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fix bugs to do with value set expansion

This commit is contained in:
Grahame Grieve 2021-09-03 17:27:23 +10:00
parent 19d255636c
commit bd6225cf9e
4 changed files with 30 additions and 13 deletions
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4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -1038,8 +1038,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
for (CanonicalType c : inc.getValueSet()) {
ValueSet vs = fetchResource(ValueSet.class, c.getValue());
if (vs != null) {
pin.addParameter().setName("tx-resource").setResource(vs);
if (isTxCaching && cacheId == null || !cached.contains(vs.getVUrl())) {
pin.addParameter().setName("tx-resource").setResource(vs);
cached.add(vs.getVUrl());
cache = true;
}
@ -1048,8 +1048,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
CodeSystem cs = fetchResource(CodeSystem.class, inc.getSystem());
if (cs != null) {
pin.addParameter().setName("tx-resource").setResource(cs);
if (isTxCaching && cacheId == null || !cached.contains(cs.getVUrl())) {
pin.addParameter().setName("tx-resource").setResource(cs);
cached.add(cs.getVUrl());
cache = true;
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetChecker.java
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@ -1,5 +1,7 @@
package org.hl7.fhir.r5.terminologies;
import java.util.List;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
@ -36,6 +38,6 @@ import org.hl7.fhir.r5.utils.EOperationOutcome;
public interface ValueSetChecker {
Boolean codeInValueSet(String system, String code) throws ETooCostly, EOperationOutcome, Exception;
Boolean codeInValueSet(String system, String code, List<String> warnings) throws ETooCostly, EOperationOutcome, Exception;
}

33
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
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@ -102,7 +102,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
Boolean result = false;
for (Coding c : code.getCoding()) {
Boolean ok = codeInValueSet(c.getSystem(), c.getCode());
Boolean ok = codeInValueSet(c.getSystem(), c.getCode(), warnings);
if (ok == null && result == false) {
result = null;
} else if (ok) {
@ -151,7 +151,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (cs == null) {
warningMessage = "Unable to resolve system "+system;
if (!inExpansion) {
if (valueset.hasExpansion()) {
if (valueset != null && valueset.hasExpansion()) {
return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.CODESYSTEM_CS_UNK_EXPANSION, valueset.getUrl(), code.getCode().toString(), code.getSystem()));
} else {
throw new FHIRException(warningMessage);
@ -187,10 +187,12 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
inInclude = checkInclude(code);
}
List<String> warnings = new ArrayList<>();
// then, if we have a value set, we check it's in the value set
if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
if ((res==null || res.isOk())) {
Boolean ok = codeInValueSet(system, code.getCode());
Boolean ok = codeInValueSet(system, code.getCode(), warnings);
if (ok == null || !ok) {
if (res == null) {
res = new ValidationResult((IssueSeverity) null, null);
@ -549,13 +551,17 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
@Override
public Boolean codeInValueSet(String system, String code) throws FHIRException {
public Boolean codeInValueSet(String system, String code, List<String> warnings) throws FHIRException {
if (valueset == null) {
return false;
}
Boolean result = false;
if (valueset.hasExpansion()) {
return checkExpansion(new Coding(system, code, null));
} else if (valueset.hasCompose()) {
for (ConceptSetComponent vsi : valueset.getCompose().getInclude()) {
Boolean ok = inComponent(vsi, system, code, valueset.getCompose().getInclude().size() == 1);
Boolean ok = inComponent(vsi, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
if (ok == null && result == false) {
result = null;
} else if (ok) {
@ -564,10 +570,10 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
}
for (ConceptSetComponent vsi : valueset.getCompose().getExclude()) {
Boolean nok = inComponent(vsi, system, code, valueset.getCompose().getInclude().size() == 1);
Boolean nok = inComponent(vsi, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
if (nok == null && result == false) {
result = null;
} else if (nok) {
} else if (nok != null && nok) {
result = false;
}
}
@ -576,7 +582,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
return result;
}
private Boolean inComponent(ConceptSetComponent vsi, String system, String code, boolean only) throws FHIRException {
private Boolean inComponent(ConceptSetComponent vsi, String system, String code, boolean only, List<String> warnings) throws FHIRException {
for (UriType uri : vsi.getValueSet()) {
if (inImport(uri.getValue(), system, code)) {
return true;
@ -607,6 +613,9 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
vs.getCompose().addInclude(vsi);
ValidationResult res = context.validateCode(options.noClient(), new Coding(system, code, null), vs);
if (res.getErrorClass() == TerminologyServiceErrorClass.UNKNOWN || res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED || res.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNSUPPORTED) {
if (warnings != null) {
warnings.add(context.formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system));
}
return null;
}
if (res.getErrorClass() == TerminologyServiceErrorClass.NOSERVICE) {
@ -705,7 +714,13 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
private boolean inImport(String uri, String system, String code) throws FHIRException {
return getVs(uri).codeInValueSet(system, code);
ValueSetCheckerSimple vs = getVs(uri);
if (vs == null) {
return false;
} else {
Boolean ok = vs.codeInValueSet(system, code, null);
return ok != null && ok;
}
}
}

2
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -603,7 +603,7 @@ BUNDLE_RULE_NONE = No Rule
BUNDLE_RULE_UNKNOWN = Bundle Rule refers to invalid resource {0}
BUNDLE_RULE_INVALID_INDEX = Bundle Rules index is invalid ({0})
BUNDLE_RULE_PROFILE_UNKNOWN = Bundle Rules profile {1} is unknown for {0}
UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_ = Unable to determine whether the provided codes are in the value set {0} because the value set or code system is not known to the validator
UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_ = Unable to determine whether the provided codes are in the value set {0} because the value set or a code system it depends on is not known to the validator
TERMINOLOGY_TX_SYSTEM_WRONG_HTML = The code system reference {0} is wrong - the code system reference cannot be to an HTML page. This may be the correct reference: {1}
TERMINOLOGY_TX_SYSTEM_WRONG_BUILD = The code system reference {0} is wrong - the code system reference cannot be a reference to build.fhir.org. This may be the correct reference: {1}
FHIRPATH_BAD_DATE = Unable to parse Date {0}