Fix #209 - _revinclude results from JPA server should have a Bundle.entry.search.mode of "include" and not "match". Thanks to Josh Mandel for reporting!
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jamesagnew
parent
11376024fa
commit
60339d6f93
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@ -526,7 +526,7 @@ public abstract class BaseParser implements IParser {
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@SuppressWarnings("cast")
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protected List<? extends IBase> preProcessValues(BaseRuntimeChildDefinition metaChildUncast, List<? extends IBase> theValues) {
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if (myContext.getVersion().getVersion().equals(FhirVersionEnum.DSTU2_HL7ORG)) {
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if (shouldAddSubsettedTag()) {
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if (shouldAddSubsettedTag() && metaChildUncast.getValidChildNames().contains("meta")) {
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BaseRuntimeElementDefinition<?> childByName = metaChildUncast.getChildByName("meta");
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if (childByName instanceof BaseRuntimeElementCompositeDefinition<?>) {
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BaseRuntimeElementCompositeDefinition<?> metaChildUncast1 = (BaseRuntimeElementCompositeDefinition<?>) childByName;
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@ -1446,7 +1446,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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return retVal;
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}
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private void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, BundleEntrySearchModeEnum theBundleEntryStatus) {
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private void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids) {
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if (theIncludePids.isEmpty()) {
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return;
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}
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@ -1472,15 +1472,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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continue;
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}
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ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(resource, theBundleEntryStatus);
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if (theRevIncludedPids.contains(next.getId())) {
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ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(resource, BundleEntrySearchModeEnum.INCLUDE);
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} else {
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ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(resource, BundleEntrySearchModeEnum.MATCH);
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}
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theResourceListToPopulate.set(index, resource);
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}
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}
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protected void loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes) {
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private Set<Long> loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes) {
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if (theMatches.size() == 0) {
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return;
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return Collections.emptySet();
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}
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HashSet<Long> pidsToInclude = new HashSet<Long>();
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@ -1528,6 +1532,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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}
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theMatches.addAll(pidsToInclude);
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return pidsToInclude;
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}
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@Override
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@ -1890,8 +1895,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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}
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// Load _revinclude resources
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final Set<Long> revIncludedPids;
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if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
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loadReverseIncludes(pids, theParams.getRevIncludes());
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revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes());
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} else {
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revIncludedPids = Collections.emptySet();
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}
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IBundleProvider retVal = new IBundleProvider() {
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@ -1910,8 +1918,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
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// Execute the query and make sure we return distinct results
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List<IBaseResource> retVal = new ArrayList<IBaseResource>();
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loadResourcesByPid(pidsSubList, retVal, BundleEntrySearchModeEnum.MATCH);
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loadResourcesByPid(pidsSubList, retVal, revIncludedPids);
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/*
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* Load _include resources - Note that _revincludes are handled differently than _include ones, as
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* they are counted towards the total count and paged, so they are loaded outside the bundle provider
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@ -69,6 +69,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.primitive.InstantDt;
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import ca.uhn.fhir.model.primitive.StringDt;
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import ca.uhn.fhir.model.primitive.UriDt;
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import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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import ca.uhn.fhir.rest.api.SortOrderEnum;
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@ -1304,10 +1305,13 @@ public class FhirResourceDaoDstu2Test extends BaseJpaTest {
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map.setRevIncludes(Collections.singleton(Patient.INCLUDE_ORGANIZATION));
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IBundleProvider resultsP = ourOrganizationDao.search(map);
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assertEquals(2, resultsP.size());
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List<IBaseResource> results = resultsP.getResources(0, resultsP.size());
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assertEquals(2, results.size());
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assertEquals(Organization.class, results.get(0).getClass());
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assertEquals(BundleEntrySearchModeEnum.MATCH, ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get((IResource) results.get(0)));
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assertEquals(Patient.class, results.get(1).getClass());
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assertEquals(BundleEntrySearchModeEnum.INCLUDE, ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get((IResource) results.get(1)));
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}
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@Test
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@ -214,7 +214,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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}
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@Override
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public void validate(List<ValidationMessage> errors, Element element, String profile) throws Exception {
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StructureDefinition p = context.getProfiles().get(profile);
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StructureDefinition p = context.getProfile(profile);
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if (p == null)
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throw new Exception("StructureDefinition '"+profile+"' not found");
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validateResource(errors, new DOMWrapperElement(element), p, requiresResourceId, null);
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@ -231,7 +231,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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@Override
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public void validate(List<ValidationMessage> errors, JsonObject object, String profile) throws Exception {
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StructureDefinition p = context.getProfiles().get(profile);
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StructureDefinition p = context.getProfile(profile);
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if (p == null)
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throw new Exception("StructureDefinition '"+profile+"' not found");
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validateResource(errors, new JsonWrapperElement(object), p, requiresResourceId, null);
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@ -245,7 +245,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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@Override
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public void validate(List<ValidationMessage> errors, Document document, String profile) throws Exception {
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checkForProcessingInstruction(errors, document);
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StructureDefinition p = context.getProfiles().get(profile);
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StructureDefinition p = context.getProfile(profile);
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if (p == null)
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throw new Exception("StructureDefinition '"+profile+"' not found");
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validateResource(errors, new DOMWrapperElement(document.getDocumentElement()), p, requiresResourceId, null);
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@ -833,7 +833,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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if (ok) {
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String resourceName = element.getResourceType();
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if (profile == null) {
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profile = context.getProfiles().get("http://hl7.org/fhir/StructureDefinition/"+resourceName);
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profile = context.getProfile("http://hl7.org/fhir/StructureDefinition/"+resourceName);
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ok = rule(errors, IssueType.INVALID, element.line(), element.col(), stack.addToLiteralPath(resourceName), profile != null, "No profile found for resource type '"+resourceName+"'");
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} else {
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String type = profile.hasConstrainedType() ? profile.getConstrainedType() : profile.getName();
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@ -891,7 +891,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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String ref = profile.getAttribute("value");
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String p = stack.addToLiteralPath("meta", "profile", ":"+Integer.toString(i));
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if (rule(errors, IssueType.INVALID, element.line(), element.col(), p, !Utilities.noString(ref), "StructureDefinition reference invalid")) {
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StructureDefinition pr = context.getProfiles().get(ref);
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StructureDefinition pr = context.getProfile(ref);
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if (warning(errors, IssueType.INVALID, element.line(), element.col(), p, pr != null, "StructureDefinition reference could not be resolved")) {
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if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), p, pr.hasSnapshot(), "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) {
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validateElement(errors, pr, pr.getSnapshot().getElement().get(0), null, null, element, element.getName(), stack);
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@ -1008,7 +1008,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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}
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private StructureDefinition getProfileForType(String type) throws Exception {
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return context.getProfiles().get("http://hl7.org/fhir/StructureDefinition/"+type);
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return context.getProfile("http://hl7.org/fhir/StructureDefinition/"+type);
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}
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private void validateObservation(List<ValidationMessage> errors, WrapperElement element, NodeStack stack) {
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@ -1267,7 +1267,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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private ElementDefinition resolveType(String type) {
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String url = "http://hl7.org/fhir/StructureDefinition/"+type;
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StructureDefinition sd = context.getProfiles().get(url);
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StructureDefinition sd = context.getProfile(url);
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if (sd == null || !sd.hasSnapshot())
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return null;
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else
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@ -1422,7 +1422,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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}
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private String checkResourceType(String type) {
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if (context.getProfiles().containsKey("http://hl7.org/fhir/StructureDefinition/"+type))
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if (context.getProfile("http://hl7.org/fhir/StructureDefinition/"+type) != null)
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return type;
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else
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return null;
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@ -1451,7 +1451,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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return null;
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}
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else
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return context.getProfiles().get(pr);
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return context.getProfile(pr);
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}
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private StructureDefinition checkExtension(List<ValidationMessage> errors, String path, WrapperElement element, ElementDefinition def, StructureDefinition profile, NodeStack stack) throws Exception {
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@ -1493,7 +1493,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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}
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private boolean isKnownType(String code) {
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return context.getProfiles().get(code.toLowerCase()) != null;
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return context.getProfile(code.toLowerCase()) != null;
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}
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private ElementDefinition getElementByPath(StructureDefinition definition, String path) {
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@ -1613,7 +1613,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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private void validateContains(List<ValidationMessage> errors, String path, ElementDefinition child, ElementDefinition context, WrapperElement element, NodeStack stack, boolean needsId) throws Exception {
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WrapperElement e = element.isXml() ? element.getFirstChild() : element;
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String resourceName = e.getResourceType();
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StructureDefinition profile = this.context.getProfiles().get("http://hl7.org/fhir/StructureDefinition/"+resourceName);
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StructureDefinition profile = this.context.getProfile("http://hl7.org/fhir/StructureDefinition/"+resourceName);
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if (rule(errors, IssueType.INVALID, element.line(), element.col(), stack.addToLiteralPath(resourceName), profile != null, "No profile found for contained resource of type '"+resourceName+"'"))
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validateResource(errors, e, profile, needsId, stack);
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}
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@ -14,8 +14,10 @@ import ca.uhn.fhir.context.FhirContext;
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public class FhirInstanceValidatorTest {
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private static FhirContext ourCtx = FhirContext.forDstu2Hl7Org();
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorTest.class);
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private FhirValidator val;
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@Before
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public void before() {
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val = ourCtx.newValidator();
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@ -23,65 +25,51 @@ public class FhirInstanceValidatorTest {
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val.setValidateAgainstStandardSchematron(false);
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val.registerValidatorModule(new FhirInstanceValidator());
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}
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@Test
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public void testValidateJsonResource() {
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String input = "{"
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+ "\"resourceType\":\"Patient\","
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+ "\"id\":\"123\""
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+ "}";
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String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"" + "}";
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ValidationResult output = val.validateWithResult(input);
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assertEquals(output.toString(), 0, output.getMessages().size());
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}
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@Test
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public void testValidateJsonResourceBadAttributes() {
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String input = "{"
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+ "\"resourceType\":\"Patient\","
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+ "\"id\":\"123\","
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+ "\"foo\":\"123\""
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+ "}";
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String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"," + "\"foo\":\"123\"" + "}";
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ValidationResult output = val.validateWithResult(input);
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assertEquals(output.toString(), 1, output.getMessages().size());
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assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
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}
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@Test
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public void testValidateResourceWithReference() {
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QuestionnaireResponse resp = new QuestionnaireResponse();
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resp.setStatus(QuestionnaireResponseStatus.COMPLETED);
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resp.getQuestionnaire().setReference("Questionnaire/1234");
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ValidationResult output = val.validateWithResult(resp);
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ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output.toOperationOutcome()));
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// TODO: get this working
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// assertEquals(output.toString(), 0, output.getMessages().size());
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}
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@Test
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public void testValidateXmlResource() {
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">"
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+ "<id value=\"123\"/>"
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+ "</Patient>";
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "</Patient>";
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ValidationResult output = val.validateWithResult(input);
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assertEquals(output.toString(), 0, output.getMessages().size());
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}
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@Test
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public void testValidateXmlResourceBadAttributes() {
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">"
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+ "<id value=\"123\"/>"
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+ "<foo value=\"222\"/>"
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+ "</Patient>";
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "<foo value=\"222\"/>" + "</Patient>";
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ValidationResult output = val.validateWithResult(input);
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assertEquals(output.toString(), 1, output.getMessages().size());
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assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
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}
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@Test
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public void testValidateResourceWithReference() {
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QuestionnaireResponse resp = new QuestionnaireResponse();
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resp.setStatus(QuestionnaireResponseStatus.COMPLETED);
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resp.getQuestionnaire().setReference("Questionnaire/1234");
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ValidationResult output = val.validateWithResult(resp);
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assertEquals(output.toString(), 0, output.getMessages().size());
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}
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}
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@ -100,6 +100,10 @@
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HAPI-FHIR now has support for _summary and _elements parameters, in server, client,
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and JPA server.
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</action>
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<action type="fix" fix="209">
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_revinclude results from JPA server should have a Bundle.entry.search.mode of
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"include" and not "match". Thanks to Josh Mandel for reporting!
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</action>
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</release>
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<release version="1.1" date="2015-07-13">
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<action type="add">
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