Examples with NarrativeDt ca.uhn.fhir.model.dstu2.composite.NarrativeDt used on opensource projects

Example 1 with NarrativeDt

use of ca.uhn.fhir.model.dstu2.composite.NarrativeDt in project cqf-ruler by DBCG.

the class CompositionSectionComponentBuilder method initializeDstu2.

@Override
protected void initializeDstu2(T theResource) {
    super.initializeDstu2(theResource);
    ca.uhn.fhir.model.dstu2.resource.Composition.Section section = (ca.uhn.fhir.model.dstu2.resource.Composition.Section) theResource;
    section.setTitle(myTitle).setElementSpecificId(getId());
    getEntries().forEach(entry -> section.addEntry().setReference(entry));
    if (myText != null) {
        section.setText(new NarrativeDt(new XhtmlDt(myText.getText()), NarrativeStatusEnum.valueOf(myText.getStatus())));
    }
// no focus
}

Example 2 with NarrativeDt

use of ca.uhn.fhir.model.dstu2.composite.NarrativeDt in project synthea by synthetichealth.

the class FhirDstu2 method careplan.

/**
 * Map the given CarePlan to a FHIR CarePlan 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 CarePlan to
 * @param encounterEntry
 *          Current Encounter entry
 * @param carePlan
 *          The CarePlan to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static Entry careplan(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, CarePlan carePlan) {
    ca.uhn.fhir.model.dstu2.resource.CarePlan careplanResource = new ca.uhn.fhir.model.dstu2.resource.CarePlan();
    careplanResource.setSubject(new ResourceReferenceDt(personEntry.getFullUrl()));
    careplanResource.setContext(new ResourceReferenceDt(encounterEntry.getFullUrl()));
    Code code = carePlan.codes.get(0);
    careplanResource.addCategory(mapCodeToCodeableConcept(code, SNOMED_URI));
    NarrativeDt narrative = new NarrativeDt();
    narrative.setStatus(NarrativeStatusEnum.GENERATED);
    narrative.setDiv(code.display);
    careplanResource.setText(narrative);
    CarePlanActivityStatusEnum activityStatus;
    GoalStatusEnum goalStatus;
    PeriodDt period = new PeriodDt().setStart(new DateTimeDt(new Date(carePlan.start)));
    careplanResource.setPeriod(period);
    if (carePlan.stop != 0L) {
        period.setEnd(new DateTimeDt(new Date(carePlan.stop)));
        careplanResource.setStatus(CarePlanStatusEnum.COMPLETED);
        activityStatus = CarePlanActivityStatusEnum.COMPLETED;
        goalStatus = GoalStatusEnum.ACHIEVED;
    } else {
        careplanResource.setStatus(CarePlanStatusEnum.ACTIVE);
        activityStatus = CarePlanActivityStatusEnum.IN_PROGRESS;
        goalStatus = GoalStatusEnum.IN_PROGRESS;
    }
    if (!carePlan.activities.isEmpty()) {
        for (Code activity : carePlan.activities) {
            Activity activityComponent = new Activity();
            ActivityDetail activityDetailComponent = new ActivityDetail();
            activityDetailComponent.setStatus(activityStatus);
            activityDetailComponent.setCode(mapCodeToCodeableConcept(activity, SNOMED_URI));
            activityDetailComponent.setProhibited(new BooleanDt(false));
            activityComponent.setDetail(activityDetailComponent);
            careplanResource.addActivity(activityComponent);
        }
    }
    if (!carePlan.reasons.isEmpty()) {
        // Only one element in list
        Code reason = carePlan.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())) {
                    careplanResource.addAddresses().setReference(entry.getFullUrl());
                }
            }
        }
    }
    for (JsonObject goal : carePlan.goals) {
        Entry goalEntry = caregoal(rand, bundle, goalStatus, goal);
        careplanResource.addGoal().setReference(goalEntry.getFullUrl());
    }
    return newEntry(rand, bundle, careplanResource);
}

Example 3 with NarrativeDt

use of ca.uhn.fhir.model.dstu2.composite.NarrativeDt in project synthea by synthetichealth.

the class FhirDstu2 method basicInfo.

/**
 * Map the given Person to a FHIR Patient resource, and add it to the given Bundle.
 *
 * @param person
 *          The Person
 * @param bundle
 *          The Bundle to add to
 * @param stopTime
 *          Time the simulation ended
 * @return The created Entry
 */
@SuppressWarnings("rawtypes")
private static Entry basicInfo(Person person, Bundle bundle, long stopTime) {
    Patient patientResource = new Patient();
    patientResource.addIdentifier().setSystem("https://github.com/synthetichealth/synthea").setValue((String) person.attributes.get(Person.ID));
    patientResource.addIdentifier().setType(IdentifierTypeCodesEnum.MR).setSystem("http://hospital.smarthealthit.org").setValue((String) person.attributes.get(Person.ID));
    patientResource.addIdentifier().setType(IdentifierTypeCodesEnum.SOCIAL_BENEFICIARY_IDENTIFIER).setSystem("http://hl7.org/fhir/sid/us-ssn").setValue((String) person.attributes.get(Person.IDENTIFIER_SSN));
    if (person.attributes.get(Person.IDENTIFIER_DRIVERS) != null) {
        patientResource.addIdentifier().setType(IdentifierTypeCodesEnum.DL).setSystem("urn:oid:2.16.840.1.113883.4.3.25").setValue((String) person.attributes.get(Person.IDENTIFIER_DRIVERS));
    }
    ExtensionDt raceExtension = new ExtensionDt();
    raceExtension.setUrl("http://hl7.org/fhir/StructureDefinition/us-core-race");
    String race = (String) person.attributes.get(Person.RACE);
    ExtensionDt ethnicityExtension = new ExtensionDt();
    ethnicityExtension.setUrl("http://hl7.org/fhir/StructureDefinition/us-core-ethnicity");
    String ethnicity = (String) person.attributes.get(Person.ETHNICITY);
    String raceDisplay;
    switch(race) {
        case "white":
            raceDisplay = "White";
            break;
        case "black":
            raceDisplay = "Black or African American";
            break;
        case "asian":
            raceDisplay = "Asian";
            break;
        case "native":
            raceDisplay = "American Indian or Alaska Native";
            break;
        case "hawaiian":
            raceDisplay = "Native Hawaiian or Other Pacific Islander";
            break;
        default:
            raceDisplay = "Other";
            break;
    }
    String ethnicityDisplay;
    if (ethnicity.equals("hispanic")) {
        ethnicityDisplay = "Hispanic or Latino";
    } else {
        ethnicityDisplay = "Not Hispanic or Latino";
    }
    Code raceCode = new Code("http://hl7.org/fhir/v3/Race", (String) raceEthnicityCodes.get(race), raceDisplay);
    Code ethnicityCode = new Code("http://hl7.org/fhir/v3/Ethnicity", (String) raceEthnicityCodes.get(ethnicity), ethnicityDisplay);
    raceExtension.setValue(mapCodeToCodeableConcept(raceCode, "http://hl7.org/fhir/v3/Race"));
    ethnicityExtension.setValue(mapCodeToCodeableConcept(ethnicityCode, "http://hl7.org/fhir/v3/Ethnicity"));
    patientResource.addUndeclaredExtension(raceExtension);
    patientResource.addUndeclaredExtension(ethnicityExtension);
    String firstLanguage = (String) person.attributes.get(Person.FIRST_LANGUAGE);
    Map languageMap = (Map) languageLookup.get(firstLanguage);
    Code languageCode = new Code((String) languageMap.get("system"), (String) languageMap.get("code"), (String) languageMap.get("display"));
    List<Communication> communication = new ArrayList<Communication>();
    Communication language = new Communication();
    language.setLanguage(mapCodeToCodeableConcept(languageCode, (String) languageMap.get("system")));
    communication.add(language);
    patientResource.setCommunication(communication);
    HumanNameDt name = patientResource.addName();
    name.setUse(NameUseEnum.OFFICIAL);
    name.addGiven((String) person.attributes.get(Person.FIRST_NAME));
    List<StringDt> officialFamilyNames = new ArrayList<StringDt>();
    officialFamilyNames.add(new StringDt((String) person.attributes.get(Person.LAST_NAME)));
    name.setFamily(officialFamilyNames);
    if (person.attributes.get(Person.NAME_PREFIX) != null) {
        name.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
    }
    if (person.attributes.get(Person.NAME_SUFFIX) != null) {
        name.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
    }
    if (person.attributes.get(Person.MAIDEN_NAME) != null) {
        HumanNameDt maidenName = patientResource.addName();
        maidenName.setUse(NameUseEnum.MAIDEN);
        maidenName.addGiven((String) person.attributes.get(Person.FIRST_NAME));
        List<StringDt> maidenFamilyNames = new ArrayList<StringDt>();
        maidenFamilyNames.add(new StringDt((String) person.attributes.get(Person.MAIDEN_NAME)));
        maidenName.setFamily(maidenFamilyNames);
        if (person.attributes.get(Person.NAME_PREFIX) != null) {
            maidenName.addPrefix((String) person.attributes.get(Person.NAME_PREFIX));
        }
        if (person.attributes.get(Person.NAME_SUFFIX) != null) {
            maidenName.addSuffix((String) person.attributes.get(Person.NAME_SUFFIX));
        }
    }
    ExtensionDt mothersMaidenNameExtension = new ExtensionDt();
    mothersMaidenNameExtension.setUrl("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");
    String mothersMaidenName = (String) person.attributes.get(Person.NAME_MOTHER);
    mothersMaidenNameExtension.setValue(new StringDt(mothersMaidenName));
    patientResource.addUndeclaredExtension(mothersMaidenNameExtension);
    long birthdate = (long) person.attributes.get(Person.BIRTHDATE);
    patientResource.setBirthDate(new DateDt(new Date(birthdate)));
    ExtensionDt birthSexExtension = new ExtensionDt();
    birthSexExtension.setUrl("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
    if (person.attributes.get(Person.GENDER).equals("M")) {
        patientResource.setGender(AdministrativeGenderEnum.MALE);
        birthSexExtension.setValue(new CodeDt("M"));
    } else if (person.attributes.get(Person.GENDER).equals("F")) {
        patientResource.setGender(AdministrativeGenderEnum.FEMALE);
        birthSexExtension.setValue(new CodeDt("F"));
    }
    patientResource.addUndeclaredExtension(birthSexExtension);
    String state = (String) person.attributes.get(Person.STATE);
    AddressDt addrResource = patientResource.addAddress();
    addrResource.addLine((String) person.attributes.get(Person.ADDRESS)).setCity((String) person.attributes.get(Person.CITY)).setPostalCode((String) person.attributes.get(Person.ZIP)).setState(state);
    if (COUNTRY_CODE != null) {
        addrResource.setCountry(COUNTRY_CODE);
    }
    Point2D.Double coord = person.getLonLat();
    if (coord != null) {
        ExtensionDt geolocationExtension = new ExtensionDt();
        geolocationExtension.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
        ExtensionDt latitudeExtension = new ExtensionDt();
        ExtensionDt longitudeExtension = new ExtensionDt();
        latitudeExtension.setUrl("latitude");
        longitudeExtension.setUrl("longitude");
        latitudeExtension.setValue(new DecimalDt(coord.getY()));
        longitudeExtension.setValue(new DecimalDt(coord.getX()));
        geolocationExtension.addUndeclaredExtension(latitudeExtension);
        geolocationExtension.addUndeclaredExtension(longitudeExtension);
        addrResource.addUndeclaredExtension(geolocationExtension);
    }
    AddressDt birthplace = new AddressDt();
    birthplace.setCity((String) person.attributes.get(Person.BIRTH_CITY)).setState((String) person.attributes.get(Person.BIRTH_STATE)).setCountry((String) person.attributes.get(Person.BIRTH_COUNTRY));
    ExtensionDt birthplaceExtension = new ExtensionDt();
    birthplaceExtension.setUrl("http://hl7.org/fhir/StructureDefinition/birthPlace");
    birthplaceExtension.setValue(birthplace);
    patientResource.addUndeclaredExtension(birthplaceExtension);
    if (person.attributes.get(Person.MULTIPLE_BIRTH_STATUS) != null) {
        patientResource.setMultipleBirth(new IntegerDt((int) person.attributes.get(Person.MULTIPLE_BIRTH_STATUS)));
    } else {
        patientResource.setMultipleBirth(new BooleanDt(false));
    }
    patientResource.addTelecom().setSystem(ContactPointSystemEnum.PHONE).setUse(ContactPointUseEnum.HOME).setValue((String) person.attributes.get(Person.TELECOM));
    String maritalStatus = ((String) person.attributes.get(Person.MARITAL_STATUS));
    if (maritalStatus != null) {
        patientResource.setMaritalStatus(MaritalStatusCodesEnum.forCode(maritalStatus.toUpperCase()));
    } else {
        patientResource.setMaritalStatus(MaritalStatusCodesEnum.S);
    }
    if (!person.alive(stopTime)) {
        patientResource.setDeceased(convertFhirDateTime((Long) person.attributes.get(Person.DEATHDATE), true));
    }
    String generatedBySynthea = "Generated by <a href=\"https://github.com/synthetichealth/synthea\">Synthea</a>." + "Version identifier: " + Utilities.SYNTHEA_VERSION + " . " + "  Person seed: " + person.seed + "  Population seed: " + person.populationSeed;
    patientResource.setText(new NarrativeDt(new XhtmlDt(generatedBySynthea), NarrativeStatusEnum.GENERATED));
    // DALY and QALY values
    // we only write the last(current) one to the patient record
    Double dalyValue = (Double) person.attributes.get("most-recent-daly");
    Double qalyValue = (Double) person.attributes.get("most-recent-qaly");
    if (dalyValue != null) {
        ExtensionDt dalyExtension = new ExtensionDt();
        dalyExtension.setUrl(SYNTHEA_EXT + "disability-adjusted-life-years");
        DecimalDt daly = new DecimalDt(dalyValue);
        dalyExtension.setValue(daly);
        patientResource.addUndeclaredExtension(dalyExtension);
        ExtensionDt qalyExtension = new ExtensionDt();
        qalyExtension.setUrl(SYNTHEA_EXT + "quality-adjusted-life-years");
        DecimalDt qaly = new DecimalDt(qalyValue);
        qalyExtension.setValue(qaly);
        patientResource.addUndeclaredExtension(qalyExtension);
    }
    return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
}