[GLT-4274] added omitted run samples to Dimsum case data

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

@@ -16,12 +16,14 @@ public class CaseData {
   private final Map<Long, Assay> assaysById;
   private final List<Case> cases;
   private final List<OmittedSample> omittedSamples;
+  private final List<OmittedRunSample> omittedRunSamples;
   private final ZonedDateTime timestamp;
 
   private CaseData(Builder builder) {
     this.assaysById = unmodifiableMap(builder.assaysById);
     this.cases = unmodifiableList(builder.cases);
     this.omittedSamples = unmodifiableList(builder.omittedSamples);
+    this.omittedRunSamples = unmodifiableList(builder.omittedRunSamples);
     this.timestamp = requireNonNull(builder.timestamp);
   }
 
@@ -37,6 +39,10 @@ public List<OmittedSample> getOmittedSamples() {
     return omittedSamples;
   }
 
+  public List<OmittedRunSample> getOmittedRunSamples() {
+    return omittedRunSamples;
+  }
+
   public ZonedDateTime getTimestamp() {
     return timestamp;
   }
@@ -46,6 +52,7 @@ public static class Builder {
     private Map<Long, Assay> assaysById;
     private List<Case> cases;
     private List<OmittedSample> omittedSamples;
+    private List<OmittedRunSample> omittedRunSamples;
     private ZonedDateTime timestamp;
 
     public CaseData build() {
@@ -67,6 +74,11 @@ public Builder omittedSamples(List<OmittedSample> omittedSamples) {
       return this;
     }
 
+    public Builder omittedRunSamples(List<OmittedRunSample> omittedRunSamples) {
+      this.omittedRunSamples = omittedRunSamples;
+      return this;
+    }
+
     public Builder timestamp(ZonedDateTime timestamp) {
       this.timestamp = timestamp;
       return this;

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

@@ -0,0 +1,172 @@
+package ca.on.oicr.gsi.cardea.data;
+
+import static java.util.Objects.requireNonNull;
+import java.time.LocalDate;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
+
+/**
+ * Immutable OmittedRunSample
+ */
+@JsonDeserialize(builder = OmittedRunSample.Builder.class)
+public class OmittedRunSample {
+
+  private final String id;
+  private final String name;
+  private final long runId;
+  private final int sequencingLane;
+  private final LocalDate qcDate;
+  private final Boolean qcPassed;
+  private final String qcReason;
+  private final String qcNote;
+  private final String qcUser;
+  private final LocalDate dataReviewDate;
+  private final Boolean dataReviewPassed;
+  private final String dataReviewUser;
+
+  private OmittedRunSample(Builder builder) {
+    this.id = requireNonNull(builder.id);
+    this.name = requireNonNull(builder.name);
+    this.runId = requireNonNull(builder.runId);
+    this.sequencingLane = requireNonNull(builder.sequencingLane);
+    this.qcPassed = builder.qcPassed;
+    this.qcReason = builder.qcReason;
+    this.qcNote = builder.qcNote;
+    this.qcUser = builder.qcUser;
+    this.qcDate = builder.qcDate;
+    this.dataReviewPassed = builder.dataReviewPassed;
+    this.dataReviewUser = builder.dataReviewUser;
+    this.dataReviewDate = builder.dataReviewDate;
+  }
+
+  public String getId() {
+    return id;
+  }
+
+  public String getName() {
+    return name;
+  }
+
+  public long getRunId() {
+    return runId;
+  }
+
+  public int getSequencingLane() {
+    return sequencingLane;
+  }
+
+  public LocalDate getQcDate() {
+    return qcDate;
+  }
+
+  public Boolean getQcPassed() {
+    return qcPassed;
+  }
+
+  public String getQcReason() {
+    return qcReason;
+  }
+
+  public String getQcNote() {
+    return qcNote;
+  }
+
+  public String getQcUser() {
+    return qcUser;
+  }
+
+  public LocalDate getDataReviewDate() {
+    return dataReviewDate;
+  }
+
+  public Boolean getDataReviewPassed() {
+    return dataReviewPassed;
+  }
+
+  public String getDataReviewUser() {
+    return dataReviewUser;
+  }
+
+  @JsonPOJOBuilder(withPrefix = "")
+  public static class Builder {
+
+    private String id;
+    private String name;
+    private Long runId;
+    private Integer sequencingLane;
+    private LocalDate qcDate;
+    private Boolean qcPassed;
+    private String qcReason;
+    private String qcNote;
+    private String qcUser;
+    private LocalDate dataReviewDate;
+    private Boolean dataReviewPassed;
+    private String dataReviewUser;
+
+    public OmittedRunSample build() {
+      return new OmittedRunSample(this);
+    }
+
+    public Builder id(String id) {
+      this.id = id;
+      return this;
+    }
+
+    public Builder name(String name) {
+      this.name = name;
+      return this;
+    }
+
+    public Builder runId(Long runId) {
+      this.runId = runId;
+      return this;
+    }
+
+    public Builder sequencingLane(Integer sequencingLane) {
+      this.sequencingLane = sequencingLane;
+      return this;
+    }
+
+    public Builder qcDate(LocalDate qcDate) {
+      this.qcDate = qcDate;
+      return this;
+    }
+
+    public Builder qcPassed(Boolean qcPassed) {
+      this.qcPassed = qcPassed;
+      return this;
+    }
+
+    public Builder qcReason(String qcReason) {
+      this.qcReason = qcReason;
+      return this;
+    }
+
+    public Builder qcNote(String qcNote) {
+      this.qcNote = qcNote;
+      return this;
+    }
+
+    public Builder qcUser(String qcUser) {
+      this.qcUser = qcUser;
+      return this;
+    }
+
+    public Builder dataReviewDate(LocalDate dataReviewDate) {
+      this.dataReviewDate = dataReviewDate;
+      return this;
+    }
+
+    public Builder dataReviewPassed(Boolean dataReviewPassed) {
+      this.dataReviewPassed = dataReviewPassed;
+      return this;
+    }
+
+    public Builder dataReviewUser(String dataReviewUser) {
+      this.dataReviewUser = dataReviewUser;
+      return this;
+    }
+
+  }
+
+}

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

@@ -10,8 +10,12 @@
 
 /**
  * Immutable RunAndLibraries
+ * 
+ * This is being moved to Dimsum because its only intended use is for data transformation within
+ * Dimsum
  */
 @JsonDeserialize(builder = RunAndLibraries.Builder.class)
+@Deprecated(forRemoval = true)
 public class RunAndLibraries {
 
   private Set<Sample> fullDepthSequencings;

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

@@ -165,6 +165,14 @@ public void testCaseSerializeDeserialize() throws Exception {
     assertCaseEqual(original, deserialized);
   }
 
+  @org.junit.jupiter.api.Test
+  public void testOmittedRunSampleSerializeDeserialize() throws Exception {
+    OmittedRunSample original = makeOmittedRunSample();
+    String serialized = mapper.writeValueAsString(original);
+    OmittedRunSample deserialized = mapper.readerFor(OmittedRunSample.class).readValue(serialized);
+    assertOmittedRunSampleEqual(original, deserialized);
+  }
+
   @org.junit.jupiter.api.Test
   public void testShesmuCaseSerializeDeserialize() throws Exception {
     ShesmuCase original = makeShesmuCase();
@@ -177,7 +185,8 @@ public void testShesmuCaseSerializeDeserialize() throws Exception {
   public void testShesmuDetailedCaseSerializeDeserialize() throws Exception {
     ShesmuDetailedCase original = makeShesmuDetailedCase();
     String serialized = mapper.writeValueAsString(original);
-    ShesmuDetailedCase deserialized = mapper.readerFor(ShesmuDetailedCase.class).readValue(serialized);
+    ShesmuDetailedCase deserialized =
+        mapper.readerFor(ShesmuDetailedCase.class).readValue(serialized);
     assertShesmuDetailedCaseEqual(original, deserialized);
   }
 
@@ -479,6 +488,21 @@ private static void assertCaseEqual(Case one, Case two) {
     assertEquals(one.getPauseDays(), two.getPauseDays());
   }
 
+  private static void assertOmittedRunSampleEqual(OmittedRunSample one, OmittedRunSample two) {
+    assertEquals(one.getId(), two.getId());
+    assertEquals(one.getName(), two.getName());
+    assertEquals(one.getRunId(), two.getRunId());
+    assertEquals(one.getSequencingLane(), two.getSequencingLane());
+    assertEquals(one.getQcPassed(), two.getQcPassed());
+    assertEquals(one.getQcReason(), two.getQcReason());
+    assertEquals(one.getQcNote(), two.getQcNote());
+    assertEquals(one.getQcUser(), two.getQcUser());
+    assertEquals(one.getQcDate(), two.getQcDate());
+    assertEquals(one.getDataReviewPassed(), two.getDataReviewPassed());
+    assertEquals(one.getDataReviewUser(), two.getDataReviewUser());
+    assertEquals(one.getDataReviewDate(), two.getDataReviewDate());
+  }
+
   private static void assertShesmuCaseEqual(ShesmuCase one, ShesmuCase two) {
     assertEquals(one.getAssayName(), two.getAssayName());
     assertEquals(one.getAssayVersion(), two.getAssayVersion());
@@ -490,7 +514,8 @@ private static void assertShesmuCaseEqual(ShesmuCase one, ShesmuCase two) {
     assertEquals(one.getRequisitionName(), two.getRequisitionName());
   }
 
-  private static void assertShesmuDetailedCaseEqual(ShesmuDetailedCase one, ShesmuDetailedCase two) {
+  private static void assertShesmuDetailedCaseEqual(ShesmuDetailedCase one,
+      ShesmuDetailedCase two) {
     assertEquals(one.getAssayName(), two.getAssayName());
     assertEquals(one.getAssayVersion(), two.getAssayVersion());
     assertEquals(one.getCaseIdentifier(), two.getCaseIdentifier());
@@ -499,7 +524,8 @@ private static void assertShesmuDetailedCaseEqual(ShesmuDetailedCase one, Shesmu
     assertEquals(one.getCaseStatus(), two.getCaseStatus());
     assertEquals(one.getCompletedDate(), two.getCompletedDate());
     assertEquals(one.getSequencing().size(), two.getSequencing().size());
-    assertShesmuTestEqual(one.getSequencing().iterator().next(), two.getSequencing().iterator().next());
+    assertShesmuTestEqual(one.getSequencing().iterator().next(),
+        two.getSequencing().iterator().next());
     assertEquals(one.getRequisitionId(), two.getRequisitionId());
     assertEquals(one.getRequisitionName(), two.getRequisitionName());
   }
@@ -796,6 +822,23 @@ private static Case makeCase() {
         .build();
   }
 
+  private static OmittedRunSample makeOmittedRunSample() {
+    return new OmittedRunSample.Builder()
+        .id("123_4_LDI567")
+        .name("Joe")
+        .runId(123L)
+        .sequencingLane(4)
+        .qcPassed(true)
+        .qcReason("Good stuff")
+        .qcNote("This is my note")
+        .qcUser("Me")
+        .qcDate(LocalDate.now().minusDays(1L))
+        .dataReviewPassed(true)
+        .dataReviewUser("Someone else")
+        .dataReviewDate(LocalDate.now())
+        .build();
+  }
+
   private static ShesmuCase makeShesmuCase() {
     Set<String> limsIds = new HashSet<>();
     limsIds.add("ID1");
@@ -817,28 +860,28 @@ private static ShesmuDetailedCase makeShesmuDetailedCase() {
     Set<ShesmuSequencing> sequencing = new HashSet<>();
     Set<ShesmuSample> limsIds = new HashSet<>();
     limsIds.add(new ShesmuSample.Builder()
-            .id("ID1")
-            .supplemental(false)
-            .build());
+        .id("ID1")
+        .supplemental(false)
+        .build());
     sequencing.add(new ShesmuSequencing.Builder()
-            .test("Some Test")
-            .limsIds(limsIds)
-            .complete(true)
-            .type(MetricCategory.LIBRARY_QUALIFICATION)
-            .build());
+        .test("Some Test")
+        .limsIds(limsIds)
+        .complete(true)
+        .type(MetricCategory.LIBRARY_QUALIFICATION)
+        .build());
 
     return new ShesmuDetailedCase.Builder()
-            .assayName("Assay")
-            .assayVersion("2.0")
-            .caseIdentifier("CASE10")
-            .stopped(false)
-            .paused(false)
-            .caseStatus(CaseStatus.COMPLETED)
-            .completedDateLocal(LocalDate.of(2024, 1, 13))
-            .sequencing(sequencing)
-            .requisitionId(1L)
-            .requisitionName("Some Req")
-            .build();
+        .assayName("Assay")
+        .assayVersion("2.0")
+        .caseIdentifier("CASE10")
+        .stopped(false)
+        .paused(false)
+        .caseStatus(CaseStatus.COMPLETED)
+        .completedDateLocal(LocalDate.of(2024, 1, 13))
+        .sequencing(sequencing)
+        .requisitionId(1L)
+        .requisitionName("Some Req")
+        .build();
   }
 
 }