Java Code Examples for ca.uhn.fhir.context.FhirContext#forDstu3()

public static void step2_search_for_patients_named_test() {
	FhirContext ctx = FhirContext.forDstu3();
	IGenericClient client = ctx.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3");

	org.hl7.fhir.r4.model.Bundle results = client
		.search()
		.forResource(Patient.class)
		.where(Patient.NAME.matches().value("test"))
		.returnBundle(org.hl7.fhir.r4.model.Bundle.class)
		.execute();

	System.out.println("First page: ");
	System.out.println(ctx.newXmlParser().encodeResourceToString(results));

	// Load the next page
	org.hl7.fhir.r4.model.Bundle nextPage = client
		.loadPage()
		.next(results)
		.execute();

	System.out.println("Next page: ");
	System.out.println(ctx.newXmlParser().encodeResourceToString(nextPage));

}
 

public static void main(String[] theArgs) {
   FhirContext ctx = FhirContext.forDstu3();
   IGenericClient client = ctx.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3");

   // Build a search and execute it
   Bundle response = client.search()
      .forResource(Patient.class)
      .where(Patient.NAME.matches().value("Test"))
      .and(Patient.BIRTHDATE.before().day("2014-01-01"))
      .count(100)
      .returnBundle(Bundle.class)
      .execute();

   // How many resources did we find?
   System.out.println("Responses: " + response.getTotal());

   // Print the ID of the first one
   System.out.println("First response ID: " + response.getEntry().get(0).getResource().getId());
}
 

private void initializeSTU3() {
  FhirContext ctx = FhirContext.forDstu3();
  validatorSTU3 = ctx.newValidator();
  org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator instanceValidator =
      new org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator();
  ValidationSupportSTU3 validationSupport = new ValidationSupportSTU3();
  org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain support =
      new org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain(
          new org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport(), validationSupport);
  instanceValidator.setValidationSupport(support);

  IValidatorModule schemaValidator = new SchemaBaseValidator(ctx);
  IValidatorModule schematronValidator = new SchematronBaseValidator(ctx);

  validatorSTU3.registerValidatorModule(schemaValidator);
  validatorSTU3.registerValidatorModule(schematronValidator);
  validatorSTU3.registerValidatorModule(instanceValidator);
}
 

public static void main(String[] args) {

      String input = "<Encounter xmlns=\"http://hl7.org/fhir\"></Encounter>";

      // Create a new validator
      FhirContext ctx = FhirContext.forDstu3();
      FhirValidator validator = ctx.newValidator();

      // Did we succeed?
      ValidationResult result = validator.validateWithResult(input);
      System.out.println("Success: " + result.isSuccessful());

      // What was the result
      OperationOutcome outcome = (OperationOutcome) result.toOperationOutcome();
      IParser parser = ctx.newXmlParser().setPrettyPrint(true);
      System.out.println(parser.encodeResourceToString(outcome));
   }
 

public static void main(String[] args) {
	
	// Create an incomplete encounter (status is required)
	Encounter enc = new Encounter();
	enc.addIdentifier().setSystem("http://acme.org/encNums").setValue("12345");
	
	// Create a new validator
	FhirContext ctx = FhirContext.forDstu3();
	FhirValidator validator = ctx.newValidator();
	
	// Did we succeed?
	ValidationResult result = validator.validateWithResult(enc);
	System.out.println("Success: " + result.isSuccessful());
	
	// What was the result
	OperationOutcome outcome = (OperationOutcome) result.toOperationOutcome();
	IParser parser = ctx.newXmlParser().setPrettyPrint(true);
	System.out.println(parser.encodeResourceToString(outcome));
}
 

public void TestCMS9v4_CQM() throws IOException, JAXBException {
      File xmlFile = new File(URLDecoder.decode(TestFhirLibrary.class.getResource("CMS9v4_CQM.xml").getFile(), "UTF-8"));
      Library library = CqlLibraryReader.read(xmlFile);

      Context context = new Context(library);

      FhirContext fhirContext = FhirContext.forDstu3();

Dstu3FhirModelResolver modelResolver = new Dstu3FhirModelResolver();
RestFhirRetrieveProvider retrieveProvider = new RestFhirRetrieveProvider(new SearchParameterResolver(fhirContext),  fhirContext.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3"));
CompositeDataProvider provider = new CompositeDataProvider(modelResolver, retrieveProvider);
      //BaseFhirDataProvider provider = new FhirDataProviderStu3().setEndpoint("http://fhirtest.uhn.ca/baseDstu3");
      //BaseFhirDataProvider provider = new FhirDataProviderStu3().setEndpoint("http://fhir3.healthintersections.com.au/open/");
      //BaseFhirDataProvider provider = new FhirDataProviderStu3().setEndpoint("http://wildfhir.aegis.net/fhir");
      context.registerDataProvider("http://hl7.org/fhir", provider);

      Object result = context.resolveExpressionRef("Breastfeeding Intention Assessment").evaluate(context);
      assertThat(result, instanceOf(Iterable.class));
      for (Object element : (Iterable)result) {
          assertThat(element, instanceOf(RiskAssessment.class));
      }
  }
 

@Test
public void testFhirHelpersStu3() throws UcumException {
    String cql = getStringFromResourceStream("stu3/TestFHIRHelpers.cql");
    Library library = translate(cql);
    Context context = new Context(library);
    context.registerLibraryLoader(getLibraryLoader());

    Dstu3FhirModelResolver modelResolver = new Dstu3FhirModelResolver();
    FhirContext fhirContext = FhirContext.forDstu3();
    RestFhirRetrieveProvider retrieveProvider = new RestFhirRetrieveProvider(new SearchParameterResolver(fhirContext),
            fhirContext.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3"));
    CompositeDataProvider provider = new CompositeDataProvider(modelResolver, retrieveProvider);
    // BaseFhirDataProvider provider = new
    // FhirDataProviderStu3().setEndpoint("http://fhirtest.uhn.ca/baseDstu3");
    context.registerDataProvider("http://hl7.org/fhir", provider);

    Object result = context.resolveExpressionRef("TestPeriodToInterval").getExpression().evaluate(context);
    // TODO - fix
    // Assert.assertEquals(((DateTime)((Interval) result).getStart()).getPartial(),
    // new Partial(DateTime.getFields(6), new int[] {2017, 5, 6, 18, 8, 0}));
    // Assert.assertEquals(((DateTime)((Interval) result).getEnd()).getPartial(),
    // new Partial(DateTime.getFields(6), new int[] {2017, 5, 6, 19, 8, 0}));
    result = context.resolveExpressionRef("TestToQuantity").getExpression().evaluate(context);
    // TODO: ModelInfo bug. Not aware of SimpleQuantity
    result = context.resolveExpressionRef("TestRangeToInterval").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToCode").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToConcept").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToString").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestRequestStatusToString").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToDateTime").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToTime").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToInteger").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToDecimal").getExpression().evaluate(context);
    result = context.resolveExpressionRef("TestToBoolean").getExpression().evaluate(context);
}
 

public static void step3_create_patient() {
	// Create a patient
	Patient newPatient = new Patient();

	// Populate the patient with fake information
	newPatient
		.addName()
			.setFamily("DevDays2015")
			.addGiven("John")
			.addGiven("Q");
	newPatient
		.addIdentifier()
			.setSystem("http://acme.org/mrn")
			.setValue("1234567");
	newPatient.setGender(Enumerations.AdministrativeGender.MALE);
	newPatient.setBirthDateElement(new DateType("2015-11-18"));

	// Create a client
	FhirContext ctx = FhirContext.forDstu3();
	IGenericClient client = ctx.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3");

	// Create the resource on the server
	MethodOutcome outcome = client
		.create()
		.resource(newPatient)
		.execute();

	// Log the ID that the server assigned
	IIdType id = outcome.getId();
	System.out.println("Created patient, got ID: " + id);
}
 

@Override
public FhirContext fhirContextDstu3() {
	FhirContext retVal = FhirContext.forDstu3();

	// Don't strip versions in some places
	ParserOptions parserOptions = retVal.getParserOptions();
	parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");

	return retVal;
}
 

@Test void testDstu3SearchParams() {
    SearchParameterResolver resolver = new SearchParameterResolver(FhirContext.forDstu3());

    RuntimeSearchParam param = resolver.getSearchParameterDefinition("Patient", "id");
    assertNotNull(param);
    assertEquals("_id", param.getName());

    
    param = resolver.getSearchParameterDefinition("MedicationAdministration", "medication", RestSearchParameterTypeEnum.TOKEN);
    assertNotNull(param);
    assertEquals("code", param.getName());

    param = resolver.getSearchParameterDefinition("MedicationAdministration", "medication", RestSearchParameterTypeEnum.REFERENCE);
    assertNotNull(param);
    assertEquals("medication", param.getName());


    param = resolver.getSearchParameterDefinition("Encounter", "period");
    assertNotNull(param);
    assertEquals("date", param.getName());

    param = resolver.getSearchParameterDefinition("Encounter", "reason");
    assertNotNull(param);
    assertEquals("reason", param.getName());

    param = resolver.getSearchParameterDefinition("Encounter", "subject");
    assertNotNull(param);
    assertEquals("patient", param.getName());

    param = resolver.getSearchParameterDefinition("Encounter", "type");
    assertNotNull(param);
    assertEquals("type", param.getName());
}
 

@Test
public void testReturnsNullPathReturnsNull() {
    SearchParameterResolver resolver = new SearchParameterResolver(FhirContext.forDstu3());

    RuntimeSearchParam param = resolver.getSearchParameterDefinition("Patient", null);
    assertNull(param);
}
 

/**
 * Get a FHIR STU3 Context for testing, but only initialize it once.
 * 
 * @return an STU3 FhirContext
 */
public static FhirContext getStu3FhirContext() {
  if (stu3FhirContext == null) {
    stu3FhirContext = FhirContext.forDstu3();
  }
  return stu3FhirContext;
}
 

public RuntimeValue<FhirContext> createDstu3FhirContext(BeanContainer container, Collection<String> resourceDefinitions) {
    FhirContext fhirContext = FhirContext.forDstu3();
    initContext(resourceDefinitions, fhirContext);
    container.instance(FhirContextProducers.class).setDstu3(fhirContext);
    return new RuntimeValue<>(fhirContext);
}
 

public R4FhirTerminologyProvider() {
    this.fhirContext = FhirContext.forDstu3();
}
 

public Dstu3FhirTerminologyProvider() {
    this.fhirContext = FhirContext.forDstu3();
}
 

public Dstu3FhirModelResolver() {
    this(FhirContext.forDstu3());
}
 

@Test
public void testObservationAttachment() throws Exception {

  Person person = new Person(0L);
  person.attributes.put(Person.GENDER, "F");
  person.attributes.put(Person.FIRST_LANGUAGE, "spanish");
  person.attributes.put(Person.RACE, "other");
  person.attributes.put(Person.ETHNICITY, "hispanic");
  person.attributes.put(Person.INCOME, Integer.parseInt(Config
      .get("generate.demographics.socioeconomic.income.poverty")) * 2);
  person.attributes.put(Person.OCCUPATION_LEVEL, 1.0);
  person.attributes.put("Pulmonary Resistance", 0.1552);
  person.attributes.put("BMI Multiplier", 0.055);
  person.setVitalSign(VitalSign.BMI, 21.0);

  person.history = new LinkedList<>();
  Provider mock = Mockito.mock(Provider.class);
  mock.uuid = "Mock-UUID";
  person.setProvider(EncounterType.AMBULATORY, mock);
  person.setProvider(EncounterType.WELLNESS, mock);
  person.setProvider(EncounterType.EMERGENCY, mock);
  person.setProvider(EncounterType.INPATIENT, mock);

  Long time = System.currentTimeMillis();
  long birthTime = time - Utilities.convertTime("years", 35);
  person.attributes.put(Person.BIRTHDATE, birthTime);

  Payer.loadNoInsurance();
  for (int i = 0; i < person.payerHistory.length; i++) {
    person.setPayerAtAge(i, Payer.noInsurance);
  }
  
  Module module = TestHelper.getFixture("observation.json");
  
  State physiology = module.getState("Simulate_CVS");
  assertTrue(physiology.process(person, time));
  person.history.add(physiology);
  
  State encounter = module.getState("SomeEncounter");
  assertTrue(encounter.process(person, time));
  person.history.add(encounter);
  
  State chartState = module.getState("ChartObservation");
  assertTrue(chartState.process(person, time));
  person.history.add(chartState);
  
  State urlState = module.getState("UrlObservation");
  assertTrue(urlState.process(person, time));
  person.history.add(urlState);
  
  FhirContext ctx = FhirContext.forDstu3();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirStu3.convertToFHIRJson(person, System.currentTimeMillis());
  Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
  
  for (BundleEntryComponent entry : bundle.getEntry()) {
    if (entry.getResource() instanceof Media) {
      Media media = (Media) entry.getResource();
      if (media.getContent().getData() != null) {
        assertEquals(400, media.getWidth());
        assertEquals(200, media.getHeight());
        assertEquals("Invasive arterial pressure", media.getReasonCode().get(0).getText());
        assertTrue(Base64.isBase64(media.getContent().getDataElement().getValueAsString()));
      } else if (media.getContent().getUrl() != null) {
        assertEquals("https://example.com/image/12498596132", media.getContent().getUrl());
        assertEquals("en-US", media.getContent().getLanguage());
        assertTrue(media.getContent().getSize() > 0);
      } else {
        fail("Invalid Media element in output JSON");
      }
    }
  }
}
 

@Test
public void testSampledDataExport() throws Exception {

  Person person = new Person(0L);
  person.attributes.put(Person.GENDER, "F");
  person.attributes.put(Person.FIRST_LANGUAGE, "spanish");
  person.attributes.put(Person.RACE, "other");
  person.attributes.put(Person.ETHNICITY, "hispanic");
  person.attributes.put(Person.INCOME, Integer.parseInt(Config
      .get("generate.demographics.socioeconomic.income.poverty")) * 2);
  person.attributes.put(Person.OCCUPATION_LEVEL, 1.0);

  person.history = new LinkedList<>();
  Provider mock = Mockito.mock(Provider.class);
  mock.uuid = "Mock-UUID";
  person.setProvider(EncounterType.AMBULATORY, mock);
  person.setProvider(EncounterType.WELLNESS, mock);
  person.setProvider(EncounterType.EMERGENCY, mock);
  person.setProvider(EncounterType.INPATIENT, mock);

  Long time = System.currentTimeMillis();
  long birthTime = time - Utilities.convertTime("years", 35);
  person.attributes.put(Person.BIRTHDATE, birthTime);

  Payer.loadNoInsurance();
  for (int i = 0; i < person.payerHistory.length; i++) {
    person.setPayerAtAge(i, Payer.noInsurance);
  }
  
  Module module = TestHelper.getFixture("observation.json");
  
  State encounter = module.getState("SomeEncounter");
  assertTrue(encounter.process(person, time));
  person.history.add(encounter);
  
  State physiology = module.getState("Simulate_CVS");
  assertTrue(physiology.process(person, time));
  person.history.add(physiology);
  
  State sampleObs = module.getState("SampledDataObservation");
  assertTrue(sampleObs.process(person, time));
  person.history.add(sampleObs);
  
  FhirContext ctx = FhirContext.forDstu3();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirStu3.convertToFHIRJson(person, System.currentTimeMillis());
  Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
  
  for (BundleEntryComponent entry : bundle.getEntry()) {
    if (entry.getResource() instanceof Observation) {
      Observation obs = (Observation) entry.getResource();
      assertTrue(obs.getValue() instanceof SampledData);
      SampledData data = (SampledData) obs.getValue();
      assertEquals(10, data.getPeriod().doubleValue(), 0.001); // 0.01s == 10ms
      assertEquals(3, (int) data.getDimensions());
    }
  }
}
 

/**
 * Constructor
 */
public ExampleRestfulServlet() {
	super(FhirContext.forDstu3()); // This is an STU3 server
}
 

@Bean(name="stu3ctx")
@Primary
public FhirContext getStu3FhirContext() {

    return FhirContext.forDstu3();
}