Java Code Examples for ca.uhn.fhir.context.FhirContext#forR4()

/**
 * This is the Java main method, which gets executed
 */
public static void main(String[] args) {

   // Create a context
   FhirContext ctx = FhirContext.forR4();

   // Create a client
   IGenericClient client = ctx.newRestfulGenericClient("https://hapi.fhir.org/baseR4");

   // Read a patient with the given ID
   Patient patient = client.read().resource(Patient.class).withId("example").execute();

   // Print the output
   String string = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
   System.out.println(string);

}
 

private void initializeR4() {
  FhirContext ctx = FhirContext.forR4();
  validatorR4 = ctx.newValidator();
  org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator instanceValidator =
      new org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator();
  ValidationSupportR4 validationSupport = new ValidationSupportR4();
  org.hl7.fhir.r4.hapi.validation.ValidationSupportChain support =
      new org.hl7.fhir.r4.hapi.validation.ValidationSupportChain(
          new org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport(), validationSupport);
  instanceValidator.setValidationSupport(support);
  instanceValidator.setNoTerminologyChecks(true);

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

  validatorR4.registerValidatorModule(schemaValidator);
  validatorR4.registerValidatorModule(schematronValidator);
  validatorR4.registerValidatorModule(instanceValidator);
}
 

public static void main(String[] theArgs) {
   // Create a client
	FhirContext ctx = FhirContext.forR4();
	IGenericClient client = ctx.newRestfulGenericClient("http://fhirtest.uhn.ca/R4");

	Patient patient = new Patient();
	patient.setId("Patient/example"); // Give the patient an ID
	patient.addName().setFamily("Simpson").addGiven("Homer");
	patient.setGender(Enumerations.AdministrativeGender.MALE);

	// Update the patient
	MethodOutcome outcome = client
        .update()
        .resource(patient)
        .execute();
	
	System.out.println("Now have ID: " + outcome.getId());
}
 

public static void main(String[] theArgs) {

      Patient pat = new Patient();
      pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");
      pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135");
      pat.setGender(AdministrativeGender.MALE);

      // Create a context
      FhirContext ctx = FhirContext.forR4();

      // Create a client
      String serverBaseUrl = "http://hapi.fhir.org/baseR4";
      IGenericClient client = ctx.newRestfulGenericClient(serverBaseUrl);

      // Use the client to store a new resource instance
      MethodOutcome outcome = client
         .create()
         .resource(pat)
         .execute();

      // Print the ID of the newly created resource
      System.out.println(outcome.getId());
   }
 

@Setup
public void setUp() {
    context = FhirContext.forR4();
    context.setParserErrorHandler(new StrictErrorHandler());
    fhirValidator = context.newValidator();
    validator = FHIRValidator.validator();
    jsonParser = FHIRParser.parser(Format.JSON);
    jsonGenerator = FHIRGenerator.generator(Format.JSON);
    xmlParser = FHIRParser.parser(Format.XML);
    xmlGenerator = FHIRGenerator.generator(Format.XML);
}
 

@Setup
public void setUp() throws Exception {
    context = FhirContext.forR4();
    fhirValidator = context.newValidator();
    baseResource = context.newJsonParser().parseResource(new StringReader(JSON_SPEC_EXAMPLE));
    validator = FHIRValidator.validator();
    resource = FHIRParser.parser(Format.JSON).parse(new StringReader(JSON_SPEC_EXAMPLE));
    evaluationContext = new EvaluationContext(resource);
}
 

@Setup
public void setUp() throws Exception {
    if (exampleName == null) {
        System.err.println("exampleName is null; if you're in Eclipse then make sure annotation processing is on and you've ran 'mvn clean package'.");
        System.exit(1);
    }
    
    // us
    String JSON_SPEC_EXAMPLE = BenchmarkUtil.getSpecExample(Format.JSON, exampleName);
    resource = FHIRParser.parser(Format.JSON).parse(new StringReader(JSON_SPEC_EXAMPLE));
    
    // HAPI
    context = FhirContext.forR4();
    baseResource = context.newJsonParser().parseResource(new StringReader(JSON_SPEC_EXAMPLE));
}
 

/**
 * Get an R4 FHIR Context for testing, but only initialize it once.
 * 
 * @return an R4 FhirContext
 */
public static FhirContext getR4FhirContext() {
  if (r4FhirContext == null) {
    r4FhirContext = FhirContext.forR4();
  }
  return r4FhirContext;
}
 

/**
 * Write the FHIR bundle including the document to the provided file.
 * 
 * @param file
 * @throws IOException
 */
public void writeTo(File file) throws IOException{
	FhirContext ctx = FhirContext.forR4();
	String serialized = ctx.newXmlParser().encodeResourceToString(bundle);
	try (FileWriter out = new FileWriter(file)) {
		out.write(serialized);
	}
}
 

@Test void testR4SearchParams() {
    SearchParameterResolver resolver = new SearchParameterResolver(FhirContext.forR4());

    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", "reasonCode");
    assertNotNull(param);
    assertEquals("reason-code", param.getName());

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

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

    param = resolver.getSearchParameterDefinition("Observation", "code");
    assertNotNull(param);
    assertEquals("code", param.getName());

    param = resolver.getSearchParameterDefinition("Observation", "subject");
    assertNotNull(param);
    assertEquals("subject", param.getName());
}
 

@Override
public FhirContext fhirContextR4() {
	FhirContext retVal = FhirContext.forR4();

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

	return retVal;
}
 

@Setup
public void setUp() throws IOException {
    if (exampleName == null) {
        System.err.println("exampleName is null; if you're in Eclipse then make sure annotation processing is on and you've ran 'mvn clean package'.");
        System.exit(1);
    }
    System.out.println("Setting up for example " + exampleName);
    context = FhirContext.forR4();
    context.setParserErrorHandler(new StrictErrorHandler());
    JSON_SPEC_EXAMPLE = BenchmarkUtil.getSpecExample(Format.JSON, exampleName);
    XML_SPEC_EXAMPLE = BenchmarkUtil.getSpecExample(Format.XML, exampleName);
}
 

public static void testRun(String exampleName, String expression) throws Exception {
    String specExample = BenchmarkUtil.getSpecExample(Format.JSON, exampleName);

    FhirContext context = FhirContext.forR4();
    IBaseResource baseResource = context.newJsonParser().parseResource(new StringReader(specExample));
    IFluentPath fluentPath = context.newFluentPath();
    System.out.println(fluentPath.evaluate(baseResource, expression, IBase.class));

    Resource resource = FHIRParser.parser(Format.JSON).parse(new StringReader(specExample));
    FHIRPathEvaluator evaluator = FHIRPathEvaluator.evaluator();
    EvaluationContext evaluationContext = new EvaluationContext(resource);
    System.out.println(evaluator.evaluate(evaluationContext, expression, singleton(evaluationContext.getTree().getRoot())));
}
 

@Setup
public void setUp() throws Exception {
    context = FhirContext.forR4();
    fluentPath = context.newFluentPath();
    resource = FHIRParser.parser(Format.JSON).parse(new StringReader(JSON_SPEC_EXAMPLE));
    evaluator = FHIRPathEvaluator.evaluator();
    evaluationContext = new EvaluationContext(resource);
    initialContext = singleton(evaluationContext.getTree().getRoot());
    baseResource = context.newJsonParser().parseResource(new StringReader(JSON_SPEC_EXAMPLE));
}
 

@Bean(name="r4ctx")
public FhirContext getR4FhirContext() {

    return FhirContext.forR4();
}
 

@Test
public void testFHIRExport() throws Exception {
  FhirContext ctx = FhirContext.forR4();
  FhirValidator validator = ctx.newValidator();
  validator.setValidateAgainstStandardSchema(true);
  validator.setValidateAgainstStandardSchematron(true);

  File tempOutputFolder = tempFolder.newFolder();
  Config.set("exporter.baseDirectory", tempOutputFolder.toString());
  Config.set("exporter.hospital.fhir.export", "true");
  Config.set("exporter.fhir.transaction_bundle", "true");
  FhirR4.TRANSACTION_BUNDLE = true; // set this manually, in case it has already been loaded.
  TestHelper.loadTestProperties();
  Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
  Location location = new Location(Generator.DEFAULT_STATE, null);
  Provider.clear();
  Provider.loadProviders(location, 1L);
  assertNotNull(Provider.getProviderList());
  assertFalse(Provider.getProviderList().isEmpty());

  Provider.getProviderList().get(0).incrementEncounters(EncounterType.WELLNESS, 0);
  HospitalExporterR4.export(0L);

  File expectedExportFolder = tempOutputFolder.toPath().resolve("fhir").toFile();
  assertTrue(expectedExportFolder.exists() && expectedExportFolder.isDirectory());

  File expectedExportFile = expectedExportFolder.toPath().resolve("hospitalInformation0.json")
      .toFile();
  assertTrue(expectedExportFile.exists() && expectedExportFile.isFile());

  FileReader fileReader = new FileReader(expectedExportFile.getPath());
  BufferedReader bufferedReader = new BufferedReader(fileReader);
  StringBuilder fhirJson = new StringBuilder();
  String line = null;
  while ((line = bufferedReader.readLine()) != null) {
    fhirJson.append(line);
  }
  bufferedReader.close();
  IBaseResource resource = ctx.newJsonParser().parseResource(fhirJson.toString());
  ValidationResult result = validator.validateWithResult(resource);
  if (result.isSuccessful() == false) {
    for (SingleValidationMessage message : result.getMessages()) {
      System.out.println(message.getSeverity().toString() + ": " + message.getMessage());
    }
  }
  assertTrue(result.isSuccessful());
}
 

public RuntimeValue<FhirContext> createR4FhirContext(BeanContainer container, Collection<String> resourceDefinitions) {
    FhirContext fhirContext = FhirContext.forR4();
    initContext(resourceDefinitions, fhirContext);
    container.instance(FhirContextProducers.class).setR4(fhirContext);
    return new RuntimeValue<>(fhirContext);
}
 

@Test
public void testFHIRR4Export() throws Exception {
  TestHelper.loadTestProperties();
  Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
  Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());

  FhirContext ctx = FhirContext.forR4();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  ValidationResources validator = new ValidationResources();
  List<String> validationErrors = new ArrayList<String>();

  int numberOfPeople = 10;
  Generator generator = new Generator(numberOfPeople);
  
  generator.options.overflow = false;

  for (int i = 0; i < numberOfPeople; i++) {
    int x = validationErrors.size();
    TestHelper.exportOff();
    Person person = generator.generatePerson(i);
    FhirR4.TRANSACTION_BUNDLE = person.random.nextBoolean();
    FhirR4.USE_US_CORE_IG = person.random.nextBoolean();
    FhirR4.USE_SHR_EXTENSIONS = false;
    String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis());
    // Check that the fhirJSON doesn't contain unresolved SNOMED-CT strings
    // (these should have been converted into URIs)
    if (fhirJson.contains("SNOMED-CT")) {
      validationErrors.add(
          "JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
    }
    // Now validate the resource...
    IBaseResource resource = ctx.newJsonParser().parseResource(fhirJson);
    ValidationResult result = validator.validateR4(resource);
    if (!result.isSuccessful()) {
      // If the validation failed, let's crack open the Bundle and validate
      // each individual entry.resource to get context-sensitive error
      // messages...
      Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
      for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
        ValidationResult eresult = validator.validateR4(entry.getResource());
        if (!eresult.isSuccessful()) {
          for (SingleValidationMessage emessage : eresult.getMessages()) {
            boolean valid = false;
            if (emessage.getMessage().contains("@ AllergyIntolerance ait-2")) {
              /*
               * The ait-2 invariant:
               * Description:
               * AllergyIntolerance.clinicalStatus SHALL NOT be present
               * if verification Status is entered-in-error
               * Expression:
               * verificationStatus!='entered-in-error' or clinicalStatus.empty()
               */
              valid = true;
            } else if (emessage.getMessage().contains("@ ExplanationOfBenefit dom-3")) {
              /*
               * For some reason, it doesn't like the contained ServiceRequest and contained
               * Coverage resources in the ExplanationOfBenefit, both of which are
               * properly referenced. Running $validate on test servers finds this valid...
               */
              valid = true;
            } else if (emessage.getMessage().contains(
                "per-1: If present, start SHALL have a lower value than end")) {
              /*
               * The per-1 invariant does not account for daylight savings time... so, if the
               * daylight savings switch happens between the start and end, the validation
               * fails, even if it is valid.
               */
              valid = true; // ignore this error
            } else if (emessage.getMessage().contains("[active, inactive, entered-in-error]")
                || emessage.getMessage().contains("MedicationStatusCodes-list")) {
              /*
               * MedicationStatement.status has more legal values than this... including
               * completed and stopped.
               */
              valid = true;
            }
            if (!valid) {
              System.out.println(parser.encodeResourceToString(entry.getResource()));
              System.out.println("ERROR: " + emessage.getMessage());
              validationErrors.add(emessage.getMessage());
            }
          }
        }
      }
    }
    int y = validationErrors.size();
    if (x != y) {
      Exporter.export(person, System.currentTimeMillis());
    }
  }
  assertTrue("Validation of exported FHIR bundle failed: "
      + String.join("|", validationErrors), validationErrors.size() == 0);
}
 

@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.forR4();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirR4.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());
    }
  }
}
 

@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.forR4();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirR4.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");
      }
    }
  }
}