ca.uhn.fhir.parser.IParser Java Examples

public static void main(String[] theArgs) {
Patient pat = new Patient();
pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");

// Add an extension on the resource
pat.addExtension()
		.setUrl("http://hl7.org/fhir/StructureDefinition/patient-importance")
		.setValue(new CodeableConcept().setText("Patient is a VIP"));

// Add an extension on a primitive
pat.getBirthDateElement().setValueAsString("1955-02-22");
pat.getBirthDateElement().addExtension()
		.setUrl("http://hl7.org/fhir/StructureDefinition/patient-birthTime")
		.setValue(new TimeType("23:30"));

    IParser parser = FhirContext.forDstu3().newJsonParser().setPrettyPrint(true);
    System.out.println(parser.encodeResourceToString(pat));
 }
 

public void beforeProducer(Exchange exchange) {
    final Message in = exchange.getIn();
    String body = in.getBody(String.class);

    if (body != null) {
        List<IBaseResource> resources = new ArrayList<>();
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        try {
            Document doc = dbf.newDocumentBuilder().parse(new ByteArrayInputStream(body.getBytes("UTF-8")));
            Node transactionElement = doc.getFirstChild();
            NodeList childNodes = transactionElement.getChildNodes();
            IParser parser = fhirContext.newXmlParser();
            for (int i = 0; i < childNodes.getLength(); i++) {
                Node resourceNode = childNodes.item(i);
                Document resourceDocument = toDocument(resourceNode, dbf);
                String resourceXml = toXml(resourceDocument);
                IBaseResource resource = parser.parseResource(resourceXml);
                resources.add(resource);
            }
        } catch (SAXException | IOException | ParserConfigurationException | TransformerException e) {
            throw new RuntimeExchangeException("Cannot convert Transaction to a list of resources", exchange, e);
        }

        in.setHeader("CamelFhir.resources", resources);
    }
}
 

public void afterProducer(Exchange exchange) {
    final Message in = exchange.getIn();
    @SuppressWarnings("unchecked")
    List<IBaseResource> body = in.getBody(List.class);

    StringBuilder transaction = new StringBuilder("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>" +
        "<Transaction xmlns=\"http://hl7.org/fhir\">");
    IParser parser = fhirContext.newXmlParser();
    for (IBaseResource resource: body) {
        String encodedResource = parser.encodeResourceToString(resource);
        transaction.append(encodedResource);
    }
    transaction.append("</Transaction>");

    in.setBody(transaction.toString());
}
 

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));
   }
 

/**
 * Loads the structure definitions from the given directory.
 * @param rootDir the directory to load structure definitions from
 * @return a list of structure definitions
 * @throws Throwable when there is an error reading the structure definitions.
 */
private void loadFromDirectory(String rootDir) throws Throwable {

  IParser jsonParser = FhirContext.forR4().newJsonParser();
  jsonParser.setParserErrorHandler(new StrictErrorHandler());

  URL profilesFolder = ClassLoader.getSystemClassLoader().getResource(rootDir);
  Path path = Paths.get(profilesFolder.toURI());
  Files.walk(path, Integer.MAX_VALUE).filter(Files::isReadable).filter(Files::isRegularFile)
      .filter(p -> p.toString().endsWith(".json")).forEach(f -> {
        try {
          IBaseResource resource = jsonParser.parseResource(new FileReader(f.toFile()));
          handleResource(resource);
        } catch (FileNotFoundException e) {
          throw new RuntimeException(e);
        }
      });
}
 

private static void load(PrePopulatedValidationSupport support,
    IParser jsonParser,
    String resource) {

  try (InputStream input = UsCoreStu3ProfileProvider.class
      .getClassLoader()
      .getResourceAsStream(resource)) {

    StructureDefinition definition = (StructureDefinition)
        jsonParser.parseResource(new InputStreamReader(input));

    support.addStructureDefinition(definition);

  } catch (IOException exception) {

    throw new RuntimeException(exception);
  }
}
 

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 static void main(String[] theArgs) {

		// Create a Patient
		Patient pat = new Patient();
		pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");
		pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135");
		pat.addTelecom().setUse(ContactPointUse.HOME).setSystem(ContactPointSystem.PHONE).setValue("1 (416) 340-4800");
		pat.setGender(AdministrativeGender.MALE);

		// Create a context
		FhirContext ctx = FhirContext.forDstu3();

		// Create a JSON parser
		IParser parser = ctx.newJsonParser();
		parser.setPrettyPrint(true);

		String encode = parser.encodeResourceToString(pat);
		System.out.println(encode);

	}
 

private static void addBunsenTestStu3ProfileDefinitions(PrePopulatedValidationSupport support,
    FhirContext context) {

  IParser parser = context.newJsonParser();

  load(support, parser, "definitions/StructureDefinition-bunsen-test-profile-booleanfield.json");
  load(support, parser, "definitions/StructureDefinition-bunsen-test-profile-integerfield.json");
  load(support, parser, "definitions/StructureDefinition-bunsen-test-profile-Patient.json");
  load(support, parser,
      "definitions/StructureDefinition-bunsen-test-profile-integerArrayField.json");
  load(support, parser,
      "definitions/StructureDefinition-bunsen-test-profile-nested-extension.json");
  load(support, parser,
      "definitions/StructureDefinition-bunsen-test-profile-codeableconcept-ext.json");
  load(support, parser,
      "definitions/StructureDefinition-bunsen-test-codeableConcept-modifierExt.json");
  load(support, parser,
      "definitions/StructureDefinition-bunsen-test-string-modifierExt.json");
}
 

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
   FhirValidator validator = FhirContext.forDstu3().newValidator();

   // Cache this object! Supplies structure definitions
   DefaultProfileValidationSupport support = new DefaultProfileValidationSupport();

   // Create the validator
   FhirInstanceValidator module = new FhirInstanceValidator(support);
   validator.registerValidatorModule(module);

   // Did we succeed?
   IParser parser = FhirContext.forDstu3().newXmlParser().setPrettyPrint(true);
   System.out.println(parser.encodeResourceToString(validator.validateWithResult(enc).toOperationOutcome()));
}
 

/**
 * Loads the structure definitions from the given directory.
 * @param rootDir the directory to load structure definitions from
 * @return a list of structure definitions
 * @throws Throwable when there is an error reading the structure definitions.
 */
private void loadFromDirectory(String rootDir) throws Throwable {

  IParser jsonParser = FhirContext.forDstu3().newJsonParser();
  jsonParser.setParserErrorHandler(new StrictErrorHandler());

  URL profilesFolder = ClassLoader.getSystemClassLoader().getResource(rootDir);
  Path path = Paths.get(profilesFolder.toURI());
  Files.walk(path, Integer.MAX_VALUE).filter(Files::isReadable).filter(Files::isRegularFile)
      .filter(p -> p.toString().endsWith(".json")).forEach(f -> {
        try {
          IBaseResource resource = jsonParser.parseResource(new FileReader(f.toFile()));
          resources.add(resource);
          if (resource instanceof CodeSystem) {
            CodeSystem cs = (CodeSystem) resource;
            resourcesMap.put(cs.getUrl(), cs);
            codeSystemMap.put(cs.getUrl(), cs);
          } else if (resource instanceof ValueSet) {
            ValueSet vs = (ValueSet) resource;
            resourcesMap.put(vs.getUrl(), vs);
          } else if (resource instanceof StructureDefinition) {
            StructureDefinition sd = (StructureDefinition) resource;
            resourcesMap.put(sd.getUrl(), sd);
            definitions.add(sd);
            definitionsMap.put(sd.getUrl(), sd);
          }
        } catch (FileNotFoundException e) {
          throw new RuntimeException(e);
        }
      });
}
 

public static void main(String[] args) {
     Example32_ExtendedPatient pat = new Example32_ExtendedPatient();
	pat.addName().setFamily("Simpson").addGiven("Homer");

	pat.setEyeColour(new CodeType("blue"));

	IParser p = FhirContext.forDstu3().newXmlParser().setPrettyPrint(true);
	String encoded = p.encodeResourceToString(pat);
	
	System.out.println(encoded);
}
 

public static void main(String[] args) {

      String input =
         "{" +
            "\"resourceType\": \"Patient\"," +
            "\"foo\": \"bar\"" +
            "}";

      FhirContext ctx = FhirContext.forDstu3();
      IParser parser = ctx.newJsonParser();
      parser.setParserErrorHandler(new StrictErrorHandler());
      IBaseResource output = parser.parseResource(input);
   }
 

public static void main(String[] args) {
	String input = "<Encounter xmlns=\"http://hl7.org/fhir\"><AAAA value=\"foo\"/></Encounter>";

	IParser p = FhirContext.forDstu3().newXmlParser();
	
	// Parse with (default) lenient error handler
	p.setParserErrorHandler(new LenientErrorHandler());
	p.parseResource(input);

	// Parse with strict error handler
	p.setParserErrorHandler(new StrictErrorHandler());
	p.parseResource(input);
}
 

private static void addUsCoreDefinitions(PrePopulatedValidationSupport support,
    FhirContext context) {

  IParser parser = context.newJsonParser();

  load(support, parser, "definitions/StructureDefinition-us-core-allergyintolerance.json");
  load(support, parser, "definitions/StructureDefinition-us-core-birthsex.json");
  load(support, parser, "definitions/StructureDefinition-us-core-careplan.json");
  load(support, parser, "definitions/StructureDefinition-us-core-careteam.json");
  load(support, parser, "definitions/StructureDefinition-us-core-condition.json");
  load(support, parser, "definitions/StructureDefinition-us-core-device.json");
  load(support, parser, "definitions/StructureDefinition-us-core-diagnosticreport.json");
  load(support, parser, "definitions/StructureDefinition-us-core-direct.json");
  load(support, parser, "definitions/StructureDefinition-us-core-documentreference.json");
  load(support, parser, "definitions/StructureDefinition-us-core-encounter.json");
  load(support, parser, "definitions/StructureDefinition-us-core-ethnicity.json");
  load(support, parser, "definitions/StructureDefinition-us-core-goal.json");
  load(support, parser, "definitions/StructureDefinition-us-core-immunization.json");
  load(support, parser, "definitions/StructureDefinition-us-core-location.json");
  load(support, parser, "definitions/StructureDefinition-us-core-medication.json");
  load(support, parser, "definitions/StructureDefinition-us-core-medicationrequest.json");
  load(support, parser, "definitions/StructureDefinition-us-core-medicationstatement.json");
  load(support, parser, "definitions/StructureDefinition-us-core-observationresults.json");
  load(support, parser, "definitions/StructureDefinition-us-core-organization.json");
  load(support, parser, "definitions/StructureDefinition-us-core-patient.json");
  load(support, parser, "definitions/StructureDefinition-us-core-practitioner.json");
  load(support, parser, "definitions/StructureDefinition-us-core-practitionerrole.json");
  load(support, parser, "definitions/StructureDefinition-us-core-procedure.json");
  load(support, parser, "definitions/StructureDefinition-us-core-profile-link.json");
  load(support, parser, "definitions/StructureDefinition-us-core-race.json");
  load(support, parser, "definitions/StructureDefinition-us-core-smokingstatus.json");

}
 

@Benchmark
public void benchmarkHAPIXMLParserValidatorGenerator(FHIRParserValidatorGeneratorBenchmarkState state) throws Exception {
    IParser parser = state.context.newXmlParser();
    IBaseResource baseResource = parser.parseResource(new StringReader(FHIRParserValidatorGeneratorBenchmarkState.XML_SPEC_EXAMPLE));
    state.fhirValidator.validateWithResult(baseResource);
    parser.encodeResourceToWriter(baseResource, FHIRParserValidatorGeneratorBenchmarkState.NOP_WRITER);
}
 

@Benchmark
public void benchmarkHAPIJsonParserValidatorGenerator(FHIRParserValidatorGeneratorBenchmarkState state) throws Exception {
    IParser parser = state.context.newJsonParser();
    IBaseResource resource = parser.parseResource(new StringReader(FHIRParserValidatorGeneratorBenchmarkState.JSON_SPEC_EXAMPLE));
    state.fhirValidator.validateWithResult(resource);
    parser.encodeResourceToWriter(resource, FHIRParserValidatorGeneratorBenchmarkState.NOP_WRITER);
}
 

public static void main(String[] theArgs) {
	
	String resourceBody = "{\"resourceType\":\"Patient\",\"identifier\":[{\"system\":\"http://acme.org/MRNs\",\"value\":\"7000135\"}],\"name\":[{\"family\":[\"Simpson\"],\"given\":[\"Homer\",\"J\"]}]}";

	// Create a context
	FhirContext ctx = FhirContext.forDstu3();
	
	// Create a JSON parser
	IParser parser = ctx.newJsonParser();
	Patient pat = parser.parseResource(Patient.class, resourceBody);
	
	List<Identifier> identifiers = pat.getIdentifier();
	String idSystemString = identifiers.get(0).getSystem();
	String idValueString = identifiers.get(0).getValue();
	
	System.out.println(idSystemString + " " + idValueString);
	
}
 

private static IParser getJsonParser() {
	return context.newJsonParser();
}
 

private static IParser getJsonParser() {
	return context.newJsonParser();
}
 

@Substitute
public IParser newRDFParser() {
    throw new UnsupportedOperationException();
}
 

public static IParser getJsonParser() {
	return context.newJsonParser();
}
 

@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 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 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 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");
      }
    }
  }
}
 

@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 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 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());
    }
  }
}