@apollo-annotation/jbrowse-plugin-apollo 0.3.7 → 0.3.8

package/src/index.ts

@@ -6,6 +6,7 @@ import {
   CDSCheck,
   CoreValidation,
   ParentChildValidation,
+  TranscriptCheck,
   changes,
   validationRegistry,
 } from '@apollo-annotation/shared'
@@ -30,6 +31,7 @@ import {
 } from '@jbrowse/core/util'
 import { type LinearGenomeViewStateModel } from '@jbrowse/plugin-linear-genome-view'
 import AddIcon from '@mui/icons-material/Add'
+import { alpha } from '@mui/material'
 
 import { version } from '../package.json'
 
@@ -51,19 +53,16 @@ import {
   configSchema as linearApolloDisplayConfigSchema,
   stateModelFactory as LinearApolloDisplayStateModelFactory,
 } from './LinearApolloDisplay'
+import {
+  LinearApolloReferenceSequenceDisplay,
+  configSchema as linearApolloReferenceSequenceDisplayConfigSchema,
+  stateModelFactory as LinearApolloReferenceSequenceDisplayStateModelFactory,
+} from './LinearApolloReferenceSequenceDisplay'
 import {
   configSchema as linearApolloSixFrameDisplayConfigSchema,
   stateModelFactory as LinearApolloSixFrameDisplayStateModelFactory,
 } from './LinearApolloSixFrameDisplay'
-import {
-  AddFeature,
-  DownloadGFF3,
-  LogOut,
-  ManageChecks,
-  OpenLocalFile,
-  ViewChangeLog,
-  ViewCheckResults,
-} from './components'
+import { AddFeature } from './components'
 import ApolloPluginConfigurationSchema from './config'
 import {
   annotationFromJBrowseFeature,
@@ -73,6 +72,7 @@ import {
   LinearApolloDisplayComponent,
   LinearApolloSixFrameDisplayComponent,
 } from './makeDisplayComponent'
+import { addTopLevelMenus } from './menus'
 import { type ApolloSessionModel, extendSession } from './session'
 
 interface RpcHandle {
@@ -106,6 +106,10 @@ for (const [changeName, change] of Object.entries(changes)) {
 
 const cdsCheck = new CDSCheck()
 checkRegistry.registerCheck(cdsCheck.name, cdsCheck)
+
+const transcriptCheck = new TranscriptCheck()
+checkRegistry.registerCheck(transcriptCheck.name, transcriptCheck)
+
 validationRegistry.registerValidation(new CoreValidation())
 validationRegistry.registerValidation(new ParentChildValidation())
 
@@ -201,6 +205,22 @@ export default class ApolloPlugin extends Plugin {
       })
     })
 
+    pluginManager.addDisplayType(() => {
+      const configSchema = linearApolloReferenceSequenceDisplayConfigSchema
+      return new DisplayType({
+        name: 'LinearApolloReferenceSequenceDisplay',
+        configSchema,
+        stateModel: LinearApolloReferenceSequenceDisplayStateModelFactory(
+          pluginManager,
+          configSchema,
+        ),
+        displayName: 'Apollo reference sequence display',
+        trackType: 'ReferenceSequenceTrack',
+        viewType: 'LinearGenomeView',
+        ReactComponent: LinearApolloReferenceSequenceDisplay,
+      })
+    })
+
     pluginManager.addToExtensionPoint(
       'Core-extendSession',
       // @ts-expect-error not sure how to deal with snapshot model types
@@ -357,103 +377,20 @@ export default class ApolloPlugin extends Plugin {
 
   configure(pluginManager: PluginManager) {
     if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToMenu('Apollo', {
-        label: 'Download GFF3',
-        onClick: (session: ApolloSessionModel) => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              DownloadGFF3,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-              },
-            ],
-          )
-        },
-      })
-      pluginManager.rootModel.appendToMenu('Apollo', {
-        label: 'Manage Checks',
-        onClick: (session: ApolloSessionModel) => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              ManageChecks,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-              },
-            ],
-          )
-        },
-      })
-      pluginManager.rootModel.appendToMenu('Apollo', {
-        label: 'View Change Log',
-        onClick: (session: ApolloSessionModel) => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              ViewChangeLog,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-              },
-            ],
-          )
-        },
-      })
-      pluginManager.rootModel.appendToMenu('Apollo', {
-        label: 'Open local GFF3 file',
-        onClick: (session: ApolloSessionModel) => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              OpenLocalFile,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-                inMemoryFileDriver: session.apolloDataStore.inMemoryFileDriver,
-              },
-            ],
-          )
-        },
-      })
-      pluginManager.rootModel.appendToMenu('Apollo', {
-        label: 'View check results',
-        onClick: (session: ApolloSessionModel) => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              ViewCheckResults,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-              },
-            ],
-          )
-        },
-      })
-      pluginManager.rootModel.appendToMenu('Apollo', {
-        label: 'Log out',
-        onClick: (session: ApolloSessionModel) => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              LogOut,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-              },
-            ],
-          )
+      pluginManager.jexl.addFunction(
+        'colorFeature',
+        (featureType: 'pseudogenic_transcript' | 'nonCodingTranscript') => {
+          if (featureType === 'pseudogenic_transcript') {
+            return alpha('rgb(148, 203, 236)', 0.6)
+          }
+          if (featureType === 'nonCodingTranscript') {
+            return alpha('rgb(194, 106, 119)', 0.6)
+          }
+          throw new Error('Invalid type')
         },
-      })
+      )
+
+      addTopLevelMenus(pluginManager.rootModel)
     }
   }
 }

package/src/makeDisplayComponent.tsx

@@ -19,7 +19,6 @@ const accordionControlHeight = 12
 const useStyles = makeStyles()((theme) => ({
   shading: {
     background: alpha(theme.palette.primary.main, 0.2),
-    overflowY: 'scroll',
     overflowX: 'hidden',
   },
   details: {

package/src/menus/index.ts

@@ -0,0 +1 @@
+export { addTopLevelMenus } from './topLevelMenu'

package/src/{ApolloInternetAccount/addMenuItems.ts → menus/topLevelMenu.ts}

@@ -2,130 +2,139 @@ import {
   type AbstractMenuManager,
   type AbstractSessionModel,
 } from '@jbrowse/core/util'
+import DownloadIcon from '@mui/icons-material/Download'
+import FactCheckIcon from '@mui/icons-material/FactCheck'
+import FileOpenIcon from '@mui/icons-material/FileOpen'
+import LogoutIcon from '@mui/icons-material/Logout'
+import RedoIcon from '@mui/icons-material/Redo'
+import TrackChangesIcon from '@mui/icons-material/TrackChanges'
+import UndoIcon from '@mui/icons-material/Undo'
 
 import {
-  AddAssembly,
-  AddRefSeqAliases,
-  DeleteAssembly,
-  ImportFeatures,
-  ManageUsers,
+  DownloadGFF3,
+  LogOut,
+  OpenLocalFile,
+  ViewChangeLog,
+  ViewCheckResults,
 } from '../components'
-import { AddAssemblyAliases } from '../components/AddAssemblyAliases'
 import { type ApolloSessionModel } from '../session'
 
-export function addMenuItems(rootModel: AbstractMenuManager) {
+export function addTopLevelMenus(rootModel: AbstractMenuManager) {
+  rootModel.insertInMenu(
+    'Apollo',
+    {
+      label: 'Redo',
+      icon: RedoIcon,
+      onClick(session: ApolloSessionModel) {
+        const { apolloDataStore } = session
+        void apolloDataStore.changeManager.redoLastChange()
+      },
+    },
+    0,
+  )
+  rootModel.insertInMenu(
+    'Apollo',
+    {
+      label: 'Undo',
+      icon: UndoIcon,
+      onClick(session: ApolloSessionModel) {
+        const { apolloDataStore } = session
+        void apolloDataStore.changeManager.undoLastChange()
+      },
+    },
+    0,
+  )
+
   rootModel.appendToMenu('Apollo', {
-    label: 'Add Assembly',
+    label: 'Download GFF3',
+    icon: DownloadIcon,
     onClick: (session: ApolloSessionModel) => {
       ;(session as unknown as AbstractSessionModel).queueDialog(
         (doneCallback) => [
-          AddAssembly,
+          DownloadGFF3,
           {
             session,
             handleClose: () => {
               doneCallback()
             },
-            changeManager: session.apolloDataStore.changeManager,
           },
         ],
       )
     },
   })
   rootModel.appendToMenu('Apollo', {
-    label: 'Delete Assembly',
+    label: 'View Change Log',
+    icon: TrackChangesIcon,
     onClick: (session: ApolloSessionModel) => {
       ;(session as unknown as AbstractSessionModel).queueDialog(
         (doneCallback) => [
-          DeleteAssembly,
+          ViewChangeLog,
           {
             session,
             handleClose: () => {
               doneCallback()
             },
-            changeManager: session.apolloDataStore.changeManager,
           },
         ],
       )
     },
   })
   rootModel.appendToMenu('Apollo', {
-    label: 'Import Features',
+    label: 'Open local GFF3 file',
+    icon: FileOpenIcon,
     onClick: (session: ApolloSessionModel) => {
       ;(session as unknown as AbstractSessionModel).queueDialog(
         (doneCallback) => [
-          ImportFeatures,
+          OpenLocalFile,
           {
             session,
             handleClose: () => {
               doneCallback()
             },
-            changeManager: session.apolloDataStore.changeManager,
+            inMemoryFileDriver: session.apolloDataStore.inMemoryFileDriver,
           },
         ],
       )
     },
   })
   rootModel.appendToMenu('Apollo', {
-    label: 'Add reference sequence aliases',
+    label: 'View check results',
+    icon: FactCheckIcon,
     onClick: (session: ApolloSessionModel) => {
       ;(session as unknown as AbstractSessionModel).queueDialog(
         (doneCallback) => [
-          AddRefSeqAliases,
+          ViewCheckResults,
           {
             session,
             handleClose: () => {
               doneCallback()
             },
-            changeManager: session.apolloDataStore.changeManager,
           },
         ],
       )
     },
   })
   rootModel.appendToMenu('Apollo', {
-    label: 'Add Assembly aliases',
+    label: 'Lock/Unlock session',
     onClick: (session: ApolloSessionModel) => {
-      ;(session as unknown as AbstractSessionModel).queueDialog(
-        (doneCallback) => [
-          AddAssemblyAliases,
-          {
-            session,
-            handleClose: () => {
-              doneCallback()
-            },
-            changeManager: session.apolloDataStore.changeManager,
-          },
-        ],
-      )
+      session.toggleLocked()
     },
   })
   rootModel.appendToMenu('Apollo', {
-    label: 'Manage Users',
+    label: 'Log out',
+    icon: LogoutIcon,
     onClick: (session: ApolloSessionModel) => {
       ;(session as unknown as AbstractSessionModel).queueDialog(
         (doneCallback) => [
-          ManageUsers,
+          LogOut,
           {
             session,
             handleClose: () => {
               doneCallback()
             },
-            changeManager: session.apolloDataStore.changeManager,
           },
         ],
       )
     },
   })
-  rootModel.appendToMenu('Apollo', {
-    label: 'Undo',
-    onClick: (session: ApolloSessionModel) => {
-      const { apolloDataStore } = session
-      const { notify } = session as unknown as AbstractSessionModel
-      if (apolloDataStore.changeManager.recentChanges.length > 0) {
-        void apolloDataStore.changeManager.revertLastChange()
-      } else {
-        notify('No changes to undo', 'info')
-      }
-    },
-  })
 }

package/src/menus/topLevelMenuAdmin.ts

@@ -0,0 +1,154 @@
+import {
+  type AbstractMenuManager,
+  type AbstractSessionModel,
+} from '@jbrowse/core/util'
+import AddIcon from '@mui/icons-material/Add'
+import AdminPanelSettingsIcon from '@mui/icons-material/AdminPanelSettings'
+import DeleteIcon from '@mui/icons-material/Delete'
+import InputIcon from '@mui/icons-material/Input'
+import PersonIcon from '@mui/icons-material/Person'
+import RuleIcon from '@mui/icons-material/Rule'
+
+import {
+  AddAssembly,
+  AddAssemblyAliases,
+  AddRefSeqAliases,
+  DeleteAssembly,
+  ImportFeatures,
+  ManageChecks,
+  ManageUsers,
+} from '../components'
+import { type ApolloSessionModel } from '../session'
+
+export function addTopLevelAdminMenus(rootModel: AbstractMenuManager) {
+  rootModel.appendToMenu('Apollo', {
+    label: 'Admin',
+    type: 'subMenu',
+    icon: AdminPanelSettingsIcon,
+    subMenu: [
+      {
+        label: 'Add Assembly',
+        icon: AddIcon,
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              AddAssembly,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager: session.apolloDataStore.changeManager,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Delete Assembly',
+        icon: DeleteIcon,
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              DeleteAssembly,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager: session.apolloDataStore.changeManager,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Import Features',
+        icon: InputIcon,
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              ImportFeatures,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager: session.apolloDataStore.changeManager,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Add reference sequence aliases',
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              AddRefSeqAliases,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager: session.apolloDataStore.changeManager,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Add Assembly aliases',
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              AddAssemblyAliases,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager: session.apolloDataStore.changeManager,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Manage Users',
+        icon: PersonIcon,
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              ManageUsers,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager: session.apolloDataStore.changeManager,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Manage Checks',
+        icon: RuleIcon,
+        onClick: (session: ApolloSessionModel) => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              ManageChecks,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+              },
+            ],
+          )
+        },
+      },
+    ],
+  })
+}