@vitessce/all 2.0.3-beta.0 → 3.0.0

package/dist-tsc/joint-file-types.js

@@ -0,0 +1,127 @@
+import { FileType } from '@vitessce/constants-internal';
+export function expandAnndataZarr(fileDef) {
+    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,
+                },
+            }]) : []),
+    ];
+}

package/dist-tsc/joint-file-types.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=joint-file-types.test.d.ts.map

package/dist-tsc/joint-file-types.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"joint-file-types.test.d.ts","sourceRoot":"","sources":["../src/joint-file-types.test.ts"],"names":[],"mappings":""}

package/dist-tsc/joint-file-types.test.js

@@ -0,0 +1,128 @@
+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/dist-tsc/latest-config-schema.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=latest-config-schema.test.d.ts.map

package/dist-tsc/latest-config-schema.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"latest-config-schema.test.d.ts","sourceRoot":"","sources":["../src/latest-config-schema.test.ts"],"names":[],"mappings":""}

package/dist-tsc/latest-config-schema.test.js

@@ -0,0 +1,19 @@
+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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "2.0.3-beta.0",
+  "version": "3.0.0",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -8,37 +8,55 @@
     "url": "git+https://github.com/vitessce/vitessce.git"
   },
   "license": "MIT",
+  "type": "module",
   "main": "dist/index.js",
   "files": [
-    "dist"
+    "src",
+    "dist",
+    "dist-tsc"
   ],
   "dependencies": {
     "@material-ui/core": "~4.12.3",
-    "@vitessce/constants-internal": "2.0.3-beta.0",
-    "@vitessce/feature-list": "2.0.3-beta.0",
-    "@vitessce/genomic-profiles": "2.0.3-beta.0",
-    "@vitessce/heatmap": "2.0.3-beta.0",
-    "@vitessce/csv": "2.0.3-beta.0",
-    "@vitessce/layer-controller": "2.0.3-beta.0",
-    "@vitessce/json": "2.0.3-beta.0",
-    "@vitessce/description": "2.0.3-beta.0",
-    "@vitessce/scatterplot-embedding": "2.0.3-beta.0",
-    "@vitessce/scatterplot-gating": "2.0.3-beta.0",
-    "@vitessce/obs-sets-manager": "2.0.3-beta.0",
-    "@vitessce/statistical-plots": "2.0.3-beta.0",
-    "@vitessce/status": "2.0.3-beta.0",
-    "@vitessce/spatial": "2.0.3-beta.0",
-    "@vitessce/zarr": "2.0.3-beta.0",
-    "@vitessce/vit-s": "2.0.3-beta.0"
+    "zod": "^3.21.4",
+    "@vitessce/constants-internal": "3.0.0",
+    "@vitessce/csv": "3.0.0",
+    "@vitessce/description": "3.0.0",
+    "@vitessce/feature-list": "3.0.0",
+    "@vitessce/genomic-profiles": "3.0.0",
+    "@vitessce/heatmap": "3.0.0",
+    "@vitessce/json": "3.0.0",
+    "@vitessce/layer-controller": "3.0.0",
+    "@vitessce/obs-sets-manager": "3.0.0",
+    "@vitessce/ome-tiff": "3.0.0",
+    "@vitessce/plugins": "3.0.0",
+    "@vitessce/scatterplot-embedding": "3.0.0",
+    "@vitessce/scatterplot-gating": "3.0.0",
+    "@vitessce/schemas": "3.0.0",
+    "@vitessce/spatial": "3.0.0",
+    "@vitessce/statistical-plots": "3.0.0",
+    "@vitessce/status": "3.0.0",
+    "@vitessce/vit-s": "3.0.0",
+    "@vitessce/zarr": "3.0.0"
   },
   "devDependencies": {
-    "react": "^18.0.0"
+    "@types/react": "^18.0.28",
+    "react": "^18.0.0",
+    "vitest": "^0.23.4"
   },
   "peerDependencies": {
     "react": "^16.8.0 || ^17.0.0 || ^18.0.0"
   },
   "scripts": {
-    "start": "tsc --watch",
-    "build": "tsc"
+    "start": "pnpm -C ../../../ run start-tsc",
+    "build": "pnpm -C ../../../ run build-tsc",
+    "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",
+    "test": "pnpm exec vitest --run -r ../../../ --dir ."
+  },
+  "module": "dist/index.js",
+  "exports": {
+    ".": {
+      "types": "./dist-tsc/index.d.ts",
+      "import": "./dist/index.js"
+    }
   }
 }

package/src/Vitessce.tsx

@@ -0,0 +1,74 @@
+/* eslint-disable max-len */
+import React, { useMemo } from 'react';
+import {
+  VitS,
+} from '@vitessce/vit-s';
+import {
+  upgradeAndParse,
+} from '@vitessce/schemas';
+import {
+  baseViewTypes,
+  baseFileTypes,
+  baseJointFileTypes,
+  baseCoordinationTypes,
+} from './base-plugins.js';
+
+export function Vitessce(props: any) {
+  const {
+    config,
+    onConfigUpgrade,
+    pluginViewTypes: pluginViewTypesProp,
+    pluginFileTypes: pluginFileTypesProp,
+    pluginCoordinationTypes: pluginCoordinationTypesProp,
+    pluginJointFileTypes: pluginJointFileTypesProp,
+  } = props;
+
+  const configUid = config?.uid;
+  const configVersion = config?.version;
+
+  const [configOrWarning, success] = useMemo(() => {
+    try {
+      const validConfig = upgradeAndParse(config, onConfigUpgrade);
+      return [validConfig, true];
+    } catch (e) {
+      console.error(e);
+      return [
+        {
+          title: 'Config validation or upgrade failed.',
+          unformatted: (e as any).message,
+        },
+        false,
+      ];
+    }
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [configUid, configVersion]);
+
+  const mergedPluginViewTypes = useMemo(() => ([
+    ...baseViewTypes, ...(pluginViewTypesProp || []),
+  ]), [pluginViewTypesProp]);
+
+  const mergedPluginFileTypes = useMemo(() => ([
+    ...baseFileTypes, ...(pluginFileTypesProp || []),
+  ]), [pluginFileTypesProp]);
+
+  const mergedPluginJointFileTypes = useMemo(() => ([
+    ...baseJointFileTypes, ...(pluginJointFileTypesProp || []),
+  ]), [pluginJointFileTypesProp]);
+
+  const mergedPluginCoordinationTypes = useMemo(() => ([
+    ...baseCoordinationTypes, ...(pluginCoordinationTypesProp || []),
+  ]), [pluginCoordinationTypesProp]);
+
+
+  return (
+    <VitS
+      {...props}
+      config={configOrWarning}
+      viewTypes={mergedPluginViewTypes}
+      fileTypes={mergedPluginFileTypes}
+      jointFileTypes={mergedPluginJointFileTypes}
+      coordinationTypes={mergedPluginCoordinationTypes}
+      warning={(success ? null : configOrWarning)}
+    />
+  );
+}