@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.7

package/src/OntologyManager/OntologyStore/indexeddb-storage.ts

@@ -1,17 +1,23 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { openLocation } from '@jbrowse/core/util/io'
 import equal from 'fast-deep-equal/es6'
-import { IDBPDatabase, IDBPTransaction, openDB } from 'idb/with-async-ittr'
+import {
+  type IDBPDatabase,
+  type IDBPTransaction,
+  openDB,
+} from 'idb/with-async-ittr'
+
+import { defaultTextIndexFields } from '..'
 
 import { PREFIXED_ID_PATH, getWords } from './fulltext'
 import {
-  OntologyDB,
+  type OntologyDB,
   isOntologyDBEdge,
   isOntologyDBNode,
 } from './indexeddb-schema'
-import { GraphDocument } from './obo-graph-json-schema'
-import OntologyStore from '.'
-import { defaultTextIndexFields } from '..'
+import { type GraphDocument } from './obo-graph-json-schema'
+
+import type OntologyStore from '.'
 
 /** schema version we are currently on, used for the IndexedDB schema open call */
 const schemaVersion = 2

package/src/OntologyManager/index.ts

@@ -1,5 +1,5 @@
 import {
-  AnyConfigurationModel,
+  type AnyConfigurationModel,
   ConfigurationSchema,
   readConfObject,
 } from '@jbrowse/core/configuration'
@@ -10,18 +10,21 @@ import {
 } from '@jbrowse/core/util/types/mst'
 import { autorun } from 'mobx'
 import {
-  Instance,
+  type Instance,
   addDisposer,
   flow,
   getRoot,
   getSnapshot,
+  isAlive,
   types,
 } from 'mobx-state-tree'
-import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
-import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
+
+import type ApolloPluginConfigurationSchema from '../config'
+import { type ApolloRootModel } from '../types'
+
+import OntologyStore, { type OntologyStoreOptions } from './OntologyStore'
+import { type OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
-import ApolloPluginConfigurationSchema from '../config'
-import { ApolloRootModel } from '../types'
 
 export { isDeprecated } from './OntologyStore/indexeddb-schema'
 
@@ -77,7 +80,9 @@ export const OntologyRecordType = types
       const equivalents: string[] = terms
         .map((term) => term.lbl)
         .filter((term) => term != undefined)
-      self.setEquivalentTypes(type, equivalents)
+      if (isAlive(self)) {
+        self.setEquivalentTypes(type, equivalents)
+      }
     }),
   }))
   .actions((self) => ({

package/src/OntologyManager/util.ts

@@ -1,6 +1,7 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+
+import type OntologyStore from './OntologyStore'
 
-import OntologyStore from './OntologyStore'
 import { isOntologyClass } from '.'
 
 export async function fetchValidDescendantTerms(

package/src/TabularEditor/HybridGrid/ChangeHandling.ts

@@ -1,11 +1,11 @@
-import type { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
   TypeChange,
 } from '@apollo-annotation/shared'
 
-import type { ChangeManager } from '../../ChangeManager'
+import { type ChangeManager } from '../../ChangeManager'
 
 export function handleFeatureTypeChange(
   changeManager: ChangeManager,

package/src/TabularEditor/HybridGrid/Feature.tsx

@@ -1,25 +1,26 @@
 /* eslint-disable unicorn/no-nested-ternary */
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { AbstractSessionModel } from '@jbrowse/core/util'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import { type AbstractSessionModel } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 import React from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { OntologyTermAutocomplete } from '../../components/OntologyTermAutocomplete'
 import { isOntologyClass } from '../../OntologyManager'
-import OntologyStore from '../../OntologyManager/OntologyStore'
-import { DisplayStateModel } from '../types'
+import type OntologyStore from '../../OntologyManager/OntologyStore'
+import { OntologyTermAutocomplete } from '../../components/OntologyTermAutocomplete'
+import { type DisplayStateModel } from '../types'
+
 import {
   handleFeatureEndChange,
   handleFeatureStartChange,
   handleFeatureTypeChange,
 } from './ChangeHandling'
 import { FeatureAttributes } from './FeatureAttributes'
-import { featureContextMenuItems } from './featureContextMenuItems'
-import type { ContextMenuState } from './HybridGrid'
+import { type ContextMenuState } from './HybridGrid'
 import { NumberCell } from './NumberCell'
+import { featureContextMenuItems } from './featureContextMenuItems'
 
 const useStyles = makeStyles()((theme) => ({
   typeContent: {
@@ -67,6 +68,8 @@ function makeContextMenuItems(
     selectedFeature,
     session,
     setSelectedFeature,
+    filteredTranscripts,
+    updateFilteredTranscripts,
   } = display
   return featureContextMenuItems(
     feature,
@@ -76,6 +79,8 @@ function makeContextMenuItems(
     setSelectedFeature,
     session,
     changeManager,
+    filteredTranscripts,
+    updateFilteredTranscripts,
   )
 }
 
@@ -132,6 +137,7 @@ export const Feature = observer(function Feature({
           displayState.setApolloHover({
             feature,
             topLevelFeature: getTopLevelFeature(feature),
+            // @ts-expect-error TODO fix in future when moving hover logic to session.
             glyph: displayState.getGlyph(getTopLevelFeature(feature)),
           })
         }}

package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx

@@ -1,5 +1,5 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { observer } from 'mobx-react'
 import { getSnapshot } from 'mobx-state-tree'
 import React from 'react'

package/src/TabularEditor/HybridGrid/HybridGrid.tsx

@@ -1,10 +1,11 @@
-import { Menu, MenuItem } from '@jbrowse/core/ui'
+import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { DisplayStateModel } from '../types'
+import { type DisplayStateModel } from '../types'
+
 import { Feature } from './Feature'
 
 const useStyles = makeStyles()((theme) => ({

package/src/TabularEditor/HybridGrid/ToolBar.tsx

@@ -6,7 +6,7 @@ import { observer } from 'mobx-react'
 import React from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { DisplayStateModel } from '../types'
+import { type DisplayStateModel } from '../types'
 
 const useStyles = makeStyles()({
   toolbar: {

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -1,14 +1,21 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { MenuItem } from '@jbrowse/core/ui'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import { type MenuItem } from '@jbrowse/core/ui'
 import {
-  AbstractSessionModel,
-  SessionWithWidgets,
+  type AbstractSessionModel,
+  type SessionWithWidgets,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
 
-import { ChangeManager } from '../../ChangeManager'
-import { AddChildFeature, CopyFeature, DeleteFeature } from '../../components'
-import { ApolloSessionModel } from '../../session'
+import { type ChangeManager } from '../../ChangeManager'
+import {
+  AddChildFeature,
+  CopyFeature,
+  DeleteFeature,
+  MergeExons,
+  MergeTranscripts,
+  SplitExon,
+} from '../../components'
+import { type ApolloSessionModel } from '../../session'
 import { getApolloInternetAccount } from '../../util'
 
 export function featureContextMenuItems(
@@ -19,6 +26,8 @@ export function featureContextMenuItems(
   setSelectedFeature: (f: AnnotationFeature | undefined) => void,
   session: ApolloSessionModel,
   changeManager: ChangeManager,
+  filteredTranscripts: string[],
+  updateFilteredTranscripts: (forms: string[]) => void,
 ) {
   const internetAccount = getApolloInternetAccount(session)
   const role = internetAccount ? internetAccount.role : 'admin'
@@ -26,6 +35,7 @@ export function featureContextMenuItems(
   const readOnly = !(role && ['admin', 'user'].includes(role))
   const menuItems: MenuItem[] = []
   if (feature) {
+    const featureID = feature.attributes.get('gff_id')?.toString()
     const sourceAssemblyId = getAssemblyId(region.assemblyName)
     const currentAssemblyId = getAssemblyId(region.assemblyName)
     menuItems.push(
@@ -111,6 +121,72 @@ export function featureContextMenuItems(
           )
         },
       },
+      {
+        label: 'Merge transcripts',
+        disabled: !admin,
+        onClick: () => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              MergeTranscripts,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager,
+                sourceFeature: feature,
+                sourceAssemblyId: currentAssemblyId,
+                selectedFeature,
+                setSelectedFeature,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Merge exons',
+        disabled: !admin,
+        onClick: () => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              MergeExons,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager,
+                sourceFeature: feature,
+                sourceAssemblyId: currentAssemblyId,
+                selectedFeature,
+                setSelectedFeature,
+              },
+            ],
+          )
+        },
+      },
+      {
+        label: 'Split exon',
+        disabled: !admin,
+        onClick: () => {
+          ;(session as unknown as AbstractSessionModel).queueDialog(
+            (doneCallback) => [
+              SplitExon,
+              {
+                session,
+                handleClose: () => {
+                  doneCallback()
+                },
+                changeManager,
+                sourceFeature: feature,
+                sourceAssemblyId: currentAssemblyId,
+                selectedFeature,
+                setSelectedFeature,
+              },
+            ],
+          )
+        },
+      },
     )
     const { featureTypeOntology } = session.apolloDataStore.ontologyManager
     if (!featureTypeOntology) {
@@ -121,22 +197,38 @@ export function featureContextMenuItems(
         featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript')) &&
       isSessionModelWithWidgets(session)
     ) {
-      menuItems.push({
-        label: 'Edit transcript details',
-        onClick: () => {
-          const apolloTranscriptWidget = session.addWidget(
-            'ApolloTranscriptDetails',
-            'apolloTranscriptDetails',
-            {
-              feature,
-              assembly: currentAssemblyId,
-              changeManager,
-              refName: region.refName,
-            },
-          )
-          session.showWidget(apolloTranscriptWidget)
+      menuItems.push(
+        {
+          label: 'Edit transcript details',
+          onClick: () => {
+            const apolloTranscriptWidget = session.addWidget(
+              'ApolloTranscriptDetails',
+              'apolloTranscriptDetails',
+              {
+                feature,
+                assembly: currentAssemblyId,
+                changeManager,
+                refName: region.refName,
+              },
+            )
+            session.showWidget(apolloTranscriptWidget)
+          },
+        },
+        {
+          label: 'Visible',
+          type: 'checkbox',
+          checked:
+            featureID && filteredTranscripts.includes(featureID) ? false : true,
+          onClick: () => {
+            if (featureID) {
+              const newForms = filteredTranscripts.includes(featureID)
+                ? filteredTranscripts.filter((form) => form !== featureID)
+                : [...filteredTranscripts, featureID]
+              updateFilteredTranscripts(newForms)
+            }
+          },
         },
-      })
+      )
     }
   }
   return menuItems

package/src/TabularEditor/TabularEditorPane.tsx

@@ -3,7 +3,7 @@ import React from 'react'
 
 import HybridGrid from './HybridGrid'
 import { ToolBar } from './HybridGrid/ToolBar'
-import { DisplayStateModel } from './types'
+import { type DisplayStateModel } from './types'
 
 function stopPropagation(e: React.MouseEvent) {
   e.stopPropagation()

package/src/TabularEditor/model.ts

@@ -1,6 +1,6 @@
-import { Instance, getParent, types } from 'mobx-state-tree'
+import { type Instance, getParent, types } from 'mobx-state-tree'
 
-import { DisplayStateModel } from './types'
+import { type DisplayStateModel } from './types'
 
 export const TabularEditorStateModelType = types
   .model('TabularEditor', {

package/src/TabularEditor/types.ts

@@ -1,3 +1,6 @@
-import { LinearApolloDisplay } from '../LinearApolloDisplay/stateModel'
+import { type LinearApolloDisplay } from '../LinearApolloDisplay/stateModel'
+import { type LinearApolloSixFrameDisplay } from '../LinearApolloSixFrameDisplay/stateModel'
 
-export type DisplayStateModel = LinearApolloDisplay
+export type DisplayStateModel =
+  | LinearApolloDisplay
+  | LinearApolloSixFrameDisplay