Jd 20241126 fix versioned refs in transaction bundles (#6521)

* tests, fix, minor refactoring

* spotless

* changelog

* changelog update

---------

Co-authored-by: jdar <justin.dar@smiledigitalhealth.com>

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ParserOptions.java

@@ -23,12 +23,14 @@ import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.util.CollectionUtil;
 import jakarta.annotation.Nonnull;
 import jakarta.annotation.Nullable;
+import org.apache.commons.lang3.Validate;
 
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 /**
  * This object supplies default configuration to all {@link IParser parser} instances
@@ -126,6 +128,17 @@ public class ParserOptions {
 		return myDontStripVersionsFromReferencesAtPaths;
 	}
 
+	/**
+	 * Returns a sub-collection of {@link #getDontStripVersionsFromReferencesAtPaths()} containing only paths
+	 * for the given resource type.
+	 */
+	public Set<String> getDontStripVersionsFromReferencesAtPathsByResourceType(String theResourceType) {
+		Validate.notEmpty(theResourceType, "theResourceType must not be null or empty");
+		return myDontStripVersionsFromReferencesAtPaths.stream()
+				.filter(referencePath -> referencePath.startsWith(theResourceType + "."))
+				.collect(Collectors.toSet());
+	}
+
 	/**
 	 * If supplied value(s), any resource references at the specified paths will have their
 	 * resource versions encoded instead of being automatically stripped during the encoding

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6519-fix-versioned-refs-from-transaction-bundles.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 6519
+jira: SMILE-8776
+title: "Previously, when posting a transaction bundle with versioned references, the server would strip versioned 
+references form the resource even when configured not to do so. This has now been fixed."

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4VersionedReferenceTest.java

@@ -26,6 +26,7 @@ import org.hl7.fhir.r4.model.MessageHeader;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Task;
@@ -42,6 +43,8 @@ import java.util.Collections;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Optional;
+import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
@@ -65,6 +68,8 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		myStorageSettings.setDeleteEnabled(new JpaStorageSettings().isDeleteEnabled());
 		myStorageSettings.setRespectVersionsForSearchIncludes(new JpaStorageSettings().isRespectVersionsForSearchIncludes());
 		myStorageSettings.setAutoVersionReferenceAtPaths(new JpaStorageSettings().getAutoVersionReferenceAtPaths());
+		myStorageSettings.setAutoCreatePlaceholderReferenceTargets(new JpaStorageSettings().isAutoCreatePlaceholderReferenceTargets());
+		myStorageSettings.setResourceClientIdStrategy(new JpaStorageSettings().getResourceClientIdStrategy());
 	}
 
 	@Nested
@@ -667,6 +672,88 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		assertEquals(patientIdString, observation.getSubject().getReference());
 	}
 
+	@Test
+	public void testDontStripVersionsFromRefsAtPaths_inTransactionBundle_shouldPreserveVersion() {
+		Set<String> referencePaths = Set.of("AuditEvent.entity.what","MessageHeader.focus","Provenance.target","Provenance.entity.what");
+
+		myFhirContext.getParserOptions().setDontStripVersionsFromReferencesAtPaths(referencePaths);
+		myStorageSettings.setAutoVersionReferenceAtPaths("Encounter.subject");
+		myStorageSettings.setAutoCreatePlaceholderReferenceTargets(true);
+		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
+
+		postBundleAndAssertProvenanceRefsPreserved("/transaction-bundles/transaction-with-client-supplied-versioned-reference.json");
+	}
+
+	@Test
+	public void testDontStripVersionsFromRefsAtAllPaths_inTransactionBundle_shouldPreserveVersion() {
+		myFhirContext.getParserOptions().setStripVersionsFromReferences(false);
+		myStorageSettings.setAutoVersionReferenceAtPaths("Encounter.subject");
+		myStorageSettings.setAutoCreatePlaceholderReferenceTargets(true);
+		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
+
+		postBundleAndAssertProvenanceRefsPreserved("/transaction-bundles/transaction-with-client-supplied-versioned-reference.json");
+	}
+
+	@Test
+	public void testDontStripVersionsFromRefsAtPaths_withTransactionBundleAndAutoVersionSet_shouldPreserveVersion() {
+		Set<String> referencePaths = Set.of("AuditEvent.entity.what","MessageHeader.focus","Provenance.target","Provenance.entity.what");
+
+		myFhirContext.getParserOptions().setDontStripVersionsFromReferencesAtPaths(referencePaths);
+		myStorageSettings.setAutoVersionReferenceAtPaths("Provenance.entity.what");
+		myStorageSettings.setAutoCreatePlaceholderReferenceTargets(true);
+		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
+
+		Encounter encounter = new Encounter();
+		encounter.setId("242976");
+		myEncounterDao.update(encounter);
+
+		postBundleAndAssertProvenanceRefsPreserved("/transaction-bundles/transaction-with-client-supplied-versioned-reference.json");
+	}
+
+	private Provenance postBundleAndAssertProvenanceRefsPreserved(String theBundlePath) {
+		Bundle bundle = myFhirContext.newJsonParser().parseResource(Bundle.class,
+			new InputStreamReader(
+				FhirResourceDaoR4VersionedReferenceTest.class.getResourceAsStream(theBundlePath)));
+
+		Bundle transaction = mySystemDao.transaction(new SystemRequestDetails(), bundle);
+
+		Optional<Bundle.BundleEntryComponent> provenanceEntry = transaction.getEntry().stream().filter(entry -> entry.getResponse().getLocation().contains("Provenance")).findFirst();
+		assertThat(provenanceEntry).isPresent();
+		String provenanceLocation = provenanceEntry.get().getResponse().getLocation();
+		Provenance provenance = myProvenanceDao.read(new IdDt(provenanceLocation));
+		assertThat(provenance.getEntity().get(0).getWhat().getReference()).isEqualTo("Encounter/242976/_history/1");
+		return provenance;
+	}
+
+	@Test
+	public void testDontStripVersionsFromRefsAtPathsAndAutoVersionSameTransaction_withTransactionBundle_shouldPreserveVersion() {
+		Set<String> referencePaths = Set.of("AuditEvent.entity.what","MessageHeader.focus","Provenance.target","Provenance.entity.what", "Provenance.agent.who");
+
+		myFhirContext.getParserOptions().setDontStripVersionsFromReferencesAtPaths(referencePaths);
+		myStorageSettings.setAutoVersionReferenceAtPaths("Provenance.agent.who");
+		myStorageSettings.setAutoCreatePlaceholderReferenceTargets(true);
+		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
+
+		Provenance provenance = postBundleAndAssertProvenanceRefsPreserved("/transaction-bundles/transaction-with-client-assigned-version-reference-and-auto-version-field.json");
+		assertThat(provenance.getAgent().get(0).getWho().getReference()).isEqualTo("Patient/237643/_history/1");
+	}
+
+	@Test
+	public void testDontStripVersionsFromRefsAtPaths_withTransactionBundleAndPreExistingReference_shouldPreserveVersion() {
+		Set<String> referencePaths = Set.of("AuditEvent.entity.what","MessageHeader.focus","Provenance.target","Provenance.entity.what");
+
+		myFhirContext.getParserOptions().setDontStripVersionsFromReferencesAtPaths(referencePaths);
+		myStorageSettings.setAutoVersionReferenceAtPaths("Provenance.entity.what");
+		myStorageSettings.setAutoCreatePlaceholderReferenceTargets(true);
+		myStorageSettings.setResourceClientIdStrategy(JpaStorageSettings.ClientIdStrategyEnum.ANY);
+
+		Encounter encounter = new Encounter();
+		encounter.setId("242976");
+		myEncounterDao.update(encounter);
+
+		postBundleAndAssertProvenanceRefsPreserved("/transaction-bundles/transaction-with-client-supplied-versioned-reference-and-pre-existing-ref.json");
+	}
+
 	@Test
 	public void testDontOverwriteExistingVersion() {
 		myFhirContext.getParserOptions().setStripVersionsFromReferences(false);

hapi-fhir-jpaserver-test-r4/src/test/resources/transaction-bundles/transaction-with-client-assigned-version-reference-and-auto-version-field.json

@@ -0,0 +1,136 @@
+{
+	"resourceType": "Bundle",
+	"type": "transaction",
+	"entry": [
+		{
+			"fullUrl": "https://smilecdrmock.harrisarc.ca/fhir-system/Encounter/242976",
+			"resource": {
+				"resourceType": "Encounter",
+				"id": "242976",
+				"meta": {
+					"versionId": "4",
+					"lastUpdated": "2024-07-26T10:43:49.287-04:00",
+					"source": "#d9d63c433c828a4d"
+				},
+				"identifier": [
+					{
+						"use": "official",
+						"type": {
+							"coding": [
+								{
+									"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+									"code": "VN"
+								}
+							]
+						},
+						"system": "https://www.ciussscentreouest.ca/ids/visit-number/iclsc/dlm",
+						"value": "ICLSCRepair1-1"
+					}
+				],
+				"status": "entered-in-error",
+				"class": {
+					"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+					"code": "AMB",
+					"display": "Ambulatory"
+				},
+				"type": [
+					{
+						"coding": [
+							{
+								"system": "https://www.ciussscentreouest.ca/codesystem/mode/iclsc",
+								"code": "1",
+								"display": "1 Rencontre présence usager"
+							}
+						]
+					}
+				],
+				"subject": {
+					"reference": "Patient/237643"
+				},
+				"period": {
+					"start": "2020-07-26T13:36:00-04:00",
+					"end": "2020-07-26T14:06:00-04:00"
+				},
+				"length": {
+					"value": 30,
+					"unit": "min"
+				}
+			},
+			"request": {
+				"method": "PUT",
+				"url": "Encounter/242976"
+			}
+		},
+		{
+			"resource": {
+				"resourceType": "Provenance",
+				"target": [
+					{
+						"reference": "#"
+					}
+				],
+				"recorded": "2024-07-26T14:51:28.222+00:00",
+				"activity": {
+					"coding": [
+						{
+							"system": "http://terminology.hl7.org/CodeSystem/v3-DataOperation",
+							"code": "CREATE",
+							"display": "Create"
+						}
+					]
+				},
+				"agent": [
+					{
+						"role": [
+							{
+								"coding": [
+									{
+										"system": "http://terminology.hl7.org/CodeSystem/v3-RoleClass",
+										"code": "AGNT",
+										"display": "Agent"
+									}
+								]
+							}
+						],
+						"who": {
+							"display": "ICLSC Encounter Repair loop",
+							"reference": "Patient/237643"
+						}
+					}
+				],
+				"entity": [
+					{
+						"role": "source",
+						"what": {
+							"reference": "Encounter/242976/_history/1"
+						}
+					}
+				]
+			},
+			"request": {
+				"method": "POST",
+				"url": "Provenance"
+			}
+		},
+		{
+			"resource": {
+				"resourceType": "Patient",
+				"id": "237643",
+				"identifier" : [{
+					"system" : "urn:oid:1.2.36.146.595.217.0.1",
+					"value" : "abc"
+				}],
+				"name": [ {
+					"family": "smith",
+					"given": [ "John" ]
+				} ],
+				"gender": "male",
+				"birthDate": "1988-08-10"
+			},
+			"request": {
+				"method": "PUT",
+				"url": "Patient/237643"
+			}
+		}
+	]
+}

hapi-fhir-jpaserver-test-r4/src/test/resources/transaction-bundles/transaction-with-client-supplied-versioned-reference-and-pre-existing-ref.json

@@ -0,0 +1,56 @@
+{
+    "resourceType": "Bundle",
+    "type": "transaction",
+    "entry": [
+        {
+            "resource": {
+                "resourceType": "Provenance",
+                "target": [
+                    {
+                        "reference": "#"
+                    }
+                ],
+                "recorded": "2024-07-26T14:51:28.222+00:00",
+                "activity": {
+                    "coding": [
+                        {
+                            "system": "http://terminology.hl7.org/CodeSystem/v3-DataOperation",
+                            "code": "CREATE",
+                            "display": "Create"
+                        }
+                    ]
+                },
+                "agent": [
+                    {
+                        "role": [
+                            {
+                                "coding": [
+                                    {
+                                        "system": "http://terminology.hl7.org/CodeSystem/v3-RoleClass",
+                                        "code": "AGNT",
+                                        "display": "Agent"
+                                    }
+                                ]
+                            }
+                        ],
+                        "who": {
+                            "display": "ICLSC Encounter Repair loop"
+                        }
+                    }
+                ],
+                "entity": [
+                    {
+                        "role": "source",
+                        "what": {
+                            "reference": "Encounter/242976/_history/1"
+                        }
+                    }
+                ]
+            },
+            "request": {
+                "method": "POST",
+                "url": "Provenance"
+            }
+        }
+    ]
+}

hapi-fhir-jpaserver-test-r4/src/test/resources/transaction-bundles/transaction-with-client-supplied-versioned-reference.json

@@ -0,0 +1,115 @@
+{
+    "resourceType": "Bundle",
+    "type": "transaction",
+    "entry": [
+        {
+            "fullUrl": "https://smilecdrmock.harrisarc.ca/fhir-system/Encounter/242976",
+            "resource": {
+                "resourceType": "Encounter",
+                "id": "242976",
+                "meta": {
+                    "versionId": "4",
+                    "lastUpdated": "2024-07-26T10:43:49.287-04:00",
+                    "source": "#d9d63c433c828a4d"
+                },
+                "identifier": [
+                    {
+                        "use": "official",
+                        "type": {
+                            "coding": [
+                                {
+                                    "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                                    "code": "VN"
+                                }
+                            ]
+                        },
+                        "system": "https://www.ciussscentreouest.ca/ids/visit-number/iclsc/dlm",
+                        "value": "ICLSCRepair1-1"
+                    }
+                ],
+                "status": "entered-in-error",
+                "class": {
+                    "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode",
+                    "code": "AMB",
+                    "display": "Ambulatory"
+                },
+                "type": [
+                    {
+                        "coding": [
+                            {
+                                "system": "https://www.ciussscentreouest.ca/codesystem/mode/iclsc",
+                                "code": "1",
+                                "display": "1 Rencontre présence usager"
+                            }
+                        ]
+                    }
+                ],
+                "subject": {
+                    "reference": "Patient/237643"
+                },
+                "period": {
+                    "start": "2020-07-26T13:36:00-04:00",
+                    "end": "2020-07-26T14:06:00-04:00"
+                },
+                "length": {
+                    "value": 30,
+                    "unit": "min"
+                }
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Encounter/242976"
+            }
+        },
+        {
+            "resource": {
+                "resourceType": "Provenance",
+                "target": [
+                    {
+                        "reference": "#"
+                    }
+                ],
+                "recorded": "2024-07-26T14:51:28.222+00:00",
+                "activity": {
+                    "coding": [
+                        {
+                            "system": "http://terminology.hl7.org/CodeSystem/v3-DataOperation",
+                            "code": "CREATE",
+                            "display": "Create"
+                        }
+                    ]
+                },
+                "agent": [
+                    {
+                        "role": [
+                            {
+                                "coding": [
+                                    {
+                                        "system": "http://terminology.hl7.org/CodeSystem/v3-RoleClass",
+                                        "code": "AGNT",
+                                        "display": "Agent"
+                                    }
+                                ]
+                            }
+                        ],
+                        "who": {
+                            "display": "ICLSC Encounter Repair loop"
+                        }
+                    }
+                ],
+                "entity": [
+                    {
+                        "role": "source",
+                        "what": {
+                            "reference": "Encounter/242976/_history/1"
+                        }
+                    }
+                ]
+            },
+            "request": {
+                "method": "POST",
+                "url": "Provenance"
+            }
+        }
+    ]
+}

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java

@@ -727,6 +727,27 @@ public abstract class BaseStorageDao {
 		ourLog.debug(msg);
 	}
 
+	/**
+	 * Extracts a list of references that have versions in their ID whose versions should not be stripped
+	 *
+	 * @return A set of references that should not have their client-given versions stripped according to the
+	 * 		   versioned references settings.
+	 */
+	public static Set<IBaseReference> extractReferencesToAvoidReplacement(
+			FhirContext theFhirContext, IBaseResource theResource) {
+		if (!theFhirContext
+				.getParserOptions()
+				.getDontStripVersionsFromReferencesAtPaths()
+				.isEmpty()) {
+			String theResourceType = theFhirContext.getResourceType(theResource);
+			Set<String> versionReferencesPaths = theFhirContext
+					.getParserOptions()
+					.getDontStripVersionsFromReferencesAtPathsByResourceType(theResourceType);
+			return getReferencesWithOrWithoutVersionId(versionReferencesPaths, theFhirContext, theResource, false);
+		}
+		return Collections.emptySet();
+	}
+
 	/**
 	 * Extracts a list of references that should be auto-versioned.
 	 *
@@ -760,7 +781,7 @@ public abstract class BaseStorageDao {
 				MetaUtil.getAutoVersionReferencesAtPath(theResource.getMeta(), resourceType);
 
 		if (!autoVersionReferencesAtPaths.isEmpty()) {
-			return getReferencesWithoutVersionId(autoVersionReferencesAtPaths, theFhirContext, theResource);
+			return getReferencesWithOrWithoutVersionId(autoVersionReferencesAtPaths, theFhirContext, theResource, true);
 		}
 		return Collections.emptySet();
 	}
@@ -776,17 +797,30 @@ public abstract class BaseStorageDao {
 			String resourceName = theFhirContext.getResourceType(theResource);
 			Set<String> autoVersionReferencesPaths =
 					theStorageSettings.getAutoVersionReferenceAtPathsByResourceType(resourceName);
-			return getReferencesWithoutVersionId(autoVersionReferencesPaths, theFhirContext, theResource);
+			return getReferencesWithOrWithoutVersionId(autoVersionReferencesPaths, theFhirContext, theResource, true);
 		}
 		return Collections.emptySet();
 	}
 
-	private static Set<IBaseReference> getReferencesWithoutVersionId(
+	/**
-			Set<String> autoVersionReferencesPaths, FhirContext theFhirContext, IBaseResource theResource) {
+	 * Extracts references from given resource and filters references by those with versions, or those without versions.
-		return autoVersionReferencesPaths.stream()
+	 *
+	 * @param theVersionReferencesPaths the paths from which to extract references from
+	 * @param theFhirContext the FHIR context
+	 * @param theResource the resource from which to extract references from
+	 * @param theShouldFilterByRefsWithoutVersionId If true, this method will return only references without a version. If false, this method will return only references with a version.
+	 * @return Set of references contained in the resource with or without versions
+	 */
+	private static Set<IBaseReference> getReferencesWithOrWithoutVersionId(
+			Set<String> theVersionReferencesPaths,
+			FhirContext theFhirContext,
+			IBaseResource theResource,
+			boolean theShouldFilterByRefsWithoutVersionId) {
+		return theVersionReferencesPaths.stream()
 				.map(fullPath -> theFhirContext.newTerser().getValues(theResource, fullPath, IBaseReference.class))
 				.flatMap(Collection::stream)
-				.filter(reference -> !reference.getReferenceElement().hasVersionIdPart())
+				.filter(reference ->
+						reference.getReferenceElement().hasVersionIdPart() ^ theShouldFilterByRefsWithoutVersionId)
 				.collect(Collectors.toMap(ref -> ref, ref -> ref, (oldRef, newRef) -> oldRef, IdentityHashMap::new))
 				.keySet();
 	}

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

@@ -274,19 +274,20 @@ public abstract class BaseTransactionProcessor {
 
 	@SuppressWarnings("unchecked")
 	private void handleTransactionCreateOrUpdateOutcome(
-			IdSubstitutionMap idSubstitutions,
+			IdSubstitutionMap theIdSubstitutions,
-			Map<IIdType, DaoMethodOutcome> idToPersistedOutcome,
+			Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
-			IIdType nextResourceId,
+			IIdType theNextResourceId,
-			DaoMethodOutcome outcome,
+			DaoMethodOutcome theOutcome,
-			IBase newEntry,
+			IBase theNewEntry,
 			String theResourceType,
 			IBaseResource theRes,
 			RequestDetails theRequestDetails) {
-		IIdType newId = outcome.getId().toUnqualified();
+		IIdType newId = theOutcome.getId().toUnqualified();
-		IIdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
+		IIdType resourceId =
-		if (newId.equals(resourceId) == false) {
+				isPlaceholder(theNextResourceId) ? theNextResourceId : theNextResourceId.toUnqualifiedVersionless();
-			if (!nextResourceId.isEmpty()) {
+		if (!newId.equals(resourceId)) {
-				idSubstitutions.put(resourceId, newId);
+			if (!theNextResourceId.isEmpty()) {
+				theIdSubstitutions.put(resourceId, newId);
 			}
 			if (isPlaceholder(resourceId)) {
 				/*
@@ -294,27 +295,27 @@ public abstract class BaseTransactionProcessor {
 				 */
 				IIdType id = myContext.getVersion().newIdType();
 				id.setValue(theResourceType + '/' + resourceId.getValue());
-				idSubstitutions.put(id, newId);
+				theIdSubstitutions.put(id, newId);
 			}
 		}
 
-		populateIdToPersistedOutcomeMap(idToPersistedOutcome, newId, outcome);
+		populateIdToPersistedOutcomeMap(theIdToPersistedOutcome, newId, theOutcome);
 
-		if (shouldSwapBinaryToActualResource(theRes, theResourceType, nextResourceId)) {
+		if (shouldSwapBinaryToActualResource(theRes, theResourceType, theNextResourceId)) {
-			theRes = idToPersistedOutcome.get(newId).getResource();
+			theRes = theIdToPersistedOutcome.get(newId).getResource();
 		}
 
-		if (outcome.getCreated()) {
+		if (theOutcome.getCreated()) {
-			myVersionAdapter.setResponseStatus(newEntry, toStatusString(Constants.STATUS_HTTP_201_CREATED));
+			myVersionAdapter.setResponseStatus(theNewEntry, toStatusString(Constants.STATUS_HTTP_201_CREATED));
 		} else {
-			myVersionAdapter.setResponseStatus(newEntry, toStatusString(Constants.STATUS_HTTP_200_OK));
+			myVersionAdapter.setResponseStatus(theNewEntry, toStatusString(Constants.STATUS_HTTP_200_OK));
 		}
 
 		Date lastModified = getLastModified(theRes);
-		myVersionAdapter.setResponseLastModified(newEntry, lastModified);
+		myVersionAdapter.setResponseLastModified(theNewEntry, lastModified);
 
-		if (outcome.getOperationOutcome() != null) {
+		if (theOutcome.getOperationOutcome() != null) {
-			myVersionAdapter.setResponseOutcome(newEntry, outcome.getOperationOutcome());
+			myVersionAdapter.setResponseOutcome(theNewEntry, theOutcome.getOperationOutcome());
 		}
 
 		if (theRequestDetails != null) {
@@ -323,9 +324,9 @@ public abstract class BaseTransactionProcessor {
 					RestfulServerUtils.parsePreferHeader(null, prefer).getReturn();
 			if (preferReturn != null) {
 				if (preferReturn == PreferReturnEnum.REPRESENTATION) {
-					if (outcome.getResource() != null) {
+					if (theOutcome.getResource() != null) {
-						outcome.fireResourceViewCallbacks();
+						theOutcome.fireResourceViewCallbacks();
-						myVersionAdapter.setResource(newEntry, outcome.getResource());
+						myVersionAdapter.setResource(theNewEntry, theOutcome.getResource());
 					}
 				}
 			}
@@ -1685,9 +1686,9 @@ public abstract class BaseTransactionProcessor {
 			IdSubstitutionMap theIdSubstitutions,
 			Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
 			StopWatch theTransactionStopWatch,
-			EntriesToProcessMap entriesToProcess,
+			EntriesToProcessMap theEntriesToProcess,
-			Set<IIdType> nonUpdatedEntities,
+			Set<IIdType> theNonUpdatedEntities,
-			Set<IBasePersistedResource> updatedEntities) {
+			Set<IBasePersistedResource> theUpdatedEntities) {
 		FhirTerser terser = myContext.newTerser();
 		theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
 		IdentityHashMap<DaoMethodOutcome, Set<IBaseReference>> deferredIndexesForAutoVersioning = null;
@@ -1712,6 +1713,9 @@ public abstract class BaseTransactionProcessor {
 
 			Set<IBaseReference> referencesToAutoVersion =
 					BaseStorageDao.extractReferencesToAutoVersion(myContext, myStorageSettings, nextResource);
+			Set<IBaseReference> referencesToKeepClientSuppliedVersion =
+					BaseStorageDao.extractReferencesToAvoidReplacement(myContext, nextResource);
+
 			if (referencesToAutoVersion.isEmpty()) {
 				// no references to autoversion - we can do the resolve and save now
 				resolveReferencesThenSaveAndIndexResource(
@@ -1719,13 +1723,14 @@ public abstract class BaseTransactionProcessor {
 						theTransactionDetails,
 						theIdSubstitutions,
 						theIdToPersistedOutcome,
-						entriesToProcess,
+						theEntriesToProcess,
-						nonUpdatedEntities,
+						theNonUpdatedEntities,
-						updatedEntities,
+						theUpdatedEntities,
 						terser,
 						nextOutcome,
 						nextResource,
-						referencesToAutoVersion); // this is empty
+						referencesToAutoVersion, // this is empty
+						referencesToKeepClientSuppliedVersion);
 			} else {
 				// we have autoversioned things to defer until later
 				if (deferredIndexesForAutoVersioning == null) {
@@ -1742,19 +1747,22 @@ public abstract class BaseTransactionProcessor {
 				DaoMethodOutcome nextOutcome = nextEntry.getKey();
 				Set<IBaseReference> referencesToAutoVersion = nextEntry.getValue();
 				IBaseResource nextResource = nextOutcome.getResource();
+				Set<IBaseReference> referencesToKeepClientSuppliedVersion =
+						BaseStorageDao.extractReferencesToAvoidReplacement(myContext, nextResource);
 
 				resolveReferencesThenSaveAndIndexResource(
 						theRequest,
 						theTransactionDetails,
 						theIdSubstitutions,
 						theIdToPersistedOutcome,
-						entriesToProcess,
+						theEntriesToProcess,
-						nonUpdatedEntities,
+						theNonUpdatedEntities,
-						updatedEntities,
+						theUpdatedEntities,
 						terser,
 						nextOutcome,
 						nextResource,
-						referencesToAutoVersion);
+						referencesToAutoVersion,
+						referencesToKeepClientSuppliedVersion);
 			}
 		}
 	}
@@ -1764,15 +1772,16 @@ public abstract class BaseTransactionProcessor {
 			TransactionDetails theTransactionDetails,
 			IdSubstitutionMap theIdSubstitutions,
 			Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
-			EntriesToProcessMap entriesToProcess,
+			EntriesToProcessMap theEntriesToProcess,
-			Set<IIdType> nonUpdatedEntities,
+			Set<IIdType> theNonUpdatedEntities,
-			Set<IBasePersistedResource> updatedEntities,
+			Set<IBasePersistedResource> theUpdatedEntities,
-			FhirTerser terser,
+			FhirTerser theTerser,
 			DaoMethodOutcome theDaoMethodOutcome,
 			IBaseResource theResource,
-			Set<IBaseReference> theReferencesToAutoVersion) {
+			Set<IBaseReference> theReferencesToAutoVersion,
+			Set<IBaseReference> theReferencesToKeepClientSuppliedVersion) {
 		// References
-		List<ResourceReferenceInfo> allRefs = terser.getAllResourceReferences(theResource);
+		List<ResourceReferenceInfo> allRefs = theTerser.getAllResourceReferences(theResource);
 		for (ResourceReferenceInfo nextRef : allRefs) {
 			IBaseReference resourceReference = nextRef.getResourceReference();
 			IIdType nextId = resourceReference.getReferenceElement();
@@ -1794,18 +1803,20 @@ public abstract class BaseTransactionProcessor {
 				}
 			}
 			if (newId != null || theIdSubstitutions.containsSource(nextId)) {
+				if (shouldReplaceResourceReference(
+						theReferencesToAutoVersion, theReferencesToKeepClientSuppliedVersion, resourceReference)) {
 					if (newId == null) {
 						newId = theIdSubstitutions.getForSource(nextId);
 					}
 					if (newId != null) {
 						ourLog.debug(" * Replacing resource ref {} with {}", nextId, newId);
-
 						if (theReferencesToAutoVersion.contains(resourceReference)) {
 							replaceResourceReference(newId, resourceReference, theTransactionDetails);
 						} else {
 							replaceResourceReference(newId.toVersionless(), resourceReference, theTransactionDetails);
 						}
 					}
+				}
 			} else if (nextId.getValue().startsWith("urn:")) {
 				throw new InvalidRequestException(
 						Msg.code(541) + "Unable to satisfy placeholder ID " + nextId.getValue()
@@ -1858,7 +1869,7 @@ public abstract class BaseTransactionProcessor {
 		// URIs
 		Class<? extends IPrimitiveType<?>> uriType = (Class<? extends IPrimitiveType<?>>)
 				myContext.getElementDefinition("uri").getImplementingClass();
-		List<? extends IPrimitiveType<?>> allUris = terser.getAllPopulatedChildElementsOfType(theResource, uriType);
+		List<? extends IPrimitiveType<?>> allUris = theTerser.getAllPopulatedChildElementsOfType(theResource, uriType);
 		for (IPrimitiveType<?> nextRef : allUris) {
 			if (nextRef instanceof IIdType) {
 				continue; // No substitution on the resource ID itself!
@@ -1886,7 +1897,7 @@ public abstract class BaseTransactionProcessor {
 		IJpaDao jpaDao = (IJpaDao) dao;
 
 		IBasePersistedResource updateOutcome = null;
-		if (updatedEntities.contains(theDaoMethodOutcome.getEntity())) {
+		if (theUpdatedEntities.contains(theDaoMethodOutcome.getEntity())) {
 			boolean forceUpdateVersion = !theReferencesToAutoVersion.isEmpty();
 			String matchUrl = theDaoMethodOutcome.getMatchUrl();
 			RestOperationTypeEnum operationType = theDaoMethodOutcome.getOperationType();
@@ -1903,7 +1914,7 @@ public abstract class BaseTransactionProcessor {
 					theTransactionDetails);
 			updateOutcome = daoMethodOutcome.getEntity();
 			theDaoMethodOutcome = daoMethodOutcome;
-		} else if (!nonUpdatedEntities.contains(theDaoMethodOutcome.getId())) {
+		} else if (!theNonUpdatedEntities.contains(theDaoMethodOutcome.getId())) {
 			updateOutcome = jpaDao.updateEntity(
 					theRequest,
 					theResource,
@@ -1920,7 +1931,7 @@ public abstract class BaseTransactionProcessor {
 		if (updateOutcome != null) {
 			IIdType newId = updateOutcome.getIdDt();
 
-			IIdType entryId = entriesToProcess.getIdWithVersionlessComparison(newId);
+			IIdType entryId = theEntriesToProcess.getIdWithVersionlessComparison(newId);
 			if (entryId != null && !StringUtils.equals(entryId.getValue(), newId.getValue())) {
 				entryId.setValue(newId.getValue());
 			}
@@ -1930,12 +1941,32 @@ public abstract class BaseTransactionProcessor {
 			theIdSubstitutions.updateTargets(newId);
 
 			if (theDaoMethodOutcome.getOperationOutcome() != null) {
-				IBase responseEntry = entriesToProcess.getResponseBundleEntryWithVersionlessComparison(newId);
+				IBase responseEntry = theEntriesToProcess.getResponseBundleEntryWithVersionlessComparison(newId);
 				myVersionAdapter.setResponseOutcome(responseEntry, theDaoMethodOutcome.getOperationOutcome());
 			}
 		}
 	}
 
+	/**
+	 * We should replace the references when
+	 * 1. It is not a reference we should keep the client-supplied version for as configured by `DontStripVersionsFromReferences` or
+	 * 2. It is a reference that has been identified for auto versioning or
+	 * 3. Is a placeholder reference
+	 * @param theReferencesToAutoVersion list of references identified for auto versioning
+	 * @param theReferencesToKeepClientSuppliedVersion list of references that we should not strip the version for
+	 * @param theResourceReference the resource reference
+	 * @return true if we should replace the resource reference, false if we should keep the client provided reference
+	 */
+	private boolean shouldReplaceResourceReference(
+			Set<IBaseReference> theReferencesToAutoVersion,
+			Set<IBaseReference> theReferencesToKeepClientSuppliedVersion,
+			IBaseReference theResourceReference) {
+		return (!theReferencesToKeepClientSuppliedVersion.contains(theResourceReference)
+						&& myContext.getParserOptions().isStripVersionsFromReferences())
+				|| theReferencesToAutoVersion.contains(theResourceReference)
+				|| isPlaceholder(theResourceReference.getReferenceElement());
+	}
+
 	private void replaceResourceReference(
 			IIdType theReferenceId, IBaseReference theResourceReference, TransactionDetails theTransactionDetails) {
 		addRollbackReferenceRestore(theTransactionDetails, theResourceReference);