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

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");
		}
	}
}
 

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;
}
 

protected String processVitalSignsObservation(Element comp, ListResource list) throws Exception {
	Element observation = cda.getChild(comp, "observation");
	cda.checkTemplateId(observation, "2.16.840.1.113883.10.20.22.4.27");
	checkNoNegationOrNullFlavor(observation, "Vital Signs Observation");
	checkNoSubject(observation, "Vital Signs Observation");

	Observation obs = new Observation();

	//	SHALL contain at least one [1..*] id (CONF:7300).
	for (Element e : cda.getChildren(observation, "id"))
		obs.getIdentifier().add(convert.makeIdentifierFromII(e));

	// SHALL contain exactly one [1..1] code, which SHOULD be selected from ValueSet Vital Sign Result Value Set 2.16.840.1.113883.3.88.12.80.62 DYNAMIC (CONF:7301).
	obs.setCode(convert.makeCodeableConceptFromCD(cda.getChild(observation, "code"))); // all loinc codes

	// SHOULD contain zero or one [0..1] text (CONF:7302).
	// The text, if present, SHOULD contain zero or one [0..1] reference (CONF:15943).
	// The reference, if present, SHOULD contain zero or one [0..1] @value (CONF:15944).
	// This reference/@value SHALL begin with a '#' and SHALL point to its corresponding narrative (using the approach defined in CDA Release 2, section 4.3.5.1) (CONF:15945).
	// todo: put this in narrative if it exists?


	// SHALL contain exactly one [1..1] statusCode (CONF:7303).	This statusCode SHALL contain exactly one [1..1] @code="completed" Completed (CodeSystem: ActStatus 2.16.840.1.113883.5.14 STATIC) (CONF:19119).
	// ignore

	// SHALL contain exactly one [1..1] effectiveTime (CONF:7304).
	obs.setEffective(convert.makeMatchingTypeFromIVL(cda.getChild(observation, "effectiveTime")));

	//	SHALL contain exactly one [1..1] value with @xsi:type="PQ" (CONF:7305).
	obs.setValue(convert.makeQuantityFromPQ(cda.getChild(observation, "value")));

	// MAY contain zero or one [0..1] interpretationCode (CONF:7307).
	obs.setInterpretation(convert.makeCodeableConceptFromCD(cda.getChild(observation, "interpretationCode")));

	//	MAY contain zero or one [0..1] methodCode (CONF:7308).
	obs.setMethod(convert.makeCodeableConceptFromCD(cda.getChild(observation, "methodCode")));

	// MAY contain zero or one [0..1] targetSiteCode (CONF:7309).
	obs.setBodySite(convert.makeCodeableConceptFromCD(cda.getChild(observation, "targetSiteCode")));

	// MAY contain zero or one [0..1] author (CONF:7310).
	if (cda.getChild(observation, "author") != null)
		obs.getPerformer().add(makeReferenceToPractitionerForAssignedEntity(cda.getChild(observation, "author"), composition));

	// make a contained practitioner
	String n = nextRef();
	obs.setId(n);
	list.getContained().add(obs);
	return n;
}
 

/**
 * 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");
}