4618 refactor searchparamwithinlinereferencesextractor to create a interface and a base class (#4619)

* Introduced new interface, refactored SearchParamWithInlineReferencesExtractor, added new test

* clean up, remove unused param

* added change log

* moved error message to properties file, made base class abstract

* fixed issue with test

* code review changes

---------

Co-authored-by: Steven Li <steven@smilecdr.com>

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -78,7 +78,8 @@ ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor.externalizedBinarySt
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
 ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
-ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlMultipleMatches=Invalid match URL "{0}" - Multiple resources match this search
+ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidMatchUrlMultipleMatches=Invalid match URL "{0}" - Multiple resources match this search
+ca.uhn.fhir.jpa.dao.BaseStorageDao.inlineMatchNotSupported=Inline match URLs are not supported on this server. Cannot process reference: "{0}"
 ca.uhn.fhir.jpa.dao.BaseStorageDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1}

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_6_0/4618-refactor-searchparamwithinlinereferencesextractor-to-create-a-interface-and-a-base-class.yaml

@@ -0,0 +1,6 @@
+---
+type: change
+issue: 4618
+title: "A new interface has been created for SearchParamWithInlineReferencesExtractor with a base implementation.
+This allows us to encapsulate logic for resolving and replacing inline resources to the same place
+is also cuts down on code duplication and allow for easier sharing of the same logic"

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

@@ -1,66 +0,0 @@
-package ca.uhn.fhir.jpa.dao.index;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2023 Smile CDR, Inc.
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-
-public class ExtractInlineReferenceParams {
-	private IBaseResource myResource;
-	private TransactionDetails myTransactionDetails;
-	private RequestDetails myRequestDetails;
-
-	public ExtractInlineReferenceParams(
-		IBaseResource theResource,
-		TransactionDetails theTransactionDetails,
-		RequestDetails theRequest
-	) {
-		myResource = theResource;
-		myTransactionDetails = theTransactionDetails;
-		myRequestDetails = theRequest;
-	}
-
-	public IBaseResource getResource() {
-		return myResource;
-	}
-
-	public void setResource(IBaseResource theResource) {
-		myResource = theResource;
-	}
-
-	public TransactionDetails getTransactionDetails() {
-		return myTransactionDetails;
-	}
-
-	public void setTransactionDetails(TransactionDetails theTransactionDetails) {
-		myTransactionDetails = theTransactionDetails;
-	}
-
-	public RequestDetails getRequestDetails() {
-		return myRequestDetails;
-	}
-
-	public void setRequestDetails(RequestDetails theRequestDetails) {
-		myRequestDetails = theRequestDetails;
-	}
-
-}

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

@@ -20,41 +20,31 @@ package ca.uhn.fhir.jpa.dao.index;
  * #L%
  */
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
-import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
-import ca.uhn.fhir.jpa.dao.BaseStorageDao;
-import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboStringUniqueDao;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
-import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.dao.JpaPid;
 import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.model.entity.ResourceIndexedComboStringUnique;
 import ca.uhn.fhir.jpa.model.entity.ResourceLink;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.searchparam.extractor.BaseSearchParamWithInlineReferencesExtractor;
+import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamWithInlineReferencesExtractor;
 import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
 import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorService;
-import ca.uhn.fhir.jpa.util.MemoryCacheService;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
 import ca.uhn.fhir.rest.api.server.storage.NotFoundPid;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.rest.server.util.ResourceSearchParams;
-import ca.uhn.fhir.util.FhirTerser;
 import com.google.common.annotations.VisibleForTesting;
-import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.stereotype.Service;
@@ -65,39 +55,24 @@ import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
 import java.util.Collection;
 import java.util.Iterator;
-import java.util.List;
-import java.util.Optional;
-import java.util.Set;
 import java.util.stream.Collectors;
 
 @Service
 @Lazy
-public class SearchParamWithInlineReferencesExtractor {
+public class SearchParamWithInlineReferencesExtractor extends BaseSearchParamWithInlineReferencesExtractor<JpaPid> implements ISearchParamWithInlineReferencesExtractor {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamWithInlineReferencesExtractor.class);
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	protected EntityManager myEntityManager;
 	@Autowired
-	private MatchResourceUrlService<JpaPid> myMatchResourceUrlService;
-	@Autowired
-	private JpaStorageSettings myStorageSettings;
-	@Autowired
-	private FhirContext myContext;
-	@Autowired
-	private IIdHelperService<JpaPid> myIdHelperService;
-	@Autowired
 	private ISearchParamRegistry mySearchParamRegistry;
 	@Autowired
 	private SearchParamExtractorService mySearchParamExtractorService;
 	@Autowired
-	private DaoResourceLinkResolver<JpaPid> myDaoResourceLinkResolver;
-	@Autowired
 	private DaoSearchParamSynchronizer myDaoSearchParamSynchronizer;
 	@Autowired
 	private IResourceIndexedComboStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
 	@Autowired
 	private PartitionSettings myPartitionSettings;
-	@Autowired
-	private MemoryCacheService myMemoryCacheService;
 
 	@VisibleForTesting
 	public void setPartitionSettings(PartitionSettings thePartitionSettings) {
@@ -116,8 +91,8 @@ public class SearchParamWithInlineReferencesExtractor {
 
 	public void populateFromResource(RequestPartitionId theRequestPartitionId, ResourceIndexedSearchParams theParams, TransactionDetails theTransactionDetails, ResourceTable theEntity, IBaseResource theResource, ResourceIndexedSearchParams theExistingParams, RequestDetails theRequest, boolean thePerformIndexing) {
 		if (thePerformIndexing) {
-			ExtractInlineReferenceParams extractParams = new ExtractInlineReferenceParams(theResource, theTransactionDetails, theRequest);
+			// Perform inline match URL substitution
-			extractInlineReferences(extractParams);
+			extractInlineReferences(theRequest, theResource, theTransactionDetails);
 		}
 
 		mySearchParamExtractorService.extractFromResource(theRequestPartitionId, theRequest, theParams, theExistingParams, theEntity, theResource, theTransactionDetails, thePerformIndexing);
@@ -183,113 +158,6 @@ public class SearchParamWithInlineReferencesExtractor {
 		return paramsListForCompositePart;
 	}
 
-	@VisibleForTesting
-	public void setStorageSettings(JpaStorageSettings theStorageSettings) {
-		myStorageSettings = theStorageSettings;
-	}
-
-	@VisibleForTesting
-	public void setContext(FhirContext theContext) {
-		myContext = theContext;
-	}
-
-	@Deprecated
-	public void extractInlineReferences(
-		IBaseResource theResource,
-		TransactionDetails theTransactionDetails,
-		RequestDetails theRequest
-	) {
-		extractInlineReferences(new ExtractInlineReferenceParams(theResource, theTransactionDetails, theRequest));
-	}
-
-	/**
-	 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo".
-	 * These match URLs are resolved and replaced with the ID of the
-	 * matching resource.
-	 * <p>
-	 * This method is *only* called from UPDATE path
-	 */
-	public void extractInlineReferences(ExtractInlineReferenceParams theParams) {
-		if (!myStorageSettings.isAllowInlineMatchUrlReferences()) {
-			return;
-		}
-		IBaseResource resource = theParams.getResource();
-		RequestDetails theRequest = theParams.getRequestDetails();
-		TransactionDetails theTransactionDetails = theParams.getTransactionDetails();
-
-		FhirTerser terser = myContext.newTerser();
-		List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(resource, IBaseReference.class);
-		for (IBaseReference nextRef : allRefs) {
-			IIdType nextId = nextRef.getReferenceElement();
-			String nextIdText = nextId.getValue();
-			if (nextIdText == null) {
-				continue;
-			}
-			int qmIndex = nextIdText.indexOf('?');
-			if (qmIndex != -1) {
-				for (int i = qmIndex - 1; i >= 0; i--) {
-					if (nextIdText.charAt(i) == '/') {
-						if (i < nextIdText.length() - 1 && nextIdText.charAt(i + 1) == '?') {
-							// Just in case the URL is in the form Patient/?foo=bar
-							continue;
-						}
-						nextIdText = nextIdText.substring(i + 1);
-						break;
-					}
-				}
-				String resourceTypeString = nextIdText.substring(0, nextIdText.indexOf('?')).replace("/", "");
-				RuntimeResourceDefinition matchResourceDef = myContext.getResourceDefinition(resourceTypeString);
-				if (matchResourceDef == null) {
-					String msg = myContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidMatchUrlInvalidResourceType", nextId.getValue(), resourceTypeString);
-					throw new InvalidRequestException(Msg.code(1090) + msg);
-				}
-				Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
-
-				JpaPid resolvedMatch = null;
-				if (theTransactionDetails != null) {
-					resolvedMatch = (JpaPid) theTransactionDetails.getResolvedMatchUrls().get(nextIdText);
-				}
-
-				//Attempt to find the target reference before creating a placeholder
-				Set<JpaPid> matches;
-				if (resolvedMatch != null && !IResourcePersistentId.NOT_FOUND.equals(resolvedMatch)) {
-					matches = Set.of(resolvedMatch);
-				} else {
-					matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theTransactionDetails, theRequest);
-				}
-
-				JpaPid match;
-				if (matches.isEmpty()) {
-					Optional<IBasePersistedResource> placeholderOpt = myDaoResourceLinkResolver.createPlaceholderTargetIfConfiguredToDoSo(matchResourceType, nextRef, null, theRequest, theTransactionDetails);
-					if (placeholderOpt.isPresent()) {
-						match = (JpaPid) placeholderOpt.get().getPersistentId();
-						match.setAssociatedResourceId(placeholderOpt.get().getIdDt());
-						theTransactionDetails.addResolvedMatchUrl(nextIdText, match);
-						myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, nextIdText, match);
-					} else {
-						String msg = myContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
-						throw new ResourceNotFoundException(Msg.code(1091) + msg);
-					}
-
-				} else if (matches.size() > 1) {
-					String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "invalidMatchUrlMultipleMatches", nextId.getValue());
-					throw new PreconditionFailedException(Msg.code(1092) + msg);
-				} else {
-					match = matches.iterator().next();
-				}
-
-				IIdType newId = myIdHelperService.translatePidIdToForcedId(myContext, resourceTypeString, match);
-				ourLog.debug("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId);
-
-				if (theTransactionDetails != null) {
-					String previousReference = nextRef.getReferenceElement().getValue();
-					theTransactionDetails.addRollbackUndoAction(()->nextRef.setReference(previousReference));
-				}
-				nextRef.setReference(newId.getValue());
-			}
-		}
-	}
-
 	@VisibleForTesting
 	public void setDaoSearchParamSynchronizer(DaoSearchParamSynchronizer theDaoSearchParamSynchronizer) {
 		myDaoSearchParamSynchronizer = theDaoSearchParamSynchronizer;
@@ -317,7 +185,7 @@ public class SearchParamWithInlineReferencesExtractor {
 							searchParameterId = next.getSearchParameterId().toUnqualifiedVersionless().getValue();
 						}
 
-						String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "uniqueIndexConflictFailure", theEntity.getResourceType(), next.getIndexString(), existing.getResource().getIdDt().toUnqualifiedVersionless().getValue(), searchParameterId);
+						String msg = myFhirContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "uniqueIndexConflictFailure", theEntity.getResourceType(), next.getIndexString(), existing.getResource().getIdDt().toUnqualifiedVersionless().getValue(), searchParameterId);
 						throw new PreconditionFailedException(Msg.code(1093) + msg);
 					}
 				}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4Test.java

@@ -1108,6 +1108,25 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 		}
 	}
 
+	@Test
+	public void testTransactionCreateInlineMatchUrlWithAllowInlineMatchUrlReferencesSettingNotEnabled() {
+		Bundle request = new Bundle();
+
+		myStorageSettings.setAllowInlineMatchUrlReferences(false);
+
+		Observation o = new Observation();
+		o.getCode().setText("Some Observation");
+		o.getSubject().setReference("Patient?identifier=urn%3Asystem%7C");
+		request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
+
+		try {
+			mySystemDao.transaction(mySrd, request);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals(Msg.code(2282) + "Inline match URLs are not supported on this server. Cannot process reference: \"Patient?identifier=urn%3Asystem%7C\"", e.getMessage());
+		}
+	}
+
 	@Test
 	public void testTransactionMissingResourceForPost() {
 		Bundle request = new Bundle();

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/BaseSearchParamWithInlineReferencesExtractor.java

@@ -0,0 +1,158 @@
+package ca.uhn.fhir.jpa.searchparam.extractor;
+
+/*-
+ * #%L
+ * HAPI FHIR Storage api
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
+import ca.uhn.fhir.jpa.dao.MatchResourceUrlService;
+import ca.uhn.fhir.jpa.dao.index.DaoResourceLinkResolver;
+import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
+import ca.uhn.fhir.jpa.util.MemoryCacheService;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.FhirTerser;
+import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+
+public abstract class BaseSearchParamWithInlineReferencesExtractor<T extends IResourcePersistentId> implements ISearchParamWithInlineReferencesExtractor {
+	private static final Logger ourLog = LoggerFactory.getLogger(BaseSearchParamWithInlineReferencesExtractor.class);
+
+	protected FhirContext myFhirContext;
+	protected JpaStorageSettings myStorageSettings;
+	@Autowired
+	private MatchResourceUrlService<T> myMatchResourceUrlService;
+	@Autowired
+	private DaoResourceLinkResolver<T> myDaoResourceLinkResolver;
+	@Autowired
+	private MemoryCacheService myMemoryCacheService;
+	@Autowired
+	private IIdHelperService<T> myIdHelperService;
+
+	@Override
+	public void extractInlineReferences(RequestDetails theRequestDetails, IBaseResource theResource, TransactionDetails theTransactionDetails) {
+		FhirTerser terser = myFhirContext.newTerser();
+		List<IBaseReference> allRefs = terser.getAllPopulatedChildElementsOfType(theResource, IBaseReference.class);
+		for (IBaseReference nextRef : allRefs) {
+			IIdType nextId = nextRef.getReferenceElement();
+			String nextIdText = nextId.getValue();
+			if (nextIdText == null) {
+				continue;
+			}
+			int qmIndex = nextIdText.indexOf('?');
+			if (qmIndex != -1) {
+				if (!myStorageSettings.isAllowInlineMatchUrlReferences()) {
+					String msg = myFhirContext.getLocalizer().getMessage(BaseStorageDao.class, "inlineMatchNotSupported", UrlUtil.sanitizeUrlPart(nextRef.getReferenceElement().getValueAsString()));
+					throw new InvalidRequestException(Msg.code(2282) + msg);
+				}
+				nextIdText = truncateReference(nextIdText, qmIndex);
+				String resourceTypeString = nextIdText.substring(0, nextIdText.indexOf('?')).replace("/", "");
+				RuntimeResourceDefinition matchResourceDef = myFhirContext.getResourceDefinition(resourceTypeString);
+				if (matchResourceDef == null) {
+					String msg = myFhirContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidMatchUrlInvalidResourceType", nextId.getValue(), resourceTypeString);
+					throw new InvalidRequestException(Msg.code(1090) + msg);
+				}
+				Class<? extends IBaseResource> matchResourceType = matchResourceDef.getImplementingClass();
+
+				T resolvedMatch = null;
+				if (theTransactionDetails != null) {
+					resolvedMatch = (T) theTransactionDetails.getResolvedMatchUrls().get(nextIdText);
+				}
+
+				Set<T> matches;
+				if (resolvedMatch != null && !IResourcePersistentId.NOT_FOUND.equals(resolvedMatch)) {
+					matches = Set.of(resolvedMatch);
+				} else {
+					matches = myMatchResourceUrlService.processMatchUrl(nextIdText, matchResourceType, theTransactionDetails, theRequestDetails);
+				}
+
+				T match;
+				if (matches.isEmpty()) {
+					Optional<IBasePersistedResource> placeholderOpt = myDaoResourceLinkResolver.createPlaceholderTargetIfConfiguredToDoSo(matchResourceType, nextRef, null, theRequestDetails, theTransactionDetails);
+					if (placeholderOpt.isPresent()) {
+						match = (T) placeholderOpt.get().getPersistentId();
+						match.setAssociatedResourceId(placeholderOpt.get().getIdDt());
+						theTransactionDetails.addResolvedMatchUrl(nextIdText, match);
+						myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.MATCH_URL, nextIdText, match);
+					} else {
+						String msg = myFhirContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidMatchUrlNoMatches", nextId.getValue());
+						throw new ResourceNotFoundException(Msg.code(1091) + msg);
+					}
+				} else if (matches.size() > 1) {
+					String msg = myFhirContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidMatchUrlMultipleMatches", nextId.getValue());
+					throw new PreconditionFailedException(Msg.code(1092) + msg);
+				} else {
+					match = matches.iterator().next();
+				}
+
+				IIdType newId = myIdHelperService.translatePidIdToForcedId(myFhirContext, resourceTypeString, match);
+				ourLog.debug("Replacing inline match URL[{}] with ID[{}}", nextId.getValue(), newId);
+
+				if (theTransactionDetails != null) {
+					String previousReference = nextRef.getReferenceElement().getValue();
+					theTransactionDetails.addRollbackUndoAction(() -> nextRef.setReference(previousReference));
+				}
+				nextRef.setReference(newId.getValue());
+			}
+		}
+	}
+
+	// Removes parts of the reference keeping only the valuable parts, the resource type and searchparam
+	private static String truncateReference(String nextIdText, int qmIndex) {
+		for (int i = qmIndex - 1; i >= 0; i--) {
+			if (nextIdText.charAt(i) == '/') {
+				if (i < nextIdText.length() - 1 && nextIdText.charAt(i + 1) == '?') {
+					// Just in case the URL is in the form Patient/?foo=bar
+					continue;
+				}
+				nextIdText = nextIdText.substring(i + 1);
+				break;
+			}
+		}
+		return nextIdText;
+	}
+
+	@Autowired
+	public void setStorageSettings(JpaStorageSettings theStorageSettings) {
+		myStorageSettings = theStorageSettings;
+	}
+
+	@Autowired
+	public void setContext(FhirContext theContext) {
+		myFhirContext = theContext;
+	}
+}

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/searchparam/extractor/ISearchParamWithInlineReferencesExtractor.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.searchparam.extractor;
+
+/*-
+ * #%L
+ * HAPI FHIR Storage api
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+public interface ISearchParamWithInlineReferencesExtractor {
+
+	/**
+	 * Handle references within the resource that are match URLs, for example references like "Patient?identifier=foo".
+	 * These match URLs are resolved and replaced with the ID of the
+	 * matching resource.
+	 */
+	void extractInlineReferences(RequestDetails theRequestDetails, IBaseResource theResource, TransactionDetails theTransactionDetails);
+}