org.hl7.fhir.r4.model.CodeableConcept Java Examples

/**
 * 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;
}
 

/**
 * 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://terminology.hl7.org/CodeSystem/supply-item-type");
  supplyResource.setType(type);
  
  SupplyDeliverySuppliedItemComponent suppliedItem = new SupplyDeliverySuppliedItemComponent();
  suppliedItem.setItem(mapCodeToCodeableConcept(supply.codes.get(0), SNOMED_URI));
  suppliedItem.setQuantity(new Quantity(supply.quantity));
  
  supplyResource.setSuppliedItem(suppliedItem);
  
  supplyResource.setOccurrence(convertFhirDateTime(supply.start, true));
  
  return newEntry(bundle, supplyResource);
}
 

private void mapRelatedContacts(IPatient source, Patient target) {
	List<ContactComponent> contacts = new ArrayList<>();

	IPerson legalGuardian = source.getLegalGuardian();
	if (legalGuardian != null) {
		ContactComponent _legalGuardian = new ContactComponent();

		CodeableConcept addCoding = new CodeableConcept().addCoding(new Coding().setCode("N"));
		_legalGuardian.setRelationship(Collections.singletonList(addCoding));
		_legalGuardian.setId(legalGuardian.getId());
		List<HumanName> humanNames = contactHelper.getHumanNames(legalGuardian);
		_legalGuardian.setName((!humanNames.isEmpty()) ? humanNames.get(0) : null);
		List<Address> addresses = contactHelper.getAddresses(legalGuardian);
		_legalGuardian.setAddress((!addresses.isEmpty()) ? addresses.get(0) : null);
		AdministrativeGender gender = contactHelper.getGender(legalGuardian.getGender());
		_legalGuardian.setGender(gender);
		List<ContactPoint> contactPoints = contactHelper.getContactPoints(legalGuardian);
		_legalGuardian.setTelecom(contactPoints);

		contacts.add(_legalGuardian);
	}

	target.setContact(contacts);
}
 

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());
  }
  // pass through line/col if they're present
  if (message.getLine() != 0)
    issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_LINE).setValue(new IntegerType(message.getLine()));
  if (message.getCol() != 0)
    issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_COL).setValue(new IntegerType(message.getCol()));
  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 CacheToken generateValidationToken(ValidationOptions options, CodeableConcept code, ValueSet vs) {
  CacheToken ct = new CacheToken();
  for (Coding c : code.getCoding()) {
    if (c.hasSystem())
      ct.setName(getNameForSystem(c.getSystem()));
  }
  JsonParser json = new JsonParser();
  json.setOutputStyle(OutputStyle.PRETTY);
  ValueSet vsc = getVSEssense(vs);
  try {
    ct.request = "{\"code\" : "+json.composeString(code, "codeableConcept")+", \"valueSet\" :"+json.composeString(vsc)+(options == null ? "" : ", "+options.toJson())+"}";
  } catch (IOException e) {
    throw new Error(e);
  }
  ct.key = String.valueOf(hashNWS(ct.request));
  return ct;
}
 

private void mapMaritalStatus(Patient source, IPatient target) {
	CodeableConcept maritalStatus = source.getMaritalStatus();
	if (maritalStatus != null && !maritalStatus.getCoding().isEmpty()) {
		String code = maritalStatus.getCoding().get(0).getCode();
		target.setMaritalStatus(MaritalStatus.byFhirCodeSafe(code));
	}
}
 

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 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 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 String summary(CodeableConcept code) {
  StringBuilder b = new StringBuilder();
  b.append("{");
  boolean first = true;
  for (Coding c : code.getCoding()) {
    if (first) first = false; else b.append(",");
    b.append(summary(c));
  }
  b.append("}: \"");
  b.append(code.getText());
  b.append("\"");
  return b.toString();
}
 

private static String renderCodeable(CodeableConcept units) {
  if (units == null || units.isEmpty())
    return "";
  String v = renderCoding(units.getCoding());
  if (units.hasText())
    v = v + " " +Utilities.escapeXml(units.getText());
  return v;
}
 

private static String renderDEUnits(Type units) {
  if (units == null || units.isEmpty())
    return "";
  if (units instanceof CodeableConcept)
    return renderCodeable((CodeableConcept) units);
  else
    return "<a href=\""+Utilities.escapeXml(((Reference) units).getReference())+"\">"+Utilities.escapeXml(((Reference) units).getReference())+"</a>";
    
}
 

public static void setAllowableUnits(ElementDefinition eld, CodeableConcept cc) {
  for (Extension e : eld.getExtension()) 
    if (e.getUrl().equals(EXT_ALLOWABLE_UNITS)) {
      e.setValue(cc);
      return;
    }
  eld.getExtension().add(new Extension().setUrl(EXT_ALLOWABLE_UNITS).setValue(cc));
}
 

private Type generateFixedValue(StructureMapGroupRuleTargetComponent tgt) {
  if (!allParametersFixed(tgt))
    return null;
  if (!tgt.hasTransform())
    return null;
  switch (tgt.getTransform()) {
  case COPY: return tgt.getParameter().get(0).getValue(); 
  case TRUNCATE: return null; 
  //case ESCAPE: 
  //case CAST: 
  //case APPEND: 
  case TRANSLATE: return null; 
//case DATEOP, 
//case UUID, 
//case POINTER, 
//case EVALUATE, 
  case CC: 
    CodeableConcept cc = new CodeableConcept();
    cc.addCoding(buildCoding(tgt.getParameter().get(0).getValue(), tgt.getParameter().get(1).getValue()));
    return cc;
  case C: 
    return buildCoding(tgt.getParameter().get(0).getValue(), tgt.getParameter().get(1).getValue());
  case QTY: return null; 
//case ID, 
//case CP, 
  default:
    return null;
  }
}
 

public static CodeableConcept readAsCodeableConcept(Element element) {
  CodeableConcept cc = new CodeableConcept();
  List<Element> list = new ArrayList<Element>();
  element.getNamedChildren("coding", list);
  for (Element item : list)
    cc.addCoding(readAsCoding(item));
  cc.setText(element.getNamedChildValue("text"));
  return cc;
}
 

private CodeableConcept makeUnits(String text, String ucum) {
	if (Utilities.noString(text) && Utilities.noString(ucum))
		return null;
	CodeableConcept cc = new CodeableConcept();
	cc.setText(text);
	cc.getCoding().add(new Coding().setCode(ucum).setSystem("http://unitsofmeasure.org"));
	return cc;
}
 

@SuppressWarnings("unchecked")
private void createBundle(){
	try {
		Date now = new Date();
		
		this.bundle = new Bundle();
		bundle.setId("BundleFromPractitioner");
		bundle.setMeta(new Meta().setLastUpdated(now).setProfile(Collections.singletonList(
			new CanonicalType("http://fhir.ch/ig/ch-crl/StructureDefinition/ch-crl-bundle"))));
		bundle.setType(BundleType.DOCUMENT);
		
		BundleEntryComponent compositionEntry = bundle.addEntry();
		Composition composition = new Composition();
		compositionEntry.setResource(composition);
		composition.setId("CompFromPractitioner");
		composition.setMeta(new Meta().setLastUpdated(now)
			.setProfile(Collections.singletonList(new CanonicalType(
				"http://fhir.ch/ig/ch-crl/StructureDefinition/ch-crl-composition"))));
		composition.setStatus(CompositionStatus.FINAL);
		composition.setType(new CodeableConcept(
			new Coding("http://loinc.org", "72134-0", "Cancer event report")));
		composition.setDate(now);
		composition.setTitle("Report to the Cancer Registry");
		
		BundleEntryComponent subjectEntry = bundle.addEntry();
		IFhirTransformer<Patient, IPatient> patientTransformer =
			(IFhirTransformer<Patient, IPatient>) FhirTransformersHolder
				.getTransformerFor(Patient.class, IPatient.class);
		Patient subject = patientTransformer.getFhirObject(patient)
			.orElseThrow(() -> new IllegalStateException("Could not create subject"));
		subject.getExtension().clear();
		fixAhvIdentifier(subject);
		
		subjectEntry.setResource(subject);
		
		BundleEntryComponent practitionerEntry = bundle.addEntry();
		IFhirTransformer<Practitioner, IMandator> practitionerTransformer =
			(IFhirTransformer<Practitioner, IMandator>) FhirTransformersHolder
				.getTransformerFor(Practitioner.class, IMandator.class);
		Practitioner practitioner = practitionerTransformer.getFhirObject(author)
			.orElseThrow(() -> new IllegalStateException("Could not create autor"));
		practitioner.getExtension().clear();
		practitioner.getIdentifier().clear();
		practitionerEntry.setResource(practitioner);
		
		BundleEntryComponent documentReferenceEntry = bundle.addEntry();
		DocumentReference documentReference = new DocumentReference();
		documentReferenceEntry.setResource(documentReference);
		documentReference.setId(document.getId());
		DocumentReferenceContentComponent content = documentReference.addContent();
		content.setAttachment(new Attachment().setContentType("application/pdf")
			.setData(IOUtils.toByteArray(document.getContent())));
		
		composition.setSubject(new Reference(subject));
		composition.setAuthor(Collections.singletonList(new Reference(practitioner)));
		SectionComponent section = composition.addSection();
		section.addEntry(new Reference(documentReference));
	} catch (IOException e) {
		LoggerFactory.getLogger(getClass()).error("Error creating FHIR bundle", e);
		throw new IllegalStateException("Error creating FHIR bundle", e);
	}
}
 

private void mapMaritalStatus(IPatient source, Patient target) {
	MaritalStatus maritalStatus = source.getMaritalStatus();
	if (maritalStatus != null) {
		target.setMaritalStatus(new CodeableConcept().addCoding(new Coding().setCode(maritalStatus.getFhirCode())));
	}
}
 

public CodeableConceptBuilder() {
    super(new CodeableConcept());
}
 

public IdentifierBuilder buildType(CodeableConcept type) {
    complexProperty.setType(type);
    return this;
}
 

/**
 * Map the given Observation with attachment 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.r4.model.Media mediaResource =
      new org.hl7.fhir.r4.model.Media();

  // Hard code as Image since we don't anticipate using video or audio any time soon
  Code mediaType = new Code("http://terminology.hl7.org/CodeSystem/media-type", "image", "Image");

  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);
  }
  mediaResource.setType(mapCodeToCodeableConcept(mediaType, MEDIA_TYPE_URI));
  mediaResource.setStatus(MediaStatus.COMPLETED);
  mediaResource.setSubject(new Reference(personEntry.getFullUrl()));
  mediaResource.setEncounter(new Reference(encounterEntry.getFullUrl()));

  Attachment content = (Attachment) obs.value;
  org.hl7.fhir.r4.model.Attachment contentResource = new org.hl7.fhir.r4.model.Attachment();
  
  contentResource.setContentType(content.contentType);
  contentResource.setLanguage(content.language);
  if (content.data != null) {
    contentResource.setDataElement(new org.hl7.fhir.r4.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.r4.model.Base64BinaryType(content.hash));
  }
  
  mediaResource.setWidth(content.width);
  mediaResource.setHeight(content.height);

  mediaResource.setContent(contentResource);

  return newEntry(bundle, mediaResource);
}
 

/**
 * Create an entry for the given Claim, which references a Medication.
 *
 * @param person         The person being prescribed medication
 * @param personEntry     Entry for the person
 * @param bundle          The Bundle to add to
 * @param encounterEntry  The current Encounter
 * @param claim           the Claim object
 * @param medicationEntry The Entry for the Medication object, previously created
 * @return the added Entry
 */
private static BundleEntryComponent medicationClaim(
    Person person, BundleEntryComponent personEntry,
    Bundle bundle, BundleEntryComponent encounterEntry, Claim claim,
    BundleEntryComponent medicationEntry) {
  
  org.hl7.fhir.r4.model.Claim claimResource = new org.hl7.fhir.r4.model.Claim();
  org.hl7.fhir.r4.model.Encounter encounterResource =
      (org.hl7.fhir.r4.model.Encounter) encounterEntry.getResource();

  claimResource.setStatus(ClaimStatus.ACTIVE);
  CodeableConcept type = new CodeableConcept();
  type.getCodingFirstRep()
    .setSystem("http://terminology.hl7.org/CodeSystem/claim-type")
    .setCode("pharmacy");
  claimResource.setType(type);
  claimResource.setUse(org.hl7.fhir.r4.model.Claim.Use.CLAIM);

  // Get the insurance info at the time that the encounter occurred.
  InsuranceComponent insuranceComponent = new InsuranceComponent();
  insuranceComponent.setSequence(1);
  insuranceComponent.setFocal(true);
  insuranceComponent.setCoverage(new Reference().setDisplay(claim.payer.getName()));
  claimResource.addInsurance(insuranceComponent);

  // duration of encounter
  claimResource.setBillablePeriod(encounterResource.getPeriod());
  claimResource.setCreated(encounterResource.getPeriod().getEnd());

  claimResource.setPatient(new Reference(personEntry.getFullUrl()));
  claimResource.setProvider(encounterResource.getServiceProvider());

  // set the required priority
  CodeableConcept priority = new CodeableConcept();
  priority.getCodingFirstRep()
    .setSystem("http://terminology.hl7.org/CodeSystem/processpriority")
    .setCode("normal");
  claimResource.setPriority(priority);

  // add item for encounter
  claimResource.addItem(new ItemComponent(new PositiveIntType(1),
        encounterResource.getTypeFirstRep())
      .addEncounter(new Reference(encounterEntry.getFullUrl())));

  // add prescription.
  claimResource.setPrescription(new Reference(medicationEntry.getFullUrl()));

  Money moneyResource = new Money();
  moneyResource.setValue(claim.getTotalClaimCost());
  moneyResource.setCurrency("USD");
  claimResource.setTotal(moneyResource);

  return newEntry(bundle, claimResource);
}
 

/**
 * Returns a FHIR Condition for testing purposes.
 */
public static Condition newCondition() {

  Condition condition = new Condition();

  // Condition based on example from FHIR:
  // https://www.hl7.org/fhir/condition-example.json.html
  condition.setId("Condition/example");

  condition.setLanguage("en_US");

  // Narrative text
  Narrative narrative = new Narrative();
  narrative.setStatusAsString("generated");
  narrative.setDivAsString("This data was generated for test purposes.");
  XhtmlNode node = new XhtmlNode();
  node.setNodeType(NodeType.Text);
  node.setValue("Severe burn of left ear (Date: 24-May 2012)");
  condition.setText(narrative);

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

  condition.setVerificationStatus(Condition.ConditionVerificationStatus.CONFIRMED);

  // Condition code
  CodeableConcept code = new CodeableConcept();
  code.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("39065001")
      .setDisplay("Severe");
  condition.setSeverity(code);

  // Severity code
  CodeableConcept severity = new CodeableConcept();
  severity.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("24484000")
      .setDisplay("Burn of ear")
      .setUserSelected(true);
  condition.setSeverity(severity);

  // Onset date time
  DateTimeType onset = new DateTimeType();
  onset.setValueAsString("2012-05-24");
  condition.setOnset(onset);

  return condition;
}
 

public static CodeableConcept codeableConcept(String system, String id, String label){
    return new CodeableConcept().addCoding(new Coding(system, id, label));
}
 

protected void decorateCodeableConcept(Complex t, CodeableConcept element) {
	for (Coding c : element.getCoding())
		decorateCoding(t, c);
}
 

/**
 * Returns a FHIR medication request for testing purposes.
 */
public static MedicationRequest newMedRequest() {

  MedicationRequest medReq = new MedicationRequest();

  medReq.setId("test-med");

  // Medication code
  CodeableConcept med = new CodeableConcept();
  med.addCoding()
      .setSystem("http://www.nlm.nih.gov/research/umls/rxnorm")
      .setCode("582620")
      .setDisplay("Nizatidine 15 MG/ML Oral Solution [Axid]");

  med.setText("Nizatidine 15 MG/ML Oral Solution [Axid]");

  medReq.setMedication(med);

  Annotation annotation = new Annotation();

  annotation.setText("Test medication note.");

  annotation.setAuthor(
      new Reference("Provider/example")
          .setDisplay("Example provider."));

  medReq.addNote(annotation);

  return medReq;
}
 

public ValidationResult validateCode(ValidationOptions options, CodeableConcept code, ValueSet vs);