Java Code Examples for ca.uhn.fhir.context.FhirContext#forDstu2()

/**
 * Get a FHIR DSTU2 Context for testing, but only initialize it once.
 * 
 * @return a DSTU2 FhirContext
 */
public static FhirContext getDstu2FhirContext() {
  if (dstu2FhirContext == null) {
    dstu2FhirContext = FhirContext.forDstu2();
  }
  return dstu2FhirContext;
}
 

@BeforeClass
public void setup() {
    dstu2ModelResolver = new Dstu2FhirModelResolver();
    FhirContext dstu2Context = FhirContext.forDstu2();
    dstu2RetrieveProvider = new RestFhirRetrieveProvider(new SearchParameterResolver(dstu2Context),
            dstu2Context.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu2"));
    dstu2Provider = new CompositeDataProvider(dstu2ModelResolver, dstu2RetrieveProvider);
    
    dstu3ModelResolver = new Dstu3FhirModelResolver();
    FhirContext dstu3Context = FhirContext.forDstu3();
    dstu3RetrieveProvider = new RestFhirRetrieveProvider(new SearchParameterResolver(dstu3Context), 
    dstu3Context.newRestfulGenericClient("http://measure.eval.kanvix.com/cqf-ruler/baseDstu3"));
    dstu3Provider = new CompositeDataProvider(dstu3ModelResolver, dstu3RetrieveProvider);

}
 

public static void main(String[] args) {
	
	// Create an encounter with an invalid status and no class
	Patient pat = new Patient();
	pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("Jay");
	pat.addAddress().addLine("342 Evergreen Terrace").addLine("Springfield");
	pat.addIdentifier().setSystem("http://acme.org/mrns").setValue("12345");
	
	// Create a new context and enable the narrative generator
	FhirContext ctx = FhirContext.forDstu2();
	ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
	
	String res = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(pat);
	System.out.println(res);
}
 

public RuntimeValue<FhirContext> createDstu2FhirContext(BeanContainer container, Collection<String> resourceDefinitions) {
    FhirContext fhirContext = FhirContext.forDstu2();
    initContext(resourceDefinitions, fhirContext);
    container.instance(FhirContextProducers.class).setDstu2(fhirContext);
    return new RuntimeValue<>(fhirContext);
}
 

@Test
public void testFHIRDSTU2Export() throws Exception {
  TestHelper.loadTestProperties();
  Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
  Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());

  FhirContext ctx = FhirContext.forDstu2();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);

  FhirValidator validator = ctx.newValidator();
  validator.setValidateAgainstStandardSchema(true);
  validator.setValidateAgainstStandardSchematron(true);

  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);
    Config.set("exporter.fhir_dstu2.export", "true");
    FhirDstu2.TRANSACTION_BUNDLE = person.random.nextBoolean();
    String fhirJson = FhirDstu2.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.validateWithResult(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 (Entry entry : bundle.getEntry()) {
        ValidationResult eresult = validator.validateWithResult(entry.getResource());
        if (!eresult.isSuccessful()) {
          for (SingleValidationMessage emessage : eresult.getMessages()) {
            System.out.println(parser.encodeResourceToString(entry.getResource()));
            System.out.println("ERROR: " + emessage.getMessage());
            validationErrors.add(emessage.getMessage());
          }
        }
        if (entry.getResource() instanceof DiagnosticReport) {
          DiagnosticReport report = (DiagnosticReport) entry.getResource();
          if (report.getPerformer().isEmpty()) {
            validationErrors.add("Performer is a required field on DiagnosticReport!");
          }
        }
      }
    }
    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.forDstu2();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirDstu2.convertToFHIRJson(person, System.currentTimeMillis());
  Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
  
  for (Entry entry : bundle.getEntry()) {
    if (entry.getResource() instanceof Observation) {
      Observation obs = (Observation) entry.getResource();
      assertTrue(obs.getValue() instanceof SampledDataDt);
      SampledDataDt data = (SampledDataDt) 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.forDstu2();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirDstu2.convertToFHIRJson(person, System.currentTimeMillis());
  Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
  
  for (Entry entry : bundle.getEntry()) {
    if (entry.getResource() instanceof Media) {
      Media media = (Media) entry.getResource();
      if (media.getContent().getData() != null) {
        assertEquals(400, (int)media.getWidth());
        assertEquals(200, (int)media.getHeight());
        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 testFHIRExport() throws Exception {
  FhirContext ctx = FhirContext.forDstu2();
  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_dstu2.export", "true");
  Config.set("exporter.fhir.transaction_bundle", "true");
  FhirDstu2.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);
  HospitalExporterDstu2.export(0L);

  File expectedExportFolder = tempOutputFolder.toPath().resolve("fhir_dstu2").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 Dstu2FhirModelResolver() {
	this(FhirContext.forDstu2());
}