@vitessce/vit-s 2.0.3-beta.0 → 2.0.3

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

@@ -0,0 +1,138 @@
+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

@@ -0,0 +1,327 @@
+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

@@ -0,0 +1,26 @@
+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();
+    });
+  });
+});