lib: the variant annotation calculator search SNP ids only if the col…

…lection snp exists, #TASK-5821, #TASK-5789
opencb · Mar 13, 2024 · f206fe5 · f206fe5
1 parent 7670702
commit f206fe5
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java b/...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
@@ -469,7 +469,7 @@ private List<VariantAnnotation> runAnnotationProcess(List<Variant> normalizedVar
 
         FutureSnpAnnotator futureSnpAnnotator = null;
         Future<List<CellBaseDataResult<Snp>>> snpFuture = null;
-        if (annotatorSet.contains("xrefs")) {
+        if (annotatorSet.contains("xrefs") && dataRelease.getCollections().containsKey(EtlCommons.SNP_COLLECTION_NAME)) {
             futureSnpAnnotator = new FutureSnpAnnotator(normalizedVariantList, dataRelease.getRelease(), variantManager, logger);
             snpFuture = CACHED_THREAD_POOL.submit(futureSnpAnnotator);
         }

diff --git a/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java b/cellbase-server/src/main/java/org/opencb/cellbase/server/rest/genomic/VariantWSServer.java
@@ -458,6 +458,9 @@ public Response getAllConsequenceTypes() {
         }
     }
 
+    //-------------------------------------------------------------------------
+    // S N P
+    //-------------------------------------------------------------------------
     @GET
     @Path("/snp/search")
     @ApiOperation(httpMethod = "GET", value = "Get SNPs", response = Snp.class, responseContainer = "QueryResponse")