use of ca.uhn.fhir.model.primitive.BooleanDt 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);
}
use of ca.uhn.fhir.model.primitive.BooleanDt in project synthea by synthetichealth.
the class FhirDstu2 method immunization.
private static Entry immunization(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, HealthRecord.Entry immunization) {
Immunization immResource = new Immunization();
immResource.setStatus("completed");
immResource.setDate(new DateTimeDt(new Date(immunization.start)));
immResource.setVaccineCode(mapCodeToCodeableConcept(immunization.codes.get(0), CVX_URI));
immResource.setReported(new BooleanDt(false));
immResource.setWasNotGiven(false);
immResource.setPatient(new ResourceReferenceDt(personEntry.getFullUrl()));
immResource.setEncounter(new ResourceReferenceDt(encounterEntry.getFullUrl()));
Entry immunizationEntry = newEntry(rand, bundle, immResource);
immunization.fullUrl = immunizationEntry.getFullUrl();
return immunizationEntry;
}
use of ca.uhn.fhir.model.primitive.BooleanDt 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));
}
use of ca.uhn.fhir.model.primitive.BooleanDt 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;
}
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