Examples with Location org.mitre.synthea.world.geography.Location used on opensource projects

Example 26 with Location

use of org.mitre.synthea.world.geography.Location in project synthea by synthetichealth.

the class EncounterModuleTest method setup.

/**
 * Setup the Encounter Module Tests.
 * @throws Exception on configuration loading error
 */
@BeforeClass
public static void setup() throws Exception {
    person = new Person(0L);
    // Give person an income to prevent null pointer.
    person.attributes.put(Person.INCOME, 100000);
    person.attributes.put(Person.BIRTHDATE, 0L);
    TestHelper.loadTestProperties();
    String testState = Config.get("test_state.default", "Massachusetts");
    location = new Location(testState, null);
    location.assignPoint(person, location.randomCityName(person));
    Provider.loadProviders(location, ProviderTest.providerRandom);
    module = new EncounterModule();
    // Ensure Person's Payer is not null.
    Payer.loadNoInsurance();
    person.coverage.setPayerAtTime(System.currentTimeMillis(), Payer.noInsurance);
}

Example 27 with Location

use of org.mitre.synthea.world.geography.Location in project synthea by synthetichealth.

the class FhirR4 method findLocationUrl.

/**
 * Find the Location entry in this bundle for the given provider, and return the
 * "fullUrl" attribute.
 *
 * @param provider A given provider.
 * @param bundle The current bundle being generated.
 * @return Location.fullUrl if found, otherwise null.
 */
private static String findLocationUrl(Provider provider, Bundle bundle) {
    for (BundleEntryComponent entry : bundle.getEntry()) {
        if (entry.getResource().fhirType().equals("Location")) {
            org.hl7.fhir.r4.model.Location location = (org.hl7.fhir.r4.model.Location) entry.getResource();
            Reference managingOrg = location.getManagingOrganization();
            if (managingOrg != null && managingOrg.getIdentifier().getValue().equals(provider.getResourceID())) {
                return entry.getFullUrl();
            }
        }
    }
    return null;
}

Example 28 with Location

use of org.mitre.synthea.world.geography.Location in project synthea by synthetichealth.

the class Generator method init.

private void init() {
    if (options.state == null) {
        options.state = DEFAULT_STATE;
    }
    int stateIndex = Location.getIndex(options.state);
    if (Config.getAsBoolean("exporter.cdw.export")) {
        CDWExporter.getInstance().setKeyStart((stateIndex * 1_000_000) + 1);
    }
    this.populationRandom = new DefaultRandomNumberGenerator(options.seed);
    this.clinicianRandom = new DefaultRandomNumberGenerator(options.clinicianSeed);
    this.timestep = Long.parseLong(Config.get("generate.timestep"));
    this.stop = options.endTime;
    this.referenceTime = options.referenceTime;
    this.location = new Location(options.state, options.city);
    this.logLevel = Config.get("generate.log_patients.detail", "simple");
    this.onlyDeadPatients = Config.getAsBoolean("generate.only_dead_patients");
    this.onlyAlivePatients = Config.getAsBoolean("generate.only_alive_patients");
    // If both values are set to true, then they are both set back to the default
    if (this.onlyDeadPatients && this.onlyAlivePatients) {
        Config.set("generate.only_dead_patients", "false");
        Config.set("generate.only_alive_patients", "false");
        this.onlyDeadPatients = false;
        this.onlyAlivePatients = false;
    }
    try {
        this.maxAttemptsToKeepPatient = Long.parseLong(Config.get("generate.max_attempts_to_keep_patient", "1000"));
        if (this.maxAttemptsToKeepPatient == 0) {
            // set it to null to make the check more clear
            this.maxAttemptsToKeepPatient = null;
        }
    } catch (Exception e) {
        this.maxAttemptsToKeepPatient = null;
    }
    this.onlyVeterans = Config.getAsBoolean("generate.veteran_population_override");
    this.totalGeneratedPopulation = new AtomicInteger(0);
    this.stats = Collections.synchronizedMap(new HashMap<String, AtomicInteger>());
    this.modulePredicate = getModulePredicate();
    stats.put("alive", new AtomicInteger(0));
    stats.put("dead", new AtomicInteger(0));
    if (Config.getAsBoolean("generate.track_detailed_transition_metrics", false)) {
        this.metrics = new TransitionMetrics();
    }
    // initialize hospitals
    Provider.loadProviders(location, this.clinicianRandom);
    // Initialize Payers
    Payer.loadPayers(location);
    // ensure modules load early
    if (options.localModuleDir != null) {
        Module.addModules(options.localModuleDir);
    }
    List<String> coreModuleNames = getModuleNames(Module.getModules(path -> false));
    List<String> moduleNames = getModuleNames(Module.getModules(modulePredicate));
    if (options.keepPatientsModulePath != null) {
        try {
            Path path = options.keepPatientsModulePath.toPath().toAbsolutePath();
            this.keepPatientsModule = Module.loadFile(path, false, null, true);
        } catch (Exception e) {
            throw new ExceptionInInitializerError(e);
        }
    }
    // ensure cost data loads early
    Costs.loadCostData();
    String locationName;
    if (options.city == null) {
        locationName = options.state;
    } else {
        locationName = options.city + ", " + options.state;
    }
    System.out.println("Running with options:");
    System.out.println(String.format("Population: %d\nSeed: %d\nProvider Seed:%d\nReference Time: %d\nLocation: %s", options.population, options.seed, options.clinicianSeed, options.referenceTime, locationName));
    System.out.println(String.format("Min Age: %d\nMax Age: %d", options.minAge, options.maxAge));
    if (options.gender != null) {
        System.out.println(String.format("Gender: %s", options.gender));
    }
    if (options.enabledModules != null) {
        moduleNames.removeAll(coreModuleNames);
        moduleNames.sort(String::compareToIgnoreCase);
        System.out.println("Modules: " + String.join("\n       & ", moduleNames));
        System.out.println(String.format("       > [%d loaded]", moduleNames.size()));
    }
    if (Config.getAsBoolean("growtherrors", false)) {
        HealthRecordEditors hrm = HealthRecordEditors.getInstance();
        hrm.registerEditor(new GrowthDataErrorsEditor());
    }
}

Example 29 with Location

use of org.mitre.synthea.world.geography.Location in project synthea by synthetichealth.

the class LifecycleModule method birth.

/**
 * For unto us a child is born.
 * @param person The baby.
 * @param time The time of birth.
 */
public static void birth(Person person, long time) {
    Map<String, Object> attributes = person.attributes;
    attributes.put(Person.ID, person.randUUID().toString());
    attributes.put(Person.BIRTHDATE, time);
    String gender = (String) attributes.get(Person.GENDER);
    String language = (String) attributes.get(Person.FIRST_LANGUAGE);
    String firstName = Names.fakeFirstName(gender, language, person);
    String lastName = Names.fakeLastName(language, person);
    attributes.put(Person.FIRST_NAME, firstName);
    attributes.put(Person.LAST_NAME, lastName);
    attributes.put(Person.NAME, firstName + " " + lastName);
    String motherFirstName = Names.fakeFirstName("F", language, person);
    String motherLastName = Names.fakeLastName(language, person);
    attributes.put(Person.NAME_MOTHER, motherFirstName + " " + motherLastName);
    String fatherFirstName = Names.fakeFirstName("M", language, person);
    // this is anglocentric where the baby gets the father's last name
    attributes.put(Person.NAME_FATHER, fatherFirstName + " " + lastName);
    double prevalenceOfTwins = (double) BiometricsConfig.get("lifecycle.prevalence_of_twins", 0.02);
    if ((person.rand() < prevalenceOfTwins)) {
        attributes.put(Person.MULTIPLE_BIRTH_STATUS, person.randInt(3) + 1);
    }
    String phoneNumber = "555-" + ((person.randInt(999 - 100 + 1) + 100)) + "-" + ((person.randInt(9999 - 1000 + 1) + 1000));
    attributes.put(Person.TELECOM, phoneNumber);
    boolean hasStreetAddress2 = person.rand() < 0.5;
    attributes.put(Person.ADDRESS, Names.fakeAddress(hasStreetAddress2, person));
    // If using FixedRecords, overwrite the person's attributes with the FixedRecord attributes.
    if (person.attributes.get(Person.RECORD_GROUP) != null) {
        FixedRecordGroup recordGroup = (FixedRecordGroup) person.attributes.get(Person.RECORD_GROUP);
        FixedRecord fr = recordGroup.records.get(0);
        attributes.putAll(fr.getFixedRecordAttributes());
    }
    String ssn = "999-" + ((person.randInt(99 - 10 + 1) + 10)) + "-" + ((person.randInt(9999 - 1000 + 1) + 1000));
    attributes.put(Person.IDENTIFIER_SSN, ssn);
    String city = (String) attributes.get(Person.CITY);
    Location location = (Location) attributes.get(Person.LOCATION);
    if (location != null) {
        // should never happen in practice, but can happen in unit tests
        location.assignPoint(person, city);
        person.attributes.put(Person.ZIP, location.getZipCode(city, person));
        String[] birthPlace;
        if ("english".equalsIgnoreCase((String) attributes.get(Person.FIRST_LANGUAGE))) {
            birthPlace = location.randomBirthPlace(person);
        } else {
            birthPlace = location.randomBirthplaceByLanguage(person, (String) person.attributes.get(Person.FIRST_LANGUAGE));
        }
        attributes.put(Person.BIRTH_CITY, birthPlace[0]);
        attributes.put(Person.BIRTH_STATE, birthPlace[1]);
        attributes.put(Person.BIRTH_COUNTRY, birthPlace[2]);
        // For CSV exports so we don't break any existing schemas
        attributes.put(Person.BIRTHPLACE, birthPlace[3]);
    }
    attributes.put(Person.ACTIVE_WEIGHT_MANAGEMENT, false);
    // TODO: Why are the percentiles a vital sign? Sounds more like an attribute?
    double heightPercentile = person.rand();
    PediatricGrowthTrajectory pgt = new PediatricGrowthTrajectory(person.getSeed(), time);
    double weightPercentile = pgt.reverseWeightPercentile(gender, heightPercentile);
    person.setVitalSign(VitalSign.HEIGHT_PERCENTILE, heightPercentile);
    person.setVitalSign(VitalSign.WEIGHT_PERCENTILE, weightPercentile);
    person.attributes.put(Person.GROWTH_TRAJECTORY, pgt);
    // Temporarily generate a mother
    Person mother = new Person(person.randLong());
    mother.attributes.put(Person.GENDER, "F");
    mother.attributes.put("pregnant", true);
    mother.attributes.put(Person.RACE, person.attributes.get(Person.RACE));
    mother.attributes.put(Person.ETHNICITY, person.attributes.get(Person.ETHNICITY));
    mother.attributes.put(BirthStatistics.BIRTH_SEX, person.attributes.get(Person.GENDER));
    BirthStatistics.setBirthStatistics(mother, time);
    person.setVitalSign(VitalSign.HEIGHT, // cm
    (double) mother.attributes.get(BirthStatistics.BIRTH_HEIGHT));
    person.setVitalSign(VitalSign.WEIGHT, // kg
    (double) mother.attributes.get(BirthStatistics.BIRTH_WEIGHT));
    // cm
    person.setVitalSign(VitalSign.HEAD, childHeadCircumference(person, time));
    attributes.put(AGE, 0);
    attributes.put(AGE_MONTHS, 0);
    boolean isRHNeg = person.rand() < 0.15;
    attributes.put("RH_NEG", isRHNeg);
    double adherenceBaseline = Config.getAsDouble("lifecycle.adherence.baseline", 0.05);
    person.attributes.put(ADHERENCE_PROBABILITY, adherenceBaseline);
    // set initial height and weight from percentiles
    grow(person, time);
    // Set initial values for many vital signs.
    calculateVitalSigns(person, time);
    String orientation = sexualOrientationData.next(person);
    attributes.put(Person.SEXUAL_ORIENTATION, orientation);
    // Setup vital signs which follow the generator approach
    setupVitalSignGenerators(person);
}

Example 30 with Location

use of org.mitre.synthea.world.geography.Location in project synthea by synthetichealth.

the class Generator method pickFixedDemographics.

/**
 * Pick a person's demographics based on their FixedRecords.
 * @param index The index to use.
 * @param random Random object.
 */
private Map<String, Object> pickFixedDemographics(int index, Random random) {
    // Get the first FixedRecord from the current RecordGroup
    FixedRecordGroup recordGroup = this.recordGroups.get(index);
    FixedRecord fr = recordGroup.records.get(0);
    // Get the city from the location in the fixed record.
    this.location = new Location(fr.state, recordGroup.getSafeCity());
    Demographics city = this.location.randomCity(random);
    // Pick the rest of the demographics based on the location of the fixed record.
    Map<String, Object> demoAttributes = pickDemographics(random, city);
    // Overwrite the person's attributes with the FixedRecord.
    demoAttributes.put(Person.BIRTHDATE, recordGroup.getValidBirthdate());
    demoAttributes.put(Person.BIRTH_CITY, city.city);
    String g = fr.gender;
    if (g.equalsIgnoreCase("None") || StringUtils.isBlank(g)) {
        g = "F";
    }
    demoAttributes.put(Person.GENDER, g);
    // Give the person their FixedRecordGroup of FixedRecords.
    demoAttributes.put(Person.RECORD_GROUP, recordGroup);
    demoAttributes.put(Person.LINK_ID, recordGroup.linkId);
    // Return the Demographic Attributes of the current person.
    return demoAttributes;
}