@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

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

@@ -0,0 +1,144 @@
+import { FileType, FILE_TYPE_DATA_TYPE_MAPPING } from '@vitessce/constants-internal';
+import {
+  JOINT_FILE_TYPES,
+  expandAnndataZarr,
+} from './joint-file-types';
+
+
+describe('src/app/joint-file-types.js', () => {
+  describe('FileType-to-DataType mappings', () => {
+    it('every file type is mapped to either a data type or a joint file type expansion function', () => {
+      const fileTypes = Object.values(FileType).sort();
+      const mappedFileTypes = [
+        ...Object.keys(FILE_TYPE_DATA_TYPE_MAPPING),
+        ...Object.keys(JOINT_FILE_TYPES),
+      ].sort();
+      expect(fileTypes.length).toEqual(mappedFileTypes.length);
+      expect(fileTypes).toEqual(mappedFileTypes);
+    });
+  });
+  describe('expandAnndataZarr', () => {
+    it('fails to expand when there are no options', () => {
+      expect(() => expandAnndataZarr({
+        fileType: 'anndata.zarr',
+        url: 'http://localhost:8000/anndata.zarr',
+      })).toThrow();
+    });
+    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/schemas.js → src/json-schemas.js}

@@ -1,4 +1,9 @@
 import rasterSchema from './schemas/raster.schema';
 import obsSetsSchema from './schemas/obsSets.schema';
 import obsSetsTabularSchema from './schemas/obsSetsTabular.schema';
-export { rasterSchema, obsSetsSchema, obsSetsTabularSchema, };
+
+export {
+  rasterSchema,
+  obsSetsSchema,
+  obsSetsTabularSchema,
+};

package/{dist → src}/plugins.js

@@ -1,6 +1,12 @@
 import { fromEntries } from '@vitessce/utils';
-import { FileType, CoordinationType, FILE_TYPE_DATA_TYPE_MAPPING, COMPONENT_COORDINATION_TYPES, DEFAULT_COORDINATION_VALUES, } from '@vitessce/constants-internal';
+import {
+  FileType, CoordinationType,
+  FILE_TYPE_DATA_TYPE_MAPPING,
+  COMPONENT_COORDINATION_TYPES,
+  DEFAULT_COORDINATION_VALUES,
+} from '@vitessce/constants-internal';
 import { JOINT_FILE_TYPES } from './joint-file-types';
+
 const PLUGINS_KEY = '__VITESSCE_PLUGINS__';
 const PLUGIN_VIEW_TYPES_KEY = 'viewTypes';
 const PLUGIN_COORDINATION_TYPES_KEY = 'coordinationTypes';
@@ -8,23 +14,31 @@ const PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY = 'coordinationTypesPerView';
 const PLUGIN_FILE_TYPES_KEY = 'fileTypes';
 const PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY = 'fileTypeDataTypeMapping';
 const PLUGIN_JOINT_FILE_TYPES_KEY = 'jointFileTypes';
+
 window[PLUGINS_KEY] = {};
 const PLUGINS = window[PLUGINS_KEY];
+
 // Reference: https://github.com/higlass/higlass-register/blob/master/src/index.js
 PLUGINS[PLUGIN_VIEW_TYPES_KEY] = PLUGINS[PLUGIN_VIEW_TYPES_KEY] || {};
 PLUGINS[PLUGIN_COORDINATION_TYPES_KEY] = PLUGINS[PLUGIN_COORDINATION_TYPES_KEY] || {};
-PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY] = (PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY] || {});
+PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY] = (
+  PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY] || {}
+);
 PLUGINS[PLUGIN_FILE_TYPES_KEY] = PLUGINS[PLUGIN_FILE_TYPES_KEY] || {};
-PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY] = (PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY] || {});
+PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY] = (
+  PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY] || {}
+);
 PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY] = PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY] || {};
+
 /**
  * Register a new coordination type.
  * @param {string} typeName Name for the new coordination type.
  * @param {*} defaultValue A default value for the coordination type.
  */
 export function registerPluginCoordinationType(typeName, defaultValue) {
-    PLUGINS[PLUGIN_COORDINATION_TYPES_KEY][typeName] = defaultValue;
+  PLUGINS[PLUGIN_COORDINATION_TYPES_KEY][typeName] = defaultValue;
 }
+
 /**
  * Register a new view type.
  * @param {string} viewType A name
@@ -32,20 +46,20 @@ export function registerPluginCoordinationType(typeName, defaultValue) {
  * @param {string[]} coordinationTypes A list of coordination types that this view supports.
  */
 export function registerPluginViewType(viewType, viewSubscriberReactComponent, coordinationTypes) {
-    PLUGINS[PLUGIN_VIEW_TYPES_KEY][viewType] = viewSubscriberReactComponent;
-    // Register the supported coordination types.
-    const pluginTypesPerView = PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY];
-    if (Array.isArray(pluginTypesPerView[viewType])) {
-        coordinationTypes.forEach((coordinationType) => {
-            if (!pluginTypesPerView[viewType].includes(coordinationType)) {
-                pluginTypesPerView[viewType].push(coordinationType);
-            }
-        });
-    }
-    else {
-        pluginTypesPerView[viewType] = coordinationTypes;
-    }
-}
+  PLUGINS[PLUGIN_VIEW_TYPES_KEY][viewType] = viewSubscriberReactComponent;
+  // Register the supported coordination types.
+  const pluginTypesPerView = PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY];
+  if (Array.isArray(pluginTypesPerView[viewType])) {
+    coordinationTypes.forEach((coordinationType) => {
+      if (!pluginTypesPerView[viewType].includes(coordinationType)) {
+        pluginTypesPerView[viewType].push(coordinationType);
+      }
+    });
+  } else {
+    pluginTypesPerView[viewType] = coordinationTypes;
+  }
+}
+
 /**
  * Register a new file type.
  * @param {string} fileTypeName Name for the new file type.
@@ -54,11 +68,13 @@ export function registerPluginViewType(viewType, viewSubscriberReactComponent, c
  * @param {class} dataLoaderClass Data loader class definition.
  */
 export function registerPluginFileType(
-// eslint-disable-next-line no-unused-vars
-fileTypeName, dataTypeName, dataLoaderClass, dataSourceClass) {
-    PLUGINS[PLUGIN_FILE_TYPES_KEY][fileTypeName] = [dataSourceClass, dataLoaderClass];
-    PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY][fileTypeName] = dataTypeName;
+  // eslint-disable-next-line no-unused-vars
+  fileTypeName, dataTypeName, dataLoaderClass, dataSourceClass,
+) {
+  PLUGINS[PLUGIN_FILE_TYPES_KEY][fileTypeName] = [dataSourceClass, dataLoaderClass];
+  PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY][fileTypeName] = dataTypeName;
 }
+
 /**
  * Register a new joint file type.
  * @param {string} fileTypeName Name for the new file type.
@@ -67,88 +83,104 @@ fileTypeName, dataTypeName, dataLoaderClass, dataSourceClass) {
  * file definitions with valid atomic fileType values.
  */
 export function registerPluginJointFileType(
-// eslint-disable-next-line no-unused-vars
-fileTypeName, expansionFunction) {
-    PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY][fileTypeName] = expansionFunction;
+  // eslint-disable-next-line no-unused-vars
+  fileTypeName, expansionFunction,
+) {
+  PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY][fileTypeName] = expansionFunction;
 }
+
+
 // Plugin getter functions.
+
 export function getPluginViewTypes() {
-    return Object.keys(PLUGINS[PLUGIN_VIEW_TYPES_KEY]);
+  return Object.keys(PLUGINS[PLUGIN_VIEW_TYPES_KEY]);
 }
+
 export function getPluginViewType(viewType) {
-    return PLUGINS[PLUGIN_VIEW_TYPES_KEY][viewType];
+  return PLUGINS[PLUGIN_VIEW_TYPES_KEY][viewType];
 }
+
 export function getPluginCoordinationTypes() {
-    return Object.keys(PLUGINS[PLUGIN_COORDINATION_TYPES_KEY]);
+  return Object.keys(PLUGINS[PLUGIN_COORDINATION_TYPES_KEY]);
 }
+
 export function getPluginCoordinationTypeDefaults() {
-    return PLUGINS[PLUGIN_COORDINATION_TYPES_KEY];
+  return PLUGINS[PLUGIN_COORDINATION_TYPES_KEY];
 }
+
 export function getPluginCoordinationTypesForViewType(viewType) {
-    if (Array.isArray(PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY][viewType])) {
-        return PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY][viewType];
-    }
-    return [];
+  if (Array.isArray(PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY][viewType])) {
+    return PLUGINS[PLUGIN_COORDINATION_TYPES_PER_VIEW_KEY][viewType];
+  }
+  return [];
 }
+
 export function getPluginFileTypes() {
-    return Object.keys(PLUGINS[PLUGIN_FILE_TYPES_KEY]);
+  return Object.keys(PLUGINS[PLUGIN_FILE_TYPES_KEY]);
 }
 export function getPluginConvenienceFileTypes() {
-    return Object.keys(PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY]);
+  return Object.keys(PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY]);
 }
+
 export function getDataTypeForPluginFileType(fileType) {
-    return PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY][fileType];
+  return PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY][fileType];
 }
 export function getLoaderClassesForPluginFileType(fileType) {
-    return PLUGINS[PLUGIN_FILE_TYPES_KEY][fileType];
+  return PLUGINS[PLUGIN_FILE_TYPES_KEY][fileType];
 }
 export function getExpansionFunctionForPluginConvenienceFileType(fileType) {
-    return PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY][fileType];
+  return PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY][fileType];
 }
+
 // Getters that depend on plugins.
 export function getFileTypes() {
-    return [
-        ...Object.values(FileType),
-        ...getPluginFileTypes(),
-    ];
+  return [
+    ...Object.values(FileType),
+    ...getPluginFileTypes(),
+  ];
 }
+
 export function getCoordinationTypes() {
-    return [
-        ...Object.values(CoordinationType),
-        ...getPluginCoordinationTypes(),
-    ];
+  return [
+    ...Object.values(CoordinationType),
+    ...getPluginCoordinationTypes(),
+  ];
 }
+
 // Need to do this in a function since the plugin coordination
 // types are dynamic.
 export function getDefaultCoordinationValues() {
-    return {
-        ...DEFAULT_COORDINATION_VALUES,
-        ...getPluginCoordinationTypeDefaults(),
-    };
+  return {
+    ...DEFAULT_COORDINATION_VALUES,
+    ...getPluginCoordinationTypeDefaults(),
+  };
 }
+
 // Need to do this in a function since the plugin coordination
 // types are dynamic.
 export function getComponentCoordinationTypes() {
-    return {
-        ...COMPONENT_COORDINATION_TYPES,
-        ...fromEntries(getPluginViewTypes().map(viewType => ([
-            viewType,
-            getPluginCoordinationTypesForViewType(viewType),
-        ]))),
-    };
-}
+  return {
+    ...COMPONENT_COORDINATION_TYPES,
+    ...fromEntries(getPluginViewTypes().map(viewType => ([
+      viewType,
+      getPluginCoordinationTypesForViewType(viewType),
+    ]))),
+  };
+}
+
 export function getFileTypeDataTypeMapping() {
-    return {
-        ...FILE_TYPE_DATA_TYPE_MAPPING,
-        ...fromEntries(getPluginFileTypes().map(fileType => ([
-            fileType,
-            getDataTypeForPluginFileType(fileType),
-        ]))),
-    };
-}
+  return {
+    ...FILE_TYPE_DATA_TYPE_MAPPING,
+    ...fromEntries(getPluginFileTypes().map(fileType => ([
+      fileType,
+      getDataTypeForPluginFileType(fileType),
+    ]))),
+  };
+}
+
 export function getJointFileTypes() {
-    return {
-        ...JOINT_FILE_TYPES,
-        ...PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY],
-    };
+  return {
+    ...JOINT_FILE_TYPES,
+    ...PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY],
+  };
 }

package/src/plugins.test.fixtures.js

@@ -0,0 +1,78 @@
+export const convenienceFileDefsCollapsed = {
+  version: '1.0.15',
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  datasets: [
+    {
+      files: [
+        {
+          fileType: 'anndata.convenience.zarr',
+          url: 'http://localhost:8000/my_anndata.zarr',
+          options: {
+            cells: {
+              xy: 'obsm/centroids',
+            },
+            cellSets: [
+              {
+                groupName: 'Leiden',
+                setName: 'obs/leiden',
+              },
+            ],
+          },
+        },
+      ],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [],
+};
+
+export function pluginExpandAnnDataConvenience(fileDef) {
+  return [
+    {
+      fileType: 'anndata-cells.zarr',
+      url: fileDef.url,
+      options: fileDef.options.cells,
+    },
+    {
+      fileType: 'anndata-cell-sets.zarr',
+      url: fileDef.url,
+      options: fileDef.options.cellSets,
+    },
+  ];
+}
+
+export const convenienceFileDefsExpanded = {
+  version: '1.0.15',
+  name: 'My config name',
+  description: 'My config description',
+  initStrategy: 'auto',
+  datasets: [
+    {
+      files: [
+        {
+          fileType: 'anndata-cells.zarr',
+          url: 'http://localhost:8000/my_anndata.zarr',
+          options: {
+            xy: 'obsm/centroids',
+          },
+        },
+        {
+          fileType: 'anndata-cell-sets.zarr',
+          url: 'http://localhost:8000/my_anndata.zarr',
+          options: [
+            {
+              groupName: 'Leiden',
+              setName: 'obs/leiden',
+            },
+          ],
+        },
+      ],
+      name: 'A',
+      uid: 'A',
+    },
+  ],
+  layout: [],
+};

package/src/plugins.test.js

@@ -0,0 +1,42 @@
+/* eslint-disable camelcase */
+import {
+  registerPluginFileType,
+  registerPluginJointFileType,
+  getFileTypeDataTypeMapping,
+  getJointFileTypes,
+} from './plugins';
+import {
+  convenienceFileDefsCollapsed,
+  convenienceFileDefsExpanded,
+  pluginExpandAnnDataConvenience,
+} from './plugins.test.fixtures';
+import {
+  initialize,
+} from './view-config-utils';
+
+describe('src/app/plugins.js', () => {
+  describe('getFileTypeDataTypeMapping', () => {
+    it('returns the correct data type for built-in file types', () => {
+      const dataType = getFileTypeDataTypeMapping()['image.raster.json'];
+      expect(dataType).toEqual('image');
+    });
+    it('returns the correct data type for plugin file types', () => {
+      registerPluginFileType('plugin-cells.json', 'cells', null, null);
+      const dataType = getFileTypeDataTypeMapping()['plugin-cells.json'];
+      expect(dataType).toEqual('cells');
+    });
+  });
+  describe('convenience file types', () => {
+    it('registers plugin convenience file types', () => {
+      registerPluginJointFileType('anndata.convenience.zarr', pluginExpandAnnDataConvenience);
+      const expansionFuncs = getJointFileTypes();
+      expect(Object.keys(expansionFuncs).includes('anndata.convenience.zarr')).toBeTruthy();
+      expect(typeof expansionFuncs['anndata.convenience.zarr']).toEqual('function');
+    });
+    it('uses plugin convenience file types in view config initialization', () => {
+      registerPluginJointFileType('anndata.convenience.zarr', pluginExpandAnnDataConvenience);
+      expect(initialize(convenienceFileDefsCollapsed).datasets)
+        .toEqual(convenienceFileDefsExpanded.datasets);
+    });
+  });
+});

package/src/schemas/config-0.1.0.schema.json

@@ -0,0 +1,85 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "https://github.com/vitessce/vitessce/#dataset",
+    "title": "Vitessce data set",
+    "type": "object",
+    "definitions": {
+      "components": {
+        "type": "array",
+        "items": {
+          "type": "object",
+          "additionalProperties": false,
+          "required": ["component", "x", "y"],
+          "properties": {
+            "component": { "type": "string" },
+            "props": { "type": "object" },
+            "x": { "type": "integer" },
+            "y": { "type": "integer" },
+            "w": { "type": "integer" },
+            "h": { "type": "integer" }
+          }
+        }
+      },
+      "requestInit": {
+        "type": "object",
+        "additionalProperties": false,
+        "required": [],
+        "properties": {
+          "method": {
+            "type": "string"
+          },
+          "headers": {
+            "type": "object"
+          },
+          "body": {
+            "type": "string"
+          },
+          "mode": {
+            "type": "string"
+          },
+          "credentials": {
+            "type": "string"
+          },
+          "cache": {
+            "type": "string"
+          },
+          "redirect": {
+            "type": "string"
+          },
+          "referrer": {
+            "type": "string"
+          },
+          "integrity": {
+            "type": "string"
+          }
+        }
+      }
+    },
+    "additionalProperties": false,
+    "required": ["version", "name", "layers"],
+    "properties": {
+      "name": { "type": "string" },
+      "public": { "type": "boolean" },
+      "description": { "type": "string" },
+      "layers": {
+        "type": "array",
+        "items": {
+          "type": "object",
+          "additionalProperties": false,
+          "required": ["name", "type", "fileType", "url"],
+          "properties": {
+            "name": { "type": "string" },
+            "type": { "type": "string" },
+            "fileType": { "type": "string" },
+            "url": { "type": "string" },
+            "requestInit": { "$ref": "#/definitions/requestInit" }
+          }
+        }
+      },
+      "staticLayout": { "$ref": "#/definitions/components" },
+      "version": {
+        "type": "string", "enum": ["0.1.0"]
+      }
+    }
+  }
+