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beef up validation of CodeSystem properties that are codes

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This commit is contained in:
Grahame Grieve 2025-01-09 17:08:28 +11:00
parent a0a6e1b65a
commit 8f6f75f4bf
5 changed files with 147 additions and 23 deletions
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8
org.hl7.fhir.utilities/src/main/resources/Messages.properties
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@ -1207,3 +1207,11 @@ EXTENSION_FHIR_VERSION_LATEST = The definition of the extension ''{0}'' specifie
VALUESET_INCLUDE_WRONG_VS = The system ''{0}'' is actually a value set
VALUESET_INCLUDE_WRONG_VS_HINT = The system ''{0}'' is actually a value set, which itself refers to the system ''{1}'' so that may be what is intended here
VALUESET_INCLUDE_WRONG_VS_MANY = The system ''{0}'' is actually a value set, which itself refers to the systems {1}
CODESYSTEM_PROPERTY_URI_UNKNOWN = The property uri ''{0}'' is not known, so the property values can not be validated fully
CODESYSTEM_PROPERTY_URI_UNKNOWN_TYPE = The property uri ''{0}'' is not known, so the property values can not be validated fully; unless specified elsewhere, codes will be treated as internal references
CODESYSTEM_PROPERTY_URI_UNKNOWN_BASE = The base property uri ''{0}'' is not known, so the property values can not be validated fully
CODESYSTEM_PROPERTY_URI_INVALID = The code ''{0}'' in the CodeSystem {2} for uri ''{1}'' is not valid
CODESYSTEM_PROPERTY_CODE_DEFAULT_WARNING = The type is ''code'', but no ValueSet information was found, so the codes will be validated as internal codes
CODESYSTEM_PROPERTY_VALUESET_NOT_FOUND = The ValueSet {0} is unknown, so the property codes cannot be validated
CODESYSTEM_PROPERTY_BAD_INTERNAL_REFERENCE = The code ''{0}'' is not a valid code in this code system
CODESYSTEM_PROPERTY_BAD_PROPERTY_CODE = The code ''{0}'' is not a valid code in the value set ''{1}''

15
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -7503,9 +7503,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (!Utilities.noString(msg)) {
msg = msg + " (log: " + msg + ")";
}
String msgId = null;
if (inv.hasSource()) {
msg = context.formatMessage(I18nConstants.INV_FAILED_SOURCE, inv.getKey() + ": '" + inv.getHuman()+"'", inv.getSource())+msg;
msg = context.formatMessage(I18nConstants.INV_FAILED_SOURCE, inv.getKey() + ": '" + inv.getHuman()+"'", inv.getSource())+msg;
msgId = inv.getSource()+"#"+inv.getKey();
} else {
msgId = profile.getUrl()+"#"+inv.getKey();
msg = context.formatMessage(I18nConstants.INV_FAILED, inv.getKey() + ": '" + inv.getHuman()+"'")+msg;
}
String invId = (inv.hasSource() ? inv.getSource() : profile.getUrl()) + "#"+inv.getKey();
@ -7514,15 +7517,15 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
ToolingExtensions.readBooleanExtension(inv, ToolingExtensions.EXT_BEST_PRACTICE)) {
msg = msg +" (Best Practice Recommendation)";
if (bpWarnings == BestPracticeWarningLevel.Hint)
hintInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId);
hintInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId, msgId);
else if (/*bpWarnings == null || */ bpWarnings == BestPracticeWarningLevel.Warning)
warningInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId);
warningInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId, msgId);
else if (bpWarnings == BestPracticeWarningLevel.Error)
ok = ruleInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId) && ok;
ok = ruleInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId, msgId) && ok;
} else if (inv.getSeverity() == ConstraintSeverity.ERROR) {
ok = ruleInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId) && ok;
ok = ruleInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId, msgId) && ok;
} else if (inv.getSeverity() == ConstraintSeverity.WARNING) {
warningInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId);
warningInv(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, invOK, msg, invId, msgId);
}
}
return ok;

124
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/CodeSystemValidator.java
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@ -8,11 +8,14 @@ import java.util.Map;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.codesystems.CodesystemAltcodeKind;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
import org.hl7.fhir.utilities.CanonicalPair;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
@ -21,6 +24,7 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.cli.model.ValidationOutcome;
import org.hl7.fhir.validation.instance.type.CodeSystemValidator.KnownProperty;
import org.hl7.fhir.validation.instance.type.CodeSystemValidator.PropertyDef;
import org.hl7.fhir.validation.instance.utils.NodeStack;
@ -60,7 +64,7 @@ public class CodeSystemValidator extends BaseValidator {
}
public enum CodeValidationRule {
NO_VALIDATION, INTERNAL_CODE, VS_ERROR, VS_WARNING
NO_VALIDATION, INTERNAL_CODE, INTERNAL_CODE_WARNING, VS_ERROR, VS_WARNING
}
public class PropertyDef {
@ -69,7 +73,7 @@ public class CodeSystemValidator extends BaseValidator {
private String type;
private CodeValidationRule rule;
private String valueset;
private ValueSet valueset;
protected PropertyDef(String uri, String code, String type) {
super();
@ -78,7 +82,7 @@ public class CodeSystemValidator extends BaseValidator {
this.type = type;
}
public void setCodeValidationRules(CodeValidationRule rule, String valueset) {
public void setCodeValidationRules(CodeValidationRule rule, ValueSet valueset) {
this.rule = rule;
this.valueset = valueset;
}
@ -92,13 +96,18 @@ public class CodeSystemValidator extends BaseValidator {
public String getType() {
return type;
}
public String getValueset() {
public ValueSet getValueset() {
return valueset;
}
public CodeValidationRule getRule() {
return rule;
}
}
private static final String VS_PROP_STATUS = null;
private Set<String> propertyCodes = new HashSet<String>();
public CodeSystemValidator(BaseValidator parent) {
super(parent);
@ -237,11 +246,48 @@ public class CodeSystemValidator extends BaseValidator {
PropertyDef pd = new PropertyDef(uri, code, type);
KnownProperty ukp = null;
KnownProperty ckp = null;
boolean foundPropDefn = false;
CodeValidationRule ruleFromUri = CodeValidationRule.INTERNAL_CODE_WARNING;
String valuesetFromUri = null;
if (uri != null) {
if (rule(errors, "2024-03-06", IssueType.BUSINESSRULE, cs.line(), cs.col(), stack.getLiteralPath(), Utilities.isAbsoluteUrl(uri), I18nConstants.CODESYSTEM_PROPERTY_ABSOLUTE_URI, uri)) {
if (rule(errors, "2024-03-06", IssueType.BUSINESSRULE, cs.line(), cs.col(), stack.getLiteralPath(), !properties.containsKey(uri), I18nConstants.CODESYSTEM_PROPERTY_DUPLICATE_URI, uri)) {
properties.put(uri, pd);
if (uri.contains("#")) {
String base = uri.substring(0, uri.indexOf("#"));
String pcode = uri.substring(uri.indexOf("#")+1);
CodeSystem pcs = context.findTxResource(CodeSystem.class, base);
if (pcs == null) {
warning(errors, "2025-01-09", IssueType.NOTFOUND, cs.line(), cs.col(), stack.getLiteralPath(), false, I18nConstants.CODESYSTEM_PROPERTY_URI_UNKNOWN_BASE, base);
} else {
ConceptDefinitionComponent cc = CodeSystemUtilities.findCode(pcs.getConcept(), pcode);
if (rule(errors, "2025-01-09", IssueType.INVALID, cs.line(), cs.col(), stack.getLiteralPath(), cc != null, I18nConstants.CODESYSTEM_PROPERTY_URI_INVALID, pcode, base, pcs.present())) {
foundPropDefn = true;
if ("code".equals(type)) {
ConceptPropertyComponent ccp = CodeSystemUtilities.getProperty(cc, "binding");
if (ccp != null && ccp.hasValue() && ccp.getValue().hasPrimitiveValue()) {
ruleFromUri = CodeValidationRule.VS_ERROR;
valuesetFromUri = ccp.getValue().primitiveValue();
} else {
ruleFromUri = CodeValidationRule.INTERNAL_CODE_WARNING;
}
}
} else {
ok = false;
if ("code".equals(type)) {
ruleFromUri = CodeValidationRule.INTERNAL_CODE_WARNING;
}
}
}
} else {
if ("code".equals(type)) {
warning(errors, "2025-01-09", IssueType.NOTFOUND, cs.line(), cs.col(), stack.getLiteralPath(), false, I18nConstants.CODESYSTEM_PROPERTY_URI_UNKNOWN_TYPE, uri);
} else {
hint(errors, "2025-01-09", IssueType.NOTFOUND, cs.line(), cs.col(), stack.getLiteralPath(), false, I18nConstants.CODESYSTEM_PROPERTY_URI_UNKNOWN, uri);
}
}
} else {
ok = false;
}
@ -352,21 +398,26 @@ public class CodeSystemValidator extends BaseValidator {
pd.setCodeValidationRules(CodeValidationRule.INTERNAL_CODE, null);
break;
case Status:
pd.setCodeValidationRules(CodeValidationRule.VS_WARNING, VS_PROP_STATUS);
pd.setCodeValidationRules(CodeValidationRule.VS_WARNING, findVS(errors, cs, stack, VS_PROP_STATUS, I18nConstants.CODESYSTEM_PROPERTY_VALUESET_NOT_FOUND));
break;
default:
break;
}
} else if ("code".equals(pd.getType())) {
if (property.hasExtension("http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet")) {
pd.setCodeValidationRules(CodeValidationRule.VS_ERROR, property.getExtensionValue("http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet").primitiveValue());
if (property.hasExtension("http://hl7.org/fhir/StructureDefinition/codesystem-property-valueset", "http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet")) {
pd.setCodeValidationRules(CodeValidationRule.VS_ERROR, findVS(errors, cs, stack,
property.getExtensionValue("http://hl7.org/fhir/StructureDefinition/codesystem-property-valueset", "http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet").primitiveValue(),
I18nConstants.CODESYSTEM_PROPERTY_VALUESET_NOT_FOUND));
} else if (foundPropDefn && valuesetFromUri != null) {
pd.setCodeValidationRules(ruleFromUri, findVS(errors, cs, stack, valuesetFromUri, I18nConstants.CODESYSTEM_PROPERTY_VALUESET_NOT_FOUND));
} else if (VersionUtilities.isR6Plus(context.getVersion())) {
hint(errors, "2024-03-18", IssueType.BUSINESSRULE, cs.line(), cs.col(), stack.getLiteralPath(), ukp != null && type.equals(ukp.getType()), I18nConstants.CODESYSTEM_PROPERTY_CODE_WARNING);
} else {
pd.setCodeValidationRules(ruleFromUri, null);
hint(errors, "2025-01-09", IssueType.BUSINESSRULE, cs.line(), cs.col(), stack.getLiteralPath(), false, I18nConstants.CODESYSTEM_PROPERTY_CODE_DEFAULT_WARNING);
}
} else if ("Coding".equals(pd.getType()) && property.hasExtension("http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet")) {
pd.setCodeValidationRules(CodeValidationRule.VS_ERROR, property.getExtensionValue("http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet").primitiveValue());
} else if ("Coding".equals(pd.getType()) && property.hasExtension("http://hl7.org/fhir/StructureDefinition/codesystem-property-valueset", "http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet")) {
pd.setCodeValidationRules(CodeValidationRule.VS_ERROR, findVS(errors, cs, stack, property.getExtensionValue("http://hl7.org/fhir/StructureDefinition/codesystem-property-valueset", "http://hl7.org/fhir/6.0/StructureDefinition/extension-CodeSystem.property.valueSet").primitiveValue(), I18nConstants.CODESYSTEM_PROPERTY_VALUESET_NOT_FOUND));
}
if (uri == null) {
@ -382,6 +433,18 @@ public class CodeSystemValidator extends BaseValidator {
return ok;
}
private ValueSet findVS(List<ValidationMessage> errors, Element cs, NodeStack stack, String url, String message) {
if (url == null) {
return null;
} else {
ValueSet vs = context.findTxResource(ValueSet.class, url);
if (vs != null) {
warning(errors, "2025-01-09", IssueType.NOTFOUND, cs.line(), cs.col(), stack.getLiteralPath(), false, message, url);
}
return vs;
}
}
private boolean isBaseSpec(String url) {
return url.startsWith("http://hl7.org/fhir/") && !url.substring(20).contains("/");
}
@ -480,7 +543,9 @@ public class CodeSystemValidator extends BaseValidator {
if (rule(errors, "2024-03-06", IssueType.BUSINESSRULE, cs.line(), cs.col(), stack.getLiteralPath(), defn != null, I18nConstants.CODESYSTEM_PROPERTY_UNDEFINED, code) &&
rule(errors, "2024-03-06", IssueType.BUSINESSRULE, cs.line(), cs.col(), stack.getLiteralPath(), value != null, I18nConstants.CODESYSTEM_PROPERTY_NO_VALUE, code) &&
rule(errors, "2024-03-06", IssueType.BUSINESSRULE, cs.line(), cs.col(), stack.getLiteralPath(), value.fhirType().equals(defn.type), I18nConstants.CODESYSTEM_PROPERTY_WRONG_TYPE, code, value.fhirType(), defn.type)) {
// nothing?
if ("code".equals(value.fhirType())) {
checkCodeProperty(errors, cs, stack, defn, value.primitiveValue(), codes);
}
} else {
ok = false;
}
@ -492,6 +557,43 @@ public class CodeSystemValidator extends BaseValidator {
return ok;
}
private void checkCodeProperty(List<ValidationMessage> errors, Element cs, NodeStack stack, PropertyDef defn, String code, Set<String> codes) {
switch (defn.getRule()) {
case INTERNAL_CODE:
if (!isSeenPropertyCode(defn, code)) {
rule(errors, "2025-01-09", IssueType.INVALID, cs.line(), cs.col(), stack.getLiteralPath(), codes.contains(code), I18nConstants.CODESYSTEM_PROPERTY_BAD_INTERNAL_REFERENCE, code);
}
break;
case INTERNAL_CODE_WARNING:
if (!isSeenPropertyCode(defn, code)) {
warning(errors, "2025-01-09", IssueType.INVALID, cs.line(), cs.col(), stack.getLiteralPath(), codes.contains(code), I18nConstants.CODESYSTEM_PROPERTY_BAD_INTERNAL_REFERENCE, code);
}
break;
case VS_ERROR:
if (defn.getValueset() != null && !isSeenPropertyCode(defn, code)) {
ValidationResult vo = context.validateCode(baseOptions, code, defn.getValueset());
rule(errors, "2025-01-09", IssueType.INVALID, cs.line(), cs.col(), stack.getLiteralPath(), vo.isOk(), I18nConstants.CODESYSTEM_PROPERTY_BAD_PROPERTY_CODE, code);
}
break;
case VS_WARNING:
if (defn.getValueset() != null && !isSeenPropertyCode(defn, code)) {
ValidationResult vo = context.validateCode(baseOptions, code, defn.getValueset());
warning(errors, "2025-01-09", IssueType.INVALID, cs.line(), cs.col(), stack.getLiteralPath(), vo.isOk(), I18nConstants.CODESYSTEM_PROPERTY_BAD_PROPERTY_CODE, code, defn.getValueset().getVersionedUrl());
}
break;
default:
case NO_VALIDATION:
break;
}
}
private boolean isSeenPropertyCode(PropertyDef defn, String code) {
String key = defn.getValueset() != null ? defn.getValueset().getVersionedUrl()+"#"+code : "null#"+code;
boolean isnew = propertyCodes.contains(key);
propertyCodes.add(key);
return isnew;
}
private boolean checkShareableCodeSystem(List<ValidationMessage> errors, Element cs, NodeStack stack) {
if (parent.isForPublication()) {
if (isHL7(cs)) {

19
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/vs-externals.json
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@ -1,17 +1,24 @@
{
"http://fhir.abda.de/eRezeptAbgabedaten/ValueSet/DAV-VS-ERP-DEUEV-Anlage-8" : null,
"http://loinc.org/vs/LL378-1" : null,
"http://loinc.org|2.76" : null,
"http://www.rfc-editor.org/bcp/bcp13.txt" : null,
"http://loinc.org/vs/LL1971-2" : null,
"#f3b2bd36-199b-4591-b4db-f49db0912b6|null" : null,
"#c1|null" : null,
"http://hl7.org/fhir/us/davinci-hrex/ValueSet/hrex-endpoint-name" : null,
"http://fhir.ch/ig/ch-ig/ValueSet/ch-ig-example" : null,
"http://hl7.org/fhir/us/qicore/ValueSet/qicore-negation-reason" : null,
"http://fhir.ch/ig/ch-ig/ValueSet/OrganizationType" : null,
"https://fhir.kbv.de/ValueSet/KBV_VS_SFHIR_ICD_SEITENLOKALISATION" : null,
"http://fhir.abda.de/eRezeptAbgabedaten/ValueSet/DAV-VS-ERP-DEUEV-Anlage-8" : null,
"http://loinc.org/vs/LL378-1" : null,
"http://something/something|null" : null,
"http://hl7.org/fhir/CodeSystem/c1|null" : null,
"http://hl7.org/fhir/uv/sdc/CodeSystem/CSPHQ9|null" : null,
"http://loinc.org/vs/LL1971-2" : null,
"#f3b2bd36-199b-4591-b4db-f49db0912b62|null" : null,
"http://hl7.org/fhir/smart-app-launch/ValueSet/user-access-category" : null,
"https://healthterminologies.gov.au/fhir/ValueSet/australian-immunisation-register-vaccine-1" : {
"server" : "https://tx.ontoserver.csiro.au/fhir",
"filename" : "vs-0ce1569f-f985-44cb-a5a0-9d205efd76b4.json"
},
"http://fhir.ch/ig/ch-ig/ValueSet/OrganizationType" : null,
"http://loinc.org/vs/LL4048-6" : null,
"https://fhir.kbv.de/ValueSet/KBV_VS_SFHIR_ICD_SEITENLOKALISATION" : null
"http://loinc.org/vs/LL4048-6" : null
}

4
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/5.0.0/vs-externals.json
View File

@ -1,8 +1,12 @@
{
"http://hl7.org/fhir/ValueSet/ucum-vitals-common|4.0.0" : null,
"http://loinc.org/vs" : null,
"#cs1|null" : null,
"#cs|null" : null,
"http://hl7.org.au/fhir/ValueSet/au-hl7v2-0203" : null,
"http://hl7.org/fhir/ValueSet/name-use|4.0.1" : null,
"http://something|null" : null,
"http://snomed.info/sct|null" : null,
"http://hl7.org/fhir/ValueSet/observation-status|4.0.0" : null,
"http://hl7.org/fhir/ValueSet/identifier-use|4.0.1" : null,
"http://snomed.info/sct?fhir_vs" : null