[GLT-4064] added assay test library qualification skipped field

oicr-gsi · Jan 2, 2024 · 7ac61ad · 7ac61ad
1 parent 6eb38fb
commit 7ac61ad
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Showing 4 changed files with 17 additions and 0 deletions.
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Test.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Test.java
@@ -24,6 +24,7 @@ public class Test {
   private final LocalDate latestActivityDate;
   private final boolean libraryPreparationSkipped;
   private final List<Sample> libraryPreparations;
+  private final boolean libraryQualificationSkipped;
   private final List<Sample> libraryQualifications;
   private final String name;
   private final String targetedSequencing;
@@ -46,6 +47,7 @@ private Test(Builder builder) {
     this.targetedSequencing = builder.targetedSequencing;
     this.extractionSkipped = builder.extractionSkipped;
     this.libraryPreparationSkipped = builder.libraryPreparationSkipped;
+    this.libraryQualificationSkipped = builder.libraryQualificationSkipped;
     this.extractions =
         builder.extractions == null ? emptyList() : unmodifiableList(builder.extractions);
     this.libraryPreparations = builder.libraryPreparations == null ? emptyList()
@@ -121,6 +123,10 @@ public boolean isLibraryPreparationSkipped() {
     return libraryPreparationSkipped;
   }
 
+  public boolean isLibraryQualificationSkipped() {
+    return libraryQualificationSkipped;
+  }
+
   public int getExtractionDaysSpent() {
     return extractionDaysSpent;
   }
@@ -147,6 +153,7 @@ public static class Builder {
     private String libraryDesignCode;
     private boolean libraryPreparationSkipped;
     private List<Sample> libraryPreparations;
+    private boolean libraryQualificationSkipped;
     private List<Sample> libraryQualifications;
     private String name;
     private String targetedSequencing;
@@ -197,6 +204,11 @@ public Builder libraryPreparations(List<Sample> libraryPreparations) {
       return this;
     }
 
+    public Builder libraryQualificationSkipped(boolean libraryQualificationSkipped) {
+      this.libraryQualificationSkipped = libraryQualificationSkipped;
+      return this;
+    }
+
     public Builder libraryQualifications(List<Sample> libraryQualifications) {
       this.libraryQualifications = libraryQualifications;
       return this;

diff --git a/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java b/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java
@@ -716,6 +716,7 @@ private List<Test> parseTests(JsonNode json, String fieldName, Map<String, Sampl
           .targetedSequencing(parseString(testNode, "targeted_sequencing"))
           .extractionSkipped(parseBoolean(testNode, "extraction_skipped"))
           .libraryPreparationSkipped(parseBoolean(testNode, "library_preparation_skipped"))
+          .libraryQualificationSkipped(parseBoolean(testNode, "library_qualification_skipped"))
           .extractions(parseIdsAndGet(testNode, "extraction_ids", JsonNode::asText, samplesById))
           .libraryPreparations(
               parseIdsAndGet(testNode, "library_preparation_ids", JsonNode::asText, samplesById))

diff --git a/cardea-server/src/test/resources/testdata/cases.json b/cardea-server/src/test/resources/testdata/cases.json
@@ -24,6 +24,7 @@
         "targeted_sequencing": null,
         "extraction_skipped": false,
         "library_preparation_skipped": false,
+        "library_qualification_skipped": false,
         "extraction_ids": ["SAM413593"],
         "library_preparation_ids": ["LIB75802"],
         "library_qualification_ids": ["5459_1_LDI73620", "5467_1_LDI73620"],
@@ -42,6 +43,7 @@
         "targeted_sequencing": null,
         "extraction_skipped": false,
         "library_preparation_skipped": false,
+        "library_qualification_skipped": false,
         "extraction_ids": ["SAM413648"],
         "library_preparation_ids": ["LIB76197"],
         "library_qualification_ids": ["5460_1_LDI73998"],
@@ -60,6 +62,7 @@
         "targeted_sequencing": null,
         "extraction_skipped": false,
         "library_preparation_skipped": false,
+        "library_qualification_skipped": false,
         "extraction_ids": ["SAM413735"],
         "library_preparation_ids": ["LIB75803"],
         "library_qualification_ids": ["5459_1_LDI73621", "5467_1_LDI73621"],

diff --git a/changes/add_libQualSkipped.md b/changes/add_libQualSkipped.md
@@ -0,0 +1 @@
+Assay test field to specify if library qualification is skipped