org.hl7.fhir.dstu3.model.CodeableConcept Java Examples

@SuppressWarnings("rawtypes")
private String describeValidationParameters(Parameters pin) {
  CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
  for (ParametersParameterComponent p : pin.getParameter()) {
    if (p.hasValue() && p.getValue() instanceof PrimitiveType) {
      b.append(p.getName() + "=" + ((PrimitiveType) p.getValue()).asStringValue());
    } else if (p.hasValue() && p.getValue() instanceof Coding) {
      b.append("system=" + ((Coding) p.getValue()).getSystem());
      b.append("code=" + ((Coding) p.getValue()).getCode());
      b.append("display=" + ((Coding) p.getValue()).getDisplay());
    } else if (p.hasValue() && p.getValue() instanceof CodeableConcept) {
      if (((CodeableConcept) p.getValue()).hasCoding()) {
        Coding c = ((CodeableConcept) p.getValue()).getCodingFirstRep();
        b.append("system=" + c.getSystem());
        b.append("code=" + c.getCode());
        b.append("display=" + c.getDisplay());
      } else if (((CodeableConcept) p.getValue()).hasText()) {
        b.append("text=" + ((CodeableConcept) p.getValue()).getText());
      }
    } else if (p.hasResource() && (p.getResource() instanceof ValueSet)) {
      b.append("valueset=" + getVSSummary((ValueSet) p.getResource()));
    }
  }
  return b.toString();
}
 

public List<ObservationComponent> getComponents(DomainResource resource){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	List<ObservationComponent> components = new ArrayList<>();
	
	for (ObservationComponentComponent o : fhirObservation.getComponent()) {
		ObservationComponent component = new ObservationComponent(o.getId());
		CodeableConcept codeableConcept = o.getCode();
		if (codeableConcept != null) {
			component.setCoding(ModelUtil.getCodingsFromConcept(codeableConcept));
			component.setExtensions(getExtensions(o));
			
			if (o.hasValueQuantity()) {
				Quantity quantity = (Quantity) o.getValue();
				component.setNumericValue(quantity.getValue());
				component.setNumericValueUnit(quantity.getUnit());
			} else if (o.hasValueStringType()) {
				StringType stringType = (StringType) o.getValue();
				component.setStringValue(stringType.getValue());
			}
		}
		components.add(component);
	}
	return components;
}
 

public static OperationOutcomeIssueComponent convertToIssue(ValidationMessage message, OperationOutcome op) {
  OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
  issue.setCode(convert(message.getType()));
  if (message.getLocation() != null) {
    // message location has a fhirPath in it. We need to populate the expression
    issue.addExpression(message.getLocation());
    // also, populate the XPath variant
    StringType s = new StringType();
    s.setValue(Utilities.fhirPathToXPath(message.getLocation())+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
    issue.getLocation().add(s);
  }
  issue.setSeverity(convert(message.getLevel()));
  CodeableConcept c = new CodeableConcept();
  c.setText(message.getMessage());
  issue.setDetails(c);
  if (message.getSource() != null) {
    issue.getExtension().add(ToolingExtensions.makeIssueSource(message.getSource()));
  }
  return issue;
}
 

public void setCategory(DomainResource resource, ObservationCategory category){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	CodeableConcept categoryCode = new CodeableConcept();
	if (category.name().startsWith("SOAP_")) {
		// elexis soap categories
		categoryCode.setCoding(
			Collections.singletonList(new Coding(IdentifierSystem.ELEXIS_SOAP.getSystem(),
				category.getCode(), category.getLocalized())));
	} else {
		org.hl7.fhir.dstu3.model.codesystems.ObservationCategory fhirCategoryCode =
			(org.hl7.fhir.dstu3.model.codesystems.ObservationCategory) categoryMapping
				.getFhirEnumValueByEnum(category);
		if (fhirCategoryCode != null) {
			// lookup matching fhir category
			categoryCode
				.setCoding(Collections.singletonList(new Coding(fhirCategoryCode.getSystem(),
					fhirCategoryCode.toCode(), fhirCategoryCode.getDisplay())));
		} else {
			throw new IllegalStateException("Unknown observation category " + category);
		}
	}
	if (!categoryCode.getCoding().isEmpty()) {
		fhirObservation.setCategory(Collections.singletonList(categoryCode));
	}
}
 

@Test
public void convertCondition20() throws IOException {
	// condition format of HAPI FHIR 2.0
	String oldContent = AllTests.getResourceAsString("/rsc/json/ConditionFormat20.json");
	assertFalse(FindingsFormatUtil.isCurrentFindingsFormat(oldContent));

	Optional<String> newContent = FindingsFormatUtil.convertToCurrentFindingsFormat(oldContent);
	assertTrue(newContent.isPresent());

	IBaseResource resource = AllTests.getJsonParser().parseResource(newContent.get());
	assertTrue(resource instanceof Condition);
	Condition condition = (Condition) resource;

	// category changed from diagnosis to problem-list-item
	List<CodeableConcept> category = condition.getCategory();
	assertFalse(category.isEmpty());
	CodeableConcept code = category.get(0);
	List<Coding> coding = code.getCoding();
	assertFalse(coding.isEmpty());
	assertTrue(coding.get(0).getCode().equals(ConditionCategory.PROBLEMLISTITEM.getCode()));
	// dateRecorded changed to assertedDate
	Date assertedDate = condition.getAssertedDate();
	assertNotNull(assertedDate);
}
 

public CodeableConcept makeCodeableConceptFromCD(Element cv) throws Exception {
		if (cv == null)
			return null;
		CodeableConcept cc = new CodeableConcept();
		cc.addCoding(makeCodingFromCV(cv));
		for (Element e : cda.getChildren(cv, "translation"))
			cc.addCoding(makeCodingFromCV(e));
		if (cda.getChild(cv, "originalText") != null) {
			Element ote = cda.getChild(cv, "originalText");
//			if (cda.getChild(ote, "reference") != null) {
//				if (cda.getChild(ote, "reference").getAttribute("value").startsWith("#")) {
//					Element t = cda.getByXmlId(cda.getChild(ote, "reference").getAttribute("value").substring(1));
//					String ot = t.getTextContent().trim();
//					cc.setText(Utilities.noString(ot) ? null : ot);
//				} else
//					throw new Exception("external references not handled yet "+cda.getChild(ote, "reference").getAttribute("value"));
//			} else {	  		
				String ot = ote.getTextContent().trim();
				cc.setText(Utilities.noString(ot) ? null : ot);
	  	//}  
	  }
	  return cc;
  }
 

public static void main(String[] theArgs) {
Patient pat = new Patient();
pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");

// Add an extension on the resource
pat.addExtension()
		.setUrl("http://hl7.org/fhir/StructureDefinition/patient-importance")
		.setValue(new CodeableConcept().setText("Patient is a VIP"));

// Add an extension on a primitive
pat.getBirthDateElement().setValueAsString("1955-02-22");
pat.getBirthDateElement().addExtension()
		.setUrl("http://hl7.org/fhir/StructureDefinition/patient-birthTime")
		.setValue(new TimeType("23:30"));

    IParser parser = FhirContext.forDstu3().newJsonParser().setPrettyPrint(true);
    System.out.println(parser.encodeResourceToString(pat));
 }
 

private CodeableConcept inspectCode(CodeableConcept cc, Coding def) {
	if (cc != null) {
		for (Coding c : cc.getCoding()) {
			if ("http://snomed.info/sct".equals(c.getSystem())) {
				if ("ASSERTION".equals(c.getCode()))
					c.setSystem("http://hl7.org/fhir/v3/ActCode");
			}
			if ("http://hl7.org/fhir/v3/ActCode".equals(c.getSystem()) && "ASSERTION".equals(c.getCode())) {
				if (def == null)
					throw new Error("need a default code");
				c.setSystem(def.getSystem());
				c.setVersion(def.getVersion());
				c.setCode(def.getCode());
				c.setDisplay(def.getDisplay());
			}
		}
	}
	return cc;
}
 

/**
 * Helper function to convert a Code into a CodeableConcept. Takes an optional system, which
 * replaces the Code.system in the resulting CodeableConcept if not null.
 *
 * @param from The Code to create a CodeableConcept from.
 * @param system The system identifier, such as a URI. Optional; may be null.
 * @return The converted CodeableConcept
 */
private static CodeableConcept mapCodeToCodeableConcept(Code from, String system) {
  CodeableConcept to = new CodeableConcept();
  system = system == null ? null : ExportHelper.getSystemURI(system);
  from.system = ExportHelper.getSystemURI(from.system);

  if (from.display != null) {
    to.setText(from.display);
  }

  Coding coding = new Coding();
  coding.setCode(from.code);
  coding.setDisplay(from.display);
  if (from.system == null) {
    coding.setSystem(system);
  } else {
    coding.setSystem(from.system);
  }

  to.addCoding(coding);

  return to;
}
 

private CodeableConcept makeClassCode(CodeableConcept type, DocumentReference ref) throws Exception {
	CodeableConcept res = new CodeableConcept();
	String cs = type.getCoding().get(0).getCode();
	if (cs.equals("18842-5") || cs.equals("34133-9"))
		return type;
	else if (cs.equals("34111-5")) {
		ref.getFormatCommentsPre().add("The underlying CDA document has the code '34111-5: Evaluation and Management Note' which is incorrect (wrong display/code combination). The type has been preserved even though it's wrong");
		res.addCoding().setSystem("http://loinc.org").setCode("34109-9").setDisplay("Evaluation and management note");
	}
	//		else if (cs.equals("34111-5") || cs.equals("5666"))
	//		  res.addCoding().setSystem("http://loinc.org").setCode("LP173418-7").setDisplay("Note");
	else
		throw new Exception("Uncategorised document type code: "+cs+": "+type.getCoding().get(0).getDisplay());
	return res;

}
 

private void makeDocumentReference(CDAUtilities cda, Convert convert, Element doc, Context context) throws Exception {
	scanSection("document", doc);
	DocumentReference ref = new DocumentReference();
	ref.setId(context.baseId+"-document");
	ref.setMasterIdentifier(convert.makeIdentifierFromII(cda.getChild(doc, "id")));
	ref.setSubject(context.subjectRef);
	ref.setType(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(doc, "code")), null));
	ref.addAuthor(context.authorRef);
	ref.setCreatedElement(convert.makeDateTimeFromTS(cda.getChild(doc, "effectiveTime")));
	ref.setIndexedElement(InstantType.now());
	ref.setStatus(DocumentReferenceStatus.CURRENT);
	ref.addSecurityLabel(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(doc, "confidentialityCode")), null));
	DocumentReferenceContentComponent cnt = ref.addContent();
	cnt.getAttachment().setContentType("application/hl7-v3+xml").setUrl("Binary/"+context.baseId).setLanguage(convertLanguage(cda.getChild(doc, "language")));
	//		for (Element ti : cda.getChildren(doc, "templateId"))
	//			cnt.addFormat().setSystem("urn:oid:1.3.6.1.4.1.19376.1.2.3").setCode(value)("urn:oid:"+ti.getAttribute("root"));
	ref.setContext(new DocumentReferenceContextComponent());
	ref.getContext().setPeriod(convert.makePeriodFromIVL(cda.getChild(cda.getChild(doc, "serviceEvent"), "effectiveTime")));
	for (CodeableConcept cc : context.encounter.getType())
		ref.getContext().addEvent(cc);
	ref.setDescription(cda.getChild(doc, "title").getTextContent());
	ref.setCustodian(new Reference().setReference("Organization/"+processOrganization(cda.getDescendent(doc, "custodian/assignedCustodian/representedCustodianOrganization"), cda, convert, context).getId()));
	Practitioner p = processPerformer(cda, convert, context, cda.getChild(doc, "legalAuthenticator"), "assignedEntity", "assignedPerson");
	ref.setAuthenticator(new Reference().setReference("Practitioner/"+p.getId()).setDisplay(p.getUserString("display")));
	saveResource(ref);
}
 

/**
 * Map the given Media element to a FHIR Media resource, and add it to the given Bundle.
 *
 * @param personEntry    The Entry for the Person
 * @param bundle         Bundle to add the Media to
 * @param encounterEntry Current Encounter entry
 * @param obs   The Observation to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static BundleEntryComponent media(BundleEntryComponent personEntry, Bundle bundle,
    BundleEntryComponent encounterEntry, Observation obs) {
  org.hl7.fhir.dstu3.model.Media mediaResource =
      new org.hl7.fhir.dstu3.model.Media();

  if (obs.codes != null && obs.codes.size() > 0) {
    List<CodeableConcept> reasonList = obs.codes.stream()
        .map(code -> mapCodeToCodeableConcept(code, SNOMED_URI)).collect(Collectors.toList());
    mediaResource.setReasonCode(reasonList);
  }
  
  // Hard code as an image
  mediaResource.setType(DigitalMediaType.PHOTO);
  mediaResource.setSubject(new Reference(personEntry.getFullUrl()));

  Attachment content = (Attachment) obs.value;
  org.hl7.fhir.dstu3.model.Attachment contentResource = new org.hl7.fhir.dstu3.model.Attachment();
  
  contentResource.setContentType(content.contentType);
  contentResource.setLanguage(content.language);
  if (content.data != null) {
    contentResource.setDataElement(new org.hl7.fhir.dstu3.model.Base64BinaryType(content.data));
  }
  contentResource.setUrl(content.url);
  contentResource.setSize(content.size);
  contentResource.setTitle(content.title);
  if (content.hash != null) {
    contentResource.setHashElement(new org.hl7.fhir.dstu3.model.Base64BinaryType(content.hash));
  }
  
  mediaResource.setWidth(content.width);
  mediaResource.setHeight(content.height);
  
  mediaResource.setContent(contentResource);

  return newEntry(bundle, mediaResource);
}
 

@Override
public void call(Row r) throws Exception {

  // Build the claim
  // ---------------

  // CLIENT_ID ....... 0
  // CLIENT_SUB_ID ... 1
  // CLAIM_SK ........ 2
  // CLAIM_NBR ....... 3
  // CLAIM_ADJ_CD,ADJ_FROM_CLAIM_SK,ADJ_FROM_CLAIM_NBR,ADJ_FROM_CLAIM_ADJ_NBR,CLAIM_STS_CD_SK,CLAIM_STS_CD,SYS_SUBSC_SK,SYS_SUBSC_ID,SYS_MBR_SK,SYS_MBR_ID,CLIENT_HIERARCHY_LVL1,CLIENT_HIERARCHY_LVL2,CLIENT_HIERARCHY_LVL3,CLIENT_HIERARCHY_LVL4,MBR_PCP_SK,MBR_PCP_NBR,PROV_SK,PROV_ID,PROV_TP_CD_SK,PROV_TP_CD,PAYEE_SK,PAYEE_ID,PAYEE_TIN,APPROVE_DAY_AMT,ACTUAL_DAY_AMT,CLAIM_BEG_SVC_DT,RECEIVE_DT,PAY_DT,DRG_CD_SK,DRG_CD,SUBMIT_DRG_CD_SK,SUBMIT_DRG_CD,BILL_CLASS_CD,FACILITY_TP_CD,HOSP_FREQ_CD,ADMIT_SRC_CD_SK,ADMIT_SRC_CD,ADMIT_TP_CD_SK,ADMIT_TP_CD,HOSP_ADMIT_DT,HOSP_ADMIT_HR,HOSP_DISCHARGE_DT,HOSP_DISCHARGE_HR,HOSP_DISCHARGE_STS_CD_SK,HOSP_DISCHARGE_STS_CD,ATTENDING_PROV_SK,ATTENDING_PROV_ID,PROV_ADDR_CD_SK,PROV_ADDR_CD,OOA_IND,EDI_REF_ID,CURRENT_IND,SENSTV_DRG_IND,CLIENT_SPECIFIC_TXT1,CLIENT_SPECIFIC_TXT2,CLIENT_SPECIFIC_TXT3,CLIENT_SPECIFIC_TXT4,CLIENT_SPECIFIC_TXT5,CLIENT_SPECIFIC_TXT6,CLIENT_SPECIFIC_TXT7,CLIENT_SPECIFIC_TXT8,CLIENT_SPECIFIC_TXT9,CLIENT_SPECIFIC_TXT10,REC_LOAD_DTTM,REC_LAST_UPD_DTTM,REC_DEL_IND,DRG_CODE_TP_CD,SUBMIT_DRG_CODE_TP_CD,QA_CURRENT_IND
  CodeableConcept cc = new CodeableConcept();
  cc.setUserData("value", r.getString(3)); // TODO check that this is how
                                           // this valued is set here

  Identifier i = new Identifier();
  i.setUse(IdentifierUse.OFFICIAL);
  i.setType(cc);
  i.setSystem("Payer Specific	 Claim Number");
  i.setValue(r.getAs("CLAIM_NBR"));
  // TODO i.setAssigner(value);

  List<Identifier> identifiers = new ArrayList<>();
  identifiers.add(i);

  Claim c = new Claim();
  c.setIdentifier(identifiers);

  // Process/send the claim
  // ----------------------

  // TODO
}
 

public static BaseServerResponseException buildOperationOutcomeException(BaseServerResponseException exception,  org.hl7.fhir.r4.model.OperationOutcome.IssueType issueType) {
    org.hl7.fhir.r4.model.CodeableConcept codeableConcept = new org.hl7.fhir.r4.model.CodeableConcept()
            .setText(exception.getMessage());


    org.hl7.fhir.r4.model.OperationOutcome operationOutcome = new org.hl7.fhir.r4.model.OperationOutcome();

    operationOutcome.addIssue()
            .setSeverity(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.ERROR)
            .setCode(issueType)
            .setDetails(codeableConcept);

     exception.setOperationOutcome(operationOutcome);
    return exception;
}
 

public LibraryBuilder buildType(LibraryType libraryType) {
    CodeableConcept codeableConcept =
            new CodeableConceptBuilder().buildCoding(
                new CodingBuilder()
                        .buildCode(libraryType.getSystem(), libraryType.toCode(), libraryType.getDisplay())
                        .build()
            ).build();
    complexProperty.setType(codeableConcept);

    return this;
}
 

public OperationOutcomeBuilder buildIssue(String severity, String code, String details)
{
    complexProperty.addIssue(
            new OperationOutcome.OperationOutcomeIssueComponent()
                    .setSeverity(OperationOutcome.IssueSeverity.fromCode(severity))
                    .setCode(OperationOutcome.IssueType.fromCode(code))
                    .setDetails(new CodeableConcept().setText(details))
    );

    return this;
}
 

public void setCategory(DomainResource resource, ConditionCategory category){
	org.hl7.fhir.dstu3.model.Condition fhirCondition =
		(org.hl7.fhir.dstu3.model.Condition) resource;
	CodeableConcept categoryCode = new CodeableConcept();
	org.hl7.fhir.dstu3.model.codesystems.ConditionCategory fhirCategoryCode =
		(org.hl7.fhir.dstu3.model.codesystems.ConditionCategory) categoryMapping
			.getFhirEnumValueByEnum(category);
	if (fhirCategoryCode != null) {
		categoryCode
			.setCoding(Collections.singletonList(new Coding(fhirCategoryCode.getSystem(),
				fhirCategoryCode.toCode(), fhirCategoryCode.getDisplay())));
		fhirCondition.setCategory(Collections.singletonList(categoryCode));
	}
}
 

public List<ICoding> getCoding(DomainResource resource){
	org.hl7.fhir.dstu3.model.Condition fhirCondition =
		(org.hl7.fhir.dstu3.model.Condition) resource;
	CodeableConcept codeableConcept = fhirCondition.getCode();
	if (codeableConcept != null) {
		return ModelUtil.getCodingsFromConcept(codeableConcept);
	}
	return Collections.emptyList();
}
 

@Test
public void testContainedResources() throws FHIRException {

  Medication testMedicationOne = (Medication) testMedicationRequest.getContained().get(0);
  String testMedicationOneId = testMedicationOne.getId();
  CodeableConcept testMedicationIngredientItem = testMedicationOne.getIngredientFirstRep()
      .getItemCodeableConcept();

  Medication decodedMedicationOne = (Medication) testMedicationRequestDecoded.getContained()
      .get(0);
  String decodedMedicationOneId = decodedMedicationOne.getId();
  CodeableConcept decodedMedicationOneIngredientItem = decodedMedicationOne
      .getIngredientFirstRep()
      .getItemCodeableConcept();

  Assert.assertEquals(testMedicationOneId, decodedMedicationOneId);
  Assert.assertTrue(decodedMedicationOneIngredientItem.equalsDeep(testMedicationIngredientItem));

  Provenance testProvenance = (Provenance) testMedicationRequest.getContained().get(1);
  String testProvenanceId = testProvenance.getId();

  Provenance decodedProvenance = (Provenance) testMedicationRequestDecoded.getContained().get(1);
  String decodedProvenanceId = decodedProvenance.getId();

  Assert.assertEquals(testProvenanceId, decodedProvenanceId);

  Medication testMedicationTwo = (Medication) testMedicationRequest.getContained().get(2);
  String testMedicationTwoId = testMedicationTwo.getId();

  Medication decodedMedicationTwo = (Medication) testMedicationRequestDecoded.getContained()
      .get(2);
  String decodedMedicationTwoId = decodedMedicationTwo.getId();

  Assert.assertEquals(testMedicationTwoId, decodedMedicationTwoId);
}
 

public static OperationOutcome createErrorOutcome(String display) {
    Coding code = new Coding().setDisplay(display);
    return new OperationOutcome().addIssue(
            new OperationOutcome.OperationOutcomeIssueComponent()
                    .setSeverity(OperationOutcome.IssueSeverity.ERROR)
                    .setCode(OperationOutcome.IssueType.PROCESSING)
                    .setDetails(new CodeableConcept().addCoding(code))
    );
}
 

public static OperationOutcome createOperationOutcome (String message) {
    OperationOutcome outcome = new OperationOutcome();

    outcome.addIssue()
            .setCode(OperationOutcome.IssueType.EXCEPTION)
            .setSeverity(OperationOutcome.IssueSeverity.FATAL)
            .setDiagnostics(message)
            .setDetails(
                    new CodeableConcept().setText(message)
            );
    return outcome;
}
 

/**
 * This is just a convenience method that creates a codeableconcept if one
 * doesn't already exist, and adds a coding to it
 */
public TranslationRequests addCode(String theSystem, String theCode) {
	Validate.notBlank(theSystem, "theSystem must not be null");
	Validate.notBlank(theCode, "theCode must not be null");
	if (getCodeableConcept() == null) {
		setCodeableConcept(new CodeableConcept());
	}
	getCodeableConcept().addCoding(new Coding().setSystem(theSystem).setCode(theCode));
	return this;
}
 

@Override
public List<ICoding> getCoding(){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		org.hl7.fhir.dstu3.model.ProcedureRequest fhirProcedureRequest =
			(org.hl7.fhir.dstu3.model.ProcedureRequest) resource.get();
		CodeableConcept codeableConcept = fhirProcedureRequest.getCode();
		if (codeableConcept != null) {
			return ModelUtil.getCodingsFromConcept(codeableConcept);
		}
	}
	return Collections.emptyList();
}
 

public List<ICoding> getCoding(DomainResource resource){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	CodeableConcept codeableConcept = fhirObservation.getCode();
	if (codeableConcept != null) {
		return ModelUtil.getCodingsFromConcept(codeableConcept);
	}
	return Collections.emptyList();
}
 

/**
 * Returns a new MedicationRequest for testing.
 *
 * @return a FHIR MedicationRequest for testing.
 */
public static MedicationRequest newMedicationRequest() {

  MedicationRequest medicationRequest = new MedicationRequest();

  medicationRequest.setId("test-medication-request");

  CodeableConcept itemCodeableConcept = new CodeableConcept();
  itemCodeableConcept.addCoding()
      .setSystem("http://www.nlm.nih.gov/research/umls/rxnorm")
      .setCode("103109")
      .setDisplay("Vitamin E 3 MG Oral Tablet [Ephynal]")
      .setUserSelected(true);

  medicationRequest.setMedication(itemCodeableConcept);

  medicationRequest
      .setSubject(new Reference("Patient/12345").setDisplay("Here is a display for you."));

  medicationRequest.setDosageInstruction(ImmutableList.of(
      new Dosage().setTiming(new Timing().setRepeat(new TimingRepeatComponent().setCount(10)))));

  medicationRequest
      .setSubstitution(new MedicationRequestSubstitutionComponent().setAllowed(true));

  return medicationRequest;
}
 

/**
 * Returns a new Medication for testing.
 *
 * @return a FHIR Medication for testing.
 */
public static Medication newMedication(String id) {

  Medication medication = new Medication();

  medication.setId(id);

  CodeableConcept itemCodeableConcept = new CodeableConcept();
  itemCodeableConcept.addCoding()
      .setSystem("http://www.nlm.nih.gov/research/umls/rxnorm")
      .setCode("103109")
      .setDisplay("Vitamin E 3 MG Oral Tablet [Ephynal]")
      .setUserSelected(true);

  MedicationIngredientComponent ingredientComponent = new MedicationIngredientComponent();
  ingredientComponent.setItem(itemCodeableConcept);

  medication.addIngredient(ingredientComponent);

  Reference itemReference = new Reference("test-item-reference");

  MedicationPackageContentComponent medicationPackageContentComponent =
      new MedicationPackageContentComponent();
  medicationPackageContentComponent.setItem(itemReference);

  MedicationPackageComponent medicationPackageComponent = new MedicationPackageComponent();
  medicationPackageComponent.addContent(medicationPackageContentComponent);

  medication.setPackage(medicationPackageComponent);

  return medication;
}
 

/**
 * Map the JsonObject for a Supply into a FHIR SupplyDelivery and add it to the Bundle.
 *
 * @param personEntry    The Person entry.
 * @param bundle         Bundle to add to.
 * @param supply         The supplied object to add.
 * @param encounter      The encounter during which the supplies were delivered
 * @return The added Entry.
 */
private static BundleEntryComponent supplyDelivery(BundleEntryComponent personEntry, 
        Bundle bundle, HealthRecord.Supply supply, Encounter encounter) {
 
  SupplyDelivery supplyResource = new SupplyDelivery();
  supplyResource.setStatus(SupplyDeliveryStatus.COMPLETED);
  supplyResource.setPatient(new Reference(personEntry.getFullUrl()));
  
  CodeableConcept type = new CodeableConcept();
  type.addCoding()
    .setCode("device")
    .setDisplay("Device")
    .setSystem("http://hl7.org/fhir/supply-item-type");
  supplyResource.setType(type);
  
  SupplyDeliverySuppliedItemComponent suppliedItem = new SupplyDeliverySuppliedItemComponent();
  suppliedItem.setItem(mapCodeToCodeableConcept(supply.codes.get(0), SNOMED_URI));
  
  SimpleQuantity quantity = new SimpleQuantity();
  quantity.setValue(supply.quantity);
  suppliedItem.setQuantity(quantity);
  
  supplyResource.setSuppliedItem(suppliedItem);
  
  supplyResource.setOccurrence(convertFhirDateTime(supply.start, true));
  
  return newEntry(bundle, supplyResource);
}
 

/**
 * Returns a new Observation for testing.
 *
 * @return a FHIR Observation for testing.
 */
public static Observation newObservation() {
  Observation observation = new Observation();

  observation.setId("blood-pressure");

  Identifier identifier = observation.addIdentifier();
  identifier.setSystem("urn:ietf:rfc:3986");
  identifier.setValue("urn:uuid:187e0c12-8dd2-67e2-99b2-bf273c878281");

  observation.setStatus(Observation.ObservationStatus.FINAL);

  CodeableConcept obsCode = new CodeableConcept();

  observation.setCode(obsCode);

  Quantity quantity = new Quantity();
  quantity.setValue(new java.math.BigDecimal("123.45"));
  quantity.setUnit("mm[Hg]");
  quantity.setSystem("http://unitsofmeasure.org");
  observation.setValue(quantity);

  ObservationComponentComponent component = observation.addComponent();

  CodeableConcept code = new CodeableConcept()
      .addCoding(new Coding()
          .setCode("abc")
          .setSystem("PLACEHOLDER"));

  component.setCode(code);

  return observation;
}
 

public static List<ICoding> getCodingsFromConcept(CodeableConcept codeableConcept){
	ArrayList<ICoding> ret = new ArrayList<>();
	List<Coding> coding = codeableConcept.getCoding();
	for (Coding code : coding) {
		ret.add(new CodingWrapper(code));
	}
	return ret;
}
 

@Test
public void testMultiModifierExtensionsWithCodeableConceptField() {

  CodeableConcept expected1 = (CodeableConcept) testBunsenTestProfilePatient
      .getModifierExtensionsByUrl(TestData.BUNSEN_TEST_CODEABLE_CONCEPT_MODIFIER_EXT_FIELD)
      .get(0).getValue();

  CodeableConcept expected2 = (CodeableConcept) testBunsenTestProfilePatient
      .getModifierExtensionsByUrl(TestData.BUNSEN_TEST_CODEABLE_CONCEPT_MODIFIER_EXT_FIELD)
      .get(1).getValue();

  CodeableConcept decodedCodeableConceptField1 =
      (CodeableConcept) testBunsenTestProfilePatientDecoded
          .getModifierExtensionsByUrl(TestData.BUNSEN_TEST_CODEABLE_CONCEPT_MODIFIER_EXT_FIELD)
          .get(0).getValue();

  CodeableConcept decodedCodeableConceptField2 =
      (CodeableConcept) testBunsenTestProfilePatientDecoded
          .getModifierExtensionsByUrl(TestData.BUNSEN_TEST_CODEABLE_CONCEPT_MODIFIER_EXT_FIELD)
          .get(1).getValue();

  Assert.assertTrue(expected1.equalsDeep(decodedCodeableConceptField1));
  Assert.assertTrue(expected2.equalsDeep(decodedCodeableConceptField2));

  final List<Row> codings = testBunsenTestProfilePatientDataset
      .select(functions.explode(functions.col("codeableConceptModifierExt.coding"))
          .alias("coding")).select("coding.code", "coding.display").collectAsList();

  Assert.assertEquals(decodedCodeableConceptField1.getCoding().get(0).getCode(),
      codings.get(0).getList(0).get(0));
  Assert.assertEquals(decodedCodeableConceptField1.getCoding().get(0).getDisplay(),
      codings.get(0).getList(1).get(0));

  Assert.assertEquals(decodedCodeableConceptField2.getCoding().get(0).getCode(),
      codings.get(1).getList(0).get(0));
  Assert.assertEquals(decodedCodeableConceptField2.getCoding().get(0).getDisplay(),
      codings.get(1).getList(1).get(0));
}