ensure all sequencings with no limids are not shown

oicr-gsi · Oct 3, 2024 · 2e852b9 · 2e852b9
1 parent bde6663
commit 2e852b9
Showing 1 changed file with 10 additions and 6 deletions.
diff --git a/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/service/CaseService.java b/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/service/CaseService.java
@@ -138,13 +138,14 @@ private Set<ShesmuSequencing> getSequencingForShesmuCase(Case kase){
 
     for (Test test : kase.getTests()) {
 
-      List<Sample> fullDepthSeqs = test.getFullDepthSequencings();
-      if (fullDepthSeqs != null && !fullDepthSeqs.isEmpty()) {
-        sequencings.add(makeShesmuSequencing(fullDepthSeqs, MetricCategory.FULL_DEPTH_SEQUENCING, reqId, test.getName()));
+      ShesmuSequencing fullDepthSeq = makeShesmuSequencing(test.getFullDepthSequencings(), MetricCategory.FULL_DEPTH_SEQUENCING, reqId, test.getName());
+      if (fullDepthSeq != null) {
+        sequencings.add(fullDepthSeq);
       }
-      List<Sample> libraryQuals = test.getLibraryQualifications();
-      if (libraryQuals != null && !libraryQuals.isEmpty()) {
-        sequencings.add(makeShesmuSequencing(libraryQuals, MetricCategory.LIBRARY_QUALIFICATION, reqId, test.getName()));
+
+      ShesmuSequencing libraryQual = makeShesmuSequencing(test.getLibraryQualifications(), MetricCategory.LIBRARY_QUALIFICATION, reqId, test.getName());
+      if (libraryQual != null) {
+        sequencings.add(libraryQual);
       }
     };
 
@@ -173,6 +174,9 @@ private ShesmuSequencing makeShesmuSequencing(List<Sample> samples, MetricCatego
       }
     }
 
+    if (shesmuSamples.isEmpty()) {
+      return null;
+    }
     return new ShesmuSequencing.Builder()
             .test(name)
             .limsIds(shesmuSamples)