Merge pull request #1179 from tadgh/allow-3-to-2-specimen

Allow specimen to be converted from STU3 -> STU2

hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_30.java

@@ -24,33 +24,26 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.commons.codec.binary.Base64;
+import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.instance.model.CodeableConcept;
 import org.hl7.fhir.instance.model.Reference;
+import org.hl7.fhir.instance.model.Resource;
 import org.hl7.fhir.instance.utils.ToolingExtensions;
 import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
-import org.hl7.fhir.dstu3.model.Annotation;
 import org.hl7.fhir.dstu3.model.CapabilityStatement.SystemRestfulInteraction;
-import org.hl7.fhir.dstu3.model.CodeSystem;
-import org.hl7.fhir.dstu3.model.Coding;
 import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
 import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionDesignationComponent;
 import org.hl7.fhir.dstu3.model.CommunicationRequest.CommunicationPriority;
-import org.hl7.fhir.dstu3.model.ConceptMap;
-import org.hl7.fhir.dstu3.model.ContactDetail;
 import org.hl7.fhir.dstu3.model.ConceptMap.ConceptMapGroupComponent;
 import org.hl7.fhir.dstu3.model.ConceptMap.SourceElementComponent;
 import org.hl7.fhir.dstu3.model.DocumentReference.ReferredDocumentStatus;
-import org.hl7.fhir.dstu3.model.Dosage;
-import org.hl7.fhir.dstu3.model.ElementDefinition;
 import org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionSlicingDiscriminatorComponent;
-import org.hl7.fhir.dstu3.model.Enumeration;
 import org.hl7.fhir.dstu3.model.Immunization.ImmunizationPractitionerComponent;
 import org.hl7.fhir.dstu3.model.ReferralRequest.ReferralPriority;
 import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionKind;
 import org.hl7.fhir.dstu3.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.dstu3.model.Timing.EventTiming;
-import org.hl7.fhir.dstu3.model.UriType;
 import org.hl7.fhir.dstu3.terminologies.CodeSystemUtilities;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.Utilities;
@@ -13102,6 +13095,8 @@ public org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionDesignationComponen
       return convertSearchParameter((org.hl7.fhir.dstu3.model.SearchParameter) src);
     if (src instanceof org.hl7.fhir.dstu3.model.Slot)
       return convertSlot((org.hl7.fhir.dstu3.model.Slot) src);
+    if (src instanceof org.hl7.fhir.dstu3.model.Specimen)
+      return convertSpecimen((org.hl7.fhir.dstu3.model.Specimen) src);
     if (src instanceof org.hl7.fhir.dstu3.model.StructureDefinition)
       return convertStructureDefinition((org.hl7.fhir.dstu3.model.StructureDefinition) src);
     if (src instanceof org.hl7.fhir.dstu3.model.Subscription)
@@ -13119,4 +13114,99 @@ public org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionDesignationComponen
     throw new Error("Unknown resource "+src.fhirType());
   }
 
+  private org.hl7.fhir.instance.model.Specimen.SpecimenStatus convertSpecimenStatus(Specimen.SpecimenStatus status) {
+    if (status == null) {
+      return null;
+    }
+    switch(status) {
+      case AVAILABLE: return org.hl7.fhir.instance.model.Specimen.SpecimenStatus.AVAILABLE;
+      case UNAVAILABLE: return org.hl7.fhir.instance.model.Specimen.SpecimenStatus.UNAVAILABLE;
+      case ENTEREDINERROR: return org.hl7.fhir.instance.model.Specimen.SpecimenStatus.ENTEREDINERROR;
+      case UNSATISFACTORY: return org.hl7.fhir.instance.model.Specimen.SpecimenStatus.UNSATISFACTORY;
+      case NULL: return org.hl7.fhir.instance.model.Specimen.SpecimenStatus.NULL;
+      default: return org.hl7.fhir.instance.model.Specimen.SpecimenStatus.NULL;
+    }
+  }
+
+  public org.hl7.fhir.instance.model.Specimen.SpecimenTreatmentComponent convertSpecimenProcessingComponent(org.hl7.fhir.dstu3.model.Specimen.SpecimenProcessingComponent src) throws FHIRException {
+    if (src == null)
+      return null;
+    org.hl7.fhir.instance.model.Specimen.SpecimenTreatmentComponent tgt = new org.hl7.fhir.instance.model.Specimen.SpecimenTreatmentComponent();
+    copyElement(src, tgt);
+    if (src.hasDescription())
+      tgt.setDescription(src.getDescription());
+    if (src.hasProcedure())
+      tgt.setProcedure(convertCodeableConcept(src.getProcedure()));
+    for (org.hl7.fhir.dstu3.model.Reference t : src.getAdditive())
+      tgt.addAdditive(convertReference(t));
+    return tgt;
+  }
+
+  public org.hl7.fhir.instance.model.Specimen.SpecimenContainerComponent convertSpecimenContainerComponent(org.hl7.fhir.dstu3.model.Specimen.SpecimenContainerComponent src) throws FHIRException {
+    if (src == null)
+      return null;
+    org.hl7.fhir.instance.model.Specimen.SpecimenContainerComponent tgt = new org.hl7.fhir.instance.model.Specimen.SpecimenContainerComponent();
+    copyElement(src, tgt);
+    for (org.hl7.fhir.dstu3.model.Identifier t : src.getIdentifier())
+      tgt.addIdentifier(convertIdentifier(t));
+    if (src.hasDescription())
+      tgt.setDescription(src.getDescription());
+    if (src.hasType())
+      tgt.setType(convertCodeableConcept(src.getType()));
+    if (src.hasCapacity())
+      tgt.setCapacity(convertSimpleQuantity(src.getCapacity()));
+    if (src.hasSpecimenQuantity())
+      tgt.setSpecimenQuantity(convertSimpleQuantity(src.getSpecimenQuantity()));
+    if (src.hasAdditive())
+      tgt.setAdditive(convertType(src.getAdditive()));
+    return tgt;
+  }
+  public org.hl7.fhir.instance.model.Specimen.SpecimenCollectionComponent convertSpecimenCollectionComponent(org.hl7.fhir.dstu3.model.Specimen.SpecimenCollectionComponent src) throws FHIRException {
+    if (src == null)
+      return null;
+    org.hl7.fhir.instance.model.Specimen.SpecimenCollectionComponent tgt = new org.hl7.fhir.instance.model.Specimen.SpecimenCollectionComponent();
+    copyElement(src, tgt);
+    if (src.hasCollector())
+      tgt.setCollector(convertReference(src.getCollector()));
+    if (src.hasCollected())
+      tgt.setCollected(convertType(src.getCollected()));
+    if (src.hasQuantity())
+      tgt.setQuantity(convertSimpleQuantity(src.getQuantity()));
+    if (src.hasMethod())
+      tgt.setMethod(convertCodeableConcept(src.getMethod()));
+    if (src.hasBodySite())
+      tgt.setBodySite(convertCodeableConcept(src.getBodySite()));
+    return tgt;
+  }
+
+  private org.hl7.fhir.instance.model.Specimen convertSpecimen(Specimen src) {
+    if (src == null) {
+      return null;
+    }
+    org.hl7.fhir.instance.model.Specimen tgt = new org.hl7.fhir.instance.model.Specimen();
+    copyDomainResource(src, tgt);
+    for (org.hl7.fhir.dstu3.model.Identifier t : src.getIdentifier())
+      tgt.addIdentifier(convertIdentifier(t));
+    if (src.hasAccessionIdentifier())
+      tgt.setAccessionIdentifier(convertIdentifier(src.getAccessionIdentifier()));
+    if (src.hasStatus())
+      tgt.setStatus(convertSpecimenStatus(src.getStatus()));
+    if (src.hasType())
+      tgt.setType(convertCodeableConcept(src.getType()));
+    if (src.hasSubject())
+      tgt.setSubject(convertReference(src.getSubject()));
+    if (src.hasReceivedTime())
+      tgt.setReceivedTime(src.getReceivedTime());
+    for (org.hl7.fhir.dstu3.model.Reference t : src.getParent())
+      tgt.addParent(convertReference(t));
+    if (src.hasCollection())
+      tgt.setCollection(convertSpecimenCollectionComponent(src.getCollection()));
+    for (org.hl7.fhir.dstu3.model.Specimen.SpecimenProcessingComponent t : src.getProcessing())
+      tgt.addTreatment(convertSpecimenProcessingComponent(t));
+    for (org.hl7.fhir.dstu3.model.Specimen.SpecimenContainerComponent t : src.getContainer())
+      tgt.addContainer(convertSpecimenContainerComponent(t));
+    return tgt;
+
+  }
+
 }

hapi-fhir-converter/src/test/java/org/hl7/fhir/convertors/VersionConvertor_10_30Test.java

@@ -2,9 +2,14 @@ package org.hl7.fhir.convertors;
 
 import static org.junit.Assert.assertEquals;
 
+import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.Resource;
 import org.junit.Test;
 
+import java.util.Collections;
+import java.util.Date;
+
 public class VersionConvertor_10_30Test {
 
 	@Test
@@ -22,4 +27,38 @@ public class VersionConvertor_10_30Test {
 		assertEquals("Encounter/123", context);
 	}
 
+	@Test
+	public void testConvertSpecimen() throws FHIRException {
+
+		NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
+		VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
+
+		Specimen spec = new Specimen();
+		CodeableConcept cc = new CodeableConcept();
+		Coding coding = new Coding();
+		coding.setSystem("test_system");
+		coding.setCode("test_code");
+		coding.setDisplay("test_display");
+		cc.addCoding(coding);
+		spec.setType(cc);
+		spec.setId("76c1143a-974a-4dfe-8f1a-4292b02d323d");
+		spec.setReceivedTime(new Date());
+		spec.addExtension().setUrl("testurl!").setValue(new StringType("Yup its an extension"));
+		spec.setSubject(new Reference("Patient/123"));
+		spec.getRequest().add(new Reference("Practitioner/321"));
+		Specimen.SpecimenCollectionComponent specimenCollectionComponent = new Specimen.SpecimenCollectionComponent();
+		specimenCollectionComponent.setCollected(new DateTimeType(new Date()));
+		SimpleQuantity simpleQuantity = new SimpleQuantity();
+		simpleQuantity.setUnit("buckets");
+		simpleQuantity.setValue(1000L);
+
+		specimenCollectionComponent.setQuantity(simpleQuantity);
+		spec.setCollection(specimenCollectionComponent);
+		Specimen.SpecimenContainerComponent specimenContainerComponent = new Specimen.SpecimenContainerComponent();
+		specimenContainerComponent.getExtension().add(new Extension().setUrl("some_url").setValue(new StringType("some_value")));
+		spec.setContainer(Collections.singletonList(specimenContainerComponent));
+		Resource resource = converter.convertResource(spec);
+	}
+
+	
 }