Examples with RandomNumberGenerator org.mitre.synthea.helpers.RandomNumberGenerator used on opensource projects

Example 1 with RandomNumberGenerator

use of org.mitre.synthea.helpers.RandomNumberGenerator in project synthea by synthetichealth.

the class HospitalExporterR4 method export.

/**
 * Export the hospital in FHIR R4 format.
 */
public static void export(RandomNumberGenerator rand, long stop) {
    if (Config.getAsBoolean("exporter.hospital.fhir.export")) {
        Bundle bundle = new Bundle();
        if (Config.getAsBoolean("exporter.fhir.transaction_bundle")) {
            bundle.setType(BundleType.BATCH);
        } else {
            bundle.setType(BundleType.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) {
                BundleEntryComponent entry = FhirR4.provider(rand, bundle, h);
                addHospitalExtensions(h, (Organization) entry.getResource());
            }
        }
        String bundleJson = FhirR4.getContext().newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
        // get output folder
        List<String> folders = new ArrayList<>();
        folders.add("fhir");
        String baseDirectory = Config.get("exporter.baseDirectory");
        File f = Paths.get(baseDirectory, folders.toArray(new String[0])).toFile();
        f.mkdirs();
        Path outFilePath = f.toPath().resolve("hospitalInformation" + stop + ".json");
        try {
            Files.write(outFilePath, Collections.singleton(bundleJson), StandardOpenOption.CREATE_NEW);
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

Example 2 with RandomNumberGenerator

use of org.mitre.synthea.helpers.RandomNumberGenerator in project synthea by synthetichealth.

the class BB2RIFExporterTest method testStaticFieldConfig.

@Test
public void testStaticFieldConfig() throws IOException, NoSuchMethodException {
    RandomNumberGenerator rand = new Person(System.currentTimeMillis());
    assertEquals("foo", StaticFieldConfig.processCell("foo", rand));
    String randomVal = StaticFieldConfig.processCell("1, 2, 3", rand);
    assertTrue(randomVal.equalsIgnoreCase("1") || randomVal.equalsIgnoreCase("2") || randomVal.equalsIgnoreCase("3"));
    StaticFieldConfig config = new StaticFieldConfig();
    assertEquals("INSERT", config.getValue("DML_IND", INPATIENT.class));
    assertEquals("82 (DMEPOS)", config.getValue("NCH_CLM_TYPE_CD", DME.class));
    assertEquals("71 (local carrier, non-DME)", config.getValue("NCH_CLM_TYPE_CD", CARRIER.class));
    HashMap<BENEFICIARY, String> values = new HashMap<>();
    config.setValues(values, BENEFICIARY.class, rand);
    assertEquals("INSERT", values.get(BENEFICIARY.DML_IND));
    String sexIdent = values.get(BENEFICIARY.BENE_SEX_IDENT_CD);
    assertTrue(sexIdent.equals("1") || sexIdent.equals("2"));
}

Example 3 with RandomNumberGenerator

use of org.mitre.synthea.helpers.RandomNumberGenerator in project synthea by synthetichealth.

the class FhirR4 method media.

/**
 * Map the given Observation with attachment element to a FHIR Media 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 Media to
 * @param encounterEntry Current Encounter entry
 * @param obs   The Observation to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static BundleEntryComponent media(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Observation obs) {
    org.hl7.fhir.r4.model.Media mediaResource = new org.hl7.fhir.r4.model.Media();
    // Hard code as Image since we don't anticipate using video or audio any time soon
    Code mediaType = new Code("http://terminology.hl7.org/CodeSystem/media-type", "image", "Image");
    if (obs.codes != null && obs.codes.size() > 0) {
        List<CodeableConcept> reasonList = obs.codes.stream().map(code -> mapCodeToCodeableConcept(code, SNOMED_URI)).collect(Collectors.toList());
        mediaResource.setReasonCode(reasonList);
    }
    mediaResource.setType(mapCodeToCodeableConcept(mediaType, MEDIA_TYPE_URI));
    mediaResource.setStatus(MediaStatus.COMPLETED);
    mediaResource.setSubject(new Reference(personEntry.getFullUrl()));
    mediaResource.setEncounter(new Reference(encounterEntry.getFullUrl()));
    Attachment content = (Attachment) obs.value;
    org.hl7.fhir.r4.model.Attachment contentResource = new org.hl7.fhir.r4.model.Attachment();
    contentResource.setContentType(content.contentType);
    contentResource.setLanguage(content.language);
    if (content.data != null) {
        contentResource.setDataElement(new org.hl7.fhir.r4.model.Base64BinaryType(content.data));
    } else {
        contentResource.setSize(content.size);
    }
    contentResource.setUrl(content.url);
    contentResource.setTitle(content.title);
    if (content.hash != null) {
        contentResource.setHashElement(new org.hl7.fhir.r4.model.Base64BinaryType(content.hash));
    }
    mediaResource.setWidth(content.width);
    mediaResource.setHeight(content.height);
    mediaResource.setContent(contentResource);
    return newEntry(rand, bundle, mediaResource);
}

Example 4 with RandomNumberGenerator

use of org.mitre.synthea.helpers.RandomNumberGenerator in project synthea by synthetichealth.

the class FhirPractitionerExporterR4 method export.

/**
 * Export the practitioner in FHIR R4 format.
 */
public static void export(RandomNumberGenerator rand, long stop) {
    if (Config.getAsBoolean("exporter.practitioner.fhir.export")) {
        Bundle bundle = new Bundle();
        if (Config.getAsBoolean("exporter.fhir.transaction_bundle")) {
            bundle.setType(BundleType.BATCH);
        } else {
            bundle.setType(BundleType.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) {
                            BundleEntryComponent entry = FhirR4.practitioner(rand, bundle, doc);
                            Practitioner practitioner = (Practitioner) entry.getResource();
                            practitioner.addExtension().setUrl(EXTENSION_URI).setValue(new IntegerType(doc.getEncounterCount()));
                        }
                    }
                }
            }
        }
        String bundleJson = FhirR4.getContext().newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
        // get output folder
        List<String> folders = new ArrayList<>();
        folders.add("fhir");
        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 5 with RandomNumberGenerator

use of org.mitre.synthea.helpers.RandomNumberGenerator in project synthea by synthetichealth.

the class FhirStu3 method media.

/**
 * Map the given Media element to a FHIR Media 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 Media to
 * @param encounterEntry Current Encounter entry
 * @param obs   The Observation to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static BundleEntryComponent media(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Observation obs) {
    org.hl7.fhir.dstu3.model.Media mediaResource = new org.hl7.fhir.dstu3.model.Media();
    if (obs.codes != null && obs.codes.size() > 0) {
        List<CodeableConcept> reasonList = obs.codes.stream().map(code -> mapCodeToCodeableConcept(code, SNOMED_URI)).collect(Collectors.toList());
        mediaResource.setReasonCode(reasonList);
    }
    // Hard code as an image
    mediaResource.setType(DigitalMediaType.PHOTO);
    mediaResource.setSubject(new Reference(personEntry.getFullUrl()));
    Attachment content = (Attachment) obs.value;
    org.hl7.fhir.dstu3.model.Attachment contentResource = new org.hl7.fhir.dstu3.model.Attachment();
    contentResource.setContentType(content.contentType);
    contentResource.setLanguage(content.language);
    if (content.data != null) {
        contentResource.setDataElement(new org.hl7.fhir.dstu3.model.Base64BinaryType(content.data));
    }
    contentResource.setUrl(content.url);
    contentResource.setSize(content.size);
    contentResource.setTitle(content.title);
    if (content.hash != null) {
        contentResource.setHashElement(new org.hl7.fhir.dstu3.model.Base64BinaryType(content.hash));
    }
    mediaResource.setWidth(content.width);
    mediaResource.setHeight(content.height);
    mediaResource.setContent(contentResource);
    return newEntry(rand, bundle, mediaResource);
}