use of org.hl7.fhir.dstu2016may.model.DecimalType in project pathling by aehrc.
the class TestData method newQuestionnaire.
/**
* Returns a FHIR Questionnaire resource for testing purposes.
*/
public static Questionnaire newQuestionnaire() {
final Questionnaire questionnaire = new Questionnaire();
questionnaire.setId("Questionnaire/1");
final QuestionnaireItemComponent item = questionnaire.addItem();
item.addEnableWhen().setAnswer(new DecimalType(TEST_VERY_SMALL_DECIMAL_SCALE_6));
item.addInitial().setValue(new DecimalType(TEST_VERY_BIG_DECIMAL));
// This nested item will be discarded on import, as we currently skip recursive elements.
final QuestionnaireItemComponent nestedItem = item.addItem();
nestedItem.addInitial().setValue(new DecimalType(TEST_SMALL_DECIMAL));
return questionnaire;
}
use of org.hl7.fhir.dstu2016may.model.DecimalType in project redmatch by aehrc.
the class FhirExporter method getValue.
/**
* Resolves a value.
*
* @param value The value specified in the transformation rules.
* @param fhirType The type of the FHIR attribute where this value will be set.
* @param vertex A vertex with patient data.
* @param recordId The id of this record. Used to create the references to FHIR ids.
* @param enumFactory If the type is an enumeration, this is the factory to create an instance.
* @param fhirPackage The target FHIR package.
* @return The value or null if the value cannot be determined. This can also be a list.
*/
private Base getValue(Value value, Class<?> fhirType, JsonObject vertex, String recordId, Class<?> enumFactory, VersionedFhirPackage fhirPackage) throws IOException {
// If this is a field-based value then make sure that there is a value and if not return null
if (value instanceof FieldBasedValue) {
FieldBasedValue fbv = (FieldBasedValue) value;
// Account for field ids of the form xx___y
String fieldId = fbv.getFieldId();
String shortFieldId = null;
String regex = "(?<fieldId>.*)___\\d+$";
Pattern pattern = Pattern.compile(regex);
Matcher matcher = pattern.matcher(fieldId);
if (matcher.find()) {
shortFieldId = matcher.group("fieldId");
log.debug("Transformed fieldId into '" + fieldId + "'");
}
boolean hasValue = false;
JsonElement jsonElement = vertex.get(fieldId);
if (jsonElement != null) {
String rawValue = jsonElement.getAsString();
if (!rawValue.isEmpty()) {
hasValue = true;
}
}
if (!hasValue && shortFieldId != null) {
jsonElement = vertex.get(shortFieldId);
if (jsonElement != null) {
String rawValue = jsonElement.getAsString();
if (!rawValue.isEmpty()) {
hasValue = true;
}
}
}
if (!hasValue) {
return null;
}
}
if (value instanceof BooleanValue) {
return new BooleanType(((BooleanValue) value).getValue());
} else if (value instanceof CodeLiteralValue) {
String code = ((CodeLiteralValue) value).getCode();
return getCode(code, enumFactory);
} else if (value instanceof ConceptLiteralValue) {
ConceptLiteralValue clv = (ConceptLiteralValue) value;
String system = clv.getSystem();
String code = clv.getCode();
String display = clv.getDisplay() != null ? clv.getDisplay() : "";
return getConcept(system, code, display, fhirType);
} else if (value instanceof DoubleValue) {
return new DecimalType(((DoubleValue) value).getValue());
} else if (value instanceof IntegerValue) {
return new IntegerType(((IntegerValue) value).getValue());
} else if (value instanceof ReferenceValue) {
ReferenceValue rv = (ReferenceValue) value;
Reference ref = new Reference();
String resourceType = rv.getResourceType();
String resourceId = rv.getResourceId();
boolean unique = uniqueIds.contains(resourceType + "<" + resourceId + ">");
CodeInfo codeInfo = terminologyService.lookup(fhirPackage, resourceType);
if (codeInfo.isProfile()) {
resourceType = StringUtils.getLastPath(codeInfo.getBaseResource());
}
if (unique) {
// This is a reference to a unique resource - no need to append row id
if (fhirResourceMap.containsKey(resourceId)) {
ref.setReference("/" + resourceType + "/" + resourceId);
} else {
log.debug("Did not find resource " + resourceType + "/" + resourceId);
}
} else {
if (fhirResourceMap.containsKey(resourceId + "-" + recordId)) {
ref.setReference("/" + resourceType + "/" + resourceId + "-" + recordId);
} else {
log.debug("Did not find resource " + resourceType + "/" + resourceId + "-" + recordId);
}
}
return ref;
} else if (value instanceof StringValue) {
if (fhirType.equals(StringType.class)) {
return new StringType(((StringValue) value).getStringValue());
} else if (fhirType.equals(MarkdownType.class)) {
return new MarkdownType(((StringValue) value).getStringValue());
} else if (fhirType.equals(IdType.class)) {
return new IdType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UriType.class)) {
return new UriType(((StringValue) value).getStringValue());
} else if (fhirType.equals(OidType.class)) {
return new OidType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UuidType.class)) {
return new UuidType(((StringValue) value).getStringValue());
} else if (fhirType.equals(CanonicalType.class)) {
return new CanonicalType(((StringValue) value).getStringValue());
} else if (fhirType.equals(UrlType.class)) {
return new UrlType(((StringValue) value).getStringValue());
} else {
throw new TransformationException("Got StringValue for FHIR type " + fhirType.getName() + ". This should not happen!");
}
} else if (value instanceof CodeSelectedValue) {
CodeSelectedValue csv = (CodeSelectedValue) value;
String fieldId = csv.getFieldId();
Mapping m = getSelectedMapping(fieldId, vertex);
if (m == null) {
throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
}
return getTarget(m).getCodeElement();
} else if (value instanceof ConceptSelectedValue) {
ConceptSelectedValue csv = (ConceptSelectedValue) value;
String fieldId = csv.getFieldId();
Mapping m = getSelectedMapping(fieldId, vertex);
if (m == null) {
throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
}
if (fhirType.isAssignableFrom(Coding.class)) {
return getTarget(m);
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(getTarget(m));
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT_SELECTED.");
}
} else if (value instanceof ConceptValue) {
// Ontoserver REDCap plugin format: 74400008|Appendicitis|http://snomed.info/sct
ConceptValue cv = (ConceptValue) value;
String fieldId = cv.getFieldId();
Mapping m = getMapping(fieldId);
if (m != null) {
if (fhirType.isAssignableFrom(Coding.class)) {
return getTarget(m);
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(getTarget(m));
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
}
} else {
au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
Coding c = field.getCoding(vertex);
if (c != null) {
if (fhirType.isAssignableFrom(Coding.class)) {
return c;
} else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
return new CodeableConcept().addCoding(c);
} else {
throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
}
}
}
throw new TransformationException("Could not get concept for field " + fieldId + ".");
} else if (value instanceof FieldValue) {
FieldValue fv = (FieldValue) value;
String fieldId = fv.getFieldId();
FieldValue.DatePrecision pr = fv.getDatePrecision();
au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
return field.getValue(vertex, fhirType, pr);
} else {
throw new TransformationException("Unable to get VALUE for " + value);
}
}
use of org.hl7.fhir.dstu2016may.model.DecimalType in project synthea by synthetichealth.
the class FhirR4 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 BundleEntryComponent basicInfo(Person person, Bundle bundle, long stopTime) {
Patient patientResource = new Patient();
patientResource.addIdentifier().setSystem(SYNTHEA_IDENTIFIER).setValue((String) person.attributes.get(Person.ID));
if (USE_US_CORE_IG) {
Meta meta = new Meta();
meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient");
patientResource.setMeta(meta);
}
Code mrnCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "MR", "Medical Record Number");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(mrnCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem("http://hospital.smarthealthit.org").setValue((String) person.attributes.get(Person.ID));
Code ssnCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "SS", "Social Security Number");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(ssnCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem("http://hl7.org/fhir/sid/us-ssn").setValue((String) person.attributes.get(Person.IDENTIFIER_SSN));
if (person.attributes.get(Person.IDENTIFIER_DRIVERS) != null) {
Code driversCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "DL", "Driver's License");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(driversCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem("urn:oid:2.16.840.1.113883.4.3.25").setValue((String) person.attributes.get(Person.IDENTIFIER_DRIVERS));
}
if (person.attributes.get(Person.IDENTIFIER_PASSPORT) != null) {
Code passportCode = new Code("http://terminology.hl7.org/CodeSystem/v2-0203", "PPN", "Passport Number");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(passportCode, "http://terminology.hl7.org/CodeSystem/v2-0203")).setSystem(SHR_EXT + "passportNumber").setValue((String) person.attributes.get(Person.IDENTIFIER_PASSPORT));
}
if (person.attributes.get(Person.CONTACT_EMAIL) != null) {
ContactComponent contact = new ContactComponent();
HumanName contactName = new HumanName();
contactName.setUse(HumanName.NameUse.OFFICIAL);
contactName.addGiven((String) person.attributes.get(Person.CONTACT_GIVEN_NAME));
contactName.setFamily((String) person.attributes.get(Person.CONTACT_FAMILY_NAME));
contact.setName(contactName);
contact.addTelecom().setSystem(ContactPointSystem.EMAIL).setUse(ContactPointUse.HOME).setValue((String) person.attributes.get(Person.CONTACT_EMAIL));
patientResource.addContact(contact);
}
if (USE_US_CORE_IG) {
// We do not yet account for mixed race
Extension raceExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race");
String race = (String) person.attributes.get(Person.RACE);
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 raceNum = (String) raceEthnicityCodes.get(race);
Extension raceCodingExtension = new Extension("ombCategory");
Coding raceCoding = new Coding();
if (raceDisplay.equals("Other")) {
raceCoding.setSystem("http://terminology.hl7.org/CodeSystem/v3-NullFlavor");
raceCoding.setCode("UNK");
raceCoding.setDisplay("Unknown");
} else {
raceCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
raceCoding.setCode(raceNum);
raceCoding.setDisplay(raceDisplay);
}
raceCodingExtension.setValue(raceCoding);
raceExtension.addExtension(raceCodingExtension);
Extension raceTextExtension = new Extension("text");
raceTextExtension.setValue(new StringType(raceDisplay));
raceExtension.addExtension(raceTextExtension);
patientResource.addExtension(raceExtension);
// We do not yet account for mixed ethnicity
Extension ethnicityExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
String ethnicity = (String) person.attributes.get(Person.ETHNICITY);
String ethnicityDisplay;
if (ethnicity.equals("hispanic")) {
ethnicity = "hispanic";
ethnicityDisplay = "Hispanic or Latino";
} else {
ethnicity = "nonhispanic";
ethnicityDisplay = "Not Hispanic or Latino";
}
String ethnicityNum = (String) raceEthnicityCodes.get(ethnicity);
Extension ethnicityCodingExtension = new Extension("ombCategory");
Coding ethnicityCoding = new Coding();
ethnicityCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
ethnicityCoding.setCode(ethnicityNum);
ethnicityCoding.setDisplay(ethnicityDisplay);
ethnicityCodingExtension.setValue(ethnicityCoding);
ethnicityExtension.addExtension(ethnicityCodingExtension);
Extension ethnicityTextExtension = new Extension("text");
ethnicityTextExtension.setValue(new StringType(ethnicityDisplay));
ethnicityExtension.addExtension(ethnicityTextExtension);
patientResource.addExtension(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<PatientCommunicationComponent> communication = new ArrayList<PatientCommunicationComponent>();
communication.add(new PatientCommunicationComponent(mapCodeToCodeableConcept(languageCode, (String) languageMap.get("system"))));
patientResource.setCommunication(communication);
HumanName name = patientResource.addName();
name.setUse(HumanName.NameUse.OFFICIAL);
name.addGiven((String) person.attributes.get(Person.FIRST_NAME));
name.setFamily((String) person.attributes.get(Person.LAST_NAME));
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) {
HumanName maidenName = patientResource.addName();
maidenName.setUse(HumanName.NameUse.MAIDEN);
maidenName.addGiven((String) person.attributes.get(Person.FIRST_NAME));
maidenName.setFamily((String) person.attributes.get(Person.MAIDEN_NAME));
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));
}
}
Extension mothersMaidenNameExtension = new Extension("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");
String mothersMaidenName = (String) person.attributes.get(Person.NAME_MOTHER);
mothersMaidenNameExtension.setValue(new StringType(mothersMaidenName));
patientResource.addExtension(mothersMaidenNameExtension);
long birthdate = (long) person.attributes.get(Person.BIRTHDATE);
patientResource.setBirthDate(new Date(birthdate));
Extension birthSexExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
if (person.attributes.get(Person.GENDER).equals("M")) {
patientResource.setGender(AdministrativeGender.MALE);
birthSexExtension.setValue(new CodeType("M"));
} else if (person.attributes.get(Person.GENDER).equals("F")) {
patientResource.setGender(AdministrativeGender.FEMALE);
birthSexExtension.setValue(new CodeType("F"));
} else if (person.attributes.get(Person.GENDER).equals("UNK")) {
patientResource.setGender(AdministrativeGender.UNKNOWN);
}
if (USE_US_CORE_IG) {
patientResource.addExtension(birthSexExtension);
}
String state = (String) person.attributes.get(Person.STATE);
if (USE_US_CORE_IG) {
state = Location.getAbbreviation(state);
}
Address 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);
}
Address birthplace = new Address();
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));
Extension birthplaceExtension = new Extension("http://hl7.org/fhir/StructureDefinition/patient-birthPlace");
birthplaceExtension.setValue(birthplace);
patientResource.addExtension(birthplaceExtension);
if (person.attributes.get(Person.MULTIPLE_BIRTH_STATUS) != null) {
patientResource.setMultipleBirth(new IntegerType((int) person.attributes.get(Person.MULTIPLE_BIRTH_STATUS)));
} else {
patientResource.setMultipleBirth(new BooleanType(false));
}
patientResource.addTelecom().setSystem(ContactPointSystem.PHONE).setUse(ContactPointUse.HOME).setValue((String) person.attributes.get(Person.TELECOM));
String maritalStatus = ((String) person.attributes.get(Person.MARITAL_STATUS));
if (maritalStatus != null) {
Code maritalStatusCode = new Code("http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", maritalStatus, maritalStatus);
patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus"));
} else {
Code maritalStatusCode = new Code("http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", "S", "Never Married");
patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus"));
}
Point2D.Double coord = person.getLonLat();
if (coord != null) {
Extension geolocation = addrResource.addExtension();
geolocation.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
geolocation.addExtension("latitude", new DecimalType(coord.getY()));
geolocation.addExtension("longitude", new DecimalType(coord.getX()));
}
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.getSeed() + " Population seed: " + person.populationSeed;
patientResource.setText(new Narrative().setStatus(NarrativeStatus.GENERATED).setDiv(new XhtmlNode(NodeType.Element).setValue(generatedBySynthea)));
if (USE_SHR_EXTENSIONS) {
patientResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Patient"));
// Patient profile requires race, ethnicity, birthsex,
// MothersMaidenName, FathersName, Person-extension
patientResource.addExtension().setUrl(SHR_EXT + "shr-actor-FictionalPerson-extension").setValue(new BooleanType(true));
String fathersName = (String) person.attributes.get(Person.NAME_FATHER);
Extension fathersNameExtension = new Extension(SHR_EXT + "shr-entity-FathersName-extension", new HumanName().setText(fathersName));
patientResource.addExtension(fathersNameExtension);
String ssn = (String) person.attributes.get(Person.IDENTIFIER_SSN);
Extension ssnExtension = new Extension(SHR_EXT + "shr-demographics-SocialSecurityNumber-extension", new StringType(ssn));
patientResource.addExtension(ssnExtension);
}
// 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) {
Extension dalyExtension = new Extension(SYNTHEA_EXT + "disability-adjusted-life-years");
DecimalType daly = new DecimalType(dalyValue);
dalyExtension.setValue(daly);
patientResource.addExtension(dalyExtension);
Extension qalyExtension = new Extension(SYNTHEA_EXT + "quality-adjusted-life-years");
DecimalType qaly = new DecimalType(qalyValue);
qalyExtension.setValue(qaly);
patientResource.addExtension(qalyExtension);
}
return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
}
use of org.hl7.fhir.dstu2016may.model.DecimalType in project synthea by synthetichealth.
the class FhirStu3 method provider.
/**
* Map the Provider into a FHIR Organization resource, and add it to the given Bundle.
* @param bundle The Bundle to add to
* @param provider The Provider
* @return The added Entry
*/
protected static BundleEntryComponent provider(Bundle bundle, Provider provider) {
org.hl7.fhir.dstu3.model.Organization organizationResource = new org.hl7.fhir.dstu3.model.Organization();
List<CodeableConcept> organizationType = new ArrayList<CodeableConcept>();
organizationType.add(mapCodeToCodeableConcept(new Code("http://hl7.org/fhir/organization-type", "prov", "Healthcare Provider"), "http://hl7.org/fhir/organization-type"));
organizationResource.addIdentifier().setSystem("https://github.com/synthetichealth/synthea").setValue((String) provider.getResourceID());
organizationResource.setId(provider.getResourceID());
organizationResource.setName(provider.name);
organizationResource.setType(organizationType);
Address address = new Address().addLine(provider.address).setCity(provider.city).setPostalCode(provider.zip).setState(provider.state);
if (COUNTRY_CODE != null) {
address.setCountry(COUNTRY_CODE);
}
organizationResource.addAddress(address);
Point2D.Double coord = provider.getLonLat();
if (coord != null) {
Extension geolocation = address.addExtension();
geolocation.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
geolocation.addExtension("latitude", new DecimalType(coord.getY()));
geolocation.addExtension("longitude", new DecimalType(coord.getX()));
}
if (provider.phone != null && !provider.phone.isEmpty()) {
ContactPoint contactPoint = new ContactPoint().setSystem(ContactPointSystem.PHONE).setValue(provider.phone);
organizationResource.addTelecom(contactPoint);
}
if (USE_SHR_EXTENSIONS) {
organizationResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Organization"));
// required fields for this profile are identifier, type, address, and contact
organizationResource.addIdentifier().setSystem("urn:ietf:rfc:3986").setValue("urn:uuid:" + provider.getResourceID());
organizationResource.addContact().setName(new HumanName().setText("Synthetic Provider"));
}
return newEntry(bundle, organizationResource, provider.getResourceID());
}
use of org.hl7.fhir.dstu2016may.model.DecimalType in project synthea by synthetichealth.
the class FhirStu3 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 BundleEntryComponent 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));
Code mrnCode = new Code("http://hl7.org/fhir/v2/0203", "MR", "Medical Record Number");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(mrnCode, "http://hl7.org/fhir/v2/0203")).setSystem("http://hospital.smarthealthit.org").setValue((String) person.attributes.get(Person.ID));
Code ssnCode = new Code("http://hl7.org/fhir/identifier-type", "SB", "Social Security Number");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(ssnCode, "http://hl7.org/fhir/identifier-type")).setSystem("http://hl7.org/fhir/sid/us-ssn").setValue((String) person.attributes.get(Person.IDENTIFIER_SSN));
if (person.attributes.get(Person.IDENTIFIER_DRIVERS) != null) {
Code driversCode = new Code("http://hl7.org/fhir/v2/0203", "DL", "Driver's License");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(driversCode, "http://hl7.org/fhir/v2/0203")).setSystem("urn:oid:2.16.840.1.113883.4.3.25").setValue((String) person.attributes.get(Person.IDENTIFIER_DRIVERS));
}
if (person.attributes.get(Person.IDENTIFIER_PASSPORT) != null) {
Code passportCode = new Code("http://hl7.org/fhir/v2/0203", "PPN", "Passport Number");
patientResource.addIdentifier().setType(mapCodeToCodeableConcept(passportCode, "http://hl7.org/fhir/v2/0203")).setSystem(SHR_EXT + "passportNumber").setValue((String) person.attributes.get(Person.IDENTIFIER_PASSPORT));
}
if (person.attributes.get(Person.CONTACT_EMAIL) != null) {
ContactComponent contact = new ContactComponent();
HumanName contactName = new HumanName();
contactName.setUse(HumanName.NameUse.OFFICIAL);
contactName.addGiven((String) person.attributes.get(Person.CONTACT_GIVEN_NAME));
contactName.setFamily((String) person.attributes.get(Person.CONTACT_FAMILY_NAME));
contact.setName(contactName);
contact.addTelecom().setSystem(ContactPointSystem.EMAIL).setUse(ContactPointUse.HOME).setValue((String) person.attributes.get(Person.CONTACT_EMAIL));
patientResource.addContact(contact);
}
// We do not yet account for mixed race
Extension raceExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race");
String race = (String) person.attributes.get(Person.RACE);
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 raceNum = (String) raceEthnicityCodes.get(race);
Extension raceCodingExtension = new Extension("ombCategory");
Coding raceCoding = new Coding();
if (raceDisplay.equals("Other")) {
raceCoding.setSystem("http://hl7.org/fhir/v3/NullFlavor");
raceCoding.setCode("UNK");
raceCoding.setDisplay("Unknown");
} else {
raceCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
raceCoding.setCode(raceNum);
raceCoding.setDisplay(raceDisplay);
}
raceCodingExtension.setValue(raceCoding);
raceExtension.addExtension(raceCodingExtension);
Extension raceTextExtension = new Extension("text");
raceTextExtension.setValue(new StringType(raceDisplay));
raceExtension.addExtension(raceTextExtension);
patientResource.addExtension(raceExtension);
// We do not yet account for mixed ethnicity
Extension ethnicityExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");
String ethnicity = (String) person.attributes.get(Person.ETHNICITY);
String ethnicityDisplay;
if (ethnicity.equals("hispanic")) {
ethnicity = "hispanic";
ethnicityDisplay = "Hispanic or Latino";
} else {
ethnicity = "nonhispanic";
ethnicityDisplay = "Not Hispanic or Latino";
}
String ethnicityNum = (String) raceEthnicityCodes.get(ethnicity);
Extension ethnicityCodingExtension = new Extension("ombCategory");
Coding ethnicityCoding = new Coding();
ethnicityCoding.setSystem("urn:oid:2.16.840.1.113883.6.238");
ethnicityCoding.setCode(ethnicityNum);
ethnicityCoding.setDisplay(ethnicityDisplay);
ethnicityCodingExtension.setValue(ethnicityCoding);
ethnicityExtension.addExtension(ethnicityCodingExtension);
Extension ethnicityTextExtension = new Extension("text");
ethnicityTextExtension.setValue(new StringType(ethnicityDisplay));
ethnicityExtension.addExtension(ethnicityTextExtension);
patientResource.addExtension(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<PatientCommunicationComponent> communication = new ArrayList<PatientCommunicationComponent>();
communication.add(new PatientCommunicationComponent(mapCodeToCodeableConcept(languageCode, (String) languageMap.get("system"))));
patientResource.setCommunication(communication);
HumanName name = patientResource.addName();
name.setUse(HumanName.NameUse.OFFICIAL);
name.addGiven((String) person.attributes.get(Person.FIRST_NAME));
name.setFamily((String) person.attributes.get(Person.LAST_NAME));
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) {
HumanName maidenName = patientResource.addName();
maidenName.setUse(HumanName.NameUse.MAIDEN);
maidenName.addGiven((String) person.attributes.get(Person.FIRST_NAME));
maidenName.setFamily((String) person.attributes.get(Person.MAIDEN_NAME));
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));
}
}
Extension mothersMaidenNameExtension = new Extension("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName");
String mothersMaidenName = (String) person.attributes.get(Person.NAME_MOTHER);
mothersMaidenNameExtension.setValue(new StringType(mothersMaidenName));
patientResource.addExtension(mothersMaidenNameExtension);
long birthdate = (long) person.attributes.get(Person.BIRTHDATE);
patientResource.setBirthDate(new Date(birthdate));
Extension birthSexExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
if (person.attributes.get(Person.GENDER).equals("M")) {
patientResource.setGender(AdministrativeGender.MALE);
birthSexExtension.setValue(new CodeType("M"));
} else if (person.attributes.get(Person.GENDER).equals("F")) {
patientResource.setGender(AdministrativeGender.FEMALE);
birthSexExtension.setValue(new CodeType("F"));
}
patientResource.addExtension(birthSexExtension);
String state = (String) person.attributes.get(Person.STATE);
Address 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);
}
Address birthplace = new Address();
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));
Extension birthplaceExtension = new Extension("http://hl7.org/fhir/StructureDefinition/birthPlace");
birthplaceExtension.setValue(birthplace);
patientResource.addExtension(birthplaceExtension);
if (person.attributes.get(Person.MULTIPLE_BIRTH_STATUS) != null) {
patientResource.setMultipleBirth(new IntegerType((int) person.attributes.get(Person.MULTIPLE_BIRTH_STATUS)));
} else {
patientResource.setMultipleBirth(new BooleanType(false));
}
patientResource.addTelecom().setSystem(ContactPoint.ContactPointSystem.PHONE).setUse(ContactPoint.ContactPointUse.HOME).setValue((String) person.attributes.get(Person.TELECOM));
String maritalStatus = ((String) person.attributes.get(Person.MARITAL_STATUS));
if (maritalStatus != null) {
Code maritalStatusCode = new Code("http://hl7.org/fhir/v3/MaritalStatus", maritalStatus, maritalStatus);
patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://hl7.org/fhir/v3/MaritalStatus"));
} else {
Code maritalStatusCode = new Code("http://hl7.org/fhir/v3/MaritalStatus", "S", "Never Married");
patientResource.setMaritalStatus(mapCodeToCodeableConcept(maritalStatusCode, "http://hl7.org/fhir/v3/MaritalStatus"));
}
Point2D.Double coord = person.getLonLat();
if (coord != null) {
Extension geolocation = addrResource.addExtension();
geolocation.setUrl("http://hl7.org/fhir/StructureDefinition/geolocation");
geolocation.addExtension("latitude", new DecimalType(coord.getY()));
geolocation.addExtension("longitude", new DecimalType(coord.getX()));
}
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.getSeed() + " Population seed: " + person.populationSeed;
patientResource.setText(new Narrative().setStatus(NarrativeStatus.GENERATED).setDiv(new XhtmlNode(NodeType.Element).setValue(generatedBySynthea)));
if (USE_SHR_EXTENSIONS) {
patientResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-entity-Patient"));
// Patient profile requires race, ethnicity, birthsex,
// MothersMaidenName, FathersName, Person-extension
patientResource.addExtension().setUrl(SHR_EXT + "shr-actor-FictionalPerson-extension").setValue(new BooleanType(true));
String fathersName = (String) person.attributes.get(Person.NAME_FATHER);
Extension fathersNameExtension = new Extension(SHR_EXT + "shr-entity-FathersName-extension", new HumanName().setText(fathersName));
patientResource.addExtension(fathersNameExtension);
String ssn = (String) person.attributes.get(Person.IDENTIFIER_SSN);
Extension ssnExtension = new Extension(SHR_EXT + "shr-demographics-SocialSecurityNumber-extension", new StringType(ssn));
patientResource.addExtension(ssnExtension);
Basic personResource = new Basic();
// the only required field on this patient resource is code
Coding fixedCode = new Coding("http://standardhealthrecord.org/fhir/basic-resource-type", "shr-entity-Person", "shr-entity-Person");
personResource.setCode(new CodeableConcept().addCoding(fixedCode));
Meta personMeta = new Meta();
personMeta.addProfile(SHR_EXT + "shr-entity-Person");
personResource.setMeta(personMeta);
BundleEntryComponent personEntry = newEntry(person, bundle, personResource);
patientResource.addExtension().setUrl(SHR_EXT + "shr-entity-Person-extension").setValue(new Reference(personEntry.getFullUrl()));
}
// 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) {
Extension dalyExtension = new Extension(SYNTHEA_EXT + "disability-adjusted-life-years");
DecimalType daly = new DecimalType(dalyValue);
dalyExtension.setValue(daly);
patientResource.addExtension(dalyExtension);
Extension qalyExtension = new Extension(SYNTHEA_EXT + "quality-adjusted-life-years");
DecimalType qaly = new DecimalType(qalyValue);
qalyExtension.setValue(qaly);
patientResource.addExtension(qalyExtension);
}
return newEntry(bundle, patientResource, (String) person.attributes.get(Person.ID));
}
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