Make core API call non-blocking (#454)

* Handle when Instant json element is a json object

The completedDate in the DB could be ISO 8601 string, or json object. I think this has to do with the recent spring boot upgrade, but I can't find the specific version of the change. I will handle both scenarios for now

* Textarea in review mode should fit text content (#427)

* Update pom version

* Fix reject cancer type name review (#428)

* Add reference to oncokb sop alteration nomenclature in add mutation modal helper (#432)

* Update pom version

* Avoid fetching management info repeatedly

* Do not rerender the side bar when loading session

The getSession is an async method which updates the loading status.

* Fix drug code not selectable (#435)

* Bump actions to latest version (#438)

* resize text area when input changes (#440)

* add sorting by firebase index (#443)

* Delete mutation/tumor/treatment as last step to avoid stale index (#444)

* break in middle of word to fix collapsible title overlfow (#442)

* Change searchEntities to readHandler instead of updateHandler (#445)

* Fixed data validation tool (#447)

* Allow curating mutation summary (#433)

* Parse protein change case insensitive (#441)

* Fix adding CDx biomarker association (#450)

* use firebase properties directly in backend (#451)

* fix references tab (#452)

* Added Heap (#448)

* Added Heap

* Updated CSP

* Reduce width so sidebar does not go offscren (#446)

* allow comma in mutation name when transcripts present (#453)

* allow comma in mutation name when transcripts present

* add missing colon

* rename transcripts to reference genomes

* Make core API call non-blocking

* Add tests for stale indices check (#455)

* Added loading icon when review is accepted

* Update setup-java action

* Update pom version

* Put feature flag in app config

* Now showing loading icon on accept all

---------

Co-authored-by: Hongxin <[email protected]>
Co-authored-by: Hongxin <[email protected]>
Co-authored-by: Calvin Lu <[email protected]>
Co-authored-by: oncokb-bot <[email protected]>
Co-authored-by: bprize15 <[email protected]>

.github/workflows/after-branch-commit.yml

@@ -93,7 +93,8 @@ jobs:
       - name: 'Setup Java'
         uses: actions/setup-java@v4
         with:
-          java-version: 8
+          distribution: 'temurin'
+          java-version: 17
 
       - name: 'Get Current Version Level'
         id: version_level

pom.xml

@@ -7,7 +7,7 @@
 
     <groupId>org.mskcc.oncokb.curation</groupId>
     <artifactId>oncokb-curation</artifactId>
-    <version>2.0.23</version>
+    <version>2.0.25</version>
     <packaging>jar</packaging>
     <name>OncoKB Curation</name>
     <description>Description for oncokb-curation</description>

src/main/java/org/mskcc/oncokb/curation/OncokbCurationApp.java

@@ -100,7 +100,7 @@ public void importOncoKbSequence() throws ApiException, IOException {
     @PostConstruct
     public void initFirebase() throws IOException {
         if (applicationProperties.getFirebase().isEnabled()) {
-            String serviceAccountPath = applicationProperties.getFrontend().getFirebase().getServiceAccountCredentialsPath();
+            String serviceAccountPath = applicationProperties.getFirebase().getServiceAccountCredentialsPath();
             if (serviceAccountPath == null) {
                 log.error("application.firebase.service-account-credentials-path is not specified");
                 return;
@@ -113,7 +113,7 @@ public void initFirebase() throws IOException {
             try {
                 FirebaseOptions options = FirebaseOptions.builder()
                     .setCredentials(GoogleCredentials.fromStream(serviceAccountFileUrl.openStream()))
-                    .setDatabaseUrl(applicationProperties.getFrontend().getFirebase().getDatabaseUrl())
+                    .setDatabaseUrl(applicationProperties.getFirebase().getDatabaseUrl())
                     .build();
 
                 FirebaseApp.initializeApp(options);

src/main/java/org/mskcc/oncokb/curation/config/application/FrontendProperties.java

@@ -21,4 +21,14 @@ public String getSentryDsn() {
     public void setSentryDsn(String sentryDsn) {
         this.sentryDsn = sentryDsn;
     }
+
+    private Boolean stopReviewIfCoreSubmissionFails;
+
+    public Boolean getStopReviewIfCoreSubmissionFails() {
+        return stopReviewIfCoreSubmissionFails;
+    }
+
+    public void setStopReviewIfCoreSubmissionFails(Boolean stopReviewIfCoreSubmissionFails) {
+        this.stopReviewIfCoreSubmissionFails = stopReviewIfCoreSubmissionFails;
+    }
 }

src/main/java/org/mskcc/oncokb/curation/service/MainService.java

@@ -149,7 +149,7 @@ public AlterationAnnotationStatus annotateAlteration(ReferenceGenome referenceGe
 
         // update associated genes
         Set<Gene> genes = alteration.getGenes();
-        if (parsedAlteration.getType().equals(STRUCTURAL_VARIANT) && !parsedAlteration.getGenes().isEmpty()) {
+        if (STRUCTURAL_VARIANT.equals(parsedAlteration.getType()) && !parsedAlteration.getGenes().isEmpty()) {
             genes = parsedAlteration.getGenes();
         }
         Set<Gene> annotatedGenes = genes
@@ -230,7 +230,8 @@ public AlterationAnnotationStatus annotateAlteration(ReferenceGenome referenceGe
                 ) {
                     String refRe = String.valueOf(canonicalSequenceOptional.orElseThrow().getSequence().charAt(alteration.getStart() - 1));
                     if (!StringUtils.isEmpty(refRe)) {
-                        if (StringUtils.isEmpty(alteration.getRefResidues())) {
+                        // only set the reference AA when the alteration happens on one position
+                        if (StringUtils.isEmpty(alteration.getRefResidues()) && alteration.getStart().equals(alteration.getEnd())) {
                             alteration.setRefResidues(refRe);
                         } else {
                             // If The AA in alteration is differed from the canonical transcript, and it's not X, we give warning