Examples with ExtensionDt ca.uhn.fhir.model.api.ExtensionDt used on opensource projects

Example 1 with ExtensionDt

use of ca.uhn.fhir.model.api.ExtensionDt in project synthea by synthetichealth.

the class FhirPractitionerExporterDstu2 method export.

/**
 * Export the practitioner in FHIR DSTU2 format.
 */
public static void export(long stop) {
    if (Config.getAsBoolean("exporter.practitioner.fhir_dstu2.export")) {
        Bundle bundle = new Bundle();
        if (Config.getAsBoolean("exporter.fhir.transaction_bundle")) {
            bundle.setType(BundleTypeEnum.BATCH);
        } else {
            bundle.setType(BundleTypeEnum.COLLECTION);
        }
        for (Provider h : Provider.getProviderList()) {
            // filter - exports only those hospitals in use
            Table<Integer, String, AtomicInteger> utilization = h.getUtilization();
            int totalEncounters = utilization.column(Provider.ENCOUNTERS).values().stream().mapToInt(ai -> ai.get()).sum();
            if (totalEncounters > 0) {
                Map<String, ArrayList<Clinician>> clinicians = h.clinicianMap;
                for (String specialty : clinicians.keySet()) {
                    ArrayList<Clinician> docs = clinicians.get(specialty);
                    for (Clinician doc : docs) {
                        if (doc.getEncounterCount() > 0) {
                            Entry entry = FhirDstu2.practitioner(bundle, doc);
                            Practitioner practitioner = (Practitioner) entry.getResource();
                            ExtensionDt extension = new ExtensionDt();
                            extension.setUrl(EXTENSION_URI);
                            extension.setValue(new IntegerDt(doc.getEncounterCount()));
                            practitioner.addUndeclaredExtension(extension);
                        }
                    }
                }
            }
        }
        String bundleJson = FhirDstu2.getContext().newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
        // get output folder
        List<String> folders = new ArrayList<>();
        folders.add("fhir_dstu2");
        String baseDirectory = Config.get("exporter.baseDirectory");
        File f = Paths.get(baseDirectory, folders.toArray(new String[0])).toFile();
        f.mkdirs();
        Path outFilePath = f.toPath().resolve("practitionerInformation" + stop + ".json");
        try {
            Files.write(outFilePath, Collections.singleton(bundleJson), StandardOpenOption.CREATE_NEW);
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

Example 2 with ExtensionDt

use of ca.uhn.fhir.model.api.ExtensionDt in project synthea by synthetichealth.

the class HospitalExporterDstu2 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();
    ExtensionDt encountersExtension = new ExtensionDt();
    encountersExtension.setUrl(SYNTHEA_URI + "utilization-encounters-extension");
    IntegerDt encountersValue = new IntegerDt(totalEncounters);
    encountersExtension.setValue(encountersValue);
    organizationResource.addUndeclaredExtension(encountersExtension);
    int totalProcedures = utilization.column(Provider.PROCEDURES).values().stream().mapToInt(ai -> ai.get()).sum();
    ExtensionDt proceduresExtension = new ExtensionDt();
    proceduresExtension.setUrl(SYNTHEA_URI + "utilization-procedures-extension");
    IntegerDt proceduresValue = new IntegerDt(totalProcedures);
    proceduresExtension.setValue(proceduresValue);
    organizationResource.addUndeclaredExtension(proceduresExtension);
    int totalLabs = utilization.column(Provider.LABS).values().stream().mapToInt(ai -> ai.get()).sum();
    ExtensionDt labsExtension = new ExtensionDt();
    labsExtension.setUrl(SYNTHEA_URI + "utilization-labs-extension");
    IntegerDt labsValue = new IntegerDt(totalLabs);
    labsExtension.setValue(labsValue);
    organizationResource.addUndeclaredExtension(labsExtension);
    int totalPrescriptions = utilization.column(Provider.PRESCRIPTIONS).values().stream().mapToInt(ai -> ai.get()).sum();
    ExtensionDt prescriptionsExtension = new ExtensionDt();
    prescriptionsExtension.setUrl(SYNTHEA_URI + "utilization-prescriptions-extension");
    IntegerDt prescriptionsValue = new IntegerDt(totalPrescriptions);
    prescriptionsExtension.setValue(prescriptionsValue);
    organizationResource.addUndeclaredExtension(prescriptionsExtension);
    Integer bedCount = h.getBedCount();
    if (bedCount != null) {
        ExtensionDt bedCountExtension = new ExtensionDt();
        bedCountExtension.setUrl(SYNTHEA_URI + "bed-count-extension");
        IntegerDt bedCountValue = new IntegerDt(bedCount);
        bedCountExtension.setValue(bedCountValue);
        organizationResource.addUndeclaredExtension(bedCountExtension);
    }
}

Example 3 with ExtensionDt

use of ca.uhn.fhir.model.api.ExtensionDt in project synthea by synthetichealth.

the class FhirDstu2 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 Entry 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));
    patientResource.addIdentifier().setType(IdentifierTypeCodesEnum.MR).setSystem("http://hospital.smarthealthit.org").setValue((String) person.attributes.get(Person.ID));
    patientResource.addIdentifier().setType(IdentifierTypeCodesEnum.SOCIAL_BENEFICIARY_IDENTIFIER).setSystem("http://hl7.org/fhir/sid/us-ssn").setValue((String) person.attributes.get(Person.IDENTIFIER_SSN));
    if (person.attributes.get(Person.IDENTIFIER_DRIVERS) != null) {
        patientResource.addIdentifier().setType(IdentifierTypeCodesEnum.DL).setSystem("urn:oid:2.16.840.1.113883.4.3.25").setValue((String) person.attributes.get(Person.IDENTIFIER_DRIVERS));
    }
    ExtensionDt raceExtension = new ExtensionDt();
    raceExtension.setUrl("http://hl7.org/fhir/StructureDefinition/us-core-race");
    String race = (String) person.attributes.get(Person.RACE);
    ExtensionDt ethnicityExtension = new ExtensionDt();
    ethnicityExtension.setUrl("http://hl7.org/fhir/StructureDefinition/us-core-ethnicity");
    String ethnicity = (String) person.attributes.get(Person.ETHNICITY);
    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 ethnicityDisplay;
    if (ethnicity.equals("hispanic")) {
        ethnicityDisplay = "Hispanic or Latino";
    } else {
        ethnicityDisplay = "Not Hispanic or Latino";
    }
    Code raceCode = new Code("http://hl7.org/fhir/v3/Race", (String) raceEthnicityCodes.get(race), raceDisplay);
    Code ethnicityCode = new Code("http://hl7.org/fhir/v3/Ethnicity", (String) raceEthnicityCodes.get(ethnicity), ethnicityDisplay);
    raceExtension.setValue(mapCodeToCodeableConcept(raceCode, "http://hl7.org/fhir/v3/Race"));
    ethnicityExtension.setValue(mapCodeToCodeableConcept(ethnicityCode, "http://hl7.org/fhir/v3/Ethnicity"));
    patientResource.addUndeclaredExtension(raceExtension);
    patientResource.addUndeclaredExtension(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<Communication> communication = new ArrayList<Communication>();
    Communication language = new Communication();
    language.setLanguage(mapCodeToCodeableConcept(languageCode, (String) languageMap.get("system")));
    communication.add(language);
    patientResource.setCommunication(communication);
    HumanNameDt name = patientResource.addName();
    name.setUse(NameUseEnum.OFFICIAL);
    name.addGiven((String) person.attributes.get(Person.FIRST_NAME));
    List<StringDt> officialFamilyNames = new ArrayList<StringDt>();
    officialFamilyNames.add(new StringDt((String) person.attributes.get(Person.LAST_NAME)));
    name.setFamily(officialFamilyNames);
    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) {
        HumanNameDt maidenName = patientResource.addName();
        maidenName.setUse(NameUseEnum.MAIDEN);
        maidenName.addGiven((String) person.attributes.get(Person.FIRST_NAME));
        List<StringDt> maidenFamilyNames = new ArrayList<StringDt>();
        maidenFamilyNames.add(new StringDt((String) person.attributes.get(Person.MAIDEN_NAME)));
        maidenName.setFamily(maidenFamilyNames);
        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));
        }
    }
    ExtensionDt mothersMaidenNameExtension = new ExtensionDt();
    mothersMaidenNameExtension.setUrl("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");
    String mothersMaidenName = (String) person.attributes.get(Person.NAME_MOTHER);
    mothersMaidenNameExtension.setValue(new StringDt(mothersMaidenName));
    patientResource.addUndeclaredExtension(mothersMaidenNameExtension);
    long birthdate = (long) person.attributes.get(Person.BIRTHDATE);
    patientResource.setBirthDate(new DateDt(new Date(birthdate)));
    ExtensionDt birthSexExtension = new ExtensionDt();
    birthSexExtension.setUrl("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
    if (person.attributes.get(Person.GENDER).equals("M")) {
        patientResource.setGender(AdministrativeGenderEnum.MALE);
        birthSexExtension.setValue(new CodeDt("M"));
    } else if (person.attributes.get(Person.GENDER).equals("F")) {
        patientResource.setGender(AdministrativeGenderEnum.FEMALE);
        birthSexExtension.setValue(new CodeDt("F"));
    }
    patientResource.addUndeclaredExtension(birthSexExtension);
    String state = (String) person.attributes.get(Person.STATE);
    AddressDt 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);
    }
    Point2D.Double coord = person.getLonLat();
    if (coord != null) {
        ExtensionDt geolocationExtension = new ExtensionDt();
        geolocationExtension.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
        ExtensionDt latitudeExtension = new ExtensionDt();
        ExtensionDt longitudeExtension = new ExtensionDt();
        latitudeExtension.setUrl("latitude");
        longitudeExtension.setUrl("longitude");
        latitudeExtension.setValue(new DecimalDt(coord.getY()));
        longitudeExtension.setValue(new DecimalDt(coord.getX()));
        geolocationExtension.addUndeclaredExtension(latitudeExtension);
        geolocationExtension.addUndeclaredExtension(longitudeExtension);
        addrResource.addUndeclaredExtension(geolocationExtension);
    }
    AddressDt birthplace = new AddressDt();
    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));
    ExtensionDt birthplaceExtension = new ExtensionDt();
    birthplaceExtension.setUrl("http://hl7.org/fhir/StructureDefinition/birthPlace");
    birthplaceExtension.setValue(birthplace);
    patientResource.addUndeclaredExtension(birthplaceExtension);
    if (person.attributes.get(Person.MULTIPLE_BIRTH_STATUS) != null) {
        patientResource.setMultipleBirth(new IntegerDt((int) person.attributes.get(Person.MULTIPLE_BIRTH_STATUS)));
    } else {
        patientResource.setMultipleBirth(new BooleanDt(false));
    }
    patientResource.addTelecom().setSystem(ContactPointSystemEnum.PHONE).setUse(ContactPointUseEnum.HOME).setValue((String) person.attributes.get(Person.TELECOM));
    String maritalStatus = ((String) person.attributes.get(Person.MARITAL_STATUS));
    if (maritalStatus != null) {
        patientResource.setMaritalStatus(MaritalStatusCodesEnum.forCode(maritalStatus.toUpperCase()));
    } else {
        patientResource.setMaritalStatus(MaritalStatusCodesEnum.S);
    }
    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.seed + "  Population seed: " + person.populationSeed;
    patientResource.setText(new NarrativeDt(new XhtmlDt(generatedBySynthea), NarrativeStatusEnum.GENERATED));
    // 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) {
        ExtensionDt dalyExtension = new ExtensionDt();
        dalyExtension.setUrl(SYNTHEA_EXT + "disability-adjusted-life-years");
        DecimalDt daly = new DecimalDt(dalyValue);
        dalyExtension.setValue(daly);
        patientResource.addUndeclaredExtension(dalyExtension);
        ExtensionDt qalyExtension = new ExtensionDt();
        qalyExtension.setUrl(SYNTHEA_EXT + "quality-adjusted-life-years");
        DecimalDt qaly = new DecimalDt(qalyValue);
        qalyExtension.setValue(qaly);
        patientResource.addUndeclaredExtension(qalyExtension);
    }
    return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
}