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

Example 91 with Encounter

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

the class FhirDstu2 method medication.

/**
 * Map the given Medication to a FHIR MedicationRequest 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 Medication to
 * @param encounterEntry
 *          Current Encounter entry
 * @param medication
 *          The Medication
 * @return The added Entry
 */
private static Entry medication(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, Medication medication) {
    MedicationOrder medicationResource = new MedicationOrder();
    medicationResource.setPatient(new ResourceReferenceDt(personEntry.getFullUrl()));
    medicationResource.setEncounter(new ResourceReferenceDt(encounterEntry.getFullUrl()));
    ca.uhn.fhir.model.dstu2.resource.Encounter encounter = (ca.uhn.fhir.model.dstu2.resource.Encounter) encounterEntry.getResource();
    medicationResource.setPrescriber(encounter.getParticipantFirstRep().getIndividual());
    Code code = medication.codes.get(0);
    String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
    medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
    medicationResource.setDateWritten(new DateTimeDt(new Date(medication.start)));
    if (medication.stop != 0L) {
        medicationResource.setStatus(MedicationOrderStatusEnum.STOPPED);
    } else {
        medicationResource.setStatus(MedicationOrderStatusEnum.ACTIVE);
    }
    if (!medication.reasons.isEmpty()) {
        // Only one element in list
        Code reason = medication.reasons.get(0);
        for (Entry entry : bundle.getEntry()) {
            if (entry.getResource().getResourceName().equals("Condition")) {
                Condition condition = (Condition) entry.getResource();
                // Only one element in list
                CodingDt coding = condition.getCode().getCoding().get(0);
                if (reason.code.equals(coding.getCode())) {
                    medicationResource.setReason(new ResourceReferenceDt(entry.getFullUrl()));
                }
            }
        }
    }
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        DosageInstruction dosage = new DosageInstruction();
        // as_needed is true if present
        dosage.setAsNeeded(new BooleanDt(rxInfo.has("as_needed")));
        // as_needed is true if present
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            TimingDt timing = new TimingDt();
            Repeat timingRepeatComponent = new Repeat();
            timingRepeatComponent.setFrequency(rxInfo.get("dosage").getAsJsonObject().get("frequency").getAsInt());
            timingRepeatComponent.setPeriod(rxInfo.get("dosage").getAsJsonObject().get("period").getAsDouble());
            timingRepeatComponent.setPeriodUnits(convertUcumCode(rxInfo.get("dosage").getAsJsonObject().get("unit").getAsString()));
            timing.setRepeat(timingRepeatComponent);
            dosage.setTiming(timing);
            QuantityDt dose = new SimpleQuantityDt().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            dosage.setDose(dose);
            if (rxInfo.has("instructions")) {
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    Code instructionCode = new Code(SNOMED_URI, instruction.get("code").getAsString(), instruction.get("display").getAsString());
                    dosage.setAdditionalInstructions(mapCodeToCodeableConcept(instructionCode, SNOMED_URI));
                }
            }
        }
        List<DosageInstruction> dosageInstruction = new ArrayList<DosageInstruction>();
        dosageInstruction.add(dosage);
        medicationResource.setDosageInstruction(dosageInstruction);
    }
    Entry medicationEntry = newEntry(rand, bundle, medicationResource);
    // create new claim for medication
    medicationClaim(rand, personEntry, bundle, encounterEntry, medication.claim, medicationEntry);
    // Create new administration for medication, if needed
    if (medication.administration) {
        medicationAdministration(rand, personEntry, bundle, encounterEntry, medication);
    }
    return medicationEntry;
}

Example 92 with Encounter

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

the class FhirDstu2 method encounterClaim.

/**
 * Create an entry for the given Claim, associated to an Encounter.
 *
 * @param rand
 *          Source of randomness to use when generating ids etc
 * @param personEntry
 *          Entry for the person
 * @param bundle
 *          The Bundle to add to
 * @param encounterEntry
 *          The current Encounter
 * @param claim
 *          the Claim object
 * @return the added Entry
 */
private static Entry encounterClaim(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, Claim claim) {
    ca.uhn.fhir.model.dstu2.resource.Claim claimResource = new ca.uhn.fhir.model.dstu2.resource.Claim();
    ca.uhn.fhir.model.dstu2.resource.Encounter encounterResource = (ca.uhn.fhir.model.dstu2.resource.Encounter) encounterEntry.getResource();
    // assume institutional claim
    claimResource.setType(ClaimTypeEnum.INSTITUTIONAL);
    claimResource.setUse(UseEnum.COMPLETE);
    claimResource.setPatient(new ResourceReferenceDt(personEntry.getFullUrl()));
    claimResource.setOrganization(encounterResource.getServiceProvider());
    // Add data for the encounter
    ca.uhn.fhir.model.dstu2.resource.Claim.Item encounterItem = new ca.uhn.fhir.model.dstu2.resource.Claim.Item();
    encounterItem.setSequence(new PositiveIntDt(1));
    // assume item type is clinical service invoice
    CodingDt itemType = new CodingDt();
    itemType.setSystem("http://hl7.org/fhir/v3/ActCode").setCode("CSINV").setDisplay("clinical service invoice");
    encounterItem.setType(itemType);
    CodingDt itemService = new CodingDt();
    ca.uhn.fhir.model.dstu2.resource.Encounter encounter = (ca.uhn.fhir.model.dstu2.resource.Encounter) encounterEntry.getResource();
    itemService.setSystem(encounter.getTypeFirstRep().getCodingFirstRep().getSystem()).setCode(encounter.getTypeFirstRep().getCodingFirstRep().getCode()).setDisplay(encounter.getTypeFirstRep().getCodingFirstRep().getDisplay());
    encounterItem.setService(itemService);
    claimResource.addItem(encounterItem);
    int itemSequence = 2;
    int conditionSequence = 1;
    for (Claim.ClaimEntry claimEntry : claim.items) {
        HealthRecord.Entry item = claimEntry.entry;
        if (Costs.hasCost(item)) {
            // update claimItems list
            ca.uhn.fhir.model.dstu2.resource.Claim.Item procedureItem = new ca.uhn.fhir.model.dstu2.resource.Claim.Item();
            procedureItem.setSequence(new PositiveIntDt(itemSequence));
            // calculate the cost of the procedure
            MoneyDt moneyResource = new MoneyDt();
            moneyResource.setCode("USD");
            moneyResource.setSystem("urn:iso:std:iso:4217");
            moneyResource.setValue(item.getCost());
            procedureItem.setNet(moneyResource);
            // assume item type is clinical service invoice
            itemType = new CodingDt();
            itemType.setSystem("http://hl7.org/fhir/v3/ActCode").setCode("CSINV").setDisplay("clinical service invoice");
            procedureItem.setType(itemType);
            // item service should match the entry code
            itemService = new CodingDt();
            Code code = item.codes.get(0);
            String system = ExportHelper.getSystemURI(code.system);
            itemService.setSystem(system).setCode(code.code).setDisplay(code.display);
            procedureItem.setService(itemService);
            claimResource.addItem(procedureItem);
        } else {
            // assume it's a Condition, we don't have a Condition class specifically
            // add diagnosisComponent to claim
            ca.uhn.fhir.model.dstu2.resource.Claim.Diagnosis diagnosisComponent = new ca.uhn.fhir.model.dstu2.resource.Claim.Diagnosis();
            diagnosisComponent.setSequence(new PositiveIntDt(conditionSequence));
            if (item.codes.size() > 0) {
                // use first code
                Code code = item.codes.get(0);
                String system = ExportHelper.getSystemURI(code.system);
                diagnosisComponent.setDiagnosis(new CodingDt(system, code.code).setDisplay(code.display));
            }
            claimResource.addDiagnosis(diagnosisComponent);
            conditionSequence++;
        }
        itemSequence++;
    }
    return newEntry(rand, bundle, claimResource);
}

Example 93 with Encounter

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

the class CCDAExporter method export.

/**
 * Export a CCDA R2.1 document for a Person at a given time.
 *
 * @param person
 *          Person to export.
 * @param time
 *          Time the record should be generated. Any content in the record AFTER this time will
 *          not be included.
 * @return String of CCDA R2.1 XML.
 */
public static String export(Person person, long time) {
    // create a super encounter... this makes it easier to access
    // all the Allergies (for example) in the export templates,
    // instead of having to iterate through all the encounters.
    Encounter superEncounter = person.record.new Encounter(time, "super");
    for (Encounter encounter : person.record.encounters) {
        if (encounter.start <= time) {
            superEncounter.observations.addAll(encounter.observations);
            superEncounter.reports.addAll(encounter.reports);
            superEncounter.conditions.addAll(encounter.conditions);
            superEncounter.allergies.addAll(encounter.allergies);
            superEncounter.procedures.addAll(encounter.procedures);
            superEncounter.immunizations.addAll(encounter.immunizations);
            superEncounter.medications.addAll(encounter.medications);
            superEncounter.careplans.addAll(encounter.careplans);
            superEncounter.imagingStudies.addAll(encounter.imagingStudies);
        } else {
            break;
        }
    }
    // The export templates fill in the record by accessing the attributes
    // of the Person, so we add a few attributes just for the purposes of export.
    person.attributes.put("UUID", new UUIDGenerator(person));
    person.attributes.put("ehr_encounters", person.record.encounters);
    person.attributes.put("ehr_observations", superEncounter.observations);
    person.attributes.put("ehr_reports", superEncounter.reports);
    person.attributes.put("ehr_conditions", superEncounter.conditions);
    person.attributes.put("ehr_allergies", superEncounter.allergies);
    person.attributes.put("ehr_procedures", superEncounter.procedures);
    person.attributes.put("ehr_immunizations", superEncounter.immunizations);
    person.attributes.put("ehr_medications", superEncounter.medications);
    person.attributes.put("ehr_careplans", superEncounter.careplans);
    person.attributes.put("ehr_imaging_studies", superEncounter.imagingStudies);
    Observation smokingHistory = person.record.getLatestObservation("72166-2");
    if (smokingHistory != null) {
        person.attributes.put("ehr_smoking_history", smokingHistory);
    }
    person.attributes.put("time", time);
    person.attributes.put("race_lookup", RaceAndEthnicity.LOOK_UP_CDC_RACE);
    person.attributes.put("ethnicity_lookup", RaceAndEthnicity.LOOK_UP_CDC_ETHNICITY_CODE);
    person.attributes.put("ethnicity_display_lookup", RaceAndEthnicity.LOOK_UP_CDC_ETHNICITY_DISPLAY);
    if (person.attributes.get(Person.PREFERREDYPROVIDER + "wellness") == null) {
        // This person does not have a preferred provider. This happens for veterans at age 20 due to
        // the provider reset and they don't have a provider until their next wellness visit. There
        // may be other cases. This ensures the preferred provider is there for the CCDA template
        Encounter encounter = person.record.lastWellnessEncounter();
        if (encounter != null) {
            person.attributes.put(Person.PREFERREDYPROVIDER + "wellness", encounter.provider);
        } else {
            throw new IllegalStateException(String.format("Unable to export to CCDA because " + "person %s %s has no preferred provider.", person.attributes.get(Person.FIRST_NAME), person.attributes.get(Person.LAST_NAME)));
        }
    }
    StringWriter writer = new StringWriter();
    try {
        Template template = TEMPLATES.getTemplate("ccda.ftl");
        template.process(person.attributes, writer);
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
    return writer.toString();
}

Example 94 with Encounter

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

the class CDWExporter 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 {
    // Ignore civilians, only consider the veteran population.
    if (!person.attributes.containsKey("veteran")) {
        return;
    }
    int primarySta3n = -1;
    Provider provider = person.getProvider(EncounterType.WELLNESS, time);
    if (provider != null) {
        String state = Location.getStateName(provider.state);
        String tz = Location.getTimezoneByState(state);
        primarySta3n = sta3n.addFact(provider.id, clean(provider.name) + "," + tz);
        location.addFact(provider.id, clean(provider.name));
    }
    int personID = patient(person, primarySta3n, time);
    for (Encounter encounter : person.record.encounters) {
        int encounterID = encounter(personID, person, encounter, primarySta3n);
        for (HealthRecord.Entry condition : encounter.conditions) {
            condition(personID, encounterID, encounter, condition, primarySta3n);
        }
        for (HealthRecord.Entry allergy : encounter.allergies) {
            allergy(personID, person, encounterID, encounter, allergy, primarySta3n);
        }
        for (HealthRecord.Report report : encounter.reports) {
            // Ignore death certificates
            if (!DeathModule.DEATH_CERTIFICATE.equals(report.codes.get(0))) {
                report(personID, encounterID, encounter, primarySta3n, report);
            }
        }
        for (Observation observation : encounter.observations) {
            observation(personID, encounterID, encounter, primarySta3n, observation);
        }
        for (Procedure procedure : encounter.procedures) {
            procedure(personID, encounterID, encounter, procedure, primarySta3n);
        }
        for (Medication medication : encounter.medications) {
            medication(personID, encounterID, encounter, medication, primarySta3n);
        }
        for (Immunization immunization : encounter.immunizations) {
            immunization(personID, person, encounterID, encounter, immunization, primarySta3n);
        }
    }
    // Patient Data
    lookuppatient.flush();
    spatient.flush();
    spatientaddress.flush();
    spatientphone.flush();
    patientrace.flush();
    patientethnicity.flush();
    // Encounter Data
    consult.flush();
    visit.flush();
    appointment.flush();
    inpatient.flush();
    // Immunization Data
    immunization.flush();
    // Allergy Data
    allergy.flush();
    allergicreaction.flush();
    allergycomment.flush();
    // Condition Data
    problemlist.flush();
    vdiagnosis.flush();
    // Medication Data
    rxoutpatient.flush();
    rxoutpatfill.flush();
    nonvamed.flush();
    cprsorder.flush();
    ordereditem.flush();
    // Diagnostic Report Data
    labchem.flush();
    labpanel.flush();
    patientlabchem.flush();
    vprocedure.flush();
    // Procedure Data
    surgeryProcedureDiagnosisCode.flush();
    surgeryPRE.flush();
    // Vital Sign Observation Data
    vitalSign.flush();
}

Example 95 with Encounter

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

the class TextExporter method exportEncounter.

/**
 * Produce and export a person's record in text format.
 *
 * @param person Person
 * @param time Time the simulation ended
 * @throws IOException if any error occurs writing to the standard export location
 */
public static void exportEncounter(Person person, long time) throws IOException {
    List<Encounter> encounters = person.record.encounters;
    List<Entry> conditions = new ArrayList<>();
    List<Entry> allergies = new ArrayList<>();
    List<Medication> medications = new ArrayList<>();
    List<CarePlan> careplans = new ArrayList<>();
    for (Encounter encounter : person.record.encounters) {
        conditions.addAll(encounter.conditions);
        allergies.addAll(encounter.allergies);
        medications.addAll(encounter.medications);
        careplans.addAll(encounter.careplans);
    }
    // reverse these items so they are displayed in reverse chrono order
    Collections.reverse(encounters);
    Collections.reverse(conditions);
    Collections.reverse(allergies);
    Collections.reverse(medications);
    Collections.reverse(careplans);
    // set an integer that will be used as a counter for file naming purposes
    int encounterNumber = 0;
    for (Encounter encounter : encounters) {
        // make a record for each encounter to write information
        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, false);
            }
        }
        breakline(textRecord);
        textRecord.add("ENCOUNTER");
        encounterReport(textRecord, person, encounter);
        breakline(textRecord);
        textRecord.add("CONTINUING");
        textRecord.add("   ");
        textRecord.add("   CONDITIONS:");
        for (Entry condition : conditions) {
            conditionpast(textRecord, condition, encounter);
        }
        textRecord.add("   ");
        textRecord.add("   MEDICATIONS:");
        for (Medication medication : medications) {
            medicationpast(textRecord, medication, encounter);
        }
        textRecord.add("   ");
        textRecord.add("   CAREPLANS:");
        for (CarePlan careplan : careplans) {
            careplanpast(textRecord, careplan, encounter);
        }
        textRecord.add("   ");
        breakline(textRecord);
        encounterNumber++;
        // write to the file
        File outDirectory2 = Exporter.getOutputFolder("text_encounters", person);
        Path outFilePath2 = outDirectory2.toPath().resolve(Exporter.filename(person, Integer.toString(encounterNumber), "txt"));
        Files.write(outFilePath2, textRecord, StandardOpenOption.CREATE_NEW);
    }
}