[GLT-4066] added sequencing subgate TAT fields

cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Run.java

@@ -16,6 +16,7 @@
 public class Run {
 
   private final Long clustersPf;
+  private final LocalDate startDate;
   private final LocalDate completionDate;
   private final String containerModel;
   private final LocalDate dataReviewDate;
@@ -44,6 +45,7 @@ private Run(Builder builder) {
     this.sequencingParameters = builder.sequencingParameters;
     this.readLength = builder.readLength;
     this.readLength2 = builder.readLength2;
+    this.startDate = builder.startDate;
     this.completionDate = builder.completionDate;
     this.percentOverQ30 = builder.percentOverQ30;
     this.clustersPf = builder.clustersPf;
@@ -72,6 +74,10 @@ public Long getClustersPf() {
     return clustersPf;
   }
 
+  public LocalDate getStartDate() {
+    return startDate;
+  }
+
   public LocalDate getCompletionDate() {
     return completionDate;
   }
@@ -145,6 +151,7 @@ public int hashCode() {
   public static class Builder {
 
     private Long clustersPf;
+    private LocalDate startDate;
     private LocalDate completionDate;
     private String containerModel;
     private LocalDate dataReviewDate;
@@ -171,6 +178,11 @@ public Builder clustersPf(Long clustersPf) {
       return this;
     }
 
+    public Builder startDate(LocalDate startDate) {
+      this.startDate = startDate;
+      return this;
+    }
+
     public Builder completionDate(LocalDate completionDate) {
       this.completionDate = completionDate;
       return this;

cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Test.java

@@ -35,7 +35,13 @@ public class Test {
   private final int extractionDaysSpent;
   private final int libraryPreparationDaysSpent;
   private final int libraryQualificationDaysSpent;
+  private final int libraryQualificationLoadingDaysSpent;
+  private final int libraryQualificationSequencingDaysSpent;
+  private final int libraryQualificationQcDaysSpent;
   private final int fullDepthSequencingDaysSpent;
+  private final int fullDepthSequencingLoadingDaysSpent;
+  private final int fullDepthSequencingSequencingDaysSpent;
+  private final int fullDepthSequencingQcDaysSpent;
 
   private Test(Builder builder) {
     this.name = requireNonNull(builder.name);
@@ -70,7 +76,13 @@ private Test(Builder builder) {
     this.extractionDaysSpent = builder.extractionDaysSpent;
     this.libraryPreparationDaysSpent = builder.libraryPreparationDaysSpent;
     this.libraryQualificationDaysSpent = builder.libraryQualificationDaysSpent;
+    this.libraryQualificationLoadingDaysSpent = builder.libraryQualificationLoadingDaysSpent;
+    this.libraryQualificationSequencingDaysSpent = builder.libraryQualificationSequencingDaysSpent;
+    this.libraryQualificationQcDaysSpent = builder.libraryQualificationQcDaysSpent;
     this.fullDepthSequencingDaysSpent = builder.fullDepthSequencingDaysSpent;
+    this.fullDepthSequencingLoadingDaysSpent = builder.fullDepthSequencingLoadingDaysSpent;
+    this.fullDepthSequencingSequencingDaysSpent = builder.fullDepthSequencingSequencingDaysSpent;
+    this.fullDepthSequencingQcDaysSpent = builder.fullDepthSequencingQcDaysSpent;
   }
 
   public List<Sample> getExtractions() {
@@ -145,10 +157,34 @@ public int getLibraryQualificationDaysSpent() {
     return libraryQualificationDaysSpent;
   }
 
+  public int getLibraryQualificationLoadingDaysSpent() {
+    return libraryQualificationLoadingDaysSpent;
+  }
+
+  public int getLibraryQualificationSequencingDaysSpent() {
+    return libraryQualificationSequencingDaysSpent;
+  }
+
+  public int getLibraryQualificationQcDaysSpent() {
+    return libraryQualificationQcDaysSpent;
+  }
+
   public int getFullDepthSequencingDaysSpent() {
     return fullDepthSequencingDaysSpent;
   }
 
+  public int getFullDepthSequencingLoadingDaysSpent() {
+    return fullDepthSequencingLoadingDaysSpent;
+  }
+
+  public int getFullDepthSequencingSequencingDaysSpent() {
+    return fullDepthSequencingSequencingDaysSpent;
+  }
+
+  public int getFullDepthSequencingQcDaysSpent() {
+    return fullDepthSequencingQcDaysSpent;
+  }
+
   @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
@@ -169,7 +205,13 @@ public static class Builder {
     private int extractionDaysSpent;
     private int libraryPreparationDaysSpent;
     private int libraryQualificationDaysSpent;
+    private int libraryQualificationLoadingDaysSpent;
+    private int libraryQualificationSequencingDaysSpent;
+    private int libraryQualificationQcDaysSpent;
     private int fullDepthSequencingDaysSpent;
+    private int fullDepthSequencingLoadingDaysSpent;
+    private int fullDepthSequencingSequencingDaysSpent;
+    private int fullDepthSequencingQcDaysSpent;
     private LocalDate latestActivityDate;
 
     public Test build() {
@@ -261,11 +303,41 @@ public Builder libraryQualificationDaysSpent(int days) {
       return this;
     }
 
+    public Builder libraryQualificationLoadingDaysSpent(int days) {
+      this.libraryQualificationLoadingDaysSpent = days;
+      return this;
+    }
+
+    public Builder libraryQualificationSequencingDaysSpent(int days) {
+      this.libraryQualificationSequencingDaysSpent = days;
+      return this;
+    }
+
+    public Builder libraryQualificationQcDaysSpent(int days) {
+      this.libraryQualificationQcDaysSpent = days;
+      return this;
+    }
+
     public Builder fullDepthSequencingDaysSpent(int days) {
       this.fullDepthSequencingDaysSpent = days;
       return this;
     }
 
+    public Builder fullDepthSequencingLoadingDaysSpent(int days) {
+      this.fullDepthSequencingLoadingDaysSpent = days;
+      return this;
+    }
+
+    public Builder fullDepthSequencingSequencingDaysSpent(int days) {
+      this.fullDepthSequencingSequencingDaysSpent = days;
+      return this;
+    }
+
+    public Builder fullDepthSequencingQcDaysSpent(int days) {
+      this.fullDepthSequencingQcDaysSpent = days;
+      return this;
+    }
+
     public Builder latestActivityDate(LocalDate latestActivityDate) {
       this.latestActivityDate = latestActivityDate;
       return this;

cardea-data/src/test/java/ca/on/oicr/gsi/cardea/JacksonTest.java

@@ -340,6 +340,7 @@ private static void assertLaneEqual(Lane one, Lane two) {
 
   private static void assertRunEqual(Run one, Run two) {
     assertEquals(one.getClustersPf(), two.getClustersPf());
+    assertEquals(one.getStartDate(), two.getStartDate());
     assertEquals(one.getCompletionDate(), two.getCompletionDate());
     assertEquals(one.getContainerModel(), two.getContainerModel());
     assertEquals(one.getDataReviewDate(), two.getDataReviewDate());
@@ -437,7 +438,18 @@ private static void assertTestEqual(Test one, Test two) {
     assertEquals(one.getExtractionDaysSpent(), two.getExtractionDaysSpent());
     assertEquals(one.getLibraryPreparationDaysSpent(), two.getLibraryPreparationDaysSpent());
     assertEquals(one.getLibraryQualificationDaysSpent(), two.getLibraryQualificationDaysSpent());
+    assertEquals(one.getLibraryQualificationLoadingDaysSpent(),
+        two.getLibraryQualificationLoadingDaysSpent());
+    assertEquals(one.getLibraryQualificationSequencingDaysSpent(),
+        two.getLibraryQualificationSequencingDaysSpent());
+    assertEquals(one.getLibraryQualificationQcDaysSpent(),
+        two.getLibraryQualificationQcDaysSpent());
     assertEquals(one.getFullDepthSequencingDaysSpent(), two.getFullDepthSequencingDaysSpent());
+    assertEquals(one.getFullDepthSequencingLoadingDaysSpent(),
+        two.getFullDepthSequencingLoadingDaysSpent());
+    assertEquals(one.getFullDepthSequencingSequencingDaysSpent(),
+        two.getFullDepthSequencingSequencingDaysSpent());
+    assertEquals(one.getFullDepthSequencingQcDaysSpent(), two.getFullDepthSequencingQcDaysSpent());
   }
 
   private static <T> void assertListsEqual(List<T> one, List<T> two, BiConsumer<T, T> assertEqual) {
@@ -630,6 +642,7 @@ private static Lane makeLane() {
   private static Run makeRun() {
     return new Run.Builder()
         .clustersPf(12L)
+        .startDate(LocalDate.of(2024, 1, 5))
         .completionDate(LocalDate.of(2024, 1, 6))
         .containerModel("Flow cell")
         .dataReviewDate(LocalDate.of(2024, 1, 10))
@@ -721,7 +734,13 @@ private static Test makeTest() {
         .extractionDaysSpent(1)
         .libraryPreparationDaysSpent(2)
         .libraryQualificationDaysSpent(3)
+        .libraryQualificationLoadingDaysSpent(1)
+        .libraryQualificationSequencingDaysSpent(0)
+        .libraryQualificationQcDaysSpent(2)
         .fullDepthSequencingDaysSpent(4)
+        .fullDepthSequencingLoadingDaysSpent(0)
+        .fullDepthSequencingSequencingDaysSpent(3)
+        .fullDepthSequencingQcDaysSpent(1)
         .build();
   }
 

cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java

@@ -331,6 +331,7 @@ protected Map<Long, Run> loadRuns(FileReader fileReader) throws DataParseExcepti
           .sequencingParameters(parseString(json, "sequencing_parameters"))
           .readLength(parseInteger(json, "read_length", false))
           .readLength2(parseInteger(json, "read_length_2", false))
+          .startDate(parseDate(json, "start_date"))
           .completionDate(parseDate(json, "completion_date"))
           .percentOverQ30(parseDecimal(json, "percent_over_q30", false))
           .clustersPf(parseLong(json, "clusters_pf", false))
@@ -732,8 +733,20 @@ private List<Test> parseTests(JsonNode json, String fieldName, Map<String, Sampl
               parseInteger(testNode, "library_preparation_days_spent", true))
           .libraryQualificationDaysSpent(
               parseInteger(testNode, "library_qualification_days_spent", true))
+          .libraryQualificationLoadingDaysSpent(
+              parseInteger(testNode, "library_qualification_loading_days_spent", true))
+          .libraryQualificationSequencingDaysSpent(
+              parseInteger(testNode, "library_qualification_sequencing_days_spent", true))
+          .libraryQualificationQcDaysSpent(
+              parseInteger(testNode, "library_qualification_qc_days_spent", true))
           .fullDepthSequencingDaysSpent(
               parseInteger(testNode, "full_depth_sequencing_days_spent", true))
+          .fullDepthSequencingLoadingDaysSpent(
+              parseInteger(testNode, "full_depth_sequencing_loading_days_spent", true))
+          .fullDepthSequencingSequencingDaysSpent(
+              parseInteger(testNode, "full_depth_sequencing_sequencing_days_spent", true))
+          .fullDepthSequencingQcDaysSpent(
+              parseInteger(testNode, "full_depth_sequencing_qc_days_spent", true))
           .build());
     }
     return tests;

cardea-server/src/test/java/ca/on/oicr/gsi/cardea/server/CaseLoaderTest.java

@@ -11,6 +11,7 @@
 import ca.on.oicr.gsi.cardea.data.CaseRelease;
 import ca.on.oicr.gsi.cardea.data.DeliverableType;
 import ca.on.oicr.gsi.cardea.data.Donor;
+import ca.on.oicr.gsi.cardea.data.Lane;
 import ca.on.oicr.gsi.cardea.data.Metric;
 import ca.on.oicr.gsi.cardea.data.MetricCategory;
 import ca.on.oicr.gsi.cardea.data.MetricSubcategory;
@@ -40,6 +41,7 @@ public class CaseLoaderTest {
   private static final String testDonorId = "SAM413576";
   private static final String testProjectName = "PROJ";
   private static final String testSampleId = "SAM413577";
+  private static final long testRunId = 5476L;
   private static File dataDirectory;
   private CaseLoader sut;
 
@@ -51,13 +53,13 @@ public static void setupClass() {
     dataDirectory = caseFile.getParentFile();
   }
 
-  private void assertDonor(Donor donor) {
+  private static void assertDonor(Donor donor) {
     assertNotNull(donor);
     assertEquals(testDonorId, donor.getId());
     assertEquals("PROJ_1289", donor.getName());
   }
 
-  private void assertOmittedSample(OmittedSample sample) {
+  private static void assertOmittedSample(OmittedSample sample) {
     assertNotNull(sample);
     assertEquals("SAM123457", sample.getId());
     assertEquals("NOCASE_0001_01", sample.getName());
@@ -69,7 +71,7 @@ private void assertOmittedSample(OmittedSample sample) {
     assertEquals(LocalDate.of(2022, 12, 13), sample.getCreatedDate());
   }
 
-  private void assertProject(Project project) {
+  private static void assertProject(Project project) {
     assertNotNull(project);
     assertEquals(testProjectName, project.getName());
     assertEquals("Research", project.getPipeline());
@@ -82,14 +84,39 @@ private void assertProject(Project project) {
     assertTrue(deliverables.contains("cBioPortal Submission"));
   }
 
-  private void assertSample(Sample sample) {
+  private static void assertSample(Sample sample) {
     assertNotNull(sample);
     assertEquals(testSampleId, sample.getId());
     assertEquals("PROJ_1289_Ly_R_nn_1-1", sample.getName());
     assertEquals(Boolean.TRUE, sample.getQcPassed());
     assertEquals(LocalDate.of(2021, 7, 19), sample.getQcDate());
   }
 
+  private static void assertRun(Run run) {
+    assertNotNull(run);
+    assertEquals(testRunId, run.getId());
+    assertEquals("210810_A00469_0195_BH2YF2DMXY", run.getName());
+    assertEquals("S2", run.getContainerModel());
+    assertFalse(run.hasJoinedLanes());
+    assertEquals("2×151", run.getSequencingParameters());
+    assertEquals(151, run.getReadLength());
+    assertEquals(151, run.getReadLength2());
+    assertEquals(LocalDate.of(2021, 8, 11), run.getStartDate());
+    assertEquals(LocalDate.of(2021, 8, 12), run.getCompletionDate());
+    assertTrue(run.getQcPassed());
+    assertEquals("Technician One", run.getQcUser());
+    assertEquals(LocalDate.of(2021, 8, 12), run.getQcDate());
+    assertEquals(new BigDecimal("89.1"), run.getPercentOverQ30());
+    assertEquals(2, run.getLanes().size());
+    Lane lane1 = run.getLanes().get(0);
+    assertEquals(1, lane1.getLaneNumber());
+    assertEquals(90, lane1.getPercentOverQ30Read1());
+    assertEquals(88, lane1.getPercentOverQ30Read2());
+    assertEquals(2163613696L, lane1.getClustersPf());
+    assertEquals(new BigDecimal("0.66"), lane1.getPercentPfixRead1());
+    assertEquals(new BigDecimal("0.65"), lane1.getPercentPfixRead2());
+  }
+
   @BeforeEach
   public void setup() {
     sut = new CaseLoader(dataDirectory, null);
@@ -135,15 +162,23 @@ public void testLoad() throws Exception {
     assertEquals(1, test.getLibraryPreparations().size());
     assertNotNull(test.getLibraryQualifications());
     assertEquals(2, test.getLibraryQualifications().size());
-    System.out
-        .println(test.getLibraryQualifications().stream().map(s -> s.getRun().getName()).reduce("",
-            String::concat));
     assertNotNull(test.getFullDepthSequencings());
     assertEquals(1, test.getFullDepthSequencings().size());
     Sample fullDepth = test.getFullDepthSequencings().get(0);
     assertEquals("5476_1_LDI73620", fullDepth.getId());
     assertEquals("PROJ_1289_Ly_R_PE_567_WG", fullDepth.getName());
     assertEquals(Boolean.TRUE, fullDepth.getQcPassed());
+    assertEquals(1, test.getExtractionDaysSpent());
+    assertEquals(2, test.getLibraryPreparationDaysSpent());
+    assertEquals(6, test.getLibraryQualificationDaysSpent());
+    assertEquals(1, test.getLibraryQualificationLoadingDaysSpent());
+    assertEquals(2, test.getLibraryQualificationSequencingDaysSpent());
+    assertEquals(3, test.getLibraryQualificationQcDaysSpent());
+    assertEquals(9, test.getFullDepthSequencingDaysSpent());
+    assertEquals(2, test.getFullDepthSequencingLoadingDaysSpent());
+    assertEquals(3, test.getFullDepthSequencingSequencingDaysSpent());
+    assertEquals(4, test.getFullDepthSequencingQcDaysSpent());
+    assertRun(fullDepth.getRun());
 
     assertNotNull(kase.getDeliverables());
     assertEquals(1, kase.getDeliverables().size());
@@ -291,4 +326,13 @@ public void testLoadSamples() throws Exception {
     }
   }
 
+  @Test
+  public void testLoadRuns() throws Exception {
+    try (FileReader reader = sut.getRunReader()) {
+      Map<Long, Run> runsById = sut.loadRuns(reader);
+      assertEquals(6, runsById.size());
+      assertRun(runsById.get(testRunId));
+    }
+  }
+
 }