validate qcFailed so cannot be null

oicr-gsi · Nov 15, 2024 · f3866a2 · f3866a2
1 parent 0ed35c7
commit f3866a2
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Showing 4 changed files with 11 additions and 9 deletions.
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/ShesmuSample.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/ShesmuSample.java
@@ -27,11 +27,11 @@ public String getId() {
     return id;
   }
 
-  public Boolean isSupplemental() {
+  public boolean isSupplemental() {
     return supplemental;
   }
 
-  public Boolean qcFailed() {
+  public boolean isQcFailed() {
     return qcFailed;
   }
 
@@ -42,7 +42,7 @@ public static class Builder {
 
     private String id;
     private boolean supplemental;
-    private boolean qcFailed;
+    private Boolean qcFailed;
 
     public ShesmuSample build() {
       return new ShesmuSample(this);
@@ -59,7 +59,7 @@ public Builder supplemental(boolean supplemental) {
       return this;
     }
 
-    public Builder qcFailed(boolean qcFailed) {
+    public Builder qcFailed(Boolean qcFailed) {
       this.qcFailed = qcFailed;
       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
@@ -533,6 +533,7 @@ private static void assertShesmuDetailedCaseEqual(ShesmuDetailedCase one,
   private static void assertShesmuSampleEqual(ShesmuSample one, ShesmuSample two) {
     assertEquals(one.getId(), two.getId());
     assertEquals(one.isSupplemental(), two.isSupplemental());
+    assertEquals(one.isQcFailed(), two.isQcFailed());
   }
 
   private static void assertShesmuTestEqual(ShesmuSequencing one, ShesmuSequencing two) {
@@ -862,6 +863,7 @@ private static ShesmuDetailedCase makeShesmuDetailedCase() {
     limsIds.add(new ShesmuSample.Builder()
         .id("ID1")
         .supplemental(false)
+        .qcFailed(false)
         .build());
     sequencing.add(new ShesmuSequencing.Builder()
         .test("Some Test")

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
@@ -195,10 +195,10 @@ private ShesmuSequencing makeShesmuSequencing(List<Sample> samples, MetricCatego
 
   private boolean getQcFailed(Sample sample) {
     Run run = sample.getRun();
-    return (!(sample.getDataReviewPassed() == null || sample.getDataReviewPassed())
-        || !(sample.getQcPassed() == null || sample.getQcPassed())
-        || !(run.getDataReviewPassed() == null || run.getDataReviewPassed())
-        || !(run.getQcPassed() == null || run.getQcPassed()));
+    return ((sample.getDataReviewPassed() == false)
+        || (sample.getQcPassed() == false)
+        || (run.getDataReviewPassed() == false)
+        || (run.getQcPassed() == false));
   }
 
   private Set<String> getLimsIusIdsForShesmu(Case kase) {

diff --git a/changes/add_qc_failed_field.md b/changes/add_qc_failed_field.md
@@ -1 +1 @@
-Field qcFailed on shesmu detailed cases
+Field qcFailed on sequencing items in shesmu detailed cases
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		Field qcFailed on shesmu detailed cases
		Field qcFailed on sequencing items in shesmu detailed cases