org.hl7.fhir.r4.model.Observation Java Examples

/**
 * Set up Spark.
 */
@BeforeClass
public static void setUp() {
  spark = SparkSession.builder()
      .master("local[*]")
      .appName("testing")
      .getOrCreate();

  patientDataset = spark.createDataset(ImmutableList.of(patient),
      encoders.of(Patient.class));
  decodedPatient = patientDataset.head();

  conditionsDataset = spark.createDataset(ImmutableList.of(condition),
      encoders.of(Condition.class));
  decodedCondition = conditionsDataset.head();

  observationsDataset = spark.createDataset(ImmutableList.of(observation),
      encoders.of(Observation.class));
  decodedObservation = observationsDataset.head();

  medDataset = spark.createDataset(ImmutableList.of(medRequest),
      encoders.of(MedicationRequest.class));

  decodedMedRequest = medDataset.head();
}
 

/**
 * Returns a FHIR Observation for testing purposes.
 */
public static Observation newObservation() {

  // Observation based on https://www.hl7.org/FHIR/observation-example-bloodpressure.json.html
  Observation observation = new Observation();

  observation.setId("blood-pressure");

  Identifier identifier = observation.addIdentifier();
  identifier.setSystem("urn:ietf:rfc:3986");
  identifier.setValue("urn:uuid:187e0c12-8dd2-67e2-99b2-bf273c878281");

  observation.setStatus(Observation.ObservationStatus.FINAL);

  Quantity quantity = new Quantity();
  quantity.setValue(new java.math.BigDecimal("123.45"));
  quantity.setUnit("mm[Hg]");
  observation.setValue(quantity);

  return observation;
}
 

@Override
public List<IAuthRule> buildRuleList(RequestDetails theRequestDetails) {

   // Process this header
   String authHeader = theRequestDetails.getHeader("Authorization");

   RuleBuilder builder = new RuleBuilder();
   builder
      .allow().metadata().andThen()
      .allow().read().allResources().withAnyId().andThen()
      .allow().write().resourcesOfType(Observation.class).inCompartment("Patient", new IdType("Patient/123"));

   return builder.build();
}
 

@Test
public void testWebsocketSubscription() throws Exception {
    /*
     * Create subscription
     */
    Subscription subscription = new Subscription();
    subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
    subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
    subscription.setCriteria("Observation?status=final");

    Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
    channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
    channel.setPayload("application/json");
    subscription.setChannel(channel);

    MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
    IIdType mySubscriptionId = methodOutcome.getId();

    // Wait for the subscription to be activated
    waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());

    /*
     * Attach websocket
     */

    WebSocketClient myWebSocketClient = new WebSocketClient();
    SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);

    myWebSocketClient.start();
    URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
    ClientUpgradeRequest request = new ClientUpgradeRequest();
    ourLog.info("Connecting to : {}", echoUri);
    Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
    Session session = connection.get(2, TimeUnit.SECONDS);

    ourLog.info("Connected to WS: {}", session.isOpen());

    /*
     * Create a matching resource
     */
    Observation obs = new Observation();
    obs.setStatus(Observation.ObservationStatus.FINAL);
    ourClient.create().resource(obs).execute();

    // Give some time for the subscription to deliver
    Thread.sleep(2000);

    /*
     * Ensure that we receive a ping on the websocket
     */
    waitForSize(1, () -> mySocketImplementation.myPingCount);

    /*
     * Clean up
     */
    ourClient.delete().resourceById(mySubscriptionId).execute();
}
 

@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());
    }
  }
}