From e30f92350127ed096141695ab7cd743cb5823e3f Mon Sep 17 00:00:00 2001
From: Dillan Cooke <dillan.cooke@oicr.on.ca>
Date: Fri, 5 Jan 2024 08:05:49 -0500
Subject: [PATCH] [GLT-4064] support tests with no library qualification step
 (#173)

---
 changes/change_libQual_skipped.md                  |  1 +
 pom.xml                                            |  4 ++--
 .../dimsum/service/filtering/CompletedGate.java    |  3 ++-
 .../gsi/dimsum/service/filtering/PendingState.java |  3 ++-
 ts/data/case.ts                                    | 14 ++++++++++++++
 5 files changed, 21 insertions(+), 4 deletions(-)
 create mode 100644 changes/change_libQual_skipped.md

diff --git a/changes/change_libQual_skipped.md b/changes/change_libQual_skipped.md
new file mode 100644
index 00000000..49792b84
--- /dev/null
+++ b/changes/change_libQual_skipped.md
@@ -0,0 +1 @@
+Some tests may not have a library qualification step
diff --git a/pom.xml b/pom.xml
index 4c4fed2e..d03c1c65 100644
--- a/pom.xml
+++ b/pom.xml
@@ -138,7 +138,7 @@
     <dependency>
       <groupId>ca.on.oicr.gsi.cardea</groupId>
       <artifactId>cardea-data</artifactId>
-      <version>1.6.0</version>
+      <version>1.7.0</version>
     </dependency>
   </dependencies>
 
@@ -184,4 +184,4 @@
     </plugins>
   </build>
 
-</project>
\ No newline at end of file
+</project>
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CompletedGate.java b/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CompletedGate.java
index 0edcaca4..ffe30bd3 100644
--- a/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CompletedGate.java
+++ b/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/CompletedGate.java
@@ -73,7 +73,8 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
   LIBRARY_QUALIFICATION("Library Qualification", true) {
     @Override
     public boolean qualifyTest(Test test) {
-      return Helpers.isCompleted(test.getLibraryQualifications());
+      return test.isLibraryQualificationSkipped()
+          || Helpers.isCompleted(test.getLibraryQualifications());
     }
 
     @Override
diff --git a/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/PendingState.java b/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/PendingState.java
index c70b6464..9acb2761 100644
--- a/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/PendingState.java
+++ b/src/main/java/ca/on/oicr/gsi/dimsum/service/filtering/PendingState.java
@@ -137,7 +137,8 @@ public boolean qualifySample(Sample sample, MetricCategory requestCategory) {
   LIBRARY_QUALIFICATION("Library Qualification", true) {
     @Override
     public boolean qualifyTest(Test test) {
-      return Helpers.hasPendingWork(test.getLibraryQualifications(), test.getLibraryPreparations());
+      return !test.isLibraryQualificationSkipped()
+          && Helpers.hasPendingWork(test.getLibraryQualifications(), test.getLibraryPreparations());
     }
 
     @Override
diff --git a/ts/data/case.ts b/ts/data/case.ts
index b8eb8988..d54bbb3d 100644
--- a/ts/data/case.ts
+++ b/ts/data/case.ts
@@ -75,6 +75,7 @@ export interface Test {
   targetedSequencing: string;
   extractionSkipped: boolean;
   libraryPreparationSkipped: boolean;
+  libraryQualificationSkipped: boolean;
   extractions: Sample[];
   libraryPreparations: Sample[];
   libraryQualifications: Sample[];
@@ -443,6 +444,13 @@ export const caseDefinition: TableDefinition<Case, Test> = {
         ) {
           return;
         }
+        if (
+          !test.libraryQualifications.length &&
+          test.libraryQualificationSkipped
+        ) {
+          addNaText(fragment);
+          return;
+        }
         addSampleIcons(kase.assayId, test.libraryQualifications, fragment);
         if (samplePhaseComplete(test.libraryPreparations)) {
           if (samplePhasePendingWorkOrQc(test.libraryQualifications)) {
@@ -468,6 +476,12 @@ export const caseDefinition: TableDefinition<Case, Test> = {
       },
       getCellHighlight(kase, test) {
         test = assertNotNull(test);
+        if (
+          !test.libraryQualifications.length &&
+          test.libraryQualificationSkipped
+        ) {
+          return "na";
+        }
         return getSamplePhaseHighlight(
           kase.requisition,
           test.libraryQualifications