[GLT-4035] added TAT and pause data (#37)

oicr-gsi · Nov 15, 2023 · 0a8b4e0 · 0a8b4e0
1 parent fe2991b
commit 0a8b4e0
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Showing 8 changed files with 193 additions and 10 deletions.
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Case.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Case.java
@@ -34,6 +34,12 @@ public class Case {
   private final String timepoint;
   private final String tissueOrigin;
   private final String tissueType;
+  private final int receiptDaysSpent;
+  private final int analysisReviewDaysSpent;
+  private final int releaseApprovalDaysSpent;
+  private final int releaseDaysSpent;
+  private final int caseDaysSpent;
+  private final int pauseDays;
 
   private Case(Builder builder) {
     this.id = requireNonNull(builder.id);
@@ -57,6 +63,12 @@ private Case(Builder builder) {
             Stream.of(requisition.getLatestActivityDate()))
         .flatMap(Function.identity()).filter(Objects::nonNull).max(LocalDate::compareTo)
         .orElse(null);
+    this.receiptDaysSpent = builder.receiptDaysSpent;
+    this.analysisReviewDaysSpent = builder.analysisReviewDaysSpent;
+    this.releaseApprovalDaysSpent = builder.releaseApprovalDaysSpent;
+    this.releaseDaysSpent = builder.releaseDaysSpent;
+    this.caseDaysSpent = builder.caseDaysSpent;
+    this.pauseDays = builder.pauseDays;
   }
 
   public long getAssayId() {
@@ -115,7 +127,30 @@ public String getTissueType() {
     return tissueType;
   }
 
-  // method used by Dimsum
+  public int getReceiptDaysSpent() {
+    return receiptDaysSpent;
+  }
+
+  public int getAnalysisReviewDaysSpent() {
+    return analysisReviewDaysSpent;
+  }
+
+  public int getReleaseApprovalDaysSpent() {
+    return releaseApprovalDaysSpent;
+  }
+
+  public int getReleaseDaysSpent() {
+    return releaseDaysSpent;
+  }
+
+  public int getCaseDaysSpent() {
+    return caseDaysSpent;
+  }
+
+  public int getPauseDays() {
+    return pauseDays;
+  }
+
   public boolean isStopped() {
     return requisition.isStopped();
   }
@@ -136,7 +171,12 @@ public static class Builder {
     private String tissueOrigin;
     private String tissueType;
     private LocalDate startDate;
-
+    private int receiptDaysSpent;
+    private int analysisReviewDaysSpent;
+    private int releaseApprovalDaysSpent;
+    private int releaseDaysSpent;
+    private int caseDaysSpent;
+    private int pauseDays;
 
     public Case build() {
       return new Case(this);
@@ -206,5 +246,35 @@ public Builder tissueType(String tissueType) {
       this.tissueType = tissueType;
       return this;
     }
+
+    public Builder receiptDaysSpent(int days) {
+      this.receiptDaysSpent = days;
+      return this;
+    }
+
+    public Builder analysisReviewDaysSpent(int days) {
+      this.analysisReviewDaysSpent = days;
+      return this;
+    }
+
+    public Builder releaseApprovalDaysSpent(int days) {
+      this.releaseApprovalDaysSpent = days;
+      return this;
+    }
+
+    public Builder releaseDaysSpent(int days) {
+      this.releaseDaysSpent = days;
+      return this;
+    }
+
+    public Builder caseDaysSpent(int days) {
+      this.caseDaysSpent = days;
+      return this;
+    }
+
+    public Builder pauseDays(int days) {
+      this.pauseDays = days;
+      return this;
+    }
   }
 }
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Requisition.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Requisition.java
@@ -28,13 +28,17 @@ public class Requisition {
   private final List<RequisitionQcGroup> qcGroups;
   private final String stopReason;
   private final boolean stopped;
+  private final boolean paused;
+  private final String pauseReason;
 
   private Requisition(Builder builder) {
     this.id = requireNonNull(builder.id);
     this.name = requireNonNull(builder.name);
     this.assayId = builder.assayId;
     this.stopped = builder.stopped;
     this.stopReason = builder.stopReason;
+    this.paused = builder.paused;
+    this.pauseReason = builder.pauseReason;
     this.qcGroups = builder.qcGroups == null ? emptyList() : unmodifiableList(builder.qcGroups);
     this.analysisReviews = builder.analysisReviews == null ? emptyList()
         : unmodifiableList(builder.analysisReviews);
@@ -92,19 +96,27 @@ public List<RequisitionQcGroup> getQcGroups() {
     return qcGroups;
   }
 
+  public boolean isStopped() {
+    return stopped;
+  }
+
   public String getStopReason() {
     return stopReason;
   }
 
+  public boolean isPaused() {
+    return paused;
+  }
+
+  public String getPauseReason() {
+    return pauseReason;
+  }
+
   @Override
   public int hashCode() {
     return Objects.hash(id);
   }
 
-  public boolean isStopped() {
-    return stopped;
-  }
-
   @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
@@ -117,6 +129,8 @@ public static class Builder {
     private List<RequisitionQcGroup> qcGroups;
     private String stopReason;
     private boolean stopped;
+    private boolean paused;
+    private String pauseReason;
 
     public Builder assayId(Long assayId) {
       this.assayId = assayId;
@@ -166,5 +180,15 @@ public Builder stopped(boolean stopped) {
       this.stopped = stopped;
       return this;
     }
+
+    public Builder paused(boolean paused) {
+      this.paused = paused;
+      return this;
+    }
+
+    public Builder pauseReason(String pauseReason) {
+      this.pauseReason = pauseReason;
+      return this;
+    }
   }
 }
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
@@ -31,6 +31,10 @@ public class Test {
   private final String tissueOrigin;
   private final String tissueType;
   private final String libraryDesignCode;
+  private final int extractionDaysSpent;
+  private final int libraryPreparationDaysSpent;
+  private final int libraryQualificationDaysSpent;
+  private final int fullDepthSequencingDaysSpent;
 
   private Test(Builder builder) {
     this.name = requireNonNull(builder.name);
@@ -55,6 +59,10 @@ private Test(Builder builder) {
             fullDepthSequencings.stream())
         .flatMap(Function.identity()).map(Sample::getLatestActivityDate).max(LocalDate::compareTo)
         .orElse(null);
+    this.extractionDaysSpent = builder.extractionDaysSpent;
+    this.libraryPreparationDaysSpent = builder.libraryPreparationDaysSpent;
+    this.libraryQualificationDaysSpent = builder.libraryQualificationDaysSpent;
+    this.fullDepthSequencingDaysSpent = builder.fullDepthSequencingDaysSpent;
   }
 
   public List<Sample> getExtractions() {
@@ -113,6 +121,22 @@ public boolean isLibraryPreparationSkipped() {
     return libraryPreparationSkipped;
   }
 
+  public int getExtractionDaysSpent() {
+    return extractionDaysSpent;
+  }
+
+  public int getLibraryPreparationDaysSpent() {
+    return libraryPreparationDaysSpent;
+  }
+
+  public int getLibraryQualificationDaysSpent() {
+    return libraryQualificationDaysSpent;
+  }
+
+  public int getFullDepthSequencingDaysSpent() {
+    return fullDepthSequencingDaysSpent;
+  }
+
   @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
@@ -129,6 +153,10 @@ public static class Builder {
     private String timepoint;
     private String tissueOrigin;
     private String tissueType;
+    private int extractionDaysSpent;
+    private int libraryPreparationDaysSpent;
+    private int libraryQualificationDaysSpent;
+    private int fullDepthSequencingDaysSpent;
 
     public Test build() {
       return new Test(this);
@@ -198,5 +226,25 @@ public Builder tissueType(String tissueType) {
       this.tissueType = tissueType;
       return this;
     }
+
+    public Builder extractionDaysSpent(int days) {
+      this.extractionDaysSpent = days;
+      return this;
+    }
+
+    public Builder libraryPreparationDaysSpent(int days) {
+      this.libraryPreparationDaysSpent = days;
+      return this;
+    }
+
+    public Builder libraryQualificationDaysSpent(int days) {
+      this.libraryQualificationDaysSpent = days;
+      return this;
+    }
+
+    public Builder fullDepthSequencingDaysSpent(int days) {
+      this.fullDepthSequencingDaysSpent = days;
+      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
@@ -228,6 +228,12 @@ private List<Case> loadCases(FileReader fileReader, Map<String, Project> project
           .tests(parseTests(json, "assay_tests", samplesById))
           .requisition(requisitionsById.get(requisitionId))
           .startDate(parseDate(json, "start_date"))
+          .receiptDaysSpent(parseInteger(json, "receipt_days_spent", true))
+          .analysisReviewDaysSpent(parseInteger(json, "analysis_review_days_spent", true))
+          .releaseApprovalDaysSpent(parseInteger(json, "release_approval_days_spent", true))
+          .releaseDaysSpent(parseInteger(json, "release_days_spent", true))
+          .caseDaysSpent(parseInteger(json, "case_days_spent", true))
+          .pauseDays(parseInteger(json, "pause_days", true))
           .build();
     });
   }
@@ -292,6 +298,8 @@ protected Map<Long, Requisition> loadRequisitions(FileReader fileReader,
           .assayId(parseLong(json, "assay_id", false))
           .stopped(parseBoolean(json, "stopped"))
           .stopReason(parseString(json, "stop_reason", false))
+          .paused(parseBoolean(json, "paused"))
+          .pauseReason(parseString(json, "pause_reason", false))
           .qcGroups(parseRequisitionQcGroups(json.get("qc_groups"), donorsById))
           .analysisReviews(parseRequisitionQcs(json, "analysis_reviews"))
           .releaseApprovals(parseRequisitionQcs(json, "release_approvals"))
@@ -707,6 +715,13 @@ private List<Test> parseTests(JsonNode json, String fieldName, Map<String, Sampl
               parseIdsAndGet(testNode, "library_qualification_ids", JsonNode::asText, samplesById))
           .fullDepthSequencings(
               parseIdsAndGet(testNode, "full_depth_sequencing_ids", JsonNode::asText, samplesById))
+          .extractionDaysSpent(parseInteger(testNode, "extraction_days_spent", true))
+          .libraryPreparationDaysSpent(
+              parseInteger(testNode, "library_preparation_days_spent", true))
+          .libraryQualificationDaysSpent(
+              parseInteger(testNode, "library_qualification_days_spent", true))
+          .fullDepthSequencingDaysSpent(
+              parseInteger(testNode, "full_depth_sequencing_days_spent", true))
           .build());
     }
     return tests;

diff --git a/cardea-server/src/test/resources/testdata/cases.json b/cardea-server/src/test/resources/testdata/cases.json
@@ -27,7 +27,11 @@
         "extraction_ids": ["SAM413593"],
         "library_preparation_ids": ["LIB75802"],
         "library_qualification_ids": ["5459_1_LDI73620", "5467_1_LDI73620"],
-        "full_depth_sequencing_ids": ["5476_1_LDI73620"]
+        "full_depth_sequencing_ids": ["5476_1_LDI73620"],
+        "extraction_days_spent": 0,
+        "library_preparation_days_spent": 0,
+        "library_qualification_days_spent": 0,
+        "full_depth_sequencing_days_spent": 0
       },
       {
         "name": "Tumour WT",
@@ -41,7 +45,11 @@
         "extraction_ids": ["SAM413648"],
         "library_preparation_ids": ["LIB76197"],
         "library_qualification_ids": ["5460_1_LDI73998"],
-        "full_depth_sequencing_ids": ["5481_1_LDI73998"]
+        "full_depth_sequencing_ids": ["5481_1_LDI73998"],
+        "extraction_days_spent": 0,
+        "library_preparation_days_spent": 0,
+        "library_qualification_days_spent": 0,
+        "full_depth_sequencing_days_spent": 0
       },
       {
         "name": "Tumour WG",
@@ -55,11 +63,21 @@
         "extraction_ids": ["SAM413735"],
         "library_preparation_ids": ["LIB75803"],
         "library_qualification_ids": ["5459_1_LDI73621", "5467_1_LDI73621"],
-        "full_depth_sequencing_ids": ["5476_1_LDI73621", "5540_1_LDI73621"]
+        "full_depth_sequencing_ids": ["5476_1_LDI73621", "5540_1_LDI73621"],
+        "extraction_days_spent": 0,
+        "library_preparation_days_spent": 0,
+        "library_qualification_days_spent": 0,
+        "full_depth_sequencing_days_spent": 0
       }
     ],
     "requisition_id": 512,
     "stopped": false,
-    "start_date": "2021-07-19"
+    "start_date": "2021-07-19",
+    "receipt_days_spent": 0,
+    "analysis_review_days_spent": 0,
+    "release_approval_days_spent": 0,
+    "release_days_spent": 0,
+    "case_days_spent": 0,
+    "pause_days": 0
   }
 ]
diff --git a/cardea-server/src/test/resources/testdata/requisitions.json b/cardea-server/src/test/resources/testdata/requisitions.json
@@ -4,6 +4,9 @@
     "name": "REQ-1",
     "assay_id": 2,
     "stopped": false,
+    "stop_reason": null,
+    "paused": false,
+    "pause_reason": null,
     "qc_groups": [
       {
         "donor_id": "SAM413576",
@@ -52,6 +55,9 @@
     "name": "REQ-X",
     "assay_id": null,
     "stopped": false,
+    "stop_reason": null,
+    "paused": false,
+    "pause_reason": null,
     "qc_groups": [],
     "analysis_reviews": [],
     "release_approvals": [],

diff --git a/changes/add_pauses.md b/changes/add_pauses.md
@@ -0,0 +1 @@
+Requisition pause status and reason
diff --git a/changes/add_tat.md b/changes/add_tat.md
@@ -0,0 +1 @@
+Days spent per QC step at case and test levels