[GLT-4049] added case deliverables

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

@@ -31,6 +31,7 @@ public class Case {
   private final Requisition requisition;
   private final LocalDate startDate;
   private final List<Test> tests;
+  private final List<Deliverable> deliverables;
   private final String timepoint;
   private final String tissueOrigin;
   private final String tissueType;
@@ -55,6 +56,8 @@ private Case(Builder builder) {
     this.timepoint = builder.timepoint;
     this.receipts = unmodifiableList(builder.receipts);
     this.tests = unmodifiableList(builder.tests);
+    this.deliverables =
+        builder.deliverables == null ? null : unmodifiableList(builder.deliverables);
     this.requisition = requireNonNull(builder.requisition);
     this.startDate = requireNonNull(builder.startDate);
     this.latestActivityDate = Stream
@@ -115,6 +118,10 @@ public List<Test> getTests() {
     return tests;
   }
 
+  public List<Deliverable> getDeliverables() {
+    return deliverables;
+  }
+
   public String getTimepoint() {
     return timepoint;
   }
@@ -167,6 +174,7 @@ public static class Builder {
     private List<Sample> receipts;
     private Requisition requisition;
     private List<Test> tests;
+    private List<Deliverable> deliverables;
     private String timepoint;
     private String tissueOrigin;
     private String tissueType;
@@ -227,6 +235,11 @@ public Builder requisition(Requisition requisition) {
       return this;
     }
 
+    public Builder deliverables(List<Deliverable> deliverables) {
+      this.deliverables = deliverables;
+      return this;
+    }
+
     public Builder tests(List<Test> tests) {
       this.tests = tests;
       return this;

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

@@ -0,0 +1,144 @@
+package ca.on.oicr.gsi.cardea.data;
+
+import static java.util.Objects.requireNonNull;
+
+import java.time.LocalDate;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
+
+public class Deliverable {
+
+  private final DeliverableType deliverableType;
+  private final LocalDate analysisReviewQcDate;
+  private final Boolean analysisReviewQcPassed;
+  private final String analysisReviewQcUser;
+  private final LocalDate releaseApprovalQcDate;
+  private final Boolean releaseApprovalQcPassed;
+  private final String releaseApprovalQcUser;
+  private final LocalDate releaseQcDate;
+  private final Boolean releaseQcPassed;
+  private final String releaseQcUser;
+
+  private Deliverable(Builder builder) {
+    this.deliverableType = requireNonNull(builder.deliverableType);
+    this.analysisReviewQcDate = builder.analysisReviewQcDate;
+    this.analysisReviewQcPassed = builder.analysisReviewQcPassed;
+    this.analysisReviewQcUser = builder.analysisReviewQcUser;
+    this.releaseApprovalQcDate = builder.releaseApprovalQcDate;
+    this.releaseApprovalQcPassed = builder.releaseApprovalQcPassed;
+    this.releaseApprovalQcUser = builder.releaseApprovalQcUser;
+    this.releaseQcDate = builder.releaseQcDate;
+    this.releaseQcPassed = builder.releaseQcPassed;
+    this.releaseQcUser = builder.releaseQcUser;
+  }
+
+  public DeliverableType getDeliverableType() {
+    return deliverableType;
+  }
+
+  public LocalDate getAnalysisReviewQcDate() {
+    return analysisReviewQcDate;
+  }
+
+  public Boolean getAnalysisReviewQcPassed() {
+    return analysisReviewQcPassed;
+  }
+
+  public String getAnalysisReviewQcUser() {
+    return analysisReviewQcUser;
+  }
+
+  public LocalDate getReleaseApprovalQcDate() {
+    return releaseApprovalQcDate;
+  }
+
+  public Boolean getReleaseApprovalQcPassed() {
+    return releaseApprovalQcPassed;
+  }
+
+  public String getReleaseApprovalQcUser() {
+    return releaseApprovalQcUser;
+  }
+
+  public LocalDate getReleaseQcDate() {
+    return releaseQcDate;
+  }
+
+  public Boolean getReleaseQcPassed() {
+    return releaseQcPassed;
+  }
+
+  public String getReleaseQcUser() {
+    return releaseQcUser;
+  }
+
+  @JsonPOJOBuilder(withPrefix = "")
+  public static class Builder {
+
+    private DeliverableType deliverableType;
+    private LocalDate analysisReviewQcDate;
+    private Boolean analysisReviewQcPassed;
+    private String analysisReviewQcUser;
+    private LocalDate releaseApprovalQcDate;
+    private Boolean releaseApprovalQcPassed;
+    private String releaseApprovalQcUser;
+    private LocalDate releaseQcDate;
+    private Boolean releaseQcPassed;
+    private String releaseQcUser;
+
+    public Builder deliverableType(DeliverableType deliverableType) {
+      this.deliverableType = deliverableType;
+      return this;
+    }
+
+    public Builder analysisReviewQcDate(LocalDate analysisReviewQcDate) {
+      this.analysisReviewQcDate = analysisReviewQcDate;
+      return this;
+    }
+
+    public Builder analysisReviewQcPassed(Boolean analysisReviewQcPassed) {
+      this.analysisReviewQcPassed = analysisReviewQcPassed;
+      return this;
+    }
+
+    public Builder analysisReviewQcUser(String analysisReviewQcUser) {
+      this.analysisReviewQcUser = analysisReviewQcUser;
+      return this;
+    }
+
+    public Builder releaseApprovalQcDate(LocalDate releaseApprovalQcDate) {
+      this.releaseApprovalQcDate = releaseApprovalQcDate;
+      return this;
+    }
+
+    public Builder releaseApprovalQcPassed(Boolean releaseApprovalQcPassed) {
+      this.releaseApprovalQcPassed = releaseApprovalQcPassed;
+      return this;
+    }
+
+    public Builder releaseApprovalQcUser(String releaseApprovalQcUser) {
+      this.releaseApprovalQcUser = releaseApprovalQcUser;
+      return this;
+    }
+
+    public Builder releaseQcDate(LocalDate releaseQcDate) {
+      this.releaseQcDate = releaseQcDate;
+      return this;
+    }
+
+    public Builder releaseQcPassed(Boolean releaseQcPassed) {
+      this.releaseQcPassed = releaseQcPassed;
+      return this;
+    }
+
+    public Builder releaseQcUser(String releaseQcUser) {
+      this.releaseQcUser = releaseQcUser;
+      return this;
+    }
+
+    public Deliverable build() {
+      return new Deliverable(this);
+    }
+
+  }
+
+}

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

@@ -0,0 +1,16 @@
+package ca.on.oicr.gsi.cardea.data;
+
+public enum DeliverableType {
+
+  CLINICAL_REPORT("Clinical Report"), DATA_RELEASE("Data Release");
+
+  private final String label;
+
+  private DeliverableType(String label) {
+    this.label = label;
+  }
+
+  public String getLabel() {
+    return label;
+  }
+}

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

@@ -4,6 +4,8 @@
 import ca.on.oicr.gsi.cardea.data.AssayTargets;
 import ca.on.oicr.gsi.cardea.data.Case;
 import ca.on.oicr.gsi.cardea.data.CaseData;
+import ca.on.oicr.gsi.cardea.data.Deliverable;
+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;
@@ -226,6 +228,7 @@ private List<Case> loadCases(FileReader fileReader, Map<String, Project> project
           .timepoint(parseString(json, "timepoint"))
           .receipts(parseIdsAndGet(json, "receipt_ids", JsonNode::asText, samplesById))
           .tests(parseTests(json, "assay_tests", samplesById))
+          .deliverables(parseDeliverables(json.get("deliverables")))
           .requisition(requisitionsById.get(requisitionId))
           .startDate(parseDate(json, "start_date"))
           .receiptDaysSpent(parseInteger(json, "receipt_days_spent", true))
@@ -324,7 +327,7 @@ protected Map<Long, Run> loadRuns(FileReader fileReader) throws DataParseExcepti
           .percentOverQ30(parseDecimal(json, "percent_over_q30", false))
           .clustersPf(parseLong(json, "clusters_pf", false))
           .lanes(parseLanes(json.get("lanes")))
-          .qcPassed(parseQcPassed(json, "qc_state"))
+          .qcPassed(parseQcPassed(json, "qc_state", true))
           .qcUser(parseString(json, "qc_user"))
           .qcDate(parseDate(json, "qc_date"))
           .dataReviewPassed(parseDataReviewPassed(json, "data_review_state"))
@@ -390,7 +393,7 @@ protected Map<String, Sample> loadSamples(FileReader fileReader, Map<String, Don
           .lambdaClusters(parseInteger(json, "lambda_clusters", false))
           .puc19Methylation(parseDecimal(json, "puc19_methylation", false))
           .puc19Clusters(parseInteger(json, "puc19_clusters", false))
-          .qcPassed(parseQcPassed(json, "qc_state"))
+          .qcPassed(parseQcPassed(json, "qc_state", true))
           .qcReason(parseString(json, "qc_reason"))
           .qcNote(parseString(json, "qc_note"))
           .qcUser(parseString(json, "qc_user"))
@@ -485,8 +488,12 @@ private static Long parseLong(JsonNode json, String fieldName, boolean required)
     return node == null ? null : node.asLong();
   }
 
-  private static Boolean parseQcPassed(JsonNode json, String fieldName) throws DataParseException {
-    String qcState = parseString(json, fieldName, true);
+  private static Boolean parseQcPassed(JsonNode json, String fieldName, boolean required)
+      throws DataParseException {
+    String qcState = parseString(json, fieldName, required);
+    if (qcState == null) {
+      return null;
+    }
     switch (qcState) {
       case "Ready":
         return Boolean.TRUE;
@@ -529,7 +536,7 @@ private static List<RequisitionQc> parseRequisitionQcs(JsonNode json, String fie
     List<RequisitionQc> qcs = new ArrayList<>();
     for (JsonNode node : arr) {
       qcs.add(new RequisitionQc.Builder()
-          .qcPassed(parseQcPassed(node, "qc_state"))
+          .qcPassed(parseQcPassed(node, "qc_state", true))
           .qcUser(parseString(node, "qc_user"))
           .qcDate(parseDate(node, "qc_date"))
           .build());
@@ -727,6 +734,28 @@ private List<Test> parseTests(JsonNode json, String fieldName, Map<String, Sampl
     return tests;
   }
 
+  private List<Deliverable> parseDeliverables(JsonNode deliverablesNode) throws DataParseException {
+    if (deliverablesNode == null) {
+      return null;
+    }
+    List<Deliverable> deliverables = new ArrayList<>();
+    for (JsonNode node : deliverablesNode) {
+      deliverables.add(new Deliverable.Builder()
+          .deliverableType(DeliverableType.valueOf(parseString(node, "deliverable_type")))
+          .analysisReviewQcDate(parseDate(node, "analysis_review_qc_date"))
+          .analysisReviewQcPassed(parseQcPassed(node, "analysis_review_qc_state", false))
+          .analysisReviewQcUser(parseString(node, "analysis_review_qc_user"))
+          .releaseApprovalQcDate(parseDate(node, "release_approval_qc_date"))
+          .releaseApprovalQcPassed(parseQcPassed(node, "release_approval_qc_state", false))
+          .releaseApprovalQcUser(parseString(node, "release_approval_qc_user"))
+          .releaseQcDate(parseDate(node, "release_qc_date"))
+          .releaseQcPassed(parseQcPassed(node, "release_qc_state", false))
+          .releaseQcUser(parseString(node, "release_qc_user"))
+          .build());
+    }
+    return deliverables;
+  }
+
   @FunctionalInterface
   private static interface ParseFunction<T, R> {
     R apply(T input) throws DataParseException;

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

@@ -8,6 +8,8 @@
 import ca.on.oicr.gsi.cardea.data.AssayTargets;
 import ca.on.oicr.gsi.cardea.data.Case;
 import ca.on.oicr.gsi.cardea.data.CaseData;
+import ca.on.oicr.gsi.cardea.data.Deliverable;
+import ca.on.oicr.gsi.cardea.data.DeliverableType;
 import ca.on.oicr.gsi.cardea.data.Donor;
 import ca.on.oicr.gsi.cardea.data.Metric;
 import ca.on.oicr.gsi.cardea.data.MetricCategory;
@@ -40,7 +42,6 @@ public class CaseLoaderTest {
   private static final String testProjectName = "PROJ";
   private static final String testSampleId = "SAM413577";
   private static File dataDirectory;
-  private List<Case> cases = MockCase.getCases();
   private CaseLoader sut;
 
   @BeforeAll
@@ -137,6 +138,14 @@ public void testLoad() throws Exception {
     assertEquals("5476_1_LDI73620", fullDepth.getId());
     assertEquals("PROJ_1289_Ly_R_PE_567_WG", fullDepth.getName());
     assertEquals(Boolean.TRUE, fullDepth.getQcPassed());
+
+    assertNotNull(kase.getDeliverables());
+    assertEquals(1, kase.getDeliverables().size());
+    Deliverable deliverable = kase.getDeliverables().get(0);
+    assertEquals(DeliverableType.CLINICAL_REPORT, deliverable.getDeliverableType());
+    assertEquals("Person", deliverable.getAnalysisReviewQcUser());
+    assertEquals(LocalDate.of(2021, 8, 10), deliverable.getAnalysisReviewQcDate());
+    assertTrue(deliverable.getAnalysisReviewQcPassed());
   }
 
   @Test

cardea-server/src/test/resources/testdata/cases.json

@@ -70,6 +70,20 @@
         "full_depth_sequencing_days_spent": 0
       }
     ],
+    "deliverables": [
+      {
+        "deliverable_type": "CLINICAL_REPORT",
+        "analysis_review_qc_state": "Ready",
+        "analysis_review_qc_user": "Person",
+        "analysis_review_qc_date": "2021-08-10",
+        "release_approval_qc_state": null,
+        "release_approval_qc_user": null,
+        "release_approval_qc_date": null,
+        "release_qc_state": null,
+        "release_qc_user": null,
+        "release_qc_date": null
+      }
+    ],
     "requisition_id": 512,
     "stopped": false,
     "start_date": "2021-07-19",

changes/add_deliverables.md

@@ -0,0 +1 @@
+Case deliverables