@vitessce/vit-s 2.0.3 → 3.0.0

package/src/component-registry.js

@@ -1,21 +0,0 @@
-import { getPluginViewType, getPluginViewTypes } from './plugins';
-
-// TODO(monorepo): this code can be simplified
-const registry = {};
-
-export function getComponent(name) {
-  let component = registry[name];
-  if (component === undefined) {
-    component = getPluginViewType(name);
-    if (component === undefined) {
-      throw new Error(
-        `Could not find definition for "${name}" in the core registry nor the plugin registry.`,
-      );
-    }
-  }
-  return component;
-}
-
-export function getViewTypes() {
-  return [...Object.keys(registry), ...getPluginViewTypes()];
-}

package/src/errors/OptionsValidationError.js

@@ -1,25 +0,0 @@
-import AbstractLoaderError from './AbstractLoaderError';
-
-export default class OptionsValidationError extends AbstractLoaderError {
-  constructor(fileType, url, options, reason) {
-    super(`Error while validating file definition options: ${fileType} from ${url}.`);
-    this.name = 'OptionsValidationError';
-
-    this.fileType = fileType;
-    this.url = url;
-    this.options = options;
-    this.reason = reason;
-  }
-
-  warnInConsole() {
-    const {
-      options, reason,
-    } = this;
-    console.warn(
-      'Received options\n',
-      JSON.stringify(options, null, 2),
-      'JSON schema validation failure reason\n',
-      JSON.stringify(reason, null, 2),
-    );
-  }
-}

package/src/file-options-schemas-legacy.js

@@ -1,139 +0,0 @@
-export const cellsJsonSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#cells-json-options',
-  title: 'cells.json options',
-  oneOf: [
-    { type: 'null' },
-    {
-      type: 'object',
-      additionalProperties: false,
-      required: [],
-      properties: {
-        obsLabelsTypes: {
-          type: 'array',
-          items: { type: 'string' },
-        },
-        embeddingTypes: {
-          type: 'array',
-          items: { type: 'string' },
-        },
-      },
-    },
-  ],
-};
-
-export const anndataCellsZarrSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#anndata-cells-zarr-options',
-  title: 'anndata-cells.zarr options',
-  type: 'object',
-  minProperties: 1,
-  additionalProperties: false,
-  required: [],
-  properties: {
-    xy: {
-      type: 'string',
-      description: "The location in the AnnData store of cell centroids, like 'obsm/X_centroids.'",
-    },
-    poly: {
-      type: 'string',
-      description: "The location in the AnnData store of cell polygon outlines, like 'obsm/X_polygons.'",
-    },
-    factors: {
-      type: 'array',
-      description: "List of locations in the AnnData store of cell sets, like 'obs/louvain'",
-      items: {
-        type: 'string',
-      },
-    },
-    mappings: {
-      patternProperties: {
-        '.': {
-          type: 'object',
-          description: "An object containing key-values for mappings like { UMAP: { key: 'obsm/X_umap', dims: [0, 1] } }.",
-          additionalProperties: false,
-          required: ['key'],
-          properties: {
-            key: {
-              type: 'string',
-              description: "Where to look in the AnnData store for this mapping, like 'obsm/X_umap.'",
-            },
-            dims: {
-              type: 'array',
-              description: 'Which indices of the obsm object to take for a scatterplot, allowing for, for example, different PCs from obsm/X_pca',
-              minItems: 2,
-              maxItems: 2,
-              items: { type: 'number' },
-            },
-          },
-        },
-      },
-    },
-  },
-};
-
-export const anndataCellSetsZarrSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#anndata-cell-sets-zarr-options',
-  title: 'anndata-cell-sets.zarr options',
-  type: 'array',
-  items: {
-    type: 'object',
-    additionalProperties: false,
-    required: ['groupName', 'setName'],
-    properties: {
-      groupName: {
-        type: 'string',
-        description: "The display name for the set, like 'Cell Type' or 'Louvain.'",
-      },
-      setName: {
-        oneOf: [
-          {
-            type: 'string',
-            description: "The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'",
-          },
-          {
-            type: 'array',
-            items: { type: 'string' },
-            description: 'An array of locations in the AnnData store for a hierarchy of set names, from coarse to fine levels.',
-          },
-        ],
-      },
-      scoreName: {
-        oneOf: [
-          {
-            type: 'string',
-            description: "The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'",
-          },
-        ],
-      },
-    },
-  },
-};
-
-export const anndataExpressionMatrixZarrSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#anndata-expression-matrix-zarr-options',
-  title: 'anndata-expression-matrix.zarr options',
-  type: 'object',
-  additionalProperties: false,
-  required: ['matrix'],
-  properties: {
-    matrix: {
-      type: 'string',
-      description: "The location in the AnnData store of the cell x gene matrix, like 'obsm/hvg_subset.' or 'X'",
-    },
-    geneFilter: {
-      type: 'string',
-      description: "The location in the AnnData store of a filter for the genes if using a subset of the data, like 'var.highly_variable.' if the matrix comes from 'obsm/hvg_subset.'",
-    },
-    matrixGeneFilter: {
-      type: 'string',
-      description: "The location in the AnnData store of a filter for the matrix data (used in heatmap and histogram), like 'var.highly_variable.''",
-    },
-    geneAlias: {
-      type: 'string',
-      description: 'The location in the AnnData store of a different list of names for gene list component, other than the `var` index',
-    },
-  },
-};

package/src/file-options-schemas-legacy.test.js

@@ -1,138 +0,0 @@
-import {
-  expandExpressionMatrixZarr,
-  expandRasterOmeZarr,
-  expandGenesJson,
-  expandCellsJson,
-  expandCellSetsJson,
-  expandMoleculesJson,
-  expandAnndataCellsZarr,
-  expandAnndataCellSetsZarr,
-  expandAnndataExpressionMatrixZarr,
-  expandClustersJson,
-} from './joint-file-types-legacy';
-
-describe('src/app/file-options-schemas-legacy.js', () => {
-  describe('Options validation for joint file type expansion functions', () => {
-    it('cells.json with extra options fails validation', () => {
-      expect(() => expandCellsJson({
-        fileType: 'cells.json',
-        url: 'http://localhost:8000/cells.json',
-        options: {
-          badKey: 'test',
-          embeddingTypes: ['UMAP', 't-SNE'],
-          obsLabelsTypes: ['cluster', 'subcluster'],
-        },
-      })).toThrow();
-    });
-    it('molecules.json with any options fails validation', () => {
-      expect(() => expandMoleculesJson({
-        fileType: 'molecules.json',
-        url: 'http://localhost:8000/molecules.json',
-        options: {},
-      })).toThrow();
-    });
-    it('expression-matrix.zarr with any options fails validation', () => {
-      expect(() => expandExpressionMatrixZarr({
-        fileType: 'expression-matrix.zarr',
-        url: 'http://localhost:8000/expression-matrix.zarr',
-        options: {},
-      })).toThrow();
-    });
-    it('raster.ome-zarr with any options fails validation', () => {
-      expect(() => expandRasterOmeZarr({
-        fileType: 'raster.ome-zarr',
-        url: 'http://localhost:8000/raster.ome-zarr',
-        options: {},
-      })).toThrow();
-    });
-    it('cell-sets.json with any options fails validation', () => {
-      expect(() => expandCellSetsJson({
-        fileType: 'cell-sets.json',
-        url: 'http://localhost:8000/cell-sets.json',
-        options: {},
-      })).toThrow();
-    });
-    it('clusters.json with any options fails validation', () => {
-      expect(() => expandClustersJson({
-        fileType: 'clusters.json',
-        url: 'http://localhost:8000/clusters.json',
-        options: {},
-      })).toThrow();
-    });
-    it('genes.json with any options fails validation', () => {
-      expect(() => expandGenesJson({
-        fileType: 'genes.json',
-        url: 'http://localhost:8000/genes.json',
-        options: {},
-      })).toThrow();
-    });
-    it('anndata-cells.zarr with extra options fails validation', () => {
-      expect(() => expandAnndataCellsZarr({
-        fileType: 'anndata-cells.zarr',
-        url: 'http://localhost:8000/anndata-cells.zarr',
-        options: {
-          poly: 'obsm/poly',
-          xy: 'obsm/xy',
-          bad: 'bad',
-        },
-      })).toThrow();
-    });
-    it('anndata-cells.zarr with invalid options fails validation', () => {
-      expect(() => expandAnndataCellsZarr({
-        fileType: 'anndata-cells.zarr',
-        url: 'http://localhost:8000/anndata-cells.zarr',
-        options: {
-          poly: 'obsm/poly',
-          xy: 'obsm/xy',
-          mappings: {
-            UMAP: ['bad'],
-          },
-        },
-      })).toThrow();
-    });
-    it('anndata-cell-sets.zarr with invalid options fails validation', () => {
-      expect(() => expandAnndataCellSetsZarr({
-        fileType: 'anndata-cell-sets.zarr',
-        url: 'http://localhost:8000/anndata-cell-sets.zarr',
-        options: {},
-      })).toThrow();
-    });
-    it('anndata-cell-sets.zarr with extra options fails validation', () => {
-      expect(() => expandAnndataCellSetsZarr({
-        fileType: 'anndata-cell-sets.zarr',
-        url: 'http://localhost:8000/anndata-cell-sets.zarr',
-        options: [
-          {
-            groupName: 'Cell Type Annotations',
-            setName: 'obs/cell_type',
-            scoreName: 'obs/score',
-            bad: 'bad',
-          },
-        ],
-      })).toThrow();
-    });
-    it('anndata-expression-matrix.zarr with invalid options fails validation', () => {
-      expect(() => expandAnndataExpressionMatrixZarr({
-        fileType: 'anndata-expression-matrix.zarr',
-        url: 'http://localhost:8000/anndata-expression-matrix.zarr',
-        options: {
-          matrix: 'good',
-          geneAlias: 1,
-        },
-      })).toThrow();
-    });
-    it('anndata-expression-matrix.zarr with extra options fails validation', () => {
-      expect(() => expandAnndataExpressionMatrixZarr({
-        fileType: 'anndata-expression-matrix.zarr',
-        url: 'http://localhost:8000/anndata-expression-matrix.zarr',
-        options: {
-          matrix: 'good',
-          geneAlias: 'good',
-          geneFilter: 'good',
-          matrixGeneFilter: 'good',
-          bad: 'bad',
-        },
-      })).toThrow();
-    });
-  });
-});

package/src/file-options-schemas.js

@@ -1,327 +0,0 @@
-import Ajv from 'ajv';
-
-export function validateOptions(optionsSchema, options) {
-  const validate = new Ajv().compile(optionsSchema);
-  const valid = validate(options || null);
-  if (!valid) {
-    console.warn(JSON.stringify(validate.errors, null, 2));
-    throw new Error(`File definition options failed schema validation (${optionsSchema.title})`);
-  }
-  return true;
-}
-
-export const emptySchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#empty-options',
-  title: 'Empty options',
-  oneOf: [
-    { type: 'null' },
-  ],
-};
-
-const sharedDefinitions = {
-  annDataObs: {
-    type: 'object',
-    additionalProperties: false,
-    required: ['path'],
-    properties: {
-      path: { type: 'string' },
-    },
-  },
-  annDataObsm: {
-    type: 'object',
-    additionalProperties: false,
-    required: ['path'],
-    properties: {
-      path: { type: 'string' },
-      dims: {
-        type: 'array',
-        description: 'Which indices of the obsm object to take for a scatterplot, allowing for, for example, different PCs from obsm/X_pca',
-        items: { type: 'number' },
-      },
-    },
-  },
-  annDataConvenienceObsLabelsItem: {
-    type: 'object',
-    additionalProperties: false,
-    required: ['path', 'obsLabelsType'],
-    properties: {
-      path: { type: 'string' },
-      obsLabelsType: { type: 'string' },
-    },
-  },
-  annDataConvenienceFeatureLabelsItem: {
-    type: 'object',
-    additionalProperties: false,
-    required: ['path', 'featureLabelsType'],
-    properties: {
-      path: { type: 'string' },
-      featureLabelsType: { type: 'string' },
-    },
-  },
-  annDataConvenienceObsEmbeddingItem: {
-    type: 'object',
-    additionalProperties: false,
-    required: ['path', 'embeddingType'],
-    properties: {
-      path: { type: 'string' },
-      dims: {
-        type: 'array',
-        description: 'Which indices of the obsm object to take for a scatterplot, allowing for, for example, different PCs from obsm/X_pca',
-        items: { type: 'number' },
-      },
-      embeddingType: { type: 'string' },
-    },
-  },
-  annDataObsLabels: { $ref: '#/definitions/annDataObs' },
-  annDataFeatureLabels: { $ref: '#/definitions/annDataObs' },
-  annDataObsFeatureMatrix: {
-    type: 'object',
-    description: 'Options for the obsFeatureMatrix.anndata.zarr file type.',
-    additionalProperties: false,
-    required: ['path'],
-    properties: {
-      path: { type: 'string' },
-      featureFilterPath: {
-        type: 'string',
-        description: 'If the feature index should be filtered, put a boolean column here (analogous to the previous geneFilter option). e.g., var/in_obsm_X_small_matrix',
-      },
-      initialFeatureFilterPath: {
-        type: 'string',
-        description: 'If only a subset of the matrix should be loaded initially, put a boolean column along the feature axis here (analogous to the previous matrixGeneFilter option). e.g., var/highly_variable',
-      },
-    },
-  },
-  annDataObsSets: {
-    type: 'array',
-    description: 'Options for the obsSets.anndata.zarr file type.',
-    items: {
-      type: 'object',
-      additionalProperties: false,
-      required: ['name', 'path'],
-      properties: {
-        name: {
-          type: 'string',
-          description: "The display name for the set, like 'Cell Type' or 'Louvain.'",
-        },
-        path: {
-          oneOf: [
-            {
-              type: 'string',
-              description: "The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'",
-            },
-            {
-              type: 'array',
-              items: { type: 'string' },
-              description: 'An array of locations in the AnnData store for a hierarchy of set names, from coarse to fine levels.',
-            },
-          ],
-        },
-        scorePath: {
-          oneOf: [
-            {
-              type: 'string',
-              description: "The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'",
-            },
-          ],
-        },
-      },
-    },
-  },
-  annDataObsLocations: { $ref: '#/definitions/annDataObsm' },
-  annDataObsEmbedding: { $ref: '#/definitions/annDataObsm' },
-  annDataObsSegmentations: { $ref: '#/definitions/annDataObs' },
-};
-
-/**
- * Options schemas for atomic file types.
- */
-// AnnData
-export const obsEmbeddingAnndataSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsEmbedding-anndata-zarr-options',
-  title: 'obsEmbedding.anndata.zarr options',
-  definitions: sharedDefinitions,
-  $ref: '#/definitions/annDataObsEmbedding',
-};
-export const obsLocationsAnndataSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsLocations-anndata-zarr-options',
-  title: 'obsLocations.anndata.zarr options',
-  definitions: sharedDefinitions,
-  $ref: '#/definitions/annDataObsLocations',
-};
-export const obsSegmentationsAnndataSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsSegmentations-anndata-zarr-options',
-  title: 'obsSegmentations.anndata.zarr options',
-  definitions: sharedDefinitions,
-  $ref: '#/definitions/annDataObsSegmentations',
-};
-export const obsSetsAnndataSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsSets-anndata-zarr-options',
-  title: 'obsSets.anndata.zarr options',
-  definitions: sharedDefinitions,
-  $ref: '#/definitions/annDataObsSets',
-};
-export const obsFeatureMatrixAnndataSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsFeatureMatrix-anndata-zarr-options',
-  title: 'obsFeatureMatrix.anndata.zarr options',
-  definitions: sharedDefinitions,
-  $ref: '#/definitions/annDataObsFeatureMatrix',
-};
-export const obsLabelsAnndataSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsLabels-anndata-zarr-options',
-  title: 'obsLabels.anndata.zarr options',
-  definitions: sharedDefinitions,
-  $ref: '#/definitions/annDataObsLabels',
-};
-export const featureLabelsAnndataSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#featureLabels-anndata-zarr-options',
-  title: 'featureLabels.anndata.zarr options',
-  definitions: sharedDefinitions,
-  $ref: '#/definitions/annDataFeatureLabels',
-};
-// CSV
-export const obsEmbeddingCsvSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsEmbedding-csv-options',
-  title: 'obsEmbedding.csv options',
-  type: 'object',
-  required: ['obsIndex', 'obsEmbedding'],
-  properties: {
-    obsIndex: { type: 'string' },
-    obsEmbedding: {
-      type: 'array',
-      items: { type: 'string' },
-      minItems: 2,
-      maxItems: 2,
-    },
-  },
-};
-export const obsLocationsCsvSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsLocations-csv-options',
-  title: 'obsLocations.csv options',
-  type: 'object',
-  required: ['obsIndex', 'obsLocations'],
-  properties: {
-    obsIndex: { type: 'string' },
-    obsLocations: {
-      type: 'array',
-      items: { type: 'string' },
-      minItems: 2,
-      maxItems: 2,
-    },
-  },
-};
-export const obsLabelsCsvSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsLabels-csv-options',
-  title: 'obsLabels.csv options',
-  type: 'object',
-  required: ['obsIndex', 'obsLabels'],
-  properties: {
-    obsIndex: { type: 'string' },
-    obsLabels: { type: 'string' },
-  },
-};
-export const featureLabelsCsvSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#featureLabels-csv-options',
-  title: 'featureLabels.csv options',
-  type: 'object',
-  required: ['featureIndex', 'featureLabels'],
-  properties: {
-    featureIndex: { type: 'string' },
-    featureLabels: { type: 'string' },
-  },
-};
-export const obsSetsCsvSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#obsLabels-csv-options',
-  title: 'obsLabels.csv options',
-  type: 'object',
-  additionalProperties: false,
-  required: ['obsIndex', 'obsSets'],
-  properties: {
-    obsIndex: { type: 'string' },
-    obsSets: {
-      type: 'array',
-      items: {
-        type: 'object',
-        additionalProperties: false,
-        required: ['name', 'column'],
-        properties: {
-          name: {
-            type: 'string',
-            description: "The display name for the set, like 'Cell Type' or 'Louvain'",
-          },
-          column: {
-            oneOf: [
-              {
-                type: 'string',
-                description: "The column for the set, like 'cell_type'",
-              },
-              {
-                type: 'array',
-                items: { type: 'string' },
-                description: 'An array of columns for a hierarchy of set names, from coarse to fine levels.',
-              },
-            ],
-          },
-          scoreColumn: {
-            oneOf: [
-              {
-                type: 'string',
-                description: "The column for the set confidence scores, like 'celltype_prediction_score'",
-              },
-            ],
-          },
-        },
-      },
-    },
-  },
-};
-
-/**
- * Options schemas for joint file types.
- */
-export const anndataZarrSchema = {
-  $schema: 'http://json-schema.org/draft-07/schema#',
-  $id: 'https://github.com/vitessce/vitessce/#anndata-zarr-options',
-  title: 'anndata.zarr options',
-  definitions: sharedDefinitions,
-  type: 'object',
-  minProperties: 1,
-  additionalProperties: false,
-  required: [],
-  properties: {
-    obsLabels: {
-      oneOf: [
-        { $ref: '#/definitions/annDataObsLabels' },
-        { type: 'array', items: { $ref: '#/definitions/annDataConvenienceObsLabelsItem' } },
-      ],
-    },
-    featureLabels: {
-      oneOf: [
-        { $ref: '#/definitions/annDataFeatureLabels' },
-        { type: 'array', items: { $ref: '#/definitions/annDataConvenienceFeatureLabelsItem' } },
-      ],
-    },
-    obsFeatureMatrix: { $ref: '#/definitions/annDataObsFeatureMatrix' },
-    obsSets: { $ref: '#/definitions/annDataObsSets' },
-    obsLocations: { $ref: '#/definitions/annDataObsLocations' },
-    obsSegmentations: { $ref: '#/definitions/annDataObsSegmentations' },
-    obsEmbedding: {
-      oneOf: [
-        { $ref: '#/definitions/annDataObsEmbedding' },
-        { type: 'array', items: { $ref: '#/definitions/annDataConvenienceObsEmbeddingItem' } },
-      ],
-    },
-  },
-};

package/src/file-options-schemas.test.js

@@ -1,26 +0,0 @@
-import {
-  expandAnndataZarr,
-} from './joint-file-types';
-
-describe('src/app/file-options-schemas.js', () => {
-  describe('Options validation for joint file type expansion functions', () => {
-    it('anndata.zarr with invalid options fails validation', () => {
-      expect(() => expandAnndataZarr({
-        fileType: 'anndata.zarr',
-        url: 'http://localhost:8000/anndata.zarr',
-        options: {
-          obsFeatureMatrix: 1,
-        },
-      })).toThrow();
-    });
-    it('anndata.zarr with extra options fails validation', () => {
-      expect(() => expandAnndataZarr({
-        fileType: 'anndata.zarr',
-        url: 'http://localhost:8000/anndata.zarr',
-        options: {
-          bad: 'bad',
-        },
-      })).toThrow();
-    });
-  });
-});