org.hl7.fhir.dstu3.model.DateTimeType 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 void execute() throws IOException, FHIRException {
  CSVReader csv = new CSVReader(new FileInputStream("c:\\temp\\nucc.csv"));
  CodeSystem cs = new CodeSystem();
  cs.setId("nucc-provider-taxonomy");
  cs.setUrl("http://nucc.org/provider-taxonomy");
  cs.setName("NUCC Provider Taxonomy");
  cs.setDateElement(new DateTimeType());
  cs.setDescription("The Health Care Provider Taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct 'Levels' including Provider Type, Classification, and Area of Specialization");
  cs.setCopyright("See NUCC copyright statement");
  cs.setStatus(PublicationStatus.ACTIVE);
  cs.setContent(CodeSystemContentMode.COMPLETE);
  cs.setExperimental(false);
  cs.setValueSet("http://hl7.org/fhir/ValueSet/nucc-provider-taxonomy"); 
  cs.setHierarchyMeaning(CodeSystemHierarchyMeaning.CLASSIFIEDWITH);
  csv.parseLine();
  while (csv.ready())
  {
    String[] values = csv.parseLine();
    processLine(cs, values);
  }     
  csv.close();
  new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("c:\\temp\\nucc.xml"), cs);
}
 

public Optional<LocalDateTime> getEffectiveTime(DomainResource resource){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	Type effective = fhirObservation.getEffective();
	if (effective instanceof DateTimeType) {
		return Optional.of(getLocalDateTime(((DateTimeType) effective).getValue()));
	} else if (effective instanceof Period) {
		Date start = ((Period) effective).getStart();
		if (start != null) {
			return Optional.of(getLocalDateTime(start));
		}
		Date end = ((Period) effective).getEnd();
		if (end != null) {
			return Optional.of(getLocalDateTime(end));
		}
	}
	return Optional.empty();
}
 

public Optional<String> getEnd(DomainResource resource){
	org.hl7.fhir.dstu3.model.Condition fhirCondition =
		(org.hl7.fhir.dstu3.model.Condition) resource;
	try {
		if (fhirCondition.hasAbatementDateTimeType()) {
			DateTimeType dateTime = fhirCondition.getAbatementDateTimeType();
			if (dateTime != null) {
				Date date = dateTime.getValue();
				SimpleDateFormat format = new SimpleDateFormat("dd.MM.yyyy");
				return Optional.of(format.format(date));
			}
		} else if (fhirCondition.hasAbatementStringType()) {
			return Optional.of(fhirCondition.getAbatementStringType().getValue());
		}
	} catch (FHIRException e) {
		LoggerFactory.getLogger(ConditionAccessor.class).error("Could not access end.", e);
	}
	return Optional.empty();
}
 

public Optional<String> getStart(DomainResource resource){
	org.hl7.fhir.dstu3.model.Condition fhirCondition =
		(org.hl7.fhir.dstu3.model.Condition) resource;
	try {
		if (fhirCondition.hasOnsetDateTimeType()) {
			DateTimeType dateTime = fhirCondition.getOnsetDateTimeType();
			if (dateTime != null) {
				Date date = dateTime.getValue();
				SimpleDateFormat format = new SimpleDateFormat("dd.MM.yyyy");
				return Optional.of(format.format(date));
			}
		} else if (fhirCondition.hasOnsetStringType()) {
			return Optional.of(fhirCondition.getOnsetStringType().getValue());
		}
	} catch (FHIRException e) {
		LoggerFactory.getLogger(ConditionAccessor.class).error("Could not access start time.",
			e);
	}
	return Optional.empty();
}
 

public static Stream<Arguments> dstu3PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(BooleanType.class.getSimpleName(), new BooleanType()),
    Arguments.arguments(CodeType.class.getSimpleName(), new CodeType()),
    Arguments.arguments(DateType.class.getSimpleName(), new DateType()),
    Arguments.arguments(DateTimeType.class.getSimpleName(), new DateTimeType()),
    Arguments.arguments(DecimalType.class.getSimpleName(), new DecimalType()),
    Arguments.arguments(InstantType.class.getSimpleName(), new InstantType()),
    Arguments.arguments(PositiveIntType.class.getSimpleName(), new PositiveIntType()),
    Arguments.arguments(UnsignedIntType.class.getSimpleName(), new UnsignedIntType()),
    Arguments.arguments(IntegerType.class.getSimpleName(), new IntegerType()),
    Arguments.arguments(MarkdownType.class.getSimpleName(), new MarkdownType()),
    Arguments.arguments(OidType.class.getSimpleName(), new OidType()),
    Arguments.arguments(StringType.class.getSimpleName(), new StringType()),
    Arguments.arguments(TimeType.class.getSimpleName(), new TimeType()),
    Arguments.arguments(UuidType.class.getSimpleName(), new UuidType()),
    Arguments.arguments(Base64BinaryType.class.getSimpleName(), new Base64BinaryType()),
    Arguments.arguments(UriType.class.getSimpleName(), new UriType()));
}
 

public static Stream<Arguments> r5PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(org.hl7.fhir.r5.model.BooleanType.class.getSimpleName(), new org.hl7.fhir.r5.model.BooleanType()),
    Arguments.arguments(org.hl7.fhir.r5.model.CodeType.class.getSimpleName(), new org.hl7.fhir.r5.model.CodeType()),
    Arguments.arguments(org.hl7.fhir.r5.model.DateType.class.getSimpleName(), new org.hl7.fhir.r5.model.DateType()),
    Arguments.arguments(org.hl7.fhir.r5.model.DateTimeType.class.getSimpleName(), new org.hl7.fhir.r5.model.DateTimeType()),
    Arguments.arguments(org.hl7.fhir.r5.model.DecimalType.class.getSimpleName(), new org.hl7.fhir.r5.model.DecimalType()),
    Arguments.arguments(org.hl7.fhir.r5.model.InstantType.class.getSimpleName(), new org.hl7.fhir.r5.model.InstantType()),
    Arguments.arguments(org.hl7.fhir.r5.model.PositiveIntType.class.getSimpleName(), new org.hl7.fhir.r5.model.PositiveIntType()),
    Arguments.arguments(org.hl7.fhir.r5.model.UnsignedIntType.class.getSimpleName(), new org.hl7.fhir.r5.model.UnsignedIntType()),
    Arguments.arguments(org.hl7.fhir.r5.model.IntegerType.class.getSimpleName(), new org.hl7.fhir.r5.model.IntegerType()),
    Arguments.arguments(org.hl7.fhir.r5.model.MarkdownType.class.getSimpleName(), new org.hl7.fhir.r5.model.MarkdownType()),
    Arguments.arguments(org.hl7.fhir.r5.model.OidType.class.getSimpleName(), new org.hl7.fhir.r5.model.OidType()),
    Arguments.arguments(org.hl7.fhir.r5.model.StringType.class.getSimpleName(), new org.hl7.fhir.r5.model.StringType()),
    Arguments.arguments(org.hl7.fhir.r5.model.TimeType.class.getSimpleName(), new org.hl7.fhir.r5.model.TimeType()),
    Arguments.arguments(org.hl7.fhir.r5.model.UuidType.class.getSimpleName(), new org.hl7.fhir.r5.model.UuidType()),
    Arguments.arguments(org.hl7.fhir.r5.model.Base64BinaryType.class.getSimpleName(), new org.hl7.fhir.r5.model.Base64BinaryType()),
    Arguments.arguments(org.hl7.fhir.r5.model.UriType.class.getSimpleName(), new org.hl7.fhir.r5.model.UriType()));
}
 

public static Stream<Arguments> dstu3PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(BooleanType.class.getSimpleName(), new BooleanType()),
    Arguments.arguments(CodeType.class.getSimpleName(), new CodeType()),
    Arguments.arguments(DateType.class.getSimpleName(), new DateType()),
    Arguments.arguments(DateTimeType.class.getSimpleName(), new DateTimeType()),
    Arguments.arguments(DecimalType.class.getSimpleName(), new DecimalType()),
    Arguments.arguments(InstantType.class.getSimpleName(), new InstantType()),
    Arguments.arguments(PositiveIntType.class.getSimpleName(), new PositiveIntType()),
    Arguments.arguments(UnsignedIntType.class.getSimpleName(), new UnsignedIntType()),
    Arguments.arguments(IntegerType.class.getSimpleName(), new IntegerType()),
    Arguments.arguments(MarkdownType.class.getSimpleName(), new MarkdownType()),
    Arguments.arguments(OidType.class.getSimpleName(), new OidType()),
    Arguments.arguments(StringType.class.getSimpleName(), new StringType()),
    Arguments.arguments(TimeType.class.getSimpleName(), new TimeType()),
    Arguments.arguments(UuidType.class.getSimpleName(), new UuidType()),
    Arguments.arguments(Base64BinaryType.class.getSimpleName(), new Base64BinaryType()),
    Arguments.arguments(UriType.class.getSimpleName(), new UriType()));
}
 

public static Stream<Arguments> r4PrimitiveTypes() {
  return Stream.of(
    Arguments.arguments(org.hl7.fhir.r4.model.BooleanType.class.getSimpleName(), new org.hl7.fhir.r4.model.BooleanType()),
    Arguments.arguments(org.hl7.fhir.r4.model.CodeType.class.getSimpleName(), new org.hl7.fhir.r4.model.CodeType()),
    Arguments.arguments(org.hl7.fhir.r4.model.DateType.class.getSimpleName(), new org.hl7.fhir.r4.model.DateType()),
    Arguments.arguments(org.hl7.fhir.r4.model.DateTimeType.class.getSimpleName(), new org.hl7.fhir.r4.model.DateTimeType()),
    Arguments.arguments(org.hl7.fhir.r4.model.DecimalType.class.getSimpleName(), new org.hl7.fhir.r4.model.DecimalType()),
    Arguments.arguments(org.hl7.fhir.r4.model.InstantType.class.getSimpleName(), new org.hl7.fhir.r4.model.InstantType()),
    Arguments.arguments(org.hl7.fhir.r4.model.PositiveIntType.class.getSimpleName(), new org.hl7.fhir.r4.model.PositiveIntType()),
    Arguments.arguments(org.hl7.fhir.r4.model.UnsignedIntType.class.getSimpleName(), new org.hl7.fhir.r4.model.UnsignedIntType()),
    Arguments.arguments(org.hl7.fhir.r4.model.IntegerType.class.getSimpleName(), new org.hl7.fhir.r4.model.IntegerType()),
    Arguments.arguments(org.hl7.fhir.r4.model.MarkdownType.class.getSimpleName(), new org.hl7.fhir.r4.model.MarkdownType()),
    Arguments.arguments(org.hl7.fhir.r4.model.OidType.class.getSimpleName(), new org.hl7.fhir.r4.model.OidType()),
    Arguments.arguments(org.hl7.fhir.r4.model.StringType.class.getSimpleName(), new org.hl7.fhir.r4.model.StringType()),
    Arguments.arguments(org.hl7.fhir.r4.model.TimeType.class.getSimpleName(), new org.hl7.fhir.r4.model.TimeType()),
    Arguments.arguments(org.hl7.fhir.r4.model.UuidType.class.getSimpleName(), new org.hl7.fhir.r4.model.UuidType()),
    Arguments.arguments(org.hl7.fhir.r4.model.Base64BinaryType.class.getSimpleName(), new org.hl7.fhir.r4.model.Base64BinaryType()),
    Arguments.arguments(org.hl7.fhir.r4.model.UriType.class.getSimpleName(), new org.hl7.fhir.r4.model.UriType()));
}
 

public void process() throws FHIRFormatError, IOException, XmlPullParserException, SAXException, ParserConfigurationException {
	log("Begin. Produce Loinc CDEs in "+dest+" from "+definitions);
	loadLoinc();
	log("LOINC loaded");

	now = DateTimeType.now();

	bundle = new Bundle();
	bundle.setId("http://hl7.org/fhir/commondataelement/loinc");
   bundle.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));

	processLoincCodes();
	if (dest != null) {
		log("Saving...");
		saveBundle();
	}
	log("Done");

}
 

public Bundle process(String sourceFile) throws FileNotFoundException, SAXException, IOException, ParserConfigurationException {
  this.definitions = sourceFile;
  log("Begin. Produce Loinc CDEs in "+dest+" from "+definitions);
  loadLoinc();
  log("LOINC loaded");

  now = DateTimeType.now();

  bundle = new Bundle();
  bundle.setType(BundleType.COLLECTION);
  bundle.setId("http://hl7.org/fhir/commondataelement/loinc");
  bundle.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));

  processLoincCodes();
  return bundle;
}
 

@Override
public void setScheduledTime(LocalDateTime time){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		org.hl7.fhir.dstu3.model.ProcedureRequest fhirProcedureRequest =
			(org.hl7.fhir.dstu3.model.ProcedureRequest) resource.get();
		fhirProcedureRequest.setOccurrence(new DateTimeType(getDate(time)));
		
		saveResource(resource.get());
	}
}
 

/**
 * Convert the timestamp into a FHIR DateType or DateTimeType.
 *
 * @param datetime Timestamp
 * @param time If true, return a DateTime; if false, return a Date.
 * @return a DateType or DateTimeType representing the given timestamp
 */
private static Type convertFhirDateTime(long datetime, boolean time) {
  Date date = new Date(datetime);

  if (time) {
    return new DateTimeType(date);
  } else {
    return new DateType(date);
  }
}
 

private ValueSet makeTypeList(StructureDefinition profile, List<TypeRefComponent> types, String path) {
  ValueSet vs = new ValueSet();
  vs.setName("Type options for "+path);
  vs.setDescription(vs.getName());
 vs.setStatus(PublicationStatus.ACTIVE);
  vs.setExpansion(new ValueSetExpansionComponent());
  vs.getExpansion().setIdentifier(Factory.createUUID());
  vs.getExpansion().setTimestampElement(DateTimeType.now());
  for (TypeRefComponent t : types) {
    ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
   if (t.getCode().equals("Reference") && (t.hasTargetProfile() && t.getTargetProfile().startsWith("http://hl7.org/fhir/StructureDefinition/"))) { 
     cc.setCode(t.getTargetProfile().substring(40));
      cc.setSystem("http://hl7.org/fhir/resource-types");
     cc.setDisplay(cc.getCode());
    } else {
      ProfileUtilities pu = new ProfileUtilities(context, null, null);
      StructureDefinition ps = null;
      if (t.hasTargetProfile()) 
        ps = pu.getProfile(profile, t.getTargetProfile());
      else if (t.hasProfile()) 
        ps = pu.getProfile(profile, t.getProfile());
      
      if (ps != null) {
       cc.setCode(t.getTargetProfile());
        cc.setDisplay(ps.getType());
        cc.setSystem("http://hl7.org/fhir/resource-types");
      } else {
       cc.setCode(t.getCode());
       cc.setDisplay(t.getCode());
        cc.setSystem("http://hl7.org/fhir/data-types");
      }
    }
   t.setUserData("text", cc.getCode());
  }

  return vs;
}
 

public static boolean isDeprecated(CodeSystem cs, ConceptDefinitionComponent def) {
  for (ConceptPropertyComponent p : def.getProperty()) {
    if (p.getCode().equals("deprecated") && p.hasValue() && p.getValue() instanceof BooleanType) 
      return ((BooleanType) p.getValue()).getValue();
    if (p.getCode().equals("deprecationDate") && p.hasValue() && p.getValue() instanceof DateTimeType) 
      return ((DateTimeType) p.getValue()).before(new DateTimeType());
  }
  return false;
}
 

private String convertForDateFormat(String fmt, String av) throws FHIRException {
 	if ("v3".equals(fmt)) {
 		DateTimeType d = DateTimeType.parseV3(av);
 		return d.asStringValue();
 	} else
 		throw new FHIRException("Unknown Data format '"+fmt+"'");
}
 

private static ConceptMap generateLoincMdcMap(CodeSystem mdc, String dst, String src) throws IOException, FHIRException {
  ConceptMap cm = new ConceptMap();
  cm.setId("loinc-mdc");
  cm.setUrl("http:/???/fhir/ConceptMap/loinc-mdc");
  cm.setVersion("[todo]");
  cm.setName("LoincMdcCrossMap");
  cm.setTitle("Cross Map between LOINC and MDC");
  cm.setStatus(PublicationStatus.DRAFT);
  cm.setExperimental(true);
  cm.setDateElement(new DateTimeType());
  cm.setPublisher("HL7, Inc");
  ContactDetail cd = cm.addContact();
  cd.setName("LOINC + IEEE");
  ContactPoint cp = cd.addTelecom();
  cp.setSystem(ContactPointSystem.URL);
  cp.setValue("http://loinc.org");
  cm.setDescription("A Cross Map between the LOINC and MDC Code systems");
  cm.setPurpose("To implementers map between medical device codes and LOINC codes");
  cm.setCopyright("This content LOINC \u00ae is copyright \u00a9 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use");
  cm.setSource(new UriType("http://loinc.org/vs"));
  cm.setTarget(new UriType(MDC_ALL_VALUES));
  ConceptMapGroupComponent g = cm.addGroup();
  g.setSource("urn:iso:std:iso:11073:10101");
  g.setTarget("http://loinc.org");

  CSVReader csv = new CSVReader(new FileInputStream(src));
  csv.readHeaders();
  while (csv.line()) {
    SourceElementComponent e = g.addElement();
    e.setCode(csv.cell("IEEE_CF_CODE10"));
    e.setDisplay(csv.cell("IEEE_DESCRIPTION"));
    TargetElementComponent t = e.addTarget();
    t.setEquivalence(ConceptMapEquivalence.EQUIVALENT);
    t.setCode(csv.cell("LOINC_NUM"));
    t.setDisplay(csv.cell("LOINC_LONG_COMMON_NAME"));
  }
  new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "conceptmap-"+cm.getId()+".xml")), cm);
  System.out.println("Done");
  return cm;
}
 

public DateTimeType makeDateTimeFromIVL(Element ivl) throws Exception {
 if (ivl == null)
 	return null;
 if (ivl.hasAttribute("value")) 
 	return makeDateTimeFromTS(ivl);
 Element high =  cda.getChild(ivl, "high");
 if (high != null)
 	return makeDateTimeFromTS(high);
 Element low =  cda.getChild(ivl, "low");
 if (low != null)
 	return makeDateTimeFromTS(low);
 return null;
}
 

public DateTimeType makeDateTimeFromTS(Element ts) throws Exception {
if (ts == null)
	return null;

  String v = ts.getAttribute("value");
  if (Utilities.noString(v))
  	return null;
  
  if (v.length() > 8 && !hasTimezone(v))
  	v += defaultTimezone;
  DateTimeType d = DateTimeType.parseV3(v);
  return d;
}
 

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;
}
 

public static void setDeprecated(CodeSystem cs, ConceptDefinitionComponent concept, DateTimeType date) throws FHIRFormatError {
  defineDeprecatedProperty(cs);
  concept.addProperty().setCode("deprecationDate").setValue(date);    
}
 

private void processLoincCodes() {
	Element row = XMLUtil.getFirstChild(xml.getDocumentElement());
	int i = 0;
	while (row != null) {
		i++;
		if (i % 1000 == 0)
			System.out.print(".");
			String code = col(row, "LOINC_NUM");
			String comp = col(row, "COMPONENT");
			DataElement de = new DataElement();
			de.setId("loinc-"+code);
	    de.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
			bundle.getEntry().add(new BundleEntryComponent().setResource(de));
			Identifier id = new Identifier();
			id.setSystem("http://hl7.org/fhir/commondataelement/loinc");
			id.setValue(code);
			de.addIdentifier(id);
			de.setPublisher("Regenstrief + FHIR Project Team");
			if (!col(row, "STATUS").equals("ACTIVE"))
 				de.setStatus(PublicationStatus.DRAFT); // till we get good at this
			else
				de.setStatus(PublicationStatus.RETIRED);
			de.setDateElement(DateTimeType.now());
			de.setName(comp);
			ElementDefinition dee = de.addElement();

			// PROPERTY	ignore
			// TIME_ASPCT	
			// SYSTEM	
			// SCALE_TYP	
			// METHOD_TYP	
			// dee.getCategory().add(new CodeableConcept().setText(col(row, "CLASS")));
			// SOURCE	
			// DATE_LAST_CHANGED - should be in ?	
			// CHNG_TYPE	
			dee.setComment(col(row , "COMMENTS"));
			if (hasCol(row, "CONSUMER_NAME"))
				dee.addAlias(col(row, "CONSUMER_NAME"));	
			// MOLAR_MASS	
			// CLASSTYPE	
			// FORMULA	
			// SPECIES	
			// EXMPL_ANSWERS	
			// ACSSYM	
			// BASE_NAME - ? this is a relationship	
			// NAACCR_ID	
			// ---------- CODE_TABLE todo	
			// SURVEY_QUEST_TEXT	
			// SURVEY_QUEST_SRC	
			if (hasCol(row, "RELATEDNAMES2")) {
        String n = col(row, "RELATEDNAMES2");
        for (String s : n.split("\\;")) {
					if (!Utilities.noString(s))
						dee.addAlias(s);	
        }
			}
			dee.addAlias(col(row, "SHORTNAME"));	
			// ORDER_OBS	
			// CDISC Code	
			// HL7_FIELD_SUBFIELD_ID	
			//  ------------------ EXTERNAL_COPYRIGHT_NOTICE todo	
			dee.setDefinition(col(row, "LONG_COMMON_NAME"));	
			// HL7_V2_DATATYPE	
			String cc = makeType(col(row, "HL7_V3_DATATYPE"), code);
			if (cc != null)
			  dee.addType().setCode(cc);	
			// todo... CURATED_RANGE_AND_UNITS	
			// todo: DOCUMENT_SECTION	
			// STATUS_REASON	
			// STATUS_TEXT	
			// CHANGE_REASON_PUBLIC	
			// COMMON_TEST_RANK	
			// COMMON_ORDER_RANK	
			// COMMON_SI_TEST_RANK	
			// HL7_ATTACHMENT_STRUCTURE

			// units:
			// UNITSREQUIRED	
			// SUBMITTED_UNITS
			ToolingExtensions.setAllowableUnits(dee, makeUnits(col(row, "EXAMPLE_UNITS"), col(row, "EXAMPLE_UCUM_UNITS")));
			// EXAMPLE_SI_UCUM_UNITS	
		
		row = XMLUtil.getNextSibling(row);
	}
	System.out.println("done");
}
 

/**
 * Returns a FHIR Condition for testing purposes.
 *
 * @return a FHIR Condition for testing.
 */
public static Condition newCondition() {

  Condition condition = new Condition();

  // Condition based on example from FHIR:
  // https://www.hl7.org/fhir/condition-example.json.html
  condition.setId("Condition/example");

  condition.setLanguage("en_US");

  // Narrative text
  Narrative narrative = new Narrative();
  narrative.setStatusAsString("generated");
  narrative.setDivAsString("This data was generated for test purposes.");
  XhtmlNode node = new XhtmlNode();
  node.setNodeType(NodeType.Text);
  node.setValue("Severe burn of left ear (Date: 24-May 2012)");
  condition.setText(narrative);

  condition.setSubject(new Reference("Patient/12345").setDisplay("Here is a display for you."));

  condition.setVerificationStatus(Condition.ConditionVerificationStatus.CONFIRMED);

  // Condition code
  CodeableConcept code = new CodeableConcept();
  code.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("39065001")
      .setDisplay("Severe");
  condition.setSeverity(code);

  // Severity code
  CodeableConcept severity = new CodeableConcept();
  severity.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("24484000")
      .setDisplay("Burn of ear")
      .setUserSelected(true);
  condition.setSeverity(severity);

  // Onset date time
  DateTimeType onset = new DateTimeType();
  onset.setValueAsString("2012-05-24");
  condition.setOnset(onset);

  return condition;
}
 

/**
 * Returns a FHIR Condition for testing purposes.
 */
public static Condition newCondition() {

  Condition condition = new Condition();

  // Condition based on example from FHIR:
  // https://www.hl7.org/fhir/condition-example.json.html
  condition.setId("Condition/example");

  condition.setLanguage("en_US");

  // Narrative text
  Narrative narrative = new Narrative();
  narrative.setStatusAsString("generated");
  narrative.setDivAsString("This data was generated for test purposes.");
  XhtmlNode node = new XhtmlNode();
  node.setNodeType(NodeType.Text);
  node.setValue("Severe burn of left ear (Date: 24-May 2012)");
  condition.setText(narrative);

  condition.setSubject(new Reference("Patient/example").setDisplay("Here is a display for you."));

  condition.setVerificationStatus(Condition.ConditionVerificationStatus.CONFIRMED);

  // Condition code
  CodeableConcept code = new CodeableConcept();
  code.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("39065001")
      .setDisplay("Severe");
  condition.setSeverity(code);

  // Severity code
  CodeableConcept severity = new CodeableConcept();
  severity.addCoding()
      .setSystem("http://snomed.info/sct")
      .setCode("24484000")
      .setDisplay("Burn of ear")
      .setUserSelected(true);
  condition.setSeverity(severity);

  // Onset date time
  DateTimeType onset = new DateTimeType();
  onset.setValueAsString("2012-05-24");
  condition.setOnset(onset);

  return condition;
}
 

/**
 * 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;
}
 

public void setEffectiveTime(DomainResource resource, LocalDateTime time){
	org.hl7.fhir.dstu3.model.Observation fhirObservation =
		(org.hl7.fhir.dstu3.model.Observation) resource;
	fhirObservation.setEffective(new DateTimeType(getDate(time)));
}