@jbrowse/plugin-data-management 2.3.4 → 2.4.1

package/esm/index.d.ts

@@ -1,8 +1,6 @@
 /// <reference types="react" />
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { AddTrackModel } from './AddTrackWidget/model';
-import { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
 declare const SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
     rootModel?: unknown;
     onClose: () => void;
@@ -27,4 +25,5 @@ export default class extends Plugin {
     configure(_pluginManager: PluginManager): void;
 }
 export { AssemblyManager, SetDefaultSession };
-export type { HierarchicalTrackSelectorModel, AddTrackModel };
+export { type AddTrackModel } from './AddTrackWidget/model';
+export { type HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,uBAAuB,MAAM,iBAAiB,CAAA;AACrD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAE9C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,gCAEN,MAAM,mCAAmC,CAAA;AAE1C,MAAM,iBAAiB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC,CAAA;AAEnE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC,CAAA;AAE/D,MAAM,CAAC,OAAO,MAAO,SAAQ,MAAM;IAAnC;;QACE,SAAI,GAAG,sBAAsB,CAAA;QAE7B,YAAO,GAAG;YACR,eAAe;YACf,iBAAiB;SAClB,CAAA;IAWH,CAAC;IATC,OAAO,CAAC,aAA4B;QAClC,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,eAAe,CAAC,aAAa,CAAC,CAAA;QAC9B,gCAAgC,CAAC,aAAa,CAAC,CAAA;QAC/C,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C;AAED,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,uBAAuB,MAAM,iBAAiB,CAAA;AACrD,OAAO,eAAe,MAAM,kBAAkB,CAAA;AAE9C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,gCAAgC,MAAM,mCAAmC,CAAA;AAEhF,MAAM,iBAAiB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC,CAAA;AAEnE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC,CAAA;AAE/D,MAAM,CAAC,OAAO,MAAO,SAAQ,MAAM;IAAnC;;QACE,SAAI,GAAG,sBAAsB,CAAA;QAE7B,YAAO,GAAG;YACR,eAAe;YACf,iBAAiB;SAClB,CAAA;IAWH,CAAC;IATC,OAAO,CAAC,aAA4B;QAClC,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,eAAe,CAAC,aAAa,CAAC,CAAA;QAC9B,gCAAgC,CAAC,aAAa,CAAC,CAAA;QAC/C,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C;AAED,OAAO,EAAE,eAAe,EAAE,iBAAiB,EAAE,CAAA"}

package/esm/ucsc-trackhub/ucscTrackHub.d.ts

@@ -1,7 +1,5 @@
 import { TrackDbFile } from '@gmod/ucsc-hub';
 import { FileLocation } from '@jbrowse/core/util';
-import ucscAssemblies from './ucscAssemblies';
-export { ucscAssemblies };
 export declare function fetchHubFile(hubLocation: FileLocation): Promise<import("@gmod/ucsc-hub").HubFile>;
 export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<import("@gmod/ucsc-hub").GenomesFile>;
 export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
@@ -22,3 +20,4 @@ export declare function makeLoc2(first: string, alt?: string): {
     locationType: string;
 };
 export declare function generateTracks(trackDb: TrackDbFile, trackDbLoc: FileLocation, assemblyName: string, sequenceAdapter: any): any;
+export { default as ucscAssemblies } from './ucscAssemblies';

package/esm/ucsc-trackhub/ucscTrackHub.js

@@ -1,8 +1,6 @@
 import { isUriLocation, objectHash } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { generateUnsupportedTrackConf, generateUnknownTrackConf, } from '@jbrowse/core/util/tracks';
-import ucscAssemblies from './ucscAssemblies';
-export { ucscAssemblies };
 export async function fetchHubFile(hubLocation) {
     try {
         const hubFileText = await openLocation(hubLocation).readFile('utf8');
@@ -44,18 +42,18 @@ export function makeLoc2(first, alt) {
         };
 }
 export function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapter) {
+    var _a;
     const tracks = [];
-    trackDb.forEach((track, trackName) => {
-        var _a;
-        const trackKeys = Array.from(track.keys());
-        const parentTrackKeys = [
+    for (const [trackName, track] of trackDb.entries()) {
+        const trackKeys = [...track.keys()];
+        const parentTrackKeys = new Set([
             'superTrack',
             'compositeTrack',
             'container',
             'view',
-        ];
-        if (trackKeys.some(key => parentTrackKeys.includes(key))) {
-            return;
+        ]);
+        if (trackKeys.some(key => parentTrackKeys.has(key))) {
+            continue;
         }
         const parentTracks = [];
         let currentTrackName = trackName;
@@ -77,7 +75,7 @@ export function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapte
             trackId: `ucsc-trackhub-${objectHash(res)}`,
             assemblyNames: [assemblyName],
         });
-    });
+    }
     return tracks;
 }
 function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter) {
@@ -289,4 +287,5 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
             return generateUnknownTrackConf(name, baseTrackType, categories);
     }
 }
+export { default as ucscAssemblies } from './ucscAssemblies';
 //# sourceMappingURL=ucscTrackHub.js.map

package/esm/ucsc-trackhub/ucscTrackHub.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.3.4",
+  "version": "2.4.1",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -61,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "98ae48be91ee2371e1b2768a907b4997995e9915"
+  "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
 }

package/src/AddConnectionWidget/components/AddConnectionWidget.test.tsx

@@ -47,8 +47,8 @@ describe('<AddConnectionWidget />', () => {
 
   it('can handle a custom UCSC trackHub URL', async () => {
     const mockFetch = async (url: RequestInfo | URL) => {
-      // @ts-ignore
-      const urlText = url.href ? url.href : url
+      // @ts-expect-error
+      const urlText = url.href || url
       let responseText = ''
       if (urlText.endsWith('hub.txt')) {
         responseText = `hub TestHub
@@ -98,8 +98,8 @@ type bigWig
 
   it('can handle a custom JBrowse 1 data directory URL', async () => {
     const mockFetch = async (url: RequestInfo | URL) => {
-      // @ts-ignore
-      const urlText = url.href ? url.href : url
+      // @ts-expect-error
+      const urlText = url.href || url
       let responseText = ''
       if (urlText.endsWith('trackList.json')) {
         responseText = '{}'

package/src/AddConnectionWidget/components/ConnectionTypeSelect.tsx

@@ -33,7 +33,6 @@ function ConnectionTypeSelect(props: {
                     href={connectionType.url}
                     rel="noopener noreferrer"
                     target="_blank"
-                    color="secondary"
                   >
                     <OpenInNewIcon />
                   </IconButton>

package/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.tsx.snap

@@ -68,7 +68,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                   class="MuiFormControl-root MuiFormControl-fullWidth MuiTextField-root css-wb57ya-MuiFormControl-root-MuiTextField-root"
                 >
                   <label
-                    class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined MuiFormLabel-colorPrimary MuiFormLabel-filled MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined css-1sumxir-MuiFormLabel-root-MuiInputLabel-root"
+                    class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined MuiFormLabel-colorPrimary MuiFormLabel-filled MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined css-1jy569b-MuiFormLabel-root-MuiInputLabel-root"
                     data-shrink="true"
                     for="mui-1"
                     id="mui-1-label"
@@ -126,7 +126,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                   >
                     A track or assembly hub in the Track Hub format
                     <a
-                      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-colorSecondary MuiIconButton-sizeMedium css-1gws2xf-MuiButtonBase-root-MuiIconButton-root"
+                      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
                       href="//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro"
                       rel="noopener noreferrer"
                       tabindex="0"

package/src/AddTrackWidget/components/ConfirmTrack.tsx

@@ -160,7 +160,7 @@ export default observer(function ConfirmTrack({
         TextFieldProps={{
           fullWidth: true,
           SelectProps: {
-            // @ts-ignore
+            // @ts-expect-error
             SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
           },
         }}

package/src/AddTrackWidget/components/TextIndexingConfig.tsx

@@ -68,7 +68,6 @@ const TextIndexingConfig = observer(({ model }: { model: AddTrackModel }) => {
                       endAdornment: (
                         <InputAdornment position="end">
                           <IconButton
-                            color="secondary"
                             onClick={() => {
                               const newAttr = section.values.filter((a, i) => {
                                 return i !== idx
@@ -113,7 +112,6 @@ const TextIndexingConfig = observer(({ model }: { model: AddTrackModel }) => {
                             }
                           }}
                           disabled={index === 0 ? value1 === '' : value2 === ''}
-                          color="secondary"
                           data-testid={`stringArrayAdd-Feat`}
                         >
                           <AddIcon />

package/src/AddTrackWidget/components/TrackAdapterSelector.tsx

@@ -44,7 +44,7 @@ const TrackAdapterSelector = observer(({ model }: { model: AddTrackModel }) => {
       fullWidth
       onChange={event => model.setAdapterHint(event.target.value)}
       SelectProps={{
-        // @ts-ignore
+        // @ts-expect-error
         SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
       }}
     >

package/src/AddTrackWidget/components/TrackTypeSelector.tsx

@@ -30,7 +30,7 @@ const TrackTypeSelector = observer(({ model }: { model: AddTrackModel }) => {
       fullWidth
       onChange={event => model.setTrackType(event.target.value)}
       SelectProps={{
-        // @ts-ignore
+        // @ts-expect-error
         SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
       }}
     >

package/src/AddTrackWidget/index.test.tsx

@@ -53,9 +53,9 @@ const realLocation = window.location
 
 // https://stackoverflow.com/a/60110508/2129219
 function setWindowLoc(loc: string) {
-  // @ts-ignore
+  // @ts-expect-error
   delete window.location
-  // @ts-ignore
+  // @ts-expect-error
   window.location = new URL(loc)
 }
 

package/src/AddTrackWidget/model.ts

@@ -104,18 +104,18 @@ export default function f(pluginManager: PluginManager) {
       get isFtp() {
         const { trackData: track, indexTrackData: index } = self
         return !!(
-          // @ts-ignore
+          // @ts-expect-error
           (index?.uri?.startsWith('ftp://') || track?.uri?.startsWith('ftp://'))
         )
       },
 
       get isRelativeTrackUrl() {
-        // @ts-ignore
+        // @ts-expect-error
         const uri = self.trackData?.uri
         return uri ? !isAbsoluteUrl(uri) : false
       },
       get isRelativeIndexUrl() {
-        // @ts-ignore
+        // @ts-expect-error
         const uri = self.indexTrackData?.uri
         return uri ? !isAbsoluteUrl(uri) : false
       },
@@ -124,11 +124,11 @@ export default function f(pluginManager: PluginManager) {
       },
 
       get trackHttp() {
-        // @ts-ignore
+        // @ts-expect-error
         return self.trackData?.uri?.startsWith('http://')
       },
       get indexHttp() {
-        // @ts-ignore
+        // @ts-expect-error
         return self.indexTrackData?.uri?.startsWith('http://')
       },
 

package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.tsx

@@ -9,7 +9,7 @@ import HierarchicalTrackSelector from './HierarchicalTrackSelector'
 
 jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
-// @ts-ignore
+// @ts-expect-error
 window.requestIdleCallback = cb => cb()
 window.cancelIdleCallback = () => {}
 
@@ -20,7 +20,7 @@ test('renders nothing with no assembly', () => {
 
   const { container } = render(
     <ThemeProvider theme={createJBrowseTheme()}>
-      {/* @ts-ignore*/}
+      {/* @ts-expect-error*/}
       <HierarchicalTrackSelector model={model} />
     </ThemeProvider>,
   )
@@ -76,7 +76,7 @@ test('renders with a couple of uncategorized tracks', async () => {
 
   const { container, findByTestId } = render(
     <ThemeProvider theme={createJBrowseTheme()}>
-      {/* @ts-ignore*/}
+      {/* @ts-expect-error*/}
       <HierarchicalTrackSelector model={model} />
     </ThemeProvider>,
   )
@@ -139,7 +139,7 @@ test('renders with a couple of categorized tracks', async () => {
 
   const { container, findByTestId } = render(
     <ThemeProvider theme={createJBrowseTheme()}>
-      {/* @ts-ignore*/}
+      {/* @ts-expect-error*/}
       <HierarchicalTrackSelector model={model} />
     </ThemeProvider>,
   )

package/src/HierarchicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.tsx.snap

@@ -31,7 +31,7 @@ exports[`renders with a couple of categorized tracks 1`] = `
     style="display: flex;"
   >
     <button
-      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1m9x3cr-MuiButtonBase-root-MuiIconButton-root-menuIcon"
+      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1kgqocu-MuiButtonBase-root-MuiIconButton-root-menuIcon"
       tabindex="0"
       type="button"
     >
@@ -75,7 +75,7 @@ exports[`renders with a couple of categorized tracks 1`] = `
           class="MuiInputAdornment-root MuiInputAdornment-positionEnd MuiInputAdornment-standard MuiInputAdornment-sizeSmall css-1laqsz7-MuiInputAdornment-root"
         >
           <button
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-colorSecondary MuiIconButton-sizeSmall css-16a6k96-MuiButtonBase-root-MuiIconButton-root"
+            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-9vna8i-MuiButtonBase-root-MuiIconButton-root"
             tabindex="0"
             type="button"
           >
@@ -119,7 +119,7 @@ exports[`renders with a couple of uncategorized tracks 1`] = `
     style="display: flex;"
   >
     <button
-      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1m9x3cr-MuiButtonBase-root-MuiIconButton-root-menuIcon"
+      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1kgqocu-MuiButtonBase-root-MuiIconButton-root-menuIcon"
       tabindex="0"
       type="button"
     >
@@ -163,7 +163,7 @@ exports[`renders with a couple of uncategorized tracks 1`] = `
           class="MuiInputAdornment-root MuiInputAdornment-positionEnd MuiInputAdornment-standard MuiInputAdornment-sizeSmall css-1laqsz7-MuiInputAdornment-root"
         >
           <button
-            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-colorSecondary MuiIconButton-sizeSmall css-16a6k96-MuiButtonBase-root-MuiIconButton-root"
+            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-9vna8i-MuiButtonBase-root-MuiIconButton-root"
             tabindex="0"
             type="button"
           >

package/src/HierarchicalTrackSelectorWidget/components/faceted/FacetFilters.tsx

@@ -65,7 +65,7 @@ function FacetFilter({
           className={classes.select}
           value={filters[column.field]}
           onChange={event => {
-            // @ts-ignore
+            // @ts-expect-error
             const { options } = event.target
             const val: string[] = []
             const len = options.length
@@ -105,28 +105,28 @@ export default function FacetFilters({
 }) {
   const facets = columns.slice(1)
   const uniqs = facets.map(() => new Map<string, number>())
-  rows.forEach(row => {
-    facets.forEach((column, index) => {
+  for (const row of rows) {
+    for (const [index, column] of facets.entries()) {
       const elt = uniqs[index]
       const key = `${row[column.field] || ''}`
       const val = elt.get(key)
       // we don't allow filtering on empty yet
       if (key) {
-        if (val !== undefined) {
-          elt.set(key, val + 1)
-        } else {
+        if (val === undefined) {
           elt.set(key, 1)
+        } else {
+          elt.set(key, val + 1)
         }
       }
-    })
-  })
+    }
+  }
 
   return (
     <div>
       {facets.map((column, index) => (
         <FacetFilter
           key={column.field}
-          vals={Array.from(uniqs[index])}
+          vals={[...uniqs[index]]}
           column={column}
           width={width}
           dispatch={dispatch}

package/src/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.tsx

@@ -99,11 +99,10 @@ export default observer(function FacetedSelector({
 
   const filteredMetadataKeys = useMemo(
     () =>
-      [...new Set(rows.map(row => getRootKeys(row.metadata)).flat())].filter(
-        f =>
-          !hideSparse
-            ? true
-            : rows.map(r => r.metadata[f]).filter(f => !!f).length > 5,
+      [...new Set(rows.flatMap(row => getRootKeys(row.metadata)))].filter(f =>
+        !hideSparse
+          ? true
+          : rows.map(r => r.metadata[f]).filter(f => !!f).length > 5,
       ),
     [hideSparse, rows],
   )

package/src/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.tsx

@@ -73,8 +73,6 @@ export default observer(function HamburgerMenu({
     deletingConnection?: boolean,
   ) {
     const name = readConfObject(connectionConf, 'name')
-
-    // @ts-ignore
     const result = session.prepareToBreakConnection(connectionConf)
     if (result) {
       const [safelyBreakConnection, dereferenceTypeCount] = result

package/src/HierarchicalTrackSelectorWidget/components/tree/HierarchicalHeader.tsx

@@ -55,10 +55,7 @@ function HierarchicalTrackSelectorHeader({
           InputProps={{
             endAdornment: (
               <InputAdornment position="end">
-                <IconButton
-                  color="secondary"
-                  onClick={() => model.clearFilterText()}
-                >
+                <IconButton onClick={() => model.clearFilterText()}>
                   <ClearIcon />
                 </IconButton>
               </InputAdornment>

package/src/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.tsx

@@ -70,7 +70,7 @@ export default observer(function HierarchicalTree({
       }
 
       while (true) {
-        // @ts-ignore
+        // @ts-expect-error
         const parentMeta = yield
 
         for (let i = 0; i < parentMeta.node.children.length; i++) {
@@ -83,7 +83,7 @@ export default observer(function HierarchicalTree({
   )
 
   useEffect(() => {
-    // @ts-ignore
+    // @ts-expect-error
     treeRef.current.recomputeTree({
       refreshNodes: true,
       useDefaultHeight: true,
@@ -91,9 +91,9 @@ export default observer(function HierarchicalTree({
   }, [tree, filterText])
   return (
     <>
-      {/* @ts-ignore */}
+      {/* @ts-expect-error */}
       <VariableSizeTree ref={treeRef} treeWalker={treeWalker} height={height}>
-        {/* @ts-ignore */}
+        {/* @ts-expect-error */}
         {Node}
       </VariableSizeTree>
     </>

package/src/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.tsx

@@ -13,7 +13,7 @@ import { getAllChildren, treeToMap, NodeData } from '../util'
 
 const useStyles = makeStyles()(theme => ({
   contrastColor: {
-    color: theme.palette.secondary.contrastText,
+    color: theme.palette.tertiary.contrastText,
   },
 
   // margin:auto 0 to center text vertically

package/src/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.tsx

@@ -15,7 +15,7 @@ import MoreHorizIcon from '@mui/icons-material/MoreHoriz'
 import { isUnsupported, NodeData } from '../util'
 import { SanitizedHTML } from '@jbrowse/core/ui'
 
-const useStyles = makeStyles()({
+const useStyles = makeStyles()(theme => ({
   compactCheckbox: {
     padding: 0,
   },
@@ -23,10 +23,10 @@ const useStyles = makeStyles()({
   checkboxLabel: {
     marginRight: 0,
     '&:hover': {
-      backgroundColor: '#eee',
+      backgroundColor: theme.palette.action.selected,
     },
   },
-})
+}))
 
 export interface InfoArgs {
   target: HTMLElement
@@ -55,7 +55,7 @@ export default function TrackLabel({ data }: { data: NodeData }) {
               onChange={() => onChange(id)}
               disabled={isUnsupported(name)}
               inputProps={{
-                // @ts-ignore
+                // @ts-expect-error
                 'data-testid': `htsTrackEntry-${id}`,
               }}
             />
@@ -70,7 +70,6 @@ export default function TrackLabel({ data }: { data: NodeData }) {
       <IconButton
         onClick={e => setInfo({ target: e.currentTarget, id, conf })}
         style={{ padding: 0 }}
-        color="secondary"
         data-testid={`htsTrackEntryMenu-${id}`}
       >
         <MoreHorizIcon />

package/src/HierarchicalTrackSelectorWidget/components/util.ts

@@ -17,7 +17,7 @@ export interface NodeData {
 }
 
 export function getAllChildren(subtree?: TreeNode): AnyConfigurationModel[] {
-  // @ts-ignore
+  // @ts-expect-error
   return (
     subtree?.children.map(t =>
       t.children.length ? getAllChildren(t) : (t.conf as AnyConfigurationModel),

package/src/HierarchicalTrackSelectorWidget/index.ts

@@ -1,12 +1,9 @@
-import stateModelFactory, { HierarchicalTrackSelectorModel } from './model'
+import stateModelFactory from './model'
 import configSchema from './configSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes'
 import { lazy } from 'react'
 
-export { stateModelFactory, configSchema }
-export type { HierarchicalTrackSelectorModel }
-
 export default (pluginManager: PluginManager) => {
   pluginManager.addWidgetType(() => {
     return new WidgetType({
@@ -20,3 +17,9 @@ export default (pluginManager: PluginManager) => {
     })
   })
 }
+
+export {
+  type HierarchicalTrackSelectorModel,
+  default as stateModelFactory,
+} from './model'
+export { default as configSchema } from './configSchema'

package/src/HierarchicalTrackSelectorWidget/model.ts

@@ -15,7 +15,14 @@ import { ElementId } from '@jbrowse/core/util/types/mst'
 import PluginManager from '@jbrowse/core/PluginManager'
 
 function hasAnyOverlap<T>(a1: T[] = [], a2: T[] = []) {
-  return !!a1.find(value => a2.includes(value))
+  // shortcut case is that arrays are single entries, and are equal
+  // long case is that we use a set
+  if (a1[0] === a2[0]) {
+    return true
+  } else {
+    const s1 = new Set(a1)
+    return a2.some(a => s1.has(a))
+  }
 }
 
 export function matches(
@@ -116,7 +123,7 @@ export function generateHierarchy(
           id: conf.trackId,
           name: getTrackName(conf, session),
           conf,
-          checked: !!tracks.find(f => f.configuration === conf),
+          checked: tracks.some(f => f.configuration === conf),
           children: [],
         },
       )
@@ -175,7 +182,7 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
           return undefined
         }
         for (const display of trackConf.displays) {
-          if (viewType.displayTypes.find(d => d.name === display.type)) {
+          if (viewType.displayTypes.some(d => d.name === display.type)) {
             return trackConf
           }
         }
@@ -194,9 +201,10 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
         const refseq = self.getRefSeqTrackConf(assemblyName)
         // filter out tracks that don't match the current assembly (check all
         // assembly aliases) and display types
-        return (refseq ? [refseq] : []).concat([
+        return [
+          ...(refseq ? [refseq] : []),
           ...filterTracks(tracks, self, assemblyName),
-        ])
+        ]
       },
 
       get assemblyNames(): string[] {
@@ -233,7 +241,7 @@ export default function stateTreeFactory(pluginManager: PluginManager) {
           (assembly &&
             connectionInstances
               ?.map(c => ({
-                // @ts-ignore
+                // @ts-expect-error
                 id: getSnapshot(c).configuration,
                 name: getConf(c, 'name'),
                 children: this.connectionHierarchy(assemblyName, c),