Examples with MR org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR used on opensource projects

Example 76 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project org.hl7.fhir.core by hapifhir.

the class MeasureValidator method validateMeasureReportGroups.

private void validateMeasureReportGroups(ValidatorHostContext hostContext, MeasureContext m, List<ValidationMessage> errors, Element mr, NodeStack stack, boolean inProgress) {
    if (m.groups().size() == 0) {
        // only validate the report groups if the measure has groups.
        return;
    }
    List<MeasureGroupComponent> groups = new ArrayList<MeasureGroupComponent>();
    List<Element> glist = mr.getChildrenByName("group");
    if (glist.size() == 1 && m.groups().size() == 1) {
        // if there's only one group, it can be ((and usually is) anonymous)
        // but we still check that the code, if both have one, is consistent.
        Element mrg = glist.get(0);
        NodeStack ns = stack.push(mrg, 0, mrg.getProperty().getDefinition(), mrg.getProperty().getDefinition());
        if (m.groups().get(0).hasCode() && mrg.hasChild("code")) {
            CodeableConcept cc = ObjectConverter.readAsCodeableConcept(mrg.getNamedChild("code"));
            if (rule(errors, IssueType.BUSINESSRULE, mrg.line(), mrg.col(), ns.getLiteralPath(), hasUseableCode(cc), I18nConstants.MEASURE_MR_GRP_NO_USABLE_CODE)) {
                rule(errors, IssueType.BUSINESSRULE, mrg.line(), mrg.col(), ns.getLiteralPath(), cc.matches(m.groups().get(0).getCode()), I18nConstants.MEASURE_MR_GRP_NO_WRONG_CODE, DataRenderer.display(context, cc), DataRenderer.display(context, m.groups().get(0).getCode()));
            }
        }
        validateMeasureReportGroup(hostContext, m, m.groups().get(0), errors, mrg, ns, inProgress);
    } else {
        int i = 0;
        for (Element mrg : glist) {
            NodeStack ns = stack.push(mrg, i, mrg.getProperty().getDefinition(), mrg.getProperty().getDefinition());
            CodeableConcept cc = ObjectConverter.readAsCodeableConcept(mrg.getNamedChild("code"));
            if (rule(errors, IssueType.BUSINESSRULE, mrg.line(), mrg.col(), ns.getLiteralPath(), cc != null, I18nConstants.MEASURE_MR_GRP_NO_CODE)) {
                MeasureGroupComponent mg = getGroupForCode(cc, m.measure());
                if (rule(errors, IssueType.BUSINESSRULE, mrg.line(), mrg.col(), ns.getLiteralPath(), mg != null, I18nConstants.MEASURE_MR_GRP_UNK_CODE)) {
                    if (rule(errors, IssueType.BUSINESSRULE, mrg.line(), mrg.col(), ns.getLiteralPath(), !groups.contains(mg), I18nConstants.MEASURE_MR_GRP_DUPL_CODE)) {
                        groups.add(mg);
                        validateMeasureReportGroup(hostContext, m, mg, errors, mrg, ns, inProgress);
                    }
                }
            }
            i++;
        }
        boolean dataCollection = isDataCollection(mr);
        for (MeasureGroupComponent mg : m.groups()) {
            if (!groups.contains(mg)) {
                rule(errors, IssueType.BUSINESSRULE, mr.line(), mr.col(), stack.getLiteralPath(), groups.contains(mg) || dataCollection, I18nConstants.MEASURE_MR_GRP_MISSING_BY_CODE, DataRenderer.display(context, mg.getCode()));
            }
        }
    }
}

Example 77 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project org.hl7.fhir.core by hapifhir.

the class ValidationTests method test.

@SuppressWarnings("deprecation")
@Test
public void test() throws Exception {
    CacheVerificationLogger logger = new CacheVerificationLogger();
    long setup = System.nanoTime();
    this.name = name;
    System.out.println("---- " + name + " ----------------------------------------------------------------");
    System.out.println("** Core: ");
    String txLog = null;
    if (content.has("txLog")) {
        txLog = content.get("txLog").getAsString();
    }
    version = "5.0";
    List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
    if (content.has("version")) {
        version = content.get("version").getAsString();
    }
    version = VersionUtilities.getMajMin(version);
    if (!ve.containsKey(version)) {
        if (version.startsWith("5.0"))
            ve.put(version, TestUtilities.getValidationEngine("hl7.fhir.r5.core#4.5.0", ValidationEngineTests.DEF_TX, txLog, FhirPublication.R5, true, "4.5.0"));
        else if (version.startsWith("4.3"))
            ve.put(version, TestUtilities.getValidationEngine("hl7.fhir.r4b.core#4.3.0", ValidationEngineTests.DEF_TX, txLog, FhirPublication.R4B, true, "4.3.0"));
        else if (version.startsWith("4.0"))
            ve.put(version, TestUtilities.getValidationEngine("hl7.fhir.r4.core#4.0.1", ValidationEngineTests.DEF_TX, txLog, FhirPublication.R4, true, "4.0.1"));
        else if (version.startsWith("3.0"))
            ve.put(version, TestUtilities.getValidationEngine("hl7.fhir.r3.core#3.0.2", ValidationEngineTests.DEF_TX, txLog, FhirPublication.STU3, true, "3.0.2"));
        else if (version.startsWith("1.4"))
            ve.put(version, TestUtilities.getValidationEngine("hl7.fhir.r2b.core#1.4.0", ValidationEngineTests.DEF_TX, txLog, FhirPublication.DSTU2016May, true, "1.4.0"));
        else if (version.startsWith("1.0"))
            ve.put(version, TestUtilities.getValidationEngine("hl7.fhir.r2.core#1.0.2", ValidationEngineTests.DEF_TX, txLog, FhirPublication.DSTU2, true, "1.0.2"));
        else
            throw new Exception("unknown version " + version);
    }
    vCurr = ve.get(version);
    vCurr.getContext().getTxClient().setLogger(logger);
    igLoader = new IgLoader(vCurr.getPcm(), vCurr.getContext(), vCurr.getVersion(), true);
    if (TestingUtilities.fcontexts == null) {
        TestingUtilities.fcontexts = new HashMap<>();
    }
    TestingUtilities.fcontexts.put(version, vCurr.getContext());
    if (content.has("use-test") && !content.get("use-test").getAsBoolean())
        return;
    byte[] testCaseContent = TestingUtilities.loadTestResource("validator", JSONUtil.str(content, "file")).getBytes(StandardCharsets.UTF_8);
    // load and process content
    FhirFormat fmt = determineFormat(content, testCaseContent);
    InstanceValidator val = vCurr.getValidator(fmt);
    val.setWantCheckSnapshotUnchanged(true);
    val.getContext().setClientRetryCount(4);
    val.setDebug(false);
    if (content.has("fetcher") && "standalone".equals(JSONUtil.str(content, "fetcher"))) {
        val.setFetcher(vCurr);
        vCurr.setFetcher(new StandAloneValidatorFetcher(vCurr.getPcm(), vCurr.getContext(), vCurr));
    } else {
        val.setFetcher(this);
    }
    val.setPolicyAdvisor(this);
    if (content.has("allowed-extension-domain"))
        val.getExtensionDomains().add(content.get("allowed-extension-domain").getAsString());
    if (content.has("allowed-extension-domains"))
        for (JsonElement a : content.getAsJsonArray("allowed-extension-domains")) val.getExtensionDomains().add(a.getAsString());
    if (content.has("language"))
        val.setValidationLanguage(content.get("language").getAsString());
    else
        val.setValidationLanguage(null);
    if (content.has("default-version")) {
        val.setBaseOptions(val.getBaseOptions().setVersionFlexible(content.get("default-version").getAsBoolean()));
    } else {
        val.setBaseOptions(val.getBaseOptions().setVersionFlexible(false));
    }
    if (content.has("packages")) {
        for (JsonElement e : content.getAsJsonArray("packages")) {
            String n = e.getAsString();
            InputStream cnt = n.endsWith(".tgz") ? TestingUtilities.loadTestResourceStream("validator", n) : null;
            if (cnt != null) {
                igLoader.loadPackage(NpmPackage.fromPackage(cnt));
            } else {
                igLoader.loadIg(vCurr.getIgs(), vCurr.getBinaries(), n, true);
            }
        }
    }
    if (content.has("crumb-trail")) {
        val.setCrumbTrails(content.get("crumb-trail").getAsBoolean());
    }
    if (content.has("supporting")) {
        for (JsonElement e : content.getAsJsonArray("supporting")) {
            String filename = e.getAsString();
            String contents = TestingUtilities.loadTestResource("validator", filename);
            CanonicalResource mr = (CanonicalResource) loadResource(filename, contents);
            val.getContext().cacheResource(mr);
            if (mr instanceof ImplementationGuide) {
                val.getImplementationGuides().add((ImplementationGuide) mr);
            }
        }
    }
    val.getBundleValidationRules().clear();
    if (content.has("bundle-param")) {
        val.getBundleValidationRules().add(new BundleValidationRule(content.getAsJsonObject("bundle-param").get("rule").getAsString(), content.getAsJsonObject("bundle-param").get("profile").getAsString()));
    }
    if (content.has("profiles")) {
        for (JsonElement je : content.getAsJsonArray("profiles")) {
            String filename = je.getAsString();
            String contents = TestingUtilities.loadTestResource("validator", filename);
            StructureDefinition sd = loadProfile(filename, contents, messages, val.isDebug());
            val.getContext().cacheResource(sd);
        }
    }
    List<ValidationMessage> errors = new ArrayList<ValidationMessage>();
    if (content.getAsJsonObject("java").has("debug")) {
        val.setDebug(content.getAsJsonObject("java").get("debug").getAsBoolean());
    } else {
        val.setDebug(false);
    }
    if (content.has("best-practice")) {
        val.setBestPracticeWarningLevel(BestPracticeWarningLevel.valueOf(content.get("best-practice").getAsString()));
    }
    if (content.has("examples")) {
        val.setAllowExamples(content.get("examples").getAsBoolean());
    } else {
        val.setAllowExamples(true);
    }
    if (content.has("security-checks")) {
        val.setSecurityChecks(content.get("security-checks").getAsBoolean());
    }
    if (content.has("logical") == false) {
        val.setAssumeValidRestReferences(content.has("assumeValidRestReferences") ? content.get("assumeValidRestReferences").getAsBoolean() : false);
        System.out.println(String.format("Start Validating (%d to set up)", (System.nanoTime() - setup) / 1000000));
        val.validate(null, errors, new ByteArrayInputStream(testCaseContent), fmt);
        System.out.println(val.reportTimes());
        checkOutcomes(errors, content, null, name);
    }
    if (content.has("profile")) {
        System.out.print("** Profile: ");
        JsonObject profile = content.getAsJsonObject("profile");
        if (profile.has("packages")) {
            for (JsonElement e : profile.getAsJsonArray("packages")) {
                igLoader.loadIg(vCurr.getIgs(), vCurr.getBinaries(), e.getAsString(), true);
            }
        }
        if (profile.getAsJsonObject("java").has("debug")) {
            val.setDebug(profile.getAsJsonObject("java").get("debug").getAsBoolean());
        }
        if (profile.has("supporting")) {
            for (JsonElement e : profile.getAsJsonArray("supporting")) {
                String filename = e.getAsString();
                String contents = TestingUtilities.loadTestResource("validator", filename);
                CanonicalResource mr = (CanonicalResource) loadResource(filename, contents);
                val.getContext().cacheResource(mr);
                if (mr instanceof ImplementationGuide) {
                    val.getImplementationGuides().add((ImplementationGuide) mr);
                }
            }
        }
        StructureDefinition sd = null;
        String filename = profile.get("source").getAsString();
        if (Utilities.isAbsoluteUrl(filename)) {
            sd = val.getContext().fetchResource(StructureDefinition.class, filename);
        } else {
            String contents = TestingUtilities.loadTestResource("validator", filename);
            System.out.println("Name: " + name + " - profile : " + profile.get("source").getAsString());
            version = content.has("version") ? content.get("version").getAsString() : Constants.VERSION;
            sd = loadProfile(filename, contents, messages, val.isDebug());
            val.getContext().cacheResource(sd);
        }
        val.setAssumeValidRestReferences(profile.has("assumeValidRestReferences") ? profile.get("assumeValidRestReferences").getAsBoolean() : false);
        List<ValidationMessage> errorsProfile = new ArrayList<ValidationMessage>();
        val.validate(null, errorsProfile, new ByteArrayInputStream(testCaseContent), fmt, asSdList(sd));
        System.out.println(val.reportTimes());
        checkOutcomes(errorsProfile, profile, filename, name);
    }
    if (content.has("logical")) {
        System.out.print("** Logical: ");
        JsonObject logical = content.getAsJsonObject("logical");
        if (logical.has("supporting")) {
            for (JsonElement e : logical.getAsJsonArray("supporting")) {
                String filename = e.getAsString();
                String contents = TestingUtilities.loadTestResource("validator", filename);
                CanonicalResource mr = (CanonicalResource) loadResource(filename, contents);
                if (mr instanceof StructureDefinition) {
                    val.getContext().generateSnapshot((StructureDefinition) mr, true);
                }
                val.getContext().cacheResource(mr);
            }
        }
        if (logical.has("packages")) {
            for (JsonElement e : logical.getAsJsonArray("packages")) {
                igLoader.loadIg(vCurr.getIgs(), vCurr.getBinaries(), e.getAsString(), true);
            }
        }
        List<ValidationMessage> errorsLogical = new ArrayList<ValidationMessage>();
        Element le = val.validate(null, errorsLogical, new ByteArrayInputStream(testCaseContent), fmt);
        if (logical.has("expressions")) {
            FHIRPathEngine fp = new FHIRPathEngine(val.getContext());
            for (JsonElement e : logical.getAsJsonArray("expressions")) {
                String exp = e.getAsString();
                Assert.assertTrue(fp.evaluateToBoolean(null, le, le, le, fp.parse(exp)));
            }
        }
        checkOutcomes(errorsLogical, logical, "logical", name);
    }
    logger.verifyHasNoRequests();
}

Example 78 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project eCRNow by drajer-health.

the class CdaHeaderGenerator method getPatientDetails.

public static String getPatientDetails(Patient p, LaunchDetails details) {
    StringBuilder patientDetails = new StringBuilder();
    patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.RECORD_TARGET_EL_NAME));
    patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.PATIENT_ROLE_EL_NAME));
    List<Identifier> ids = CdaFhirUtilities.getIdentifierForType(p.getIdentifier(), CdaFhirEnumConstants.FHIR_ID_TYPE_MR);
    Boolean addOnce = true;
    if (ids != null && !ids.isEmpty()) {
        for (Identifier id : ids) {
            if (!StringUtils.isEmpty(id.getSystem()) && !StringUtils.isEmpty(id.getValue())) {
                logger.debug("Found Identifier with Type MR");
                String system = CdaGeneratorUtils.getRootOid(id.getSystem(), details.getAssigningAuthorityId());
                patientDetails.append(CdaGeneratorUtils.getXmlForII(system, id.getValue()));
            } else {
                logger.debug("Using Resource Identifier as id");
                if (addOnce) {
                    patientDetails.append(CdaGeneratorUtils.getXmlForII(details.getAssigningAuthorityId(), p.getId()));
                    addOnce = false;
                }
            }
        }
    } else {
        logger.debug("Using Resource Identifier as id");
        patientDetails.append(CdaGeneratorUtils.getXmlForII(details.getAssigningAuthorityId(), p.getId()));
    }
    // Add Address.
    patientDetails.append(CdaFhirUtilities.getAddressXml(p.getAddress()));
    // Add Telecom (Phone)
    patientDetails.append(CdaFhirUtilities.getTelecomXml(p.getTelecom(), false));
    // Add Telecom (Email)
    patientDetails.append(CdaFhirUtilities.getEmailXml(p.getTelecom()));
    // Add patient
    patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.PATIENT_EL_NAME));
    patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.NAME_EL_NAME));
    patientDetails.append(CdaFhirUtilities.getNameXml(p.getName()));
    patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.NAME_EL_NAME));
    patientDetails.append(CdaFhirUtilities.getGenderXml(p.getGenderElement().getValue()));
    patientDetails.append(CdaFhirUtilities.getDateTypeXml(p.getBirthDateElement(), CdaGeneratorConstants.BIRTH_TIME_EL_NAME));
    if (p.getDeceased() == null || (p.getDeceased() != null && p.getDeceased().isEmpty())) {
        patientDetails.append(CdaGeneratorUtils.getXmlForValue(CdaGeneratorConstants.SDTC_DECEASED_IND, CdaGeneratorConstants.CCDA_FALSE));
    } else {
        patientDetails.append(CdaGeneratorUtils.getXmlForValue(CdaGeneratorConstants.SDTC_DECEASED_IND, CdaGeneratorConstants.CCDA_TRUE));
        if (p.getDeceased() instanceof DateTimeType) {
            DateTimeType d = (DateTimeType) p.getDeceased();
            patientDetails.append(CdaFhirUtilities.getDateTimeTypeXml(d, CdaGeneratorConstants.SDTC_DECEASED_TIME));
        } else {
            patientDetails.append(CdaGeneratorUtils.getXmlForNullEffectiveTime(CdaGeneratorConstants.SDTC_DECEASED_TIME, CdaGeneratorConstants.NF_NI));
        }
    }
    Coding race = CdaFhirUtilities.getCodingExtension(p.getExtension(), CdaGeneratorConstants.FHIR_USCORE_RACE_EXT_URL, CdaGeneratorConstants.OMB_RACE_CATEGORY_URL);
    if (race != null && race.getCode() != null) {
        patientDetails.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.RACE_CODE_EL_NAME, race.getCode(), CdaGeneratorConstants.RACE_CODE_SYSTEM, CdaGeneratorConstants.RACE_CODE_SYSTEM_NAME, race.getDisplay()));
    } else {
        patientDetails.append(CdaGeneratorUtils.getXmlForNullCD(CdaGeneratorConstants.RACE_CODE_EL_NAME, CdaGeneratorConstants.NF_NI));
    }
    Coding ethnicity = CdaFhirUtilities.getCodingExtension(p.getExtension(), CdaGeneratorConstants.FHIR_USCORE_ETHNICITY_EXT_URL, CdaGeneratorConstants.OMB_RACE_CATEGORY_URL);
    if (ethnicity != null && ethnicity.getCode() != null) {
        patientDetails.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.ETHNIC_CODE_EL_NAME, ethnicity.getCode(), CdaGeneratorConstants.RACE_CODE_SYSTEM, CdaGeneratorConstants.RACE_CODE_SYSTEM_NAME, ethnicity.getDisplay()));
    } else {
        patientDetails.append(CdaGeneratorUtils.getXmlForNullCD(CdaGeneratorConstants.ETHNIC_CODE_EL_NAME, CdaGeneratorConstants.NF_NI));
    }
    // Adding Guardian
    if (p.getContact() != null && !p.getContact().isEmpty()) {
        ContactComponent guardianContact = CdaFhirUtilities.getGuardianContact(p.getContact());
        if (guardianContact != null) {
            patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.GUARDIAN_EL_NAME));
            // Add address if found
            if (guardianContact.getAddress() != null) {
                logger.debug("Adding Address for Guardian");
                List<Address> addrs = new ArrayList<>();
                addrs.add(guardianContact.getAddress());
                patientDetails.append(CdaFhirUtilities.getAddressXml(addrs));
            }
            // Add Telecom
            patientDetails.append(CdaFhirUtilities.getTelecomXml(guardianContact.getTelecom(), false));
            patientDetails.append(CdaFhirUtilities.getEmailXml(guardianContact.getTelecom()));
            patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.GUARDIAN_PERSON_EL_NAME));
            patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.NAME_EL_NAME));
            List<HumanName> names = new ArrayList<>();
            names.add(guardianContact.getName());
            patientDetails.append(CdaFhirUtilities.getNameXml(names));
            patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.NAME_EL_NAME));
            patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.GUARDIAN_PERSON_EL_NAME));
            patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.GUARDIAN_EL_NAME));
        }
    }
    patientDetails.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.LANGUAGE_COMM_EL_NAME));
    Coding language = CdaFhirUtilities.getLanguageForCodeSystem(p.getCommunication(), CdaGeneratorConstants.FHIR_LANGUAGE_CODESYSTEM_URL);
    if (language != null && language.getCode() != null) {
        patientDetails.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.LANGUAGE_CODE_EL_NAME, language.getCode()));
    } else {
        patientDetails.append(CdaGeneratorUtils.getXmlForNullCD(CdaGeneratorConstants.LANGUAGE_CODE_EL_NAME, CdaGeneratorConstants.NF_NI));
    }
    patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.LANGUAGE_COMM_EL_NAME));
    patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.PATIENT_EL_NAME));
    patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.PATIENT_ROLE_EL_NAME));
    patientDetails.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.RECORD_TARGET_EL_NAME));
    return patientDetails.toString();
}

Example 79 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project synthea by synthetichealth.

the class FhirR4 method basicInfo.

/**
 * Map the given Person to a FHIR Patient resource, and add it to the given Bundle.
 *
 * @param person   The Person
 * @param bundle   The Bundle to add to
 * @param stopTime Time the simulation ended
 * @return The created Entry
 */
@SuppressWarnings("rawtypes")
private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long stopTime) {
    Patient patientResource = new Patient();
    patientResource.addIdentifier().setSystem(SYNTHEA_IDENTIFIER).setValue((String) person.attributes.get(Person.ID));
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient");
        patientResource.setMeta(meta);
    }
    Code mrnCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "MR", "Medical Record Number");
    patientResource.addIdentifier().setType(mapCodeToCodeableConcept(mrnCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem("http://hospital.smarthealthit.org").setValue((String) person.attributes.get(Person.ID));
    Code ssnCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "SS", "Social Security Number");
    patientResource.addIdentifier().setType(mapCodeToCodeableConcept(ssnCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem("http://hl7.org/fhir/sid/us-ssn").setValue((String) person.attributes.get(Person.IDENTIFIER_SSN));
    if (person.attributes.get(Person.IDENTIFIER_DRIVERS) != null) {
        Code driversCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "DL", "Driver's License");
        patientResource.addIdentifier().setType(mapCodeToCodeableConcept(driversCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem("urn:oid:2.16.840.1.113883.4.3.25").setValue((String) person.attributes.get(Person.IDENTIFIER_DRIVERS));
    }
    if (person.attributes.get(Person.IDENTIFIER_PASSPORT) != null) {
        Code passportCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "PPN", "Passport Number");
        patientResource.addIdentifier().setType(mapCodeToCodeableConcept(passportCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem(SHR_EXT + "passportNumber").setValue((String) person.attributes.get(Person.IDENTIFIER_PASSPORT));
    }
    if (person.attributes.get(Person.CONTACT_EMAIL) != null) {
        ContactComponent contact = new ContactComponent();
        HumanName contactName = new HumanName();
        contactName.setUse(HumanName.NameUse.OFFICIAL);
        contactName.addGiven((String) person.attributes.get(Person.CONTACT_GIVEN_NAME));
        contactName.setFamily((String) person.attributes.get(Person.CONTACT_FAMILY_NAME));
        contact.setName(contactName);
        contact.addTelecom().setSystem(ContactPointSystem.EMAIL).setUse(ContactPointUse.HOME).setValue((String) person.attributes.get(Person.CONTACT_EMAIL));
        patientResource.addContact(contact);
    }
    if (USE_US_CORE_IG) {
        // We do not yet account for mixed race
        Extension raceExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race");
        String race = (String) person.attributes.get(Person.RACE);
        String raceDisplay;
        switch(race) {
            case "white":
                raceDisplay = "White";
                break;
            case "black":
                raceDisplay = "Black or African American";
                break;
            case "asian":
                raceDisplay = "Asian";
                break;
            case "native":
                raceDisplay = "American Indian or Alaska Native";
                break;
            case "hawaiian":
                raceDisplay = "Native Hawaiian or Other Pacific Islander";
                break;
            default:
                raceDisplay = "Other";
                break;
        }
        String raceNum = (String) raceEthnicityCodes.get(race);
        Extension raceCodingExtension = new Extension("ombCategory");
        Coding raceCoding = new Coding();
        if (raceDisplay.equals("Other")) {
            raceCoding.setSystem("http://terminology.hl7.org/CodeSystem/v3-NullFlavor");
            raceCoding.setCode("UNK");
            raceCoding.setDisplay("Unknown");
        } else {
            raceCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
            raceCoding.setCode(raceNum);
            raceCoding.setDisplay(raceDisplay);
        }
        raceCodingExtension.setValue(raceCoding);
        raceExtension.addExtension(raceCodingExtension);
        Extension raceTextExtension = new Extension("text");
        raceTextExtension.setValue(new StringType(raceDisplay));
        raceExtension.addExtension(raceTextExtension);
        patientResource.addExtension(raceExtension);
        // We do not yet account for mixed ethnicity
        Extension ethnicityExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
        String ethnicity = (String) person.attributes.get(Person.ETHNICITY);
        String ethnicityDisplay;
        if (ethnicity.equals("hispanic")) {
            ethnicity = "hispanic";
            ethnicityDisplay = "Hispanic or Latino";
        } else {
            ethnicity = "nonhispanic";
            ethnicityDisplay = "Not Hispanic or Latino";
        }
        String ethnicityNum = (String) raceEthnicityCodes.get(ethnicity);
        Extension ethnicityCodingExtension = new Extension("ombCategory");
        Coding ethnicityCoding = new Coding();
        ethnicityCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
        ethnicityCoding.setCode(ethnicityNum);
        ethnicityCoding.setDisplay(ethnicityDisplay);
        ethnicityCodingExtension.setValue(ethnicityCoding);
        ethnicityExtension.addExtension(ethnicityCodingExtension);
        Extension ethnicityTextExtension = new Extension("text");
        ethnicityTextExtension.setValue(new StringType(ethnicityDisplay));
        ethnicityExtension.addExtension(ethnicityTextExtension);
        patientResource.addExtension(ethnicityExtension);
    }
    String firstLanguage = (String) person.attributes.get(Person.FIRST_LANGUAGE);
    Map languageMap = (Map) languageLookup.get(firstLanguage);
    Code languageCode = new Code((String) languageMap.get("system"), (String) languageMap.get("code"), (String) languageMap.get("display"));
    List<PatientCommunicationComponent> communication = new ArrayList<PatientCommunicationComponent>();
    communication.add(new PatientCommunicationComponent(mapCodeToCodeableConcept(languageCode, (String) languageMap.get("system"))));
    patientResource.setCommunication(communication);
    HumanName name = patientResource.addName();
    name.setUse(HumanName.NameUse.OFFICIAL);
    name.addGiven((String) person.attributes.get(Person.FIRST_NAME));
    name.setFamily((String) person.attributes.get(Person.LAST_NAME));
    if (person.attributes.get(Person.NAME_PREFIX) != null) {
        name.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
    }
    if (person.attributes.get(Person.NAME_SUFFIX) != null) {
        name.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
    }
    if (person.attributes.get(Person.MAIDEN_NAME) != null) {
        HumanName maidenName = patientResource.addName();
        maidenName.setUse(HumanName.NameUse.MAIDEN);
        maidenName.addGiven((String) person.attributes.get(Person.FIRST_NAME));
        maidenName.setFamily((String) person.attributes.get(Person.MAIDEN_NAME));
        if (person.attributes.get(Person.NAME_PREFIX) != null) {
            maidenName.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
        }
        if (person.attributes.get(Person.NAME_SUFFIX) != null) {
            maidenName.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
        }
    }
    Extension mothersMaidenNameExtension = new Extension("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");
    String mothersMaidenName = (String) person.attributes.get(Person.NAME_MOTHER);
    mothersMaidenNameExtension.setValue(new StringType(mothersMaidenName));
    patientResource.addExtension(mothersMaidenNameExtension);
    long birthdate = (long) person.attributes.get(Person.BIRTHDATE);
    patientResource.setBirthDate(new Date(birthdate));
    Extension birthSexExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
    if (person.attributes.get(Person.GENDER).equals("M")) {
        patientResource.setGender(AdministrativeGender.MALE);
        birthSexExtension.setValue(new CodeType("M"));
    } else if (person.attributes.get(Person.GENDER).equals("F")) {
        patientResource.setGender(AdministrativeGender.FEMALE);
        birthSexExtension.setValue(new CodeType("F"));
    } else if (person.attributes.get(Person.GENDER).equals("UNK")) {
        patientResource.setGender(AdministrativeGender.UNKNOWN);
    }
    if (USE_US_CORE_IG) {
        patientResource.addExtension(birthSexExtension);
    }
    String state = (String) person.attributes.get(Person.STATE);
    if (USE_US_CORE_IG) {
        state = Location.getAbbreviation(state);
    }
    Address addrResource = patientResource.addAddress();
    addrResource.addLine((String) person.attributes.get(Person.ADDRESS)).setCity((String) person.attributes.get(Person.CITY)).setPostalCode((String) person.attributes.get(Person.ZIP)).setState(state);
    if (COUNTRY_CODE != null) {
        addrResource.setCountry(COUNTRY_CODE);
    }
    Address birthplace = new Address();
    birthplace.setCity((String) person.attributes.get(Person.BIRTH_CITY)).setState((String) person.attributes.get(Person.BIRTH_STATE)).setCountry((String) person.attributes.get(Person.BIRTH_COUNTRY));
    Extension birthplaceExtension = new Extension("http://hl7.org/fhir/StructureDefinition/patient-birthPlace");
    birthplaceExtension.setValue(birthplace);
    patientResource.addExtension(birthplaceExtension);
    if (person.attributes.get(Person.MULTIPLE_BIRTH_STATUS) != null) {
        patientResource.setMultipleBirth(new IntegerType((int) person.attributes.get(Person.MULTIPLE_BIRTH_STATUS)));
    } else {
        patientResource.setMultipleBirth(new BooleanType(false));
    }
    patientResource.addTelecom().setSystem(ContactPointSystem.PHONE).setUse(ContactPointUse.HOME).setValue((String) person.attributes.get(Person.TELECOM));
    String maritalStatus = ((String) person.attributes.get(Person.MARITAL_STATUS));
    if (maritalStatus != null) {
        Code maritalStatusCode = new Code("http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", maritalStatus, maritalStatus);
        patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus"));
    } else {
        Code maritalStatusCode = new Code("http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", "S", "Never Married");
        patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus"));
    }
    Point2D.Double coord = person.getLonLat();
    if (coord != null) {
        Extension geolocation = addrResource.addExtension();
        geolocation.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
        geolocation.addExtension("latitude", new DecimalType(coord.getY()));
        geolocation.addExtension("longitude", new DecimalType(coord.getX()));
    }
    if (!person.alive(stopTime)) {
        patientResource.setDeceased(convertFhirDateTime((Long) person.attributes.get(Person.DEATHDATE), true));
    }
    String generatedBySynthea = "Generated by <a href=\"https://github.com/synthetichealth/synthea\">Synthea</a>." + "Version identifier: " + Utilities.SYNTHEA_VERSION + " . " + "  Person seed: " + person.getSeed() + "  Population seed: " + person.populationSeed;
    patientResource.setText(new Narrative().setStatus(NarrativeStatus.GENERATED).setDiv(new XhtmlNode(NodeType.Element).setValue(generatedBySynthea)));
    if (USE_SHR_EXTENSIONS) {
        patientResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Patient"));
        // Patient profile requires race, ethnicity, birthsex,
        // MothersMaidenName, FathersName, Person-extension
        patientResource.addExtension().setUrl(SHR_EXT + "shr-actor-FictionalPerson-extension").setValue(new BooleanType(true));
        String fathersName = (String) person.attributes.get(Person.NAME_FATHER);
        Extension fathersNameExtension = new Extension(SHR_EXT + "shr-entity-FathersName-extension", new HumanName().setText(fathersName));
        patientResource.addExtension(fathersNameExtension);
        String ssn = (String) person.attributes.get(Person.IDENTIFIER_SSN);
        Extension ssnExtension = new Extension(SHR_EXT + "shr-demographics-SocialSecurityNumber-extension", new StringType(ssn));
        patientResource.addExtension(ssnExtension);
    }
    // DALY and QALY values
    // we only write the last(current) one to the patient record
    Double dalyValue = (Double) person.attributes.get("most-recent-daly");
    Double qalyValue = (Double) person.attributes.get("most-recent-qaly");
    if (dalyValue != null) {
        Extension dalyExtension = new Extension(SYNTHEA_EXT + "disability-adjusted-life-years");
        DecimalType daly = new DecimalType(dalyValue);
        dalyExtension.setValue(daly);
        patientResource.addExtension(dalyExtension);
        Extension qalyExtension = new Extension(SYNTHEA_EXT + "quality-adjusted-life-years");
        DecimalType qaly = new DecimalType(qalyValue);
        qalyExtension.setValue(qaly);
        patientResource.addExtension(qalyExtension);
    }
    return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
}

Example 80 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project synthea by synthetichealth.

the class FhirStu3 method basicInfo.

/**
 * Map the given Person to a FHIR Patient resource, and add it to the given Bundle.
 *
 * @param person The Person
 * @param bundle The Bundle to add to
 * @param stopTime Time the simulation ended
 * @return The created Entry
 */
@SuppressWarnings("rawtypes")
private static BundleEntryComponent basicInfo(Person person, Bundle bundle, long stopTime) {
    Patient patientResource = new Patient();
    patientResource.addIdentifier().setSystem("https://github.com/synthetichealth/synthea").setValue((String) person.attributes.get(Person.ID));
    Code mrnCode = new Code("http://hl7.org/fhir/v2/0203", "MR", "Medical Record Number");
    patientResource.addIdentifier().setType(mapCodeToCodeableConcept(mrnCode, "http://hl7.org/fhir/v2/0203")).setSystem("http://hospital.smarthealthit.org").setValue((String) person.attributes.get(Person.ID));
    Code ssnCode = new Code("http://hl7.org/fhir/identifier-type", "SB", "Social Security Number");
    patientResource.addIdentifier().setType(mapCodeToCodeableConcept(ssnCode, "http://hl7.org/fhir/identifier-type")).setSystem("http://hl7.org/fhir/sid/us-ssn").setValue((String) person.attributes.get(Person.IDENTIFIER_SSN));
    if (person.attributes.get(Person.IDENTIFIER_DRIVERS) != null) {
        Code driversCode = new Code("http://hl7.org/fhir/v2/0203", "DL", "Driver's License");
        patientResource.addIdentifier().setType(mapCodeToCodeableConcept(driversCode, "http://hl7.org/fhir/v2/0203")).setSystem("urn:oid:2.16.840.1.113883.4.3.25").setValue((String) person.attributes.get(Person.IDENTIFIER_DRIVERS));
    }
    if (person.attributes.get(Person.IDENTIFIER_PASSPORT) != null) {
        Code passportCode = new Code("http://hl7.org/fhir/v2/0203", "PPN", "Passport Number");
        patientResource.addIdentifier().setType(mapCodeToCodeableConcept(passportCode, "http://hl7.org/fhir/v2/0203")).setSystem(SHR_EXT + "passportNumber").setValue((String) person.attributes.get(Person.IDENTIFIER_PASSPORT));
    }
    if (person.attributes.get(Person.CONTACT_EMAIL) != null) {
        ContactComponent contact = new ContactComponent();
        HumanName contactName = new HumanName();
        contactName.setUse(HumanName.NameUse.OFFICIAL);
        contactName.addGiven((String) person.attributes.get(Person.CONTACT_GIVEN_NAME));
        contactName.setFamily((String) person.attributes.get(Person.CONTACT_FAMILY_NAME));
        contact.setName(contactName);
        contact.addTelecom().setSystem(ContactPointSystem.EMAIL).setUse(ContactPointUse.HOME).setValue((String) person.attributes.get(Person.CONTACT_EMAIL));
        patientResource.addContact(contact);
    }
    // We do not yet account for mixed race
    Extension raceExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race");
    String race = (String) person.attributes.get(Person.RACE);
    String raceDisplay;
    switch(race) {
        case "white":
            raceDisplay = "White";
            break;
        case "black":
            raceDisplay = "Black or African American";
            break;
        case "asian":
            raceDisplay = "Asian";
            break;
        case "native":
            raceDisplay = "American Indian or Alaska Native";
            break;
        case "hawaiian":
            raceDisplay = "Native Hawaiian or Other Pacific Islander";
            break;
        default:
            raceDisplay = "Other";
            break;
    }
    String raceNum = (String) raceEthnicityCodes.get(race);
    Extension raceCodingExtension = new Extension("ombCategory");
    Coding raceCoding = new Coding();
    if (raceDisplay.equals("Other")) {
        raceCoding.setSystem("http://hl7.org/fhir/v3/NullFlavor");
        raceCoding.setCode("UNK");
        raceCoding.setDisplay("Unknown");
    } else {
        raceCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
        raceCoding.setCode(raceNum);
        raceCoding.setDisplay(raceDisplay);
    }
    raceCodingExtension.setValue(raceCoding);
    raceExtension.addExtension(raceCodingExtension);
    Extension raceTextExtension = new Extension("text");
    raceTextExtension.setValue(new StringType(raceDisplay));
    raceExtension.addExtension(raceTextExtension);
    patientResource.addExtension(raceExtension);
    // We do not yet account for mixed ethnicity
    Extension ethnicityExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
    String ethnicity = (String) person.attributes.get(Person.ETHNICITY);
    String ethnicityDisplay;
    if (ethnicity.equals("hispanic")) {
        ethnicity = "hispanic";
        ethnicityDisplay = "Hispanic or Latino";
    } else {
        ethnicity = "nonhispanic";
        ethnicityDisplay = "Not Hispanic or Latino";
    }
    String ethnicityNum = (String) raceEthnicityCodes.get(ethnicity);
    Extension ethnicityCodingExtension = new Extension("ombCategory");
    Coding ethnicityCoding = new Coding();
    ethnicityCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
    ethnicityCoding.setCode(ethnicityNum);
    ethnicityCoding.setDisplay(ethnicityDisplay);
    ethnicityCodingExtension.setValue(ethnicityCoding);
    ethnicityExtension.addExtension(ethnicityCodingExtension);
    Extension ethnicityTextExtension = new Extension("text");
    ethnicityTextExtension.setValue(new StringType(ethnicityDisplay));
    ethnicityExtension.addExtension(ethnicityTextExtension);
    patientResource.addExtension(ethnicityExtension);
    String firstLanguage = (String) person.attributes.get(Person.FIRST_LANGUAGE);
    Map languageMap = (Map) languageLookup.get(firstLanguage);
    Code languageCode = new Code((String) languageMap.get("system"), (String) languageMap.get("code"), (String) languageMap.get("display"));
    List<PatientCommunicationComponent> communication = new ArrayList<PatientCommunicationComponent>();
    communication.add(new PatientCommunicationComponent(mapCodeToCodeableConcept(languageCode, (String) languageMap.get("system"))));
    patientResource.setCommunication(communication);
    HumanName name = patientResource.addName();
    name.setUse(HumanName.NameUse.OFFICIAL);
    name.addGiven((String) person.attributes.get(Person.FIRST_NAME));
    name.setFamily((String) person.attributes.get(Person.LAST_NAME));
    if (person.attributes.get(Person.NAME_PREFIX) != null) {
        name.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
    }
    if (person.attributes.get(Person.NAME_SUFFIX) != null) {
        name.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
    }
    if (person.attributes.get(Person.MAIDEN_NAME) != null) {
        HumanName maidenName = patientResource.addName();
        maidenName.setUse(HumanName.NameUse.MAIDEN);
        maidenName.addGiven((String) person.attributes.get(Person.FIRST_NAME));
        maidenName.setFamily((String) person.attributes.get(Person.MAIDEN_NAME));
        if (person.attributes.get(Person.NAME_PREFIX) != null) {
            maidenName.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
        }
        if (person.attributes.get(Person.NAME_SUFFIX) != null) {
            maidenName.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
        }
    }
    Extension mothersMaidenNameExtension = new Extension("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");
    String mothersMaidenName = (String) person.attributes.get(Person.NAME_MOTHER);
    mothersMaidenNameExtension.setValue(new StringType(mothersMaidenName));
    patientResource.addExtension(mothersMaidenNameExtension);
    long birthdate = (long) person.attributes.get(Person.BIRTHDATE);
    patientResource.setBirthDate(new Date(birthdate));
    Extension birthSexExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
    if (person.attributes.get(Person.GENDER).equals("M")) {
        patientResource.setGender(AdministrativeGender.MALE);
        birthSexExtension.setValue(new CodeType("M"));
    } else if (person.attributes.get(Person.GENDER).equals("F")) {
        patientResource.setGender(AdministrativeGender.FEMALE);
        birthSexExtension.setValue(new CodeType("F"));
    }
    patientResource.addExtension(birthSexExtension);
    String state = (String) person.attributes.get(Person.STATE);
    Address addrResource = patientResource.addAddress();
    addrResource.addLine((String) person.attributes.get(Person.ADDRESS)).setCity((String) person.attributes.get(Person.CITY)).setPostalCode((String) person.attributes.get(Person.ZIP)).setState(state);
    if (COUNTRY_CODE != null) {
        addrResource.setCountry(COUNTRY_CODE);
    }
    Address birthplace = new Address();
    birthplace.setCity((String) person.attributes.get(Person.BIRTH_CITY)).setState((String) person.attributes.get(Person.BIRTH_STATE)).setCountry((String) person.attributes.get(Person.BIRTH_COUNTRY));
    Extension birthplaceExtension = new Extension("http://hl7.org/fhir/StructureDefinition/birthPlace");
    birthplaceExtension.setValue(birthplace);
    patientResource.addExtension(birthplaceExtension);
    if (person.attributes.get(Person.MULTIPLE_BIRTH_STATUS) != null) {
        patientResource.setMultipleBirth(new IntegerType((int) person.attributes.get(Person.MULTIPLE_BIRTH_STATUS)));
    } else {
        patientResource.setMultipleBirth(new BooleanType(false));
    }
    patientResource.addTelecom().setSystem(ContactPoint.ContactPointSystem.PHONE).setUse(ContactPoint.ContactPointUse.HOME).setValue((String) person.attributes.get(Person.TELECOM));
    String maritalStatus = ((String) person.attributes.get(Person.MARITAL_STATUS));
    if (maritalStatus != null) {
        Code maritalStatusCode = new Code("http://hl7.org/fhir/v3/MaritalStatus", maritalStatus, maritalStatus);
        patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://hl7.org/fhir/v3/MaritalStatus"));
    } else {
        Code maritalStatusCode = new Code("http://hl7.org/fhir/v3/MaritalStatus", "S", "Never Married");
        patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://hl7.org/fhir/v3/MaritalStatus"));
    }
    Point2D.Double coord = person.getLonLat();
    if (coord != null) {
        Extension geolocation = addrResource.addExtension();
        geolocation.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
        geolocation.addExtension("latitude", new DecimalType(coord.getY()));
        geolocation.addExtension("longitude", new DecimalType(coord.getX()));
    }
    if (!person.alive(stopTime)) {
        patientResource.setDeceased(convertFhirDateTime((Long) person.attributes.get(Person.DEATHDATE), true));
    }
    String generatedBySynthea = "Generated by <a href=\"https://github.com/synthetichealth/synthea\">Synthea</a>." + "Version identifier: " + Utilities.SYNTHEA_VERSION + " . " + "  Person seed: " + person.getSeed() + "  Population seed: " + person.populationSeed;
    patientResource.setText(new Narrative().setStatus(NarrativeStatus.GENERATED).setDiv(new XhtmlNode(NodeType.Element).setValue(generatedBySynthea)));
    if (USE_SHR_EXTENSIONS) {
        patientResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Patient"));
        // Patient profile requires race, ethnicity, birthsex,
        // MothersMaidenName, FathersName, Person-extension
        patientResource.addExtension().setUrl(SHR_EXT + "shr-actor-FictionalPerson-extension").setValue(new BooleanType(true));
        String fathersName = (String) person.attributes.get(Person.NAME_FATHER);
        Extension fathersNameExtension = new Extension(SHR_EXT + "shr-entity-FathersName-extension", new HumanName().setText(fathersName));
        patientResource.addExtension(fathersNameExtension);
        String ssn = (String) person.attributes.get(Person.IDENTIFIER_SSN);
        Extension ssnExtension = new Extension(SHR_EXT + "shr-demographics-SocialSecurityNumber-extension", new StringType(ssn));
        patientResource.addExtension(ssnExtension);
        Basic personResource = new Basic();
        // the only required field on this patient resource is code
        Coding fixedCode = new Coding("http://standardhealthrecord.org/fhir/basic-resource-type", "shr-entity-Person", "shr-entity-Person");
        personResource.setCode(new CodeableConcept().addCoding(fixedCode));
        Meta personMeta = new Meta();
        personMeta.addProfile(SHR_EXT + "shr-entity-Person");
        personResource.setMeta(personMeta);
        BundleEntryComponent personEntry = newEntry(person, bundle, personResource);
        patientResource.addExtension().setUrl(SHR_EXT + "shr-entity-Person-extension").setValue(new Reference(personEntry.getFullUrl()));
    }
    // DALY and QALY values
    // we only write the last(current) one to the patient record
    Double dalyValue = (Double) person.attributes.get("most-recent-daly");
    Double qalyValue = (Double) person.attributes.get("most-recent-qaly");
    if (dalyValue != null) {
        Extension dalyExtension = new Extension(SYNTHEA_EXT + "disability-adjusted-life-years");
        DecimalType daly = new DecimalType(dalyValue);
        dalyExtension.setValue(daly);
        patientResource.addExtension(dalyExtension);
        Extension qalyExtension = new Extension(SYNTHEA_EXT + "quality-adjusted-life-years");
        DecimalType qaly = new DecimalType(qalyValue);
        qalyExtension.setValue(qaly);
        patientResource.addExtension(qalyExtension);
    }
    return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
}