[skip ci] Use dedupe

Misc

UseSWR for interval polling

Favs

Updates

Add tableContainer

Misc

Lint

Remove update preconfigured sessions

Move go button

Rm

Less progress

Use deferred value

Move files around

Updates

WOrking

Updates

Updates

Updates

Misc

Allow sorting complete genome

Delay bar

Simplified

More info

Simplify

Standardize

Misc

Preference

Re-org

Wow

Aggregate field back to geneName2

Aggregate field

Author: cmdcolin

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} />}
+    />
+  )
+}