private Device initializeDevice(Patient p) {
log("Initializing device");
Device d = newDevice();
d.setManufacturer(deviceInfo.getManufacturerName());
d.setModel(deviceInfo.getModelNumber());
d.setVersion(deviceInfo.getFirmwareRevision());
NarrativeDt n = getNarrative(d);
n.setDiv(
n.getDiv()
.getValueAsString()
.substring(5, n.getDiv().getValueAsString().length() - 6)
.concat("<strong>Serial Number: </strong>")
.concat(deviceInfo.getSerialNumber())
.concat("<br /><strong>Name: </strong>")
.concat(deviceInfo.getName())
.concat("<br /><strong>MAC Address: </strong>")
.concat(deviceInfo.getAddress()));
d.setText(n);
CodeableConceptDt type = new CodeableConceptDt();
// TODO find valid url
type.addCoding()
.setCode("15-102")
.setDisplay("Glukose-Analysegerät")
.setSystem("http://umdns.org");
d.setType(type);
d.setPatient(newResourceReference(p.getId()));
d.setIdentifier(Arrays.asList(getIdentifier("/devices/", "" + deviceInfo.getSysID())));
log("Initializing device done");
return d;
}
private DeviceMetric initializeDeviceMetric(Device d) {
log("Initializing device metric");
DeviceMetric metric = new DeviceMetric();
CodeableConceptDt metricType = new CodeableConceptDt();
// TODO is this the right code and display?
metricType
.addCoding()
.setCode("160020")
.setSystem("https://rtmms.nist.gov")
.setDisplay("MDC_CONC_GLU_GEN");
metric.setType(metricType);
metric.setSource(newResourceReference(d.getId()));
metric.setText(getNarrative(metric));
metric.setCategory(DeviceMetricCategoryEnum.MEASUREMENT);
CodeableConceptDt unitConcept = new CodeableConceptDt();
unitConcept
.addCoding()
.setDisplay("MDC_DIM_MILLI_MOLE_PER_L")
.setSystem("https://rtmms.nist.gov")
.setCode("266866");
metric.setUnit(unitConcept);
// TODO what is the identifier here??? especially the value
metric.setIdentifier(
new IdentifierDt().setSystem(SYSTEM_URL + "/metric/").setValue("glucosemillimolperliter"));
log("Initializing device metric done.");
return metric;
}
public CodeableConceptDt addTRCodingOrDisplay(Concept concept) {
CodeableConceptDt codeableConceptDt = addTRCoding(concept);
if (CollectionUtils.isEmpty(codeableConceptDt.getCoding())) {
CodingDt coding = codeableConceptDt.addCoding();
coding.setDisplay(concept.getName().getName());
}
return codeableConceptDt;
}
public void addFHIRCoding(
CodeableConceptDt codeableConcept, String code, String system, String display) {
CodingDt coding = codeableConcept.addCoding();
coding.setCode(code);
coding.setSystem(system);
coding.setDisplay(display);
}
public CodeableConceptDt getTRValueSetCodeableConcept(
Concept concept, String valueSetURL, CodeableConceptDt codeableConcept) {
CodingDt coding = codeableConcept.addCoding();
if (null != idMappingsRepository.findByInternalId(concept.getUuid())) {
coding.setCode(getTRValueSetCode(concept));
coding.setSystem(valueSetURL);
}
coding.setDisplay(concept.getName().getName());
return codeableConcept;
}
private CodeableConceptDt createCode(int unit) {
log("get code done");
CodeableConceptDt codeableConceptDt = new CodeableConceptDt();
CodingDt coding = new CodingDt();
String code = "", display = "";
switch (unit) {
case GlucoseRecord.UNIT_kgpl:
code = "2339-0";
display = "Glucose [Mass/volume] in Blood";
break;
case GlucoseRecord.UNIT_molpl:
code = "15074-8";
display = "Glucose [Moles/volume] in Blood";
break;
}
codeableConceptDt.addCoding().setSystem("http://loinc.org").setCode(code).setDisplay(display);
log("get code done");
return codeableConceptDt;
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(
List<ExpansionContains> contains,
String theSystem,
String theCode,
CodingDt theCoding,
CodeableConceptDt theCodeableConcept) {
for (ExpansionContains nextCode : contains) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult result =
validateCodeIsInContains(
nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
return result;
}
String system = nextCode.getSystem();
String code = nextCode.getCode();
if (isNotBlank(theCode)) {
if (theCode.equals(code) && (isBlank(theSystem) || theSystem.equals(system))) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else if (theCoding != null) {
if (StringUtils.equals(system, theCoding.getSystem())
&& StringUtils.equals(code, theCoding.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
} else {
for (CodingDt next : theCodeableConcept.getCoding()) {
if (StringUtils.equals(system, next.getSystem())
&& StringUtils.equals(code, next.getCode())) {
return new ValidateCodeResult(true, "Validation succeeded", nextCode.getDisplay());
}
}
}
}
return null;
}
@Override
public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(
UriDt theValueSetIdentifier,
IIdType theId,
CodeDt theCode,
UriDt theSystem,
StringDt theDisplay,
CodingDt theCoding,
CodeableConceptDt theCodeableConcept) {
List<IIdType> valueSetIds;
boolean haveCodeableConcept =
theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
boolean haveCoding = theCoding != null && theCoding.isEmpty() == false;
boolean haveCode = theCode != null && theCode.isEmpty() == false;
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
}
if (!(haveCodeableConcept ^ haveCoding ^ haveCode)) {
throw new InvalidRequestException(
"$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
boolean haveIdentifierParam =
theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
if (theId != null) {
valueSetIds = Collections.singletonList(theId);
} else if (haveIdentifierParam) {
Set<Long> ids =
searchForIds(
ValueSet.SP_IDENTIFIER, new TokenParam(null, theValueSetIdentifier.getValue()));
valueSetIds = new ArrayList<IIdType>();
for (Long next : ids) {
valueSetIds.add(new IdDt("ValueSet", next));
}
} else {
if (theCode == null || theCode.isEmpty()) {
throw new InvalidRequestException(
"Either ValueSet ID or ValueSet identifier or system and code must be provided. Unable to validate.");
}
Set<Long> ids =
searchForIds(
ValueSet.SP_CODE, new TokenParam(toStringOrNull(theSystem), theCode.getValue()));
valueSetIds = new ArrayList<IIdType>();
for (Long next : ids) {
valueSetIds.add(new IdDt("ValueSet", next));
}
}
for (IIdType nextId : valueSetIds) {
ValueSet expansion = expand(nextId, null);
List<ExpansionContains> contains = expansion.getExpansion().getContains();
ValidateCodeResult result =
validateCodeIsInContains(
contains,
toStringOrNull(theSystem),
toStringOrNull(theCode),
theCoding,
theCodeableConcept);
if (result != null) {
if (theDisplay != null
&& isNotBlank(theDisplay.getValue())
&& isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
return new ValidateCodeResult(
false, "Display for code does not match", result.getDisplay());
}
}
return result;
}
}
return new ValidateCodeResult(false, "Code not found", null);
}