[GLT-4129] added tests for Jackson serial/deserialization (#50)

oicr-gsi · May 3, 2024 · 15d7961 · 15d7961
1 parent 7fa3091
commit 15d7961
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Showing 11 changed files with 878 additions and 32 deletions.
diff --git a/cardea-data/pom.xml b/cardea-data/pom.xml
@@ -23,7 +23,8 @@
         <artifactId>maven-surefire-plugin</artifactId>
         <configuration>
           <!-- explicitly control property locations, so local config is never included -->
-          <argLine>-Dspring.config.location=classpath:/application.yml,classpath:/application-noauth.yml,classpath:/application-test.properties</argLine>
+          <argLine>
+            -Dspring.config.location=classpath:/application.yml,classpath:/application-noauth.yml,classpath:/application-test.properties</argLine>
         </configuration>
         <groupId>org.apache.maven.plugins</groupId>
       </plugin>
@@ -42,9 +43,19 @@
     <dependency>
       <artifactId>javax.annotation-api</artifactId>
       <groupId>javax.annotation</groupId>
-<!--      <scope>provided</scope>-->
       <version>1.3.2</version>
     </dependency>
+
+    <dependency>
+      <artifactId>spring-boot-starter-json</artifactId>
+      <groupId>org.springframework.boot</groupId>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <artifactId>spring-boot-starter-test</artifactId>
+      <groupId>org.springframework.boot</groupId>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
 
-</project>
+</project>
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Assay.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Assay.java
@@ -21,7 +21,7 @@ public class Assay {
   private final String version;
   private final AssayTargets targets;
 
-  public Assay(Builder builder) {
+  private Assay(Builder builder) {
     this.id = requireNonNull(builder.id);
     this.name = requireNonNull(builder.name);
     this.description = builder.description;

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
@@ -3,6 +3,7 @@
 import java.time.LocalDate;
 import java.util.List;
 import java.util.Set;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 
 @JsonDeserialize(as = CaseImpl.class)
@@ -52,6 +53,7 @@ public interface Case {
 
   int getPauseDays();
 
+  @JsonIgnore
   boolean isStopped();
 
 }
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/CaseDeliverableImpl.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/CaseDeliverableImpl.java
@@ -45,13 +45,18 @@ private CaseDeliverableImpl(Builder builder) {
     this.releaseApprovalDaysSpent = builder.releaseApprovalDaysSpent;
     this.releaseDaysSpent = builder.releaseDaysSpent;
     this.deliverableDaysSpent = builder.deliverableDaysSpent;
-    this.latestActivityDate = Stream
-        .concat(
-            releases == null ? Stream.empty() : releases.stream().map(CaseRelease::getQcDate),
-            Stream.of(analysisReviewQcDate, releaseApprovalQcDate))
-        .filter(Objects::nonNull)
-        .max(LocalDate::compareTo)
-        .orElse(null);
+
+    if (builder.latestActivityDate != null) {
+      this.latestActivityDate = builder.latestActivityDate;
+    } else {
+      this.latestActivityDate = Stream
+          .concat(
+              releases == null ? Stream.empty() : releases.stream().map(CaseRelease::getQcDate),
+              Stream.of(analysisReviewQcDate, releaseApprovalQcDate))
+          .filter(Objects::nonNull)
+          .max(LocalDate::compareTo)
+          .orElse(null);
+    }
   }
 
   @Override
@@ -146,6 +151,7 @@ public static class Builder {
     private int releaseApprovalDaysSpent;
     private int releaseDaysSpent;
     private int deliverableDaysSpent;
+    private LocalDate latestActivityDate;
 
     public Builder deliverableType(DeliverableType deliverableType) {
       this.deliverableType = deliverableType;
@@ -217,6 +223,11 @@ public Builder deliverableDaysSpent(int deliverableDaysSpent) {
       return this;
     }
 
+    public Builder latestActivityDate(LocalDate latestActivityDate) {
+      this.latestActivityDate = latestActivityDate;
+      return this;
+    }
+
     public CaseDeliverableImpl build() {
       return new CaseDeliverableImpl(this);
     }

diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/CaseImpl.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/CaseImpl.java
@@ -64,14 +64,18 @@ private CaseImpl(Builder builder) {
     this.requisition = requireNonNull(builder.requisition);
     this.startDate = requireNonNull(builder.startDate);
 
-    this.latestActivityDate = Stream
-        .concat(Stream.of(receipts.stream().map(Sample::getLatestActivityDate),
-            tests.stream().map(Test::getLatestActivityDate))
-            .flatMap(Function.identity()),
-            deliverables == null ? Stream.empty()
-                : deliverables.stream().map(CaseDeliverable::getLatestActivityDate))
-        .filter(Objects::nonNull).max(LocalDate::compareTo)
-        .orElse(null);
+    if (builder.latestActivityDate != null) {
+      this.latestActivityDate = builder.latestActivityDate;
+    } else {
+      this.latestActivityDate = Stream
+          .concat(Stream.of(receipts.stream().map(Sample::getLatestActivityDate),
+              tests.stream().map(Test::getLatestActivityDate))
+              .flatMap(Function.identity()),
+              deliverables == null ? Stream.empty()
+                  : deliverables.stream().map(CaseDeliverable::getLatestActivityDate))
+          .filter(Objects::nonNull).max(LocalDate::compareTo)
+          .orElse(null);
+    }
     this.receiptDaysSpent = builder.receiptDaysSpent;
     this.analysisReviewDaysSpent = builder.analysisReviewDaysSpent;
     this.releaseApprovalDaysSpent = builder.releaseApprovalDaysSpent;
@@ -219,6 +223,7 @@ public static class Builder {
     private int releaseDaysSpent;
     private int caseDaysSpent;
     private int pauseDays;
+    private LocalDate latestActivityDate;
 
     public Case build() {
       return new CaseImpl(this);
@@ -328,5 +333,10 @@ public Builder pauseDays(int days) {
       this.pauseDays = days;
       return this;
     }
+
+    public Builder latestActivityDate(LocalDate latestActivityDate) {
+      this.latestActivityDate = latestActivityDate;
+      return this;
+    }
   }
 }
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/CaseStatus.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/CaseStatus.java
@@ -1,9 +1,18 @@
 package ca.on.oicr.gsi.cardea.data;
 
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonValue;
+
 public enum CaseStatus {
   ACTIVE, COMPLETED, STOPPED;
 
+  @JsonValue
   public String getLabel() {
     return name().toLowerCase();
   }
-}
+
+  @JsonCreator
+  public static CaseStatus fromString(String string) {
+    return string == null ? null : CaseStatus.valueOf(string.toUpperCase());
+  }
+}
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
@@ -118,8 +118,12 @@ private Sample(Builder builder) {
     this.dataReviewUser = builder.dataReviewUser;
     this.dataReviewDate = builder.dataReviewDate;
     this.sequencingLane = builder.sequencingLane;
-    this.latestActivityDate = Stream.of(createdDate, qcDate, dataReviewDate)
-        .filter(Objects::nonNull).max(LocalDate::compareTo).orElseThrow();
+    if (builder.latestActivityDate != null) {
+      this.latestActivityDate = builder.latestActivityDate;
+    } else {
+      this.latestActivityDate = Stream.of(createdDate, qcDate, dataReviewDate)
+          .filter(Objects::nonNull).max(LocalDate::compareTo).orElseThrow();
+    }
   }
 
   @Override
@@ -393,6 +397,7 @@ public static class Builder {
     private BigDecimal relativeCpgInRegions;
     private BigDecimal methylationBeta;
     private Integer peReads;
+    private LocalDate latestActivityDate;
 
     public Sample build() {
       return new Sample(this);
@@ -652,5 +657,10 @@ public Builder peReads(Integer peReads) {
       return this;
     }
 
+    public Builder latestActivityDate(LocalDate latestActivityDate) {
+      this.latestActivityDate = latestActivityDate;
+      return this;
+    }
+
   }
 }
diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/ShesmuCase.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/ShesmuCase.java
@@ -11,16 +11,19 @@
 
 import java.util.Optional;
 import java.util.Set;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable ShesmuCase
  */
+@JsonDeserialize(builder = ShesmuCase.Builder.class)
 public class ShesmuCase {
 
   private final String assayName;
   private final String assayVersion;
   private final String caseIdentifier;
-  private final String caseStatus;
+  private final CaseStatus caseStatus;
   private final Optional<Instant> completedDate;
   private final Set<String> limsIds;
   private final long requisitionId;
@@ -30,7 +33,7 @@ private ShesmuCase(Builder builder) {
     this.assayName = requireNonNull(builder.assayName);
     this.assayVersion = requireNonNull(builder.assayVersion);
     this.caseIdentifier = requireNonNull(builder.caseIdentifier);
-    this.caseStatus = requireNonNull(builder.caseStatus.getLabel());
+    this.caseStatus = requireNonNull(builder.caseStatus);
     this.completedDate = builder.completedDate;
     this.limsIds = unmodifiableSet(requireNonNull(builder.limsIds));
     this.requisitionId = requireNonNull(builder.requisitionId);
@@ -49,7 +52,7 @@ public String getCaseIdentifier() {
     return caseIdentifier;
   }
 
-  public String getCaseStatus() {
+  public CaseStatus getCaseStatus() {
     return caseStatus;
   }
 
@@ -69,6 +72,7 @@ public String getRequisitionName() {
     return requisitionName;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private String assayName;
@@ -104,7 +108,12 @@ public Builder caseIdentifier(String caseIdentifier) {
       return this;
     }
 
-    public Builder completedDate(LocalDate completedDate) {
+    public Builder completedDate(Instant completedDate) {
+      this.completedDate = completedDate == null ? Optional.empty() : Optional.of(completedDate);
+      return this;
+    }
+
+    public Builder completedDateLocal(LocalDate completedDate) {
       this.completedDate = convertCompletedDate(completedDate);
       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
@@ -56,11 +56,17 @@ private Test(Builder builder) {
         : unmodifiableList(builder.libraryQualifications);
     this.fullDepthSequencings = builder.fullDepthSequencings == null ? emptyList()
         : unmodifiableList(builder.fullDepthSequencings);
-    this.latestActivityDate = Stream
-        .of(extractions.stream(), libraryPreparations.stream(), libraryQualifications.stream(),
-            fullDepthSequencings.stream())
-        .flatMap(Function.identity()).map(Sample::getLatestActivityDate).max(LocalDate::compareTo)
-        .orElse(null);
+
+    if (builder.latestActivityDate != null) {
+      this.latestActivityDate = builder.latestActivityDate;
+    } else {
+      this.latestActivityDate = Stream
+          .of(extractions.stream(), libraryPreparations.stream(), libraryQualifications.stream(),
+              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;
@@ -164,6 +170,7 @@ public static class Builder {
     private int libraryPreparationDaysSpent;
     private int libraryQualificationDaysSpent;
     private int fullDepthSequencingDaysSpent;
+    private LocalDate latestActivityDate;
 
     public Test build() {
       return new Test(this);
@@ -258,5 +265,10 @@ public Builder fullDepthSequencingDaysSpent(int days) {
       this.fullDepthSequencingDaysSpent = days;
       return this;
     }
+
+    public Builder latestActivityDate(LocalDate latestActivityDate) {
+      this.latestActivityDate = latestActivityDate;
+      return this;
+    }
   }
 }