org.hl7.fhir.dstu3.model.Quantity Java Examples

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);
}
 

public Quantity makeQuantityFromPQ(Element pq, String units) throws Exception {
if (pq == null)
   return null;
Quantity qty = new Quantity();
String n = pq.getAttribute("value").replace(",", "").trim();
try {
  qty.setValue(new BigDecimal(n));
} catch (Exception e) {
	throw new Exception("Unable to process value '"+n+"'", e);
}			
units = Utilities.noString(pq.getAttribute("unit")) ? units : pq.getAttribute("unit");
if (!Utilities.noString(units)) {
	if (ucumSvc == null || ucumSvc.validate(units) != null)
		qty.setUnit(units);
	else {
		qty.setCode(units);
		qty.setSystem("http://unitsofmeasure.org");
		qty.setUnit(ucumSvc.getCommonDisplay(units));
	}
}
return qty;		
}
 

private boolean instanceOf(TypeRefComponent t, Element obj) {
  if (t.getCode().equals("Reference")) {
    if (!(obj instanceof Reference)) {
      return false;
    } else {
      String url = ((Reference) obj).getReference();
      // there are several problems here around profile matching. This process is degenerative, and there's probably nothing we can do to solve it
      if (url.startsWith("http:") || url.startsWith("https:"))
          return true;
      else if (t.hasProfile() && t.getProfile().startsWith("http://hl7.org/fhir/StructureDefinition/")) 
        return url.startsWith(t.getProfile().substring(40)+'/');
      else
        return true;
    }
  } else if (t.getCode().equals("Quantity")) {
    return obj instanceof Quantity;
  } else
    throw new NotImplementedException("Not Done Yet");
}
 

public List<ObservationComponent> getComponents(DomainResource resource){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	List<ObservationComponent> components = new ArrayList<>();
	
	for (ObservationComponentComponent o : fhirObservation.getComponent()) {
		ObservationComponent component = new ObservationComponent(o.getId());
		CodeableConcept codeableConcept = o.getCode();
		if (codeableConcept != null) {
			component.setCoding(ModelUtil.getCodingsFromConcept(codeableConcept));
			component.setExtensions(getExtensions(o));
			
			if (o.hasValueQuantity()) {
				Quantity quantity = (Quantity) o.getValue();
				component.setNumericValue(quantity.getValue());
				component.setNumericValueUnit(quantity.getUnit());
			} else if (o.hasValueStringType()) {
				StringType stringType = (StringType) o.getValue();
				component.setStringValue(stringType.getValue());
			}
		}
		components.add(component);
	}
	return components;
}
 

@Override
public ConceptEntity findAddCode(Quantity quantity) {
    Coding code = new Coding().setCode(quantity.getCode()).setSystem(quantity.getSystem());
    ConceptEntity conceptEntity = findCode(code);

    // 12/Jan/2018 KGM to cope with LOINC codes and depreciated SNOMED codes.
    if (conceptEntity == null) {
        CodeSystemEntity system = codeSystemRepository.findBySystem(quantity.getSystem());
        if (system !=null) {
            conceptEntity = new ConceptEntity();
            conceptEntity.setCode(quantity.getCode());
            conceptEntity.setDescription(quantity.getUnit());
            conceptEntity.setDisplay(quantity.getUnit());
            conceptEntity.setCodeSystem(system);
            em.persist(conceptEntity);
        } else {
            throw new IllegalArgumentException("Unsupported system "+quantity.getSystem());
        }
    }
    return conceptEntity;
}
 

@Test
public void testDecimal() {

  BigDecimal originalDecimal = ((Quantity) testObservation.getValue()).getValue();

  // Decode the Avro decimal to ensure the expected value is there.
  BigDecimal avroDecimal  = (BigDecimal) ((Record)
      ((Record) avroObservation.get("value"))
      .get("quantity"))
      .get("value");

  Assert.assertEquals(originalDecimal.compareTo(avroDecimal), 0);

  Assert.assertEquals(originalDecimal.compareTo(
      ((Quantity) testObservationDecoded
          .getValue())
          .getValue()), 0);
}
 

/**
 * 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;
}
 

@Test
public void testDecimal() {

  BigDecimal originalDecimal = ((org.hl7.fhir.dstu3.model.Quantity)
      testObservation.getValue()).getValue();

  // Decode the Avro decimal to ensure the expected value is there.
  BigDecimal avroDecimal  = avroObservation.getValue().getQuantity().getValue();

  Assert.assertEquals(originalDecimal.compareTo(avroDecimal), 0);

  Assert.assertEquals(originalDecimal.compareTo(
      ((Quantity) testObservationDecoded
          .getValue())
          .getValue()), 0);
}
 

public Optional<String> getNumericValueUnit(DomainResource resource){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	if (fhirObservation.hasValueQuantity()) {
		Quantity quantity = (Quantity) fhirObservation.getValue();
		if (quantity.getUnit() != null) {
			return Optional.of(quantity.getUnit());
		}
	}
	return Optional.empty();
}
 

private static Type makeQty(int sat, String human, String ucum) {
  Quantity q = new Quantity();
  q.setCode(ucum);
  q.setSystem("http://unitsofmeasure.org");
  q.setUnit(human);
  q.setValue(new BigDecimal(sat));
  return q;
}
 

public Optional<BigDecimal> getNumericValue(DomainResource resource){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	if (fhirObservation.hasValueQuantity()) {
		Quantity quantity = (Quantity) fhirObservation.getValue();
		if (quantity.getValue() != null) {
			return Optional.of(quantity.getValue());
		}
	}
	return Optional.empty();
}
 

public void setNumericValue(DomainResource resource, BigDecimal value, String unit){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	Quantity q = new Quantity();
	q.setUnit(unit);
	q.setValue(value);
	fhirObservation.setValue(q);
}
 

static Type mapValueToFHIRType(Object value, String unit) {
  if (value == null) {
    return null;

  } else if (value instanceof Condition) {
    Code conditionCode = ((HealthRecord.Entry) value).codes.get(0);
    return mapCodeToCodeableConcept(conditionCode, SNOMED_URI);

  } else if (value instanceof Code) {
    return mapCodeToCodeableConcept((Code) value, SNOMED_URI);

  } else if (value instanceof String) {
    return new StringType((String) value);

  } else if (value instanceof Number) {
    double dblVal = ((Number) value).doubleValue();
    PlainBigDecimal bigVal = new PlainBigDecimal(dblVal);
    return new Quantity().setValue(bigVal)
        .setCode(unit).setSystem(UNITSOFMEASURE_URI)
        .setUnit(unit);
  } else if (value instanceof Components.SampledData) {
    return mapValueToSampledData((Components.SampledData) value, unit);
  } else {
    throw new IllegalArgumentException("unexpected observation value class: "
        + value.getClass().toString() + "; " + value);
  }
}
 

@Test
public void testDecimal() {

  BigDecimal originalDecimal = ((Quantity) testObservation.getValue()).getValue();

  // Use compareTo since equals checks scale as well.
  Assert.assertTrue(originalDecimal.compareTo(
      (BigDecimal) testObservationDataset.select(
          "value.quantity.value").head().get(0)) == 0);

  Assert.assertEquals(originalDecimal.compareTo(
      ((Quantity) testObservationDecoded
          .getValue())
          .getValue()), 0);
}
 

/**
 * 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;
}
 

public String genType(Type type) throws DefinitionException {
  if (type instanceof Coding)
    return gen((Coding) type);
  if (type instanceof CodeableConcept)
    return displayCodeableConcept((CodeableConcept) type);
  if (type instanceof Quantity)
    return displayQuantity((Quantity) type);
  if (type instanceof Range)
    return displayRange((Range) type);
  return null;
}
 

private String displayQuantity(Quantity q) {
  StringBuilder s = new StringBuilder();

  s.append("(system = '").append(describeSystem(q.getSystem()))
      .append("' code ").append(q.getCode())
      .append(" = '").append(lookupCode(q.getSystem(), q.getCode())).append("')");

  return s.toString();
}
 

private void renderQuantity(Quantity q, XhtmlNode x, boolean showCodeDetails) {
  if (q.hasComparator())
    x.addText(q.getComparator().toCode());
  x.addText(q.getValue().toString());
  if (q.hasUnit())
    x.tx(" "+q.getUnit());
  else if (q.hasCode())
    x.tx(" "+q.getCode());
  if (showCodeDetails && q.hasCode()) {
    x.span("background: LightGoldenRodYellow", null).tx(" (Details: "+describeSystem(q.getSystem())+" code "+q.getCode()+" = '"+lookupCode(q.getSystem(), q.getCode())+"')");
  }
}
 

private static Type makeQty(double val, String human, String ucum) {
  Quantity q = new Quantity();
  q.setCode(ucum);
  q.setSystem("http://unitsofmeasure.org");
  q.setUnit(human);
  q.setValue(new BigDecimal(val));
  return q;
}
 

/**
 * Add a MedicationAdministration if needed for the given medication.
 * 
 * @param personEntry       The Entry for the Person
 * @param bundle            Bundle to add the MedicationAdministration to
 * @param encounterEntry    Current Encounter entry
 * @param medication        The Medication
 * @param medicationRequest The related medicationRequest
 * @return The added Entry
 */
private static BundleEntryComponent medicationAdministration(
    BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry,
    Medication medication, MedicationRequest medicationRequest) {

  MedicationAdministration medicationResource = new MedicationAdministration();

  medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
  medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));

  Code code = medication.codes.get(0);
  String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;

  medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
  medicationResource.setEffective(new DateTimeType(new Date(medication.start)));

  medicationResource.setStatus(MedicationAdministrationStatus.fromCode("completed"));

  if (medication.prescriptionDetails != null) {
    JsonObject rxInfo = medication.prescriptionDetails;
    MedicationAdministrationDosageComponent dosage =
        new MedicationAdministrationDosageComponent();

    // as_needed is true if present
    if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
      Quantity dose = new SimpleQuantity().setValue(
          rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
      dosage.setDose((SimpleQuantity) dose);

      if (rxInfo.has("instructions")) {
        for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
          JsonObject instruction = instructionElement.getAsJsonObject();

          dosage.setText(instruction.get("display").getAsString());
        }
      }
    }
    medicationResource.setDosage(dosage);
  }

  if (!medication.reasons.isEmpty()) {
    // Only one element in list
    Code reason = medication.reasons.get(0);
    for (BundleEntryComponent entry : bundle.getEntry()) {
      if (entry.getResource().fhirType().equals("Condition")) {
        Condition condition = (Condition) entry.getResource();
        // Only one element in list
        Coding coding = condition.getCode().getCoding().get(0);
        if (reason.code.equals(coding.getCode())) {
          medicationResource.addReasonReference().setReference(entry.getFullUrl());
        }
      }
    }
  }

  BundleEntryComponent medicationAdminEntry = newEntry(bundle, medicationResource);
  return medicationAdminEntry;
}
 

private boolean isCoded(Type fixed) {
  return (fixed instanceof Coding) || (fixed instanceof CodeableConcept) || (fixed instanceof CodeType) || (fixed instanceof Quantity);
}
 

public Quantity makeQuantityFromPQ(Element pq) throws Exception {
return makeQuantityFromPQ(pq, null);
}
 

ConceptEntity findAddCode(Quantity quantity);