Gp 4415.detailed case format

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

@@ -0,0 +1,167 @@
+package ca.on.oicr.gsi.cardea.data;
+
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
+
+import java.time.*;
+import java.util.Optional;
+import java.util.Set;
+
+import static java.util.Collections.unmodifiableSet;
+import static java.util.Objects.requireNonNull;
+
+/**
+ * Immutable ShesmuCase
+ */
+@JsonDeserialize(builder = ShesmuDetailedCase.Builder.class)
+public class ShesmuDetailedCase {
+
+  private final String assayName;
+  private final String assayVersion;
+  private final String caseIdentifier;
+  private final CaseStatus caseStatus;
+  private final boolean stopped;
+  private final boolean paused;
+  private final Optional<Instant> completedDate;
+  private final long requisitionId;
+  private final String requisitionName;
+  private final Set<ShesmuSequencing> sequencing;
+
+  private ShesmuDetailedCase(Builder builder) {
+    this.assayName = requireNonNull(builder.assayName);
+    this.assayVersion = requireNonNull(builder.assayVersion);
+    this.caseIdentifier = requireNonNull(builder.caseIdentifier);
+    this.caseStatus = requireNonNull(builder.caseStatus);
+    this.completedDate = builder.completedDate;
+    this.stopped = builder.stopped;
+    this.paused = builder.paused;
+    this.requisitionId = requireNonNull(builder.requisitionId);
+    this.requisitionName = requireNonNull(builder.requisitionName);
+    this.sequencing = unmodifiableSet(requireNonNull(builder.sequencing));
+  }
+
+  public String getAssayName() {
+    return assayName;
+  }
+
+  public String getAssayVersion() {
+    return assayVersion;
+  }
+
+  public String getCaseIdentifier() {
+    return caseIdentifier;
+  }
+
+  public CaseStatus getCaseStatus() {
+    return caseStatus;
+  }
+
+  public boolean isStopped() {
+    return stopped;
+  }
+
+  public boolean isPaused() {
+    return paused;
+  }
+
+  public Optional<Instant> getCompletedDate() {
+    return completedDate;
+  }
+
+  public long getRequisitionId() {
+    return requisitionId;
+  }
+
+  public String getRequisitionName() {
+    return requisitionName;
+  }
+
+  public Set<ShesmuSequencing> getSequencing() {
+    return sequencing;
+  }
+
+  @JsonPOJOBuilder(withPrefix = "")
+  public static class Builder {
+
+    private String assayName;
+    private String assayVersion;
+    private String caseIdentifier;
+    private CaseStatus caseStatus;
+    private boolean paused;
+    private boolean stopped;
+    private Optional<Instant> completedDate;
+    private long requisitionId;
+    private String requisitionName;
+    private Set<ShesmuSequencing> sequencing;
+
+    public ShesmuDetailedCase build() {
+      return new ShesmuDetailedCase(this);
+    }
+
+    public Builder assayName(String assayName) {
+      this.assayName = assayName;
+      return this;
+    }
+
+    public Builder assayVersion(String assayVersion) {
+      this.assayVersion = assayVersion;
+      return this;
+    }
+
+    public Builder caseStatus(CaseStatus caseStatus) {
+      this.caseStatus = caseStatus;
+      return this;
+    }
+
+    public Builder paused(boolean paused) {
+      this.paused = paused;
+      return this;
+    }
+
+    public Builder stopped(boolean stopped) {
+      this.stopped = stopped;
+      return this;
+    }
+
+    public Builder caseIdentifier(String caseIdentifier) {
+      this.caseIdentifier = caseIdentifier;
+      return this;
+    }
+
+    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;
+    }
+
+    public Builder requisitionId(long requisitionId) {
+      this.requisitionId = requisitionId;
+      return this;
+    }
+
+    public Builder requisitionName(String requisitionName) {
+      this.requisitionName = requisitionName;
+      return this;
+    }
+
+    public Builder sequencing(Set<ShesmuSequencing> sequencing){
+      this.sequencing = sequencing;
+      return this;
+    }
+
+    private Optional<Instant> convertCompletedDate(LocalDate completedDate) {
+      if (completedDate == null) {
+        return Optional.empty();
+      }
+      return Optional.of(
+          ZonedDateTime.of(
+              completedDate,
+              LocalTime.MIDNIGHT,
+              ZoneId.of("UTC")).toInstant());
+    }
+  }
+}

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

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+package ca.on.oicr.gsi.cardea.data;
+
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
+
+import java.util.Set;
+
+import static java.util.Collections.unmodifiableSet;
+import static java.util.Objects.requireNonNull;
+
+/**
+ * Immutable Test
+ */
+@JsonDeserialize(builder = ShesmuSample.Builder.class)
+public class ShesmuSample {
+
+  private final String id;
+  private final boolean supplemental;
+
+
+  private ShesmuSample(Builder builder) {
+    this.id = requireNonNull(builder.id);
+    this.supplemental = requireNonNull(builder.supplemental);
+  }
+
+
+  public String getId() {
+    return id;
+  }
+
+  public Boolean isSupplemental() {
+    return supplemental;
+  }
+
+
+
+  @JsonPOJOBuilder(withPrefix = "")
+  public static class Builder {
+
+    private String id;
+    private boolean supplemental;
+
+    public ShesmuSample build() {
+      return new ShesmuSample(this);
+    }
+
+
+    public Builder id(String id) {
+      this.id = id;
+      return this;
+    }
+
+    public Builder supplemental(boolean supplemental) {
+      this.supplemental = supplemental;
+      return this;
+    }
+
+  }
+}

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

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+package ca.on.oicr.gsi.cardea.data;
+
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
+
+import java.util.Set;
+
+import static java.util.Collections.*;
+import static java.util.Objects.requireNonNull;
+
+/**
+ * Immutable Test
+ */
+@JsonDeserialize(builder = ShesmuSequencing.Builder.class)
+public class ShesmuSequencing {
+
+  private final String test;
+  private final MetricCategory type;
+  private final Set<ShesmuSample> limsIds;
+  private final boolean complete;
+
+
+  private ShesmuSequencing(Builder builder) {
+    this.test = requireNonNull(builder.test);
+    this.type = requireNonNull(builder.type);
+    this.limsIds = unmodifiableSet(requireNonNull(builder.limsIds));
+    this.complete = requireNonNull(builder.complete);
+  }
+
+
+  public String getTest() {
+    return test;
+  }
+
+  public MetricCategory getType() {
+    return type;
+  }
+
+  public Set<ShesmuSample> getLimsIds() {
+    return limsIds;
+  }
+
+  public Boolean isComplete() {
+    return complete;
+  }
+
+
+
+  @JsonPOJOBuilder(withPrefix = "")
+  public static class Builder {
+
+    private String test;
+    private Set<ShesmuSample> limsIds;
+    private MetricCategory type;
+    private boolean complete;
+
+    public ShesmuSequencing build() {
+      return new ShesmuSequencing(this);
+    }
+
+    public Builder test(String test) {
+      this.test = test;
+      return this;
+    }
+
+    public Builder type(MetricCategory type) {
+      this.type = type;
+      return this;
+    }
+
+    public Builder limsIds(Set<ShesmuSample> limsIds) {
+      this.limsIds = limsIds;
+      return this;
+    }
+
+    public Builder complete(boolean complete) {
+      this.complete = complete;
+      return this;
+    }
+
+  }
+}