honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fix handling of Coding Validation when code system is unknown

This commit is contained in:
Grahame Grieve 2022-10-05 21:16:57 +11:00
parent e74c4c98fa
commit 21848fc9af
5 changed files with 54 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
org.hl7.fhir.core.generator/configuration/CodeableConcept.java
View File

@ -94,3 +94,8 @@ public boolean hasCoding(String system, String code) {
getCoding().add(new Coding(system, code, display));
}
@Override
public String toString() {
return hasCoding() ? getCoding().toString() : "["+getText()+"]";
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
View File

@ -365,11 +365,12 @@ public class XmlParser extends ParserBase {
} else
ok = ok || (attr.getLocalName().equals("schemaLocation")); // xsi:schemalocation allowed for non FHIR content
ok = ok || (hasTypeAttr(element) && attr.getLocalName().equals("type") && FormatUtilities.NS_XSI.equals(attr.getNamespaceURI())); // xsi:type allowed if element says so
if (!ok)
if (!ok) {
logError(line(node, false), col(node, false), path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.UNDEFINED_ATTRIBUTE__ON__FOR_TYPE__PROPERTIES__, attr.getNodeName(), node.getNodeName(), element.fhirType(), properties), IssueSeverity.ERROR);
}
}
}
}
String lastName = null;
int repeatCount = 0;

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeableConcept.java
View File

@ -405,6 +405,11 @@ public boolean hasCoding(String system, String code) {
getCoding().add(new Coding(system, code, display));
}
@Override
public String toString() {
return hasCoding() ? getCoding().toString() : "["+getText()+"]";
}
// end addition
}

17
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetChecker.java
View File

@ -1,5 +1,6 @@
package org.hl7.fhir.r5.terminologies;
import java.util.ArrayList;
import java.util.List;
/*
@ -34,10 +35,24 @@ import java.util.List;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ETooCostly;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.EOperationOutcome;
public interface ValueSetChecker {
Boolean codeInValueSet(String system, String code, List<String> warnings) throws ETooCostly, EOperationOutcome, Exception;
public static class ValidationProcessInfo {
private TerminologyServiceErrorClass err;
private List<String> warnings = new ArrayList<>();
public TerminologyServiceErrorClass getErr() {
return err;
}
public void setErr(TerminologyServiceErrorClass err) {
this.err = err;
}
public List<String> getWarnings() {
return warnings;
}
}
Boolean codeInValueSet(String system, String code, ValidationProcessInfo info) throws ETooCostly, EOperationOutcome, Exception;
}

43
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -61,6 +61,7 @@ import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceDesignationComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetChecker.ValidationProcessInfo;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
@ -129,11 +130,11 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
public ValidationResult validateCode(CodeableConcept code) throws FHIRException {
// first, we validate the codings themselves
List<String> errors = new ArrayList<String>();
List<String> warnings = new ArrayList<String>();
ValidationProcessInfo info = new ValidationProcessInfo();
if (options.getValueSetMode() != ValueSetMode.CHECK_MEMERSHIP_ONLY) {
for (Coding c : code.getCoding()) {
if (!c.hasSystem()) {
warnings.add(context.formatMessage(I18nConstants.CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE));
info.getWarnings().add(context.formatMessage(I18nConstants.CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE));
}
CodeSystem cs = resolveCodeSystem(c.getSystem());
ValidationResult res = null;
@ -145,7 +146,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
if (!res.isOk()) {
errors.add(res.getMessage());
} else if (res.getMessage() != null) {
warnings.add(res.getMessage());
info.getWarnings().add(res.getMessage());
}
}
}
@ -153,7 +154,7 @@ 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(), warnings);
Boolean ok = codeInValueSet(c.getSystem(), c.getCode(), info);
if (ok == null && result == false) {
result = null;
} else if (ok) {
@ -162,15 +163,15 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
}
if (result == null) {
warnings.add(0, context.formatMessage(I18nConstants.UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));
info.getWarnings().add(0, context.formatMessage(I18nConstants.UNABLE_TO_CHECK_IF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));
} else if (!result) {
errors.add(0, context.formatMessage(I18nConstants.NONE_OF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getUrl()));
}
}
if (errors.size() > 0) {
return new ValidationResult(IssueSeverity.ERROR, errors.toString());
} else if (warnings.size() > 0) {
return new ValidationResult(IssueSeverity.WARNING, warnings.toString());
} else if (info.getWarnings().size() > 0) {
return new ValidationResult(IssueSeverity.WARNING, info.getWarnings().toString());
} else {
ConceptDefinitionComponent cd = new ConceptDefinitionComponent(foundCoding.getCode());
cd.setDisplay(foundCoding.getDisplay());
@ -251,19 +252,24 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
inInclude = checkInclude(code);
}
List<String> warnings = new ArrayList<>();
ValidationProcessInfo info = new ValidationProcessInfo();
// 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(), warnings);
Boolean ok = codeInValueSet(system, code.getCode(), info);
if (ok == null || !ok) {
if (res == null) {
res = new ValidationResult((IssueSeverity) null, null);
}
if (!inExpansion && !inInclude) {
if (warnings != null) {
res.setMessage("Not in value set "+valueset.getUrl()+" ("+warnings+")").setSeverity(IssueSeverity.ERROR);
if (info.getErr() != null) {
res.setErrorClass(info.getErr());
}
if (ok == null) {
res.setMessage("Unable to check whether code is in value set "+valueset.getUrl()+": "+info.getWarnings()).setSeverity(IssueSeverity.WARNING);
} else if (!inExpansion && !inInclude) {
if (!info.getWarnings().isEmpty()) {
res.setMessage("Not in value set "+valueset.getUrl()+": "+info.getWarnings()).setSeverity(IssueSeverity.ERROR);
} else {
res.setMessage("Not in value set "+valueset.getUrl()).setSeverity(IssueSeverity.ERROR);
}
@ -640,7 +646,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
@Override
public Boolean codeInValueSet(String system, String code, List<String> warnings) throws FHIRException {
public Boolean codeInValueSet(String system, String code, ValidationProcessInfo info) throws FHIRException {
if (valueset == null) {
return false;
}
@ -651,7 +657,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
} else if (valueset.hasCompose()) {
int i = 0;
for (ConceptSetComponent vsi : valueset.getCompose().getInclude()) {
Boolean ok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
Boolean ok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, info);
i++;
if (ok == null && result == false) {
result = null;
@ -662,7 +668,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
}
i = valueset.getCompose().getInclude().size();
for (ConceptSetComponent vsi : valueset.getCompose().getExclude()) {
Boolean nok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, warnings);
Boolean nok = inComponent(vsi, i, system, code, valueset.getCompose().getInclude().size() == 1, info);
i++;
if (nok == null && result == false) {
result = null;
@ -675,7 +681,7 @@ public class ValueSetCheckerSimple extends ValueSetWorker implements ValueSetChe
return result;
}
private Boolean inComponent(ConceptSetComponent vsi, int vsiIndex, String system, String code, boolean only, List<String> warnings) throws FHIRException {
private Boolean inComponent(ConceptSetComponent vsi, int vsiIndex, String system, String code, boolean only, ValidationProcessInfo info) throws FHIRException {
boolean ok = true;
if (vsi.hasValueSet()) {
@ -721,8 +727,9 @@ 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 && res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
warnings.add(context.formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system));
if (info != null && res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED) {
info.getWarnings().add(context.formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, system));
info.setErr(TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED);
}
return null;
}