Menu item redesign and sessions are manually saved to filesystem

packages/core/ui/Icons.tsx

@@ -34,3 +34,47 @@ export function TrackSelector(props: SvgIconProps) {
     </SvgIcon>
   )
 }
+
+//  content-save-edit from https://materialdesignicons.com/
+export function SaveAs(props: SvgIconProps) {
+  return (
+    <SvgIcon {...props}>
+      <path
+        fill="currentColor"
+        d="M10,19L10.14,18.86C8.9,18.5 8,17.36 8,16A3,3 0 0,1 11,13C12.36,13 13.5,13.9 13.86,15.14L20,9V7L16,3H4C2.89,3 2,3.9 2,5V19A2,2 0 0,0 4,21H10V19M4,5H14V9H4V5M20.04,12.13C19.9,12.13 19.76,12.19 19.65,12.3L18.65,13.3L20.7,15.35L21.7,14.35C21.92,14.14 21.92,13.79 21.7,13.58L20.42,12.3C20.31,12.19 20.18,12.13 20.04,12.13M18.07,13.88L12,19.94V22H14.06L20.12,15.93L18.07,13.88Z"
+      />
+    </SvgIcon>
+  )
+}
+
+//  content-save from https://materialdesignicons.com/
+export function Save(props: SvgIconProps) {
+  return (
+    <SvgIcon {...props}>
+      <path
+        fill="currentColor"
+        d="M15,9H5V5H15M12,19A3,3 0 0,1 9,16A3,3 0 0,1 12,13A3,3 0 0,1 15,16A3,3 0 0,1 12,19M17,3H5C3.89,3 3,3.9 3,5V19A2,2 0 0,0 5,21H19A2,2 0 0,0 21,19V7L17,3Z"
+      />
+    </SvgIcon>
+  )
+}
+
+//  dna from https://materialdesignicons.com/
+export function DNA(props: SvgIconProps) {
+  return (
+    <SvgIcon {...props}>
+      <path
+        fill="currentColor"
+        d="M4,2H6V4C6,5.44 6.68,6.61 7.88,7.78C8.74,8.61 9.89,9.41 11.09,10.2L9.26,11.39C8.27,10.72 7.31,10 6.5,9.21C5.07,7.82 4,6.1 4,4V2M18,2H20V4C20,6.1 18.93,7.82 17.5,9.21C16.09,10.59 14.29,11.73 12.54,12.84C10.79,13.96 9.09,15.05 7.88,16.22C6.68,17.39 6,18.56 6,20V22H4V20C4,17.9 5.07,16.18 6.5,14.79C7.91,13.41 9.71,12.27 11.46,11.16C13.21,10.04 14.91,8.95 16.12,7.78C17.32,6.61 18,5.44 18,4V2M14.74,12.61C15.73,13.28 16.69,14 17.5,14.79C18.93,16.18 20,17.9 20,20V22H18V20C18,18.56 17.32,17.39 16.12,16.22C15.26,15.39 14.11,14.59 12.91,13.8L14.74,12.61M7,3H17V4L16.94,4.5H7.06L7,4V3M7.68,6H16.32C16.08,6.34 15.8,6.69 15.42,7.06L14.91,7.5H9.07L8.58,7.06C8.2,6.69 7.92,6.34 7.68,6M9.09,16.5H14.93L15.42,16.94C15.8,17.31 16.08,17.66 16.32,18H7.68C7.92,17.66 8.2,17.31 8.58,16.94L9.09,16.5M7.06,19.5H16.94L17,20V21H7V20L7.06,19.5Z"
+      />
+    </SvgIcon>
+  )
+}
+
+export function Cable(props: SvgIconProps) {
+  return (
+    <SvgIcon {...props}>
+      <path d="M20 5V4c0-.55-.45-1-1-1h-2c-.55 0-1 .45-1 1v1h-1v4c0 .55.45 1 1 1h1v7c0 1.1-.9 2-2 2s-2-.9-2-2V7c0-2.21-1.79-4-4-4S5 4.79 5 7v7H4c-.55 0-1 .45-1 1v4h1v1c0 .55.45 1 1 1h2c.55 0 1-.45 1-1v-1h1v-4c0-.55-.45-1-1-1H7V7c0-1.1.9-2 2-2s2 .9 2 2v10c0 2.21 1.79 4 4 4s4-1.79 4-4v-7h1c.55 0 1-.45 1-1V5h-1z" />
+    </SvgIcon>
+  )
+}

packages/core/ui/Snackbar.tsx

@@ -1,10 +1,9 @@
-import IconButton from '@material-ui/core/IconButton'
-import Snackbar from '@material-ui/core/Snackbar'
+import React, { useEffect, useState } from 'react'
+import { IconButton, Snackbar } from '@material-ui/core'
 import CloseIcon from '@material-ui/icons/Close'
 import Alert from '@material-ui/lab/Alert'
 import { observer } from 'mobx-react'
 import { IAnyStateTreeNode } from 'mobx-state-tree'
-import React, { useEffect, useState } from 'react'
 import { AbstractSessionModel, NotificationLevel } from '../util'
 
 type SnackbarMessage = [string, NotificationLevel]
@@ -20,9 +19,7 @@ function MessageSnackbar({
   session: SnackbarSession & IAnyStateTreeNode
 }) {
   const [open, setOpen] = useState(false)
-  const [snackbarMessage, setSnackbarMessage] = useState<
-    SnackbarMessage | undefined
-  >()
+  const [snackbarMessage, setSnackbarMessage] = useState<SnackbarMessage>()
 
   const { popSnackbarMessage, snackbarMessages } = session
 

plugins/circular-view/src/index.ts

@@ -24,7 +24,7 @@ export default class CircularViewPlugin extends Plugin {
 
   configure(pluginManager: PluginManager) {
     if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['File', 'Add'], {
+      pluginManager.rootModel.appendToSubMenu(['Add'], {
         label: 'Circular view',
         icon: DataUsageIcon,
         onClick: (session: AbstractSessionModel) => {

plugins/data-management/src/AssemblyManager/AssemblyAddForm.tsx

@@ -149,6 +149,8 @@ const AdapterInput = observer(
   },
 )
 
+const blank = { uri: '' } as FileLocation
+
 const AssemblyAddForm = observer(
   ({
     rootModel,
@@ -169,48 +171,17 @@ const AssemblyAddForm = observer(
     const [assemblyName, setAssemblyName] = useState('')
     const [assemblyDisplayName, setAssemblyDisplayName] = useState('')
     const [adapterSelection, setAdapterSelection] = useState(adapterTypes[0])
-    const [fastaLocation, setFastaLocation] = useState<{
-      uri: string
-      locationType: 'UriLocation'
-    }>({
-      uri: '',
-      locationType: 'UriLocation',
-    })
-    const [faiLocation, setFaiLocation] = useState<{
-      uri: string
-      locationType: 'UriLocation'
-    }>({
-      uri: '',
-      locationType: 'UriLocation',
-    })
-    const [gziLocation, setGziLocation] = useState<{
-      uri: string
-      locationType: 'UriLocation'
-    }>({
-      uri: '',
-      locationType: 'UriLocation',
-    })
-    const [twoBitLocation, setTwoBitLocation] = useState<{
-      uri: string
-      locationType: 'UriLocation'
-    }>({
-      uri: '',
-      locationType: 'UriLocation',
-    })
-    const [chromSizesLocation, setChromSizesLocation] = useState<{
-      uri: string
-      locationType: 'UriLocation'
-    }>({
-      uri: '',
-      locationType: 'UriLocation',
-    })
+    const [fastaLocation, setFastaLocation] = useState(blank)
+    const [faiLocation, setFaiLocation] = useState(blank)
+    const [gziLocation, setGziLocation] = useState(blank)
+    const [twoBitLocation, setTwoBitLocation] = useState(blank)
+    const [chromSizesLocation, setChromSizesLocation] = useState(blank)
 
     function createAssembly() {
       if (assemblyName === '') {
         rootModel.session.notify("Can't create an assembly without a name")
       } else {
         setFormOpen(false)
-        // setIsAssemblyBeingEdited(true)
         let newAssembly
         if (adapterSelection === 'IndexedFastaAdapter') {
           newAssembly = {

plugins/data-management/src/index.ts

@@ -3,10 +3,6 @@ import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType'
 import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { SessionWithWidgets, isAbstractMenuManager } from '@jbrowse/core/util'
-import NoteAddIcon from '@material-ui/icons/NoteAdd'
-import InputIcon from '@material-ui/icons/Input'
-import ExtensionIcon from '@material-ui/icons/Extension'
 import {
   configSchema as ucscConfigSchema,
   modelFactory as ucscModelFactory,
@@ -105,53 +101,7 @@ export default class extends Plugin {
     })
   }
 
-  configure(pluginManager: PluginManager) {
-    if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToMenu('File', {
-        label: 'Open track',
-        icon: NoteAddIcon,
-        onClick: (session: SessionWithWidgets) => {
-          if (session.views.length === 0) {
-            session.notify('Please open a view to add a track first')
-          } else if (session.views.length >= 1) {
-            const widget = session.addWidget(
-              'AddTrackWidget',
-              'addTrackWidget',
-              { view: session.views[0].id },
-            )
-            session.showWidget(widget)
-            if (session.views.length > 1) {
-              session.notify(
-                `This will add a track to the first view. Note: if you want to open a track in a specific view open the track selector for that view and use the add track (plus icon) in the bottom right`,
-              )
-            }
-          }
-        },
-      })
-      pluginManager.rootModel.appendToMenu('File', {
-        label: 'Open connection',
-        icon: InputIcon,
-        onClick: (session: SessionWithWidgets) => {
-          const widget = session.addWidget(
-            'AddConnectionWidget',
-            'addConnectionWidget',
-          )
-          session.showWidget(widget)
-        },
-      })
-      pluginManager.rootModel.appendToMenu('File', {
-        label: 'Plugin store',
-        icon: ExtensionIcon,
-        onClick: (session: SessionWithWidgets) => {
-          const widget = session.addWidget(
-            'PluginStoreWidget',
-            'pluginStoreWidget',
-          )
-          session.showWidget(widget)
-        },
-      })
-    }
-  }
+  configure(pluginManager: PluginManager) {}
 }
 
 export { AssemblyManager, SetDefaultSession }

plugins/dotplot-view/src/index.ts

@@ -386,7 +386,7 @@ export default class DotplotPlugin extends Plugin {
 
   configure(pluginManager: PluginManager) {
     if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['File', 'Add'], {
+      pluginManager.rootModel.appendToSubMenu(['Add'], {
         label: 'Dotplot view',
         icon: TimelineIcon,
         onClick: (session: AbstractSessionModel) => {

plugins/linear-comparative-view/src/index.tsx

@@ -13,9 +13,7 @@ import {
   DialogTitle,
   IconButton,
 } from '@material-ui/core'
-import CloseIcon from '@material-ui/icons/Close'
-import AddIcon from '@material-ui/icons/Add'
-import CalendarIcon from '@material-ui/icons/CalendarViewDay'
+
 import { ConfigurationSchema, getConf } from '@jbrowse/core/configuration'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
@@ -34,12 +32,20 @@ import {
   getContainingTrack,
   isAbstractMenuManager,
 } from '@jbrowse/core/util'
-
 import {
   MismatchParser,
   LinearPileupDisplayModel,
 } from '@jbrowse/plugin-alignments'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+import { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
+import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
+
+// icons
+import CloseIcon from '@material-ui/icons/Close'
+import AddIcon from '@material-ui/icons/Add'
+import CalendarIcon from '@material-ui/icons/CalendarViewDay'
+// locals
+//
 import {
   configSchemaFactory as linearComparativeDisplayConfigSchemaFactory,
   ReactComponent as LinearComparativeDisplayReactComponent,
@@ -59,9 +65,6 @@ import {
   AdapterClass as MCScanAnchorsAdapter,
   configSchema as MCScanAnchorsConfigSchema,
 } from './MCScanAnchorsAdapter'
-import { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
-import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
-
 const { parseCigar } = MismatchParser
 
 function getLengthOnRef(cigar: string) {
@@ -189,14 +192,17 @@ interface BasicFeature {
   refName: string
 }
 
+// hashmap of refName->array of features
+type FeaturesPerRef = { [key: string]: BasicFeature[] }
+
 function gatherOverlaps(regions: BasicFeature[]) {
   const groups = regions.reduce((memo, x) => {
     if (!memo[x.refName]) {
       memo[x.refName] = []
     }
     memo[x.refName].push(x)
     return memo
-  }, {} as { [key: string]: BasicFeature[] })
+  }, {} as FeaturesPerRef)
 
   return Object.values(groups)
     .map(group => mergeIntervals(group.sort((a, b) => a.start - b.start)))
@@ -707,7 +713,7 @@ export default class extends Plugin {
 
   configure(pluginManager: PluginManager) {
     if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['File', 'Add'], {
+      pluginManager.rootModel.appendToSubMenu(['Add'], {
         label: 'Linear synteny view',
         icon: CalendarIcon,
         onClick: (session: AbstractSessionModel) => {

plugins/linear-genome-view/src/index.ts

@@ -121,7 +121,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
 
   configure(pluginManager: PluginManager) {
     if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['File', 'Add'], {
+      pluginManager.rootModel.appendToSubMenu(['Add'], {
         label: 'Linear genome view',
         icon: LineStyleIcon,
         onClick: (session: AbstractSessionModel) => {

plugins/spreadsheet-view/src/index.ts

@@ -23,7 +23,7 @@ export default class SpreadsheetViewPlugin extends Plugin {
 
   configure(pluginManager: PluginManager) {
     if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['File', 'Add'], {
+      pluginManager.rootModel.appendToSubMenu(['Add'], {
         label: 'Spreadsheet view',
         icon: ViewComfyIcon,
         onClick: (session: AbstractSessionModel) => {

plugins/sv-inspector/src/index.ts

@@ -18,7 +18,7 @@ export default class SvInspectorViewPlugin extends Plugin {
 
   configure(pluginManager: PluginManager) {
     if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['File', 'Add'], {
+      pluginManager.rootModel.appendToSubMenu(['Add'], {
         label: 'SV inspector',
         icon: TableChartIcon,
         onClick: (session: AbstractSessionModel) => {