@vitessce/vit-s 3.5.1 → 3.5.3

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

@@ -1 +1 @@
-{"version":3,"file":"VitessceGrid.d.ts","sourceRoot":"","sources":["../src/VitessceGrid.js"],"names":[],"mappings":"AA4BA;;;;;;;;;;;;GAYG;AACH,4CAVG;IAAsB,SAAS,EAAvB,MAAM;IACQ,MAAM,EAApB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,MAAM,EAApB,MAAM;IACU,MAAM;IACE,SAAS,EAAjC,cAAc,EAAE;IACQ,SAAS,EAAjC,cAAc,EAAE;IACgB,iBAAiB,EAAjD,sBAAsB,EAAE;IACT,QAAQ,EAAvB,OAAO;CACjB,eAkGA"}
+{"version":3,"file":"VitessceGrid.d.ts","sourceRoot":"","sources":["../src/VitessceGrid.js"],"names":[],"mappings":"AA4BA;;;;;;;;;;;;GAYG;AACH,4CAVG;IAAsB,SAAS,EAAvB,MAAM;IACQ,MAAM,EAApB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,MAAM,EAApB,MAAM;IACU,MAAM;IACE,SAAS,EAAjC,cAAc,EAAE;IACQ,SAAS,EAAjC,cAAc,EAAE;IACgB,iBAAiB,EAAjD,sBAAsB,EAAE;IACT,QAAQ,EAAvB,OAAO;CACjB,eAqGA"}

package/dist-tsc/VitessceGrid.js

@@ -62,5 +62,5 @@ export default function VitessceGrid(props) {
         setLoaders(newLoaders);
         // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [success, configKey]);
-    return (_jsx("div", { ref: containerRef, className: clsx(VITESSCE_CONTAINER, classes.vitessceContainer), role: "group", "aria-label": altText, children: layout ? (_jsx(VitessceGridLayout, { pageMode: pageMode, role: "group", layout: layout, height: height, rowHeight: rowHeight, theme: theme, viewTypes: viewTypes, draggableHandle: titleClasses.title, margin: margin, padding: padding, onRemoveComponent: removeComponent, onLayoutChange: changeLayoutPostMount, isBounded: isBounded, onResize: onResize, onResizeStop: onResize, children: children })) : null }));
+    return (_jsx("div", { ref: containerRef, className: clsx(VITESSCE_CONTAINER, classes.vitessceContainer), role: "group", "aria-label": altText, children: layout ? (_jsx(VitessceGridLayout, { pageMode: pageMode, role: "group", layout: layout, height: height, rowHeight: rowHeight, theme: theme, viewTypes: viewTypes, fileTypes: fileTypes, coordinationTypes: coordinationTypes, stores: stores, draggableHandle: titleClasses.title, margin: margin, padding: padding, onRemoveComponent: removeComponent, onLayoutChange: changeLayoutPostMount, isBounded: isBounded, onResize: onResize, onResizeStop: onResize, children: children })) : null }));
 }

package/dist-tsc/data-hook-utils.d.ts

@@ -62,5 +62,5 @@ export function useDataType(dataType: any, loaders: object, dataset: string, isR
  */
 export function useDataTypeMulti(dataType: any, loaders: object, dataset: string, isRequired: boolean, coordinationSetters: object, initialCoordinationValues: object, matchOnObj: any, mergeCoordination: any, viewUid: any): array;
 export function useHasLoader(loaders: any, dataset: any, dataType: any, matchOn: any): boolean;
-import { AbstractLoaderError } from './errors/index.js';
+import { AbstractLoaderError } from '@vitessce/abstract';
 //# sourceMappingURL=data-hook-utils.d.ts.map

package/dist-tsc/data-hook-utils.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"data-hook-utils.d.ts","sourceRoot":"","sources":["../src/data-hook-utils.js"],"names":[],"mappings":"AAiBA;;;;GAIG;AACH,4BAFW,mBAAmB,yBAS7B;AAED;;;;;;;;;;GAUG;AACH,8CATW,MAAM,WAGN,MAAM,iBAGN,MAAM,QAiBhB;AAGD,oDAuBC;AAED;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,oDAhBW,MAAM,WAEN,MAAM,cAEN,OAAO,uBAEP,MAAM,6BAGN,MAAM,iBAGJ,KAAK,CAiDjB;AAED;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,yDAhBW,MAAM,WAEN,MAAM,cAEN,OAAO,uBAEP,MAAM,6BAGN,MAAM,0DAGJ,KAAK,CAsFjB;AAED,+FAGC;oCArPM,mBAAmB"}
+{"version":3,"file":"data-hook-utils.d.ts","sourceRoot":"","sources":["../src/data-hook-utils.js"],"names":[],"mappings":"AAiBA;;;;GAIG;AACH,4BAFW,mBAAmB,yBAS7B;AAED;;;;;;;;;;GAUG;AACH,8CATW,MAAM,WAGN,MAAM,iBAGN,MAAM,QAiBhB;AAGD,oDAuBC;AAED;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,oDAhBW,MAAM,WAEN,MAAM,cAEN,OAAO,uBAEP,MAAM,6BAGN,MAAM,iBAGJ,KAAK,CAiDjB;AAED;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,yDAhBW,MAAM,WAEN,MAAM,cAEN,OAAO,uBAEP,MAAM,6BAGN,MAAM,0DAGJ,KAAK,CAsFjB;AAED,+FAGC;oCA1PM,oBAAoB"}

package/dist-tsc/data-hook-utils.js

@@ -2,8 +2,8 @@ import { useEffect, useMemo } from 'react';
 import { useQuery, useQueries } from '@tanstack/react-query';
 import { capitalize, getInitialCoordinationScopePrefix, } from '@vitessce/utils';
 import { STATUS } from '@vitessce/constants-internal';
+import { AbstractLoaderError, LoaderNotFoundError, } from '@vitessce/abstract';
 import { getMatchingLoader, useMatchingLoader, useSetWarning, } from './state/hooks.js';
-import { AbstractLoaderError, LoaderNotFoundError, } from './errors/index.js';
 /**
  * Warn via publishing to the console
  * and to the global warning store.

package/dist-tsc/data-hooks-multilevel-utils.js

@@ -2,8 +2,8 @@ import { useEffect, useMemo } from 'react';
 import { useQueries } from '@tanstack/react-query';
 import { extent } from 'd3-array';
 import { DataType, STATUS } from '@vitessce/constants-internal';
+import { LoaderNotFoundError, } from '@vitessce/abstract';
 import { getMatchingLoader, useSetWarning, } from './state/hooks.js';
-import { LoaderNotFoundError, } from './errors/index.js';
 import { warn, dataQueryFn, } from './data-hook-utils.js';
 function getFeatureSelectionQueryKeyScopeTuplesAux(allSelections, allMatchOnObj, depth, dataset, dataType, isRequired, prevLevelScopes, currSelection, currMatchOn) {
     // Base case

package/dist-tsc/data-hooks.js

@@ -1,8 +1,8 @@
 import { useState, useEffect, useMemo } from 'react';
 import { CoordinationType, DataType, STATUS } from '@vitessce/constants-internal';
 import { useQuery, useQueries } from '@tanstack/react-query';
+import { LoaderNotFoundError, } from '@vitessce/abstract';
 import { useMultiCoordinationValues, useComplexCoordination, useSetWarning, getMatchingLoader, } from './state/hooks.js';
-import { LoaderNotFoundError, } from './errors/index.js';
 import { warn, useDataType, useDataTypeMulti, } from './data-hook-utils.js';
 /**
  * Get the dataset description string.

package/dist-tsc/hooks.d.ts

@@ -82,4 +82,18 @@ export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, exp
 }): any;
 export function useGetObsMembership(obsSetsMembership: any): any;
 export function useGetObsInfo(obsType: any, obsLabelsTypes: any, obsLabelsData: any, obsSetsMembership: any): any;
+/**
+ * This hook expands a featureLabelsMap
+ * by including mappings from ENSEMBL to HGNC IDs.
+ * User-provided mappings should take precedence,
+ * but they are not always provided in the config or contained
+ * in a column of the AnnData.var dataframe, for example.
+ * @param {string} featureType A feature type. Fetching is only done for 'gene'.
+ * @param {Map|null} featureLabelsMap An optional user-supplied feature labels
+ * mapping from the dataset.
+ * @returns {{ stripCuriePrefixes: boolean }|null} An options object.
+ */
+export function useExpandedFeatureLabelsMap(featureType: string, featureLabelsMap: Map<any, any> | null, options: any): {
+    stripCuriePrefixes: boolean;
+} | null;
 //# sourceMappingURL=hooks.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../src/hooks.js"],"names":[],"mappings":"AAkBA,oDAOC;AAED;;;;GAIG;AACH,uCAHa,KAAK,CAmBjB;AAED;;;;GAIG;AACH,mCAHa,KAAK,CAoCjB;AAED;;;;;GAKG;AACH,qCAJa,KAAK,CAqCjB;AAED;;;;;;GAMG;AACH,uCAHW,MAAM,EAAE,GACN,OAAO,CAOnB;AAED;;;;GAIG;AACH,8BAHW,CAAC,IAAI,GAAC,MAAM,EAAE,CAAC,EAAE,GACf,KAAK,CAYjB;AAED;;;;;;GAMG;AACH,qDAJW,GAAG,GACD,KAAK,CA0BjB;AAED;;;;;;;;;;GAUG;AACH,+DARG;IAAuB,gBAAgB,EAA/B,MAAM;CAEd,GAAU,KAAK,CAmBjB;AAED;;;;;;;;;;;;;;;GAeG;AACH,yDAbW,YAAY,EAAE,GAAG,IAAI,GAInB;IACZ,QAAW,EAAE,UAAU,EAAE,GAAG,IAAI,CAAC;IACjC,OAAU,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,GAAG,IAAI,CAAC;IACtC,OAAU,EAAE,MAAM,EAAE,CAAA;CACjB,CAwBH;AAED;;;;QA2BC;AAED,iEAOC;AAED,kHA4BC"}
+{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../src/hooks.js"],"names":[],"mappings":"AAqBA,oDAOC;AAED;;;;GAIG;AACH,uCAHa,KAAK,CAmBjB;AAED;;;;GAIG;AACH,mCAHa,KAAK,CAoCjB;AAED;;;;;GAKG;AACH,qCAJa,KAAK,CAqCjB;AAED;;;;;;GAMG;AACH,uCAHW,MAAM,EAAE,GACN,OAAO,CAOnB;AAED;;;;GAIG;AACH,8BAHW,CAAC,IAAI,GAAC,MAAM,EAAE,CAAC,EAAE,GACf,KAAK,CAYjB;AAED;;;;;;GAMG;AACH,qDAJW,GAAG,GACD,KAAK,CA0BjB;AAED;;;;;;;;;;GAUG;AACH,+DARG;IAAuB,gBAAgB,EAA/B,MAAM;CAEd,GAAU,KAAK,CAmBjB;AAED;;;;;;;;;;;;;;;GAeG;AACH,yDAbW,YAAY,EAAE,GAAG,IAAI,GAInB;IACZ,QAAW,EAAE,UAAU,EAAE,GAAG,IAAI,CAAC;IACjC,OAAU,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,GAAG,IAAI,CAAC;IACtC,OAAU,EAAE,MAAM,EAAE,CAAA;CACjB,CAwBH;AAED;;;;QA2BC;AAED,iEAOC;AAED,kHA4BC;AAED;;;;;;;;;;GAUG;AACH,yDALW,MAAM,oBACN,gBAAI,IAAI,iBAEN;IAAE,kBAAkB,EAAE,OAAO,CAAA;CAAE,GAAC,IAAI,CA4BhD"}

package/dist-tsc/hooks.js

@@ -1,10 +1,12 @@
 import { useRef, useState, useEffect, useCallback, useMemo, } from 'react';
 import { debounce, every } from 'lodash-es';
 import { extent } from 'd3-array';
+import { useQuery } from '@tanstack/react-query';
 import { capitalize } from '@vitessce/utils';
-import { STATUS } from '@vitessce/constants-internal';
+import { STATUS, AsyncFunctionType } from '@vitessce/constants-internal';
 import { useGridResize, useEmitGridResize } from './state/hooks.js';
 import { VITESSCE_CONTAINER } from './classNames.js';
+import { useAsyncFunction } from './contexts.js';
 function getWindowDimensions() {
     const { innerWidth: width, innerHeight: height } = window;
     return {
@@ -273,3 +275,39 @@ export function useGetObsInfo(obsType, obsLabelsTypes, obsLabelsData, obsSetsMem
         return null;
     }, [obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership]);
 }
+/**
+ * This hook expands a featureLabelsMap
+ * by including mappings from ENSEMBL to HGNC IDs.
+ * User-provided mappings should take precedence,
+ * but they are not always provided in the config or contained
+ * in a column of the AnnData.var dataframe, for example.
+ * @param {string} featureType A feature type. Fetching is only done for 'gene'.
+ * @param {Map|null} featureLabelsMap An optional user-supplied feature labels
+ * mapping from the dataset.
+ * @returns {{ stripCuriePrefixes: boolean }|null} An options object.
+ */
+export function useExpandedFeatureLabelsMap(featureType, featureLabelsMap, options) {
+    // TODO: Should this be done via a hook?
+    // We could alternatively expand these types of mappings in the featureLabels data loader class.
+    // TODO: Add an option to opt-out?
+    const { stripCuriePrefixes = true } = options || {};
+    const getTermMapping = useAsyncFunction(AsyncFunctionType.GET_TERM_MAPPING);
+    const termMappingQuery = useQuery({
+        enabled: (featureType === 'gene'),
+        queryKey: ['useExpandedFeatureLabelsMap', 'ensembl', 'hgnc'],
+        queryFn: async () => getTermMapping('ensembl', 'hgnc'),
+    });
+    const { data: fetchedMapping, status, isFetching } = termMappingQuery;
+    const updatedFeatureLabelsMap = useMemo(() => {
+        if (!fetchedMapping)
+            return featureLabelsMap;
+        return new Map([
+            ...(stripCuriePrefixes
+                ? Array.from(fetchedMapping).map(([k, v]) => ([k.split(':')[1], v.split(':')[1]]))
+                : fetchedMapping),
+            ...(featureLabelsMap || []),
+        ]);
+    }, [fetchedMapping, featureLabelsMap, stripCuriePrefixes]);
+    const dataStatus = isFetching ? STATUS.LOADING : status;
+    return [updatedFeatureLabelsMap, dataStatus];
+}

package/dist-tsc/index.d.ts

@@ -3,12 +3,11 @@ export { TitleInfo } from "./TitleInfo.js";
 export { PopperMenu } from "./shared-mui/components.js";
 export { useHasLoader } from "./data-hook-utils.js";
 export { logConfig } from "./view-config-utils.js";
-export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize } from "./hooks.js";
+export { createLoaders } from "./vitessce-grid-utils.js";
+export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, useExpandedFeatureLabelsMap } from "./hooks.js";
 export { useCoordinationScopes, useCoordinationScopesBy, useInitialCoordination, useCoordination, useComplexCoordination, useComplexCoordinationSecondary, useMultiCoordinationScopes, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondary, useMultiCoordinationScopesSecondaryNonNull, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMergeCoordination, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useViewConfig, useSetViewConfig, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, useRemoveImageChannelInMetaCoordinationScopes, useAddImageChannelInMetaCoordinationScopes } from "./state/hooks.js";
 export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useSampleSetsData, useSampleEdgesData, useMultiObsLabels, useMultiObsSpots, useMultiObsPoints, useSpotMultiObsSets, useSpotMultiFeatureLabels, useMultiObsSegmentations, useMultiImages, useObsSpotsData, useObsPointsData, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData } from "./data-hooks.js";
 export { usePointMultiObsLabels, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets } from "./data-hooks-multilevel.js";
-export { AbstractLoader, AbstractTwoStepLoader, LoaderResult } from "./data/index.js";
-export { AbstractLoaderError, DatasetNotFoundError, LoaderNotFoundError, LoaderValidationError, DataSourceFetchError } from "./errors/index.js";
 export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles } from "./shared-plot-options/index.js";
 export { useAsyncFunction, usePageModeView } from "./contexts.js";
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.js

@@ -2,13 +2,12 @@ export { VitS } from './VitS.js';
 export { TitleInfo } from './TitleInfo.js';
 export { PopperMenu } from './shared-mui/components.js';
 // For plugin view types:
-export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, } from './hooks.js';
+export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, useExpandedFeatureLabelsMap, } from './hooks.js';
 export { useCoordinationScopes, useCoordinationScopesBy, useInitialCoordination, useCoordination, useComplexCoordination, useComplexCoordinationSecondary, useMultiCoordinationScopes, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondary, useMultiCoordinationScopesSecondaryNonNull, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMergeCoordination, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useViewConfig, useSetViewConfig, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, useRemoveImageChannelInMetaCoordinationScopes, useAddImageChannelInMetaCoordinationScopes, } from './state/hooks.js';
 export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useSampleSetsData, useSampleEdgesData, useMultiObsLabels, useMultiObsSpots, useMultiObsPoints, useSpotMultiObsSets, useSpotMultiFeatureLabels, useMultiObsSegmentations, useMultiImages, useObsSpotsData, useObsPointsData, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, } from './data-hooks.js';
 export { usePointMultiObsLabels, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets, } from './data-hooks-multilevel.js';
 export { useHasLoader, } from './data-hook-utils.js';
-export { AbstractLoader, AbstractTwoStepLoader, LoaderResult, } from './data/index.js';
-export { AbstractLoaderError, DatasetNotFoundError, LoaderNotFoundError, LoaderValidationError, DataSourceFetchError, } from './errors/index.js';
 export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles, } from './shared-plot-options/index.js';
 export { logConfig } from './view-config-utils.js';
 export { useAsyncFunction, usePageModeView } from './contexts.js';
+export { createLoaders } from './vitessce-grid-utils.js';

package/dist-tsc/state/hooks.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../../src/state/hooks.js"],"names":[],"mappings":"AAmCA;;;;;;GAMG;AACH,8CAJW,GAAC,mBAEC,MAAM,GAAC,SAAS,CA4B5B;AAED;;;;;;;GAOG;AACH,gDALW,GAAC,wBACD,GAAC,qBAEC,MAAM,GAAC,SAAS,CA0C5B;AAED;;;;;GAKG;AACH,6CAJW,MAAM,sBACN,GAAC,GACC,MAAM,GAAC,SAAS,CAI5B;AAED;;;;;;GAMG;AACH,+CALW,MAAM,mDACN,GAAC,wBACD,GAAC,GACC,MAAM,GAAC,SAAS,CAc5B;AA4RD;;;;;;;;;GASG;AACH,mDALW,MAAM,EAAE,sBACR,MAAM,GAEJ,MAAM,CAclB;AAED;;;;;;;;;;;;;;;GAeG;AACH,4CATW,MAAM,EAAE,sBACR,MAAM,GAEJ,KAAK,CAmCjB;AAED,yFAKC;AAED,gGAqBC;AAED,0IA4BC;AAED,iJAkEC;AAED,yFAmBC;AAED;;;;GAIG;AACH,mDAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;;;;;;;;;;;;GAaG;AACH,mDAXW,MAAM,EAAE,sBACR,MAAM,wBACN,MAAM,UAEN,MAAM,GAEJ,KAAK,CA2EjB;AAED;;;;;GAKG;AACH,0DAHW,MAAM,GACJ,MAAM,CAiBlB;AAED;;;;;;GAMG;AACH,4DAJW,MAAM,wBACN,MAAM,GACJ,MAAM,CAgBlB;AAED;;;;;;;GAOG;AACH,4DANW,MAAM,EAAE,iDACR,MAAM,eACN,MAAM,iBACN,MAAM,SAuEhB;AAGD;;;;;;;;;;;GAWG;AACH,wDATW,MAAM,EAAE,sBACR,MAAM,wBACN,MAAM,GAEJ,KAAK,CAUjB;AA6BD;;;;;;;;;;;;;;;GAeG;AACH,qDATW,MAAM,EAAE,sBACR,MAAM,GAEJ,KAAK,CAgCjB;AAED;;;;;GAKG;AACH,8BAHa,MAAM,CAKlB;AAGD;;;;;;;;;;;;GAYG;AACH,2CARW,MAAM,WACN,MAAM,YACN,MAAM,0BACN,MAAM,OAoBhB;AAED;;;;;;;;;;;;GAYG;AACH,2CARW,MAAM,WACN,MAAM,YACN,MAAM,0BACN,MAAM,OAShB;AAED;;;;;GAKG;AACH,6BAHa,MAAM,EAAE,CAKpB;AAED;;;;;GAKG;AACH,+CAEC;AAED;;;;;GAKG;AACH,0EAEC;AAED;;;;;GAKG;AACH,uEAEC;AAED;;;;;GAKG;AACH,4CAEC;AAED;;;;;GAKG;AACH,0CAEC;AAED;;;;;GAKG;AACH,iDAEC;AAED;;;;;GAKG;AACH,iCAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,oEAIC;AAGD;;;;;GAKG;AACH,qCAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,iDAEC;AAED;;;;;GAKG;AACH,8BAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,0CAEC;AAED;;;;;GAKG;AACH,iDAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,6DAOC;AAED;;;;GAIG;AACH,iCAFa,MAAM,CAIlB;AAED;;;;;GAKG;AACH,8CAEC;AAvpCD;;;;aAPG,OAAO,kCAAkC,OAAO,sEAOO;AAC1D,mFAA0D;AAC1D;;;;;EAAgE;AAOhE;;;;mIAAwD;AACxD,kFAAwD;AAiIjD,yFA+KJ;AAOI,0FAFM,MAAM,CAOlB;AAcM,iDAUJ"}
+{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../../src/state/hooks.js"],"names":[],"mappings":"AAmCA;;;;;;GAMG;AACH,8CAJW,GAAC,mBAEC,MAAM,GAAC,SAAS,CA4B5B;AAED;;;;;;;GAOG;AACH,gDALW,GAAC,wBACD,GAAC,qBAEC,MAAM,GAAC,SAAS,CA0C5B;AAED;;;;;GAKG;AACH,6CAJW,MAAM,sBACN,GAAC,GACC,MAAM,GAAC,SAAS,CAI5B;AAED;;;;;;GAMG;AACH,+CALW,MAAM,mDACN,GAAC,wBACD,GAAC,GACC,MAAM,GAAC,SAAS,CAc5B;AAySD;;;;;;;;;GASG;AACH,mDALW,MAAM,EAAE,sBACR,MAAM,GAEJ,MAAM,CAclB;AAED;;;;;;;;;;;;;;;GAeG;AACH,4CATW,MAAM,EAAE,sBACR,MAAM,GAEJ,KAAK,CAmCjB;AAED,yFAKC;AAED,gGAqBC;AAED,0IA4BC;AAED,iJAkEC;AAED,yFAmBC;AAED;;;;GAIG;AACH,mDAHW,MAAM,GACJ,MAAM,CAIlB;AAED;;;;;;;;;;;;;GAaG;AACH,mDAXW,MAAM,EAAE,sBACR,MAAM,wBACN,MAAM,UAEN,MAAM,GAEJ,KAAK,CA2EjB;AAED;;;;;GAKG;AACH,0DAHW,MAAM,GACJ,MAAM,CAiBlB;AAED;;;;;;GAMG;AACH,4DAJW,MAAM,wBACN,MAAM,GACJ,MAAM,CAgBlB;AAED;;;;;;;GAOG;AACH,4DANW,MAAM,EAAE,iDACR,MAAM,eACN,MAAM,iBACN,MAAM,SAuEhB;AAGD;;;;;;;;;;;GAWG;AACH,wDATW,MAAM,EAAE,sBACR,MAAM,wBACN,MAAM,GAEJ,KAAK,CAUjB;AA6BD;;;;;;;;;;;;;;;GAeG;AACH,qDATW,MAAM,EAAE,sBACR,MAAM,GAEJ,KAAK,CAgCjB;AAED;;;;;GAKG;AACH,8BAHa,MAAM,CAKlB;AAGD;;;;;;;;;;;;GAYG;AACH,2CARW,MAAM,WACN,MAAM,YACN,MAAM,0BACN,MAAM,OAoBhB;AAED;;;;;;;;;;;;GAYG;AACH,2CARW,MAAM,WACN,MAAM,YACN,MAAM,0BACN,MAAM,OAShB;AAED;;;;;GAKG;AACH,6BAHa,MAAM,EAAE,CAKpB;AAED;;;;;GAKG;AACH,+CAEC;AAED;;;;;GAKG;AACH,0EAEC;AAED;;;;;GAKG;AACH,uEAEC;AAED;;;;;GAKG;AACH,4CAEC;AAED;;;;;GAKG;AACH,0CAEC;AAED;;;;;GAKG;AACH,iDAEC;AAED;;;;;GAKG;AACH,iCAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,oEAIC;AAGD;;;;;GAKG;AACH,qCAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,iDAEC;AAED;;;;;GAKG;AACH,8BAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,0CAEC;AAED;;;;;GAKG;AACH,iDAHa,MAAM,CAKlB;AAED;;;;;GAKG;AACH,6DAOC;AAED;;;;GAIG;AACH,iCAFa,MAAM,CAIlB;AAED;;;;;GAKG;AACH,8CAEC;AApqCD;;;;aAPG,OAAO,kCAAkC,OAAO,sEAOO;AAC1D,mFAA0D;AAC1D;;;;;EAAgE;AAOhE;;;;mIAAwD;AACxD,kFAAwD;AAiIjD,yFA4LJ;AAOI,0FAFM,MAAM,CAOlB;AAcM,iDAUJ"}

package/dist-tsc/state/hooks.js

@@ -149,7 +149,14 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
     loaders: initialLoaders,
     // Reducer functions which update the state
     // (although technically also part of state):
-    setViewConfig: viewConfig => set({ viewConfig, initialViewConfig: viewConfig }),
+    setViewConfig: viewConfig => set({
+        viewConfig,
+        initialViewConfig: viewConfig,
+        // mostRecentConfigSource is used by the LinkController to determine
+        // whether the config was set by this instance or an external linked
+        // instance of Vitessce, and used to prevent infinite loops.
+        mostRecentConfigSource: 'internal',
+    }),
     setLoaders: loaders => set({ loaders }),
     setCoordinationValue: ({ parameter, value, coordinationScopes, byType, typeScope, coordinationScopesBy, }) => set((state) => {
         const { coordinationSpace } = state.viewConfig;
@@ -175,6 +182,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
                     },
                 },
             },
+            mostRecentConfigSource: 'internal',
         };
     }),
     mergeCoordination: (newCoordinationValues, scopePrefix, viewUid) => set((state) => {
@@ -253,7 +261,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
         };
         // console.log('newViewConfig', newViewConfig);
         return {
-            viewConfig: newViewConfig,
+            viewConfig: newViewConfig, mostRecentConfigSource: 'internal',
         };
     }),
     removeImageChannelInMetaCoordinationScopes: (coordinationScopesRaw, layerScope, channelScope) => set((state) => {
@@ -263,6 +271,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
                 ...state.viewConfig,
                 coordinationSpace: removeImageChannelInMetaCoordinationScopesHelper(coordinationScopesRaw, layerScope, channelScope, coordinationSpace),
             },
+            mostRecentConfigSource: 'internal',
         };
     }),
     addImageChannelInMetaCoordinationScopes: (coordinationScopesRaw, layerScope) => set((state) => {
@@ -272,6 +281,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
                 ...state.viewConfig,
                 coordinationSpace: addImageChannelInMetaCoordinationScopesHelper(coordinationScopesRaw, layerScope, coordinationSpace),
             },
+            mostRecentConfigSource: 'internal',
         };
     }),
     removeComponent: uid => set((state) => {
@@ -281,6 +291,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
                 ...state.viewConfig,
                 layout: newLayout,
             },
+            mostRecentConfigSource: 'internal',
         };
     }),
     changeLayout: newComponentProps => set((state) => {
@@ -295,6 +306,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
                 ...state.viewConfig,
                 layout: newLayout,
             },
+            mostRecentConfigSource: 'internal',
         };
     }),
 }));

package/dist-tsc/vitessce-grid-layout/VitessceGridLayout.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"VitessceGridLayout.d.ts","sourceRoot":"","sources":["../../src/vitessce-grid-layout/VitessceGridLayout.js"],"names":[],"mappings":"AAgBA,oDAwLC"}
+{"version":3,"file":"VitessceGridLayout.d.ts","sourceRoot":"","sources":["../../src/vitessce-grid-layout/VitessceGridLayout.js"],"names":[],"mappings":"AAgBA,oDAmMC"}

package/dist-tsc/vitessce-grid-layout/VitessceGridLayout.js

@@ -13,7 +13,7 @@ class ResponsiveHeightGridLayout extends ResponsiveGridLayout {
     }
 }
 export function VitessceGridLayout(props) {
-    const { layout, viewTypes, padding, margin: marginProp, draggableHandle: draggableHandleClass, onResize, onResizeStop, rowHeight, theme, height, onRemoveComponent, onLayoutChange: onLayoutChangeProp, isBounded, pageMode, children, } = props;
+    const { layout, viewTypes, coordinationTypes, fileTypes, stores, padding, margin: marginProp, draggableHandle: draggableHandleClass, onResize, onResizeStop, rowHeight, theme, height, onRemoveComponent, onLayoutChange: onLayoutChangeProp, isBounded, pageMode, children, } = props;
     const getComponent = useCallback((viewType) => {
         if (Array.isArray(viewTypes)) {
             const matchingViewType = viewTypes.find(v => v.name === viewType);
@@ -102,7 +102,9 @@ export function VitessceGridLayout(props) {
         const gridComponentsValues = Object.values(gridComponents);
         const contextValue = Object.fromEntries(gridComponentsValues.map((v) => {
             const Component = getComponent(v.component);
-            return [v.uid, () => (_jsx("div", { style: { display: 'flex', flexDirection: 'column', height: '100%' }, children: _jsx(Component, { ...v.props, uuid: v.uid, coordinationScopes: v.coordinationScopes, coordinationScopesBy: v.coordinationScopesBy, theme: theme, removeGridComponent: null }) }, v.uid))];
+            return [v.uid, () => (_jsx("div", { style: { display: 'flex', flexDirection: 'column', height: '100%' }, children: _jsx(Component, { ...v.props, uuid: v.uid, coordinationScopes: v.coordinationScopes, coordinationScopesBy: v.coordinationScopesBy, theme: theme, removeGridComponent: null, 
+                        // Props used by LinkControllerSubscriber:
+                        viewTypes: viewTypes, fileTypes: fileTypes, coordinationTypes: coordinationTypes, stores: stores }) }, v.uid))];
         }));
         // Not pageMode, so no children to render.
         // We render the grid components based on the layout information.
@@ -111,7 +113,9 @@ export function VitessceGridLayout(props) {
                 const removeGridComponent = () => {
                     onRemoveComponent(v.uid);
                 };
-                return (_jsx("div", { children: _jsx(Component, { ...v.props, uuid: v.uid, coordinationScopes: v.coordinationScopes, coordinationScopesBy: v.coordinationScopesBy, theme: theme, removeGridComponent: removeGridComponent }) }, v.uid));
+                return (_jsx("div", { children: _jsx(Component, { ...v.props, uuid: v.uid, coordinationScopes: v.coordinationScopes, coordinationScopesBy: v.coordinationScopesBy, theme: theme, removeGridComponent: removeGridComponent, 
+                        // Props used by LinkControllerSubscriber:
+                        viewTypes: viewTypes, fileTypes: fileTypes, coordinationTypes: coordinationTypes, stores: stores }) }, v.uid));
             }), contextValue];
     }, [gridComponents, getComponent, onRemoveComponent, theme]);
     return (pageMode

package/dist-tsc/vitessce-grid-utils.js

@@ -2,7 +2,7 @@ import { useState, useEffect, useRef, } from 'react';
 import { InternMap } from 'internmap';
 import { isEqual, pick } from 'lodash-es';
 import { DATA_TYPE_COORDINATION_VALUE_USAGE } from '@vitessce/constants-internal';
-import { getSourceAndLoaderFromFileType, getDataTypeFromFileType } from './data/loader-registry.js';
+import { getSourceAndLoaderFromFileType, getDataTypeFromFileType } from '@vitessce/abstract';
 /**
  * Return the bottom coordinate of the layout.
  * https://github.com/STRML/react-grid-layout/blob/20dac73f91274526034c00968b5bedb9c2ed36b9/lib/utils.js#L82

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vit-s",
-  "version": "3.5.1",
+  "version": "3.5.3",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -29,12 +29,13 @@
     "uuid": "^9.0.0",
     "zustand": "^3.5.10",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.5.1",
-    "@vitessce/plugins": "3.5.1",
-    "@vitessce/schemas": "3.5.1",
-    "@vitessce/utils": "3.5.1",
-    "@vitessce/sets-utils": "3.5.1",
-    "@vitessce/config": "3.5.1"
+    "@vitessce/abstract": "3.5.3",
+    "@vitessce/constants-internal": "3.5.3",
+    "@vitessce/plugins": "3.5.3",
+    "@vitessce/schemas": "3.5.3",
+    "@vitessce/utils": "3.5.3",
+    "@vitessce/sets-utils": "3.5.3",
+    "@vitessce/config": "3.5.3"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.4",
@@ -42,7 +43,7 @@
     "react": "^18.0.0",
     "vite": "^4.3.0",
     "vitest": "^0.32.2",
-    "@vitessce/types": "3.5.1"
+    "@vitessce/types": "3.5.3"
   },
   "peerDependencies": {
     "react": "^16.8.0 || ^17.0.0 || ^18.0.0"

package/src/VitessceGrid.js

@@ -122,6 +122,9 @@ export default function VitessceGrid(props) {
           rowHeight={rowHeight}
           theme={theme}
           viewTypes={viewTypes}
+          fileTypes={fileTypes}
+          coordinationTypes={coordinationTypes}
+          stores={stores}
           draggableHandle={titleClasses.title}
           margin={margin}
           padding={padding}

package/src/data-hook-utils.js

@@ -5,15 +5,15 @@ import {
   getInitialCoordinationScopePrefix,
 } from '@vitessce/utils';
 import { STATUS } from '@vitessce/constants-internal';
+import {
+  AbstractLoaderError,
+  LoaderNotFoundError,
+} from '@vitessce/abstract';
 import {
   getMatchingLoader,
   useMatchingLoader,
   useSetWarning,
 } from './state/hooks.js';
-import {
-  AbstractLoaderError,
-  LoaderNotFoundError,
-} from './errors/index.js';
 
 /**
  * Warn via publishing to the console

package/src/data-hooks-multilevel-utils.js

@@ -2,13 +2,13 @@ import { useEffect, useMemo } from 'react';
 import { useQueries } from '@tanstack/react-query';
 import { extent } from 'd3-array';
 import { DataType, STATUS } from '@vitessce/constants-internal';
+import {
+  LoaderNotFoundError,
+} from '@vitessce/abstract';
 import {
   getMatchingLoader,
   useSetWarning,
 } from './state/hooks.js';
-import {
-  LoaderNotFoundError,
-} from './errors/index.js';
 import {
   warn,
   dataQueryFn,

package/src/data-hooks.js

@@ -1,15 +1,15 @@
 import { useState, useEffect, useMemo } from 'react';
 import { CoordinationType, DataType, STATUS } from '@vitessce/constants-internal';
 import { useQuery, useQueries } from '@tanstack/react-query';
+import {
+  LoaderNotFoundError,
+} from '@vitessce/abstract';
 import {
   useMultiCoordinationValues,
   useComplexCoordination,
   useSetWarning,
   getMatchingLoader,
 } from './state/hooks.js';
-import {
-  LoaderNotFoundError,
-} from './errors/index.js';
 import {
   warn,
   useDataType,

package/src/hooks.js

@@ -3,10 +3,13 @@ import {
 } from 'react';
 import { debounce, every } from 'lodash-es';
 import { extent } from 'd3-array';
+import { useQuery } from '@tanstack/react-query';
 import { capitalize } from '@vitessce/utils';
-import { STATUS } from '@vitessce/constants-internal';
+import { STATUS, AsyncFunctionType } from '@vitessce/constants-internal';
 import { useGridResize, useEmitGridResize } from './state/hooks.js';
 import { VITESSCE_CONTAINER } from './classNames.js';
+import { useAsyncFunction } from './contexts.js';
+
 
 function getWindowDimensions() {
   const { innerWidth: width, innerHeight: height } = window;
@@ -322,3 +325,42 @@ export function useGetObsInfo(obsType, obsLabelsTypes, obsLabelsData, obsSetsMem
     return null;
   }, [obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership]);
 }
+
+/**
+ * This hook expands a featureLabelsMap
+ * by including mappings from ENSEMBL to HGNC IDs.
+ * User-provided mappings should take precedence,
+ * but they are not always provided in the config or contained
+ * in a column of the AnnData.var dataframe, for example.
+ * @param {string} featureType A feature type. Fetching is only done for 'gene'.
+ * @param {Map|null} featureLabelsMap An optional user-supplied feature labels
+ * mapping from the dataset.
+ * @returns {{ stripCuriePrefixes: boolean }|null} An options object.
+ */
+export function useExpandedFeatureLabelsMap(featureType, featureLabelsMap, options) {
+  // TODO: Should this be done via a hook?
+  // We could alternatively expand these types of mappings in the featureLabels data loader class.
+  // TODO: Add an option to opt-out?
+  const { stripCuriePrefixes = true } = options || {};
+  const getTermMapping = useAsyncFunction(AsyncFunctionType.GET_TERM_MAPPING);
+
+  const termMappingQuery = useQuery({
+    enabled: (featureType === 'gene'),
+    queryKey: ['useExpandedFeatureLabelsMap', 'ensembl', 'hgnc'],
+    queryFn: async () => getTermMapping('ensembl', 'hgnc'),
+  });
+  const { data: fetchedMapping, status, isFetching } = termMappingQuery;
+
+  const updatedFeatureLabelsMap = useMemo(() => {
+    if (!fetchedMapping) return featureLabelsMap;
+    return new Map([
+      ...(stripCuriePrefixes
+        ? Array.from(fetchedMapping).map(([k, v]) => ([k.split(':')[1], v.split(':')[1]]))
+        : fetchedMapping
+      ),
+      ...(featureLabelsMap || []),
+    ]);
+  }, [fetchedMapping, featureLabelsMap, stripCuriePrefixes]);
+  const dataStatus = isFetching ? STATUS.LOADING : status;
+  return [updatedFeatureLabelsMap, dataStatus];
+}

package/src/index.js

@@ -15,6 +15,7 @@ export {
   useClosestVitessceContainerSize,
   useWindowDimensions,
   useGridItemSize,
+  useExpandedFeatureLabelsMap,
 } from './hooks.js';
 export {
   useCoordinationScopes,
@@ -88,18 +89,6 @@ export {
 export {
   useHasLoader,
 } from './data-hook-utils.js';
-export {
-  AbstractLoader,
-  AbstractTwoStepLoader,
-  LoaderResult,
-} from './data/index.js';
-export {
-  AbstractLoaderError,
-  DatasetNotFoundError,
-  LoaderNotFoundError,
-  LoaderValidationError,
-  DataSourceFetchError,
-} from './errors/index.js';
 export {
   CellColorEncodingOption,
   OptionsContainer,
@@ -108,3 +97,4 @@ export {
 } from './shared-plot-options/index.js';
 export { logConfig } from './view-config-utils.js';
 export { useAsyncFunction, usePageModeView } from './contexts.js';
+export { createLoaders } from './vitessce-grid-utils.js';

package/src/state/hooks.js

@@ -172,7 +172,15 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
   loaders: initialLoaders,
   // Reducer functions which update the state
   // (although technically also part of state):
-  setViewConfig: viewConfig => set({ viewConfig, initialViewConfig: viewConfig }),
+  setViewConfig: viewConfig => set({
+    viewConfig,
+    initialViewConfig:
+    viewConfig,
+    // mostRecentConfigSource is used by the LinkController to determine
+    // whether the config was set by this instance or an external linked
+    // instance of Vitessce, and used to prevent infinite loops.
+    mostRecentConfigSource: 'internal',
+  }),
   setLoaders: loaders => set({ loaders }),
   setCoordinationValue: ({
     parameter, value, coordinationScopes,
@@ -202,6 +210,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
           },
         },
       },
+      mostRecentConfigSource: 'internal',
     };
   }),
   mergeCoordination: (newCoordinationValues, scopePrefix, viewUid) => set((state) => {
@@ -282,7 +291,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
     };
     // console.log('newViewConfig', newViewConfig);
     return {
-      viewConfig: newViewConfig,
+      viewConfig: newViewConfig, mostRecentConfigSource: 'internal',
     };
   }),
   removeImageChannelInMetaCoordinationScopes: (coordinationScopesRaw, layerScope, channelScope) => set((state) => {
@@ -297,6 +306,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
           coordinationSpace,
         ),
       },
+      mostRecentConfigSource: 'internal',
     };
   }),
   addImageChannelInMetaCoordinationScopes: (coordinationScopesRaw, layerScope) => set((state) => {
@@ -310,6 +320,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
           coordinationSpace,
         ),
       },
+      mostRecentConfigSource: 'internal',
     };
   }),
   removeComponent: uid => set((state) => {
@@ -319,6 +330,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
         ...state.viewConfig,
         layout: newLayout,
       },
+      mostRecentConfigSource: 'internal',
     };
   }),
   changeLayout: newComponentProps => set((state) => {
@@ -333,6 +345,7 @@ export const createViewConfigStore = (initialLoaders, initialConfig) => create(s
         ...state.viewConfig,
         layout: newLayout,
       },
+      mostRecentConfigSource: 'internal',
     };
   }),
 }));

package/src/vitessce-grid-layout/VitessceGridLayout.js

@@ -17,7 +17,8 @@ class ResponsiveHeightGridLayout extends ResponsiveGridLayout {
 export function VitessceGridLayout(props) {
   const {
     layout,
-    viewTypes, padding, margin: marginProp, draggableHandle: draggableHandleClass,
+    viewTypes, coordinationTypes, fileTypes, stores,
+    padding, margin: marginProp, draggableHandle: draggableHandleClass,
     onResize, onResizeStop, rowHeight, theme, height,
     onRemoveComponent, onLayoutChange: onLayoutChangeProp,
     isBounded,
@@ -137,6 +138,11 @@ export function VitessceGridLayout(props) {
             coordinationScopesBy={v.coordinationScopesBy}
             theme={theme}
             removeGridComponent={null}
+            // Props used by LinkControllerSubscriber:
+            viewTypes={viewTypes}
+            fileTypes={fileTypes}
+            coordinationTypes={coordinationTypes}
+            stores={stores}
           />
         </div>
       )];
@@ -152,12 +158,17 @@ export function VitessceGridLayout(props) {
       return (
         <div key={v.uid}>
           <Component
-            {... v.props}
+            {...v.props}
             uuid={v.uid}
             coordinationScopes={v.coordinationScopes}
             coordinationScopesBy={v.coordinationScopesBy}
             theme={theme}
             removeGridComponent={removeGridComponent}
+            // Props used by LinkControllerSubscriber:
+            viewTypes={viewTypes}
+            fileTypes={fileTypes}
+            coordinationTypes={coordinationTypes}
+            stores={stores}
           />
         </div>
       );
@@ -179,11 +190,11 @@ export function VitessceGridLayout(props) {
           breakpoints={gridBreakpoints}
           height={height}
           rowHeight={
-          rowHeight
-          || (
-            (window.innerHeight - 2 * padding - (maxRows - 1) * margin)
-            / maxRows
-          )}
+            rowHeight
+            || (
+              (window.innerHeight - 2 * padding - (maxRows - 1) * margin)
+              / maxRows
+            )}
           containerPadding={containerPadding}
           margin={margin}
           draggableHandle={draggableHandle}

package/src/vitessce-grid-utils.js

@@ -4,7 +4,7 @@ import {
 import { InternMap } from 'internmap';
 import { isEqual, pick } from 'lodash-es';
 import { DATA_TYPE_COORDINATION_VALUE_USAGE } from '@vitessce/constants-internal';
-import { getSourceAndLoaderFromFileType, getDataTypeFromFileType } from './data/loader-registry.js';
+import { getSourceAndLoaderFromFileType, getDataTypeFromFileType } from '@vitessce/abstract';
 
 /**
  * Return the bottom coordinate of the layout.