[GLT-4012] added assay turn-around time targets (#35)

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

@@ -19,6 +19,7 @@ public class Assay {
   private final Map<MetricCategory, List<MetricSubcategory>> metricCategories;
   private final String name;
   private final String version;
+  private final AssayTargets targets;
 
   public Assay(Builder builder) {
     this.id = requireNonNull(builder.id);
@@ -30,6 +31,7 @@ public Assay(Builder builder) {
             .collect(Collectors.toMap(entry -> entry.getKey(),
                 entry -> Collections.unmodifiableList(entry.getValue())));
     this.metricCategories = Collections.unmodifiableMap(tempMap);
+    this.targets = requireNonNull(builder.targets);
   }
 
   public String getDescription() {
@@ -52,6 +54,10 @@ public String getVersion() {
     return version;
   }
 
+  public AssayTargets getTargets() {
+    return targets;
+  }
+
   @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
@@ -60,6 +66,7 @@ public static class Builder {
     private Map<MetricCategory, List<MetricSubcategory>> metricCategories;
     private String name;
     private String version;
+    private AssayTargets targets;
 
     public Assay build() {
       return new Assay(this);
@@ -90,6 +97,11 @@ public Builder version(String version) {
       return this;
     }
 
+    public Builder targets(AssayTargets targets) {
+      this.targets = targets;
+      return this;
+    }
+
   }
 
 }

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

@@ -0,0 +1,134 @@
+package ca.on.oicr.gsi.cardea.data;
+
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
+
+/**
+ * Immutable Assay Targets
+ */
+@JsonDeserialize(builder = AssayTargets.Builder.class)
+public class AssayTargets {
+
+  private final Integer caseDays;
+  private final Integer receiptDays;
+  private final Integer extractionDays;
+  private final Integer libraryPreparationDays;
+  private final Integer libraryQualificationDays;
+  private final Integer fullDepthSequencingDays;
+  private final Integer analysisReviewDays;
+  private final Integer releaseApprovalDays;
+  private final Integer releaseDays;
+
+  private AssayTargets(Builder builder) {
+    this.caseDays = builder.caseDays;
+    this.receiptDays = builder.receiptDays;
+    this.extractionDays = builder.extractionDays;
+    this.libraryPreparationDays = builder.libraryPreparationDays;
+    this.libraryQualificationDays = builder.libraryQualificationDays;
+    this.fullDepthSequencingDays = builder.fullDepthSequencingDays;
+    this.analysisReviewDays = builder.analysisReviewDays;
+    this.releaseApprovalDays = builder.releaseApprovalDays;
+    this.releaseDays = builder.releaseDays;
+  }
+
+  public Integer getCaseDays() {
+    return caseDays;
+  }
+
+  public Integer getReceiptDays() {
+    return receiptDays;
+  }
+
+  public Integer getExtractionDays() {
+    return extractionDays;
+  }
+
+  public Integer getLibraryPreparationDays() {
+    return libraryPreparationDays;
+  }
+
+  public Integer getLibraryQualificationDays() {
+    return libraryQualificationDays;
+  }
+
+  public Integer getFullDepthSequencingDays() {
+    return fullDepthSequencingDays;
+  }
+
+  public Integer getAnalysisReviewDays() {
+    return analysisReviewDays;
+  }
+
+  public Integer getReleaseApprovalDays() {
+    return releaseApprovalDays;
+  }
+
+  public Integer getReleaseDays() {
+    return releaseDays;
+  }
+
+  @JsonPOJOBuilder(withPrefix = "")
+  public static class Builder {
+
+    private Integer caseDays;
+    private Integer receiptDays;
+    private Integer extractionDays;
+    private Integer libraryPreparationDays;
+    private Integer libraryQualificationDays;
+    private Integer fullDepthSequencingDays;
+    private Integer analysisReviewDays;
+    private Integer releaseApprovalDays;
+    private Integer releaseDays;
+
+    public Builder caseDays(Integer caseDays) {
+      this.caseDays = caseDays;
+      return this;
+    }
+
+    public Builder receiptDays(Integer receiptDays) {
+      this.receiptDays = receiptDays;
+      return this;
+    }
+
+    public Builder extractionDays(Integer extractionDays) {
+      this.extractionDays = extractionDays;
+      return this;
+    }
+
+    public Builder libraryPreparationDays(Integer libraryPreparationDays) {
+      this.libraryPreparationDays = libraryPreparationDays;
+      return this;
+    }
+
+    public Builder libraryQualificationDays(Integer libraryQualificationDays) {
+      this.libraryQualificationDays = libraryQualificationDays;
+      return this;
+    }
+
+    public Builder fullDepthSequencingDays(Integer fullDepthSequencingDays) {
+      this.fullDepthSequencingDays = fullDepthSequencingDays;
+      return this;
+    }
+
+    public Builder analysisReviewDays(Integer analysisReviewDays) {
+      this.analysisReviewDays = analysisReviewDays;
+      return this;
+    }
+
+    public Builder releaseApprovalDays(Integer releaseApprovalDays) {
+      this.releaseApprovalDays = releaseApprovalDays;
+      return this;
+    }
+
+    public Builder releaseDays(Integer releaseDays) {
+      this.releaseDays = releaseDays;
+      return this;
+    }
+
+    public AssayTargets build() {
+      return new AssayTargets(this);
+    }
+
+  }
+
+}

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

@@ -11,7 +11,6 @@
 import java.util.function.Function;
 import java.util.stream.Stream;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 

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

@@ -1,6 +1,7 @@
 package ca.on.oicr.gsi.cardea.server;
 
 import ca.on.oicr.gsi.cardea.data.Assay;
+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.Donor;
@@ -199,6 +200,7 @@ protected Map<Long, Assay> loadAssays(FileReader fileReader)
         .description(parseString(json, "description", false))
         .version(parseString(json, "version", true))
         .metricCategories(parseMetricCategories(json.get("metric_categories")))
+        .targets(parseAssayTargets(json.get("targets")))
         .build());
     return assays.stream().collect(Collectors.toMap(Assay::getId, Function.identity()));
   }
@@ -650,6 +652,22 @@ private List<Metric> parseMetrics(JsonNode json) throws DataParseException {
     return metrics;
   }
 
+  private AssayTargets parseAssayTargets(JsonNode json) throws DataParseException {
+    AssayTargets.Builder builder = new AssayTargets.Builder();
+    if (json != null && json.isObject()) {
+      builder.caseDays(parseInteger(json, "case_days", false))
+          .receiptDays(parseInteger(json, "receipt_days", false))
+          .extractionDays(parseInteger(json, "extraction_days", false))
+          .libraryPreparationDays(parseInteger(json, "library_preparation_days", false))
+          .libraryQualificationDays(parseInteger(json, "library_qualification_days", false))
+          .fullDepthSequencingDays(parseInteger(json, "full_depth_sequencing_days", false))
+          .analysisReviewDays(parseInteger(json, "analysis_review_days", false))
+          .releaseApprovalDays(parseInteger(json, "release_approval_days", false))
+          .releaseDays(parseInteger(json, "release_days", false));
+    }
+    return builder.build();
+  }
+
   private Set<Project> parseProjects(JsonNode json, String fieldName,
       Map<String, Project> projectsByName) throws DataParseException {
     JsonNode projectsNode = json.get(fieldName);

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

@@ -5,6 +5,7 @@
 import static org.mockito.Mockito.when;
 
 import ca.on.oicr.gsi.cardea.data.Assay;
+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.Donor;
@@ -166,6 +167,17 @@ public void testLoadAssays() throws Exception {
           .orElse(null);
       assertNotNull(metric);
       assertEquals(new BigDecimal("0.7"), metric.getMinimum());
+      AssayTargets targets = assay.getTargets();
+      assertNotNull(targets);
+      assertEquals(Integer.valueOf(45), targets.getCaseDays());
+      assertEquals(Integer.valueOf(2), targets.getReceiptDays());
+      assertEquals(Integer.valueOf(3), targets.getExtractionDays());
+      assertEquals(Integer.valueOf(3), targets.getLibraryPreparationDays());
+      assertEquals(Integer.valueOf(4), targets.getLibraryQualificationDays());
+      assertEquals(Integer.valueOf(7), targets.getFullDepthSequencingDays());
+      assertEquals(Integer.valueOf(2), targets.getAnalysisReviewDays());
+      assertEquals(Integer.valueOf(3), targets.getReleaseApprovalDays());
+      assertEquals(Integer.valueOf(3), targets.getReleaseDays());
     }
   }
 

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

@@ -933,6 +933,17 @@
           ]
         }
       ]
+    },
+    "targets": {
+      "case_days": 45,
+      "receipt_days": 2,
+      "extraction_days": 3,
+      "library_preparation_days": 3,
+      "library_qualification_days": 4,
+      "full_depth_sequencing_days": 7,
+      "analysis_review_days": 2,
+      "release_approval_days": 3,
+      "release_days": 3
     }
   }
 ]

changes/add_tatTargets.md

@@ -0,0 +1 @@
+Assay turn-around time targets