Fix opening local files in the multi-wiggle add track selector (#4634)

GMOD · Nov 3, 2024 · 6c5407f · 6c5407f
1 parent be177a4
commit 6c5407f
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Showing 5 changed files with 403 additions and 373 deletions.
diff --git a/package.json b/package.json
@@ -100,7 +100,7 @@
     "dependency-graph": "^1.0.0",
     "dotenv": "^16.3.1",
     "dotenv-expand": "^11.0.3",
-    "electron": "32.1.0",
+    "electron": "33.0.2",
     "electron-builder": "^25.1.6",
     "electron-mock-ipc": "^0.3.8",
     "eslint": "^9.0.0",

diff --git a/plugins/wiggle/src/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.tsx b/plugins/wiggle/src/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.tsx
@@ -11,9 +11,6 @@ import { storeBlobLocation } from '@jbrowse/core/util/tracks'
 import { AddTrackModel } from '@jbrowse/plugin-data-management'
 
 const useStyles = makeStyles()(theme => ({
-  textbox: {
-    width: '100%',
-  },
   paper: {
     margin: theme.spacing(),
     padding: theme.spacing(),
@@ -25,6 +22,17 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
+// on electron, use path to LocalFileLocation, on web, use the BlobLocation
+function makeFileLocation(file: File) {
+  const { webUtils } = window.require('electron')
+  return isElectron
+    ? {
+        localPath: webUtils.getPathForFile(file),
+        locationType: 'LocalPathLocation',
+      }
+    : storeBlobLocation({ blob: file })
+}
+
 export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
   const { classes } = useStyles()
   const [val, setVal] = useState('')
@@ -41,14 +49,14 @@ export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
 
       <TextField
         multiline
+        fullWidth
         rows={10}
         value={val}
+        placeholder="Paste list of URLs here, or use file selector below"
+        variant="outlined"
         onChange={event => {
           setVal(event.target.value)
         }}
-        placeholder={'Paste list of URLs here, or use file selector below'}
-        variant="outlined"
-        className={classes.textbox}
       />
 
       <Button variant="outlined" component="label">
@@ -60,12 +68,7 @@ export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
           onChange={({ target }) => {
             const res = [...(target.files || [])].map(file => ({
               type: 'BigWigAdapter',
-              bigWigLocation: isElectron
-                ? {
-                    localPath: (file as File & { path: string }).path,
-                    locationType: 'LocalPathLocation',
-                  }
-                : storeBlobLocation({ blob: file }),
+              bigWigLocation: makeFileLocation(file),
               source: file.name,
             }))
             setVal(JSON.stringify(res, null, 2))
@@ -74,54 +77,58 @@ export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
       </Button>
       <TextField
         value={trackName}
+        helperText="Track name"
         onChange={event => {
           setTrackName(event.target.value)
         }}
-        helperText="Track name"
       />
       <Button
         variant="contained"
         className={classes.submit}
         onClick={() => {
           const session = getSession(model)
-
-          const trackId = [
-            `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
-            session.adminMode ? '' : '-sessionTrack',
-          ].join('')
-
-          // allow list of bigwigs in JSON format or line-by-line
-          let bigWigs: unknown[]
           try {
-            bigWigs = JSON.parse(val)
-          } catch (e) {
-            bigWigs = val
-              .split(/\n|\r\n|\r/)
-              .map(f => f.trim())
-              .filter(f => !!f)
-          }
-          const obj =
-            typeof bigWigs[0] === 'string'
-              ? { bigWigs }
-              : { subadapters: bigWigs }
+            const trackId = [
+              `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+              session.adminMode ? '' : '-sessionTrack',
+            ].join('')
 
-          if (isSessionWithAddTracks(session)) {
-            session.addTrackConf({
-              trackId,
-              type: 'MultiQuantitativeTrack',
-              name: trackName,
-              assemblyNames: [model.assembly],
-              adapter: {
-                type: 'MultiWiggleAdapter',
-                ...obj,
-              },
-            })
+            // allow list of bigwigs in JSON format or line-by-line
+            let bigWigs: unknown[]
+            try {
+              bigWigs = JSON.parse(val)
+            } catch (e) {
+              bigWigs = val
+                .split(/\n|\r\n|\r/)
+                .map(f => f.trim())
+                .filter(f => !!f)
+            }
+            const obj =
+              typeof bigWigs[0] === 'string'
+                ? { bigWigs }
+                : { subadapters: bigWigs }
 
-            model.view?.showTrack(trackId)
-          }
-          model.clearData()
-          if (isSessionModelWithWidgets(session)) {
-            session.hideWidget(model)
+            if (isSessionWithAddTracks(session)) {
+              session.addTrackConf({
+                trackId,
+                type: 'MultiQuantitativeTrack',
+                name: trackName,
+                assemblyNames: [model.assembly],
+                adapter: {
+                  type: 'MultiWiggleAdapter',
+                  ...obj,
+                },
+              })
+
+              model.view?.showTrack(trackId)
+            }
+            model.clearData()
+            if (isSessionModelWithWidgets(session)) {
+              session.hideWidget(model)
+            }
+          } catch (e) {
+            console.error(e)
+            session.notifyError(`${e}`, e)
           }
         }}
       >

diff --git a/products/jbrowse-desktop/package.json b/products/jbrowse-desktop/package.json
@@ -102,13 +102,13 @@
     "use-query-params": "^2.0.0"
   },
   "devDependencies": {
-    "electron": "32.1.0"
+    "electron": "33.0.2"
   },
   "browserslist": [
     "last 1 chrome version"
   ],
   "build": {
-    "electronVersion": "32.1.0",
+    "electronVersion": "33.0.2",
     "extraMetadata": {
       "main": "build/electron.js"
     },

diff --git a/website/docs/tutorials/desktop_spec_plugin_tutorial.md b/website/docs/tutorials/desktop_spec_plugin_tutorial.md
@@ -288,13 +288,24 @@ We'll add some more UI elements that allow us to do something more interesting:
 
 **./src/MyToolWidget/MyToolWidget.tsx**
 
-```jsx
+```tsx
 import React, { useEffect, useState } from 'react'
-import { Box, Button, FormControl, Paper, TextField, Typography } from '@mui/material'
+import {
+  Box,
+  Button,
+  FormControl,
+  Paper,
+  TextField,
+  Typography,
+} from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 import { getSession } from '@jbrowse/core/util'
 import { AddTrackModel } from '@jbrowse/plugin-data-management'
-import { LocalPathLocation, FileLocation, BlobLocation } from '@jbrowse/core/util/types'
+import {
+  LocalPathLocation,
+  FileLocation,
+  BlobLocation,
+} from '@jbrowse/core/util/types'
 import { getBlob, storeBlobLocation } from '@jbrowse/core/util/tracks'
 import { isElectron } from '@jbrowse/core/util'
 
@@ -331,27 +342,26 @@ export default function MyToolWidget({ model }: { model: AddTrackModel }) {
   }, [model.trackData])
 
   return (
-    { /* formatting using paper and other mui elements */ }
     <Paper className={classes.paper}>
       <p>
         This desktop plugin widget will allow you to submit an unindexed{' '}
         <code>.vcf</code> file to JBrowse which will then use a script to sort,
         index, and zip the file. This circumvents any CLI operations you may
         have otherwise needed to do!
       </p>
-      { /* LocalFileChooser is a component we define below, it allows us to select local files only */ }
+      {/* LocalFileChooser is a component we define below, it allows us to select local files only */}
       <LocalFileChooser
         location={model.trackData}
         setLocation={model.setTrackData}
         setName={setTrackName}
       />
-      { /* displays the track name and lets the user edit it to something they wish */ }
+      {/* displays the track name and lets the user edit it to something they wish */}
       <TextField
         value={trackName}
         onChange={event => setTrackName(event.target.value)}
         helperText="Track name"
       />
-      { /* the submit button will eventually be responsible for executing our script */ }
+      {/* the submit button will eventually be responsible for executing our script */}
       <Button variant="contained" className={classes.submit} onClick={() => {}}>
         Submit
       </Button>
@@ -371,7 +381,7 @@ function LocalFileChooser(props: {
 }) {
   const { classes } = useStyles()
   const { location, setLocation, setName } = props
-  const [filename, setFilename] = useState(``)
+  const [filename, setFilename] = useState('')
 
   const needToReload =
     location && isBlobLocation(location) && !getBlob(location.blobId)
@@ -390,17 +400,19 @@ function LocalFileChooser(props: {
                 const file = target && target.files && target.files[0]
                 if (file) {
                   if (isElectron) {
+                    const { webUtils } = window.require('electron')
+                    const path = webUtils.getPathForFile(file)
                     // here we are setting the location information for the file selected
                     // these features are necessary for the VcfTabixAdapter
                     setLocation({
-                      localPath: (file as File & { path: string }).path,
+                      localPath: path,
                       locationType: 'LocalPathLocation',
                     })
                   } else {
                     setLocation(storeBlobLocation({ blob: file }))
                   }
                   // these set ui elements
-                  setFilename((file as File & { path: string }).path)
+                  setFilename(file.name)
                   setName(file.name)
                 }
               }}