Fixed merge conflicts

jfkonecn · Oct 14, 2024 · 5451d14 · 5451d14
2 parents 5ebc9a8 + f4e870b
commit 5451d14
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Showing 30 changed files with 986 additions and 366 deletions.
diff --git a/.github/workflows/after-branch-commit.yml b/.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

diff --git a/pom.xml b/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>

diff --git a/src/main/java/org/mskcc/oncokb/curation/OncokbCurationApp.java b/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);

diff --git a/src/main/java/org/mskcc/oncokb/curation/service/MainService.java b/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