Better ontology loading error handling

GMOD · Nov 6, 2024 · 93a9011 · 93a9011
1 parent 203b778
commit 93a9011
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Showing 2 changed files with 31 additions and 15 deletions.
diff --git 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
@@ -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()