@vitessce/constants-internal 2.0.3-beta.0 → 3.0.0

package/dist-tsc/constants.d.ts

@@ -0,0 +1,150 @@
+export namespace ViewType {
+    const DESCRIPTION: string;
+    const STATUS: string;
+    const SCATTERPLOT: string;
+    const SPATIAL: string;
+    const HEATMAP: string;
+    const LAYER_CONTROLLER: string;
+    const GENOMIC_PROFILES: string;
+    const GATING: string;
+    const FEATURE_LIST: string;
+    const OBS_SETS: string;
+    const OBS_SET_SIZES: string;
+    const OBS_SET_FEATURE_VALUE_DISTRIBUTION: string;
+    const FEATURE_VALUE_HISTOGRAM: string;
+}
+export namespace DataType {
+    export const OBS_LABELS: string;
+    export const OBS_EMBEDDING: string;
+    export const OBS_LOCATIONS: string;
+    export const OBS_FEATURE_MATRIX: string;
+    const OBS_SETS_1: string;
+    export { OBS_SETS_1 as OBS_SETS };
+    export const FEATURE_LABELS: string;
+    export const IMAGE: string;
+    export const OBS_SEGMENTATIONS: string;
+    export const NEIGHBORHOODS: string;
+    const GENOMIC_PROFILES_1: string;
+    export { GENOMIC_PROFILES_1 as GENOMIC_PROFILES };
+}
+export namespace FileType {
+    const ANNDATA_ZARR: string;
+    const OBS_EMBEDDING_CSV: string;
+    const OBS_LOCATIONS_CSV: string;
+    const OBS_LABELS_CSV: string;
+    const FEATURE_LABELS_CSV: string;
+    const OBS_FEATURE_MATRIX_CSV: string;
+    const OBS_SEGMENTATIONS_JSON: string;
+    const OBS_SETS_CSV: string;
+    const OBS_SETS_JSON: string;
+    const IMAGE_OME_ZARR: string;
+    const OBS_FEATURE_MATRIX_ANNDATA_ZARR: string;
+    const OBS_SETS_ANNDATA_ZARR: string;
+    const OBS_EMBEDDING_ANNDATA_ZARR: string;
+    const OBS_LOCATIONS_ANNDATA_ZARR: string;
+    const OBS_SEGMENTATIONS_ANNDATA_ZARR: string;
+    const OBS_LABELS_ANNDATA_ZARR: string;
+    const FEATURE_LABELS_ANNDATA_ZARR: string;
+    const OBS_FEATURE_MATRIX_MUDATA_ZARR: string;
+    const OBS_SETS_MUDATA_ZARR: string;
+    const OBS_EMBEDDING_MUDATA_ZARR: string;
+    const OBS_LOCATIONS_MUDATA_ZARR: string;
+    const OBS_SEGMENTATIONS_MUDATA_ZARR: string;
+    const OBS_LABELS_MUDATA_ZARR: string;
+    const FEATURE_LABELS_MUDATA_ZARR: string;
+    const GENOMIC_PROFILES_ZARR: string;
+    const NEIGHBORHOODS_JSON: string;
+    const IMAGE_OME_TIFF: string;
+    const OBS_SEGMENTATIONS_OME_TIFF: string;
+    const OBS_EMBEDDING_CELLS_JSON: string;
+    const OBS_SEGMENTATIONS_CELLS_JSON: string;
+    const OBS_LOCATIONS_CELLS_JSON: string;
+    const OBS_LABELS_CELLS_JSON: string;
+    const OBS_SETS_CELL_SETS_JSON: string;
+    const OBS_FEATURE_MATRIX_GENES_JSON: string;
+    const OBS_FEATURE_MATRIX_CLUSTERS_JSON: string;
+    const OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR: string;
+    const IMAGE_RASTER_JSON: string;
+    const OBS_SEGMENTATIONS_RASTER_JSON: string;
+    const OBS_LOCATIONS_MOLECULES_JSON: string;
+    const OBS_LABELS_MOLECULES_JSON: string;
+    const CELLS_JSON: string;
+    const CELL_SETS_JSON: string;
+    const ANNDATA_CELL_SETS_ZARR: string;
+    const ANNDATA_CELLS_ZARR: string;
+    const EXPRESSION_MATRIX_ZARR: string;
+    const MOLECULES_JSON: string;
+    const RASTER_JSON: string;
+    const RASTER_OME_ZARR: string;
+    const CLUSTERS_JSON: string;
+    const GENES_JSON: string;
+    const ANNDATA_EXPRESSION_MATRIX_ZARR: string;
+}
+export namespace CoordinationType {
+    const DATASET: string;
+    const OBS_TYPE: string;
+    const FEATURE_TYPE: string;
+    const FEATURE_VALUE_TYPE: string;
+    const OBS_LABELS_TYPE: string;
+    const EMBEDDING_TYPE: string;
+    const EMBEDDING_ZOOM: string;
+    const EMBEDDING_ROTATION: string;
+    const EMBEDDING_TARGET_X: string;
+    const EMBEDDING_TARGET_Y: string;
+    const EMBEDDING_TARGET_Z: string;
+    const EMBEDDING_OBS_SET_POLYGONS_VISIBLE: string;
+    const EMBEDDING_OBS_SET_LABELS_VISIBLE: string;
+    const EMBEDDING_OBS_SET_LABEL_SIZE: string;
+    const EMBEDDING_OBS_RADIUS: string;
+    const EMBEDDING_OBS_RADIUS_MODE: string;
+    const EMBEDDING_OBS_OPACITY: string;
+    const EMBEDDING_OBS_OPACITY_MODE: string;
+    const SPATIAL_ZOOM: string;
+    const SPATIAL_ROTATION: string;
+    const SPATIAL_TARGET_X: string;
+    const SPATIAL_TARGET_Y: string;
+    const SPATIAL_TARGET_Z: string;
+    const SPATIAL_ROTATION_X: string;
+    const SPATIAL_ROTATION_Y: string;
+    const SPATIAL_ROTATION_Z: string;
+    const SPATIAL_ROTATION_ORBIT: string;
+    const SPATIAL_ORBIT_AXIS: string;
+    const SPATIAL_AXIS_FIXED: string;
+    const HEATMAP_ZOOM_X: string;
+    const HEATMAP_ZOOM_Y: string;
+    const HEATMAP_TARGET_X: string;
+    const HEATMAP_TARGET_Y: string;
+    const OBS_FILTER: string;
+    const OBS_HIGHLIGHT: string;
+    const OBS_SET_SELECTION: string;
+    const OBS_SET_HIGHLIGHT: string;
+    const OBS_SET_EXPANSION: string;
+    const OBS_SET_COLOR: string;
+    const FEATURE_FILTER: string;
+    const FEATURE_HIGHLIGHT: string;
+    const FEATURE_SELECTION: string;
+    const FEATURE_VALUE_COLORMAP: string;
+    const FEATURE_VALUE_TRANSFORM: string;
+    const FEATURE_VALUE_COLORMAP_RANGE: string;
+    const OBS_COLOR_ENCODING: string;
+    const SPATIAL_IMAGE_LAYER: string;
+    const SPATIAL_SEGMENTATION_LAYER: string;
+    const SPATIAL_POINT_LAYER: string;
+    const SPATIAL_NEIGHBORHOOD_LAYER: string;
+    const GENOMIC_ZOOM_X: string;
+    const GENOMIC_ZOOM_Y: string;
+    const GENOMIC_TARGET_X: string;
+    const GENOMIC_TARGET_Y: string;
+    const ADDITIONAL_OBS_SETS: string;
+    const MOLECULE_HIGHLIGHT: string;
+    const GATING_FEATURE_SELECTION_X: string;
+    const GATING_FEATURE_SELECTION_Y: string;
+    const FEATURE_VALUE_TRANSFORM_COEFFICIENT: string;
+    const TOOLTIPS_VISIBLE: string;
+}
+export namespace STATUS {
+    const LOADING: string;
+    const SUCCESS: string;
+    const ERROR: string;
+}
+//# sourceMappingURL=constants.d.ts.map

package/dist-tsc/constants.d.ts.map

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

package/{dist → dist-tsc}/constants.js

@@ -43,6 +43,7 @@ export const FileType = {
     OBS_SETS_CSV: 'obsSets.csv',
     OBS_SETS_JSON: 'obsSets.json',
     IMAGE_OME_ZARR: 'image.ome-zarr',
+    // AnnData
     OBS_FEATURE_MATRIX_ANNDATA_ZARR: 'obsFeatureMatrix.anndata.zarr',
     OBS_SETS_ANNDATA_ZARR: 'obsSets.anndata.zarr',
     OBS_EMBEDDING_ANNDATA_ZARR: 'obsEmbedding.anndata.zarr',
@@ -50,8 +51,19 @@ export const FileType = {
     OBS_SEGMENTATIONS_ANNDATA_ZARR: 'obsSegmentations.anndata.zarr',
     OBS_LABELS_ANNDATA_ZARR: 'obsLabels.anndata.zarr',
     FEATURE_LABELS_ANNDATA_ZARR: 'featureLabels.anndata.zarr',
+    // MuData
+    OBS_FEATURE_MATRIX_MUDATA_ZARR: 'obsFeatureMatrix.mudata.zarr',
+    OBS_SETS_MUDATA_ZARR: 'obsSets.mudata.zarr',
+    OBS_EMBEDDING_MUDATA_ZARR: 'obsEmbedding.mudata.zarr',
+    OBS_LOCATIONS_MUDATA_ZARR: 'obsLocations.mudata.zarr',
+    OBS_SEGMENTATIONS_MUDATA_ZARR: 'obsSegmentations.mudata.zarr',
+    OBS_LABELS_MUDATA_ZARR: 'obsLabels.mudata.zarr',
+    FEATURE_LABELS_MUDATA_ZARR: 'featureLabels.mudata.zarr',
     GENOMIC_PROFILES_ZARR: 'genomic-profiles.zarr',
     NEIGHBORHOODS_JSON: 'neighborhoods.json',
+    // OME-TIFF
+    IMAGE_OME_TIFF: 'image.ome-tiff',
+    OBS_SEGMENTATIONS_OME_TIFF: 'obsSegmentations.ome-tiff',
     // New file types to support old file types:
     // - cells.json
     OBS_EMBEDDING_CELLS_JSON: 'obsEmbedding.cells.json',
@@ -129,6 +141,7 @@ export const CoordinationType = {
     OBS_HIGHLIGHT: 'obsHighlight',
     OBS_SET_SELECTION: 'obsSetSelection',
     OBS_SET_HIGHLIGHT: 'obsSetHighlight',
+    OBS_SET_EXPANSION: 'obsSetExpansion',
     OBS_SET_COLOR: 'obsSetColor',
     FEATURE_FILTER: 'featureFilter',
     FEATURE_HIGHLIGHT: 'featureHighlight',
@@ -151,6 +164,7 @@ export const CoordinationType = {
     GATING_FEATURE_SELECTION_X: 'gatingFeatureSelectionX',
     GATING_FEATURE_SELECTION_Y: 'gatingFeatureSelectionY',
     FEATURE_VALUE_TRANSFORM_COEFFICIENT: 'featureValueTransformCoefficient',
+    TOOLTIPS_VISIBLE: 'tooltipsVisible',
 };
 export const STATUS = {
     LOADING: 'loading',

package/dist-tsc/coordination.d.ts

@@ -0,0 +1,14 @@
+export const AUTO_INDEPENDENT_COORDINATION_TYPES: string[];
+/**
+   * Mapping from component type to
+   * supported coordination object types.
+   * This mapping can be used to determine
+   * which pieces of state that a component will
+   * need to get/set.
+   * Keys here are the component registry keys.
+   */
+export const COMPONENT_COORDINATION_TYPES: {
+    [x: string]: string[];
+    higlass: string[];
+};
+//# sourceMappingURL=coordination.d.ts.map

package/dist-tsc/coordination.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"coordination.d.ts","sourceRoot":"","sources":["../src/coordination.js"],"names":[],"mappings":"AASA,2DAcE;AAEF;;;;;;;KAOK;AACL;;;EA8OE"}

package/{dist → dist-tsc}/coordination.js

@@ -1,73 +1,11 @@
-import { CoordinationType, ViewType } from './constants';
-/**
- * Coordination types may have default values,
- * which can be defined here, and used by the
- * auto initialization strategy.
- */
-export const DEFAULT_COORDINATION_VALUES = {
-    [CoordinationType.OBS_TYPE]: 'cell',
-    [CoordinationType.FEATURE_TYPE]: 'gene',
-    [CoordinationType.FEATURE_VALUE_TYPE]: 'expression',
-    [CoordinationType.OBS_LABELS_TYPE]: null,
-    [CoordinationType.EMBEDDING_ZOOM]: null,
-    [CoordinationType.EMBEDDING_ROTATION]: 0,
-    [CoordinationType.EMBEDDING_TARGET_X]: null,
-    [CoordinationType.EMBEDDING_TARGET_Y]: null,
-    [CoordinationType.EMBEDDING_TARGET_Z]: 0,
-    [CoordinationType.EMBEDDING_OBS_SET_POLYGONS_VISIBLE]: false,
-    [CoordinationType.EMBEDDING_OBS_SET_LABELS_VISIBLE]: false,
-    [CoordinationType.EMBEDDING_OBS_SET_LABEL_SIZE]: 14,
-    [CoordinationType.EMBEDDING_OBS_RADIUS]: 1,
-    [CoordinationType.EMBEDDING_OBS_RADIUS_MODE]: 'auto',
-    [CoordinationType.EMBEDDING_OBS_OPACITY]: 1,
-    [CoordinationType.EMBEDDING_OBS_OPACITY_MODE]: 'auto',
-    [CoordinationType.SPATIAL_ZOOM]: null,
-    [CoordinationType.SPATIAL_ROTATION]: 0,
-    [CoordinationType.SPATIAL_TARGET_X]: null,
-    [CoordinationType.SPATIAL_TARGET_Y]: null,
-    [CoordinationType.SPATIAL_TARGET_Z]: null,
-    [CoordinationType.SPATIAL_ROTATION_X]: null,
-    [CoordinationType.SPATIAL_ROTATION_Y]: null,
-    [CoordinationType.SPATIAL_ROTATION_Z]: null,
-    [CoordinationType.SPATIAL_AXIS_FIXED]: false,
-    [CoordinationType.SPATIAL_ROTATION_ORBIT]: 0,
-    [CoordinationType.SPATIAL_ORBIT_AXIS]: 'Y',
-    [CoordinationType.SPATIAL_IMAGE_LAYER]: null,
-    [CoordinationType.SPATIAL_SEGMENTATION_LAYER]: null,
-    [CoordinationType.SPATIAL_POINT_LAYER]: null,
-    [CoordinationType.SPATIAL_NEIGHBORHOOD_LAYER]: null,
-    [CoordinationType.HEATMAP_ZOOM_X]: 0,
-    [CoordinationType.HEATMAP_ZOOM_Y]: 0,
-    [CoordinationType.HEATMAP_TARGET_X]: 0,
-    [CoordinationType.HEATMAP_TARGET_Y]: 0,
-    [CoordinationType.FEATURE_VALUE_COLORMAP]: 'plasma',
-    [CoordinationType.FEATURE_VALUE_COLORMAP_RANGE]: [0.0, 1.0],
-    [CoordinationType.FEATURE_VALUE_TRANSFORM]: null,
-    [CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT]: 1,
-    [CoordinationType.FEATURE_FILTER]: null,
-    [CoordinationType.FEATURE_HIGHLIGHT]: null,
-    [CoordinationType.FEATURE_SELECTION]: null,
-    [CoordinationType.OBS_FILTER]: null,
-    [CoordinationType.OBS_HIGHLIGHT]: null,
-    [CoordinationType.OBS_SET_SELECTION]: null,
-    [CoordinationType.OBS_SET_HIGHLIGHT]: null,
-    [CoordinationType.OBS_SET_COLOR]: null,
-    [CoordinationType.OBS_COLOR_ENCODING]: 'cellSetSelection',
-    [CoordinationType.GENOMIC_ZOOM_X]: 0,
-    [CoordinationType.GENOMIC_ZOOM_Y]: 0,
-    [CoordinationType.GENOMIC_TARGET_X]: 1549999999.5,
-    [CoordinationType.GENOMIC_TARGET_Y]: 1549999999.5,
-    [CoordinationType.ADDITIONAL_OBS_SETS]: null,
-    [CoordinationType.MOLECULE_HIGHLIGHT]: null,
-    [CoordinationType.GATING_FEATURE_SELECTION_X]: null,
-    [CoordinationType.GATING_FEATURE_SELECTION_Y]: null,
-};
+import { CoordinationType, ViewType } from './constants.js';
 // The following coordination types should be
 // initialized to independent scopes when
 // initialized automatically.
 // These make the resulting view config
 // (after auto-initialization) behave
 // like "legacy" Vitessce (pre-coordination model).
+// TODO: delegate to PluginCoordinationType class
 export const AUTO_INDEPENDENT_COORDINATION_TYPES = [
     CoordinationType.HEATMAP_ZOOM_X,
     CoordinationType.HEATMAP_ZOOM_Y,
@@ -122,6 +60,7 @@ export const COMPONENT_COORDINATION_TYPES = {
         CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
         CoordinationType.OBS_COLOR_ENCODING,
         CoordinationType.ADDITIONAL_OBS_SETS,
+        CoordinationType.TOOLTIPS_VISIBLE,
     ],
     [ViewType.GATING]: [
         CoordinationType.DATASET,
@@ -190,6 +129,7 @@ export const COMPONENT_COORDINATION_TYPES = {
         CoordinationType.OBS_COLOR_ENCODING,
         CoordinationType.ADDITIONAL_OBS_SETS,
         CoordinationType.MOLECULE_HIGHLIGHT,
+        CoordinationType.TOOLTIPS_VISIBLE,
     ],
     [ViewType.HEATMAP]: [
         CoordinationType.DATASET,
@@ -213,11 +153,13 @@ export const COMPONENT_COORDINATION_TYPES = {
         CoordinationType.FEATURE_VALUE_COLORMAP_RANGE,
         CoordinationType.OBS_COLOR_ENCODING,
         CoordinationType.ADDITIONAL_OBS_SETS,
+        CoordinationType.TOOLTIPS_VISIBLE,
     ],
     [ViewType.OBS_SETS]: [
         CoordinationType.DATASET,
         CoordinationType.OBS_TYPE,
         CoordinationType.OBS_SET_SELECTION,
+        CoordinationType.OBS_SET_EXPANSION,
         CoordinationType.OBS_SET_HIGHLIGHT,
         CoordinationType.OBS_SET_COLOR,
         CoordinationType.OBS_COLOR_ENCODING,
@@ -228,6 +170,7 @@ export const COMPONENT_COORDINATION_TYPES = {
         CoordinationType.DATASET,
         CoordinationType.OBS_TYPE,
         CoordinationType.OBS_SET_SELECTION,
+        CoordinationType.OBS_SET_EXPANSION,
         CoordinationType.OBS_SET_HIGHLIGHT,
         CoordinationType.OBS_SET_COLOR,
         CoordinationType.ADDITIONAL_OBS_SETS,
@@ -269,6 +212,10 @@ export const COMPONENT_COORDINATION_TYPES = {
         CoordinationType.FEATURE_TYPE,
         CoordinationType.FEATURE_VALUE_TYPE,
         CoordinationType.FEATURE_SELECTION,
+        CoordinationType.ADDITIONAL_OBS_SETS,
+        CoordinationType.OBS_SET_COLOR,
+        CoordinationType.OBS_COLOR_ENCODING,
+        CoordinationType.OBS_SET_SELECTION,
     ],
     [ViewType.LAYER_CONTROLLER]: [
         CoordinationType.DATASET,

package/dist-tsc/index.d.ts

@@ -0,0 +1,4 @@
+export { ViewType, DataType, FileType, CoordinationType, STATUS } from "./constants.js";
+export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE } from "./constant-relationships.js";
+export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from "./coordination.js";
+//# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.d.ts.map

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

package/dist-tsc/index.js

@@ -0,0 +1,4 @@
+export { ViewType, DataType, FileType, CoordinationType, STATUS, } from './constants.js';
+export { FILE_TYPE_DATA_TYPE_MAPPING, DATA_TYPE_COORDINATION_VALUE_USAGE } from './constant-relationships.js';
+export { AUTO_INDEPENDENT_COORDINATION_TYPES, COMPONENT_COORDINATION_TYPES } from './coordination.js';
+export { default as META_VERSION } from './version.json';

package/dist-tsc/version.json

@@ -0,0 +1,7 @@
+{
+    "note": "This file is regenerated by push-demo.sh.",
+    "version": "3.0.0",
+    "branch": "release-v3.0.0",
+    "date": "2023-06-05",
+    "hash": "74d01aab"
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/constants-internal",
-  "version": "2.0.3-beta.0",
+  "version": "3.0.0",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -8,17 +8,26 @@
     "url": "git+https://github.com/vitessce/vitessce.git"
   },
   "license": "MIT",
+  "type": "module",
   "main": "dist/index.js",
   "files": [
-    "dist"
+    "src",
+    "dist",
+    "dist-tsc"
   ],
   "devDependencies": {
-    "vite": "^3.0.0",
+    "vite": "^4.3.0",
     "vitest": "^0.23.4"
   },
   "scripts": {
-    "start": "tsc --watch",
-    "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/constant-relationships.js

@@ -0,0 +1,87 @@
+import { FileType, DataType, CoordinationType } from './constants.js';
+
+/**
+ * Mapping from file types to data types. Each file type
+ * should correspond to one data type. Multiple file types
+ * can map onto the same data type.
+ */
+export const FILE_TYPE_DATA_TYPE_MAPPING = {
+  // For new file types
+  [FileType.OBS_EMBEDDING_CSV]: DataType.OBS_EMBEDDING,
+  [FileType.OBS_LOCATIONS_CSV]: DataType.OBS_LOCATIONS,
+  [FileType.OBS_LABELS_CSV]: DataType.OBS_LABELS,
+  [FileType.FEATURE_LABELS_CSV]: DataType.FEATURE_LABELS,
+  [FileType.OBS_FEATURE_MATRIX_CSV]: DataType.OBS_FEATURE_MATRIX,
+  [FileType.OBS_SEGMENTATIONS_JSON]: DataType.OBS_SEGMENTATIONS,
+  [FileType.OBS_SETS_CSV]: DataType.OBS_SETS,
+  [FileType.OBS_SETS_JSON]: DataType.OBS_SETS,
+  [FileType.IMAGE_OME_ZARR]: DataType.IMAGE,
+  [FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
+  [FileType.OBS_SETS_ANNDATA_ZARR]: DataType.OBS_SETS,
+  [FileType.OBS_EMBEDDING_ANNDATA_ZARR]: DataType.OBS_EMBEDDING,
+  [FileType.OBS_LOCATIONS_ANNDATA_ZARR]: DataType.OBS_LOCATIONS,
+  [FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR]: DataType.OBS_SEGMENTATIONS,
+  [FileType.OBS_LABELS_ANNDATA_ZARR]: DataType.OBS_LABELS,
+  [FileType.FEATURE_LABELS_ANNDATA_ZARR]: DataType.FEATURE_LABELS,
+  [FileType.IMAGE_OME_TIFF]: DataType.IMAGE,
+  [FileType.OBS_SEGMENTATIONS_OME_TIFF]: DataType.OBS_SEGMENTATIONS,
+  [FileType.OBS_FEATURE_MATRIX_MUDATA_ZARR]: DataType.OBS_FEATURE_MATRIX,
+  [FileType.OBS_SETS_MUDATA_ZARR]: DataType.OBS_SETS,
+  [FileType.OBS_EMBEDDING_MUDATA_ZARR]: DataType.OBS_EMBEDDING,
+  [FileType.OBS_LOCATIONS_MUDATA_ZARR]: DataType.OBS_LOCATIONS,
+  [FileType.OBS_SEGMENTATIONS_MUDATA_ZARR]: DataType.OBS_SEGMENTATIONS,
+  [FileType.OBS_LABELS_MUDATA_ZARR]: DataType.OBS_LABELS,
+  [FileType.FEATURE_LABELS_MUDATA_ZARR]: DataType.FEATURE_LABELS,
+  // For new file types to support old file types
+  [FileType.OBS_EMBEDDING_CELLS_JSON]: DataType.OBS_EMBEDDING,
+  [FileType.OBS_LOCATIONS_CELLS_JSON]: DataType.OBS_LOCATIONS,
+  [FileType.OBS_SEGMENTATIONS_CELLS_JSON]: DataType.OBS_SEGMENTATIONS,
+  [FileType.OBS_LABELS_CELLS_JSON]: DataType.OBS_LABELS,
+  [FileType.OBS_SETS_CELL_SETS_JSON]: DataType.OBS_SETS,
+  [FileType.OBS_FEATURE_MATRIX_GENES_JSON]: DataType.OBS_FEATURE_MATRIX,
+  [FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON]: DataType.OBS_FEATURE_MATRIX,
+  [FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR]: DataType.OBS_FEATURE_MATRIX,
+  [FileType.IMAGE_RASTER_JSON]: DataType.IMAGE,
+  [FileType.OBS_SEGMENTATIONS_RASTER_JSON]: DataType.OBS_SEGMENTATIONS,
+  [FileType.OBS_LOCATIONS_MOLECULES_JSON]: DataType.OBS_LOCATIONS,
+  [FileType.OBS_LABELS_MOLECULES_JSON]: DataType.OBS_LABELS,
+  // For old file types
+  [FileType.GENOMIC_PROFILES_ZARR]: DataType.GENOMIC_PROFILES,
+  [FileType.NEIGHBORHOODS_JSON]: DataType.NEIGHBORHOODS,
+};
+
+/**
+ * Store a mapping from data types to the coordination types used
+ * for matching using the coordinationValues field of file definitions.
+ * This enables inferring default values, simplifying view config writing.
+ */
+export const DATA_TYPE_COORDINATION_VALUE_USAGE = {
+  [DataType.OBS_SEGMENTATIONS]: [
+    CoordinationType.OBS_TYPE,
+  ],
+  [DataType.OBS_EMBEDDING]: [
+    CoordinationType.OBS_TYPE,
+    CoordinationType.EMBEDDING_TYPE,
+  ],
+  [DataType.OBS_LOCATIONS]: [
+    CoordinationType.OBS_TYPE,
+  ],
+  [DataType.OBS_LABELS]: [
+    CoordinationType.OBS_TYPE,
+    CoordinationType.OBS_LABELS_TYPE,
+  ],
+  [DataType.FEATURE_LABELS]: [
+    CoordinationType.FEATURE_TYPE,
+  ],
+  [DataType.OBS_SETS]: [
+    CoordinationType.OBS_TYPE,
+  ],
+  [DataType.OBS_FEATURE_MATRIX]: [
+    CoordinationType.OBS_TYPE,
+    CoordinationType.FEATURE_TYPE,
+    CoordinationType.FEATURE_VALUE_TYPE,
+  ],
+  [DataType.GENOMIC_PROFILES]: [],
+  [DataType.IMAGE]: [],
+  [DataType.NEIGHBORHOODS]: [],
+};

package/src/constant-relationships.test.js

@@ -0,0 +1,14 @@
+import { DataType } from './constants.js';
+import {
+  DATA_TYPE_COORDINATION_VALUE_USAGE,
+} from './constant-relationships.js';
+
+describe('src/app/constant-relationships.js', () => {
+  describe('DataType-to-CoordinationType usage mapping', () => {
+    it('every data type is mapped to an array of coordination types', () => {
+      const dataTypes = Object.values(DataType).sort();
+      const mappedDataTypes = Object.keys(DATA_TYPE_COORDINATION_VALUE_USAGE).sort();
+      expect(dataTypes.length).toEqual(mappedDataTypes.length);
+    });
+  });
+});