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Fix issues with inferSystem

This commit is contained in:
Grahame Grieve 2024-02-12 16:20:34 +11:00
parent b8a9b94b45
commit 5b323644de
1 changed files with 39 additions and 50 deletions
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89
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValueSetValidator.java
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@ -481,7 +481,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
VersionInfo vi = new VersionInfo(this);
checkCanonical(issues, path, valueset, valueset);
String system = code.hasSystem() ? code.getSystem() : getValueSetSystemOrNull();
String system = code.getSystem();
if (!options.isMembershipOnly()) {
if (system == null && !code.hasDisplay() && options.isGuessSystem()) { // dealing with just a plain code (enum)
List<StringWithCode> problems = new ArrayList<>();
@ -490,7 +490,10 @@ public class ValueSetValidator extends ValueSetProcessBase {
if (problems.size() == 0) {
throw new Error("Unable to resolve systems but no reason why"); // this is an error in the java code
} else if (problems.size() == 1) {
return new ValidationResult(IssueSeverity.ERROR, problems.get(0).getMessage(), makeIssue(IssueSeverity.ERROR, IssueType.UNKNOWN, path, problems.get(0).getMessage(), problems.get(0).getCode(), null));
String msg = context.formatMessagePlural(1, I18nConstants.NONE_OF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getVersionedUrl(), "'"+code.toString()+"'");
issues.addAll(makeIssue(IssueSeverity.ERROR, IssueType.CODEINVALID, "code", msg, OpIssueCode.NotInVS, null));
issues.addAll(makeIssue(IssueSeverity.ERROR, IssueType.NOTFOUND, "code", problems.get(0).getMessage(), problems.get(0).getCode(), null));
return new ValidationResult(IssueSeverity.ERROR, problems.get(0).getMessage()+"; "+msg, issues);
} else {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder("; ");
for (StringWithCode s : problems) {
@ -986,40 +989,6 @@ public class ValueSetValidator extends ValueSetProcessBase {
return null;
}
private String getValueSetSystemOrNull() throws FHIRException {
if (valueset == null) {
return null;
}
if (!options.isGuessSystem()) {
return null;
}
if (valueset.getCompose().getInclude().size() == 0) {
if (!valueset.hasExpansion() || valueset.getExpansion().getContains().size() == 0) {
return null;
} else {
String cs = valueset.getExpansion().getContains().get(0).getSystem();
if (cs != null && checkSystem(valueset.getExpansion().getContains(), cs)) {
return cs;
} else {
return null;
}
}
}
for (ConceptSetComponent inc : valueset.getCompose().getInclude()) {
if (inc.hasValueSet()) {
return null;
}
if (!inc.hasSystem()) {
return null;
}
}
if (valueset.getCompose().getInclude().size() == 1) {
return valueset.getCompose().getInclude().get(0).getSystem();
}
return null;
}
/*
* Check that all system values within an expansion correspond to the specified system value
*/
@ -1087,10 +1056,10 @@ public class ValueSetValidator extends ValueSetProcessBase {
return null;
}
if (sys.size() == 0) {
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_NO_MATCHES, code)));
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_NO_MATCHES, code, valueset.getVersionedUrl())));
return null;
} else if (sys.size() > 1) {
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_MULTIPLE_MATCHES, sys.toString())));
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_MULTIPLE_MATCHES, code, valueset.getVersionedUrl(), sys.toString())));
return null;
} else {
return sys.iterator().next();
@ -1101,7 +1070,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
if (valueset.hasCompose()) {
// ignore excludes - they can't make any difference
if (!valueset.getCompose().hasInclude() && !valueset.getExpansion().hasContains()) {
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_NO_INCLUDES_OR_EXPANSION, valueset.getVersionedUrl())));
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_NO_INCLUDES_OR_EXPANSION, code, valueset.getVersionedUrl())));
}
int i = 0;
@ -1114,19 +1083,29 @@ public class ValueSetValidator extends ValueSetProcessBase {
}
}
} else if (!vsi.hasSystem()) {
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_INCLUDE_WITH_NO_SYSTEM, valueset.getVersionedUrl(), i)));
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_INCLUDE_WITH_NO_SYSTEM, code, valueset.getVersionedUrl(), i)));
return false;
}
if (vsi.hasSystem()) {
if (vsi.hasFilter()) {
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_INCLUDE_WITH_FILTER, valueset.getVersionedUrl(), i, vsi.getSystem())));
return false;
ValueSet vsDummy = new ValueSet();
vsDummy.setUrl(Utilities.makeUuidUrn());
vsDummy.setStatus(PublicationStatus.ACTIVE);
vsDummy.getCompose().addInclude(vsi);
Coding c = new Coding().setCode(code).setSystem(vsi.getSystem());
ValidationResult vr = context.validateCode(options.withGuessSystem(false), c, vsDummy);
if (vr.isOk()) {
sys.add(vsi.getSystem());
} else {
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_INCLUDE_WITH_FILTER, code, valueset.getVersionedUrl(), i, vsi.getSystem())));
return false;
}
}
CodeSystemProvider csp = CodeSystemProvider.factory(vsi.getSystem());
if (csp != null) {
Boolean ok = csp.checkCode(code);
if (ok == null) {
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM_SYSTEM_IS_INDETERMINATE, valueset.getVersionedUrl(), vsi.getSystem())));
problems.add(new StringWithCode(OpIssueCode.InferFailed, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM_SYSTEM_IS_INDETERMINATE, code, valueset.getVersionedUrl(), vsi.getSystem())));
sys.add(vsi.getSystem());
} else if (ok) {
sys.add(vsi.getSystem());
@ -1156,15 +1135,25 @@ public class ValueSetValidator extends ValueSetProcessBase {
}
}
} else {
// we'll try to expand this one then
ValueSetExpansionOutcome vse = context.expandVS(vsi, false, false);
if (vse.isOk()) {
if (!checkSystems(vse.getValueset().getExpansion().getContains(), code, sys, problems)) {
ValueSet vsDummy = new ValueSet();
vsDummy.setUrl(Utilities.makeUuidUrn());
vsDummy.setStatus(PublicationStatus.ACTIVE);
vsDummy.getCompose().addInclude(vsi);
ValidationResult vr = context.validateCode(options.withNoClient(), code, vsDummy);
if (vr.isOk()) {
sys.add(vsi.getSystem());
} else {
// ok, we'll try to expand this one then
ValueSetExpansionOutcome vse = context.expandVS(vsi, false, false);
if (vse.isOk()) {
if (!checkSystems(vse.getValueset().getExpansion().getContains(), code, sys, problems)) {
return false;
}
} else {
problems.add(new StringWithCode(OpIssueCode.NotFound, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_INCLUDE_WITH_UNKNOWN_SYSTEM, code, valueset.getVersionedUrl(), i, vsi.getSystem(), vse.getAllErrors().toString())));
return false;
}
} else {
problems.add(new StringWithCode(OpIssueCode.NotFound, context.formatMessage(I18nConstants.UNABLE_TO_RESOLVE_SYSTEM__VALUE_SET_HAS_INCLUDE_WITH_UNKNOWN_SYSTEM, valueset.getVersionedUrl(), i, vsi.getSystem(), vse.getAllErrors().toString())));
return false;
}
}
}