Examples with Encounter org.mitre.synthea.world.concepts.HealthRecord.Encounter used on opensource projects

Example 11 with Encounter

use of org.mitre.synthea.world.concepts.HealthRecord.Encounter in project synthea by synthetichealth.

the class FhirDstu2 method report.

/**
 * Map the given Report to a FHIR DiagnosticReport 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 Report to
 * @param encounterEntry
 *          Current Encounter entry
 * @param report
 *          The Report
 * @return The added Entry
 */
private static Entry report(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, Report report) {
    DiagnosticReport reportResource = new DiagnosticReport();
    reportResource.setStatus(DiagnosticReportStatusEnum.FINAL);
    /*
     * Technically, the CodeableConcept system should be "http://hl7.org/fhir/v2/0074"
     * But the official Argonauts profiles incorrectly list the category pattern as
     * the ValueSet (which contains the above system) as
     * "http://hl7.org/fhir/ValueSet/diagnostic-service-sections", so we repeat the
     * error here.
     */
    CodeableConceptDt category = new CodeableConceptDt("http://hl7.org/fhir/ValueSet/diagnostic-service-sections", "LAB");
    reportResource.setCategory(category);
    reportResource.setCode(mapCodeToCodeableConcept(report.codes.get(0), LOINC_URI));
    reportResource.setSubject(new ResourceReferenceDt(personEntry.getFullUrl()));
    reportResource.setEncounter(new ResourceReferenceDt(encounterEntry.getFullUrl()));
    reportResource.setEffective(convertFhirDateTime(report.start, true));
    reportResource.setIssued(new InstantDt(new Date(report.start)));
    ca.uhn.fhir.model.dstu2.resource.Encounter encounter = (ca.uhn.fhir.model.dstu2.resource.Encounter) encounterEntry.getResource();
    reportResource.setPerformer(encounter.getServiceProvider());
    for (Observation observation : report.observations) {
        ResourceReferenceDt reference = new ResourceReferenceDt(observation.fullUrl);
        reference.setDisplay(observation.codes.get(0).display);
        List<ResourceReferenceDt> result = new ArrayList<ResourceReferenceDt>();
        result.add(reference);
        reportResource.setResult(result);
    }
    return newEntry(rand, bundle, reportResource);
}

Example 12 with Encounter

use of org.mitre.synthea.world.concepts.HealthRecord.Encounter in project synthea by synthetichealth.

the class FhirDstu2 method encounter.

/**
 * Map the given Encounter into a FHIR Encounter resource, and add it to the given Bundle.
 *
 * @param person
 *          Patient at the encounter.
 * @param personEntry
 *          Entry for the Person
 * @param bundle
 *          The Bundle to add to
 * @param encounter
 *          The current Encounter
 * @return The added Entry
 */
private static Entry encounter(Person person, Entry personEntry, Bundle bundle, Encounter encounter) {
    ca.uhn.fhir.model.dstu2.resource.Encounter encounterResource = new ca.uhn.fhir.model.dstu2.resource.Encounter();
    encounterResource.setPatient(new ResourceReferenceDt(personEntry.getFullUrl()));
    encounterResource.setStatus(EncounterStateEnum.FINISHED);
    if (encounter.codes.isEmpty()) {
        // wellness encounter
        encounterResource.addType().addCoding().setCode("185349003").setDisplay("Encounter for check up").setSystem(SNOMED_URI);
    } else {
        Code code = encounter.codes.get(0);
        encounterResource.addType(mapCodeToCodeableConcept(code, SNOMED_URI));
    }
    EncounterClassEnum encounterClass = EncounterClassEnum.forCode(encounter.type);
    if (encounterClass == null) {
        encounterClass = EncounterClassEnum.AMBULATORY;
    }
    encounterResource.setClassElement(encounterClass);
    encounterResource.setPeriod(new PeriodDt().setStart(new DateTimeDt(new Date(encounter.start))).setEnd(new DateTimeDt(new Date(encounter.stop))));
    if (encounter.reason != null) {
        encounterResource.addReason().addCoding().setCode(encounter.reason.code).setDisplay(encounter.reason.display).setSystem(SNOMED_URI);
    }
    Provider provider = encounter.provider;
    if (provider == null) {
        // no associated provider, patient goes to wellness provider
        provider = person.getProvider(EncounterType.WELLNESS, encounter.start);
    }
    if (TRANSACTION_BUNDLE) {
        encounterResource.setServiceProvider(new ResourceReferenceDt(ExportHelper.buildFhirSearchUrl("Organization", provider.getResourceID())));
    } else {
        String providerFullUrl = findProviderUrl(provider, bundle);
        if (providerFullUrl != null) {
            encounterResource.setServiceProvider(new ResourceReferenceDt(providerFullUrl));
        } else {
            Entry providerOrganization = provider(bundle, provider);
            encounterResource.setServiceProvider(new ResourceReferenceDt(providerOrganization.getFullUrl()));
        }
    }
    encounterResource.getServiceProvider().setDisplay(provider.name);
    if (encounter.clinician != null) {
        if (TRANSACTION_BUNDLE) {
            encounterResource.addParticipant().setIndividual(new ResourceReferenceDt(ExportHelper.buildFhirNpiSearchUrl(encounter.clinician)));
        } else {
            String practitionerFullUrl = findPractitioner(encounter.clinician, bundle);
            if (practitionerFullUrl != null) {
                encounterResource.addParticipant().setIndividual(new ResourceReferenceDt(practitionerFullUrl));
            } else {
                Entry practitioner = practitioner(bundle, encounter.clinician);
                encounterResource.addParticipant().setIndividual(new ResourceReferenceDt(practitioner.getFullUrl()));
            }
        }
        encounterResource.getParticipantFirstRep().getIndividual().setDisplay(encounter.clinician.getFullname());
    }
    if (encounter.discharge != null) {
        Hospitalization hospitalization = new Hospitalization();
        Code dischargeDisposition = new Code(DISCHARGE_URI, encounter.discharge.code, encounter.discharge.display);
        hospitalization.setDischargeDisposition(mapCodeToCodeableConcept(dischargeDisposition, DISCHARGE_URI));
        encounterResource.setHospitalization(hospitalization);
    }
    return newEntry(person, bundle, encounterResource);
}

Example 13 with Encounter

use of org.mitre.synthea.world.concepts.HealthRecord.Encounter in project synthea by synthetichealth.

the class CPCDSExporter method export.

/**
 * Add a single Person's health record info to the CSV records.
 *
 * @param person Person to write record data for
 * @param time   Time the simulation ended
 * @throws IOException if any IO error occurs
 */
public void export(Person person, long time) throws IOException {
    String personID = patient(person, time);
    String payerId = "";
    String payerName = "";
    String type = COVERAGE_TYPES[(int) randomLongWithBounds(0, COVERAGE_TYPES.length - 1)];
    int groupSelect = (int) randomLongWithBounds(0, GROUPIDS.length - 1);
    UUID groupId = GROUPIDS[groupSelect];
    String groupName = GROUP_NAMES[groupSelect];
    int planSelect = (int) randomLongWithBounds(0, PLAN_NAMES.length - 1);
    String planName = PLAN_NAMES[planSelect];
    String planId = PLAN_IDS[planSelect];
    long start = 999999999999999999L;
    long end = 0;
    for (Encounter encounter : person.record.encounters) {
        String encounterID = person.randUUID().toString();
        UUID medRecordNumber = person.randUUID();
        CPCDSAttributes encounterAttributes = new CPCDSAttributes(encounter);
        if (Config.getAsBoolean("exporter.cpcds.single_payer")) {
            payerId = "b1c428d6-4f07-31e0-90f0-68ffa6ff8c76";
            payerName = clean(Config.get("single_payer.name"));
        } else {
            payerId = encounter.claim.payer.uuid.toString();
            payerName = encounter.claim.payer.getName();
        }
        for (CarePlan careplan : encounter.careplans) {
            if (careplan.start < start) {
                start = careplan.start;
            }
            if (careplan.stop > end) {
                end = careplan.stop;
            }
        }
        if (start == 999999999999999999L) {
            start = end;
        }
        String coverageID = coverage(person, personID, start, end, payerId, type, groupId, groupName, planName, planId);
        claim(person, encounter, personID, encounterID, medRecordNumber, encounterAttributes, payerId, coverageID);
        hospital(encounter, encounterAttributes, payerName);
    }
    patients.flush();
    coverages.flush();
    claims.flush();
    practitioners.flush();
    hospitals.flush();
}

Example 14 with Encounter

use of org.mitre.synthea.world.concepts.HealthRecord.Encounter in project synthea by synthetichealth.

the class TextExporter method exportAll.

/**
 * Produce and export a person's record in the text format.
 *
 * @param person Person to export
 * @param fileTag Tag to add to the filename
 * @param time Time the simulation ended
 * @throws IOException if any error occurs writing to the standard export location
 */
public static void exportAll(Person person, String fileTag, long time) throws IOException {
    List<Encounter> encounters = person.record.encounters;
    List<Entry> conditions = new ArrayList<>();
    List<Entry> allergies = new ArrayList<>();
    List<Report> reports = new ArrayList<>();
    List<Observation> observations = new ArrayList<>();
    List<Procedure> procedures = new ArrayList<>();
    List<Medication> medications = new ArrayList<>();
    List<Entry> immunizations = new ArrayList<>();
    List<CarePlan> careplans = new ArrayList<>();
    List<ImagingStudy> imagingStudies = new ArrayList<>();
    for (Encounter encounter : person.record.encounters) {
        conditions.addAll(encounter.conditions);
        allergies.addAll(encounter.allergies);
        reports.addAll(encounter.reports);
        observations.addAll(encounter.observations);
        procedures.addAll(encounter.procedures);
        medications.addAll(encounter.medications);
        immunizations.addAll(encounter.immunizations);
        careplans.addAll(encounter.careplans);
        imagingStudies.addAll(encounter.imagingStudies);
    }
    // reverse these items so they are displayed in reverse chrono order
    Collections.reverse(encounters);
    Collections.reverse(conditions);
    Collections.reverse(allergies);
    Collections.reverse(reports);
    Collections.reverse(observations);
    Collections.reverse(procedures);
    Collections.reverse(medications);
    Collections.reverse(immunizations);
    Collections.reverse(careplans);
    Collections.reverse(imagingStudies);
    // now we finally start writing things
    List<String> textRecord = new LinkedList<>();
    basicInfo(textRecord, person, time);
    breakline(textRecord);
    textRecord.add("ALLERGIES:");
    if (allergies.isEmpty()) {
        textRecord.add("No Known Allergies");
    } else {
        for (Entry allergy : allergies) {
            condition(textRecord, allergy, true);
        }
    }
    breakline(textRecord);
    textRecord.add("MEDICATIONS:");
    for (Medication medication : medications) {
        medication(textRecord, medication, true);
    }
    breakline(textRecord);
    textRecord.add("CONDITIONS:");
    for (Entry condition : conditions) {
        condition(textRecord, condition, true);
    }
    breakline(textRecord);
    textRecord.add("CARE PLANS:");
    for (CarePlan careplan : careplans) {
        careplan(textRecord, careplan, true);
    }
    breakline(textRecord);
    textRecord.add("REPORTS:");
    for (Report report : reports) {
        diagnosticReport(textRecord, report);
    }
    breakline(textRecord);
    textRecord.add("OBSERVATIONS:");
    for (Observation observation : observations) {
        observation(textRecord, observation);
    }
    breakline(textRecord);
    textRecord.add("PROCEDURES:");
    for (Procedure procedure : procedures) {
        procedure(textRecord, procedure);
    }
    breakline(textRecord);
    textRecord.add("IMMUNIZATIONS:");
    for (Entry immunization : immunizations) {
        immunization(textRecord, immunization);
    }
    breakline(textRecord);
    textRecord.add("ENCOUNTERS:");
    for (Encounter encounter : encounters) {
        encounter(textRecord, encounter);
    }
    breakline(textRecord);
    textRecord.add("IMAGING STUDIES:");
    for (ImagingStudy imagingStudy : imagingStudies) {
        imagingStudy(textRecord, imagingStudy);
    }
    breakline(textRecord);
    // finally write to the file
    File outDirectory = Exporter.getOutputFolder("text", person);
    Path outFilePath = outDirectory.toPath().resolve(Exporter.filename(person, fileTag, "txt"));
    Files.write(outFilePath, textRecord, StandardOpenOption.CREATE_NEW);
}

Example 15 with Encounter

use of org.mitre.synthea.world.concepts.HealthRecord.Encounter in project synthea by synthetichealth.

the class CodeResolveAndExportTest method resolveAndExportEncounterCodes.

@Test
public void resolveAndExportEncounterCodes() throws IOException, SAXException, ParserConfigurationException, XPathExpressionException {
    Encounter encounter = person.encounterStart(time, EncounterType.EMERGENCY);
    String reasonCode = "417981005";
    String reasonDisplay = "Exposure to blood and/or body fluid";
    encounter.reason = new Code(SNOMED_URI, reasonCode, reasonDisplay);
    encounter.reason.valueSet = SNOMED_URI + "?fhir_vs=ecl/<418307001";
    encounter.codes.add(encounter.reason);
    String observationDisplay = OBSERVATION_DISPLAY;
    Code observationType = new Code(LOINC_URI, OBSERVATION_CODE, observationDisplay);
    String observationValueCode = "LA14088-1";
    String observationValueDisplay = "Sports or recreational area";
    Code observationValue = new Code(LOINC_URI, observationValueCode, observationValueDisplay);
    observationValue.valueSet = "http://loinc.org/vs/LL1051-3";
    encounter.addObservation(time, observationType.code, observationValue, observationDisplay);
    Exporter.export(person, time);
    verifyEncounterCodeStu3();
    verifyEncounterCodeR4();
    verifyEncounterCodeDstu2();
    verifyEncounterCodeCcda();
}