Add jobmanager for #457

GMOD · Nov 15, 2024 · c6157ef · c6157ef
1 parent a59fef7
commit c6157ef
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Showing 2 changed files with 27 additions and 2 deletions.
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.ts
@@ -76,6 +76,7 @@ export interface OntologyStoreOptions {
     indexFields?: { displayName: string; jsonPath: string }[]
   }
   maxSearchResults?: number
+  update?(message: string, progress: number): void
 }
 
 export interface PropertiesOptions {
@@ -115,8 +116,8 @@ export default class OntologyStore {
     this.ontologyName = name
     this.ontologyVersion = version
     this.sourceLocation = source
-    this.db = this.prepareDatabase()
     this.options = options ?? {}
+    this.db = this.prepareDatabase()
   }
 
   /**
@@ -182,8 +183,12 @@ export default class OntologyStore {
     }
 
     try {
-      const { sourceLocation, sourceType } = this
+      const { options, sourceLocation, sourceType } = this
       if (sourceType === 'obo-graph-json') {
+        if (options.update) {
+          options.update('Importing', 0)
+        }
+        // add more updates inside `loadOboGraphJson`
         await this.loadOboGraphJson(db)
       } else {
         throw new Error(

diff --git a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
@@ -42,6 +42,7 @@ import {
 } from '../OntologyManager'
 import { ApolloRootModel } from '../types'
 import { autorun } from 'mobx'
+import { ApolloSessionModel } from './session'
 
 export function clientDataStoreFactory(
   AnnotationFeatureExtended: typeof AnnotationFeatureModel,
@@ -164,8 +165,27 @@ export function clientDataStoreFactory(
                 ) as TextIndexFieldDefinition[],
               ]
               if (!ontologyManager.findOntology(name)) {
+                // eslint-disable-next-line no-inner-declarations
+                function update(message: string, progress: number) {
+                  const session = getSession(
+                    self,
+                  ) as unknown as ApolloSessionModel
+                  const { jobsManager } = session
+                  const controller = new AbortController()
+                  const job = {
+                    name: message,
+                    statusMessage: 'Uploading ontology, this may take awhile',
+                    progressPct: progress,
+                    cancelCallback: () => {
+                      controller.abort()
+                      jobsManager.abortJob(job.name)
+                    },
+                  }
+                  jobsManager.runJob(job)
+                }
                 ontologyManager.addOntology(name, version, source, {
                   textIndexing: { indexFields },
+                  update,
                 })
               }
             }