Specimen script fnusa

src/main/groovy/projects/patientfinder/freeTextDiagnosticReport.groovy

@@ -1,12 +1,12 @@
 package projects.patientfinder
 
-
 import de.kairos.fhir.centraxx.metamodel.Episode
 import de.kairos.fhir.centraxx.metamodel.LaborFindingLaborValue
 import de.kairos.fhir.centraxx.metamodel.LaborMethod
 import de.kairos.fhir.centraxx.metamodel.LaborValue
 import de.kairos.fhir.centraxx.metamodel.MultilingualEntry
 import de.kairos.fhir.centraxx.metamodel.PrecisionDate
+import de.kairos.fhir.centraxx.metamodel.enums.LaborMappingType
 import de.kairos.fhir.centraxx.metamodel.enums.LaborValueDType
 import org.hl7.fhir.r4.model.DiagnosticReport
 
@@ -15,7 +15,6 @@ import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.PSN
 import static de.kairos.fhir.centraxx.metamodel.CrfTemplateField.LABOR_VALUE
 import static de.kairos.fhir.centraxx.metamodel.LaborFindingLaborValue.CRF_TEMPLATE_FIELD
 import static de.kairos.fhir.centraxx.metamodel.RootEntities.laborMapping
-
 /**
  * represented by CXX LaborMapping
  * @author Mike Wähnert
@@ -49,6 +48,12 @@ diagnosticReport {
 
   id = "DiagnosticReport/" + context.source[laborMapping().laborFinding().id()]
 
+  if (context.source[laborMapping().mappingType()].toString().equalsIgnoreCase(LaborMappingType.SAMPLELABORMAPPING.toString())) {
+    specimen {
+      reference = "Specimen/" + context.source[laborMapping().relatedOid()]
+    }
+  }
+
   identifier {
     system = "urn:centraxx"
     value = context.source[laborMapping().laborFinding().laborFindingId()]

src/main/groovy/projects/patientfinder/freeTextFilteredObservation.groovy

@@ -12,6 +12,7 @@ import de.kairos.fhir.centraxx.metamodel.LaborValue
 import de.kairos.fhir.centraxx.metamodel.LaborValueNumeric
 import de.kairos.fhir.centraxx.metamodel.PrecisionDate
 import de.kairos.fhir.centraxx.metamodel.ValueReference
+import de.kairos.fhir.centraxx.metamodel.enums.LaborMappingType
 import de.kairos.fhir.centraxx.metamodel.enums.LaborValueDType
 import org.hl7.fhir.r4.model.Observation
 
@@ -42,6 +43,12 @@ observation {
     return
   }
 
+  if (context.source[laborMapping().mappingType()].toString().equalsIgnoreCase(LaborMappingType.SAMPLELABORMAPPING.toString())) {
+    specimen {
+      reference = "Specimen/" + context.source[laborMapping().relatedOid()]
+    }
+  }
+
   id = "Observation/" + context.source[laborMapping().laborFinding().id()]
 
   status = Observation.ObservationStatus.UNKNOWN

src/main/groovy/projects/patientfinder/specimen.groovy

@@ -0,0 +1,59 @@
+package projects.patientfinder
+
+import de.kairos.centraxx.fhir.r4.utils.FhirUrls
+import de.kairos.fhir.centraxx.metamodel.AbstractSample
+
+import static de.kairos.fhir.centraxx.metamodel.AbstractCode.CODE
+import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.ID_CONTAINER_TYPE
+import static de.kairos.fhir.centraxx.metamodel.AbstractIdContainer.PSN
+import static de.kairos.fhir.centraxx.metamodel.IdContainerType.DECISIVE
+import static de.kairos.fhir.centraxx.metamodel.RootEntities.sample
+
+specimen {
+
+  id = "Specimen/" + context.source[sample().id()]
+
+  context.source[sample().idContainer()].each { final idContainer ->
+    final boolean isDecisive = idContainer[ID_CONTAINER_TYPE]?.getAt(DECISIVE)
+    if (isDecisive) {
+      identifier {
+        value = idContainer[PSN]
+        type {
+          coding {
+            system = FhirUrls.System.IdContainerType.BASE_URL
+            code = idContainer[ID_CONTAINER_TYPE]?.getAt(CODE)
+          }
+        }
+      }
+    }
+  }
+
+  type {
+    coding {
+      system = FhirUrls.System.Sample.SampleKind.BASE_URL
+      code = context.source[sample().sampleKind()]
+    }
+  }
+
+  subject {
+    reference = "Patient/" + context.source[sample().patientContainer().id()]
+  }
+
+  final def parentSample = context.source[sample().parent()]
+
+  if (parentSample != null){
+    parent {
+      reference = "Specimen/" + parentSample[AbstractSample.ID]
+    }
+  }
+
+  collection {
+    collectedDateTime {
+      date = context.source[sample().samplingDate().date()]
+      quantity {
+        value = context.source[sample().initialAmount().amount()] as Number
+        unit = context.source[sample().initialAmount().unit()]
+      }
+    }
+  }
+}