Add ability to connect to genark and UCSC browsers to jbrowse desktop

packages/core/ui/ConfirmDialog.tsx

@@ -0,0 +1,51 @@
+import { Button, DialogActions, DialogContent } from '@mui/material'
+import { observer } from 'mobx-react'
+
+import Dialog from './Dialog'
+
+import type { DialogProps } from '@mui/material'
+
+interface Props extends DialogProps {
+  header?: React.ReactNode
+  onCancel: () => void
+  onSubmit: () => void
+  cancelText?: string
+  submitText?: string
+}
+
+const ConfirmDialog = observer(function (props: Props) {
+  const {
+    onSubmit,
+    onCancel,
+    cancelText = 'Cancel',
+    submitText = 'OK',
+    children,
+  } = props
+  return (
+    <Dialog onClose={onCancel} {...props}>
+      <DialogContent>{children}</DialogContent>
+      <DialogActions>
+        <Button
+          color="secondary"
+          variant="contained"
+          onClick={() => {
+            onCancel()
+          }}
+        >
+          {cancelText}
+        </Button>
+        <Button
+          color="primary"
+          variant="contained"
+          onClick={() => {
+            onSubmit()
+          }}
+        >
+          {submitText}
+        </Button>
+      </DialogActions>
+    </Dialog>
+  )
+})
+
+export default ConfirmDialog

packages/core/util/cluster.ts

@@ -52,16 +52,19 @@ export function clusterData({
 }) {
   // compute distance between each data point and every other data point
   // N x N matrix where N = data.length
-  let start = performance.now()
+  let stopTokenCheckerStart = performance.now()
+  let progressStart = performance.now()
   const distances: number[][] = []
 
   for (let i = 0; i < data.length; i++) {
-    if (performance.now() - start > 400) {
+    const r = performance.now()
+    if (r - stopTokenCheckerStart > 400) {
       checkStopToken(stopToken)
-      start = performance.now()
+      stopTokenCheckerStart = performance.now()
     }
-    if (onProgress) {
-      onProgress(`Making distance matrix: ${toP(i / (data.length - 1))}%`)
+    if (r - progressStart > 50) {
+      onProgress?.(`Making distance matrix: ${toP(i / (data.length - 1))}%`)
+      progressStart = performance.now()
     }
 
     // create a row for this data point
@@ -85,14 +88,17 @@ export function clusterData({
   // keep track of all tree slices
   let clustersGivenK = []
 
-  start = performance.now()
+  stopTokenCheckerStart = performance.now()
+  progressStart = performance.now()
   for (let iteration = 0; iteration < data.length; iteration++) {
-    if (performance.now() - start > 400) {
+    const r = performance.now()
+    if (r - stopTokenCheckerStart > 400) {
       checkStopToken(stopToken)
-      start = performance.now()
+      stopTokenCheckerStart = performance.now()
     }
-    if (onProgress) {
-      onProgress(`Clustering: ${toP((iteration + 1) / data.length)}%`)
+    if (r - progressStart > 50) {
+      onProgress?.(`Clustering: ${toP((iteration + 1) / data.length)}%`)
+      progressStart = performance.now()
     }
 
     // add current tree slice

plugins/menus/src/SessionManager/components/SessionManager.tsx

@@ -56,7 +56,7 @@ const SessionManager = observer(function ({
               }}
             />
           }
-          label="Show only favorites?"
+          label="Show favorites only?"
         />
 
         <Button

products/jbrowse-desktop/electron/electron.ts

@@ -156,31 +156,8 @@ interface SessionSnap {
 
 let mainWindow: electron.BrowserWindow | null
 
-async function updatePreconfiguredSessions() {
-  try {
-    const response = await fetch('https://jbrowse.org/genomes/sessions.json')
-    if (!response.ok) {
-      throw new Error(`HTTP ${response.status} ${response.statusText}`)
-    }
-    const data = await response.json()
-    for (const [key, value] of Object.entries(data)) {
-      // if there is not a 'gravestone' (.deleted file), then repopulate it on
-      // startup, this allows the user to delete even defaults if they want to
-      if (!fs.existsSync(`${getQuickstartPath(key)}.deleted`)) {
-        fs.writeFileSync(getQuickstartPath(key), JSON.stringify(value, null, 2))
-      }
-    }
-  } catch (e) {
-    // just console.error
-    console.error('Failed to fetch sessions.json', e)
-  }
-}
-
 async function createWindow() {
   // no need to await, just update in background
-  // eslint-disable-next-line @typescript-eslint/no-floating-promises
-  updatePreconfiguredSessions()
-
   const mainWindowState = windowStateKeeper({
     defaultWidth: 1400,
     defaultHeight: 800,

products/jbrowse-desktop/package.json

@@ -97,6 +97,7 @@
     "rxjs": "^7.0.0",
     "sanitize-filename": "^1.6.3",
     "semver": "^7.3.5",
+    "swr": "^2.3.3",
     "tss-react": "^4.4.1",
     "use-query-params": "^2.0.0"
   },

products/jbrowse-desktop/src/components/Loader.tsx

@@ -8,7 +8,7 @@ import { observer } from 'mobx-react'
 import { StringParam, useQueryParam } from 'use-query-params'
 
 import JBrowse from './JBrowse'
-import StartScreen from './StartScreen'
+import StartScreen from './StartScreen/StartScreen'
 import { loadPluginManager } from './StartScreen/util'
 
 import type PluginManager from '@jbrowse/core/PluginManager'

products/jbrowse-desktop/src/components/StartScreen/Checkbox2.tsx

@@ -0,0 +1,24 @@
+import { Checkbox, FormControlLabel } from '@mui/material'
+
+export default function Checkbox2({
+  checked,
+  disabled,
+  label,
+  onChange,
+  className,
+}: {
+  checked: boolean
+  disabled?: boolean
+  label: React.ReactNode
+  onChange: (event: React.ChangeEvent<HTMLInputElement>) => void
+  className?: string
+}) {
+  return (
+    <FormControlLabel
+      className={className}
+      disabled={disabled}
+      label={label}
+      control={<Checkbox checked={checked} onChange={onChange} />}
+    />
+  )
+}