@jbrowse/plugin-data-management 2.5.0 → 2.6.1

package/esm/PluginStoreWidget/components/InstalledPlugin.d.ts

@@ -1,3 +1,4 @@
+import React from 'react';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { BasePlugin } from '@jbrowse/core/util/types';
 import { PluginStoreModel } from '../model';
@@ -5,6 +6,6 @@ declare function InstalledPlugin({ plugin, model, pluginManager, }: {
     plugin: BasePlugin;
     model: PluginStoreModel;
     pluginManager: PluginManager;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof InstalledPlugin;
 export default _default;

package/esm/PluginStoreWidget/components/InstalledPluginsList.d.ts

@@ -1,8 +1,9 @@
+import React from 'react';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { PluginStoreModel } from '../model';
 declare function InstalledPluginsList({ pluginManager, model, }: {
     pluginManager: PluginManager;
     model: PluginStoreModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof InstalledPluginsList;
 export default _default;

package/esm/PluginStoreWidget/components/PluginCard.d.ts

@@ -1,8 +1,9 @@
+import React from 'react';
 import { JBrowsePlugin } from '@jbrowse/core/util/types';
 import { PluginStoreModel } from '../model';
 declare const _default: ({ plugin, model, adminMode, }: {
     plugin: JBrowsePlugin;
     model: PluginStoreModel;
     adminMode: boolean;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

package/esm/PluginStoreWidget/components/PluginStoreWidget.d.ts

@@ -1,6 +1,7 @@
+import React from 'react';
 import { PluginStoreModel } from '../model';
 declare function PluginStoreWidget({ model }: {
     model: PluginStoreModel;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof PluginStoreWidget;
 export default _default;

package/esm/SetDefaultSession/SetDefaultSession.d.ts

@@ -1,5 +1,6 @@
+import React from 'react';
 declare const SetDefaultSession: ({ rootModel, onClose }: {
     rootModel?: unknown;
     onClose: () => void;
-}) => JSX.Element | null;
+}) => React.JSX.Element | null;
 export default SetDefaultSession;

package/esm/index.d.ts

@@ -4,22 +4,22 @@ import PluginManager from '@jbrowse/core/PluginManager';
 declare const SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
     rootModel?: unknown;
     onClose: () => void;
-}) => JSX.Element | null>;
+}) => import("react").JSX.Element | null>;
 declare const AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
     rootModel: any;
     onClose: (arg: boolean) => void;
-}) => JSX.Element>;
+}) => import("react").JSX.Element>;
 export default class extends Plugin {
     name: string;
     exports: {
         AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
             rootModel: any;
             onClose: (arg: boolean) => void;
-        }) => JSX.Element>;
+        }) => import("react").JSX.Element>;
         SetDefaultSession: import("react").LazyExoticComponent<({ rootModel, onClose }: {
             rootModel?: unknown;
             onClose: () => void;
-        }) => JSX.Element | null>;
+        }) => import("react").JSX.Element | null>;
     };
     install(pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;

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

@@ -2,6 +2,18 @@ import PluginManager from '@jbrowse/core/PluginManager';
 export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        name: {
+            type: string;
+            defaultValue: string;
+            description: string;
+        };
+        assemblyNames: {
+            type: string;
+            defaultValue: never[];
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         hubTxtLocation: {

package/esm/ucsc-trackhub/model.js

@@ -4,7 +4,6 @@ import { getSession } from '@jbrowse/core/util';
 import { types } from 'mobx-state-tree';
 // locals
 import configSchema from './configSchema';
-import { fetchGenomesFile, fetchHubFile, fetchTrackDbFile, generateTracks, } from './ucscTrackHub';
 export default function UCSCTrackHubConnection(pluginManager) {
     return types
         .compose('UCSCTrackHubConnection', BaseConnectionModelFactory(pluginManager), types.model({
@@ -15,9 +14,10 @@ export default function UCSCTrackHubConnection(pluginManager) {
         async connect() {
             var _a;
             const session = getSession(self);
+            const notLoadedAssemblies = [];
             try {
-                const connectionName = getConf(self, 'name'); // NOTE: name comes from the base configuration
                 const hubFileLocation = getConf(self, 'hubTxtLocation');
+                const { generateTracks, fetchGenomesFile, fetchTrackDbFile, fetchHubFile, } = await import('./ucscTrackHub');
                 const hubFile = await fetchHubFile(hubFileLocation);
                 const genomeFile = hubFile.get('genomesFile');
                 if (!genomeFile) {
@@ -34,7 +34,7 @@ export default function UCSCTrackHubConnection(pluginManager) {
                         locationType: 'LocalPathLocation',
                     };
                 const genomesFile = await fetchGenomesFile(genomesFileLocation);
-                const trackDbData = [];
+                const map = {};
                 for (const [genomeName, genome] of genomesFile) {
                     const assemblyNames = getConf(self, 'assemblyNames');
                     if (assemblyNames.length > 0 &&
@@ -43,14 +43,15 @@ export default function UCSCTrackHubConnection(pluginManager) {
                     }
                     const conf = (_a = session.assemblyManager.get(genomeName)) === null || _a === void 0 ? void 0 : _a.configuration;
                     if (!conf) {
-                        throw new Error(`Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`);
+                        notLoadedAssemblies.push(genomeName);
+                        continue;
                     }
                     const db = genome.get('trackDb');
                     if (!db) {
                         throw new Error('genomesFile not found on hub');
                     }
                     const base = new URL(genomeFile, hubUri);
-                    const trackDbLoc = hubUri
+                    const loc = hubUri
                         ? {
                             uri: new URL(db, base).href,
                             locationType: 'UriLocation',
@@ -59,13 +60,22 @@ export default function UCSCTrackHubConnection(pluginManager) {
                             localPath: db,
                             locationType: 'LocalPathLocation',
                         };
-                    const trackDb = await fetchTrackDbFile(trackDbLoc);
-                    trackDbData.push([trackDbLoc, trackDb, genomeName, conf]);
-                }
-                for (const [trackDbLoc, trackDbFile, genomeName, conf,] of trackDbData) {
+                    const trackDb = await fetchTrackDbFile(loc);
                     const seqAdapter = readConfObject(conf, ['sequence', 'adapter']);
-                    self.addTrackConfs(generateTracks(trackDbFile, trackDbLoc, genomeName, seqAdapter));
+                    const tracks = generateTracks(trackDb, loc, genomeName, seqAdapter);
+                    self.addTrackConfs(tracks);
+                    map[genomeName] = tracks.length;
                 }
+                const loadedAssemblies = Object.entries(map);
+                const str1 = loadedAssemblies.length
+                    ? `Loaded data from these assemblies: ${loadedAssemblies
+                        .map(([key, val]) => `${key} (${val} tracks)`)
+                        .join(', ')}`
+                    : '';
+                const str2 = notLoadedAssemblies.length
+                    ? `Skipped data from these assemblies: ${notLoadedAssemblies.join(', ')}`
+                    : '';
+                session.notify([str1, str2].filter(f => !!f).join('. '), 'success');
             }
             catch (e) {
                 console.error(e);

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

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/model.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,0BAA0B,EAAE,MAAM,4CAA4C,CAAA;AACvF,OAAO,EACL,sBAAsB,EACtB,cAAc,EACd,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAAC,aAA4B;IACzE,OAAO,KAAK;SACT,OAAO,CACN,wBAAwB,EACxB,0BAA0B,CAAC,aAAa,CAAC,EACzC,KAAK,CAAC,KAAK,CAAC;QACV,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,wBAAwB,CAAC;KAC9C,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,OAAO;;YACX,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,MAAM,mBAAmB,GAAG,EAAc,CAAA;YAC1C,IAAI;gBACF,MAAM,eAAe,GAAG,OAAO,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;gBACvD,MAAM,EACJ,cAAc,EACd,gBAAgB,EAChB,gBAAgB,EAChB,YAAY,GACb,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAA;gBAClC,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,eAAe,CAAC,CAAA;gBACnD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;gBAC7C,IAAI,CAAC,UAAU,EAAE;oBACf,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;iBAChD;gBAED,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAA;gBACpE,MAAM,mBAAmB,GAAG,MAAM;oBAChC,CAAC,CAAC;wBACE,GAAG,EAAE,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,IAAI;wBACrC,YAAY,EAAE,aAAsB;qBACrC;oBACH,CAAC,CAAC;wBACE,SAAS,EAAE,UAAU;wBACrB,YAAY,EAAE,mBAA4B;qBAC3C,CAAA;gBACL,MAAM,WAAW,GAAG,MAAM,gBAAgB,CAAC,mBAAmB,CAAC,CAAA;gBAC/D,MAAM,GAAG,GAAG,EAA+B,CAAA;gBAC3C,KAAK,MAAM,CAAC,UAAU,EAAE,MAAM,CAAC,IAAI,WAAW,EAAE;oBAC9C,MAAM,aAAa,GAAG,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,CAAA;oBACpD,IACE,aAAa,CAAC,MAAM,GAAG,CAAC;wBACxB,CAAC,aAAa,CAAC,QAAQ,CAAC,UAAU,CAAC,EACnC;wBACA,SAAQ;qBACT;oBAED,MAAM,IAAI,GAAG,MAAA,OAAO,CAAC,eAAe,CAAC,GAAG,CAAC,UAAU,CAAC,0CAAE,aAAa,CAAA;oBACnE,IAAI,CAAC,IAAI,EAAE;wBACT,mBAAmB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;wBACpC,SAAQ;qBACT;oBACD,MAAM,EAAE,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;oBAChC,IAAI,CAAC,EAAE,EAAE;wBACP,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;qBAChD;oBACD,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,CAAA;oBACxC,MAAM,GAAG,GAAG,MAAM;wBAChB,CAAC,CAAC;4BACE,GAAG,EAAE,IAAI,GAAG,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,IAAI;4BAC3B,YAAY,EAAE,aAAsB;yBACrC;wBACH,CAAC,CAAC;4BACE,SAAS,EAAE,EAAE;4BACb,YAAY,EAAE,mBAA4B;yBAC3C,CAAA;oBACL,MAAM,OAAO,GAAG,MAAM,gBAAgB,CAAC,GAAG,CAAC,CAAA;oBAC3C,MAAM,UAAU,GAAG,cAAc,CAAC,IAAI,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC,CAAA;oBAChE,MAAM,MAAM,GAAG,cAAc,CAAC,OAAO,EAAE,GAAG,EAAE,UAAU,EAAE,UAAU,CAAC,CAAA;oBACnE,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC,CAAA;oBAC1B,GAAG,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;iBAChC;gBAED,MAAM,gBAAgB,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;gBAC5C,MAAM,IAAI,GAAG,gBAAgB,CAAC,MAAM;oBAClC,CAAC,CAAC,sCAAsC,gBAAgB;yBACnD,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,KAAK,GAAG,UAAU,CAAC;yBAC7C,IAAI,CAAC,IAAI,CAAC,EAAE;oBACjB,CAAC,CAAC,EAAE,CAAA;gBACN,MAAM,IAAI,GAAG,mBAAmB,CAAC,MAAM;oBACrC,CAAC,CAAC,uCAAuC,mBAAmB,CAAC,IAAI,CAC7D,IAAI,CACL,EAAE;oBACL,CAAC,CAAC,EAAE,CAAA;gBACN,OAAO,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,SAAS,CAAC,CAAA;aACpE;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,MAAM,CACZ,yDAAyD,IAAI,CAAC,aAAa,CAAC,IAAI,6FAA6F,CAAC,GAAG,EACjL,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;aAC5C;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.5.0",
+  "version": "2.6.1",
   "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": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
 }

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

@@ -79,7 +79,7 @@ type bigWig
     expect(session.connections.length).toBe(0)
     fireEvent.mouseDown(getAllByRole('button')[0])
     const ucscTrackHubSelection = await findAllByText('UCSC Track Hub')
-    fireEvent.click(ucscTrackHubSelection[ucscTrackHubSelection.length - 1])
+    fireEvent.click(ucscTrackHubSelection.at(-1)!)
     fireEvent.click(await findByTestId('addConnectionNext'))
     fireEvent.change(await findByDisplayValue('nameOfConnection'), {
       target: { value: 'Test UCSC connection name' },

package/src/AddTrackWidget/components/DefaultAddTrackWorkflow.tsx

@@ -81,7 +81,7 @@ function AddTrackWorkflow({ model }: { model: AddTrackModel }) {
     }
 
     const trackId = [
-      `${trackName.toLowerCase().replace(/ /g, '_')}-${Date.now()}`,
+      `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
       `${session.adminMode ? '' : '-sessionTrack'}`,
     ].join('')
 

package/src/AddTrackWidget/components/PasteConfigWorkflow.tsx

@@ -52,6 +52,7 @@ function AddTrackWorkflow({ model }: { model: AddTrackModel }) {
             model.clearData()
             session.hideWidget(model)
           } catch (e) {
+            console.error(e)
             setError(e)
           }
         }}

package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.tsx

@@ -21,15 +21,13 @@ const AutoSizedHierarchicalTree = ({
 }) => {
   return typeof jest === 'undefined' ? (
     <AutoSizer disableWidth>
-      {({ height }) => {
-        return (
-          <HierarchicalTree
-            height={(height || offset) - offset}
-            model={model}
-            tree={tree}
-          />
-        )
-      }}
+      {args => (
+        <HierarchicalTree
+          height={(args.height || offset) - offset}
+          model={model}
+          tree={tree}
+        />
+      )}
     </AutoSizer>
   ) : (
     <HierarchicalTree height={9000} model={model} tree={tree} />
@@ -73,25 +71,17 @@ const HierarchicalTrackSelector = observer(function ({
   model: HierarchicalTrackSelectorModel
   toolbarHeight?: number
 }) {
-  const [assemblyIdx, setAssemblyIdx] = useState(0)
   const [headerHeight, setHeaderHeight] = useState(0)
-
-  const { assemblyNames } = model
-  const assemblyName = assemblyNames[assemblyIdx]
-  return assemblyName ? (
+  return (
     <>
-      <HierarchicalHeader
-        model={model}
-        setHeaderHeight={setHeaderHeight}
-        setAssemblyIdx={setAssemblyIdx}
-      />
+      <HierarchicalHeader model={model} setHeaderHeight={setHeaderHeight} />
       <AutoSizedHierarchicalTree
-        tree={model.hierarchy(assemblyName)}
+        tree={model.hierarchy}
         model={model}
         offset={toolbarHeight + headerHeight}
       />
     </>
-  ) : null
+  )
 })
 
 export default HierarchicalTrackSelectorContainer

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

@@ -1,26 +1,91 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`renders nothing with no assembly 1`] = `
-<button
-  class="MuiButtonBase-root MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary MuiFab-root MuiFab-circular MuiFab-sizeSmall MuiFab-secondary css-15opis6-MuiButtonBase-root-MuiFab-root-fab"
-  tabindex="0"
-  type="button"
+<div
+  data-testid="hierarchical_track_selector"
 >
-  <svg
-    aria-hidden="true"
-    class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
-    data-testid="AddIcon"
-    focusable="false"
-    viewBox="0 0 24 24"
+  <div
+    style="display: flex;"
   >
-    <path
-      d="M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6v2z"
-    />
-  </svg>
-  <span
-    class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
-  />
-</button>
+    <button
+      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-1kgqocu-MuiButtonBase-root-MuiIconButton-root-menuIcon"
+      tabindex="0"
+      type="button"
+    >
+      <svg
+        aria-hidden="true"
+        class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
+        data-testid="MenuIcon"
+        focusable="false"
+        viewBox="0 0 24 24"
+      >
+        <path
+          d="M3 18h18v-2H3v2zm0-5h18v-2H3v2zm0-7v2h18V6H3z"
+        />
+      </svg>
+      <span
+        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
+      />
+    </button>
+    <div
+      class="MuiFormControl-root MuiFormControl-marginDense MuiFormControl-fullWidth MuiTextField-root css-rlnh8o-MuiFormControl-root-MuiTextField-root-searchBox"
+    >
+      <label
+        class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard MuiFormLabel-colorPrimary MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard css-1s1jvl0-MuiFormLabel-root-MuiInputLabel-root"
+        data-shrink="false"
+        for="mui-1"
+        id="mui-1-label"
+      >
+        Filter tracks
+      </label>
+      <div
+        class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-sizeSmall MuiInputBase-adornedEnd css-1blad95-MuiInputBase-root-MuiInput-root"
+      >
+        <input
+          aria-invalid="false"
+          class="MuiInputBase-input MuiInput-input MuiInputBase-inputSizeSmall MuiInputBase-inputAdornedEnd css-nz481w-MuiInputBase-input-MuiInput-input"
+          id="mui-1"
+          type="text"
+          value=""
+        />
+        <div
+          class="MuiInputAdornment-root MuiInputAdornment-positionEnd MuiInputAdornment-standard MuiInputAdornment-sizeSmall css-1laqsz7-MuiInputAdornment-root"
+        >
+          <button
+            class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeSmall css-9vna8i-MuiButtonBase-root-MuiIconButton-root"
+            tabindex="0"
+            type="button"
+          >
+            <svg
+              aria-hidden="true"
+              class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-havevq-MuiSvgIcon-root"
+              data-testid="ClearIcon"
+              focusable="false"
+              viewBox="0 0 24 24"
+            >
+              <path
+                d="M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"
+              />
+            </svg>
+            <span
+              class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
+            />
+          </button>
+        </div>
+      </div>
+    </div>
+    <button
+      class="MuiButtonBase-root MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeSmall MuiButton-textSizeSmall css-1c8zr45-MuiButtonBase-root-MuiButton-root-menuIcon"
+      tabindex="0"
+      type="button"
+    >
+      Open faceted selector
+      <span
+        class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
+      />
+    </button>
+  </div>
+</div>
 `;
 
 exports[`renders with a couple of categorized tracks 1`] = `
@@ -56,8 +121,8 @@ exports[`renders with a couple of categorized tracks 1`] = `
       <label
         class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard MuiFormLabel-colorPrimary MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard css-1s1jvl0-MuiFormLabel-root-MuiInputLabel-root"
         data-shrink="false"
-        for="mui-5"
-        id="mui-5-label"
+        for="mui-6"
+        id="mui-6-label"
       >
         Filter tracks
       </label>
@@ -67,7 +132,7 @@ exports[`renders with a couple of categorized tracks 1`] = `
         <input
           aria-invalid="false"
           class="MuiInputBase-input MuiInput-input MuiInputBase-inputSizeSmall MuiInputBase-inputAdornedEnd css-nz481w-MuiInputBase-input-MuiInput-input"
-          id="mui-5"
+          id="mui-6"
           type="text"
           value=""
         />
@@ -144,8 +209,8 @@ exports[`renders with a couple of uncategorized tracks 1`] = `
       <label
         class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard MuiFormLabel-colorPrimary MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-sizeSmall MuiInputLabel-standard css-1s1jvl0-MuiFormLabel-root-MuiInputLabel-root"
         data-shrink="false"
-        for="mui-1"
-        id="mui-1-label"
+        for="mui-2"
+        id="mui-2-label"
       >
         Filter tracks
       </label>
@@ -155,7 +220,7 @@ exports[`renders with a couple of uncategorized tracks 1`] = `
         <input
           aria-invalid="false"
           class="MuiInputBase-input MuiInput-input MuiInputBase-inputSizeSmall MuiInputBase-inputAdornedEnd css-nz481w-MuiInputBase-input-MuiInput-input"
-          id="mui-1"
+          id="mui-2"
           type="text"
           value=""
         />

package/src/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.tsx

@@ -1,7 +1,5 @@
 import React from 'react'
 import {
-  Dialog,
-  DialogTitle,
   DialogContent,
   DialogContentText,
   Button,
@@ -9,23 +7,23 @@ import {
   ListItem,
   DialogActions,
 } from '@mui/material'
+import { Dialog } from '@jbrowse/core/ui'
 import { observer } from 'mobx-react'
 
-function CloseConnectionDialog({
+export default observer(function CloseConnectionDialog({
   modalInfo = {},
-  setModalInfo,
+  onClose,
 }: {
   modalInfo?: {
     name?: string
     dereferenceTypeCount?: { [key: string]: number }
-    safelyBreakConnection?: Function
+    safelyBreakConnection?: () => void
   }
-  setModalInfo: Function
+  onClose: () => void
 }) {
   const { name, dereferenceTypeCount, safelyBreakConnection } = modalInfo
   return (
-    <Dialog open>
-      <DialogTitle>Close connection &quot;{name}&quot;</DialogTitle>
+    <Dialog open maxWidth="lg" title={`Close connection "${name}"`}>
       <DialogContent>
         {dereferenceTypeCount ? (
           <>
@@ -44,7 +42,7 @@ function CloseConnectionDialog({
         </DialogContentText>
       </DialogContent>
       <DialogActions>
-        <Button onClick={() => setModalInfo()} color="primary">
+        <Button onClick={() => onClose()} color="primary">
           Cancel
         </Button>
         <Button
@@ -53,7 +51,7 @@ function CloseConnectionDialog({
             modalInfo
               ? () => {
                   safelyBreakConnection?.()
-                  setModalInfo()
+                  onClose()
                 }
               : () => {}
           }
@@ -64,6 +62,4 @@ function CloseConnectionDialog({
       </DialogActions>
     </Dialog>
   )
-}
-
-export default observer(CloseConnectionDialog)
+})

package/src/HierarchicalTrackSelectorWidget/components/dialogs/ToggleConnectionsDialog.tsx

@@ -27,7 +27,73 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
-function ToggleConnectionDialog({
+const ConnectionRow = observer(function ConnectionRow({
+  conf,
+  session,
+  breakConnection,
+}: {
+  conf: AnyConfigurationModel
+  session: AbstractSessionModel
+  breakConnection: (arg: AnyConfigurationModel) => void
+}) {
+  const { connectionInstances: instances = [] } = session
+  const name = readConfObject(conf, 'name')
+  const assemblyNames = readConfObject(conf, 'assemblyNames')
+  const found = instances.find(conn => name === conn.name)
+  return (
+    <FormControlLabel
+      key={conf.connectionId}
+      control={
+        <Checkbox
+          checked={!!found}
+          onChange={() => {
+            if (found) {
+              breakConnection(conf)
+            } else {
+              session.makeConnection?.(conf)
+            }
+          }}
+          color="primary"
+        />
+      }
+      label={[
+        name,
+        assemblyNames.length ? `(${ellipses(assemblyNames.join(','))})` : '',
+      ]
+        .filter(f => !!f)
+        .join(' ')}
+    />
+  )
+})
+
+const ConnectionList = observer(function ConnectionsList({
+  session,
+  breakConnection,
+}: {
+  session: AbstractSessionModel
+  breakConnection: (arg: AnyConfigurationModel) => void
+}) {
+  const { classes } = useStyles()
+  return (
+    <div className={classes.connectionContainer}>
+      {!session.connections.length ? (
+        <Typography>No connections found</Typography>
+      ) : (
+        session.connections.map((conf, idx) => (
+          <div key={conf.name + '_' + idx}>
+            <ConnectionRow
+              conf={conf}
+              session={session}
+              breakConnection={breakConnection}
+            />
+          </div>
+        ))
+      )}
+    </div>
+  )
+})
+
+export default observer(function ToggleConnectionDialog({
   session,
   handleClose,
   breakConnection,
@@ -36,8 +102,6 @@ function ToggleConnectionDialog({
   session: AbstractSessionModel
   breakConnection: (arg: AnyConfigurationModel) => void
 }) {
-  const { classes } = useStyles()
-  const { connections, connectionInstances: instances = [] } = session
   return (
     <Dialog
       open
@@ -47,39 +111,7 @@ function ToggleConnectionDialog({
     >
       <DialogContent>
         <Typography>Use the checkbox to turn on/off connections</Typography>
-        <div className={classes.connectionContainer}>
-          {connections.map(conf => {
-            const name = readConfObject(conf, 'name')
-            const assemblyNames = readConfObject(conf, 'assemblyNames')
-            const found = instances.find(conn => name === conn.name)
-            return (
-              <FormControlLabel
-                key={conf.connectionId}
-                control={
-                  <Checkbox
-                    checked={!!found}
-                    onChange={() => {
-                      if (found) {
-                        breakConnection(conf)
-                      } else {
-                        session.makeConnection?.(conf)
-                      }
-                    }}
-                    color="primary"
-                  />
-                }
-                label={`${name} ${
-                  assemblyNames.length
-                    ? '(' + ellipses(assemblyNames.join(',')) + ')'
-                    : ''
-                }`}
-              />
-            )
-          })}
-          {!connections.length ? (
-            <Typography>No connections found</Typography>
-          ) : null}
-        </div>
+        <ConnectionList session={session} breakConnection={breakConnection} />
       </DialogContent>
       <DialogActions>
         <Button
@@ -92,6 +124,4 @@ function ToggleConnectionDialog({
       </DialogActions>
     </Dialog>
   )
-}
-
-export default observer(ToggleConnectionDialog)
+})