From eb301ba32f7120a01848ad6383dce5388f2fd856 Mon Sep 17 00:00:00 2001
From: Dario Beraldi <dario.beraldi@gmail.com>
Date: Wed, 6 Nov 2024 02:42:02 +0000
Subject: [PATCH] Display message if sequence ontology is unavailable (#453)
 (#459)

* Display message if sequence ontology is unavailable (#453)

* Use Alert component

* Better ontology loading error handling

---------

Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>
---
 .../OntologyManager/OntologyStore/index.ts    | 35 ++++++++++++-------
 .../OntologyStore/indexeddb-storage.ts        | 11 ++++--
 .../src/makeDisplayComponent.tsx              | 23 +++++++++++-
 3 files changed, 53 insertions(+), 16 deletions(-)

diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts
index 48fa34042..09763c1a2 100644
--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts
@@ -7,7 +7,12 @@ import {
   UriLocation,
   isUriLocation,
 } from '@jbrowse/core/util'
-import { IDBPTransaction, IndexNames, StoreNames } from 'idb/with-async-ittr'
+import {
+  deleteDB,
+  IDBPTransaction,
+  IndexNames,
+  StoreNames,
+} from 'idb/with-async-ittr'
 
 import { textSearch } from './fulltext'
 import { OntologyDB, OntologyDBEdge, isDeprecated } from './indexeddb-schema'
@@ -176,18 +181,24 @@ export default class OntologyStore {
       return db
     }
 
-    const { sourceLocation, sourceType } = this
-    if (sourceType === 'obo-graph-json') {
-      await this.loadOboGraphJson(db)
-    } else {
-      throw new Error(
-        `ontology source file ${JSON.stringify(
-          sourceLocation,
-        )} has type ${sourceType}, which is not yet supported`,
-      )
-    }
+    try {
+      const { sourceLocation, sourceType } = this
+      if (sourceType === 'obo-graph-json') {
+        await this.loadOboGraphJson(db)
+      } else {
+        throw new Error(
+          `ontology source file ${JSON.stringify(
+            sourceLocation,
+          )} has type ${sourceType}, which is not yet supported`,
+        )
+      }
 
-    return db
+      return db
+    } catch (error) {
+      db.close()
+      await deleteDB(this.dbName)
+      throw error
+    }
   }
 
   async termCount(tx?: Transaction<['nodes']>) {
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
index dff8b7edf..2e0beab78 100644
--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
@@ -84,9 +84,14 @@ export async function loadOboGraphJson(this: OntologyStore, db: Database) {
   // TODO: using file streaming along with an event-based json parser
   // instead of JSON.parse and .readFile could probably make this faster
   // and less memory intensive
-  const oboGraph = JSON.parse(
-    await openLocation(this.sourceLocation).readFile('utf8'),
-  ) as GraphDocument
+  let oboGraph: GraphDocument
+  try {
+    oboGraph = JSON.parse(
+      await openLocation(this.sourceLocation).readFile('utf8'),
+    ) as GraphDocument
+  } catch {
+    throw new Error('Error in loading ontology')
+  }
 
   const parseTime = Date.now()
 
diff --git a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx b/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx
index 117e30fcd..6cb76a645 100644
--- a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx
+++ b/packages/jbrowse-plugin-apollo/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(
@@ -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