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Merge pull request #940 from hapifhir/gg-202210-coding-validation

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Gg 202210 coding validation
This commit is contained in:
Grahame Grieve 2022-10-05 23:20:52 +11:00 committed by GitHub
commit 53c65d857b
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GPG Key ID: 4AEE18F83AFDEB23
14 changed files with 206 additions and 58 deletions
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7
org.hl7.fhir.core.generator/configuration/CodeableConcept.java
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@ -93,4 +93,9 @@ public boolean hasCoding(String system, String code) {
public void addCoding(String system, String code, String display) {
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

@ -365,8 +365,9 @@ 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);
}
}
}
}

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

@ -404,6 +404,11 @@ public boolean hasCoding(String system, String code) {
public void addCoding(String system, String code, String display) {
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
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@ -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;
}

13
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -4503,7 +4503,18 @@ public class FHIRPathEngine {
return makeBoolean(false);
}
} else if (ns.equals("FHIR")) {
return makeBoolean(n.equals(focus.get(0).fhirType()));
if (n.equals(focus.get(0).fhirType())) {
return makeBoolean(true);
} else {
StructureDefinition sd = worker.fetchTypeDefinition(focus.get(0).fhirType());
while (sd != null) {
if (n.equals(sd.getType())) {
return makeBoolean(true);
}
sd = worker.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return makeBoolean(false);
}
} else {
return makeBoolean(false);
}

20
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLSchemaGenerator.java
View File

@ -103,6 +103,9 @@ public class GraphQLSchemaGenerator {
if (sd.getKind() == StructureDefinitionKind.COMPLEXTYPE && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
tl.put(sd.getName(), sd);
}
if (sd.getKind() == StructureDefinitionKind.RESOURCE && sd.getDerivation() != TypeDerivationRule.CONSTRAINT && sd.getAbstract()) {
tl.put(sd.getName(), sd);
}
}
writer.write("# FHIR GraphQL Schema. Version " + version + "\r\n\r\n");
writer.write("# FHIR Defined Primitive types\r\n");
@ -290,16 +293,17 @@ public class GraphQLSchemaGenerator {
}
private void generateType(Map<String, String> existingTypeNames, Writer writer, StructureDefinition sd, EnumSet<FHIROperationType> operations) throws IOException {
if (sd.getAbstract()) {
return;
}
if (operations.contains(FHIROperationType.READ) || operations.contains(FHIROperationType.SEARCH)) {
List<StringBuilder> list = new ArrayList<>();
StringBuilder b = new StringBuilder();
list.add(b);
b.append("type ");
b.append(sd.getName());
StructureDefinition sdp = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
if (sdp != null) {
b.append(" implements ");
b.append(sdp.getType());
}
b.append(" {\r\n");
ElementDefinition ed = sd.getSnapshot().getElementFirstRep();
generateProperties(existingTypeNames, list, b, sd.getName(), sd, ed, "type", "");
@ -370,7 +374,13 @@ public class GraphQLSchemaGenerator {
if (suffix)
b.append(Utilities.capitalize(typeDetails.getWorkingCode()));
b.append(": ");
b.append(n);
if (!child.getMax().equals("1")) {
b.append("[");
b.append(n);
b.append("]");
} else {
b.append(n);
}
if (!child.getPath().endsWith(".id")) {
b.append(" _");
b.append(tail(child.getPath(), suffix));

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ToolingExtensions.java
View File

@ -205,6 +205,7 @@ public class ToolingExtensions {
public static final String EXT_REND_MD = "http://hl7.org/fhir/StructureDefinition/rendering-markdown";
public static final String EXT_CAP_STMT_EXPECT = "http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation";
public static final String EXT_ED_HEIRARCHY = "http://hl7.org/fhir/StructureDefinition/elementdefinition-heirarchy";
public static final String EXT_SD_DEPENDENCY = "http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies";
// in the tooling IG
public static final String EXT_BINDING_ADDITIONAL = "http://hl7.org/fhir/tools/StructureDefinition/additional-binding";

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -611,6 +611,7 @@ public class I18nConstants {
public static final String VALIDATION_VAL_PROFILE_SIGNPOST = "VALIDATION_VAL_PROFILE_SIGNPOST";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL = "VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_META = "VALIDATION_VAL_PROFILE_SIGNPOST_META";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_DEP = "VALIDATION_VAL_PROFILE_SIGNPOST_DEP";
public static final String VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM = "VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM";
public static final String VALIDATION_VAL_PROFILE_SLICEORDER = "Validation_VAL_Profile_SliceOrder";
public static final String VALIDATION_VAL_PROFILE_OTHER_VERSION = "VALIDATION_VAL_PROFILE_OTHER_VERSION";
@ -622,6 +623,7 @@ public class I18nConstants {
public static final String VALIDATION_VAL_PROFILE_WRONGTYPE = "Validation_VAL_Profile_WrongType";
public static final String VALIDATION_VAL_PROFILE_WRONGTYPE2 = "Validation_VAL_Profile_WrongType2";
public static final String VALIDATION_VAL_UNKNOWN_PROFILE = "Validation_VAL_Unknown_Profile";
public static final String VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED = "VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED";
public static final String VALUESET_INCLUDE_INVALID_CONCEPT_CODE = "VALUESET_INCLUDE_INVALID_CONCEPT_CODE";
public static final String VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER = "VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER";

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

@ -236,6 +236,7 @@ Validation_VAL_Profile_Unknown = Profile reference ''{0}'' has not been checked
VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY = Profile reference ''{0}'' has not been checked because it is unknown, and the validator is set to not fetch unknown profiles
VALIDATION_VAL_PROFILE_UNKNOWN_ERROR = Profile reference ''{0}'' has not been checked because it is unknown, and fetching it resulted in the error {1}
Validation_VAL_Unknown_Profile = Unknown profile {0}
VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED = Profile {1} identifies {2} as a dependency (using the extension http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies), but this profile could not be found
XHTML_XHTML_Attribute_Illegal = Illegal attribute name in the XHTML (''{0}'' on ''{1}'')
XHTML_XHTML_Element_Illegal = Illegal element name in the XHTML (''{0}'')
XHTML_XHTML_NS_InValid = Wrong namespace on the XHTML (''{0}'', should be ''{1}'')
@ -536,6 +537,7 @@ VALIDATION_VAL_GLOBAL_PROFILE_UNKNOWN = Global Profile reference ''{0}'' from IG
VALIDATION_VAL_PROFILE_SIGNPOST_BASE = Validate resource against profile
VALIDATION_VAL_PROFILE_SIGNPOST = Validate resource against profile {0}
VALIDATION_VAL_PROFILE_SIGNPOST_META = Validate resource against profile {0} (per meta)
VALIDATION_VAL_PROFILE_SIGNPOST_DEP = Validate resource against profile {0} (per http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies in {1})
VALIDATION_VAL_PROFILE_SIGNPOST_BUNDLE_PARAM = Validate resource against profile {0} - provided as bundle param
VALIDATION_VAL_PROFILE_SIGNPOST_GLOBAL = Validate resource against profile {0} - a global profile in {1}
ERROR_GENERATING_SNAPSHOT = Error generating Snapshot: {0} (this usually arises from a problem in the differential)

100
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -818,15 +818,31 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
setParents(element);
long t = System.nanoTime();
NodeStack stack = new NodeStack(context, path, element, validationLanguage);
if (profiles == null || profiles.isEmpty()) {
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, new NodeStack(context, path, element, validationLanguage).resetIds(), null);
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, stack.resetIds(), null);
} else {
int i = 0;
while (i < profiles.size()) {
StructureDefinition sd = profiles.get(i);
if (sd.hasExtension(ToolingExtensions.EXT_SD_DEPENDENCY)) {
for (Extension ext : sd.getExtensionsByUrl(ToolingExtensions.EXT_SD_DEPENDENCY)) {
StructureDefinition dep = context.fetchResource( StructureDefinition.class, ext.getValue().primitiveValue());
if (dep == null) {
warning(errors, IssueType.BUSINESSRULE, element.line(), element.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED, ext.getValue().primitiveValue(), sd.getUrl());
} else if (!profiles.contains(dep)) {
profiles.add(dep);
}
}
}
i++;
}
for (StructureDefinition defn : profiles) {
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, new NodeStack(context, path, element, validationLanguage).resetIds(), null);
validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, stack.resetIds(), null);
}
}
if (hintAboutNonMustSupport) {
checkElementUsage(errors, element, new NodeStack(context, path, element, validationLanguage));
checkElementUsage(errors, element, stack);
}
errors.removeAll(messagesToRemove);
timeTracker.overall(t);
@ -1217,7 +1233,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
checkBindings(errors, path, element, stack, valueset, nextCoding);
}
}
timeTracker.tx(t, "vc "+DataRenderer.display(context, cc));
timeTracker.tx(t, "vc "+cc.toString());
}
}
} catch (Exception e) {
@ -1692,6 +1708,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOVALID_14, describeReference(binding.getValueSet(), valueset), getErrorMessage(vr.getMessage()), theSystem+"#"+theCode);
}
}
} else if (vr != null && vr.getMessage() != null) {
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage());
}
} catch (Exception e) {
if (STACK_TRACE) e.printStackTrace();
@ -3713,7 +3731,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
private String getErrorMessage(String message) {
return message != null ? " (error message = " + message + ")" : "";
return message != null ? " (error message = " + message + ")" : "";
}
public boolean isSuppressLoincSnomedMessages() {
@ -4517,28 +4535,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (!fetcher.fetchesCanonicalResource(this, profile.primitiveValue())) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY, profile.primitiveValue());
} else {
sd = null;
String url = profile.primitiveValue();
CanonicalResourceLookupResult cr = crLookups.get(url);
if (cr != null) {
if (cr.error != null) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, url, cr.error);
} else {
sd = (StructureDefinition) cr.resource;
}
} else {
try {
sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, url);
crLookups.put(url, new CanonicalResourceLookupResult(sd));
} catch (Exception e) {
if (STACK_TRACE) { e.printStackTrace(); }
crLookups.put(url, new CanonicalResourceLookupResult(e.getMessage()));
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());
}
if (sd != null) {
context.cacheResource(sd);
}
}
sd = lookupProfileReference(errors, element, stack, i, profile, sd);
}
}
if (sd != null) {
@ -4553,6 +4550,27 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (pctOwned) {
pct.done();
}
if (sd.hasExtension(ToolingExtensions.EXT_SD_DEPENDENCY)) {
for (Extension ext : sd.getExtensionsByUrl(ToolingExtensions.EXT_SD_DEPENDENCY)) {
StructureDefinition sdi = context.fetchResource(StructureDefinition.class, ext.getValue().primitiveValue());
if (sdi == null) {
warning(errors, IssueType.BUSINESSRULE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED, ext.getValue().primitiveValue(), sd.getUrl());
} else {
if (crumbTrails) {
element.addMessage(signpost(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), I18nConstants.VALIDATION_VAL_PROFILE_SIGNPOST_DEP, sdi.getUrl(), sd.getUrl()));
}
stack.resetIds();
if (pctOwned) {
pct = new PercentageTracker(resource.countDescendents(), resource.fhirType(), sdi.getUrl(), logProgress);
}
startInner(hostContext, errors, resource, element, sdi, stack, false, pct);
if (pctOwned) {
pct.done();
}
}
}
}
}
}
}
@ -4583,6 +4601,32 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
// System.out.println("start: "+(System.currentTimeMillis()-st)+" ("+resource.fhirType()+")");
}
private StructureDefinition lookupProfileReference(List<ValidationMessage> errors, Element element, NodeStack stack,
int i, Element profile, StructureDefinition sd) {
String url = profile.primitiveValue();
CanonicalResourceLookupResult cr = crLookups.get(url);
if (cr != null) {
if (cr.error != null) {
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, url, cr.error);
} else {
sd = (StructureDefinition) cr.resource;
}
} else {
try {
sd = (StructureDefinition) fetcher.fetchCanonicalResource(this, url);
crLookups.put(url, new CanonicalResourceLookupResult(sd));
} catch (Exception e) {
if (STACK_TRACE) { e.printStackTrace(); }
crLookups.put(url, new CanonicalResourceLookupResult(e.getMessage()));
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", false, I18nConstants.VALIDATION_VAL_PROFILE_UNKNOWN_ERROR, profile.primitiveValue(), e.getMessage());
}
if (sd != null) {
context.cacheResource(sd);
}
}
return sd;
}
// private void plog(String msg) {
// long n = System.currentTimeMillis();
// String elapsed = Utilities.padLeft(Long.toString(n-start), ' ', 5);
@ -5720,7 +5764,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
boolean ok;
try {
long t = System.nanoTime();
ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n);
ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n);
timeTracker.fpe(t);
msg = fpe.forLog();
} catch (Exception ex) {

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/FHIRPathExpressionFixer.java
View File

@ -45,6 +45,13 @@ public class FHIRPathExpressionFixer {
return ("name.exists() implies name.matches('[A-Z]([A-Za-z0-9_]){0,254}')");
}
// R5 ballot
if (expr.equals("url.matches('([^|#])*')")) {
return ("$this.matches('([^|#])*')");
}
// clarification in FHIRPath spec
if ("eld-19".equals(key)) {

36
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/r5/test/GeneralTests.java Normal file
View File

@ -0,0 +1,36 @@
package org.hl7.fhir.r5.test;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.jupiter.api.Test;
public class GeneralTests {
@Test
void testXMLParse() throws IOException {
System.out.println(System.getProperty("java.vm.name"));
InputStream stream = TestingUtilities.loadTestResourceStream("validator",
"xml_v10.xml");
org.hl7.fhir.r5.elementmodel.XmlParser xp = new org.hl7.fhir.r5.elementmodel.XmlParser(TestingUtilities.getSharedWorkerContext());
xp.setAllowXsiLocation(true);
List<ValidationMessage> errorList = new ArrayList<>();
xp.setupValidation(ValidationPolicy.EVERYTHING, errorList);
try {
Object resource = xp.parse(stream);
} catch (Exception e) {
e.printStackTrace();
}
for (ValidationMessage message : errorList) {
System.out.println(message.getMessage());
}
}
}

8
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -419,7 +419,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
private void checkOutcomes(List<ValidationMessage> errors, JsonObject focus, String profile, String name) throws IOException {
JsonObject java = focus.getAsJsonObject("java");
OperationOutcome goal = (OperationOutcome) new JsonParser().parse(java.getAsJsonObject("outcome"));
OperationOutcome goal = java.has("outcome") ? (OperationOutcome) new JsonParser().parse(java.getAsJsonObject("outcome")) : new OperationOutcome();
OperationOutcome actual = OperationOutcomeUtilities.createOutcomeSimple(errors);
actual.setText(null);
String json = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(actual);
@ -521,8 +521,10 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
if (java.has("outcome")) {
java.remove("outcome");
}
JsonObject oj = JsonTrackingParser.parse(json, null);
java.add("outcome", oj);
if (actual.hasIssue()) {
JsonObject oj = JsonTrackingParser.parse(json, null);
java.add("outcome", oj);
}
}
}