@apollo-annotation/jbrowse-plugin-apollo 0.3.4 → 0.3.6

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 +10,20 @@ import {
 } from '@jbrowse/core/util/types/mst'
 import { autorun } from 'mobx'
 import {
-  Instance,
+  type Instance,
   addDisposer,
   flow,
   getRoot,
   getSnapshot,
   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'
 
@@ -87,7 +89,9 @@ export const OntologyRecordType = types
           return
         }
         void self.loadEquivalentTypes('gene')
+        void self.loadEquivalentTypes('pseudogene')
         void self.loadEquivalentTypes('transcript')
+        void self.loadEquivalentTypes('pseudogenic_transcript')
         void self.loadEquivalentTypes('CDS')
         void self.loadEquivalentTypes('mRNA')
         reaction.dispose()

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

@@ -1,26 +1,26 @@
-/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* 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: {
@@ -133,6 +133,7 @@ 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/NumberCell.tsx

@@ -1,5 +1,4 @@
 /* eslint-disable @typescript-eslint/unbound-method */
-/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
@@ -37,6 +36,14 @@ export const NumberCell = observer(function NumberCell({
   const [blur, setBlur] = useState(false)
   const [inputNode, setInputNode] = useState<HTMLInputElement | null>(null)
   const { classes } = useStyles()
+
+  useEffect(() => {
+    if (initialValue !== value) {
+      setValue(initialValue)
+    }
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [initialValue])
+
   useEffect(() => {
     if (blur) {
       inputNode?.blur()

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: {
@@ -47,18 +47,20 @@ export const ToolBar = observer(function ToolBar({
         onChange={(event) => {
           model.setFilterText(event.target.value)
         }}
-        InputProps={{
-          endAdornment: (
-            <InputAdornment position="end">
-              <IconButton
-                onClick={() => {
-                  model.clearFilterText()
-                }}
-              >
-                <ClearIcon />
-              </IconButton>
-            </InputAdornment>
-          ),
+        slotProps={{
+          input: {
+            endAdornment: (
+              <InputAdornment position="end">
+                <IconButton
+                  onClick={() => {
+                    model.clearFilterText()
+                  }}
+                >
+                  <ClearIcon />
+                </IconButton>
+              </InputAdornment>
+            ),
+          },
         }}
       />
     </div>

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -1,19 +1,14 @@
-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,
-  ModifyFeatureAttribute,
-} from '../../components'
-import { ApolloSessionModel } from '../../session'
+import { type ChangeManager } from '../../ChangeManager'
+import { AddChildFeature, CopyFeature, DeleteFeature } from '../../components'
+import { type ApolloSessionModel } from '../../session'
 import { getApolloInternetAccount } from '../../util'
 
 export function featureContextMenuItems(
@@ -116,33 +111,14 @@ export function featureContextMenuItems(
           )
         },
       },
-      {
-        label: 'Edit attributes',
-        disabled: readOnly,
-        onClick: () => {
-          ;(session as unknown as AbstractSessionModel).queueDialog(
-            (doneCallback) => [
-              ModifyFeatureAttribute,
-              {
-                session,
-                handleClose: () => {
-                  doneCallback()
-                },
-                changeManager,
-                sourceFeature: feature,
-                sourceAssemblyId: currentAssemblyId,
-              },
-            ],
-          )
-        },
-      },
     )
     const { featureTypeOntology } = session.apolloDataStore.ontologyManager
     if (!featureTypeOntology) {
       throw new Error('featureTypeOntology is undefined')
     }
     if (
-      featureTypeOntology.isTypeOf(feature.type, 'transcript') &&
+      (featureTypeOntology.isTypeOf(feature.type, 'transcript') ||
+        featureTypeOntology.isTypeOf(feature.type, 'pseudogenic_transcript')) &&
       isSessionModelWithWidgets(session)
     ) {
       menuItems.push({

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