Examples with IntegerType org.hl7.fhir.dstu2016may.model.IntegerType used on opensource projects

Example 61 with IntegerType

use of org.hl7.fhir.dstu2016may.model.IntegerType 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 62 with IntegerType

use of org.hl7.fhir.dstu2016may.model.IntegerType in project synthea by synthetichealth.

the class HospitalExporterStu3 method addHospitalExtensions.

/**
 * Add FHIR extensions to capture additional information.
 */
public static void addHospitalExtensions(Provider h, Organization organizationResource) {
    Table<Integer, String, AtomicInteger> utilization = h.getUtilization();
    // calculate totals for utilization
    int totalEncounters = utilization.column(Provider.ENCOUNTERS).values().stream().mapToInt(ai -> ai.get()).sum();
    Extension encountersExtension = new Extension(SYNTHEA_URI + "utilization-encounters-extension");
    IntegerType encountersValue = new IntegerType(totalEncounters);
    encountersExtension.setValue(encountersValue);
    organizationResource.addExtension(encountersExtension);
    int totalProcedures = utilization.column(Provider.PROCEDURES).values().stream().mapToInt(ai -> ai.get()).sum();
    Extension proceduresExtension = new Extension(SYNTHEA_URI + "utilization-procedures-extension");
    IntegerType proceduresValue = new IntegerType(totalProcedures);
    proceduresExtension.setValue(proceduresValue);
    organizationResource.addExtension(proceduresExtension);
    int totalLabs = utilization.column(Provider.LABS).values().stream().mapToInt(ai -> ai.get()).sum();
    Extension labsExtension = new Extension(SYNTHEA_URI + "utilization-labs-extension");
    IntegerType labsValue = new IntegerType(totalLabs);
    labsExtension.setValue(labsValue);
    organizationResource.addExtension(labsExtension);
    int totalPrescriptions = utilization.column(Provider.PRESCRIPTIONS).values().stream().mapToInt(ai -> ai.get()).sum();
    Extension prescriptionsExtension = new Extension(SYNTHEA_URI + "utilization-prescriptions-extension");
    IntegerType prescriptionsValue = new IntegerType(totalPrescriptions);
    prescriptionsExtension.setValue(prescriptionsValue);
    organizationResource.addExtension(prescriptionsExtension);
    Integer bedCount = h.getBedCount();
    if (bedCount != null) {
        Extension bedCountExtension = new Extension(SYNTHEA_URI + "bed-count-extension");
        IntegerType bedCountValue = new IntegerType(bedCount);
        bedCountExtension.setValue(bedCountValue);
        organizationResource.addExtension(bedCountExtension);
    }
}

Example 63 with IntegerType

use of org.hl7.fhir.dstu2016may.model.IntegerType in project bunsen by cerner.

the class TestData method newPatient.

/**
 * Returns a FHIR Patient for testing purposes.
 */
public static Patient newPatient() {
    Patient patient = new Patient();
    patient.setId("test-patient");
    patient.setMultipleBirth(new IntegerType(1));
    return patient;
}

Example 64 with IntegerType

use of org.hl7.fhir.dstu2016may.model.IntegerType 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 65 with IntegerType

use of org.hl7.fhir.dstu2016may.model.IntegerType in project hapi-fhir-jpaserver-starter by hapifhir.

the class ElasticsearchLastNR4IT method testLastN.

@Test
void testLastN() throws IOException, InterruptedException {
    Thread.sleep(2000);
    Patient pt = new Patient();
    pt.addName().setFamily("Lastn").addGiven("Arthur");
    IIdType id = ourClient.create().resource(pt).execute().getId().toUnqualifiedVersionless();
    Observation obs = new Observation();
    obs.getSubject().setReferenceElement(id);
    String observationCode = "testobservationcode";
    String codeSystem = "http://testobservationcodesystem";
    obs.getCode().addCoding().setCode(observationCode).setSystem(codeSystem);
    obs.setValue(new StringType(observationCode));
    Date effectiveDtm = new GregorianCalendar().getTime();
    obs.setEffective(new DateTimeType(effectiveDtm));
    obs.getCategoryFirstRep().addCoding().setCode("testcategorycode").setSystem("http://testcategorycodesystem");
    IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless();
    myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
    Parameters output = ourClient.operation().onType(Observation.class).named("lastn").withParameter(Parameters.class, "max", new IntegerType(1)).andParameter("subject", new StringType("Patient/" + id.getIdPart())).execute();
    Bundle b = (Bundle) output.getParameter().get(0).getResource();
    assertEquals(1, b.getTotal());
    assertEquals(obsId, b.getEntry().get(0).getResource().getIdElement().toUnqualifiedVersionless());
}