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fix bugs with extension context checking

This commit is contained in:
Grahame Grieve 2020-01-19 16:53:48 +11:00
parent fa3c8305bf
commit 2ce844175f
5 changed files with 57 additions and 16 deletions
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8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
View File

@ -849,9 +849,11 @@ public class Element extends Base {
}
public boolean hasDescendant(Element element) {
for (Element child : children) {
if (element == child || child.hasDescendant(element)) {
return true;
if (children != null) {
for (Element child : children) {
if (element == child || child.hasDescendant(element)) {
return true;
}
}
}
return false;

45
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java
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@ -1613,7 +1613,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
CommaSeparatedStringBuilder contexts = new CommaSeparatedStringBuilder();
List<String> plist = new ArrayList<>();
for (StructureDefinitionContextComponent ctxt : definition.getContext()) {
for (StructureDefinitionContextComponent ctxt : fixContexts(extUrl, definition.getContext())) {
if (ok) { break; }
if (ctxt.getType() == ExtensionContextType.ELEMENT) {
if (plist.isEmpty()) {
@ -1624,7 +1624,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
String en = ctxt.getExpression();
contexts.append("e:"+en);
if (en.equals("Element") && !container.isResource()) {
if (en.equals("Element")) {
ok = true;
} else if (en.equals("Resource") && container.isResource()) {
ok = true;
@ -1662,7 +1662,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (ctxt.getType() == ExtensionContextType.FHIRPATH) {
contexts.append("p:"+ctxt.getExpression());
// The context is all elements that match the FHIRPath query found in the expression.
List<Base> res = fpe.evaluate(hostContext, resource, hostContext.rootResource, resource, fpe.parse(ctxt.getExpression()));
List<Base> res = fpe.evaluate(hostContext, resource, hostContext.rootResource, container, fpe.parse(ctxt.getExpression()));
if (res.contains(container)) {
ok = true;
}
@ -1670,15 +1670,15 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
throw new Error("Unrecognised extension context "+ctxt.getTypeElement().asStringValue());
}
}
if (!rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, ok,
"The extension " + extUrl + " is not allowed to be used at this point (allowed = "+ contexts.toString() + ")")) {
if (!ok) {
rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, false, "The extension " + extUrl + " is not allowed to be used at this point (allowed = "+ contexts.toString() + "; this element is ["+plist.toString()+")");
return false;
} else {
if (definition.hasContextInvariant()) {
for (StringType s : definition.getContextInvariant()) {
if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.rootResource, resource, fpe.parse(s.getValue()))) {
if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.rootResource, container, fpe.parse(s.getValue()))) {
rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, false,
"The extension " + extUrl + " is not allowed to be used at this point (bsed on context invariant '"+s.getValue()+"')");
"The extension " + extUrl + " is not allowed to be used at this point (based on context invariant '"+s.getValue()+"')");
return false;
}
}
@ -1687,6 +1687,20 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
private List<StructureDefinitionContextComponent> fixContexts(String extUrl, List<StructureDefinitionContextComponent> list) {
List<StructureDefinitionContextComponent> res = new ArrayList<>();
for (StructureDefinitionContextComponent ctxt : list) {
res.add(ctxt.copy());
}
if ("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type".equals(extUrl)) {
list.get(0).setExpression("ElementDefinition.type");
}
if ("http://hl7.org/fhir/StructureDefinition/regex".equals(extUrl)) {
list.get(1).setExpression("ElementDefinition.type");
}
return list;
}
private String stripIndexes(String path) {
boolean skip = false;
StringBuilder b = new StringBuilder();
@ -2205,7 +2219,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} catch (IOException e) {
throw new FHIRException(e);
}
fetchCache.put(ref, ext);
if (ext != null) {
fetchCache.put(ref, ext);
}
}
we = ext == null ? null : makeExternalRef(ext, path);
}
@ -5325,6 +5341,10 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
this.element = element;
literalPath = element.getName();
workingLang = validationLanguage;
if (!element.getName().equals(element.fhirType())) {
logicalPaths = new ArrayList<>();
logicalPaths.add(element.fhirType());
}
}
public NodeStack(Element element, String refPath) {
@ -5399,13 +5419,17 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
if (type != null) {
// type will be bull if we on a stitching point of a contained resource, or if....
res.type = type;
String tn = res.type.getPath();
String t = tail(definition.getPath());
if ("Resource".equals(tn)) {
tn = element.fhirType();
}
for (String lp : getLogicalPaths()) {
res.logicalPaths.add(lp + "." + t);
if (t.endsWith("[x]"))
res.logicalPaths.add(lp + "." + t.substring(0, t.length() - 3) + type.getPath());
}
res.logicalPaths.add(type.getPath());
res.logicalPaths.add(tn);
} else if (definition != null) {
for (String lp : getLogicalPaths()) {
res.logicalPaths.add(lp + "." + element.getName());
@ -5514,6 +5538,9 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
// this is a hack work around for past publication of wrong FHIRPath expressions
// R4
// waiting for 4.0.2
if ("(probability is decimal) implies ((probability as decimal) <= 100)".equals(expr)) {
return "probablility.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))";
}
// handled in 4.0.1
if ("(component.empty() and hasMember.empty()) implies (dataAbsentReason or value)".equals(expr))

16
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
View File

@ -109,6 +109,7 @@ import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.JsonParser;
@ -1616,12 +1617,23 @@ public class ValidationEngine implements IValidatorResourceFetcher {
}
@Override
public Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
return fetcher != null ? fetcher.fetch(appContext, url) : null;
public Element fetch(Object appContext, String url) throws FHIRException, IOException {
Resource resource = context.fetchResource(Resource.class, url);
if (resource != null) {
return new ObjectConverter(context).convert(resource);
}
if (fetcher != null) {
return fetcher.fetch(appContext, url);
}
return null;
}
@Override
public ReferenceValidationPolicy validationPolicy(Object appContext, String path, String url) {
Resource resource = context.fetchResource(StructureDefinition.class, url);
if (resource != null) {
return ReferenceValidationPolicy.CHECK_VALID;
}
if (!url.startsWith("http://hl7.org/fhir")) {
return ReferenceValidationPolicy.IGNORE;
} else if (fetcher != null) {

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java
View File

@ -97,7 +97,7 @@ public class ValidationEngineTests {
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient102.xml"), null);
if (!TestUtilities.silent)
for (OperationOutcomeIssueComponent iss : op.getIssue()) {
System.out.println(" "+iss.getDetails().getText());
System.out.println(" "+iss.getSeverity().toCode()+": "+iss.getDetails().getText());
}
int e = errors(op);
int w = warnings(op);

2
pom.xml
View File

@ -17,7 +17,7 @@
<properties>
<hapi_fhir_version>4.1.0</hapi_fhir_version>
<validator_test_case_version>1.0.32-SNAPSHOT</validator_test_case_version>
<validator_test_case_version>1.0.33-SNAPSHOT</validator_test_case_version>
</properties>
<artifactId>org.hl7.fhir.core</artifactId>