@jbrowse/plugin-data-management 2.4.0 → 2.4.2

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),

package/src/PluginStoreWidget/components/InstalledPluginsList.tsx

@@ -14,17 +14,19 @@ function InstalledPluginsList({
 }) {
   const { plugins } = pluginManager
 
-  const corePlugins = plugins
-    .filter(p => pluginManager.pluginMetadata[p.name]?.isCore)
-    .map(p => p.name)
+  const corePlugins = new Set(
+    plugins
+      .filter(p => pluginManager.pluginMetadata[p.name]?.isCore)
+      .map(p => p.name),
+  )
 
   const externalPlugins = plugins.filter(
-    plugin => !corePlugins.includes(plugin.name),
+    plugin => !corePlugins.has(plugin.name),
   )
 
   return (
     <List>
-      {externalPlugins.length ? (
+      {externalPlugins.length > 0 ? (
         externalPlugins
           .filter(plugin =>
             plugin.name.toLowerCase().includes(model.filterText.toLowerCase()),

package/src/PluginStoreWidget/components/PluginCard.tsx

@@ -54,9 +54,8 @@ export default observer(function PluginCard({
   const { classes } = useStyles()
   const session = getSession(model)
   const { pluginManager } = getEnv(model)
-  const isInstalled = Boolean(
-    pluginManager.runtimePluginDefinitions.find(def => def.url === plugin.url),
-  )
+  const { runtimePluginDefinitions } = pluginManager
+  const isInstalled = runtimePluginDefinitions.some(d => d.url === plugin.url)
   const [tempDisabled, setTempDisabled] = useState(false)
   const disableButton = isInstalled || tempDisabled
 

package/src/PluginStoreWidget/components/PluginStoreWidget.test.tsx

@@ -34,17 +34,17 @@ beforeEach(() => {
   model = session.addWidget('PluginStoreWidget', 'pluginStoreWidget')
   const { location } = window
 
-  // @ts-ignore
+  // @ts-expect-error
   delete window.location
   window.location = {
     ...location,
     reload: jest.fn(),
   }
 
-  // @ts-ignore
+  // @ts-expect-error
   fetch.resetMocks()
 
-  // @ts-ignore
+  // @ts-expect-error
   fetch.mockResponse(JSON.stringify(plugins))
 })
 

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

@@ -789,7 +789,7 @@ exports[`renders with the available plugins 1`] = `
                     class="MuiTypography-root MuiTypography-h5 css-1ldbtdh-MuiTypography-root"
                   >
                     <a
-                      class="MuiTypography-root MuiTypography-inherit MuiLink-root MuiLink-underlineAlways css-1py4a5k-MuiTypography-root-MuiLink-root"
+                      class="MuiTypography-root MuiTypography-inherit MuiLink-root MuiLink-underlineAlways css-ygjubp-MuiTypography-root-MuiLink-root"
                       href="https://github.com/GMOD/jbrowse-plugin-msaview#readme"
                       rel="noopener"
                       target="_blank"

package/src/index.ts

@@ -3,12 +3,10 @@ import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import UCSCTrackHubConnectionF from './ucsc-trackhub'
 import AddTrackWidgetF from './AddTrackWidget'
-import { AddTrackModel } from './AddTrackWidget/model'
+
 import AddConnectionWidgetF from './AddConnectionWidget'
 import PluginStoreWidgetF from './PluginStoreWidget'
-import HierarchicalTrackSelectorWidgetF, {
-  HierarchicalTrackSelectorModel,
-} from './HierarchicalTrackSelectorWidget'
+import HierarchicalTrackSelectorWidgetF from './HierarchicalTrackSelectorWidget'
 
 const SetDefaultSession = lazy(() => import('./SetDefaultSession'))
 
@@ -34,4 +32,6 @@ export default class extends Plugin {
 }
 
 export { AssemblyManager, SetDefaultSession }
-export type { HierarchicalTrackSelectorModel, AddTrackModel }
+
+export { type AddTrackModel } from './AddTrackWidget/model'
+export { type HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget'

package/src/ucsc-trackhub/ucscTrackHub.ts

@@ -6,9 +6,6 @@ import {
   generateUnsupportedTrackConf,
   generateUnknownTrackConf,
 } from '@jbrowse/core/util/tracks'
-import ucscAssemblies from './ucscAssemblies'
-
-export { ucscAssemblies }
 
 export async function fetchHubFile(hubLocation: FileLocation) {
   try {
@@ -63,16 +60,16 @@ export function generateTracks(
 ) {
   const tracks: any = []
 
-  trackDb.forEach((track, trackName) => {
-    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
@@ -99,7 +96,7 @@ export function generateTracks(
       trackId: `ucsc-trackhub-${objectHash(res)}`,
       assemblyNames: [assemblyName],
     })
-  })
+  }
 
   return tracks
 }
@@ -324,3 +321,5 @@ function makeTrackConfig(
       return generateUnknownTrackConf(name, baseTrackType, categories)
   }
 }
+
+export { default as ucscAssemblies } from './ucscAssemblies'