From f3866a2484d6bfc9ab25cf1d91d3d9897f4ff733 Mon Sep 17 00:00:00 2001
From: grapigeau <gpigeau@oicr.on.ca>
Date: Thu, 14 Nov 2024 16:21:09 -0500
Subject: [PATCH] validate qcFailed so cannot be null

---
 .../java/ca/on/oicr/gsi/cardea/data/ShesmuSample.java     | 8 ++++----
 .../src/test/java/ca/on/oicr/gsi/cardea/JacksonTest.java  | 2 ++
 .../ca/on/oicr/gsi/cardea/server/service/CaseService.java | 8 ++++----
 changes/add_qc_failed_field.md                            | 2 +-
 4 files changed, 11 insertions(+), 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
index df08ee0..6b8ea8e 100644
--- 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
index b5cc6cf..037dfb1 100644
--- 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
index 898b2fc..7fac1dc 100644
--- 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
index ba89108..4f21e5a 100644
--- a/changes/add_qc_failed_field.md
+++ b/changes/add_qc_failed_field.md
@@ -1 +1 @@
-Field qcFailed on shesmu detailed cases
\ No newline at end of file
+Field qcFailed on sequencing items in shesmu detailed cases
\ No newline at end of file