@jbrowse/plugin-data-management 2.3.4 → 2.4.1

package/src/PluginStoreWidget/components/InstalledPluginsList.tsx

@@ -12,19 +12,21 @@ function InstalledPluginsList({
   pluginManager: PluginManager
   model: PluginStoreModel
 }) {
-  const { plugins } = pluginManager as PluginManager
+  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

@@ -20,9 +20,11 @@ import { makeStyles } from 'tss-react/mui'
 import PersonIcon from '@mui/icons-material/Person'
 import AddIcon from '@mui/icons-material/Add'
 import CheckIcon from '@mui/icons-material/Check'
+
+// locals
 import { PluginStoreModel } from '../model'
 
-const useStyles = makeStyles()(() => ({
+const useStyles = makeStyles()({
   card: {
     margin: '1em',
   },
@@ -38,9 +40,9 @@ const useStyles = makeStyles()(() => ({
     alignItems: 'center',
     margin: '0.4em 0em',
   },
-}))
+})
 
-function PluginCard({
+export default observer(function PluginCard({
   plugin,
   model,
   adminMode,
@@ -52,9 +54,8 @@ 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
 
@@ -86,7 +87,6 @@ function PluginCard({
       <CardActions>
         <Button
           variant="contained"
-          color="primary"
           disabled={disableButton}
           startIcon={isInstalled ? <CheckIcon /> : <AddIcon />}
           onClick={() => {
@@ -103,6 +103,4 @@ function PluginCard({
       </CardActions>
     </Card>
   )
-}
-
-export default observer(PluginCard)
+})

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/PluginStoreWidget.tsx

@@ -32,7 +32,7 @@ const useStyles = makeStyles()(theme => ({
     margin: theme.spacing(1),
   },
   expandIcon: {
-    color: '#fff',
+    color: theme.palette.tertiary.contrastText,
   },
   adminBadge: {
     margin: '0.5em',
@@ -106,7 +106,6 @@ function PluginStoreWidget({ model }: { model: PluginStoreModel }) {
           <div className={classes.customPluginButton}>
             <Button
               variant="contained"
-              color="primary"
               onClick={() => setCustomPluginFormOpen(true)}
             >
               Add custom plugin
@@ -127,10 +126,7 @@ function PluginStoreWidget({ model }: { model: PluginStoreModel }) {
         InputProps={{
           endAdornment: (
             <InputAdornment position="end">
-              <IconButton
-                color="secondary"
-                onClick={() => model.clearFilterText()}
-              >
+              <IconButton onClick={() => model.clearFilterText()}>
                 <ClearIcon />
               </IconButton>
             </InputAdornment>
@@ -171,7 +167,7 @@ function PluginStoreWidget({ model }: { model: PluginStoreModel }) {
             })
             .map(plugin => (
               <PluginCard
-                key={(plugin as JBrowsePlugin).name}
+                key={plugin.name}
                 plugin={plugin}
                 model={model}
                 adminMode={!!adminMode}

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

@@ -29,7 +29,7 @@ exports[`renders with the available plugins 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"
         >
@@ -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()) as string[]
-    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'