Examples with BooleanType org.hl7.fhir.dstu2.model.BooleanType used on opensource projects

Example 91 with BooleanType

use of org.hl7.fhir.dstu2.model.BooleanType in project synthea by synthetichealth.

the class FhirR4 method practitioner.

/**
 * Map the clinician into a FHIR Practitioner resource, and add it to the given Bundle.
 * @param rand   Source of randomness to use when generating ids etc
 * @param bundle The Bundle to add to
 * @param clinician The clinician
 * @return The added Entry
 */
protected static BundleEntryComponent practitioner(RandomNumberGenerator rand, Bundle bundle, Clinician clinician) {
    Practitioner practitionerResource = new Practitioner();
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner");
        practitionerResource.setMeta(meta);
    }
    practitionerResource.addIdentifier().setSystem("http://hl7.org/fhir/sid/us-npi").setValue(clinician.npi);
    practitionerResource.setActive(true);
    practitionerResource.addName().setFamily((String) clinician.attributes.get(Clinician.LAST_NAME)).addGiven((String) clinician.attributes.get(Clinician.FIRST_NAME)).addPrefix((String) clinician.attributes.get(Clinician.NAME_PREFIX));
    String email = (String) clinician.attributes.get(Clinician.FIRST_NAME) + "." + (String) clinician.attributes.get(Clinician.LAST_NAME) + "@example.com";
    practitionerResource.addTelecom().setSystem(ContactPointSystem.EMAIL).setUse(ContactPointUse.WORK).setValue(email);
    if (USE_US_CORE_IG) {
        practitionerResource.getTelecomFirstRep().addExtension().setUrl("http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct").setValue(new BooleanType(true));
    }
    Address address = new Address().addLine((String) clinician.attributes.get(Clinician.ADDRESS)).setCity((String) clinician.attributes.get(Clinician.CITY)).setPostalCode((String) clinician.attributes.get(Clinician.ZIP)).setState((String) clinician.attributes.get(Clinician.STATE));
    if (COUNTRY_CODE != null) {
        address.setCountry(COUNTRY_CODE);
    }
    practitionerResource.addAddress(address);
    if (clinician.attributes.get(Person.GENDER).equals("M")) {
        practitionerResource.setGender(AdministrativeGender.MALE);
    } else if (clinician.attributes.get(Person.GENDER).equals("F")) {
        practitionerResource.setGender(AdministrativeGender.FEMALE);
    }
    BundleEntryComponent practitionerEntry = newEntry(bundle, practitionerResource, clinician.getResourceID());
    if (USE_US_CORE_IG) {
        // generate an accompanying PractitionerRole resource
        PractitionerRole practitionerRole = new PractitionerRole();
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole");
        practitionerRole.setMeta(meta);
        practitionerRole.setPractitioner(new Reference().setIdentifier(new Identifier().setSystem("http://hl7.org/fhir/sid/us-npi").setValue(clinician.npi)).setDisplay(practitionerResource.getNameFirstRep().getNameAsSingleString()));
        practitionerRole.setOrganization(new Reference().setIdentifier(new Identifier().setSystem(SYNTHEA_IDENTIFIER).setValue(clinician.getOrganization().getResourceID())).setDisplay(clinician.getOrganization().name));
        practitionerRole.addCode(mapCodeToCodeableConcept(new Code("http://nucc.org/provider-taxonomy", "208D00000X", "General Practice"), null));
        practitionerRole.addSpecialty(mapCodeToCodeableConcept(new Code("http://nucc.org/provider-taxonomy", "208D00000X", "General Practice"), null));
        practitionerRole.addLocation().setIdentifier(new Identifier().setSystem(SYNTHEA_IDENTIFIER).setValue(clinician.getOrganization().getResourceLocationID())).setDisplay(clinician.getOrganization().name);
        if (clinician.getOrganization().phone != null && !clinician.getOrganization().phone.isEmpty()) {
            practitionerRole.addTelecom(new ContactPoint().setSystem(ContactPointSystem.PHONE).setValue(clinician.getOrganization().phone));
        }
        practitionerRole.addTelecom(practitionerResource.getTelecomFirstRep());
        newEntry(rand, bundle, practitionerRole);
    }
    return practitionerEntry;
}

Example 92 with BooleanType

use of org.hl7.fhir.dstu2.model.BooleanType in project bunsen by cerner.

the class TestData method newBunsenTestProfilePatient.

/**
 * Returns a new Patient from Bunsen Test profile for testing.
 *
 * @return a FHIR Patient for testing.
 */
public static Patient newBunsenTestProfilePatient() {
    Patient patient = new Patient();
    patient.setId("test-bunsen-test-profile-patient");
    patient.setGender(AdministrativeGender.MALE);
    patient.setActive(true);
    patient.setMultipleBirth(new IntegerType(1));
    patient.setBirthDateElement(new DateType("1945-01-01"));
    // set extension field
    Extension booleanField = patient.addExtension();
    booleanField.setUrl(BUNSEN_TEST_BOOLEAN_FIELD);
    booleanField.setValue(new BooleanType(true));
    Extension integerField = patient.addExtension();
    integerField.setUrl(BUNSEN_TEST_INTEGER_FIELD);
    integerField.setValue(new IntegerType(45678));
    Extension integerArrayField1 = patient.addExtension();
    integerArrayField1.setUrl(BUNSEN_TEST_INTEGER_ARRAY_FIELD);
    integerArrayField1.setValue(new IntegerType(6666));
    Extension integerArrayField2 = patient.addExtension();
    integerArrayField2.setUrl(BUNSEN_TEST_INTEGER_ARRAY_FIELD);
    integerArrayField2.setValue(new IntegerType(9999));
    // add multiple nested extensions
    final Extension nestedExtension1 = patient.addExtension();
    nestedExtension1.setUrl(BUNSEN_TEST_NESTED_EXT_FIELD);
    nestedExtension1.setValue(null);
    final Extension nestedExtension2 = patient.addExtension();
    nestedExtension2.setUrl(BUNSEN_TEST_NESTED_EXT_FIELD);
    nestedExtension2.setValue(null);
    // add text as sub-extension to nestedExtension
    final Extension textExt1 = nestedExtension1.addExtension();
    textExt1.setUrl("text");
    textExt1.setValue(new StringType("Text1 Sub-extension of nestedExtension1 field"));
    final Extension textExt2 = nestedExtension1.addExtension();
    textExt2.setUrl("text");
    textExt2.setValue(new StringType("Text2 Sub-extension of nestedExtension1 field"));
    final Extension textExt3 = nestedExtension2.addExtension();
    textExt3.setUrl("text");
    textExt3.setValue(new StringType("Text3 Sub-extension of nestedExtension2 field"));
    // add multiple codeableConcept extensions to nestedExtension
    final CodeableConcept codeableconcept1 = new CodeableConcept();
    codeableconcept1.addCoding().setSystem("http://snomed.info/sct").setCode("CC1").setDisplay("CC1 - Codeable Concept Extension").setUserSelected(true);
    final CodeableConcept codeableconcept2 = new CodeableConcept();
    codeableconcept2.addCoding().setSystem("http://snomed.info/sct").setCode("CC2").setDisplay("CC2 - Codeable Concept Extension").setUserSelected(true);
    final CodeableConcept codeableconcept3 = new CodeableConcept();
    codeableconcept3.addCoding().setSystem("http://snomed.info/sct").setCode("CC3").setDisplay("CC3 - Codeable Concept Extension").setUserSelected(true);
    final Extension codeableConceptExt1 = nestedExtension1.addExtension();
    codeableConceptExt1.setUrl(BUNSEN_TEST_CODEABLE_CONCEPT_EXT_FIELD);
    codeableConceptExt1.setValue(codeableconcept1);
    final Extension codeableConceptExt2 = nestedExtension1.addExtension();
    codeableConceptExt2.setUrl(BUNSEN_TEST_CODEABLE_CONCEPT_EXT_FIELD);
    codeableConceptExt2.setValue(codeableconcept2);
    final Extension codeableConceptExt3 = nestedExtension2.addExtension();
    codeableConceptExt3.setUrl(BUNSEN_TEST_CODEABLE_CONCEPT_EXT_FIELD);
    codeableConceptExt3.setValue(codeableconcept3);
    // add multiple ModifierExtension fields
    Extension stringModifierExtension = patient.addModifierExtension();
    stringModifierExtension.setUrl(BUNSEN_TEST_STRING_MODIFIER_EXT_FIELD);
    stringModifierExtension.setValue(new StringType("test string modifier value"));
    CodeableConcept concept1 = new CodeableConcept();
    concept1.addCoding().setSystem("http://snomed.info/sct").setCode("C-1").setDisplay("C-1 Codeable Concept Modifier Extension").setUserSelected(true);
    Extension codeableConceptField = patient.addModifierExtension();
    codeableConceptField.setUrl(BUNSEN_TEST_CODEABLE_CONCEPT_MODIFIER_EXT_FIELD);
    codeableConceptField.setValue(concept1);
    CodeableConcept concept2 = new CodeableConcept();
    concept2.addCoding().setSystem("http://snomed.info/sct").setCode("C-2").setDisplay("C-2 Codeable Concept Modifier Extension").setUserSelected(true);
    Extension codeableConceptField2 = patient.addModifierExtension();
    codeableConceptField2.setUrl(BUNSEN_TEST_CODEABLE_CONCEPT_MODIFIER_EXT_FIELD);
    codeableConceptField2.setValue(concept2);
    return patient;
}

Example 93 with BooleanType

use of org.hl7.fhir.dstu2.model.BooleanType in project synthea by synthetichealth.

the class FhirR4 method medicationRequest.

/**
 * Map the given Medication to a FHIR MedicationRequest resource, and add it to the given Bundle.
 *
 * @param person         The person being prescribed medication
 * @param personEntry    The Entry for the Person
 * @param bundle         Bundle to add the Medication to
 * @param encounterEntry Current Encounter entry
 * @param medication     The Medication
 * @return The added Entry
 */
private static BundleEntryComponent medicationRequest(Person person, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication) {
    MedicationRequest medicationResource = new MedicationRequest();
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest");
        medicationResource.setMeta(meta);
    } else if (USE_SHR_EXTENSIONS) {
        medicationResource.addExtension().setUrl(SHR_EXT + "shr-base-ActionCode-extension").setValue(PRESCRIPTION_OF_DRUG_CC);
        medicationResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-medication-MedicationRequested"));
        Extension requestedContext = new Extension();
        requestedContext.setUrl(SHR_EXT + "shr-action-RequestedContext-extension");
        requestedContext.addExtension(SHR_EXT + "shr-action-Status-extension", new CodeType("completed"));
        requestedContext.addExtension(SHR_EXT + "shr-action-RequestIntent-extension", new CodeType("original-order"));
        medicationResource.addExtension(requestedContext);
    }
    medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
    medicationResource.setEncounter(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));
    if (USE_US_CORE_IG && medication.administration) {
        // Occasionally, rather than use medication codes, we want to use a Medication
        // Resource. We only want to do this when we use US Core, to make sure we
        // sometimes produce a resource for the us-core-medication profile, and the
        // 'administration' flag is an arbitrary way to decide without flipping a coin.
        org.hl7.fhir.r4.model.Medication drugResource = new org.hl7.fhir.r4.model.Medication();
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication");
        drugResource.setMeta(meta);
        drugResource.setCode(mapCodeToCodeableConcept(code, system));
        drugResource.setStatus(MedicationStatus.ACTIVE);
        BundleEntryComponent drugEntry = newEntry(person, bundle, drugResource);
        medicationResource.setMedication(new Reference(drugEntry.getFullUrl()));
    }
    medicationResource.setAuthoredOn(new Date(medication.start));
    medicationResource.setIntent(MedicationRequestIntent.ORDER);
    org.hl7.fhir.r4.model.Encounter encounter = (org.hl7.fhir.r4.model.Encounter) encounterEntry.getResource();
    medicationResource.setRequester(encounter.getParticipantFirstRep().getIndividual());
    if (medication.stop != 0L) {
        medicationResource.setStatus(MedicationRequestStatus.STOPPED);
    } else {
        medicationResource.setStatus(MedicationRequestStatus.ACTIVE);
    }
    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());
                }
            }
        }
    }
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        Dosage dosage = new Dosage();
        dosage.setSequence(1);
        // as_needed is true if present
        dosage.setAsNeeded(new BooleanType(rxInfo.has("as_needed")));
        if (rxInfo.has("as_needed")) {
            dosage.setText("Take as needed.");
        }
        // as_needed is false
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Timing timing = new Timing();
            TimingRepeatComponent timingRepeatComponent = new TimingRepeatComponent();
            timingRepeatComponent.setFrequency(rxInfo.get("dosage").getAsJsonObject().get("frequency").getAsInt());
            timingRepeatComponent.setPeriod(rxInfo.get("dosage").getAsJsonObject().get("period").getAsDouble());
            timingRepeatComponent.setPeriodUnit(convertUcumCode(rxInfo.get("dosage").getAsJsonObject().get("unit").getAsString()));
            timing.setRepeat(timingRepeatComponent);
            dosage.setTiming(timing);
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            DosageDoseAndRateComponent dosageDetails = new DosageDoseAndRateComponent();
            dosageDetails.setType(new CodeableConcept().addCoding(new Coding().setCode(DoseRateType.ORDERED.toCode()).setSystem(DoseRateType.ORDERED.getSystem()).setDisplay(DoseRateType.ORDERED.getDisplay())));
            dosageDetails.setDose(dose);
            List<DosageDoseAndRateComponent> details = new ArrayList<DosageDoseAndRateComponent>();
            details.add(dosageDetails);
            dosage.setDoseAndRate(details);
            if (rxInfo.has("instructions")) {
                String text = "";
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    Code instructionCode = new Code(SNOMED_URI, instruction.get("code").getAsString(), instruction.get("display").getAsString());
                    text += instructionCode.display + "\n";
                    dosage.addAdditionalInstruction(mapCodeToCodeableConcept(instructionCode, SNOMED_URI));
                }
                dosage.setText(text);
            }
        }
        List<Dosage> dosageInstruction = new ArrayList<Dosage>();
        dosageInstruction.add(dosage);
        medicationResource.setDosageInstruction(dosageInstruction);
    }
    BundleEntryComponent medicationEntry = newEntry(person, bundle, medicationResource);
    // create new claim for medication
    medicationClaim(person, personEntry, bundle, encounterEntry, medication.claim, medicationEntry);
    // Create new administration for medication, if needed
    if (medication.administration) {
        medicationAdministration(person, personEntry, bundle, encounterEntry, medication, medicationResource);
    }
    return medicationEntry;
}

Example 94 with BooleanType

use of org.hl7.fhir.dstu2.model.BooleanType in project synthea by synthetichealth.

the class FhirStu3 method medication.

/**
 * Map the given Medication to a FHIR MedicationRequest resource, and add it to the given Bundle.
 *
 * @param rand Source of randomness to use when generating ids etc
 * @param personEntry The Entry for the Person
 * @param bundle Bundle to add the Medication to
 * @param encounterEntry Current Encounter entry
 * @param medication The Medication
 * @return The added Entry
 */
private static BundleEntryComponent medication(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication) {
    MedicationRequest medicationResource = new MedicationRequest();
    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.setAuthoredOn(new Date(medication.start));
    medicationResource.setIntent(MedicationRequestIntent.ORDER);
    org.hl7.fhir.dstu3.model.Encounter encounter = (org.hl7.fhir.dstu3.model.Encounter) encounterEntry.getResource();
    MedicationRequestRequesterComponent requester = new MedicationRequestRequesterComponent();
    requester.setAgent(encounter.getParticipantFirstRep().getIndividual());
    requester.setOnBehalfOf(encounter.getServiceProvider());
    medicationResource.setRequester(requester);
    if (medication.stop != 0L) {
        medicationResource.setStatus(MedicationRequestStatus.STOPPED);
    } else {
        medicationResource.setStatus(MedicationRequestStatus.ACTIVE);
    }
    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());
                }
            }
        }
    }
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        Dosage dosage = new Dosage();
        dosage.setSequence(1);
        // as_needed is true if present
        dosage.setAsNeeded(new BooleanType(rxInfo.has("as_needed")));
        // as_needed is true if present
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Timing timing = new Timing();
            TimingRepeatComponent timingRepeatComponent = new TimingRepeatComponent();
            timingRepeatComponent.setFrequency(rxInfo.get("dosage").getAsJsonObject().get("frequency").getAsInt());
            timingRepeatComponent.setPeriod(rxInfo.get("dosage").getAsJsonObject().get("period").getAsDouble());
            timingRepeatComponent.setPeriodUnit(convertUcumCode(rxInfo.get("dosage").getAsJsonObject().get("unit").getAsString()));
            timing.setRepeat(timingRepeatComponent);
            dosage.setTiming(timing);
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            dosage.setDose(dose);
            if (rxInfo.has("instructions")) {
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    Code instructionCode = new Code(SNOMED_URI, instruction.get("code").getAsString(), instruction.get("display").getAsString());
                    dosage.addAdditionalInstruction(mapCodeToCodeableConcept(instructionCode, SNOMED_URI));
                }
            }
        }
        List<Dosage> dosageInstruction = new ArrayList<Dosage>();
        dosageInstruction.add(dosage);
        medicationResource.setDosageInstruction(dosageInstruction);
    }
    if (USE_SHR_EXTENSIONS) {
        medicationResource.addExtension().setUrl(SHR_EXT + "shr-base-ActionCode-extension").setValue(PRESCRIPTION_OF_DRUG_CC);
        medicationResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-medication-MedicationRequested"));
        // required fields for this profile are status, action-RequestedContext-extension,
        // medication[x]subject, authoredOn, requester
        Extension requestedContext = new Extension();
        requestedContext.setUrl(SHR_EXT + "shr-action-RequestedContext-extension");
        requestedContext.addExtension(SHR_EXT + "shr-action-Status-extension", new CodeType("completed"));
        requestedContext.addExtension(SHR_EXT + "shr-action-RequestIntent-extension", new CodeType("original-order"));
        medicationResource.addExtension(requestedContext);
    }
    BundleEntryComponent medicationEntry = newEntry(rand, bundle, medicationResource);
    // create new claim for medication
    medicationClaim(rand, personEntry, bundle, encounterEntry, medication.claim, medicationEntry);
    // Create new administration for medication, if needed
    if (medication.administration) {
        medicationAdministration(rand, personEntry, bundle, encounterEntry, medication, medicationResource);
    }
    return medicationEntry;
}

Example 95 with BooleanType

use of org.hl7.fhir.dstu2.model.BooleanType 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));
}