exclude sequencings without limdids

oicr-gsi · Oct 3, 2024 · bde6663 · bde6663
1 parent 0a8df4e
commit bde6663
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Showing 3 changed files with 31 additions and 31 deletions.
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/ShesmuSequencing.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/ShesmuSequencing.java
@@ -14,26 +14,26 @@
 @JsonDeserialize(builder = ShesmuSequencing.Builder.class)
 public class ShesmuSequencing {
 
-  private final String name;
-  private final MetricCategory test;
+  private final String test;
+  private final MetricCategory type;
   private final Set<ShesmuSample> limsIds;
   private final boolean complete;
 
 
   private ShesmuSequencing(Builder builder) {
-    this.name = requireNonNull(builder.name);
     this.test = requireNonNull(builder.test);
+    this.type = requireNonNull(builder.type);
     this.limsIds = unmodifiableSet(requireNonNull(builder.limsIds));
     this.complete = requireNonNull(builder.complete);
   }
 
 
-  public String getName() {
-    return name;
+  public String getTest() {
+    return test;
   }
 
-  public MetricCategory getTest() {
-    return test;
+  public MetricCategory getType() {
+    return type;
   }
 
   public Set<ShesmuSample> getLimsIds() {
@@ -49,26 +49,22 @@ public Boolean isComplete() {
   @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
-    private String name;
+    private String test;
     private Set<ShesmuSample> limsIds;
-    private MetricCategory test;
+    private MetricCategory type;
     private boolean complete;
 
-
-
-
     public ShesmuSequencing build() {
       return new ShesmuSequencing(this);
     }
 
-
-    public Builder name(String name) {
-      this.name = name;
+    public Builder test(String test) {
+      this.test = test;
       return this;
     }
 
-    public Builder test(MetricCategory test) {
-      this.test = test;
+    public Builder type(MetricCategory type) {
+      this.type = type;
       return this;
     }
 

diff --git a/cardea-data/src/test/java/ca/on/oicr/gsi/cardea/JacksonTest.java b/cardea-data/src/test/java/ca/on/oicr/gsi/cardea/JacksonTest.java
@@ -510,8 +510,8 @@ private static void assertShesmuSampleEqual(ShesmuSample one, ShesmuSample two)
   }
 
   private static void assertShesmuTestEqual(ShesmuSequencing one, ShesmuSequencing two) {
-    assertEquals(one.getName(), two.getName());
     assertEquals(one.getTest(), two.getTest());
+    assertEquals(one.getType(), two.getType());
     assertEquals(one.isComplete(), two.isComplete());
     assertEquals(one.getLimsIds().size(), two.getLimsIds().size());
     assertShesmuSampleEqual(one.getLimsIds().iterator().next(), two.getLimsIds().iterator().next());
@@ -821,10 +821,10 @@ private static ShesmuDetailedCase makeShesmuDetailedCase() {
             .supplemental(false)
             .build());
     sequencing.add(new ShesmuSequencing.Builder()
-            .name("Some Test")
+            .test("Some Test")
             .limsIds(limsIds)
             .complete(true)
-            .test(MetricCategory.LIBRARY_QUALIFICATION)
+            .type(MetricCategory.LIBRARY_QUALIFICATION)
             .build());
 
     return new ShesmuDetailedCase.Builder()

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
@@ -133,22 +133,27 @@ public Set<ShesmuDetailedCase> getShesmuDetailedCases() {
 
   private Set<ShesmuSequencing> getSequencingForShesmuCase(Case kase){
 
-    Set<ShesmuSequencing> sTests = new HashSet<>();
+    Set<ShesmuSequencing> sequencings = new HashSet<>();
     final long reqId = kase.getRequisition().getId();
 
     for (Test test : kase.getTests()) {
 
-      sTests.add(makeShesmuSequencing(test.getFullDepthSequencings(), MetricCategory.FULL_DEPTH_SEQUENCING, reqId, test.getName()));
-      sTests.add(makeShesmuSequencing(test.getLibraryQualifications(), MetricCategory.LIBRARY_QUALIFICATION, reqId, test.getName()));
-
+      List<Sample> fullDepthSeqs = test.getFullDepthSequencings();
+      if (fullDepthSeqs != null && !fullDepthSeqs.isEmpty()) {
+        sequencings.add(makeShesmuSequencing(fullDepthSeqs, MetricCategory.FULL_DEPTH_SEQUENCING, reqId, test.getName()));
+      }
+      List<Sample> libraryQuals = test.getLibraryQualifications();
+      if (libraryQuals != null && !libraryQuals.isEmpty()) {
+        sequencings.add(makeShesmuSequencing(libraryQuals, MetricCategory.LIBRARY_QUALIFICATION, reqId, test.getName()));
+      }
     };
 
-    return sTests;
+    return sequencings;
   }
 
   private ShesmuSequencing makeShesmuSequencing(List<Sample> samples, MetricCategory type, long reqId, String name){
 
-    var lims = new HashSet<ShesmuSample>();
+    Set<ShesmuSample> shesmuSamples = new HashSet<>();
 
     boolean hasPassed = false;
     boolean hasWaiting = false;
@@ -161,20 +166,19 @@ private ShesmuSequencing makeShesmuSequencing(List<Sample> samples, MetricCatego
       }
 
       if (!(sample.getRun() == null && type.equals(MetricCategory.LIBRARY_QUALIFICATION))) {
-        lims.add(new ShesmuSample.Builder()
+        shesmuSamples.add(new ShesmuSample.Builder()
                 .id(sample.getId())
                 .supplemental(!Objects.equals(sample.getRequisitionId(), reqId))
                 .build());
       }
     }
 
     return new ShesmuSequencing.Builder()
-            .name(name)
-            .limsIds(lims)
+            .test(name)
+            .limsIds(shesmuSamples)
             .complete((hasPassed && !hasWaiting))
-            .test(type)
+            .type(type)
             .build();
-
   }
 
   private Set<String> getLimsIusIdsForShesmu(Case kase) {