Report progress percent

GMOD · Nov 25, 2024 · a4c195b · a4c195b
1 parent 6ebba39
commit a4c195b
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Showing 2 changed files with 40 additions and 16 deletions.
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
@@ -81,7 +81,8 @@ function serializeWords(foundWords: Iterable<[string, string]>): string[] {
 export async function loadOboGraphJson(this: OntologyStore, db: Database) {
   const startTime = Date.now()
 
-  this.options.update?.('Parsing JSON', 1)
+  let percent_progress = 1
+  this.options.update?.('Parsing JSON', percent_progress)
   // 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
@@ -93,7 +94,9 @@ export async function loadOboGraphJson(this: OntologyStore, db: Database) {
   } catch {
     throw new Error('Error in loading ontology')
   }
-  this.options.update?.('Parsing JSON complete', 10)
+
+  percent_progress += 5
+  this.options.update?.('Parsing JSON complete', percent_progress)
 
   const parseTime = Date.now()
 
@@ -116,25 +119,46 @@ export async function loadOboGraphJson(this: OntologyStore, db: Database) {
     const fullTextIndexPaths = getTextIndexFields
       .call(this)
       .map((def) => def.jsonPath)
-    for (const node of graph.nodes ?? []) {
-      if (isOntologyDBNode(node)) {
-        await nodeStore.add({
-          ...node,
-          fullTextWords: serializeWords(
-            getWords(node, fullTextIndexPaths, this.prefixes),
-          ),
-        })
+    if (graph.nodes) {
+      let last_progress = Math.round(percent_progress)
+      for (const [, node] of graph.nodes.entries()) {
+        percent_progress += 64 * (1 / graph.nodes.length)
+        if (
+          Math.round(percent_progress) != last_progress &&
+          percent_progress < 100
+        ) {
+          this.options.update?.('Processing nodes', percent_progress)
+          last_progress = Math.round(percent_progress)
+        }
+        if (isOntologyDBNode(node)) {
+          await nodeStore.add({
+            ...node,
+            fullTextWords: serializeWords(
+              getWords(node, fullTextIndexPaths, this.prefixes),
+            ),
+          })
+        }
       }
     }
 
     // load edges
     const edgeStore = tx.objectStore('edges')
-    for (const edge of graph.edges ?? []) {
-      if (isOntologyDBEdge(edge)) {
-        await edgeStore.add(edge)
+    if (graph.edges) {
+      let last_progress = Math.round(percent_progress)
+      for (const [, edge] of graph.edges.entries()) {
+        percent_progress += 30 * (1 / graph.edges.length)
+        if (
+          Math.round(percent_progress) != last_progress &&
+          percent_progress < 100
+        ) {
+          this.options.update?.('Processing edges', percent_progress)
+          last_progress = Math.round(percent_progress)
+        }
+        if (isOntologyDBEdge(edge)) {
+          await edgeStore.add(edge)
+        }
       }
     }
-
     await tx.done
 
     // record some metadata about this ontology and load operation

diff --git a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
@@ -165,7 +165,6 @@ export function clientDataStoreFactory(
                 ) as TextIndexFieldDefinition[],
               ]
               if (!ontologyManager.findOntology(name)) {
-                // eslint-disable-next-line no-inner-declarations
                 const session = getSession(
                   self,
                 ) as unknown as ApolloSessionModel
@@ -181,7 +180,7 @@ export function clientDataStoreFactory(
                     jobsManager.abortJob(job.name)
                   },
                 }
-                const update = (message: string, progress: number) => {
+                const update = (message: string, progress: number): void => {
                   if (progress === 0) {
                     jobsManager.runJob(job)
                     return
@@ -191,6 +190,7 @@ export function clientDataStoreFactory(
                     return
                   }
                   jobsManager.update(jobName, message, progress)
+                  return
                 }
                 ontologyManager.addOntology(name, version, source, {
                   textIndexing: { indexFields },