From 75e340fb1d73e39c8a04e12c376f06e04d4264ec Mon Sep 17 00:00:00 2001
From: grapigeau <gpigeau@oicr.on.ca>
Date: Thu, 14 Nov 2024 10:01:05 -0500
Subject: [PATCH] add qcFaield field to the case_detailed_summmary format

---
 changes/add_qcFailed_detailed_cases.md                   | 1 +
 .../ca/on/oicr/gsi/shesmu/cardea/LimsSequencingInfo.java | 9 ++++++++-
 .../on/oicr/gsi/shesmu/cardea/SequencingTestValue.java   | 4 +++-
 3 files changed, 12 insertions(+), 2 deletions(-)
 create mode 100644 changes/add_qcFailed_detailed_cases.md

diff --git a/changes/add_qcFailed_detailed_cases.md b/changes/add_qcFailed_detailed_cases.md
new file mode 100644
index 000000000..1f95c21b9
--- /dev/null
+++ b/changes/add_qcFailed_detailed_cases.md
@@ -0,0 +1 @@
+qcFailed field to the case_detailed_summary input format
\ No newline at end of file
diff --git a/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/LimsSequencingInfo.java b/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/LimsSequencingInfo.java
index f0a76dc8e..962490011 100644
--- a/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/LimsSequencingInfo.java
+++ b/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/LimsSequencingInfo.java
@@ -5,11 +5,13 @@
 public class LimsSequencingInfo {
   private final String id;
   private final boolean supplemental;
+  private final boolean qcFailed;
 
-  public LimsSequencingInfo(String id, boolean supplemental) {
+  public LimsSequencingInfo(String id, boolean supplemental, boolean qcFailed) {
     super();
     this.id = id;
     this.supplemental = supplemental;
+    this.qcFailed = qcFailed;
   }
 
   @ShesmuVariable
@@ -21,4 +23,9 @@ public String id() {
   public boolean supplemental() {
     return supplemental;
   }
+
+  @ShesmuVariable
+  public boolean qcFailed() {
+    return qcFailed;
+  }
 }
diff --git a/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/SequencingTestValue.java b/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/SequencingTestValue.java
index 0e046b883..0833fbbd6 100644
--- a/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/SequencingTestValue.java
+++ b/plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/SequencingTestValue.java
@@ -18,7 +18,9 @@ public SequencingTestValue(
     this.test = test;
     this.type = type;
     this.limsIds =
-        limsIds.map(info -> new Tuple(info.id(), info.supplemental())).collect(Collectors.toSet());
+        limsIds
+            .map(info -> new Tuple(info.id(), info.supplemental(), info.qcFailed()))
+            .collect(Collectors.toSet());
     this.complete = complete;
   }