[GLT-4065] added extraction substep TAT fields (#52)

oicr-gsi · Jun 13, 2024 · 9c34ee4 · 9c34ee4
1 parent 7663ba6
commit 9c34ee4
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Showing 9 changed files with 98 additions and 1 deletion.
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Sample.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Sample.java
@@ -66,6 +66,7 @@ public class Sample {
   private final BigDecimal relativeCpgInRegions;
   private final BigDecimal methylationBeta;
   private final Integer peReads;
+  private final LocalDate transferDate;
 
   private Sample(Builder builder) {
     this.id = requireNonNull(builder.id);
@@ -124,6 +125,7 @@ private Sample(Builder builder) {
       this.latestActivityDate = Stream.of(createdDate, qcDate, dataReviewDate)
           .filter(Objects::nonNull).max(LocalDate::compareTo).orElseThrow();
     }
+    this.transferDate = builder.transferDate;
   }
 
   @Override
@@ -340,6 +342,10 @@ public Integer getPeReads() {
     return peReads;
   }
 
+  public LocalDate getTransferDate() {
+    return transferDate;
+  }
+
   @Override
   public int hashCode() {
     return Objects.hash(id, run, sequencingLane);
@@ -398,6 +404,7 @@ public static class Builder {
     private BigDecimal methylationBeta;
     private Integer peReads;
     private LocalDate latestActivityDate;
+    private LocalDate transferDate;
 
     public Sample build() {
       return new Sample(this);
@@ -662,5 +669,10 @@ public Builder latestActivityDate(LocalDate latestActivityDate) {
       return this;
     }
 
+    public Builder transferDate(LocalDate transferDate) {
+      this.transferDate = transferDate;
+      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
@@ -33,6 +33,9 @@ public class Test {
   private final String tissueType;
   private final String libraryDesignCode;
   private final int extractionDaysSpent;
+  private final int extractionPreparationDaysSpent;
+  private final int extractionQcDaysSpent;
+  private final int extractionTransferDaysSpent;
   private final int libraryPreparationDaysSpent;
   private final int libraryQualificationDaysSpent;
   private final int libraryQualificationLoadingDaysSpent;
@@ -74,6 +77,9 @@ private Test(Builder builder) {
     }
 
     this.extractionDaysSpent = builder.extractionDaysSpent;
+    this.extractionPreparationDaysSpent = builder.extractionPreparationDaysSpent;
+    this.extractionQcDaysSpent = builder.extractionQcDaysSpent;
+    this.extractionTransferDaysSpent = builder.extractionTransferDaysSpent;
     this.libraryPreparationDaysSpent = builder.libraryPreparationDaysSpent;
     this.libraryQualificationDaysSpent = builder.libraryQualificationDaysSpent;
     this.libraryQualificationLoadingDaysSpent = builder.libraryQualificationLoadingDaysSpent;
@@ -149,6 +155,18 @@ public int getExtractionDaysSpent() {
     return extractionDaysSpent;
   }
 
+  public int getExtractionPreparationDaysSpent() {
+    return extractionPreparationDaysSpent;
+  }
+
+  public int getExtractionQcDaysSpent() {
+    return extractionQcDaysSpent;
+  }
+
+  public int getExtractionTransferDaysSpent() {
+    return extractionTransferDaysSpent;
+  }
+
   public int getLibraryPreparationDaysSpent() {
     return libraryPreparationDaysSpent;
   }
@@ -203,6 +221,9 @@ public static class Builder {
     private String tissueOrigin;
     private String tissueType;
     private int extractionDaysSpent;
+    private int extractionPreparationDaysSpent;
+    private int extractionQcDaysSpent;
+    private int extractionTransferDaysSpent;
     private int libraryPreparationDaysSpent;
     private int libraryQualificationDaysSpent;
     private int libraryQualificationLoadingDaysSpent;
@@ -293,6 +314,21 @@ public Builder extractionDaysSpent(int days) {
       return this;
     }
 
+    public Builder extractionPreparationDaysSpent(int days) {
+      this.extractionPreparationDaysSpent = days;
+      return this;
+    }
+
+    public Builder extractionQcDaysSpent(int days) {
+      this.extractionQcDaysSpent = days;
+      return this;
+    }
+
+    public Builder extractionTransferDaysSpent(int days) {
+      this.extractionTransferDaysSpent = days;
+      return this;
+    }
+
     public Builder libraryPreparationDaysSpent(int days) {
       this.libraryPreparationDaysSpent = days;
       return this;

diff --git a/cardea-data/src/test/java/ca/on/oicr/gsi/cardea/JacksonTest.java b/cardea-data/src/test/java/ca/on/oicr/gsi/cardea/JacksonTest.java
@@ -414,6 +414,7 @@ private static void assertSampleEqual(Sample one, Sample two) {
     assertEquals(one.getRelativeCpgInRegions(), two.getRelativeCpgInRegions());
     assertEquals(one.getMethylationBeta(), two.getMethylationBeta());
     assertEquals(one.getPeReads(), two.getPeReads());
+    assertEquals(one.getTransferDate(), two.getTransferDate());
   }
 
   private static void assertTestEqual(Test one, Test two) {
@@ -436,6 +437,9 @@ private static void assertTestEqual(Test one, Test two) {
     assertEquals(one.getTissueType(), two.getTissueType());
     assertEquals(one.getLibraryDesignCode(), two.getLibraryDesignCode());
     assertEquals(one.getExtractionDaysSpent(), two.getExtractionDaysSpent());
+    assertEquals(one.getExtractionPreparationDaysSpent(), two.getExtractionPreparationDaysSpent());
+    assertEquals(one.getExtractionQcDaysSpent(), two.getExtractionQcDaysSpent());
+    assertEquals(one.getExtractionTransferDaysSpent(), two.getExtractionTransferDaysSpent());
     assertEquals(one.getLibraryPreparationDaysSpent(), two.getLibraryPreparationDaysSpent());
     assertEquals(one.getLibraryQualificationDaysSpent(), two.getLibraryQualificationDaysSpent());
     assertEquals(one.getLibraryQualificationLoadingDaysSpent(),
@@ -712,6 +716,7 @@ private static Sample makeSample(String name) {
         .relativeCpgInRegions(new BigDecimal("6.66"))
         .methylationBeta(new BigDecimal("7.77"))
         .peReads(35)
+        .transferDate(LocalDate.of(2024, 06, 11))
         .build();
   }
 
@@ -731,7 +736,10 @@ private static Test makeTest() {
         .tissueOrigin("Lv")
         .tissueType("P")
         .libraryDesignCode("WG")
-        .extractionDaysSpent(1)
+        .extractionDaysSpent(3)
+        .extractionPreparationDaysSpent(1)
+        .extractionQcDaysSpent(0)
+        .extractionTransferDaysSpent(2)
         .libraryPreparationDaysSpent(2)
         .libraryQualificationDaysSpent(3)
         .libraryQualificationLoadingDaysSpent(1)

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
@@ -414,6 +414,7 @@ protected Map<String, Sample> loadSamples(FileReader fileReader, Map<String, Don
           .dataReviewUser(parseString(json, "data_review_user"))
           .dataReviewDate(parseDate(json, "data_review_date"))
           .sequencingLane(parseString(json, "sequencing_lane"))
+          .transferDate(parseDate(json, "transfer_date"))
           .build();
     });
 
@@ -729,6 +730,11 @@ private List<Test> parseTests(JsonNode json, String fieldName, Map<String, Sampl
           .fullDepthSequencings(
               parseIdsAndGet(testNode, "full_depth_sequencing_ids", JsonNode::asText, samplesById))
           .extractionDaysSpent(parseInteger(testNode, "extraction_days_spent", true))
+          .extractionPreparationDaysSpent(
+              parseInteger(testNode, "extraction_preparation_days_spent", true))
+          .extractionQcDaysSpent(parseInteger(testNode, "extraction_qc_days_spent", true))
+          .extractionTransferDaysSpent(
+              parseInteger(testNode, "extraction_transfer_days_spent", true))
           .libraryPreparationDaysSpent(
               parseInteger(testNode, "library_preparation_days_spent", true))
           .libraryQualificationDaysSpent(

diff --git a/cardea-server/src/test/java/ca/on/oicr/gsi/cardea/server/CaseLoaderTest.java b/cardea-server/src/test/java/ca/on/oicr/gsi/cardea/server/CaseLoaderTest.java
@@ -90,6 +90,7 @@ private static void assertSample(Sample sample) {
     assertEquals("PROJ_1289_Ly_R_nn_1-1", sample.getName());
     assertEquals(Boolean.TRUE, sample.getQcPassed());
     assertEquals(LocalDate.of(2021, 7, 19), sample.getQcDate());
+    assertNull(sample.getTransferDate());
   }
 
   private static void assertRun(Run run) {
@@ -169,6 +170,9 @@ public void testLoad() throws Exception {
     assertEquals("PROJ_1289_Ly_R_PE_567_WG", fullDepth.getName());
     assertEquals(Boolean.TRUE, fullDepth.getQcPassed());
     assertEquals(1, test.getExtractionDaysSpent());
+    assertEquals(0, test.getExtractionPreparationDaysSpent());
+    assertEquals(0, test.getExtractionQcDaysSpent());
+    assertEquals(1, test.getExtractionTransferDaysSpent());
     assertEquals(2, test.getLibraryPreparationDaysSpent());
     assertEquals(6, test.getLibraryQualificationDaysSpent());
     assertEquals(1, test.getLibraryQualificationLoadingDaysSpent());

diff --git a/cardea-server/src/test/resources/testdata/cases.json b/cardea-server/src/test/resources/testdata/cases.json
@@ -30,6 +30,9 @@
         "library_qualification_ids": ["5459_1_LDI73620", "5467_1_LDI73620"],
         "full_depth_sequencing_ids": ["5476_1_LDI73620"],
         "extraction_days_spent": 1,
+        "extraction_preparation_days_spent": 0,
+        "extraction_qc_days_spent": 0,
+        "extraction_transfer_days_spent": 1,
         "library_preparation_days_spent": 2,
         "library_qualification_days_spent": 6,
         "library_qualification_loading_days_spent": 1,
@@ -55,6 +58,9 @@
         "library_qualification_ids": ["5460_1_LDI73998"],
         "full_depth_sequencing_ids": ["5481_1_LDI73998"],
         "extraction_days_spent": 0,
+        "extraction_preparation_days_spent": 0,
+        "extraction_qc_days_spent": 0,
+        "extraction_transfer_days_spent": 0,
         "library_preparation_days_spent": 0,
         "library_qualification_days_spent": 0,
         "library_qualification_loading_days_spent": 0,
@@ -80,6 +86,9 @@
         "library_qualification_ids": ["5459_1_LDI73621", "5467_1_LDI73621"],
         "full_depth_sequencing_ids": ["5476_1_LDI73621", "5540_1_LDI73621"],
         "extraction_days_spent": 0,
+        "extraction_preparation_days_spent": 0,
+        "extraction_qc_days_spent": 0,
+        "extraction_transfer_days_spent": 0,
         "library_preparation_days_spent": 0,
         "library_qualification_days_spent": 0,
         "library_qualification_loading_days_spent": 0,

diff --git a/cardea-server/src/test/resources/testdata/samples.json b/cardea-server/src/test/resources/testdata/samples.json
@@ -43,6 +43,7 @@
     "requisitioned": true,
     "requisition_id": 512,
     "qcable_type": "receipt_inspection",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -98,6 +99,7 @@
     "requisitioned": true,
     "requisition_id": 512,
     "qcable_type": "receipt_inspection",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -153,6 +155,7 @@
     "requisitioned": true,
     "requisition_id": 512,
     "qcable_type": "receipt_inspection",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -208,6 +211,7 @@
     "requisitioned": true,
     "requisition_id": 512,
     "qcable_type": "receipt_inspection",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -263,6 +267,7 @@
     "requisitioned": true,
     "requisition_id": 512,
     "qcable_type": "receipt_inspection",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -318,6 +323,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "extraction",
+    "transfer_date": "2021-07-19T19:01:38-04:00",
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -373,6 +379,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_preparation",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -428,6 +435,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_qualification",
+    "transfer_date": null,
     "mean_insert": 303.2,
     "clusters_per_sample": 116636,
     "preliminary_clusters_per_sample": null,
@@ -480,6 +488,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_qualification",
+    "transfer_date": null,
     "mean_insert": 298.9,
     "clusters_per_sample": 150570,
     "preliminary_clusters_per_sample": null,
@@ -535,6 +544,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "full_depth_sequencing",
+    "transfer_date": null,
     "mean_insert": 311.2,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -590,6 +600,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "extraction",
+    "transfer_date": "2021-07-19T19:56:00-04:00",
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -645,6 +656,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_preparation",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -700,6 +712,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_preparation",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -755,6 +768,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_qualification",
+    "transfer_date": null,
     "mean_insert": null,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -810,6 +824,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_qualification",
+    "transfer_date": null,
     "mean_insert": 325.9,
     "clusters_per_sample": 41082,
     "preliminary_clusters_per_sample": null,
@@ -865,6 +880,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "library_qualification",
+    "transfer_date": null,
     "mean_insert": 321.6,
     "clusters_per_sample": 190218,
     "preliminary_clusters_per_sample": null,
@@ -920,6 +936,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "full_depth_sequencing",
+    "transfer_date": null,
     "mean_insert": 780.5,
     "clusters_per_sample": 152050691,
     "preliminary_clusters_per_sample": null,
@@ -975,6 +992,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "full_depth_sequencing",
+    "transfer_date": null,
     "mean_insert": 342.1,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -1030,6 +1048,7 @@
     "requisitioned": false,
     "requisition_id": 512,
     "qcable_type": "full_depth_sequencing",
+    "transfer_date": null,
     "mean_insert": 342.1,
     "clusters_per_sample": null,
     "preliminary_clusters_per_sample": null,
@@ -1084,6 +1103,7 @@
     "ghost": false,
     "requisitioned": false,
     "requisition_id": 512,
+    "transfer_date": null,
     "qcable_type": "extraction",
     "mean_insert": null,
     "clusters_per_sample": null,

diff --git a/changes/add_sample_transferTime.md b/changes/add_sample_transferTime.md
@@ -0,0 +1 @@
+Sample transferDate field for extractions
diff --git a/changes/add_transferSubstep.md b/changes/add_transferSubstep.md
@@ -0,0 +1 @@
+Test fields for extraction TAT breakdown of days spent on preparation, QC, and transfer