Java Code Examples for org.hl7.fhir.dstu3.model.Identifier#setSystem()

/**
 * 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 void setConsultationId(DomainResource resource, String consultationId) {
	org.hl7.fhir.dstu3.model.Encounter fhirEncounter = (org.hl7.fhir.dstu3.model.Encounter) resource;
	boolean identifierFound = false;
	List<Identifier> existing = fhirEncounter.getIdentifier();
	for (Identifier existingIdentifier : existing) {
		if (IdentifierSystem.ELEXIS_CONSID.getSystem().equals(existingIdentifier.getSystem())) {
			existingIdentifier.setValue(consultationId);
			identifierFound = true;
			break;
		}
	}
	if (!identifierFound) {
		Identifier identifier = fhirEncounter.addIdentifier();
		identifier.setSystem(IdentifierSystem.ELEXIS_CONSID.getSystem());
		identifier.setValue(consultationId);
	}
}
 

public Identifier makeIdentifierFromII(Element e) throws Exception {
	Identifier id = new Identifier();
	String r = e.getAttribute("root");
	String ex;
	if (e.hasAttribute("extension") && Utilities.noString(e.getAttribute("extension"))) {
		if (generateMissingExtensions) 
			ex = UUID.randomUUID().toString();
		else
			throw new Exception("Broken identifier - extension is blank");
	} else 
		ex = e.getAttribute("extension");
     
	if (Utilities.noString(ex)) {
		id.setSystem("urn:ietf:rfc:3986");
		if (isGuid(r)) 
			id.setValue("urn:uuid:"+r);
		else if (UriForOid(r) != null)
			id.setValue(UriForOid(r));
		else 
			id.setValue(UriForOid(r));
	} else {
		if (isGuid(r)) 
			id.setSystem("urn:uuid:"+r);
		else if (UriForOid(r) != null)
			id.setSystem(UriForOid(r));
		else 
			id.setSystem("urn:oid:"+r);
		id.setValue(ex);
	}
	return id;
}
 

/**
 * 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 static Identifier getIdentifierStrict(BaseIdentifier2 baseIdentifier, Identifier identifier) {
    if (baseIdentifier.getSystem() != null) identifier.setSystem(baseIdentifier.getSystemValue());
    if (baseIdentifier.getValue() != null) identifier.setValue(baseIdentifier.getValue());
    if (baseIdentifier.getUse() != null) {
        identifier.setUse(baseIdentifier.getIdentifierUse());
    }

    return identifier;
}
 

public static Identifier getIdentifier(BaseIdentifier baseIdentifier, Identifier identifier) {
    if (baseIdentifier.getSystem() != null) identifier.setSystem(baseIdentifier.getSystem().getUri());
    if (baseIdentifier.getValue() != null) identifier.setValue(baseIdentifier.getValue());
    if (baseIdentifier.getUse() != null) {
        identifier.setUse(baseIdentifier.getIdentifierUse());
    }
    if (baseIdentifier.getIdentifierType() != null) {
        identifier.getType()
                .addCoding()
                    .setCode(baseIdentifier.getIdentifierType().getCode())
                    .setDisplay(baseIdentifier.getIdentifierType().getDisplay())
                    .setSystem(baseIdentifier.getIdentifierType().getSystem());
    }
    return identifier;
}
 

@Override
public void call(Row r) throws Exception {

  // Build the claim
  // ---------------

  // CLIENT_ID ....... 0
  // CLIENT_SUB_ID ... 1
  // CLAIM_SK ........ 2
  // CLAIM_NBR ....... 3
  // CLAIM_ADJ_CD,ADJ_FROM_CLAIM_SK,ADJ_FROM_CLAIM_NBR,ADJ_FROM_CLAIM_ADJ_NBR,CLAIM_STS_CD_SK,CLAIM_STS_CD,SYS_SUBSC_SK,SYS_SUBSC_ID,SYS_MBR_SK,SYS_MBR_ID,CLIENT_HIERARCHY_LVL1,CLIENT_HIERARCHY_LVL2,CLIENT_HIERARCHY_LVL3,CLIENT_HIERARCHY_LVL4,MBR_PCP_SK,MBR_PCP_NBR,PROV_SK,PROV_ID,PROV_TP_CD_SK,PROV_TP_CD,PAYEE_SK,PAYEE_ID,PAYEE_TIN,APPROVE_DAY_AMT,ACTUAL_DAY_AMT,CLAIM_BEG_SVC_DT,RECEIVE_DT,PAY_DT,DRG_CD_SK,DRG_CD,SUBMIT_DRG_CD_SK,SUBMIT_DRG_CD,BILL_CLASS_CD,FACILITY_TP_CD,HOSP_FREQ_CD,ADMIT_SRC_CD_SK,ADMIT_SRC_CD,ADMIT_TP_CD_SK,ADMIT_TP_CD,HOSP_ADMIT_DT,HOSP_ADMIT_HR,HOSP_DISCHARGE_DT,HOSP_DISCHARGE_HR,HOSP_DISCHARGE_STS_CD_SK,HOSP_DISCHARGE_STS_CD,ATTENDING_PROV_SK,ATTENDING_PROV_ID,PROV_ADDR_CD_SK,PROV_ADDR_CD,OOA_IND,EDI_REF_ID,CURRENT_IND,SENSTV_DRG_IND,CLIENT_SPECIFIC_TXT1,CLIENT_SPECIFIC_TXT2,CLIENT_SPECIFIC_TXT3,CLIENT_SPECIFIC_TXT4,CLIENT_SPECIFIC_TXT5,CLIENT_SPECIFIC_TXT6,CLIENT_SPECIFIC_TXT7,CLIENT_SPECIFIC_TXT8,CLIENT_SPECIFIC_TXT9,CLIENT_SPECIFIC_TXT10,REC_LOAD_DTTM,REC_LAST_UPD_DTTM,REC_DEL_IND,DRG_CODE_TP_CD,SUBMIT_DRG_CODE_TP_CD,QA_CURRENT_IND
  CodeableConcept cc = new CodeableConcept();
  cc.setUserData("value", r.getString(3)); // TODO check that this is how
                                           // this valued is set here

  Identifier i = new Identifier();
  i.setUse(IdentifierUse.OFFICIAL);
  i.setType(cc);
  i.setSystem("Payer Specific	 Claim Number");
  i.setValue(r.getAs("CLAIM_NBR"));
  // TODO i.setAssigner(value);

  List<Identifier> identifiers = new ArrayList<>();
  identifiers.add(i);

  Claim c = new Claim();
  c.setIdentifier(identifiers);

  // Process/send the claim
  // ----------------------

  // TODO
}
 

public static Identifier readAsIdentifier(Element item) {
  Identifier r = new Identifier();
  r.setSystem(item.getNamedChildValue("system"));
  r.setValue(item.getNamedChildValue("value"));
  return r;
}
 

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");
}