Fixes

Author: cmdcolin

.github/workflows/push.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - '*'
-      - '!winelectron'
     tags:
       - '*'
 

.github/workflows/windows-electron.yml

@@ -3,7 +3,7 @@ name: Windows Electron Tests
 on:
   push:
     branches:
-      - winelectron
+      - main
 
 permissions:
   contents: read

packages/core/src/util/tracks.ts

@@ -181,12 +181,24 @@ export function getFileName(track: FileLocation) {
   const uri = 'uri' in track ? track.uri : undefined
   const localPath = 'localPath' in track ? track.localPath : undefined
   const blob = 'blobId' in track ? track : undefined
-  return (
-    blob?.name ||
-    uri?.slice(uri.lastIndexOf('/') + 1) ||
-    localPath?.slice(localPath.replace(/\\/g, '/').lastIndexOf('/') + 1) ||
-    ''
-  )
+
+  if (blob?.name) {
+    return blob.name
+  }
+
+  if (uri) {
+    // Normalize path separators and find the last one
+    // This handles both forward slashes and Windows backslashes in file:// URLs
+    const normalized = uri.replace(/\\/g, '/')
+    return normalized.slice(normalized.lastIndexOf('/') + 1)
+  }
+
+  if (localPath) {
+    const normalized = localPath.replace(/\\/g, '/')
+    return normalized.slice(normalized.lastIndexOf('/') + 1)
+  }
+
+  return ''
 }
 
 export function guessAdapter(

packages/text-indexing/src/TextIndexing.ts

@@ -7,7 +7,7 @@ import { checkStopToken } from '@jbrowse/core/util/stopToken'
 import { ixIxxStream } from 'ixixx'
 
 // misc
-import { generateMeta } from './types/common.ts'
+import { generateMeta, sanitizeForFilename } from './types/common.ts'
 import { indexGff3 } from './types/gff3Adapter.ts'
 import { indexVcf } from './types/vcfAdapter.ts'
 
@@ -290,7 +290,8 @@ function getLoc(attr: string, config: Track) {
 }
 
 function runIxIxx(readStream: Readable, idxLocation: string, name: string) {
-  const ixFilename = path.join(idxLocation, 'trix', `${name}.ix`)
-  const ixxFilename = path.join(idxLocation, 'trix', `${name}.ixx`)
+  const safeName = sanitizeForFilename(name)
+  const ixFilename = path.join(idxLocation, 'trix', `${safeName}.ix`)
+  const ixxFilename = path.join(idxLocation, 'trix', `${safeName}.ixx`)
   return ixIxxStream(readStream, ixFilename, ixxFilename)
 }

packages/text-indexing/src/types/common.ts

@@ -153,6 +153,12 @@ export function guessAdapterFromFileName(filePath: string): Track {
   }
 }
 
+// Sanitize a string to be safe for use in filenames on all platforms
+// Replaces characters that are invalid in Windows filenames: \ / : * ? " < > |
+export function sanitizeForFilename(name: string) {
+  return name.replace(/[\\/:*?"<>|]/g, '_')
+}
+
 /**
  * Generates metadata of index given a filename (trackId or assembly)
  */
@@ -171,8 +177,9 @@ export async function generateMeta({
   featureTypesToExclude: string[]
   assemblyNames: string[]
 }) {
+  const safeName = sanitizeForFilename(name)
   fs.writeFileSync(
-    path.join(outDir, 'trix', `${name}_meta.json`),
+    path.join(outDir, 'trix', `${safeName}_meta.json`),
     JSON.stringify(
       {
         dateCreated: new Date().toISOString(),

products/jbrowse-desktop/electron/autoUpdater.ts

@@ -19,13 +19,16 @@ export function setupAutoUpdater(
   autoUpdater.autoDownload = false
 
   autoUpdater.on('error', (error: Error) => {
+    const errorMessage = `Error in auto-updater: ${error}`
+    sendStatusToWindow(getMainWindow(), errorMessage)
+
     // Skip dialogs in CI environments to avoid blocking tests
     if (process.env.CI) {
       console.error('Auto-updater error (CI mode, skipping dialog):', error)
       return
     }
     dialog.showErrorBox(
-      'Error: ',
+      'Update Error',
       // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       error == null ? 'unknown' : (error.stack || error).toString(),
     )
@@ -34,6 +37,7 @@ export function setupAutoUpdater(
   autoUpdater.on('update-available', async () => {
     // Skip dialogs in CI environments
     if (process.env.CI) {
+      // eslint-disable-next-line no-console
       console.log('Update available (CI mode, skipping dialog)')
       return
     }
@@ -56,13 +60,10 @@ export function setupAutoUpdater(
     sendStatusToWindow(getMainWindow(), 'Checking for update...')
   })
 
-  autoUpdater.on('error', (err: Error) => {
-    sendStatusToWindow(getMainWindow(), `Error in auto-updater: ${err}`)
-  })
-
   autoUpdater.on('update-downloaded', () => {
     // Skip dialogs in CI environments
     if (process.env.CI) {
+      // eslint-disable-next-line no-console
       console.log('Update downloaded (CI mode, skipping dialog)')
       return
     }

products/jbrowse-desktop/electron/electron.ts

@@ -1,4 +1,4 @@
-import { app, ipcMain } from 'electron'
+import { app, dialog, ipcMain } from 'electron'
 import contextMenu from 'electron-context-menu'
 import debug from 'electron-debug'
 import pkg from 'electron-updater'
@@ -11,6 +11,7 @@ import { registerSessionHandlers } from './ipc/sessionHandlers.ts'
 import { initializePaths } from './paths.ts'
 import { createAuthWindow, createMainWindow } from './window.ts'
 
+import type { AppPaths } from './paths.ts'
 import type { BrowserWindow } from 'electron'
 
 const { autoUpdater } = pkg
@@ -22,31 +23,41 @@ debug({ showDevTools: false, isEnabled: true })
 // Environment variables
 const DEV_SERVER_URL = process.env.DEV_SERVER_URL
 
-// Initialize paths once
-const paths = initializePaths()
-
 // Main window reference
 let mainWindow: BrowserWindow | null = null
 
+// Paths - initialized after app is ready
+let paths: AppPaths
+
 function getMainWindow() {
   return mainWindow
 }
 
+/**
+ * Shows an error dialog to the user and optionally quits the app
+ */
+function showFatalError(title: string, error: unknown, shouldQuit = true) {
+  const message = error instanceof Error ? error.message : String(error)
+  const detail = error instanceof Error ? error.stack : undefined
+  console.error(`${title}:`, error)
+
+  dialog.showErrorBox(title, detail ? `${message}\n\n${detail}` : message)
+
+  if (shouldQuit) {
+    app.quit()
+  }
+}
+
 /**
  * Creates the main window and initializes the application
  */
 async function initialize() {
-  try {
-    await initializeFileSystem(paths)
-    mainWindow = await createMainWindow(autoUpdater, DEV_SERVER_URL)
+  await initializeFileSystem(paths)
+  mainWindow = await createMainWindow(autoUpdater, DEV_SERVER_URL)
 
-    mainWindow.on('closed', () => {
-      mainWindow = null
-    })
-  } catch (error) {
-    console.error('Failed to initialize application:', error)
-    throw error
-  }
+  mainWindow.on('closed', () => {
+    mainWindow = null
+  })
 }
 
 /**
@@ -72,15 +83,19 @@ function registerIpcHandlers() {
   )
 }
 
-// Setup auto-updater
+// Setup auto-updater (just registers event listeners, safe before ready)
 setupAutoUpdater(autoUpdater, getMainWindow)
 
-// Register IPC handlers
-registerIpcHandlers()
-
 // App lifecycle handlers
 app.on('ready', async () => {
-  await initialize()
+  try {
+    // Initialize paths after app is ready to ensure app.getPath() works reliably
+    paths = initializePaths()
+    registerIpcHandlers()
+    await initialize()
+  } catch (error) {
+    showFatalError('Failed to initialize application', error)
+  }
 })
 
 app.on('window-all-closed', () => {
@@ -91,6 +106,10 @@ app.on('window-all-closed', () => {
 
 app.on('activate', async () => {
   if (mainWindow === null) {
-    await initialize()
+    try {
+      await initialize()
+    } catch (error) {
+      showFatalError('Failed to create window', error)
+    }
   }
 })

products/jbrowse-desktop/electron/window.ts

@@ -1,5 +1,5 @@
 import path from 'path'
-import url from 'url'
+import url, { pathToFileURL } from 'url'
 
 import electron, { BrowserWindow, Menu, app, shell } from 'electron'
 import windowStateKeeper from 'electron-window-state'
@@ -15,9 +15,7 @@ const DEFAULT_DEV_SERVER_URL = 'http://localhost:3000'
 
 function getAppUrl(devServerUrl: URL): URL {
   if (app.isPackaged) {
-    return new URL(
-      `file://${path.join(app.getAppPath(), 'build', 'index.html')}`,
-    )
+    return pathToFileURL(path.join(app.getAppPath(), 'build', 'index.html'))
   }
   return devServerUrl
 }