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fix bug in code system handling (NPE) + add support for json test cases in fhirpath tests + fix error validating references in bundles

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This commit is contained in:
Grahame Grieve 2021-11-30 15:37:12 +11:00
parent 7f5a1d95cc
commit b4597687b8
3 changed files with 17 additions and 9 deletions
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3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -498,6 +498,9 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
@Override
public CodeSystem fetchCodeSystem(String system) {
if (system == null) {
return null;
}
if (system.contains("|")) {
String s = system.substring(0, system.indexOf("|"));
String v = system.substring(system.indexOf("|")+1);

7
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/FHIRPathTests.java
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@ -15,6 +15,7 @@ import org.apache.commons.lang3.NotImplementedException;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BooleanType;
@ -187,7 +188,11 @@ public class FHIRPathTests {
} else {
res = resources.get(input);
if (res == null) {
res = new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", input));
if (input.endsWith(".json")) {
res = new JsonParser().parse(TestingUtilities.loadTestResourceStream("r5", input));
} else {
res = new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", input));
}
resources.put(input, res);
}
fp.check(res, res.getResourceType().toString(), res.getResourceType().toString(), node);

16
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -302,7 +302,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
} else if (item instanceof Element) {
Element e = (Element) item;
if (e.getName().equals("contained")) {
if (e.getSpecial() != null) {
self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e, ctxt.getRootResource()), valerrors, e, e, sd, IdStatus.OPTIONAL, new NodeStack(context, null, e, validationLanguage));
} else {
self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL, new NodeStack(context, null, e, validationLanguage));
@ -2732,7 +2732,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !isSuspiciousReference(ref), I18nConstants.REFERENCE_REF_SUSPICIOUS, ref);
ResolvedReference we = localResolve(ref, stack, errors, path, (Element) hostContext.getAppContext(), element);
ResolvedReference we = localResolve(ref, stack, errors, path, hostContext.getRootResource(), element);
String refType;
if (ref.startsWith("#")) {
refType = "contained";
@ -3420,7 +3420,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return true;
}
private ResolvedReference localResolve(String ref, NodeStack stack, List<ValidationMessage> errors, String path, Element hostContext, Element source) {
private ResolvedReference localResolve(String ref, NodeStack stack, List<ValidationMessage> errors, String path, Element rootResource, Element source) {
if (ref.startsWith("#")) {
// work back through the parent list.
// really, there should only be one level for this (contained resources cannot contain
@ -3520,11 +3520,11 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
stack = stack.getParent();
}
// we can get here if we got called via FHIRPath conformsTo which breaks the stack continuity.
if (hostContext != null && BUNDLE.equals(hostContext.fhirType())) {
String type = hostContext.getChildValue(TYPE);
Element entry = getEntryForSource(hostContext, source);
if (rootResource != null && BUNDLE.equals(rootResource.fhirType())) {
String type = rootResource.getChildValue(TYPE);
Element entry = getEntryForSource(rootResource, source);
fullUrl = entry.getChildValue(FULL_URL);
IndexedElement res = getFromBundle(hostContext, ref, fullUrl, errors, path, type, "transaction".equals(type));
IndexedElement res = getFromBundle(rootResource, ref, fullUrl, errors, path, type, "transaction".equals(type));
if (res == null) {
return null;
} else {
@ -3532,7 +3532,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
rr.setResource(res.getMatch());
rr.setFocus(res.getMatch());
rr.setExternal(false);
rr.setStack(new NodeStack(context, null, hostContext, validationLanguage).push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(),
rr.setStack(new NodeStack(context, null, rootResource, validationLanguage).push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(),
res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1,
res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition()));
rr.getStack().qualifyPath(".ofType("+rr.getResource().fhirType()+")");