[GLT-3983] model changes for dimsum

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

@@ -5,10 +5,13 @@
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Assay
  */
+@JsonDeserialize(builder = Assay.Builder.class)
 public class Assay {
 
   private final String description;
@@ -22,9 +25,10 @@ public Assay(Builder builder) {
     this.name = requireNonNull(builder.name);
     this.description = builder.description;
     this.version = requireNonNull(builder.version);
-    Map<MetricCategory, List<MetricSubcategory>> tempMap = builder.metricCategories.entrySet().stream()
-        .collect(Collectors.toMap(entry -> entry.getKey(),
-            entry -> Collections.unmodifiableList(entry.getValue())));
+    Map<MetricCategory, List<MetricSubcategory>> tempMap =
+        builder.metricCategories.entrySet().stream()
+            .collect(Collectors.toMap(entry -> entry.getKey(),
+                entry -> Collections.unmodifiableList(entry.getValue())));
     this.metricCategories = Collections.unmodifiableMap(tempMap);
   }
 
@@ -48,6 +52,7 @@ public String getVersion() {
     return version;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private String description;

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

@@ -12,10 +12,13 @@
 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;
 
 /**
  * Immutable case
  */
+@JsonDeserialize(builder = Case.Builder.class)
 public class Case {
 
   private final Assay assay;
@@ -36,16 +39,21 @@ private Case(Builder builder) {
     this.id = requireNonNull(builder.id);
     this.donor = requireNonNull(builder.donor);
     this.projects = unmodifiableSet(builder.projects);
-    this.assay = requireNonNull(builder.assay);
-    this.assayId = this.assay.getId();
+    this.assay = builder.assay;
+    if (this.assay != null) {
+      this.assayId = this.assay.getId();
+    } else {
+      this.assayId = builder.assayId;
+    }
     this.tissueOrigin = requireNonNull(builder.tissueOrigin);
     this.tissueType = requireNonNull(builder.tissueType);
     this.timepoint = builder.timepoint;
     this.receipts = unmodifiableList(builder.receipts);
     this.tests = unmodifiableList(builder.tests);
     this.requisition = builder.requisition;
     this.startDate = builder.receipts.stream()
-        .filter(sample -> sample.getRequisitionId().longValue() == builder.requisition.getId())
+        .filter(sample -> sample.getRequisitionId() != null
+            && sample.getRequisitionId().longValue() == builder.requisition.getId())
         .map(Sample::getCreatedDate)
         .min(LocalDate::compareTo).orElse(null);
     this.latestActivityDate = Stream
@@ -114,9 +122,11 @@ public boolean isStopped() {
     return requisition.isStopped();
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private Assay assay;
+    private long assayId;
     private Donor donor;
     private String id;
     private Set<Project> projects;
@@ -127,13 +137,18 @@ public static class Builder {
     private String tissueOrigin;
     private String tissueType;
 
+    public Case build() {
+      return new Case(this);
+    }
+
     public Builder assay(Assay assay) {
       this.assay = assay;
       return this;
     }
 
-    public Case build() {
-      return new Case(this);
+    public Builder assayId(long assayId) {
+      this.assayId = assayId;
+      return this;
     }
 
     public Builder donor(Donor donor) {

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

@@ -1,10 +1,13 @@
 package ca.on.oicr.gsi.cardea.data;
 
 import static java.util.Objects.requireNonNull;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Donor
  */
+@JsonDeserialize(builder = Donor.Builder.class)
 public class Donor {
 
   private final String externalName;
@@ -29,6 +32,7 @@ public String getName() {
     return name;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private String externalName;

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

@@ -2,10 +2,13 @@
 
 import java.math.BigDecimal;
 import java.util.Objects;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Lane
  */
+@JsonDeserialize(builder = Lane.Builder.class)
 public class Lane {
 
   private final Long clustersPf;
@@ -48,6 +51,7 @@ public BigDecimal getPercentPfixRead2() {
     return percentPfixRead2;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private Long clustersPf;

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

@@ -3,10 +3,13 @@
 import static java.util.Objects.requireNonNull;
 
 import java.math.BigDecimal;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Metric
  */
+@JsonDeserialize(builder = Metric.Builder.class)
 public class Metric {
 
   private final String containerModel;
@@ -97,6 +100,7 @@ public boolean isNegateTissueType() {
     return negateTissueType;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private String containerModel;

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

@@ -2,10 +2,13 @@
 
 import java.util.Collections;
 import java.util.List;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable MetricSubcategory
  */
+@JsonDeserialize(builder = MetricSubcategory.Builder.class)
 public class MetricSubcategory {
 
   private final String libraryDesignCode;
@@ -36,6 +39,7 @@ public Integer getSortPriority() {
     return sortPriority;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private String libraryDesignCode;

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

@@ -3,10 +3,13 @@
 import static java.util.Objects.requireNonNull;
 
 import java.time.LocalDate;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable OmittedSample
  */
+@JsonDeserialize(builder = OmittedSample.Builder.class)
 public class OmittedSample {
 
   private final Long assayId;
@@ -61,6 +64,7 @@ public String getRequisitionName() {
     return requisitionName;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private LocalDate createdDate;

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

@@ -1,10 +1,13 @@
 package ca.on.oicr.gsi.cardea.data;
 
 import static java.util.Objects.requireNonNull;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Project
  */
+@JsonDeserialize(builder = Project.Builder.class)
 public class Project {
 
   private final String name;
@@ -23,6 +26,7 @@ public String getPipeline() {
     return pipeline;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private String name;

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

@@ -9,10 +9,13 @@
 import java.util.Objects;
 import java.util.function.Function;
 import java.util.stream.Stream;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Requisition
  */
+@JsonDeserialize(builder = Requisition.Builder.class)
 public class Requisition {
 
   private final Long assayId;
@@ -35,11 +38,14 @@ private Requisition(Builder builder) {
     this.qcGroups = builder.qcGroups == null ? emptyList() : unmodifiableList(builder.qcGroups);
     this.informaticsReviews = builder.informaticsReviews == null ? emptyList()
         : unmodifiableList(builder.informaticsReviews);
-    this.draftReports = builder.draftReports == null ? emptyList() : unmodifiableList(builder.draftReports);
-    this.finalReports = builder.finalReports == null ? emptyList() : unmodifiableList(builder.finalReports);
-    this.latestActivityDate = Stream.of(informaticsReviews.stream(), draftReports.stream(), finalReports.stream())
-        .flatMap(Function.identity()).map(RequisitionQc::getQcDate).max(LocalDate::compareTo)
-        .orElse(null);
+    this.draftReports =
+        builder.draftReports == null ? emptyList() : unmodifiableList(builder.draftReports);
+    this.finalReports =
+        builder.finalReports == null ? emptyList() : unmodifiableList(builder.finalReports);
+    this.latestActivityDate =
+        Stream.of(informaticsReviews.stream(), draftReports.stream(), finalReports.stream())
+            .flatMap(Function.identity()).map(RequisitionQc::getQcDate).max(LocalDate::compareTo)
+            .orElse(null);
   }
 
   @Override
@@ -99,6 +105,7 @@ public boolean isStopped() {
     return stopped;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private Long assayId;

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

@@ -3,10 +3,13 @@
 import static java.util.Objects.requireNonNull;
 
 import java.time.LocalDate;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable RequisitionQc
  */
+@JsonDeserialize(builder = RequisitionQc.Builder.class)
 public class RequisitionQc {
 
   private final LocalDate qcDate;
@@ -31,6 +34,7 @@ public boolean isQcPassed() {
     return qcPassed;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private LocalDate qcDate;

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

@@ -3,10 +3,13 @@
 import static java.util.Objects.requireNonNull;
 
 import java.math.BigDecimal;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable RequisitionQcGroup
  */
+@JsonDeserialize(builder = RequisitionQcGroup.Builder.class)
 public class RequisitionQcGroup {
 
   private final BigDecimal callability;
@@ -61,6 +64,7 @@ public String getTissueType() {
     return tissueType;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private BigDecimal callability;

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

@@ -6,10 +6,13 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Objects;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Run
  */
+@JsonDeserialize(builder = Run.Builder.class)
 public class Run {
 
   private final Long clustersPf;
@@ -138,6 +141,7 @@ public int hashCode() {
     return Objects.hash(id);
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private Long clustersPf;

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

@@ -5,10 +5,13 @@
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable RunAndLibraries
  */
+@JsonDeserialize(builder = RunAndLibraries.Builder.class)
 public class RunAndLibraries {
 
   private Set<Sample> fullDepthSequencings;
@@ -33,6 +36,7 @@ public Run getRun() {
     return run;
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private Set<Sample> fullDepthSequencings = new HashSet<>();

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

@@ -5,10 +5,13 @@
 import java.time.LocalDate;
 import java.util.Objects;
 import java.util.stream.Stream;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 
 /**
  * Immutable Sample
  */
+@JsonDeserialize(builder = Sample.Builder.class)
 public class Sample {
 
   private final Long assayId;
@@ -317,6 +320,7 @@ public int hashCode() {
     return Objects.hash(id, run, sequencingLane);
   }
 
+  @JsonPOJOBuilder(withPrefix = "")
   public static class Builder {
 
     private Integer clustersPerSample;