },
+        },
+      ]);
+    });
+  });
+});

package/src/joint-file-types.ts

@@ -0,0 +1,142 @@
+import type { z } from 'zod';
+import type { latestFileDefSchema } from '@vitessce/schemas';
+import { FileType } from '@vitessce/constants-internal';
+
+type BaseFileDef = {
+  url?: string;
+  requestInit?: any;
+  coordinationValues: Record<string, string>;
+};
+
+export function expandAnndataZarr(fileDef: z.infer<typeof latestFileDefSchema>) {
+  const baseFileDef: 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: any) => ({
+        // 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: any) => ({
+        // 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: any) => ({
+        // 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,
+        },
+      }]
+    ) : []),
+  ];
+}

package/src/latest-config-schema.test.ts

@@ -0,0 +1,26 @@
+import { describe, expect, it } from 'vitest';
+
+import { CoordinationType } from '@vitessce/constants-internal';
+import {
+  baseCoordinationTypes,
+} from './base-plugins.js';
+
+describe('view config schema', () => {
+  describe('coordination types', () => {
+    it('defines schema for all valid coordination types', () => {
+      const coordinationTypeNamesFromConstants = Object.values(CoordinationType).sort();
+      const coordinationTypeNamesFromBasePlugins = baseCoordinationTypes.map(ct => ct.name).sort();
+
+      expect(coordinationTypeNamesFromConstants)
+        .toEqual(expect.arrayContaining(coordinationTypeNamesFromBasePlugins));
+    });
+
+    it('defines schema for only valid coordination types (does not have extra)', () => {
+      const coordinationTypeNamesFromConstants = Object.values(CoordinationType).sort();
+      const coordinationTypeNamesFromBasePlugins = baseCoordinationTypes.map(ct => ct.name).sort();
+
+      expect(coordinationTypeNamesFromBasePlugins)
+        .toEqual(expect.arrayContaining(coordinationTypeNamesFromConstants));
+    });
+  });
+});

package/dist/setup.js

@@ -1,96 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-/* eslint-disable max-len */
-import { useState, useLayoutEffect } from 'react';
-import { VitS, registerPluginFileType } from '@vitessce/vit-s';
-// Register view type plugins
-import { register as registerDescription } from '@vitessce/description';
-import { register as registerObsSetsManager } from '@vitessce/obs-sets-manager';
-import { register as registerScatterplotEmbedding } from '@vitessce/scatterplot-embedding';
-import { register as registerScatterplotGating } from '@vitessce/scatterplot-gating';
-import { register as registerSpatial } from '@vitessce/spatial';
-import { register as registerHeatmap } from '@vitessce/heatmap';
-import { register as registerFeatureList } from '@vitessce/feature-list';
-import { register as registerLayerController } from '@vitessce/layer-controller';
-import { register as registerStatus } from '@vitessce/status';
-import { registerCellSetExpression, registerCellSetSizes, registerExpressionHistogram } from '@vitessce/statistical-plots';
-import { registerHiglass, registerGenomicProfiles } from '@vitessce/genomic-profiles';
-// Register file type plugins
-import { 
-// CSV
-CsvSource, ObsSetsCsvLoader, ObsEmbeddingCsvLoader, ObsLocationsCsvLoader, ObsLabelsCsvLoader, ObsFeatureMatrixCsvLoader, FeatureLabelsCsvLoader, } from '@vitessce/csv';
-import { 
-// JSON
-JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader, 
-// Legacy
-RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
-import { 
-// AnnData
-AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsEmbeddingAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader, 
-// OME
-OmeZarrLoader, 
-// Legacy
-ZarrDataSource, MatrixZarrAsObsFeatureMatrixLoader, GenomicProfilesZarrLoader, } from '@vitessce/zarr';
-import { FileType, DataType } from '@vitessce/constants-internal';
-function setup() {
-    // View types
-    registerDescription();
-    registerObsSetsManager();
-    registerScatterplotEmbedding();
-    registerScatterplotGating();
-    registerSpatial();
-    registerHeatmap();
-    registerFeatureList();
-    registerLayerController();
-    registerStatus();
-    // Statistical plots
-    registerCellSetExpression();
-    registerCellSetSizes();
-    registerExpressionHistogram();
-    // Higlass
-    registerHiglass();
-    registerGenomicProfiles();
-    // File types
-    // All CSV file types
-    registerPluginFileType(FileType.OBS_SETS_CSV, DataType.OBS_SETS, ObsSetsCsvLoader, CsvSource);
-    registerPluginFileType(FileType.OBS_EMBEDDING_CSV, DataType.OBS_EMBEDDING, ObsEmbeddingCsvLoader, CsvSource);
-    registerPluginFileType(FileType.OBS_LOCATIONS_CSV, DataType.OBS_LOCATIONS, ObsLocationsCsvLoader, CsvSource);
-    registerPluginFileType(FileType.OBS_LABELS_CSV, DataType.OBS_LABELS, ObsLabelsCsvLoader, CsvSource);
-    registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CSV, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixCsvLoader, CsvSource);
-    registerPluginFileType(FileType.FEATURE_LABELS_CSV, DataType.FEATURE_LABELS, FeatureLabelsCsvLoader, CsvSource);
-    // All JSON file types
-    registerPluginFileType(FileType.OBS_SEGMENTATIONS_JSON, DataType.OBS_SEGMENTATIONS, ObsSegmentationsJsonLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
-    // All AnnData file types
-    registerPluginFileType(FileType.OBS_SETS_ANNDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, AnnDataSource);
-    registerPluginFileType(FileType.OBS_EMBEDDING_ANNDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, AnnDataSource);
-    registerPluginFileType(FileType.OBS_LOCATIONS_ANNDATA_ZARR, DataType.OBS_LOCATIONS, ObsLocationsAnndataLoader, AnnDataSource);
-    registerPluginFileType(FileType.OBS_LABELS_ANNDATA_ZARR, DataType.OBS_LABELS, ObsLabelsAnndataLoader, AnnDataSource);
-    registerPluginFileType(FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR, DataType.OBS_FEATURE_MATRIX, ObsFeatureMatrixAnndataLoader, AnnDataSource);
-    registerPluginFileType(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource);
-    registerPluginFileType(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource);
-    // All OME file types
-    registerPluginFileType(FileType.IMAGE_OME_ZARR, DataType.IMAGE, OmeZarrLoader, ZarrDataSource);
-    // All legacy file types
-    registerPluginFileType(FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR, DataType.OBS_FEATURE_MATRIX, MatrixZarrAsObsFeatureMatrixLoader, ZarrDataSource);
-    registerPluginFileType(FileType.IMAGE_RASTER_JSON, DataType.IMAGE, RasterJsonAsImageLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_SEGMENTATIONS_RASTER_JSON, DataType.OBS_SEGMENTATIONS, RasterJsonAsObsSegmentationsLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_SETS_CELL_SETS_JSON, DataType.OBS_SETS, ObsSetsJsonLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON, DataType.OBS_FEATURE_MATRIX, ClustersJsonAsObsFeatureMatrixLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_FEATURE_MATRIX_GENES_JSON, DataType.OBS_FEATURE_MATRIX, GenesJsonAsObsFeatureMatrixLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_LABELS_CELLS_JSON, DataType.OBS_LABELS, CellsJsonAsObsLabelsLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_EMBEDDING_CELLS_JSON, DataType.OBS_EMBEDDING, CellsJsonAsObsEmbeddingLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_LOCATIONS_CELLS_JSON, DataType.OBS_LOCATIONS, CellsJsonAsObsLocationsLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_SEGMENTATIONS_CELLS_JSON, DataType.OBS_SEGMENTATIONS, CellsJsonAsObsSegmentationsLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_LOCATIONS_MOLECULES_JSON, DataType.OBS_LOCATIONS, MoleculesJsonAsObsLocationsLoader, JsonSource);
-    registerPluginFileType(FileType.OBS_LABELS_MOLECULES_JSON, DataType.OBS_LABELS, MoleculesJsonAsObsLabelsLoader, JsonSource);
-    registerPluginFileType(FileType.NEIGHBORHOODS_JSON, DataType.NEIGHBORHOODS, JsonLoader, JsonSource);
-    registerPluginFileType(FileType.GENOMIC_PROFILES_ZARR, DataType.GENOMIC_PROFILES, GenomicProfilesZarrLoader, ZarrDataSource);
-}
-export function Vitessce(props) {
-    const [ready, setReady] = useState(false);
-    useLayoutEffect(() => {
-        setup();
-        setReady(true);
-    }, []);
-    return (ready ? (_jsx(VitS, { ...props })) : null);
-}