[GLT-4064] support tests with no library qualification step (#173)

changes/change_libQual_skipped.md

@@ -0,0 +1 @@
+Some tests may not have a library qualification step

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>
+</project>

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

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

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