Java Code Examples for org.hl7.fhir.dstu3.model.Observation#setStatus()

private static void addAge(Bundle b, int y, int m, String v) throws FHIRException {
  Observation obs = new Observation();
  obs.setId("obs-example-age-weight-"+Integer.toString(y)+"-"+Integer.toString(m));
  obs.setSubject(new Reference().setReference("Patient/123"));
  obs.setStatus(ObservationStatus.FINAL);
  Calendar when = Calendar.getInstance();
  when.add(Calendar.YEAR, -y);
  when.add(Calendar.MONTH, m);
  obs.setEffective(new DateTimeType(when));
  obs.getCode().addCoding().setCode("29463-7").setSystem("http://loinc.org");
  obs.setValue(new Quantity());
  obs.getValueQuantity().setCode("kg");
  obs.getValueQuantity().setSystem("http://unitsofmeasure.org");
  obs.getValueQuantity().setUnit("kg");
  obs.getValueQuantity().setValue(new BigDecimal(v));
  b.addEntry().setFullUrl("http://hl7.org/fhir/Observation/"+obs.getId()).setResource(obs);
}
 

private void processSocialHistorySection(CDAUtilities cda, Convert convert, Element section, Context context) throws Exception {
	scanSection("Social History", section);
	int i = 0;
	for (Element c : cda.getChildren(section, "entry")) {
		Element o = cda.getChild(c, "observation");
		Observation obs = new Observation();
		obs.setId(context.baseId+"-smoking-"+(i == 0 ? "" : Integer.toString(i)));
		obs.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/observation-daf-smokingstatus-dafsmokingstatus");
		i++;
		obs.setSubject(context.subjectRef);
		obs.setContext(new Reference().setReference("Encounter/"+context.encounter.getId()));
		obs.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(o, "code")), new Coding().setSystem("http://loinc.org").setCode("72166-2")));

		boolean found = false;
		for (Element e : cda.getChildren(o, "id")) {
			Identifier id = convert.makeIdentifierFromII(e);
			obs.getIdentifier().add(convert.makeIdentifierFromII(e));
		}
		if (!found) {
			obs.setStatus(ObservationStatus.FINAL);
			obs.setEffective(convert.makeDateTimeFromTS(cda.getChild(o, "effectiveTime")));
			obs.setValue(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(o, "value")), null));
			saveResource(obs, "-sh");
		}
	}
}
 

/**
 * 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;
}
 

public static void main(String[] args) {

      // Create an Observation
      Observation obs = new Observation();
      obs.setStatus(Observation.ObservationStatus.FINAL);
      obs.setValue(new StringType("This is a value"));

      // Create a Patient
      Patient pat = new Patient();
      pat.addName().setFamily("Simpson").addGiven("Homer");

      // Assign the Patient to the Observation
      obs.getSubject().setResource(pat);

      FhirContext ctx = FhirContext.forDstu3();
      String output = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs);
      System.out.println(output);

   }
 

private static Observation baseVitals(Bundle b, Calendar when, int min, String name, String lCode, String text) throws FHIRFormatError {
  Observation obs = new Observation();
  obs.setId("obs-vitals-"+name+"-"+Integer.toString(min));
  obs.setSubject(new Reference().setReference("Patient/123"));
  obs.setStatus(ObservationStatus.FINAL);
  obs.setEffective(new DateTimeType(when));
  obs.addCategory().setText("Vital Signs").addCoding().setSystem("http://hl7.org/fhir/observation-category").setCode("vital-signs").setDisplay("Vital Signs");
  obs.getCode().setText(text).addCoding().setCode(lCode).setSystem("http://loinc.org");
  b.addEntry().setFullUrl("http://hl7.org/fhir/Observation/"+obs.getId()).setResource(obs);
  return obs;
}
 

private Observation processObservation(CDAUtilities cda, Convert convert, Context context, Element o) throws Exception {
	Observation obs = new Observation();
	obs.setId(context.baseId+"-results-"+Integer.toString(context.obsId));
	context.obsId++;
	obs.setSubject(context.subjectRef);
	obs.setContext(new Reference().setReference("Encounter/"+context.encounter.getId()));
	obs.setStatus(ObservationStatus.FINAL);
	obs.setEffective(convert.makeDateTimeFromTS(cda.getChild(o, "effectiveTime")));
	obs.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(o, "code")), null));
	obs.setInterpretation(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(o, "interpretationCode")), null));
	Element rr = cda.getChild(o, "referenceRange");
	if (rr != null)
		obs.addReferenceRange().setText(cda.getChild(cda.getChild(rr, "observationRange"), "text").getTextContent());

	Element v = cda.getChild(o, "value");
	String type = v.getAttribute("xsi:type");
	if ("ST".equals(type)) {
		obs.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/observation-daf-results-dafresultobsother");
		obs.setValue(new StringType(v.getTextContent()));
	} else if ("CD".equals(type)) {
		obs.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/observation-daf-results-dafresultobscode");
		obs.setValue(inspectCode(convert.makeCodeableConceptFromCD(v), null));
	} else if ("PQ".equals(type)) {
		obs.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/observation-daf-results-dafresultobsquantity");
		String va = cda.getChild(o, "value").getAttribute("value");
		if (!Utilities.isDecimal(va, true)) {
			obs.setDataAbsentReason(inspectCode(new CodeableConcept().setText(va), null));
		} else
			obs.setValue(convert.makeQuantityFromPQ(cda.getChild(o, "value"), null));
	} else
		throw new Exception("Unknown type '"+type+"'");

	for (Element e : cda.getChildren(o, "id")) {
		Identifier id = convert.makeIdentifierFromII(e);
		obs.getIdentifier().add(id);
	}
	saveResource(obs, "-gen");
	return obs;
}
 

/**
 * Returns a new Observation for testing.
 *
 * @return a FHIR Observation for testing.
 */
public static Observation newObservation() {
  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);

  CodeableConcept obsCode = new CodeableConcept();

  observation.setCode(obsCode);

  Quantity quantity = new Quantity();
  quantity.setValue(new java.math.BigDecimal("123.45"));
  quantity.setUnit("mm[Hg]");
  quantity.setSystem("http://unitsofmeasure.org");
  observation.setValue(quantity);

  ObservationComponentComponent component = observation.addComponent();

  CodeableConcept code = new CodeableConcept()
      .addCoding(new Coding()
          .setCode("abc")
          .setSystem("PLACEHOLDER"));

  component.setCode(code);

  return observation;
}
 

private void processVitalSignsSection(CDAUtilities cda, Convert convert, Element section, Context context) throws Exception {
	scanSection("Vital Signs", section);
	ListResource list = new ListResource();
	list.setId(context.baseId+"-list-vitalsigns");
	//. list.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/list-daf-dafproblemlist"); no list
	list.setSubject(context.subjectRef);
	list.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")), null));
	list.setTitle(cda.getChild(section, "title").getTextContent());
	list.setStatus(ListStatus.CURRENT);
	list.setMode(ListMode.SNAPSHOT);
	list.setDateElement(context.now);
	list.setSource(context.authorRef);
	buildNarrative(list, cda.getChild(section, "text"));

	int i = 0;
	for (Element c : cda.getChildren(section, "entry")) {
		Element org = cda.getChild(c, "organizer"); // problem concern act
		for (Element oc : cda.getChildren(org, "component")) {
			Element o = cda.getChild(oc, "observation"); // problem concern act
			Observation obs = new Observation();
			obs.setId(context.baseId+"-vitals-"+Integer.toString(i));
			obs.setUserData("profile", "http://hl7.org/fhir/StructureDefinition/observation-daf-vitalsigns-dafvitalsigns");
			i++;
			obs.setSubject(context.subjectRef);
			obs.setContext(new Reference().setReference("Encounter/"+context.encounter.getId()));
			obs.setCode(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(o, "code")), null));

			boolean found = false;
			for (Element e : cda.getChildren(o, "id")) {
				Identifier id = convert.makeIdentifierFromII(e);
				obs.getIdentifier().add(id);
			}

			if (!found) {
				list.addEntry().setItem(new Reference().setReference("Observation/"+obs.getId()));
				obs.setStatus(ObservationStatus.FINAL);
				obs.setEffective(convert.makeDateTimeFromTS(cda.getChild(o, "effectiveTime")));
				String v = cda.getChild(o, "value").getAttribute("value");
				if (!Utilities.isDecimal(v, true)) {
					obs.setDataAbsentReason(inspectCode(new CodeableConcept().setText(v), null));
				} else
					obs.setValue(convert.makeQuantityFromPQ(cda.getChild(o, "value")));
				saveResource(obs, "-vs");
			}
		}
	}
	saveResource(list, "-vs");
}
 

@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();
}