@vitessce/vit-s 2.0.3 → 3.0.1

package/src/joint-file-types.js

@@ -1,171 +0,0 @@
-import { FileType } from '@vitessce/constants-internal';
-import {
-  validateOptions,
-  anndataZarrSchema,
-} from './file-options-schemas';
-import {
-  expandMoleculesJson,
-  expandExpressionMatrixZarr,
-  expandRasterJson,
-  expandRasterOmeZarr,
-  expandCellSetsJson,
-  expandCellsJson,
-  expandClustersJson,
-  expandGenesJson,
-  expandAnndataCellsZarr,
-  expandAnndataCellSetsZarr,
-  expandAnndataExpressionMatrixZarr,
-} from './joint-file-types-legacy';
-
-export function expandAnndataZarr(fileDef) {
-  validateOptions(anndataZarrSchema, fileDef.options);
-  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,
-        },
-      }]
-    ) : []),
-  ];
-}
-
-/**
- * Built-in joint file type
- * expansion functions.
- */
-export const JOINT_FILE_TYPES = {
-  [FileType.ANNDATA_ZARR]: expandAnndataZarr,
-  [FileType.ANNDATA_CELLS_ZARR]: expandAnndataCellsZarr,
-  [FileType.ANNDATA_CELL_SETS_ZARR]: expandAnndataCellSetsZarr,
-  [FileType.ANNDATA_EXPRESSION_MATRIX_ZARR]: expandAnndataExpressionMatrixZarr,
-  [FileType.EXPRESSION_MATRIX_ZARR]: expandExpressionMatrixZarr,
-  [FileType.RASTER_JSON]: expandRasterJson,
-  [FileType.RASTER_OME_ZARR]: expandRasterOmeZarr,
-  [FileType.CELL_SETS_JSON]: expandCellSetsJson,
-  [FileType.CLUSTERS_JSON]: expandClustersJson,
-  [FileType.GENES_JSON]: expandGenesJson,
-  [FileType.CELLS_JSON]: expandCellsJson,
-  [FileType.MOLECULES_JSON]: expandMoleculesJson,
-};

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

@@ -1,144 +0,0 @@
-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/src/json-schemas.js

@@ -1,9 +0,0 @@
-import rasterSchema from './schemas/raster.schema';
-import obsSetsSchema from './schemas/obsSets.schema';
-import obsSetsTabularSchema from './schemas/obsSetsTabular.schema';
-
-export {
-  rasterSchema,
-  obsSetsSchema,
-  obsSetsTabularSchema,
-};

package/src/plugins.js

@@ -1,186 +0,0 @@
-import { fromEntries } from '@vitessce/utils';
-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';
-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_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_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;
-}
-
-/**
- * Register a new view type.
- * @param {string} viewType A name
- * @param {function} viewSubscriberReactComponent A react component.
- * @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;
-  }
-}
-
-/**
- * Register a new file type.
- * @param {string} fileTypeName Name for the new file type.
- * @param {string} dataTypeName Name for the data type associated with the file type.
- * @param {class} dataSourceClass Data source class definition.
- * @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;
-}
-
-/**
- * Register a new joint file type.
- * @param {string} fileTypeName Name for the new file type.
- * @param {function} expansionFunction The joint file type expansion function.
- * Should take in a single file definition and return an array of
- * 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;
-}
-
-
-// Plugin getter functions.
-
-export function getPluginViewTypes() {
-  return Object.keys(PLUGINS[PLUGIN_VIEW_TYPES_KEY]);
-}
-
-export function getPluginViewType(viewType) {
-  return PLUGINS[PLUGIN_VIEW_TYPES_KEY][viewType];
-}
-
-export function getPluginCoordinationTypes() {
-  return Object.keys(PLUGINS[PLUGIN_COORDINATION_TYPES_KEY]);
-}
-
-export function getPluginCoordinationTypeDefaults() {
-  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 [];
-}
-
-export function getPluginFileTypes() {
-  return Object.keys(PLUGINS[PLUGIN_FILE_TYPES_KEY]);
-}
-export function getPluginConvenienceFileTypes() {
-  return Object.keys(PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY]);
-}
-
-export function getDataTypeForPluginFileType(fileType) {
-  return PLUGINS[PLUGIN_FILE_TYPE_DATA_TYPE_MAPPING_KEY][fileType];
-}
-export function getLoaderClassesForPluginFileType(fileType) {
-  return PLUGINS[PLUGIN_FILE_TYPES_KEY][fileType];
-}
-export function getExpansionFunctionForPluginConvenienceFileType(fileType) {
-  return PLUGINS[PLUGIN_JOINT_FILE_TYPES_KEY][fileType];
-}
-
-// Getters that depend on plugins.
-export function getFileTypes() {
-  return [
-    ...Object.values(FileType),
-    ...getPluginFileTypes(),
-  ];
-}
-
-export function getCoordinationTypes() {
-  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(),
-  };
-}
-
-// 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),
-    ]))),
-  };
-}
-
-export function getFileTypeDataTypeMapping() {
-  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],
-  };
-}

package/src/plugins.test.js

@@ -1,42 +0,0 @@
-/* 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

@@ -1,85 +0,0 @@
-{
-    "$schema": "http://json-schema.org/draft-07/schema#",
-    "$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"]
-      }
-    }
-  }
-