org.hl7.fhir.r4.model.Coding 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;
}
 

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 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 CacheToken generateValidationToken(ValidationOptions options, Coding code, ValueSet vs) {
  CacheToken ct = new CacheToken();
  if (code.hasSystem())
    ct.name = getNameForSystem(code.getSystem());
  else
    ct.name = NAME_FOR_NO_SYSTEM;
  JsonParser json = new JsonParser();
  json.setOutputStyle(OutputStyle.PRETTY);
  ValueSet vsc = getVSEssense(vs);
  try {
    ct.request = "{\"code\" : "+json.composeString(code, "code")+", \"valueSet\" :"+(vsc == null ? "null" : json.composeString(vsc))+(options == null ? "" : ", "+options.toJson())+"}";
  } catch (IOException e) {
    throw new Error(e);
  }
  ct.key = String.valueOf(hashNWS(ct.request));
  return ct;
}
 

public ConceptMap updateClosure(String name, Coding coding) {
  Parameters params = new Parameters();
  params.addParameter().setName("name").setValue(new StringType(name));
  params.addParameter().setName("concept").setValue(coding);
  List<Header> headers = null;
  ResourceRequest<Resource> result = utils.issuePostRequest(resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
      utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers);
  result.addErrorStatus(410);//gone
  result.addErrorStatus(404);//unknown
  result.addErrorStatus(405);
  result.addErrorStatus(422);//Unprocessable Entity
  result.addSuccessStatus(200);
  result.addSuccessStatus(201);
  if(result.isUnsuccessfulRequest()) {
    throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
  }
  return (ConceptMap) result.getPayload();
}
 

@SuppressWarnings("rawtypes")
private String describeTransformCCorC(StructureMapGroupRuleTargetComponent tgt) throws FHIRException {
  if (tgt.getParameter().size() < 2)
    return null;
  Type p1 = tgt.getParameter().get(0).getValue();
  Type p2 = tgt.getParameter().get(1).getValue();
  if (p1 instanceof IdType || p2 instanceof IdType)
    return null;
  if (!(p1 instanceof PrimitiveType) || !(p2 instanceof PrimitiveType))
    return null;
  String uri = ((PrimitiveType) p1).asStringValue();
  String code = ((PrimitiveType) p2).asStringValue();
  if (Utilities.noString(uri))
    throw new FHIRException("Describe Transform, but the uri is blank");
  if (Utilities.noString(code))
    throw new FHIRException("Describe Transform, but the code is blank");
  Coding c = buildCoding(uri, code);
  return NarrativeGenerator.describeSystem(c.getSystem())+"#"+c.getCode()+(c.hasDisplay() ? "("+c.getDisplay()+")" : "");
}
 

public ServiceRequestBuilder buildCode(Coding coding) {
    complexProperty.setCode(
            new CodeableConceptBuilder()
                    .buildCoding(coding)
                    .build()
    );
    return  this;
}
 

@Test
public void coding() {

  Coding expectedCoding = condition.getSeverity().getCodingFirstRep();
  Coding actualCoding = decodedCondition.getSeverity().getCodingFirstRep();

  // Codings are a nested array, so we explode them into a table of the coding
  // fields so we can easily select and compare individual fields.
  Dataset<Row> severityCodings = conditionsDataset
      .select(functions.explode(conditionsDataset.col("severity.coding"))
          .alias("coding"))
      .select("coding.*") // Pull all fields in the coding to the top level.
      .cache();

  Assert.assertEquals(expectedCoding.getCode(),
      severityCodings.select("code").head().get(0));
  Assert.assertEquals(expectedCoding.getCode(),
      actualCoding.getCode());

  Assert.assertEquals(expectedCoding.getSystem(),
      severityCodings.select("system").head().get(0));
  Assert.assertEquals(expectedCoding.getSystem(),
      actualCoding.getSystem());

  Assert.assertEquals(expectedCoding.getUserSelected(),
      severityCodings.select("userSelected").head().get(0));
  Assert.assertEquals(expectedCoding.getUserSelected(),
      actualCoding.getUserSelected());

  Assert.assertEquals(expectedCoding.getDisplay(),
      severityCodings.select("display").head().get(0));
  Assert.assertEquals(expectedCoding.getDisplay(),
      actualCoding.getDisplay());
}
 

private void processIndexTerm(org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, JsonObject child) {
  String s = readString(child, "label");
  if (s != null) {
    if (!s.equals(cc.getDisplay())) {
      cc.addDesignation().setValue(s).setUse(new Coding().setSystem("http://id.who.int/icd11/mms/designation").setCode("term"));        
    }
  }    
}
 

@Test
public void testMetaSecurity() {
  Meta meta = new Meta();
  Coding coding = meta.addSecurity().setSystem(TEST_SYSTEM).setCode(TEST_CODE);
  Assertions.assertTrue(meta.hasSecurity());
  Assertions.assertNotNull(meta.getSecurity());
  Assertions.assertNotNull(meta.getSecurity(TEST_SYSTEM, TEST_CODE));
  Assertions.assertEquals(1, meta.getSecurity().size());
  Assertions.assertEquals(meta.getSecurity().get(0), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
  Assertions.assertEquals(meta.getSecurityFirstRep(), meta.getSecurity(TEST_SYSTEM, TEST_CODE));
  Assertions.assertEquals(coding, meta.getSecurity(TEST_SYSTEM, TEST_CODE));
}
 

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 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();
}
 

public static void setExtension(Element focus, String url, Coding c) {
  for (Extension e : focus.getExtension()) 
    if (e.getUrl().equals(url)) {
      e.setValue(c);
      return;
    }
  focus.getExtension().add(new Extension().setUrl(url).setValue(c));    
}
 

public CodeableConceptBuilder buildCoding(Coding coding) {
    if (!complexProperty.hasCoding()) {
        complexProperty.setCoding(new ArrayList<>());
    }

    complexProperty.addCoding(coding);
    return this;
}
 

private Coding buildCoding(String uri, String code) throws FHIRException {
 // if we can get this as a valueSet, we will
 String system = null;
 String display = null;
 ValueSet vs = Utilities.noString(uri) ? null : worker.fetchResourceWithException(ValueSet.class, uri);
 if (vs != null) {
   ValueSetExpansionOutcome vse = worker.expandVS(vs, true, false);
   if (vse.getError() != null)
     throw new FHIRException(vse.getError());
   CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
   for (ValueSetExpansionContainsComponent t : vse.getValueset().getExpansion().getContains()) {
     if (t.hasCode())
       b.append(t.getCode());
     if (code.equals(t.getCode()) && t.hasSystem()) {
       system = t.getSystem();
        display = t.getDisplay();
       break;
     }
      if (code.equalsIgnoreCase(t.getDisplay()) && t.hasSystem()) {
        system = t.getSystem();
        display = t.getDisplay();
        break;
      }
   }
   if (system == null)
     throw new FHIRException("The code '"+code+"' is not in the value set '"+uri+"' (valid codes: "+b.toString()+"; also checked displays)");
 } else
   system = uri;
 ValidationResult vr = worker.validateCode(terminologyServiceOptions, system, code, null);
 if (vr != null && vr.getDisplay() != null)
   display = vr.getDisplay();
 return new Coding().setSystem(system).setCode(code).setDisplay(display);
}
 

private List<Coding> mergeCodings(List<Coding> left, List<Coding> right) {
  List<Coding> result = new ArrayList<Coding>();
  result.addAll(left);
  for (Coding c : right) {
    boolean found = false;
    for (Coding ct : left)
      if (Utilities.equals(c.getSystem(), ct.getSystem()) && Utilities.equals(c.getCode(), ct.getCode()))
        found = true;
    if (!found)
      result.add(c);
  }
  return result;
}
 

protected void decorateCoding(Complex t, Coding element) {
	if (!element.hasSystem())
		return;
	if ("http://snomed.info/sct".equals(element.getSystem())) {
		t.prefix("sct", "http://snomed.info/sct/");
		t.predicate("a", "sct:"+element.getCode());
	} else if ("http://snomed.info/sct".equals(element.getSystem())) {
		t.prefix("loinc", "http://loinc.org/rdf#");
		t.predicate("a", "loinc:"+element.getCode());
	}  
}
 

public static Coding readAsCoding(Element item) {
  Coding c = new Coding();
  c.setSystem(item.getNamedChildValue("system"));
  c.setVersion(item.getNamedChildValue("version"));
  c.setCode(item.getNamedChildValue("code"));
  c.setDisplay(item.getNamedChildValue("display"));
  return c;
}
 

private Coding translateByJustCode(ConceptMap cm, String code) throws FHIRException {
  SourceElementComponent ct = null;
  ConceptMapGroupComponent cg = null;
  for (ConceptMapGroupComponent g : cm.getGroup()) {
    for (SourceElementComponent e : g.getElement()) {
      if (code.equals(e.getCode())) {
        if (e != null)
          throw new FHIRException("Unable to process translate "+code+" because multiple candidate matches were found in concept map "+cm.getUrl());
        ct = e;
        cg = g;
      }
    }
  }
  if (ct == null)
    return null;
  TargetElementComponent tt = null;
  for (TargetElementComponent t : ct.getTarget()) {
    if (!t.hasDependsOn() && !t.hasProduct() && isOkEquivalence(t.getEquivalence())) {
      if (tt != null)
        throw new FHIRException("Unable to process translate "+code+" because multiple targets were found in concept map "+cm.getUrl());
      tt = t;       
    }
  }
  if (tt == null)
    return null;
  return new Coding().setSystem(cg.getTarget()).setVersion(cg.getTargetVersion()).setCode(tt.getCode()).setDisplay(tt.getDisplay());
}
 

public Coding translate(Coding source, String url) throws FHIRException {
  ConceptMap cm = context.fetchResource(ConceptMap.class, url);
  if (cm == null)
    throw new FHIRException("Unable to find ConceptMap '"+url+"'");
  if (source.hasSystem()) 
    return translateBySystem(cm, source.getSystem(), source.getCode());
  else
    return translateByJustCode(cm, source.getCode());
}
 

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;
}
 

public CodeableConceptBuilder buildCoding(List<Coding> coding) {
    complexProperty.setCoding(coding);
    return this;
}
 

@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);
	}
}
 

public CodingBuilder() {
    super(new Coding());
}
 

public ActivityDefinitionBuilder buildBodySite(Coding coding) {
    complexProperty.getBodySite().add(new CodeableConceptBuilder().buildCoding(coding).build());
    return this;
}
 

public ActivityDefinitionBuilder buildCode(Coding coding) {
    complexProperty.getCode().addCoding(coding);
    return this;
}
 

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

/**
 * Add a MedicationAdministration if needed for the given medication.
 * 
 * @param personEntry       The Entry for the Person
 * @param bundle            Bundle to add the MedicationAdministration to
 * @param encounterEntry    Current Encounter entry
 * @param medication        The Medication
 * @param medicationRequest The related medicationRequest
 * @return The added Entry
 */
private static BundleEntryComponent medicationAdministration(
    BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry,
    Medication medication, MedicationRequest medicationRequest) {

  MedicationAdministration medicationResource = new MedicationAdministration();

  medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
  medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));

  Code code = medication.codes.get(0);
  String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;

  medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
  medicationResource.setEffective(new DateTimeType(new Date(medication.start)));

  medicationResource.setStatus("completed");

  if (medication.prescriptionDetails != null) {
    JsonObject rxInfo = medication.prescriptionDetails;
    MedicationAdministrationDosageComponent dosage =
        new MedicationAdministrationDosageComponent();

    // as_needed is false
    if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
      Quantity dose = new SimpleQuantity()
          .setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
      dosage.setDose((SimpleQuantity) dose);

      if (rxInfo.has("instructions")) {
        for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
          JsonObject instruction = instructionElement.getAsJsonObject();

          dosage.setText(instruction.get("display").getAsString());
        }
      }
    }
    if (rxInfo.has("refills")) {
      SimpleQuantity rate = new SimpleQuantity();
      rate.setValue(rxInfo.get("refills").getAsLong());
      dosage.setRate(rate);
    }
    medicationResource.setDosage(dosage);
  }

  if (!medication.reasons.isEmpty()) {
    // Only one element in list
    Code reason = medication.reasons.get(0);
    for (BundleEntryComponent entry : bundle.getEntry()) {
      if (entry.getResource().fhirType().equals("Condition")) {
        Condition condition = (Condition) entry.getResource();
        // Only one element in list
        Coding coding = condition.getCode().getCoding().get(0);
        if (reason.code.equals(coding.getCode())) {
          medicationResource.addReasonReference().setReference(entry.getFullUrl());
        }
      }
    }
  }

  BundleEntryComponent medicationAdminEntry = newEntry(bundle, medicationResource);
  return medicationAdminEntry;
}
 

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

private void addDesignation(String v, org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent cc, String system, String code) {
  if (v != null) {
    cc.addDesignation().setValue(v.replace("\r", "").replace("\n", "")).setUse(new Coding().setSystem(system).setCode(code));
  }
}