@apollo-annotation/jbrowse-plugin-apollo 0.1.21 → 0.2.0

package/src/makeDisplayComponent.tsx

@@ -3,7 +3,7 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
 import ExpandLessIcon from '@mui/icons-material/ExpandLess'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
-import { Typography, alpha } from '@mui/material'
+import { Alert, Typography, alpha } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useCallback, useEffect, useRef } from 'react'
 import { makeStyles } from 'tss-react/mui'
@@ -14,6 +14,9 @@ import { TrackLines } from './SixFrameFeatureDisplay/components'
 import { SixFrameFeatureDisplay } from './SixFrameFeatureDisplay/stateModel'
 import { TabularEditorPane } from './TabularEditor'
 
+import { getSession } from '@jbrowse/core/util'
+import { ApolloSessionModel } from './session'
+
 const accordionControlHeight = 12
 
 const useStyles = makeStyles()((theme) => ({
@@ -52,6 +55,11 @@ const useStyles = makeStyles()((theme) => ({
     // position: 'relative',
     userSelect: 'none',
   },
+  alertContainer: {
+    display: 'flex',
+    alignItems: 'center',
+    justifyContent: 'center',
+  },
 }))
 
 function scrollSelectedFeatureIntoView(
@@ -87,9 +95,9 @@ const ResizeHandle = ({
     (event: MouseEvent) => {
       event.stopPropagation()
       event.preventDefault()
-      window.removeEventListener('mousemove', mouseMove)
-      window.removeEventListener('mouseup', cancelDrag)
-      window.removeEventListener('mouseleave', cancelDrag)
+      globalThis.removeEventListener('mousemove', mouseMove)
+      globalThis.removeEventListener('mouseup', cancelDrag)
+      globalThis.removeEventListener('mouseleave', cancelDrag)
     },
     [mouseMove],
   )
@@ -99,9 +107,9 @@ const ResizeHandle = ({
     <div
       onMouseDown={(event: React.MouseEvent) => {
         event.stopPropagation()
-        window.addEventListener('mousemove', mouseMove)
-        window.addEventListener('mouseup', cancelDrag)
-        window.addEventListener('mouseleave', cancelDrag)
+        globalThis.addEventListener('mousemove', mouseMove)
+        globalThis.addEventListener('mouseup', cancelDrag)
+        globalThis.addEventListener('mouseleave', cancelDrag)
       }}
       onClick={(e) => {
         e.stopPropagation()
@@ -155,6 +163,11 @@ export const DisplayComponent = observer(function DisplayComponent({
 }: {
   model: LinearApolloDisplayI
 }) {
+  const session = getSession(model) as unknown as ApolloSessionModel
+  const { ontologyManager } = session.apolloDataStore
+  const { featureTypeOntology } = ontologyManager
+  const ontologyStore = featureTypeOntology?.dataStore
+
   const { classes } = useStyles()
 
   const {
@@ -177,6 +190,14 @@ export const DisplayComponent = observer(function DisplayComponent({
     model.setDetailsHeight(detailsHeight - delta)
   }
 
+  if (!ontologyStore) {
+    return (
+      <div className={classes.alertContainer}>
+        <Alert severity="error">Could not load feature type ontology.</Alert>
+      </div>
+    )
+  }
+
   if (graphical && table) {
     const tabularHeight = tabularEditor.isShown ? detailsHeight : 0
     const featureAreaHeight = isShown

package/src/session/ClientDataStore.ts

@@ -51,6 +51,7 @@ export function clientDataStoreFactory(
       typeName: types.optional(types.literal('Client'), 'Client'),
       assemblies: types.map(ApolloAssembly),
       checkResults: types.map(CheckResult),
+      ontologyManager: types.optional(OntologyManagerType, {}),
     })
     .views((self) => ({
       get internetAccounts() {
@@ -136,7 +137,6 @@ export function clientDataStoreFactory(
       desktopFileDriver: isElectron
         ? new DesktopFileDriver(self as unknown as ClientDataStoreType)
         : undefined,
-      ontologyManager: OntologyManagerType.create(),
     }))
     .actions((self) => ({
       afterCreate() {

package/src/session/session.ts

@@ -419,6 +419,7 @@ export function extendSession(
           ([, assembly]) => assembly.backendDriverType === 'InMemoryFileDriver',
         ),
       )
+      // @ts-expect-error ontologyManager isn't actually required
       snap.apolloDataStore = {
         typeName: 'Client',
         assemblies,
@@ -433,5 +434,5 @@ export type ApolloSessionStateModel = ReturnType<typeof extendSession>
 // @ts-expect-error Snapshots seem to mess up types here
 // eslint disable because of
 // https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
-// eslint-disable-next-line @typescript-eslint/no-empty-interface
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface ApolloSessionModel extends Instance<ApolloSessionStateModel> {}