Add text searching to desktop and allow it to reload after installing…

… plugins

products/jbrowse-desktop/public/electron.ts

@@ -221,12 +221,13 @@ ipcMain.handle('listSessions', async () => {
   )
 })
 
-ipcMain.handle('loadExternalConfig', (_event: unknown, sessionPath) =>
-  readFile(sessionPath, 'utf8'),
-)
-ipcMain.handle('loadSession', (_event: unknown, sessionName: string) =>
-  readFile(getPath(sessionName), 'utf8'),
-)
+ipcMain.handle('loadExternalConfig', (_event: unknown, sessionPath) => {
+  return readFile(sessionPath, 'utf8')
+})
+
+ipcMain.handle('loadSession', (_event: unknown, sessionName: string) => {
+  return readFile(getPath(sessionName), 'utf8')
+})
 
 ipcMain.on('saveSession', async (_event: unknown, snap: SessionSnap) => {
   const page = await mainWindow?.capturePage()

products/jbrowse-desktop/src/Loader.tsx

@@ -1,23 +1,62 @@
-import React, { useState } from 'react'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { CssBaseline, ThemeProvider } from '@material-ui/core'
+import React, { useState, useEffect } from 'react'
 import { observer } from 'mobx-react'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { CssBaseline, ThemeProvider, Typography } from '@material-ui/core'
+import { createJBrowseTheme } from '@jbrowse/core/ui'
+import {
+  StringParam,
+  QueryParamProvider,
+  useQueryParam,
+} from 'use-query-params'
+import { ipcRenderer } from 'electron'
+
+import { createPluginManager } from './StartScreen/util'
+
 import JBrowse from './JBrowse'
 import StartScreen from './StartScreen'
-import { createJBrowseTheme } from '@jbrowse/core/ui'
 
-function Loader() {
+const Loader = observer(() => {
   const [pluginManager, setPluginManager] = useState<PluginManager>()
+  const [config, setConfig] = useQueryParam('config', StringParam)
+  const [error, setError] = useState<Error>()
+
+  useEffect(() => {
+    ;(async () => {
+      if (config) {
+        try {
+          const data = await ipcRenderer.invoke('loadSession', config)
+          const pm = await createPluginManager(JSON.parse(data))
+          setPluginManager(pm)
+          setConfig('')
+        } catch (e) {
+          console.error(e)
+          setError(e)
+        }
+      }
+    })()
+  }, [config, setConfig])
+
   return (
     <ThemeProvider theme={createJBrowseTheme()}>
       <CssBaseline />
+      {error ? (
+        <Typography variant="h6" color="error">{`${error}`}</Typography>
+      ) : null}
       {pluginManager?.rootModel?.session ? (
         <JBrowse pluginManager={pluginManager} />
-      ) : (
+      ) : !config || error ? (
         <StartScreen setPluginManager={setPluginManager} />
-      )}
+      ) : null}
     </ThemeProvider>
   )
+})
+
+function Wrapper() {
+  return (
+    <QueryParamProvider>
+      <Loader />
+    </QueryParamProvider>
+  )
 }
 
-export default observer(Loader)
+export default Wrapper

products/jbrowse-desktop/src/StartScreen/data/preloadedConfigs.js

@@ -203,11 +203,47 @@ const preloadedConfigs = {
           },
         },
       },
+      {
+        type: 'FeatureTrack',
+        trackId: 'ncbi_refseq_109_hg38_latest',
+        name: 'NCBI RefSeq',
+        assemblyNames: ['hg38'],
+        category: ['Annotation'],
+        adapter: {
+          type: 'Gff3TabixAdapter',
+          gffGzLocation: {
+            uri:
+              'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GRCh38_latest_genomic.sort.gff.gz',
+          },
+          index: {
+            location: {
+              uri:
+                'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GRCh38_latest_genomic.sort.gff.gz.tbi',
+            },
+          },
+        },
+      },
     ],
 
     defaultSession: {
       name: 'New Session',
     },
+    aggregateTextSearchAdapters: [
+      {
+        type: 'TrixTextSearchAdapter',
+        textSearchAdapterId: 'hg38-index',
+        ixFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/trix/hg38.ix',
+        },
+        ixxFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/trix/hg38.ixx',
+        },
+        metaFilePath: {
+          uri: 'https://jbrowse.org/genomes/GRCh38/trix/meta.json',
+        },
+        assemblyNames: ['hg38'],
+      },
+    ],
   },
   hg19: {
     assemblies: [
@@ -243,6 +279,30 @@ const preloadedConfigs = {
       },
     ],
     tracks: [
+      {
+        type: 'FeatureTrack',
+        trackId: 'ncbi_gff_hg19',
+        name: 'NCBI RefSeq',
+        assemblyNames: ['hg19'],
+        category: ['Annotation'],
+        metadata: {
+          source: 'https://www.ncbi.nlm.nih.gov/genome/guide/human/',
+          dateaccessed: '12/03/2020',
+        },
+        adapter: {
+          type: 'Gff3TabixAdapter',
+          gffGzLocation: {
+            uri:
+              'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz',
+          },
+          index: {
+            location: {
+              uri:
+                'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi',
+            },
+          },
+        },
+      },
       {
         type: 'FeatureTrack',
         trackId: 'repeats_hg19',
@@ -397,6 +457,23 @@ const preloadedConfigs = {
     defaultSession: {
       name: 'New Session',
     },
+
+    aggregateTextSearchAdapters: [
+      {
+        type: 'TrixTextSearchAdapter',
+        textSearchAdapterId: 'hg19-index',
+        ixFilePath: {
+          uri: 'https://jbrowse.org/genomes/hg19/trix/hg19.ix',
+        },
+        ixxFilePath: {
+          uri: 'https://jbrowse.org/genomes/hg19/trix/hg19.ixx',
+        },
+        metaFilePath: {
+          uri: 'https://jbrowse.org/genomes/hg19/trix/meta.json',
+        },
+        assemblyNames: ['hg19'],
+      },
+    ],
   },
   mm10: {
     assemblies: [

products/jbrowse-desktop/src/corePlugins.ts

@@ -20,6 +20,7 @@ import Wiggle from '@jbrowse/plugin-wiggle'
 import SpreadsheetViewPlugin from '@jbrowse/plugin-spreadsheet-view'
 import SvInspectorPlugin from '@jbrowse/plugin-sv-inspector'
 import HicPlugin from '@jbrowse/plugin-hic'
+import TrixPlugin from '@jbrowse/plugin-trix'
 import GridBookmarkPlugin from '@jbrowse/plugin-grid-bookmark'
 
 const corePlugins = [
@@ -45,6 +46,7 @@ const corePlugins = [
   SvInspectorPlugin,
   BreakpointSplitView,
   HicPlugin,
+  TrixPlugin,
   GridBookmarkPlugin,
 ]
 

products/jbrowse-desktop/src/jbrowseModel.js

@@ -58,6 +58,9 @@ export default function JBrowseDesktop(
       // track configuration is an array of track config schemas. multiple
       // instances of a track can exist that use the same configuration
       tracks: types.array(pluginManager.pluggableConfigSchemaType('track')),
+      aggregateTextSearchAdapters: types.array(
+        pluginManager.pluggableConfigSchemaType('text search adapter'),
+      ),
       connections: types.array(
         pluginManager.pluggableConfigSchemaType('connection'),
       ),

products/jbrowse-desktop/src/rootModel.ts

@@ -5,8 +5,8 @@ import { autorun } from 'mobx'
 import PluginManager from '@jbrowse/core/PluginManager'
 import RpcManager from '@jbrowse/core/rpc/RpcManager'
 import { MenuItem } from '@jbrowse/core/ui'
-import AddIcon from '@material-ui/icons/Add'
 import SettingsIcon from '@material-ui/icons/Settings'
+import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager'
 import AppsIcon from '@material-ui/icons/Apps'
 import electron from 'electron'
 import {
@@ -58,6 +58,7 @@ export default function rootModelFactory(pluginManager: PluginManager) {
     .volatile(() => ({
       pluginsUpdated: false,
       error: undefined as Error | undefined,
+      textSearchManager: new TextSearchManager(pluginManager),
     }))
     .actions(self => ({
       setSavedSessionNames(sessionNames: string[]) {
@@ -109,13 +110,6 @@ export default function rootModelFactory(pluginManager: PluginManager) {
         {
           label: 'File',
           menuItems: [
-            {
-              label: 'New Session',
-              icon: AddIcon,
-              onClick: (session: { setDefaultSession: () => void }) => {
-                session.setDefaultSession()
-              },
-            },
             {
               label: 'Return to start screen',
               icon: AppsIcon,
@@ -294,15 +288,19 @@ export default function rootModelFactory(pluginManager: PluginManager) {
           self,
           autorun(
             () => {
-              // if (self.session) {
-              //   ipcRenderer.send('saveSession', getSnapshot(self.session))
-              // }
               if (self.session) {
                 ipcRenderer.send('saveSession', {
                   ...getSnapshot(self.jbrowse),
                   defaultSession: getSnapshot(self.session),
                 })
               }
+              if (self.pluginsUpdated) {
+                const url = window.location.href.split('?')[0]
+
+                window.location.href = `${url}?config=${encodeURIComponent(
+                  self.session?.name || '',
+                )}`
+              }
             },
             { delay: 1000 },
           ),