Examples with Clinician org.mitre.synthea.world.agents.Clinician used on opensource projects

Example 1 with Clinician

use of org.mitre.synthea.world.agents.Clinician 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 Clinician

use of org.mitre.synthea.world.agents.Clinician in project synthea by synthetichealth.

the class BB2RIFExporter method exportNPIs.

/**
 * Export NPI writer with synthetic providers.
 * @throws IOException if something goes horribly wrong.
 */
public void exportNPIs() throws IOException {
    HashMap<NPI, String> fieldValues = new HashMap<>();
    SynchronizedBBLineWriter rifWriter = rifWriters.getOrCreateWriter(NPI.class, RifEntryStatus.INITIAL, "tsv", "\t");
    for (Provider h : Provider.getProviderList()) {
        // filter - exports only those organizations 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) {
            // export organization
            fieldValues.clear();
            fieldValues.put(NPI.NPI, h.npi);
            fieldValues.put(NPI.ENTITY_TYPE_CODE, "2");
            fieldValues.put(NPI.EIN, "<UNAVAIL>");
            fieldValues.put(NPI.ORG_NAME, h.name);
            rifWriter.writeValues(fieldValues);
            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) {
                        // export each doc
                        Map<String, Object> attributes = doc.getAttributes();
                        fieldValues.clear();
                        fieldValues.put(NPI.NPI, doc.npi);
                        fieldValues.put(NPI.ENTITY_TYPE_CODE, "1");
                        fieldValues.put(NPI.LAST_NAME, attributes.get(Clinician.LAST_NAME).toString());
                        fieldValues.put(NPI.FIRST_NAME, attributes.get(Clinician.FIRST_NAME).toString());
                        fieldValues.put(NPI.PREFIX, attributes.get(Clinician.NAME_PREFIX).toString());
                        fieldValues.put(NPI.CREDENTIALS, "M.D.");
                        rifWriter.writeValues(fieldValues);
                    }
                }
            }
        }
    }
}

Example 3 with Clinician

use of org.mitre.synthea.world.agents.Clinician in project synthea by synthetichealth.

the class CSVExporter method exportOrganizationsAndProviders.

/**
 * Export the organizations.csv and providers.csv files. This method should be
 * called once after all the Patient records have been exported using the
 * export(Person,long) method.
 *
 * @throws IOException if any IO errors occur.
 */
public void exportOrganizationsAndProviders() throws IOException {
    for (Provider org : Provider.getProviderList()) {
        // Check utilization for hospital before we export
        Table<Integer, String, AtomicInteger> utilization = org.getUtilization();
        int totalEncounters = utilization.column(Provider.ENCOUNTERS).values().stream().mapToInt(ai -> ai.get()).sum();
        if (totalEncounters > 0) {
            organization(org, totalEncounters);
            Map<String, ArrayList<Clinician>> providers = org.clinicianMap;
            for (String speciality : providers.keySet()) {
                ArrayList<Clinician> clinicians = providers.get(speciality);
                for (Clinician clinician : clinicians) {
                    provider(clinician, org.getResourceID());
                }
            }
        }
        organizations.flush();
        providers.flush();
    }
}

Example 4 with Clinician

use of org.mitre.synthea.world.agents.Clinician in project synthea by synthetichealth.

the class FhirPractitionerExporterStu3 method export.

/**
 * Export the practitioner in FHIR STU3 format.
 */
public static void export(long stop) {
    if (Config.getAsBoolean("exporter.practitioner.fhir_stu3.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 = FhirStu3.practitioner(bundle, doc);
                            Practitioner practitioner = (Practitioner) entry.getResource();
                            practitioner.addExtension().setUrl(EXTENSION_URI).setValue(new IntegerType(doc.getEncounterCount()));
                        }
                    }
                }
            }
        }
        String bundleJson = FhirStu3.getContext().newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle);
        // get output folder
        List<String> folders = new ArrayList<>();
        folders.add("fhir_stu3");
        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 Clinician

use of org.mitre.synthea.world.agents.Clinician 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();
        }
    }
}