Add changelog

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2868-bug-in-conditional-create.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 2876
+jira: SMILE-1153
+title: "Fixed a bug in transaction bundle processing, specifically for bundles which contained both a conditional create, and a resource which relied on this conditional create as a reference.
+This would cause the referring resource to generate a contained resource instead of appropriately referencing the existing patient."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -94,6 +94,7 @@ import com.google.common.collect.Sets;
 import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hashing;
 import org.apache.commons.lang3.NotImplementedException;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBase;
@@ -1162,10 +1163,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 					validateResourceForStorage((T) theResource, entity);
 				}
 			}
-			String resourceType = myContext.getResourceType(theResource);
+			if (!StringUtils.isBlank(entity.getResourceType())) {
-			if (isNotBlank(entity.getResourceType()) && !entity.getResourceType().equals(resourceType)) {
+				validateIncomingResourceTypeMatchesExisting(theResource, entity);
-				throw new UnprocessableEntityException(
-					"Existing resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + entity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
 			}
 		}
 
@@ -1206,6 +1205,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			if (thePerformIndexing || ((ResourceTable) theEntity).getVersion() == 1) {
 
 				newParams = new ResourceIndexedSearchParams();
+
 				mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing);
 
 				changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);
@@ -1415,6 +1415,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 		return entity;
 	}
 
+	private void validateIncomingResourceTypeMatchesExisting(IBaseResource theResource, ResourceTable entity) {
+		String resourceType = myContext.getResourceType(theResource);
+		if (!resourceType.equals(entity.getResourceType())) {
+			throw new UnprocessableEntityException(
+				"Existing resource ID[" + entity.getIdDt().toUnqualifiedVersionless() + "] is of type[" + entity.getResourceType() + "] - Cannot update with [" + resourceType + "]");
+		}
+	}
+
 	@Override
 	public ResourceTable updateInternal(RequestDetails theRequestDetails, T theResource, boolean thePerformIndexing, boolean theForceUpdateVersion,
 													IBasePersistedResource theEntity, IIdType theResourceId, IBaseResource theOldResource, TransactionDetails theTransactionDetails) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java

@@ -262,7 +262,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		entity.setCreatedByMatchUrl(theIfNoneExist);
 		entity.setVersion(1);
 
-		//FIXME GGG is this possibly where we are fetching the thing?
 		if (isNotBlank(theIfNoneExist)) {
 			Set<ResourcePersistentId> match = myMatchResourceUrlService.processMatchUrl(theIfNoneExist, myResourceType, theTransactionDetails, theRequest);
 			if (match.size() > 1) {
@@ -279,7 +278,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 				};
 
 				Supplier<IIdType> idSupplier = () -> {
-					return myTxTemplate.execute(tx -> {
+					myTxTemplate.execute(tx -> {
 						IIdType retVal = myIdHelperService.translatePidIdToForcedId(myFhirContext, myResourceName, pid);
 						if (!retVal.hasVersionIdPart()) {
 							IIdType idWithVersion = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_CONDITIONAL_CREATE_VERSION, pid.getIdAsLong());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseTransactionProcessor.java

@@ -791,6 +791,8 @@ public abstract class BaseTransactionProcessor {
 						String matchUrl = myVersionAdapter.getEntryRequestIfNoneExist(nextReqEntry);
 						matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
 						outcome = resourceDao.create(res, matchUrl, false, theTransactionDetails, theRequest);
+						// IS THIS THE MAGIC SAUCE?
+					 	res.setId(outcome.getId());
 						if (nextResourceId != null) {
 							handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequest);
 						}
@@ -865,7 +867,6 @@ public abstract class BaseTransactionProcessor {
 								matchUrl = parts.getResourceType();
 							}
 							matchUrl = performIdSubstitutionsInMatchUrl(theIdSubstitutions, matchUrl);
-							//TODO FIXME GGG This update call comes back with a contained resource.
 							outcome = resourceDao.update(res, matchUrl, false, false, theRequest, theTransactionDetails);
 							if (Boolean.TRUE.equals(outcome.getCreated())) {
 								conditionalRequestUrls.put(matchUrl, res.getClass());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/SearchParamWithInlineReferencesExtractor.java

@@ -129,6 +129,7 @@ public class SearchParamWithInlineReferencesExtractor {
 			partitionId = RequestPartitionId.allPartitions();
 		}
 
+		//THIS IS THE NEW SPOT
 		mySearchParamExtractorService.extractFromResource(partitionId, theRequest, theParams, theEntity, theResource, theTransactionDetails, theFailOnInvalidReference);
 
 		Set<Map.Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).entrySet();

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamExtractor.java

@@ -78,6 +78,7 @@ import java.util.Collections;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
 import java.util.TreeSet;
@@ -964,6 +965,17 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		return retVal;
 	}
 
+
+	/**
+	 * Helper function to determine if a set of SPs for a resource uses a resolve as part of its fhir path.
+	 */
+	private boolean anySearchParameterUsesResolve(Collection<RuntimeSearchParam> searchParams, RestSearchParameterTypeEnum theSearchParamType) {
+		return searchParams.stream()
+			.filter(param -> param.getParamType() != theSearchParamType)
+			.filter(Objects::nonNull)
+			.anyMatch(param -> param.getPath().contains("resolve"));
+	}
+
 	/**
 	 * HAPI FHIR Reference objects (e.g. {@link org.hl7.fhir.r4.model.Reference}) can hold references either by text
 	 * (e.g. "#3") or by resource (e.g. "new Reference(patientInstance)"). The FHIRPath evaluator only understands the
@@ -974,17 +986,12 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 	 * if we think there's actually a chance
 	 */
 	private void cleanUpContainedResourceReferences(IBaseResource theResource, RestSearchParameterTypeEnum theSearchParamType, Collection<RuntimeSearchParam> searchParams) {
-		boolean havePathWithResolveExpression = myModelConfig.isIndexOnContainedResources();
+		boolean havePathWithResolveExpression =
-		for (RuntimeSearchParam nextSpDef : searchParams) {
+			myModelConfig.isIndexOnContainedResources()
-			if (nextSpDef.getParamType() != theSearchParamType) {
+			|| anySearchParameterUsesResolve(searchParams, theSearchParamType);
-				continue;
+
-			}
-			if (defaultString(nextSpDef.getPath()).contains("resolve")) {
-				havePathWithResolveExpression = true;
-				break;
-			}
-		}
 		if (havePathWithResolveExpression) {
+			//FIXME GGG/JA: At this point, if the Task.basedOn.reference.resource does _not_ have an ID, we will attempt to contain it internally.
 			myContext.newTerser().containResources(theResource, FhirTerser.OptionsEnum.MODIFY_RESOURCE, FhirTerser.OptionsEnum.STORE_AND_REUSE_RESULTS);
 		}
 	}