@Override
public ValueSet expandByIdentifier(String theUri, String theFilter) {
if (isBlank(theUri)) {
throw new InvalidRequestException("URI must not be blank or missing");
}
ValueSet source = new ValueSet();
source.getCompose().addImport(theUri);
if (isNotBlank(theFilter)) {
ConceptSetComponent include = source.getCompose().addInclude();
ConceptSetFilterComponent filter = include.addFilter();
filter.setProperty("display");
filter.setOp(FilterOperator.EQUAL);
filter.setValue(theFilter);
}
ValueSet retVal = doExpand(source);
return retVal;
// if (defaultValueSet != null) {
// source = getContext().newJsonParser().parseResource(ValueSet.class,
// getContext().newJsonParser().encodeResourceToString(defaultValueSet));
// } else {
// IBundleProvider ids = search(ValueSet.SP_URL, new UriParam(theUri));
// if (ids.size() == 0) {
// throw new InvalidRequestException("Unknown ValueSet URI: " + theUri);
// }
// source = (ValueSet) ids.getResources(0, 1).get(0);
// }
//
// return expand(defaultValueSet, theFilter);
}
private String getVSSummary(ValueSet vs) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (ConceptSetComponent cc : vs.getCompose().getInclude())
b.append("Include " + getIncSummary(cc));
for (ConceptSetComponent cc : vs.getCompose().getExclude())
b.append("Exclude " + getIncSummary(cc));
return b.toString();
}
private boolean notcomplete(ValueSet vs) {
if (!vs.hasExpansion()) return true;
if (!vs.getExpansion()
.getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/valueset-unclosed")
.isEmpty()) return true;
if (!vs.getExpansion()
.getExtensionsByUrl("http://hl7.org/fhir/StructureDefinition/valueset-toocostly")
.isEmpty()) return true;
return false;
}
/**
* Only produce the v3 vocabulary for appending to rim.ttl
*
* @throws Exception
*/
public void executeV3(Map<String, ValueSet> valuesets, Map<String, CodeSystem> codeSystems)
throws Exception {
for (ValueSet vs : this.valuesets.values()) {
valuesets.put("vs:" + tail(vs.getUrl()), vs);
}
// for (String n : sorted(valuesets.keySet()))
// gen(n, valuesets.get(n));
commit(false);
}
private ValidationResult verifyCodeInExpansion(ValueSet vs, String code) throws FHIRException {
if (vs.getExpansion()
.hasExtension("http://hl7.org/fhir/StructureDefinition/valueset-toocostly")) {
throw new FHIRException("Unable to validate core - value set is too costly to expand");
} else {
ValueSetExpansionContainsComponent cc = findCode(vs.getExpansion().getContains(), code);
if (cc == null)
return new ValidationResult(
IssueSeverity.ERROR, "Unknown Code " + code + " in " + vs.getUrl());
return null;
}
}
@Override
public ValueSetExpansionComponent expandVS(ConceptSetComponent inc, boolean heirachical)
throws TerminologyServiceException {
ValueSet vs = new ValueSet();
vs.setCompose(new ValueSetComposeComponent());
vs.getCompose().getInclude().add(inc);
ValueSetExpansionOutcome vse = expandVS(vs, true, heirachical);
ValueSet valueset = vse.getValueset();
if (valueset == null)
throw new TerminologyServiceException("Error Expanding ValueSet: " + vse.getError());
return valueset.getExpansion();
}
@Override
public ValidationResult validateCode(
String system, String code, String display, ConceptSetComponent vsi) {
try {
ValueSet vs = new ValueSet();
vs.setUrl(Utilities.makeUuidUrn());
vs.getCompose().addInclude(vsi);
return verifyCodeExternal(
vs, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
} catch (Exception e) {
return new ValidationResult(
IssueSeverity.FATAL,
"Error validating code \"" + code + "\" in system \"" + system + "\": " + e.getMessage());
}
}
private ValueSet doExpand(ValueSet theSource) {
validateIncludes("include", theSource.getCompose().getInclude());
validateIncludes("exclude", theSource.getCompose().getExclude());
HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
ValueSetExpansionOutcome outcome = workerContext.expand(theSource);
ValueSetExpansionComponent expansion = outcome.getValueset().getExpansion();
ValueSet retVal = new ValueSet();
retVal.getMeta().setLastUpdated(new Date());
retVal.setExpansion(expansion);
return retVal;
}
@Override
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical) {
try {
if (vs.hasExpansion()) {
return new ValueSetExpansionOutcome(vs.copy());
}
String cacheFn = null;
if (cache != null) {
cacheFn = Utilities.path(cache, determineCacheId(vs, heirarchical) + ".json");
if (new File(cacheFn).exists()) return loadFromCache(vs.copy(), cacheFn);
}
if (cacheOk && vs.hasUrl()) {
if (expProfile == null) throw new Exception("No ExpansionProfile provided");
ValueSetExpansionOutcome vse =
expansionCache.getExpander().expand(vs, expProfile.setExcludeNested(!heirarchical));
if (vse.getValueset() != null) {
if (cache != null) {
FileOutputStream s = new FileOutputStream(cacheFn);
newJsonParser().compose(new FileOutputStream(cacheFn), vse.getValueset());
s.close();
}
}
return vse;
} else {
ValueSetExpansionOutcome res = expandOnServer(vs, cacheFn);
if (cacheFn != null) {
if (res.getValueset() != null) {
saveToCache(res.getValueset(), cacheFn);
} else {
OperationOutcome oo = new OperationOutcome();
oo.addIssue().getDetails().setText(res.getError());
saveToCache(oo, cacheFn);
}
}
return res;
}
} catch (NoTerminologyServiceException e) {
return new ValueSetExpansionOutcome(
e.getMessage() == null ? e.getClass().getName() : e.getMessage(),
TerminologyServiceErrorClass.NOSERVICE);
} catch (Exception e) {
return new ValueSetExpansionOutcome(
e.getMessage() == null ? e.getClass().getName() : e.getMessage(),
TerminologyServiceErrorClass.UNKNOWN);
}
}
private ValidationResult verifyCodeInternal(ValueSet vs, String code)
throws FileNotFoundException, ETooCostly, IOException, FHIRException {
if (vs.hasExpansion()) return verifyCodeInExpansion(vs, code);
else {
ValueSetExpansionOutcome vse = expansionCache.getExpander().expand(vs, null);
if (vse.getValueset() == null)
return new ValidationResult(IssueSeverity.ERROR, vse.getError(), vse.getErrorClass());
else return verifyCodeInExpansion(vse.getValueset(), code);
}
}
private ValidationResult verifyCodeInExpansion(
ValueSet vs, String system, String code, String display) {
ValueSetExpansionContainsComponent cc = findCode(vs.getExpansion().getContains(), code);
if (cc == null)
return new ValidationResult(
IssueSeverity.ERROR, "Unknown Code " + code + " in " + vs.getUrl());
if (display == null)
return new ValidationResult(
new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
if (cc.hasDisplay()) {
if (display.equalsIgnoreCase(cc.getDisplay()))
return new ValidationResult(
new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
return new ValidationResult(
IssueSeverity.WARNING,
"Display Name for " + code + " must be '" + cc.getDisplay() + "'",
new ConceptDefinitionComponent().setCode(code).setDisplay(cc.getDisplay()));
}
return null;
}
private ValidationResult verifyCodeInternal(
ValueSet vs, String system, String code, String display) throws Exception {
if (vs.hasExpansion()) return verifyCodeInExpansion(vs, system, code, display);
else {
ValueSetExpansionOutcome vse = expansionCache.getExpander().expand(vs, null);
if (vse.getValueset() != null)
return verifyCodeExternal(
vs, new Coding().setSystem(system).setCode(code).setDisplay(display), false);
else return verifyCodeInExpansion(vse.getValueset(), system, code, display);
}
}
private ValidationResult handleByCache(ValueSet vs, Coding coding, boolean tryCache) {
String cacheId = cacheId(coding);
Map<String, ValidationResult> cache = validationCache.get(vs.getUrl());
if (cache == null) {
cache = new HashMap<String, IWorkerContext.ValidationResult>();
validationCache.put(vs.getUrl(), cache);
}
if (cache.containsKey(cacheId)) return cache.get(cacheId);
if (!tryCache) return null;
if (!cacheValidation) return null;
if (failed.contains(vs.getUrl())) return null;
ValueSetExpansionOutcome vse = expandVS(vs, true, false);
if (vse.getValueset() == null || notcomplete(vse.getValueset())) {
failed.add(vs.getUrl());
return null;
}
ValidationResult res = validateCode(coding, vse.getValueset());
cache.put(cacheId, res);
return res;
}
private ValidationResult verifyCodeExternal(ValueSet vs, CodeableConcept cc, boolean tryCache)
throws Exception {
ValidationResult res = handleByCache(vs, cc, tryCache);
if (res != null) return res;
Parameters pin = new Parameters();
pin.addParameter().setName("codeableConcept").setValue(cc);
pin.addParameter().setName("valueSet").setResource(vs);
res = serverValidateCode(pin, false);
Map<String, ValidationResult> cache = validationCache.get(vs.getUrl());
cache.put(cacheId(cc), res);
return res;
}
private String determineCacheId(ValueSet vs, boolean heirarchical) throws Exception {
// just the content logical definition is hashed
ValueSet vsid = new ValueSet();
vsid.setCompose(vs.getCompose());
JsonParser parser = new JsonParser();
parser.setOutputStyle(OutputStyle.NORMAL);
ByteArrayOutputStream b = new ByteArrayOutputStream();
parser.compose(b, vsid);
b.close();
String s = new String(b.toByteArray(), Charsets.UTF_8);
// any code systems we can find, we add these too.
for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
CodeSystem cs = fetchCodeSystem(inc.getSystem());
if (cs != null) {
String css = cacheValue(cs);
s = s + css;
}
}
s = s + "-" + Boolean.toString(heirarchical);
String r = Integer.toString(s.hashCode());
// TextFile.stringToFile(s, Utilities.path(cache, r+".id.json"));
return r;
}
private ValidationResult verifyCodeExternal(ValueSet vs, Coding coding, boolean tryCache)
throws Exception {
ValidationResult res = vs == null ? null : handleByCache(vs, coding, tryCache);
if (res != null) return res;
Parameters pin = new Parameters();
pin.addParameter().setName("coding").setValue(coding);
if (vs != null) pin.addParameter().setName("valueSet").setResource(vs);
res = serverValidateCode(pin, vs == null);
if (vs != null) {
Map<String, ValidationResult> cache = validationCache.get(vs.getUrl());
cache.put(cacheId(coding), res);
}
return res;
}
private ValueSetExpansionOutcome loadFromCache(ValueSet vs, String cacheFn)
throws FileNotFoundException, Exception {
JsonParser parser = new JsonParser();
Resource r = parser.parse(new FileInputStream(cacheFn));
if (r instanceof OperationOutcome)
return new ValueSetExpansionOutcome(
((OperationOutcome) r).getIssue().get(0).getDetails().getText(),
TerminologyServiceErrorClass.UNKNOWN);
else {
vs.setExpansion(
((ValueSet) r)
.getExpansion()); // because what is cached might be from a different value set
return new ValueSetExpansionOutcome(vs);
}
}
@Override
public ValidationResult validateCode(String system, String code, String display, ValueSet vs) {
try {
if (system == null && display == null) return verifyCodeInternal(vs, code);
if ((codeSystems.containsKey(system) && codeSystems.get(system) != null) || vs.hasExpansion())
return verifyCodeInternal(vs, system, code, display);
else
return verifyCodeExternal(
vs, new Coding().setSystem(system).setCode(code).setDisplay(display), true);
} catch (Exception e) {
return new ValidationResult(
IssueSeverity.FATAL,
"Error validating code \"" + code + "\" in system \"" + system + "\": " + e.getMessage(),
TerminologyServiceErrorClass.SERVER_ERROR);
}
}
@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());
}
}
public ValueSetExpansionOutcome expandOnServer(ValueSet vs, String fn) throws Exception {
if (noTerminologyServer)
return new ValueSetExpansionOutcome(
"Error expanding ValueSet: running without terminology services",
TerminologyServiceErrorClass.NOSERVICE);
if (expProfile == null) throw new Exception("No ExpansionProfile provided");
try {
Map<String, String> params = new HashMap<String, String>();
params.put("_limit", Integer.toString(expandCodesLimit));
params.put("_incomplete", "true");
log("Terminology Server: $expand on " + getVSSummary(vs));
ValueSet result = txServer.expandValueset(vs, expProfile.setIncludeDefinition(false), params);
return new ValueSetExpansionOutcome(result);
} catch (Exception e) {
return new ValueSetExpansionOutcome(
"Error expanding ValueSet \"" + vs.getUrl() + ": " + e.getMessage(),
TerminologyServiceErrorClass.UNKNOWN);
}
}
private String gen(Section section, CodeSystem cs, ValueSet vs) {
String bn = getPNameForUri(cs.getUrl());
if (!bn.startsWith("<")) {
section.triple(bn + ".system", "a", "fhir:CodeSystem");
if (cs.hasVersion()) section.triple(bn + ".system", "fhir:version", literal(cs.getVersion()));
if (vs.hasName()) section.label(bn + ".system", vs.getName());
if (vs.hasDescription())
section.comment(
bn + ".system",
vs.getDescription()
.replace("value set", "code system")
.replace("Value Set", "Code System")
.replace("Value set", "Code system"));
if (vs.hasCopyright())
section.triple(bn + ".system", "dc:rights", literal(vs.getCopyright()));
if (vs.hasDate()) section.triple(bn + ".system", "dc:date", literal(vs.getDate().toString()));
section.triple(bn, "a", "fhir:Concept");
gen(section, bn, bn, cs.getConcept());
}
return bn;
}
@Override
public ValueSet expand(ValueSet source, String theFilter) {
ValueSet toExpand = new ValueSet();
for (UriType next : source.getCompose().getImport()) {
ConceptSetComponent include = toExpand.getCompose().addInclude();
include.setSystem(next.getValue());
addFilterIfPresent(theFilter, include);
}
for (ConceptSetComponent next : source.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
if (toExpand.getCompose().isEmpty()) {
throw new InvalidRequestException(
"ValueSet does not have any compose.include or compose.import values, can not expand");
}
toExpand.getCompose().getExclude().addAll(source.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand);
return retVal;
}
@Override
public ValidationResult validateCode(CodeableConcept code, ValueSet vs) {
try {
if (vs.hasExpansion()) return verifyCodeInternal(vs, code);
else {
// we'll try expanding first; if that doesn't work, then we'll just pass it to the server to
// validate
// ... could be a problem if the server doesn't have the code systems we have locally, so we
// try not to depend on the server
try {
ValueSetExpansionOutcome vse = expandVS(vs, true, false);
if (vse.getValueset() != null) return verifyCodeInternal(vse.getValueset(), code);
} catch (Exception e) {
// failed? we'll just try the server
}
return verifyCodeExternal(vs, code, true);
}
} catch (Exception e) {
return new ValidationResult(
IssueSeverity.FATAL,
"Error validating code \"" + code.toString() + "\": " + e.getMessage(),
TerminologyServiceErrorClass.SERVER_ERROR);
}
}
private void gen(String bn, ValueSet vs) throws FHIRException {
Section section = section(bn);
section.triple(bn, "a", "fhir:ValueSet");
if (vs.hasVersion()) section.triple(bn, "fhir:version", literal(vs.getVersion()));
if (vs.hasName()) section.label(bn, vs.getName());
if (vs.hasDescription())
section.comment(
bn,
vs.getDescription()
.replace("code system", "value set")
.replace("Code System", "Value Set")
.replace("Code system", "Value set"));
if (vs.hasCopyright()) section.triple(bn, "dc:rights", literal(vs.getCopyright()));
if (vs.hasDate()) section.triple(bn, "dc:date", literal(vs.getDateElement().asStringValue()));
for (UsageContext cc : vs.getUseContext())
codedTriple(section, bn, "fhir:useContext", cc.getValueCodeableConcept());
section.triple(
bn,
"fhir:status",
complex().predicate("a", "fhir:conformance-resource-status\\#" + vs.getStatus().toCode()));
section.triple(
bn,
"fhir:canonicalStatus",
complex().predicate("a", getCanonicalStatus("ValueSet.status", vs.getStatus().toCode())));
}
@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);
}