Examples with GrowthDataErrorsEditor org.mitre.synthea.editors.GrowthDataErrorsEditor used on opensource projects

Example 1 with GrowthDataErrorsEditor

use of org.mitre.synthea.editors.GrowthDataErrorsEditor in project synthea by synthetichealth.

the class GrowthDataErrorsEditorTest method encountersWithObservationsOfCode.

@Test
public void encountersWithObservationsOfCode() {
    GrowthDataErrorsEditor mod = new GrowthDataErrorsEditor();
    List<HealthRecord.Encounter> es = mod.encountersWithObservationsOfCode(record.encounters, GrowthDataErrorsEditor.HEIGHT_LOINC_CODE);
    assertEquals(2, es.size());
}

Example 2 with GrowthDataErrorsEditor

use of org.mitre.synthea.editors.GrowthDataErrorsEditor in project synthea by synthetichealth.

the class GrowthDataErrorsEditorTest method process.

@Test
public void process() {
    GrowthDataErrorsEditor m = new GrowthDataErrorsEditor();
    m.process(new Person(1), record.encounters, 100000);
}

Example 3 with GrowthDataErrorsEditor

use of org.mitre.synthea.editors.GrowthDataErrorsEditor 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());
    }
}