Merge remote-tracking branch 'origin/5745-ready-state-batch2' into 5818-update-batch2-framework-with-gate_waiting-state

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java

@@ -609,34 +609,35 @@ public abstract class BaseParser implements IParser {
 	private boolean isStripVersionsFromReferences(
 			CompositeChildElement theCompositeChildElement, IBaseResource theResource) {
 
-		Set<String> autoVersionReferencesAtPathExtensions =
+		if (theResource != null) {
-				MetaUtil.getAutoVersionReferencesAtPath(theResource.getMeta(), myContext.getResourceType(theResource));
+			Set<String> autoVersionReferencesAtPathExtensions = MetaUtil.getAutoVersionReferencesAtPath(
+					theResource.getMeta(), myContext.getResourceType(theResource));
 
 			if (!autoVersionReferencesAtPathExtensions.isEmpty()
 					&& theCompositeChildElement.anyPathMatches(autoVersionReferencesAtPathExtensions)) {
 				return false;
 			}
+		}
 
 		Boolean stripVersionsFromReferences = myStripVersionsFromReferences;
 		if (stripVersionsFromReferences != null) {
 			return stripVersionsFromReferences;
 		}
 
-		if (myContext.getParserOptions().isStripVersionsFromReferences() == false) {
+		if (!myContext.getParserOptions().isStripVersionsFromReferences()) {
 			return false;
 		}
 
 		Set<String> dontStripVersionsFromReferencesAtPaths = myDontStripVersionsFromReferencesAtPaths;
-		if (dontStripVersionsFromReferencesAtPaths != null) {
+		if (dontStripVersionsFromReferencesAtPaths != null
-			if (dontStripVersionsFromReferencesAtPaths.isEmpty() == false
+				&& !dontStripVersionsFromReferencesAtPaths.isEmpty()
 				&& theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths)) {
 			return false;
 		}
-		}
 
 		dontStripVersionsFromReferencesAtPaths =
 				myContext.getParserOptions().getDontStripVersionsFromReferencesAtPaths();
-		return dontStripVersionsFromReferencesAtPaths.isEmpty() != false
+		return dontStripVersionsFromReferencesAtPaths.isEmpty()
 				|| !theCompositeChildElement.anyPathMatches(dontStripVersionsFromReferencesAtPaths);
 	}
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/5842-json-parser-npe.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5842
+title: "Fixed a bug where an NPE was being thrown when trying to serialize a FHIR fragment (e.g., backboneElement
+, compound datatype) to a string representation if the fragment contains a `Reference`."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -127,7 +127,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 
 		Builder version = forVersion(VersionEnum.V7_2_0);
 
-		// allow null codes in concept map targets
+		// allow null codes in concept map targets (see comment on "20190722.27" if you are going to change this)
 		version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
 				.modifyColumn("20240327.1", "TARGET_CODE")
 				.nullable()
@@ -2497,10 +2497,26 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 				.modifyColumn("20190722.26", "SYSTEM_VERSION")
 				.nullable()
 				.withType(ColumnTypeEnum.STRING, 200);
+
+		/*
+		DISABLED THIS STEP (20190722.27) ON PURPOSE BECAUSE IT STARTED CAUSING FAILURES ON MSSQL FOR A FRESH DB.
+		I left it here for historical purposes.
+		The reason for the failure is as follows. The TARGET_CODE column was originally 'not nullable' when it was
+		first introduced. And in 7_2_0, it is being changed to a nullable column (see 20240327.1 in init720()).
+		Starting with 7_2_0, on a fresh db, we create the table with nullable TARGET_CODE (as it is made nullable now).
+		Since we run all migration steps on fresh db, this step will try to convert the column which is created as nullable
+		to not nullable (which will then need to be coverted back to nullable in 7_2_0 migration).
+		Changing a nullable column to not nullable is not allowed in
+		MSSQL if there is an index on the column, which is the case here, as there is IDX_CNCPT_MP_GRP_ELM_TGT_CD
+		on this column. Since init720() has the right migration
+		step, where the column is set to nullable and has the right type and length, this statement is also
+		not necessary anymore even for not fresh dbs.
+
 		version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
 				.modifyColumn("20190722.27", "TARGET_CODE")
 				.nonNullable()
 				.withType(ColumnTypeEnum.STRING, 500);
+		*/
 		version.onTable("TRM_CONCEPT_MAP_GRP_ELM_TGT")
 				.modifyColumn("20190722.28", "VALUESET_URL")
 				.nullable()

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/StorageSettings.java

@@ -97,7 +97,7 @@ public class StorageSettings {
 	private boolean myDefaultSearchParamsCanBeOverridden = true;
 	private Set<Subscription.SubscriptionChannelType> mySupportedSubscriptionTypes = new HashSet<>();
 	private boolean myAutoCreatePlaceholderReferenceTargets;
-	private boolean myCrossPartitionSubscriptionEnabled = false;
+	private boolean myCrossPartitionSubscriptionEnabled = true;
 	private Integer myBundleBatchPoolSize = DEFAULT_BUNDLE_BATCH_POOL_SIZE;
 	private Integer myBundleBatchMaxPoolSize = DEFAULT_BUNDLE_BATCH_MAX_POOL_SIZE;
 	private boolean myEnableInMemorySubscriptionMatching = true;

hapi-fhir-jpaserver-subscription/src/main/java/ca/uhn/fhir/jpa/subscription/model/config/SubscriptionModelConfig.java

@@ -20,6 +20,7 @@
 package ca.uhn.fhir.jpa.subscription.model.config;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
 import org.springframework.context.annotation.Bean;
@@ -29,8 +30,9 @@ import org.springframework.context.annotation.Configuration;
 public class SubscriptionModelConfig {
 
 	@Bean
-	public SubscriptionCanonicalizer subscriptionCanonicalizer(FhirContext theFhirContext) {
+	public SubscriptionCanonicalizer subscriptionCanonicalizer(
-		return new SubscriptionCanonicalizer(theFhirContext);
+			FhirContext theFhirContext, StorageSettings theStorageSettings) {
+		return new SubscriptionCanonicalizer(theFhirContext, theStorageSettings);
 	}
 
 	@Bean

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/match/matcher/subscriber/SubscriptionRegisteringSubscriberTest.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionRegistry;
 import ca.uhn.fhir.jpa.subscription.model.ResourceModifiedJsonMessage;
@@ -50,7 +51,7 @@ public class SubscriptionRegisteringSubscriberTest {
 	@Mock
 	private SubscriptionRegistry mySubscriptionRegistry;
 	@Spy
-	private SubscriptionCanonicalizer mySubscriptionCanonicalizer = new SubscriptionCanonicalizer(myFhirContext);
+	private SubscriptionCanonicalizer mySubscriptionCanonicalizer = new SubscriptionCanonicalizer(myFhirContext, new StorageSettings());
 	@Mock
 	private DaoRegistry myDaoRegistry;
 	@Mock

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionRegistryTest.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.subscription.match.registry;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.ISubscriptionDeliveryChannelNamer;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionChannelRegistry;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
@@ -33,7 +34,7 @@ public class SubscriptionRegistryTest {
 	static FhirContext ourFhirContext = FhirContext.forR4Cached();
 
 	@Spy
-	SubscriptionCanonicalizer mySubscriptionCanonicalizer = new SubscriptionCanonicalizer(ourFhirContext);
+	SubscriptionCanonicalizer mySubscriptionCanonicalizer = new SubscriptionCanonicalizer(ourFhirContext, new StorageSettings());
 
 	@Spy
 	ISubscriptionDeliveryChannelNamer mySubscriptionDeliveryChannelNamer = new TestChannelNamer();

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/CanonicalSubscriptionTest.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.subscription.module;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
 import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryJsonMessage;
@@ -8,12 +9,15 @@ import ca.uhn.fhir.jpa.subscription.model.ResourceDeliveryMessage;
 import ca.uhn.fhir.util.HapiExtensions;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import jakarta.annotation.Nonnull;
 import org.assertj.core.util.Lists;
 import org.hamcrest.Matchers;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -66,7 +70,7 @@ public class CanonicalSubscriptionTest {
 
 	@Test
 	public void testCanonicalSubscriptionRetainsMetaTags() throws IOException {
-		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4());
+		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4(), new StorageSettings());
 		CanonicalSubscription sub1 = canonicalizer.canonicalize(makeMdmSubscription());
 		assertTrue(sub1.getTags().keySet().contains(TAG_SYSTEM));
 		assertEquals(sub1.getTags().get(TAG_SYSTEM), TAG_VALUE);
@@ -74,7 +78,7 @@ public class CanonicalSubscriptionTest {
 
 	@Test
 	public void emailDetailsEquals() {
-		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4());
+		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4(), new StorageSettings());
 		CanonicalSubscription sub1 = canonicalizer.canonicalize(makeEmailSubscription());
 		CanonicalSubscription sub2 = canonicalizer.canonicalize(makeEmailSubscription());
 		assertTrue(sub1.equals(sub2));
@@ -82,7 +86,7 @@ public class CanonicalSubscriptionTest {
 
 	@Test
 	public void testSerializeMultiPartitionSubscription(){
-		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4());
+		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4(), new StorageSettings());
 		Subscription subscription = makeEmailSubscription();
 		subscription.addExtension(HapiExtensions.EXTENSION_SUBSCRIPTION_CROSS_PARTITION, new BooleanType().setValue(true));
 		CanonicalSubscription canonicalSubscription = canonicalizer.canonicalize(subscription);
@@ -90,28 +94,30 @@ public class CanonicalSubscriptionTest {
 		assertEquals(canonicalSubscription.getCrossPartitionEnabled(), true);
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSerializeIncorrectMultiPartitionSubscription(){
+	@ValueSource(booleans = {true, false})
-		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4());
+	public void testSerializeIncorrectMultiPartitionSubscription(boolean theIsCrossPartitionEnabled){
+		final StorageSettings storageSettings = buildStorageSettings(theIsCrossPartitionEnabled);
+		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4(), storageSettings);
 		Subscription subscription = makeEmailSubscription();
 		subscription.addExtension(HapiExtensions.EXTENSION_SUBSCRIPTION_CROSS_PARTITION, new StringType().setValue("false"));
 		CanonicalSubscription canonicalSubscription = canonicalizer.canonicalize(subscription);
 
-		System.out.print(canonicalSubscription);
+		assertEquals(canonicalSubscription.getCrossPartitionEnabled(), theIsCrossPartitionEnabled);
-
-		assertEquals(canonicalSubscription.getCrossPartitionEnabled(), false);
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSerializeNonMultiPartitionSubscription(){
+	@ValueSource(booleans = {true, false})
-		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4());
+	public void testSerializeNonMultiPartitionSubscription(boolean theIsCrossPartitionEnabled){
+		final StorageSettings storageSettings = buildStorageSettings(theIsCrossPartitionEnabled);
+		SubscriptionCanonicalizer canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4(), storageSettings);
 		Subscription subscription = makeEmailSubscription();
 		subscription.addExtension(HapiExtensions.EXTENSION_SUBSCRIPTION_CROSS_PARTITION, new BooleanType().setValue(false));
 		CanonicalSubscription canonicalSubscription = canonicalizer.canonicalize(subscription);
 
 		System.out.print(canonicalSubscription);
 
-		assertEquals(canonicalSubscription.getCrossPartitionEnabled(), false);
+		assertEquals(canonicalSubscription.getCrossPartitionEnabled(), theIsCrossPartitionEnabled);
 	}
 
 	@Test
@@ -154,4 +160,11 @@ public class CanonicalSubscriptionTest {
 		ResourceDeliveryMessage payload = resourceDeliveryMessage.getPayload();
 		return payload.getSubscription();
 	}
+
+	@Nonnull
+	private static StorageSettings buildStorageSettings(boolean theIsCrossPartitionEnabled) {
+		final StorageSettings storageSettings = new StorageSettings();
+		storageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
+		return storageSettings;
+	}
 }

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/module/subscriber/SubscriptionMatchingSubscriberTest.java

@@ -27,6 +27,8 @@ import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Nested;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.mockito.Answers;
 import org.mockito.InjectMocks;
 import org.mockito.Mock;
@@ -38,6 +40,7 @@ import java.util.Optional;
 
 import static ca.uhn.fhir.jpa.subscription.match.matcher.subscriber.SubscriptionCriteriaParser.TypeEnum.STARTYPE_EXPRESSION;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.ArgumentMatchers.eq;
 import static org.mockito.Mockito.atLeastOnce;
@@ -227,8 +230,10 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		ourObservationListener.awaitExpected();
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSubscriptionAndResourceOnDiffPartitionNotMatch() throws InterruptedException {
+	@ValueSource(booleans = {true, false})
+	public void testSubscriptionAndResourceOnDiffPartitionNotMatch(boolean theIsCrossPartitionEnabled) throws InterruptedException {
+		myStorageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
 		myPartitionSettings.setPartitioningEnabled(true);
 		String payload = "application/fhir+json";
 
@@ -240,13 +245,18 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		mockSubscriptionRead(requestPartitionId, subscription);
 		sendSubscription(subscription, requestPartitionId, true);
 
-		mySubscriptionResourceNotMatched.setExpectedCount(1);
+		final ThrowsInterrupted throwsInterrupted = () -> sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionId(0));
-		sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionId(0));
+		if (theIsCrossPartitionEnabled) {
-		mySubscriptionResourceNotMatched.awaitExpected();
+			runWithinLatchLogicExpectSuccess(throwsInterrupted);
+		} else {
+			runWithLatchLogicExpectFailure(throwsInterrupted);
+		}
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSubscriptionAndResourceOnDiffPartitionNotMatchPart2() throws InterruptedException {
+	@ValueSource(booleans = {true, false})
+	public void testSubscriptionAndResourceOnDiffPartitionNotMatchPart2(boolean theIsCrossPartitionEnabled) throws InterruptedException {
+		myStorageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
 		myPartitionSettings.setPartitioningEnabled(true);
 		String payload = "application/fhir+json";
 
@@ -258,13 +268,19 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		mockSubscriptionRead(requestPartitionId, subscription);
 		sendSubscription(subscription, requestPartitionId, true);
 
-		mySubscriptionResourceNotMatched.setExpectedCount(1);
+		final ThrowsInterrupted throwsInterrupted = () -> sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionId(1));
-		sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionId(1));
+
-		mySubscriptionResourceNotMatched.awaitExpected();
+		if (theIsCrossPartitionEnabled) {
+			runWithinLatchLogicExpectSuccess(throwsInterrupted);
+		} else {
+			runWithLatchLogicExpectFailure(throwsInterrupted);
+		}
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSubscriptionOnDefaultPartitionAndResourceOnDiffPartitionNotMatch() throws InterruptedException {
+	@ValueSource(booleans = {true, false})
+	public void testSubscriptionOnDefaultPartitionAndResourceOnDiffPartitionNotMatch(boolean theIsCrossPartitionEnabled) throws InterruptedException {
+		myStorageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
 		myPartitionSettings.setPartitioningEnabled(true);
 		String payload = "application/fhir+json";
 
@@ -276,13 +292,19 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		mockSubscriptionRead(requestPartitionId, subscription);
 		sendSubscription(subscription, requestPartitionId, true);
 
-		mySubscriptionResourceNotMatched.setExpectedCount(1);
+		final ThrowsInterrupted throwsInterrupted = () -> sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionId(1));
-		sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionId(1));
+
-		mySubscriptionResourceNotMatched.awaitExpected();
+		if (theIsCrossPartitionEnabled) {
+			runWithinLatchLogicExpectSuccess(throwsInterrupted);
+		} else {
+			runWithLatchLogicExpectFailure(throwsInterrupted);
+		}
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSubscriptionOnAPartitionAndResourceOnDefaultPartitionNotMatch() throws InterruptedException {
+	@ValueSource(booleans = {true, false})
+	public void testSubscriptionOnAPartitionAndResourceOnDefaultPartitionNotMatch(boolean theIsCrossPartitionEnabled) throws InterruptedException {
+		myStorageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
 		myPartitionSettings.setPartitioningEnabled(true);
 		String payload = "application/fhir+json";
 
@@ -294,9 +316,13 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		mockSubscriptionRead(requestPartitionId, subscription);
 		sendSubscription(subscription, requestPartitionId, true);
 
-		mySubscriptionResourceNotMatched.setExpectedCount(1);
+		final ThrowsInterrupted throwsInterrupted = () -> sendObservation(code, "SNOMED-CT", RequestPartitionId.defaultPartition());
-		sendObservation(code, "SNOMED-CT", RequestPartitionId.defaultPartition());
+
-		mySubscriptionResourceNotMatched.awaitExpected();
+		if (theIsCrossPartitionEnabled) {
+			runWithinLatchLogicExpectSuccess(throwsInterrupted);
+		} else {
+			runWithLatchLogicExpectFailure(throwsInterrupted);
+		}
 	}
 
 	@Test
@@ -320,8 +346,10 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		ourObservationListener.awaitExpected();
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testSubscriptionOnOnePartitionDoNotMatchResourceOnMultiplePartitions() throws InterruptedException {
+	@ValueSource(booleans = {true, false})
+	public void testSubscriptionOnOnePartitionDoNotMatchResourceOnMultiplePartitions(boolean theIsCrossPartitionEnabled) throws InterruptedException {
+		myStorageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
 		myPartitionSettings.setPartitioningEnabled(true);
 		String payload = "application/fhir+json";
 
@@ -333,10 +361,13 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 		mockSubscriptionRead(requestPartitionId, subscription);
 		sendSubscription(subscription, requestPartitionId, true);
 
-		mySubscriptionResourceNotMatched.setExpectedCount(1);
+		final ThrowsInterrupted throwsInterrupted = () -> sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionIds(Collections.synchronizedList(Lists.newArrayList(0, 2))));
-		List<Integer> partitionId = Collections.synchronizedList(Lists.newArrayList(0, 2));
+
-		sendObservation(code, "SNOMED-CT", RequestPartitionId.fromPartitionIds(partitionId));
+		if (theIsCrossPartitionEnabled) {
-		mySubscriptionResourceNotMatched.awaitExpected();
+			runWithinLatchLogicExpectSuccess(throwsInterrupted);
+		} else {
+			runWithLatchLogicExpectFailure(throwsInterrupted);
+		}
 	}
 
 	@Test
@@ -519,4 +550,31 @@ public class SubscriptionMatchingSubscriberTest extends BaseBlockingQueueSubscri
 			verify(message, atLeastOnce()).getPayloadId(null);
 		}
 	}
+
+	private interface ThrowsInterrupted {
+		void runOrThrow() throws InterruptedException;
+	}
+
+	private void runWithLatchLogicExpectFailure(ThrowsInterrupted theRunnable) {
+		try {
+			mySubscriptionResourceNotMatched.setExpectedCount(1);
+			theRunnable.runOrThrow();
+			mySubscriptionResourceNotMatched.awaitExpected();
+		} catch (InterruptedException exception) {
+			Thread.currentThread().interrupt();
+		}
+	}
+
+	private void runWithinLatchLogicExpectSuccess(ThrowsInterrupted theRunnable) {
+		try {
+			ourObservationListener.setExpectedCount(1);
+			mySubscriptionResourceMatched.setExpectedCount(1);
+			theRunnable.runOrThrow();
+			mySubscriptionResourceMatched.awaitExpected();
+			ourObservationListener.awaitExpected();
+		} catch (InterruptedException exception) {
+			fail();
+			Thread.currentThread().interrupt();
+		}
+	}
 }

hapi-fhir-jpaserver-subscription/src/test/java/ca/uhn/fhir/jpa/subscription/submit/interceptor/SubscriptionValidatingInterceptorTest.java

@@ -6,6 +6,7 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
 import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionCanonicalizer;
@@ -226,7 +227,7 @@ public class SubscriptionValidatingInterceptorTest {
 
 		@Bean
 		SubscriptionCanonicalizer subscriptionCanonicalizer(FhirContext theFhirContext) {
-			return new SubscriptionCanonicalizer(theFhirContext);
+			return new SubscriptionCanonicalizer(theFhirContext, new StorageSettings());
 		}
 
 		@Bean

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/partition/PartitionedSubscriptionTriggeringR4Test.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.interceptor.api.Interceptor;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.dao.r4.BasePartitioningR4Test;
@@ -24,15 +25,13 @@ import jakarta.servlet.ServletException;
 import org.awaitility.core.ConditionTimeoutException;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.Observation;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.ValueSource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -41,6 +40,7 @@ import java.time.LocalDate;
 import java.time.Month;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Stream;
 
 import static org.awaitility.Awaitility.await;
 import static org.hamcrest.CoreMatchers.containsString;
@@ -146,8 +146,10 @@ public class PartitionedSubscriptionTriggeringR4Test extends BaseSubscriptionsR4
 		Assertions.assertEquals(Constants.CT_FHIR_JSON_NEW, BaseSubscriptionsR4Test.ourRestfulServer.getRequestContentTypes().get(0));
 	}
 
-	@Test
+	@ParameterizedTest
-	public void testCreateSubscriptionInPartitionAndResourceInDifferentPartition() throws Exception {
+	@ValueSource(booleans = {true, false})
+	public void testCreateSubscriptionInPartitionAndResourceInDifferentPartition(boolean theIsCrossPartitionEnabled) throws Exception {
+		myStorageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
 		String payload = "application/fhir+json";
 
 		String code = "1000000050";
@@ -169,28 +171,37 @@ public class PartitionedSubscriptionTriggeringR4Test extends BaseSubscriptionsR4
 		Assertions.assertEquals(0, BaseSubscriptionsR4Test.ourPatientProvider.getCountCreate());
 
 		try {
-			// Should have 0 matching subscription, if we get 1 update count then the test fails
 			BaseSubscriptionsR4Test.ourPatientProvider.waitForUpdateCount(1);
-			fail();
+			if (!theIsCrossPartitionEnabled) {
+				fail("Expecting a timeout and 0 matching subscriptions and thus a timeout if cross partition is DISabled");
+			}
+			Assertions.assertEquals(1, BaseSubscriptionsR4Test.ourRestfulServer.getRequestContentTypes().size());
 		} catch (ConditionTimeoutException e) {
+			if (theIsCrossPartitionEnabled) {
+				fail("Expecting no timeout and 1 matching subscriptions and thus a timeout if cross partition is enabled");
+			} else {
+				// Should have 0 matching subscription, if we get 1 update count then the test fails
 				Assertions.assertEquals(0, BaseSubscriptionsR4Test.ourRestfulServer.getRequestContentTypes().size());
 			}
 		}
+	}
 
-
+	@ParameterizedTest
-	@Test
+	@ValueSource(booleans = {true, false})
-	public void testManualTriggeredSubscriptionDoesNotCheckOutsideOfPartition() throws Exception {
+	public void testManualTriggeredSubscriptionDoesNotCheckOutsideOfPartition(boolean theIsCrossPartitionEnabled) throws Exception {
+		myStorageSettings.setCrossPartitionSubscriptionEnabled(theIsCrossPartitionEnabled);
 		String payload = "application/fhir+json";
 		String code = "1000000050";
 		String criteria1 = "Observation?code=SNOMED-CT|" + code + "&_format=xml";
 
 		//Given: We store a resource in partition 2
 		myPartitionInterceptor.setRequestPartitionId(REQ_PART_2);
-		IIdType observationIdPartitionTwo = myDaoRegistry.getResourceDao("Observation").create(createBaseObservation(code, "SNOMED-CT"), mySrd).getId();
+		final IFhirResourceDao observation = myDaoRegistry.getResourceDao("Observation");
+		IIdType observationIdPartitionTwo = observation.create(createBaseObservation(code, "SNOMED-CT"), mySrd).getId();
 
 		//Given: We store a similar resource in partition 1
 		myPartitionInterceptor.setRequestPartitionId(REQ_PART_1);
-		IIdType observationIdPartitionOne = myDaoRegistry.getResourceDao("Observation").create(createBaseObservation(code, "SNOMED-CT"), mySrd).getId();
+		IIdType observationIdPartitionOne = observation.create(createBaseObservation(code, "SNOMED-CT"), mySrd).getId();
 
 		//Given: We create a subscrioption on Partition 1
 		IIdType subscriptionId = myDaoRegistry.getResourceDao("Subscription").create(newSubscription(criteria1, payload), mySrd).getId();
@@ -204,8 +215,14 @@ public class PartitionedSubscriptionTriggeringR4Test extends BaseSubscriptionsR4
 
 		waitForQueueToDrain();
 		List<Observation> resourceUpdates = BaseSubscriptionsR4Test.ourObservationProvider.getResourceUpdates();
+		if (theIsCrossPartitionEnabled) {
+			assertThat(resourceUpdates.size(), is(equalTo(2)));
+			assertThat(resourceUpdates.stream().map(Resource::getId).sorted().toList(),
+				is(equalTo(Stream.of(observationIdPartitionOne, observationIdPartitionTwo).map(Object::toString).sorted().toList())));
+		} else {
 			assertThat(resourceUpdates.size(), is(equalTo(1)));
 			assertThat(resourceUpdates.get(0).getId(), is(equalTo(observationIdPartitionOne.toString())));
+		}
 
 		String responseValue = resultParameters.getParameter().get(0).getValue().primitiveValue();
 		assertThat(responseValue, containsString("Subscription triggering job submitted as JOB ID"));

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/subscription/SubscriptionValidatingInterceptorTest.java

@@ -5,6 +5,7 @@ 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.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionMatchingStrategy;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionStrategyEvaluator;
@@ -63,7 +64,7 @@ public class SubscriptionValidatingInterceptorTest {
 	@BeforeEach
 	public void before() {
 		mySvc = new SubscriptionValidatingInterceptor();
-		mySubscriptionCanonicalizer = spy(new SubscriptionCanonicalizer(myCtx));
+		mySubscriptionCanonicalizer = spy(new SubscriptionCanonicalizer(myCtx, new StorageSettings()));
 		mySvc.setSubscriptionCanonicalizerForUnitTest(mySubscriptionCanonicalizer);
 		mySvc.setDaoRegistryForUnitTest(myDaoRegistry);
 		mySvc.setSubscriptionStrategyEvaluatorForUnitTest(mySubscriptionStrategyEvaluator);

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplPatch.java

@@ -27,6 +27,11 @@ import org.hl7.fhir.instance.model.api.IIdType;
 
 import java.util.Set;
 
+/**
+ * @deprecated Users should be instead be granted more granular write permissions that cover PATCH operations.
+ * @since 7.2.0
+ */
+@Deprecated
 class RuleImplPatch extends BaseRule {
 	private boolean myAllRequests;
 

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/api/config/JpaStorageSettings.java

@@ -48,6 +48,7 @@ import java.util.TreeSet;
 
 @SuppressWarnings("JavadocLinkAsPlainText")
 public class JpaStorageSettings extends StorageSettings {
+	private static final Logger ourLog = LoggerFactory.getLogger(JpaStorageSettings.class);
 
 	/**
 	 * Default value for {@link #getBulkExportFileMaximumSize()}: 100 MB
@@ -105,7 +106,6 @@ public class JpaStorageSettings extends StorageSettings {
 	 */
 	private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
 
-	private static final Logger ourLog = LoggerFactory.getLogger(JpaStorageSettings.class);
 	private static final int DEFAULT_REINDEX_BATCH_SIZE = 800;
 	private static final int DEFAULT_MAXIMUM_DELETE_CONFLICT_COUNT = 60;
 	/**

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionCanonicalizer.java

@@ -23,6 +23,7 @@ import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.match.matcher.matching.SubscriptionMatchingStrategy;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
@@ -68,10 +69,23 @@ public class SubscriptionCanonicalizer {
 	private static final Logger ourLog = LoggerFactory.getLogger(SubscriptionCanonicalizer.class);
 
 	final FhirContext myFhirContext;
+	private final StorageSettings myStorageSettings;
 
 	@Autowired
+	public SubscriptionCanonicalizer(FhirContext theFhirContext, StorageSettings theStorageSettings) {
+		myFhirContext = theFhirContext;
+		myStorageSettings = theStorageSettings;
+	}
+
+	// TODO:  LD:  remove this constructor once all callers call the 2 arg constructor above
+
+	/**
+	 * @deprecated All callers should invoke {@link SubscriptionCanonicalizer()} instead.
+	 */
+	@Deprecated
 	public SubscriptionCanonicalizer(FhirContext theFhirContext) {
 		myFhirContext = theFhirContext;
+		myStorageSettings = new StorageSettings();
 	}
 
 	public CanonicalSubscription canonicalize(IBaseResource theSubscription) {
@@ -109,7 +123,7 @@ public class SubscriptionCanonicalizer {
 			retVal.setIdElement(subscription.getIdElement());
 			retVal.setPayloadString(channel.getPayload());
 			retVal.setTags(extractTags(subscription));
-			retVal.setCrossPartitionEnabled(SubscriptionUtil.isCrossPartition(theSubscription));
+			handleCrossPartition(theSubscription, retVal);
 			retVal.setSendDeleteMessages(extractDeleteExtensionDstu2(subscription));
 		} catch (FHIRException theE) {
 			throw new InternalErrorException(Msg.code(557) + theE);
@@ -161,7 +175,7 @@ public class SubscriptionCanonicalizer {
 			retVal.setPayloadSearchCriteria(
 					getExtensionString(subscription, HapiExtensions.EXT_SUBSCRIPTION_PAYLOAD_SEARCH_CRITERIA));
 			retVal.setTags(extractTags(subscription));
-			retVal.setCrossPartitionEnabled(SubscriptionUtil.isCrossPartition(theSubscription));
+			handleCrossPartition(theSubscription, retVal);
 
 			if (retVal.getChannelType() == CanonicalSubscriptionChannelType.EMAIL) {
 				String from;
@@ -292,7 +306,7 @@ public class SubscriptionCanonicalizer {
 				getExtensionString(subscription, HapiExtensions.EXT_SUBSCRIPTION_PAYLOAD_SEARCH_CRITERIA));
 		retVal.setTags(extractTags(subscription));
 		setPartitionIdOnReturnValue(theSubscription, retVal);
-		retVal.setCrossPartitionEnabled(SubscriptionUtil.isCrossPartition(theSubscription));
+		handleCrossPartition(theSubscription, retVal);
 
 		List<org.hl7.fhir.r4.model.CanonicalType> profiles =
 				subscription.getMeta().getProfile();
@@ -497,6 +511,8 @@ public class SubscriptionCanonicalizer {
 			retVal.setSendDeleteMessages(extension.getValueBooleanType().booleanValue());
 		}
 
+		handleCrossPartition(theSubscription, retVal);
+
 		return retVal;
 	}
 
@@ -561,6 +577,8 @@ public class SubscriptionCanonicalizer {
 
 		setR5FlagsBasedOnChannelType(subscription, retVal);
 
+		handleCrossPartition(theSubscription, retVal);
+
 		return retVal;
 	}
 
@@ -762,4 +780,12 @@ public class SubscriptionCanonicalizer {
 		}
 		return status.getValueAsString();
 	}
+
+	private void handleCrossPartition(IBaseResource theSubscription, CanonicalSubscription retVal) {
+		if (myStorageSettings.isCrossPartitionSubscriptionEnabled()) {
+			retVal.setCrossPartitionEnabled(true);
+		} else {
+			retVal.setCrossPartitionEnabled(SubscriptionUtil.isCrossPartition(theSubscription));
+		}
+	}
 }

hapi-fhir-storage/src/test/java/ca/uhn/fhir/jpa/subscription/match/registry/SubscriptionCanonicalizerTest.java

@@ -1,23 +1,35 @@
 package ca.uhn.fhir.jpa.subscription.match.registry;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.model.entity.StorageSettings;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscription;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalSubscriptionChannelType;
 import ca.uhn.fhir.jpa.subscription.model.CanonicalTopicSubscriptionFilter;
 import ca.uhn.fhir.model.api.ExtensionDt;
+import ca.uhn.fhir.model.api.IFhirVersion;
+import ca.uhn.fhir.model.dstu2.FhirDstu2;
 import ca.uhn.fhir.model.primitive.BooleanDt;
 import ca.uhn.fhir.subscription.SubscriptionConstants;
 import ca.uhn.fhir.subscription.SubscriptionTestDataHelper;
+import org.hl7.fhir.dstu3.hapi.ctx.FhirDstu3;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.hapi.ctx.FhirR4;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.Subscription;
+import org.hl7.fhir.r4b.hapi.ctx.FhirR4B;
+import org.hl7.fhir.r5.hapi.ctx.FhirR5;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.Enumerations;
 import org.jetbrains.annotations.NotNull;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
 import org.junit.jupiter.params.provider.ValueSource;
 
+import java.util.stream.Stream;
+
 import static ca.uhn.fhir.rest.api.Constants.CT_FHIR_JSON_NEW;
 import static ca.uhn.fhir.util.HapiExtensions.EX_SEND_DELETE_MESSAGES;
 import static org.hamcrest.MatcherAssert.assertThat;
@@ -26,12 +38,13 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.params.provider.Arguments.arguments;
 
 class SubscriptionCanonicalizerTest {
 
 	FhirContext r4Context = FhirContext.forR4();
 
-	private final SubscriptionCanonicalizer testedSC = new SubscriptionCanonicalizer(r4Context);
+	private final SubscriptionCanonicalizer testedSC = new SubscriptionCanonicalizer(r4Context, new StorageSettings());
 
 	@Test
 	void testCanonicalizeR4SendDeleteMessagesSetsExtensionValueNotPresent() {
@@ -72,7 +85,7 @@ class SubscriptionCanonicalizerTest {
 	@Test
 	public void testCanonicalizeDstu2SendDeleteMessages() {
 		//setup
-		SubscriptionCanonicalizer dstu2Canonicalizer = new SubscriptionCanonicalizer(FhirContext.forDstu2Cached());
+		SubscriptionCanonicalizer dstu2Canonicalizer = new SubscriptionCanonicalizer(FhirContext.forDstu2Cached(), new StorageSettings());
 		ca.uhn.fhir.model.dstu2.resource.Subscription dstu2Sub = new ca.uhn.fhir.model.dstu2.resource.Subscription();
 		ExtensionDt extensionDt = new ExtensionDt();
 		extensionDt.setUrl(EX_SEND_DELETE_MESSAGES);
@@ -108,7 +121,7 @@ class SubscriptionCanonicalizerTest {
 	@ValueSource(strings = {"full-resource", "id-only", "empty"})
 	public void testR5Canonicalize_returnsCorrectCanonicalSubscription(String thePayloadContent) {
 		// setup
-		SubscriptionCanonicalizer r5Canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR5Cached());
+		SubscriptionCanonicalizer r5Canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR5Cached(), new StorageSettings());
 		org.hl7.fhir.r5.model.Subscription.SubscriptionPayloadContent payloadContent =
 				org.hl7.fhir.r5.model.Subscription.SubscriptionPayloadContent.fromCode(thePayloadContent);
 		org.hl7.fhir.r5.model.Subscription subscription = buildR5Subscription(payloadContent);
@@ -148,7 +161,7 @@ class SubscriptionCanonicalizerTest {
 		// Example drawn from http://build.fhir.org/ig/HL7/fhir-subscription-backport-ig/Subscription-subscription-zulip.json.html
 
 		// setup
-		SubscriptionCanonicalizer r4bCanonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4BCached());
+		SubscriptionCanonicalizer r4bCanonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4BCached(), new StorageSettings());
 		org.hl7.fhir.r4b.model.Subscription subscription = buildR4BSubscription(thePayloadContent);
 
 		// execute
@@ -160,6 +173,46 @@ class SubscriptionCanonicalizerTest {
 		verifyChannelParameters(canonical, thePayloadContent);
 	}
 
+
+	private static Stream<Arguments> crossPartitionParams() {
+		return Stream.of(
+			arguments(true, FhirContext.forDstu2Cached()),
+			arguments(false, FhirContext.forDstu2Cached()),
+			arguments(true, FhirContext.forDstu3Cached()),
+			arguments(false, FhirContext.forDstu3Cached()),
+			arguments(true, FhirContext.forR4Cached()),
+			arguments(false, FhirContext.forR4Cached()),
+			arguments(true, FhirContext.forR4BCached()),
+			arguments(false, FhirContext.forR4BCached()),
+			arguments(true, FhirContext.forR5Cached()),
+			arguments(false, FhirContext.forR5Cached())
+		);
+	}
+	@ParameterizedTest
+	@MethodSource("crossPartitionParams")
+	void testCrossPartition(boolean theCrossPartitionSubscriptionEnabled, FhirContext theFhirContext) {
+		final IFhirVersion version = theFhirContext.getVersion();
+		IBaseResource subscription = null;
+		if (version instanceof FhirDstu2){
+			subscription = new ca.uhn.fhir.model.dstu2.resource.Subscription();
+		} else if (version instanceof FhirDstu3){
+			subscription = new org.hl7.fhir.dstu3.model.Subscription();
+		} else if (version instanceof FhirR4){
+			subscription = new Subscription();
+		} else if (version instanceof FhirR4B){
+			subscription = new org.hl7.fhir.r4b.model.Subscription();
+		} else if (version instanceof FhirR5){
+			subscription = new org.hl7.fhir.r5.model.Subscription();
+		}
+
+		final StorageSettings storageSettings = new StorageSettings();
+		storageSettings.setCrossPartitionSubscriptionEnabled(theCrossPartitionSubscriptionEnabled);
+		final SubscriptionCanonicalizer subscriptionCanonicalizer = new SubscriptionCanonicalizer(theFhirContext, storageSettings);
+		final CanonicalSubscription canonicalSubscription = subscriptionCanonicalizer.canonicalize(subscription);
+
+		assertEquals(theCrossPartitionSubscriptionEnabled, canonicalSubscription.getCrossPartitionEnabled());
+	}
+
 	private org.hl7.fhir.r4b.model.Subscription buildR4BSubscription(String thePayloadContent) {
 		org.hl7.fhir.r4b.model.Subscription subscription = new org.hl7.fhir.r4b.model.Subscription();
 
@@ -195,7 +248,7 @@ class SubscriptionCanonicalizerTest {
 		// Example drawn from http://build.fhir.org/ig/HL7/fhir-subscription-backport-ig/Subscription-subscription-zulip.json.html
 
 		// setup
-		SubscriptionCanonicalizer r4Canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4Cached());
+		SubscriptionCanonicalizer r4Canonicalizer = new SubscriptionCanonicalizer(FhirContext.forR4Cached(), new StorageSettings());
 
 		// execute
 		Subscription subscription = SubscriptionTestDataHelper.buildR4TopicSubscriptionWithContent(thePayloadContent);

hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/JsonParserR4Test.java

@@ -1168,6 +1168,18 @@ public class JsonParserR4Test extends BaseTest {
 		assertEquals(expected, actual);
 	}
 
+	@Test
+	public void testEncodeToString_CompoundTypeWithReference() {
+		Identifier identifier = new Identifier();
+		identifier.setSystem("http://system.org");
+		identifier.setValue("123");
+		Reference reference = new Reference("Organization/1");
+		identifier.setAssigner(reference);
+		String expected = "{\"system\":\"http://system.org\",\"value\":\"123\",\"assigner\":{\"reference\":\"Organization/1\"}}";
+		String actual = ourCtx.newJsonParser().encodeToString(identifier);
+		assertEquals(expected, actual);
+	}
+
 	@Test
 	public void testEncodeToString_Resource() {
 		Patient p = new Patient();