add in detailed case summary input format to cardea plugin

plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/CaseSummaryDetailedFormatDefinition.java

@@ -0,0 +1,10 @@
+package ca.on.oicr.gsi.shesmu.cardea;
+
+import ca.on.oicr.gsi.shesmu.plugin.input.InputFormat;
+
+public class CaseSummaryDetailedFormatDefinition extends InputFormat {
+
+  public CaseSummaryDetailedFormatDefinition() {
+    super("case_detailed_summary", CaseSummaryDetailedValue.class);
+  }
+}

plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/CaseSummaryDetailedValue.java

@@ -0,0 +1,105 @@
+package ca.on.oicr.gsi.shesmu.cardea;
+
+import ca.on.oicr.gsi.shesmu.plugin.Tuple;
+import ca.on.oicr.gsi.shesmu.plugin.input.ShesmuVariable;
+import java.time.Instant;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class CaseSummaryDetailedValue {
+  private final String assayName;
+  private final String assayVersion;
+  private final String caseIdentifier;
+  private final String caseStatus;
+  private final Optional<Instant> completedDate;
+  private final Set<Tuple> sequencing;
+  private final long requisitionId;
+  private final String requisitionName;
+  private final boolean stopped;
+  private final boolean paused;
+
+  public CaseSummaryDetailedValue(
+      String assayName,
+      String assayVersion,
+      String caseIdentifier,
+      String caseStatus,
+      Optional<Instant> completedDate,
+      Stream<SequencingTestValue> sequencingTestValueStream,
+      long requisitionId,
+      String requisitionName,
+      boolean stopped,
+      boolean paused) {
+    super();
+    this.assayName = assayName;
+    this.assayVersion = assayVersion;
+    this.caseIdentifier = caseIdentifier;
+    this.caseStatus = caseStatus;
+    this.completedDate = completedDate;
+    this.sequencing =
+        sequencingTestValueStream
+            .map(
+                sequencingTest ->
+                    new Tuple(
+                        sequencingTest.test(),
+                        sequencingTest.type(),
+                        sequencingTest.isComplete(),
+                        sequencingTest.limsIds()))
+            .collect(Collectors.toSet());
+    this.requisitionId = requisitionId;
+    this.requisitionName = requisitionName;
+    this.stopped = stopped;
+    this.paused = paused;
+  }
+
+  @ShesmuVariable
+  public String assay_name() {
+    return assayName;
+  }
+
+  @ShesmuVariable
+  public String assay_version() {
+    return assayVersion;
+  }
+
+  @ShesmuVariable
+  public String case_identifier() {
+    return caseIdentifier;
+  }
+
+  @ShesmuVariable
+  public String case_status() {
+    return caseStatus;
+  }
+
+  @ShesmuVariable
+  public Optional<Instant> completed_date() {
+    return completedDate;
+  }
+
+  @ShesmuVariable(type = "ao4test$stype$sis_complete$blims_ids$ao2lims_id$ssupplemental$b")
+  public Set<Tuple> sequencing() {
+    return sequencing;
+  }
+
+  @ShesmuVariable
+  public long requisition_id() {
+    return requisitionId;
+  }
+
+  @ShesmuVariable
+  public String requisition_name() {
+    return requisitionName;
+  }
+
+  @ShesmuVariable
+  public boolean stopped() {
+    return stopped;
+  }
+
+  @ShesmuVariable
+  public boolean paused() {
+    return paused;
+  }
+}

plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/LimsSequencingInfo.java

@@ -0,0 +1,24 @@
+package ca.on.oicr.gsi.shesmu.cardea;
+
+import ca.on.oicr.gsi.shesmu.plugin.input.ShesmuVariable;
+
+public class LimsSequencingInfo {
+  private final String limsId;
+  private final boolean supplemental;
+
+  public LimsSequencingInfo(String limsId, boolean supplemental) {
+    super();
+    this.limsId = limsId;
+    this.supplemental = supplemental;
+  }
+
+  @ShesmuVariable
+  public String limsId() {
+    return limsId;
+  }
+
+  @ShesmuVariable
+  public boolean supplemental() {
+    return supplemental;
+  }
+}

plugin-cardea/src/main/java/ca/on/oicr/gsi/shesmu/cardea/SequencingTestValue.java

@@ -0,0 +1,46 @@
+package ca.on.oicr.gsi.shesmu.cardea;
+
+import ca.on.oicr.gsi.shesmu.plugin.Tuple;
+import ca.on.oicr.gsi.shesmu.plugin.input.ShesmuVariable;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public class SequencingTestValue {
+  private final String test;
+  private final String type;
+  private final Set<Tuple> limsIds;
+  private final boolean isComplete;
+
+  public SequencingTestValue(
+      String test, String type, Stream<LimsSequencingInfo> limsIds, boolean isComplete) {
+    super();
+    this.test = test;
+    this.type = type;
+    this.limsIds =
+        limsIds
+            .map(info -> new Tuple(info.limsId(), info.supplemental()))
+            .collect(Collectors.toSet());
+    this.isComplete = isComplete;
+  }
+
+  @ShesmuVariable
+  public String test() {
+    return test;
+  }
+
+  @ShesmuVariable
+  public String type() {
+    return type;
+  }
+
+  @ShesmuVariable
+  public Set<Tuple> limsIds() {
+    return limsIds;
+  }
+
+  @ShesmuVariable
+  public boolean isComplete() {
+    return isComplete;
+  }
+}

plugin-cardea/src/main/java/module-info.java

@@ -1,3 +1,4 @@
+import ca.on.oicr.gsi.shesmu.cardea.CaseSummaryDetailedFormatDefinition;
 import ca.on.oicr.gsi.shesmu.cardea.CaseSummaryFormatDefinition;
 import ca.on.oicr.gsi.shesmu.plugin.input.InputFormat;
 
@@ -7,5 +8,6 @@
   requires ca.on.oicr.gsi.shesmu;
 
   provides InputFormat with
-      CaseSummaryFormatDefinition;
+      CaseSummaryFormatDefinition,
+      CaseSummaryDetailedFormatDefinition;
 }