@SuppressWarnings("rawtypes")
private String describeValidationParameters(Parameters pin) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (ParametersParameterComponent p : pin.getParameter()) {
if (p.hasValue() && p.getValue() instanceof PrimitiveType) {
b.append(p.getName() + "=" + ((PrimitiveType) p.getValue()).asStringValue());
} else if (p.hasValue() && p.getValue() instanceof Coding) {
b.append("system=" + ((Coding) p.getValue()).getSystem());
b.append("code=" + ((Coding) p.getValue()).getCode());
b.append("display=" + ((Coding) p.getValue()).getDisplay());
} else if (p.hasValue() && p.getValue() instanceof CodeableConcept) {
if (((CodeableConcept) p.getValue()).hasCoding()) {
Coding c = ((CodeableConcept) p.getValue()).getCodingFirstRep();
b.append("system=" + c.getSystem());
b.append("code=" + c.getCode());
b.append("display=" + c.getDisplay());
} else if (((CodeableConcept) p.getValue()).hasText()) {
b.append("text=" + ((CodeableConcept) p.getValue()).getText());
}
} else if (p.hasResource() && (p.getResource() instanceof ValueSet)) {
b.append("valueset=" + getVSSummary((ValueSet) p.getResource()));
}
}
return b.toString();
}
protected void codedTriple(Subject subject, String predicate, CodeableConcept cc) {
for (Coding c : cc.getCoding()) {
String s = getLinkedForm(c);
if (s != null)
subject.predicate(
predicate, new StringType(s), c.hasDisplay() ? c.getDisplay() : cc.getText());
}
}
protected void codedTriple(
Section section, String subject, String predicate, CodeableConcept cc) {
for (Coding c : cc.getCoding()) {
String s = getLinkedForm(c);
if (s != null)
section.triple(subject, predicate, s, c.hasDisplay() ? c.getDisplay() : cc.getText());
}
}
protected String getLinkedForm(Coding c) {
if (c.hasSystem()) {
if (c.getSystem().equals("http://loinc.org")) {
prefixes.put("loinc", "http://loinc.org/");
return "loinc:" + c.getCode();
}
}
return null;
}
private String cacheId(Coding coding) {
return "|"
+ coding.getSystem()
+ "|"
+ coding.getVersion()
+ "|"
+ coding.getCode()
+ "|"
+ coding.getDisplay();
}
private ValidationResult verifyCodeInternal(ValueSet vs, CodeableConcept code) throws Exception {
for (Coding c : code.getCoding()) {
ValidationResult res = verifyCodeInternal(vs, c.getSystem(), c.getCode(), c.getDisplay());
if (res.isOk()) return res;
}
if (code.getCoding().isEmpty())
return new ValidationResult(IssueSeverity.ERROR, "None code provided");
else
return new ValidationResult(
IssueSeverity.ERROR, "None of the codes are in the specified value set");
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(
List<ValueSetExpansionContainsComponent> contains,
String theSystem,
String theCode,
Coding theCoding,
CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent 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 (Coding 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(
IPrimitiveType<String> theValueSetIdentifier,
IIdType theId,
IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem,
IPrimitiveType<String> theDisplay,
Coding theCoding,
CodeableConcept theCodeableConcept,
RequestDetails theRequestDetails) {
List<IIdType> valueSetIds = Collections.emptyList();
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 (!LogicUtil.multiXor(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 IdType("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.");
}
// String code = theCode.getValue();
// String system = toStringOrNull(theSystem);
LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
if (result.isFound()) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult retVal =
new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
return retVal;
}
}
// if (valueSetIds.isEmpty()) {
// if (haveIdentifierParam) {
// myValidationSupport.expandValueSet(getContext(), include);
// if (myValidationSupport.isCodeSystemSupported(getContext(),
// theValueSetIdentifier.getValue())) {
// String system = toStringOrNull(theSystem);
// String code = toStringOrNull(theCode);
// String display = toStringOrNull(theDisplay);
// CodeValidationResult result = myValidationSupport.validateCode(getContext(), system,
// code, display);
// 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 new ValidateCodeResult(true, "Code validates", result.getDisplay());
// }
// }
// }
// }
for (IIdType nextId : valueSetIds) {
ValueSet expansion = expand(nextId, null, theRequestDetails);
List<ValueSetExpansionContainsComponent> 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);
}
@Override
public ValidationResult validateCode(Coding code, ValueSet vs) {
if (codeSystems.containsKey(code.getSystem()) && codeSystems.get(code.getSystem()) != null)
try {
return verifyCodeInCodeSystem(
codeSystems.get(code.getSystem()), code.getSystem(), code.getCode(), code.getDisplay());
} catch (Exception e) {
return new ValidationResult(
IssueSeverity.FATAL,
"Error validating code \""
+ code
+ "\" in system \""
+ code.getSystem()
+ "\": "
+ e.getMessage());
}
else if (vs.hasExpansion())
try {
return verifyCodeInternal(vs, code.getSystem(), code.getCode(), code.getDisplay());
} catch (Exception e) {
return new ValidationResult(
IssueSeverity.FATAL,
"Error validating code \""
+ code
+ "\" in system \""
+ code.getSystem()
+ "\": "
+ e.getMessage());
}
else
try {
return verifyCodeExternal(vs, code, true);
} catch (Exception e) {
return new ValidationResult(
IssueSeverity.WARNING,
"Error validating code \""
+ code
+ "\" in system \""
+ code.getSystem()
+ "\": "
+ e.getMessage());
}
}
