Merge branch 'master' into 2958-consistent-error-handling

hapi-deployable-pom/pom.xml

@@ -4,7 +4,7 @@
     <parent>
 		 <groupId>ca.uhn.hapi.fhir</groupId>
 		 <artifactId>hapi-fhir</artifactId>
-		 <version>5.6.0-PRE3-SNAPSHOT</version>
+		 <version>5.6.0-PRE4-SNAPSHOT</version>
 		 <relativePath>../pom.xml</relativePath>
 	 </parent>
 

hapi-fhir-android/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FhirTerser.java

@@ -961,6 +961,7 @@ public class FhirTerser {
 				for (BaseRuntimeChildDefinition nextChild : childDef.getChildrenAndExtension()) {
 
 					List<?> values = nextChild.getAccessor().getValues(theElement);
+
 					if (values != null) {
 						for (Object nextValueObject : values) {
 							IBase nextValue;

hapi-fhir-bom/pom.xml

@@ -3,14 +3,14 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>ca.uhn.hapi.fhir</groupId>
     <artifactId>hapi-fhir-bom</artifactId>
-    <version>5.6.0-PRE3-SNAPSHOT</version>
+    <version>5.6.0-PRE4-SNAPSHOT</version>
     <packaging>pom</packaging>
 	 <name>HAPI FHIR BOM</name>
 
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
     

hapi-fhir-cli/hapi-fhir-cli-api/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java

@@ -282,7 +282,7 @@ public abstract class BaseApp {
 	}
 
 	private Optional<BaseCommand> parseCommand(String[] theArgs) {
-		Optional<BaseCommand> commandOpt = getNextCommand(theArgs);
+		Optional<BaseCommand> commandOpt = getNextCommand(theArgs, 0);
 
 		if (! commandOpt.isPresent()) {
 			String message = "Unrecognized command: " + ansi().bold().fg(Ansi.Color.RED) + theArgs[0] + ansi().boldOff().fg(Ansi.Color.WHITE);
@@ -294,8 +294,8 @@ public abstract class BaseApp {
 		return commandOpt;
 	}
 
-	private Optional<BaseCommand> getNextCommand(String[] theArgs) {
+	private Optional<BaseCommand> getNextCommand(String[] theArgs, int thePosition) {
-		return ourCommands.stream().filter(cmd -> cmd.getCommandName().equals(theArgs[0])).findFirst();
+		return ourCommands.stream().filter(cmd -> cmd.getCommandName().equals(theArgs[thePosition])).findFirst();
 	}
 
 	private void processHelp(String[] theArgs) {
@@ -303,7 +303,7 @@ public abstract class BaseApp {
 			logUsage();
 			return;
 		}
-		Optional<BaseCommand> commandOpt = getNextCommand(theArgs);
+		Optional<BaseCommand> commandOpt = getNextCommand(theArgs, 1);
 		if (! commandOpt.isPresent()) {
 			String message = "Unknown command: " + theArgs[1];
 			System.err.println(message);

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/BaseAppTest.java

@@ -0,0 +1,31 @@
+package ca.uhn.fhir.cli;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import java.io.ByteArrayOutputStream;
+import java.io.PrintStream;
+
+import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+public class BaseAppTest {
+
+	private final PrintStream standardOut = System.out;
+	private final ByteArrayOutputStream outputStreamCaptor = new ByteArrayOutputStream();
+
+	@BeforeEach
+	public void setUp() {
+		System.setOut(new PrintStream(outputStreamCaptor));
+	}
+
+	@AfterEach
+	public void tearDown() {
+		System.setOut(standardOut);
+	}
+
+	@Test
+	public void testHelpOption() {
+		App.main(new String[]{"help", "create-package"});
+		assertThat(outputStreamCaptor.toString().trim(), outputStreamCaptor.toString().trim(), containsString("Usage"));
+	}
+}

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir-cli</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../../hapi-deployable-pom</relativePath>
 	</parent>
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -30,6 +30,7 @@ import org.apache.commons.lang3.time.DateUtils;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -65,8 +66,8 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(myDataSource);
 		retVal.setJpaProperties(myJpaProperties);

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java

@@ -30,6 +30,7 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -62,8 +63,8 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(myDataSource);
 		retVal.setJpaProperties(myJpaProperties);

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java

@@ -28,6 +28,7 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -60,8 +61,8 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(myDataSource);
 		retVal.setJpaProperties(myJpaProperties);

hapi-fhir-cli/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client-okhttp/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-client/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-converter/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-dist/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2901-autoversionatpaths-with-autocreateplaceholders-no-null-pointer.yml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 2901
+jira: SMILE-3004
+title: "Processing transactions with AutoversionAtPaths set should create those resources (if AutoCreatePlaceholders is set) and use latest version as expected"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2962-custom-elastic-prefixes.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 2962
+jira: SMILE-720
+title: "Added a new DaoConfig setting called `setElasticSearchIndexPrefix(String prefix)` which will cause Hibernate search to prefix all of its tables with the provided value."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2967-hybrid-search-chain.yaml

@@ -0,0 +1,7 @@
+---
+type: fix
+issue: 2967
+jira: SMILE-2899
+title: "Previously, the system would only traverse references to discrete resources while performing a chained search.
+This fix adds support for traversing references to contained resources as well, with the limitation that the reference
+to the contained resource must be the last reference in the chain."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2973-CLI-option-help-fails.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 2973
+title: "CLI `smileutil help {command}` returns `Unknown command` which should return the usage of `command`. This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2975-elastic-improvements.yaml

@@ -0,0 +1,5 @@
+---
+type: add
+issue: 2975
+title: "Two improvements have been made to the connection to Elasticsearch. First, null username and password values are now permitted. Second, multiple hosts are now permitted via the `setHosts()` method on the ElasticHibernatePropertiesBuilder, allowing you to
+ connect to multiple elasticsearch clusters at once. Thanks to Dušan Marković for the contribution!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/2978-bundle-batch-tag-bug.yaml

@@ -0,0 +1,3 @@
+---
+type: fix
+title: "Fixed a bug where two identical tags in parallel entries being created in a batch would fail."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/lastn.md

@@ -31,12 +31,11 @@ In addition, the Elasticsearch client service, `ElasticsearchSvcImpl` will need
 ```java
   @Bean()
   public ElasticsearchSvcImpl elasticsearchSvc() {
-     String elasticsearchHost = "localhost";
+     String elasticsearchHost = "localhost:9200";
-     String elasticsearchUserId = "elastic";
+     String elasticsearchUsername = "elastic";
      String elasticsearchPassword = "changeme";
-     int elasticsearchPort = 9301;
 
-     return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUserId, elasticsearchPassword);
+     return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
   }
 ```
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/schema.md

@@ -302,6 +302,14 @@ If the server has been configured with a [Resource Server ID Strategy](/apidocs/
                 Contains the specific version (starting with 1) of the resource that this row corresponds to. 
             </td>        
         </tr>
+        <tr>
+            <td>RESOURCE_TYPE</td>
+            <td></td>
+            <td>String</td>
+            <td>
+                Contains the string specifying the type of the resource (Patient, Observation, etc).
+            </td>
+        </tr>
     </tbody>
 </table>
 
@@ -476,7 +484,7 @@ The following columns are common to **all HFJ_SPIDX_xxx tables**.
         <tr>
             <td>RES_ID</td>
             <td>FK to <a href="#HFJ_RESOURCE">HFJ_RESOURCE</a></td>
-            <td>String</td>
+            <td>Long</td>
             <td></td>
             <td>
                 Contains the PID of the resource being indexed.  

hapi-fhir-jacoco/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jaxrsserver-base/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-api/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/config/DaoConfig.java

@@ -258,6 +258,11 @@ public class DaoConfig {
 	private boolean myAccountForDateIndexNulls;
 	private boolean myTriggerSubscriptionsForNonVersioningChanges;
 
+	/**
+	 * @since 5.6.0
+	 */
+	private String myElasicSearchIndexPrefix;
+
 	/**
 	 * @since 5.6.0
 	 */
@@ -269,6 +274,7 @@ public class DaoConfig {
 	private Integer myBundleBatchPoolSize = DEFAULT_BUNDLE_BATCH_POOL_SIZE;
 	private Integer myBundleBatchMaxPoolSize = DEFAULT_BUNDLE_BATCH_MAX_POOL_SIZE;
 
+
 	/**
 	 * Constructor
 	 */
@@ -2643,6 +2649,28 @@ public class DaoConfig {
 		return retval;
 	}
 
+	/**
+	 *
+	 * Sets a prefix for any indexes created when interacting with elasticsearch. This will apply to fulltext search indexes
+	 * and terminology expansion indexes.
+	 *
+	 * @since 5.6.0
+	 */
+	public String getElasticSearchIndexPrefix() {
+		return myElasicSearchIndexPrefix;
+	}
+
+	/**
+	 *
+	 * Sets a prefix for any indexes created when interacting with elasticsearch. This will apply to fulltext search indexes
+	 * and terminology expansion indexes.
+	 *
+	 * @since 5.6.0
+	 */
+	public void setElasticSearchIndexPrefix(String thePrefix) {
+		myElasicSearchIndexPrefix = thePrefix;
+	}
+
     public enum StoreMetaSourceInformationEnum {
 		NONE(false, false),
 		SOURCE_URI(true, false),

hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirSystemDao.java

@@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.api.dao;
 
 import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
 import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
-import ca.uhn.fhir.rest.annotation.Offset;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import org.hl7.fhir.instance.model.api.IBaseBundle;

hapi-fhir-jpaserver-base/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/cache/ResourceVersionSvcDaoImpl.java

@@ -24,18 +24,23 @@ 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.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.util.QueryChunker;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.slf4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 import javax.annotation.Nonnull;
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Optional;
 import java.util.stream.Collectors;
 
 import static org.slf4j.LoggerFactory.getLogger;
@@ -52,17 +57,19 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
 	DaoRegistry myDaoRegistry;
 	@Autowired
 	IResourceTableDao myResourceTableDao;
+	@Autowired
+	IdHelperService myIdHelperService;
 
 	@Override
 	@Nonnull
-	public ResourceVersionMap getVersionMap(String theResourceName, SearchParameterMap theSearchParamMap) {
+	public ResourceVersionMap getVersionMap(RequestPartitionId theRequestPartitionId, String theResourceName, SearchParameterMap theSearchParamMap) {
 		IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(theResourceName);
 
 		if (ourLog.isDebugEnabled()) {
 			ourLog.debug("About to retrieve version map for resource type: {}", theResourceName);
 		}
 
-		List<Long> matchingIds = dao.searchForIds(theSearchParamMap, new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.allPartitions())).stream()
+		List<Long> matchingIds = dao.searchForIds(theSearchParamMap, new SystemRequestDetails().setRequestPartitionId(theRequestPartitionId)).stream()
 			.map(ResourcePersistentId::getIdAsLong)
 			.collect(Collectors.toList());
 
@@ -74,4 +81,95 @@ public class ResourceVersionSvcDaoImpl implements IResourceVersionSvc {
 
 		return ResourceVersionMap.fromResourceTableEntities(allById);
 	}
+
+	@Override
+	/**
+	 * Retrieves the latest versions for any resourceid that are found.
+	 * If they are not found, they will not be contained in the returned map.
+	 * The key should be the same value that was passed in to allow
+	 * consumer to look up the value using the id they already have.
+	 *
+	 * This method should not throw, so it can safely be consumed in
+	 * transactions.
+	 *
+	 * @param theRequestPartitionId - request partition id
+	 * @param theIds - list of IIdTypes for resources of interest.
+	 * @return
+	 */
+	public ResourcePersistentIdMap getLatestVersionIdsForResourceIds(RequestPartitionId theRequestPartitionId, List<IIdType> theIds) {
+		ResourcePersistentIdMap idToPID = new ResourcePersistentIdMap();
+		HashMap<String, List<IIdType>> resourceTypeToIds = new HashMap<>();
+
+		for (IIdType id : theIds) {
+			String resourceType = id.getResourceType();
+			if (!resourceTypeToIds.containsKey(resourceType)) {
+				resourceTypeToIds.put(resourceType, new ArrayList<>());
+			}
+			resourceTypeToIds.get(resourceType).add(id);
+		}
+
+		for (String resourceType : resourceTypeToIds.keySet()) {
+			ResourcePersistentIdMap idAndPID = getIdsOfExistingResources(theRequestPartitionId,
+				resourceTypeToIds.get(resourceType));
+			idToPID.putAll(idAndPID);
+		}
+
+		return idToPID;
+	}
+
+	/**
+	 * Helper method to determine if some resources exist in the DB (without throwing).
+	 * Returns a set that contains the IIdType for every resource found.
+	 * If it's not found, it won't be included in the set.
+	 *
+	 * @param theIds - list of IIdType ids (for the same resource)
+	 * @return
+	 */
+	private ResourcePersistentIdMap getIdsOfExistingResources(RequestPartitionId thePartitionId,
+																				 Collection<IIdType> theIds) {
+		// these are the found Ids that were in the db
+		ResourcePersistentIdMap retval = new ResourcePersistentIdMap();
+
+		if (theIds == null || theIds.isEmpty()) {
+			return retval;
+		}
+
+		List<ResourcePersistentId> resourcePersistentIds = myIdHelperService.resolveResourcePersistentIdsWithCache(thePartitionId,
+			theIds.stream().collect(Collectors.toList()));
+
+		// we'll use this map to fetch pids that require versions
+		HashMap<Long, ResourcePersistentId> pidsToVersionToResourcePid = new HashMap<>();
+
+		// fill in our map
+		for (ResourcePersistentId pid : resourcePersistentIds) {
+			if (pid.getVersion() == null) {
+				pidsToVersionToResourcePid.put(pid.getIdAsLong(), pid);
+			}
+			Optional<IIdType> idOp = theIds.stream()
+				.filter(i -> i.getIdPart().equals(pid.getAssociatedResourceId().getIdPart()))
+				.findFirst();
+			// this should always be present
+			// since it was passed in.
+			// but land of optionals...
+			idOp.ifPresent(id -> {
+				retval.put(id, pid);
+			});
+		}
+
+		// set any versions we don't already have
+		if (!pidsToVersionToResourcePid.isEmpty()) {
+			Collection<Object[]> resourceEntries = myResourceTableDao
+				.getResourceVersionsForPid(new ArrayList<>(pidsToVersionToResourcePid.keySet()));
+
+			for (Object[] record : resourceEntries) {
+				// order matters!
+				Long retPid = (Long) record[0];
+				String resType = (String) record[1];
+				Long version = (Long) record[2];
+				pidsToVersionToResourcePid.get(retPid).setVersion(version);
+			}
+		}
+
+		return retval;
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java

@@ -122,6 +122,7 @@ import ca.uhn.fhir.jpa.search.cache.DatabaseSearchCacheSvcImpl;
 import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
 import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
 import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
+import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
 import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
 import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
@@ -155,6 +156,7 @@ import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
 import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -288,8 +290,8 @@ public abstract class BaseConfig {
 	 * bean, but it provides a partially completed entity manager
 	 * factory with HAPI FHIR customizations
 	 */
-	protected LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	protected LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory);
 		configureEntityManagerFactory(retVal, fhirContext());
 		return retVal;
 	}
@@ -919,6 +921,11 @@ public abstract class BaseConfig {
 		return new PredicateBuilderFactory(theApplicationContext);
 	}
 
+	@Bean
+	public IndexNamePrefixLayoutStrategy indexLayoutStrategy() {
+		return new IndexNamePrefixLayoutStrategy();
+	}
+
 	@Bean
 	public JpaResourceLoader jpaResourceLoader() {
 		return new JpaResourceLoader();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirLocalContainerEntityManagerFactoryBean.java

@@ -23,6 +23,9 @@ package ca.uhn.fhir.jpa.config;
 import org.hibernate.cfg.AvailableSettings;
 import org.hibernate.query.criteria.LiteralHandlingMode;
 import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
+import org.springframework.orm.hibernate5.SpringBeanContainer;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
 import java.util.Map;
@@ -32,6 +35,14 @@ import java.util.Map;
  * that sets some sensible default property values
  */
 public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContainerEntityManagerFactoryBean {
+
+	//https://stackoverflow.com/questions/57902388/how-to-inject-spring-beans-into-the-hibernate-envers-revisionlistener
+	ConfigurableListableBeanFactory myConfigurableListableBeanFactory;
+
+	public HapiFhirLocalContainerEntityManagerFactoryBean(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
+		myConfigurableListableBeanFactory = theConfigurableListableBeanFactory;
+	}
+
 	@Override
 	public Map<String, Object> getJpaPropertyMap() {
 		Map<String, Object> retVal = super.getJpaPropertyMap();
@@ -63,6 +74,11 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
 		if (!retVal.containsKey(AvailableSettings.BATCH_VERSIONED_DATA)) {
 			retVal.put(AvailableSettings.BATCH_VERSIONED_DATA, "true");
 		}
+		// Why is this here, you ask? LocalContainerEntityManagerFactoryBean actually clobbers the setting hibernate needs
+		// in order to be able to resolve beans, so we add it back in manually here
+		if (!retVal.containsKey(AvailableSettings.BEAN_CONTAINER)) {
+			retVal.put(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(myConfigurableListableBeanFactory));
+		}
 
 		return retVal;
 	}

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

@@ -1207,7 +1207,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
 			if (thePerformIndexing || ((ResourceTable) theEntity).getVersion() == 1) {
 
 				newParams = new ResourceIndexedSearchParams();
-
 				mySearchParamWithInlineReferencesExtractor.populateFromResource(newParams, theTransactionDetails, entity, theResource, existingParams, theRequest, thePerformIndexing);
 
 				changed = populateResourceIntoEntity(theTransactionDetails, theRequest, theResource, entity, true);

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

@@ -136,9 +136,12 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
+import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 import java.util.UUID;

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

@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.util.ResourceCountCache;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.util.StopWatch;
 import com.google.common.annotations.VisibleForTesting;

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

@@ -25,19 +25,18 @@ import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
+import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
+import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
-import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
-import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
-import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
 import ca.uhn.fhir.model.api.IQueryParameterAnd;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
 import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
@@ -45,12 +44,16 @@ import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
 import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.param.QualifierDetails;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.OperationOutcomeUtil;
@@ -91,6 +94,10 @@ public abstract class BaseStorageDao {
 	protected DaoRegistry myDaoRegistry;
 	@Autowired
 	protected ModelConfig myModelConfig;
+	@Autowired
+	protected IResourceVersionSvc myResourceVersionSvc;
+	@Autowired
+	protected DaoConfig myDaoConfig;
 
 	@VisibleForTesting
 	public void setSearchParamRegistry(ISearchParamRegistry theSearchParamRegistry) {
@@ -204,10 +211,33 @@ public abstract class BaseStorageDao {
 			for (IBaseReference nextReference : referencesToVersion) {
 				IIdType referenceElement = nextReference.getReferenceElement();
 				if (!referenceElement.hasBaseUrl()) {
-					String resourceType = referenceElement.getResourceType();
+
-					IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
+					ResourcePersistentIdMap resourceVersionMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
-					String targetVersionId = dao.getCurrentVersionId(referenceElement);
+						Collections.singletonList(referenceElement)
-					String newTargetReference = referenceElement.withVersion(targetVersionId).getValue();
+					);
+
+					// 3 cases:
+					// 1) there exists a resource in the db with some version (use this version)
+					// 2) no resource exists, but we will create one (eventually). The version is 1
+					// 3) no resource exists, and none will be made -> throw
+					Long version;
+					if (resourceVersionMap.containsKey(referenceElement)) {
+						// the resource exists... latest id
+						// will be the value in the ResourcePersistentId
+						version = resourceVersionMap.getResourcePersistentId(referenceElement).getVersion();
+					} else if (myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) {
+						// if idToPID doesn't contain object
+						// but autcreateplaceholders is on
+						// then the version will be 1 (the first version)
+						version = 1L;
+					}
+					else {
+						// resource not found
+						// and no autocreateplaceholders set...
+						// we throw
+						throw new ResourceNotFoundException(referenceElement);
+					}
+					String newTargetReference = referenceElement.withVersion(version.toString()).getValue();
 					nextReference.setReference(newTargetReference);
 				}
 			}

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.interceptor.api.HookParams;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.interceptor.model.TransactionWriteOperationsDetails;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
@@ -34,6 +35,8 @@ import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.api.model.DeleteConflict;
 import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
 import ca.uhn.fhir.jpa.api.model.DeleteMethodOutcome;
+import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
+import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
 import ca.uhn.fhir.jpa.delete.DeleteConflictService;
 import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
@@ -68,11 +71,11 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.servlet.ServletSubRequestDetails;
 import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
 import ca.uhn.fhir.rest.server.util.ServletRequestUtil;
+import ca.uhn.fhir.util.AsyncUtil;
 import ca.uhn.fhir.util.ElementUtil;
 import ca.uhn.fhir.util.FhirTerser;
 import ca.uhn.fhir.util.ResourceReferenceInfo;
 import ca.uhn.fhir.util.StopWatch;
-import ca.uhn.fhir.util.AsyncUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.ArrayListMultimap;
@@ -90,7 +93,6 @@ 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.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.model.Task;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -117,11 +119,11 @@ import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 import java.util.TreeSet;
-import java.util.concurrent.Callable;
-import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.TimeUnit;
 import java.util.regex.Pattern;
+import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.util.StringUtil.toUtf8String;
 import static org.apache.commons.lang3.StringUtils.defaultString;
@@ -157,6 +159,9 @@ public abstract class BaseTransactionProcessor {
 
 	private TaskExecutor myExecutor ;
 
+	@Autowired
+	private IResourceVersionSvc myResourceVersionSvc;
+
 	@VisibleForTesting
 	public void setDaoConfig(DaoConfig theDaoConfig) {
 		myDaoConfig = theDaoConfig;
@@ -252,8 +257,10 @@ public abstract class BaseTransactionProcessor {
 		myVersionAdapter.populateEntryWithOperationOutcome(caughtEx, nextEntry);
 	}
 
-	private void handleTransactionCreateOrUpdateOutcome(Map<IIdType, IIdType> idSubstitutions, Map<IIdType, DaoMethodOutcome> idToPersistedOutcome, IIdType nextResourceId, DaoMethodOutcome outcome,
+	private void handleTransactionCreateOrUpdateOutcome(Map<IIdType, IIdType> idSubstitutions, Map<IIdType, DaoMethodOutcome> idToPersistedOutcome,
-																		 IBase newEntry, String theResourceType, IBaseResource theRes, RequestDetails theRequestDetails) {
+																		 IIdType nextResourceId, DaoMethodOutcome outcome,
+																		 IBase newEntry, String theResourceType,
+																		 IBaseResource theRes, RequestDetails theRequestDetails) {
 		IIdType newId = outcome.getId().toUnqualified();
 		IIdType resourceId = isPlaceholder(nextResourceId) ? nextResourceId : nextResourceId.toUnqualifiedVersionless();
 		if (newId.equals(resourceId) == false) {
@@ -359,8 +366,8 @@ public abstract class BaseTransactionProcessor {
 		IBase nextRequestEntry = null;
 		for (int i=0; i<requestEntriesSize; i++ ) {
 			nextRequestEntry = requestEntries.get(i);
-			BundleTask bundleTask = new BundleTask(completionLatch, theRequestDetails, responseMap, i, nextRequestEntry, theNestedMode);
+			RetriableBundleTask retriableBundleTask = new RetriableBundleTask(completionLatch, theRequestDetails, responseMap, i, nextRequestEntry, theNestedMode);
-			getTaskExecutor().execute(bundleTask);
+			getTaskExecutor().execute(retriableBundleTask);
 		}
 
 		// waiting for all tasks to be completed
@@ -394,7 +401,8 @@ public abstract class BaseTransactionProcessor {
 		myHapiTransactionService = theHapiTransactionService;
 	}
 
-	private IBaseBundle processTransaction(final RequestDetails theRequestDetails, final IBaseBundle theRequest, final String theActionName, boolean theNestedMode) {
+	private IBaseBundle processTransaction(final RequestDetails theRequestDetails, final IBaseBundle theRequest,
+														final String theActionName, boolean theNestedMode) {
 		validateDependencies();
 
 		String transactionType = myVersionAdapter.getBundleType(theRequest);
@@ -412,7 +420,8 @@ public abstract class BaseTransactionProcessor {
 			throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType);
 		}
 
-		int numberOfEntries = myVersionAdapter.getEntries(theRequest).size();
+		List<IBase> requestEntries = myVersionAdapter.getEntries(theRequest);
+		int numberOfEntries = requestEntries.size();
 
 		if (myDaoConfig.getMaximumTransactionBundleSize() != null && numberOfEntries > myDaoConfig.getMaximumTransactionBundleSize()) {
 			throw new PayloadTooLargeException("Transaction Bundle Too large.  Transaction bundle contains " +
@@ -425,8 +434,6 @@ public abstract class BaseTransactionProcessor {
 		final TransactionDetails transactionDetails = new TransactionDetails();
 		final StopWatch transactionStopWatch = new StopWatch();
 
-		List<IBase> requestEntries = myVersionAdapter.getEntries(theRequest);
-
 		// Do all entries have a verb?
 		for (int i = 0; i < numberOfEntries; i++) {
 			IBase nextReqEntry = requestEntries.get(i);
@@ -450,10 +457,11 @@ public abstract class BaseTransactionProcessor {
 		List<IBase> getEntries = new ArrayList<>();
 		final IdentityHashMap<IBase, Integer> originalRequestOrder = new IdentityHashMap<>();
 		for (int i = 0; i < requestEntries.size(); i++) {
-			originalRequestOrder.put(requestEntries.get(i), i);
+			IBase requestEntry = requestEntries.get(i);
+			originalRequestOrder.put(requestEntry, i);
 			myVersionAdapter.addEntry(response);
-			if (myVersionAdapter.getEntryRequestVerb(myContext, requestEntries.get(i)).equals("GET")) {
+			if (myVersionAdapter.getEntryRequestVerb(myContext, requestEntry).equals("GET")) {
-				getEntries.add(requestEntries.get(i));
+				getEntries.add(requestEntry);
 			}
 		}
 
@@ -472,16 +480,43 @@ public abstract class BaseTransactionProcessor {
 		}
 		entries.sort(new TransactionSorter(placeholderIds));
 
-		doTransactionWriteOperations(theRequestDetails, theActionName, transactionDetails, transactionStopWatch, response, originalRequestOrder, entries);
+		// perform all writes
+		doTransactionWriteOperations(theRequestDetails, theActionName,
+			transactionDetails, transactionStopWatch,
+			response, originalRequestOrder, entries);
+
+		// perform all gets
+		// (we do these last so that the gets happen on the final state of the DB;
+		// see above note)
+		doTransactionReadOperations(theRequestDetails, response,
+			getEntries, originalRequestOrder,
+			transactionStopWatch, theNestedMode);
+
+		// Interceptor broadcast: JPA_PERFTRACE_INFO
+		if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequestDetails)) {
+			String taskDurations = transactionStopWatch.formatTaskDurations();
+			StorageProcessingMessage message = new StorageProcessingMessage();
+			message.setMessage("Transaction timing:\n" + taskDurations);
+			HookParams params = new HookParams()
+				.add(RequestDetails.class, theRequestDetails)
+				.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
+				.add(StorageProcessingMessage.class, message);
+			CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_INFO, params);
+		}
+
+		return response;
+	}
+
+	private void doTransactionReadOperations(final RequestDetails theRequestDetails, IBaseBundle theResponse,
+														  List<IBase> theGetEntries, IdentityHashMap<IBase, Integer> theOriginalRequestOrder,
+														  StopWatch theTransactionStopWatch, boolean theNestedMode) {
+		if (theGetEntries.size() > 0) {
+			theTransactionStopWatch.startTask("Process " + theGetEntries.size() + " GET entries");
 
 			/*
 			 * Loop through the request and process any entries of type GET
 			 */
-		if (getEntries.size() > 0) {
+			for (IBase nextReqEntry : theGetEntries) {
-			transactionStopWatch.startTask("Process " + getEntries.size() + " GET entries");
-		}
-		for (IBase nextReqEntry : getEntries) {
-
 				if (theNestedMode) {
 					throw new InvalidRequestException("Can not invoke read operation on nested transaction");
 				}
@@ -491,8 +526,8 @@ public abstract class BaseTransactionProcessor {
 				}
 
 				ServletRequestDetails srd = (ServletRequestDetails) theRequestDetails;
-			Integer originalOrder = originalRequestOrder.get(nextReqEntry);
+				Integer originalOrder = theOriginalRequestOrder.get(nextReqEntry);
-			IBase nextRespEntry = (IBase) myVersionAdapter.getEntries(response).get(originalOrder);
+				IBase nextRespEntry = (IBase) myVersionAdapter.getEntries(theResponse).get(originalOrder);
 
 				ArrayListMultimap<String, String> paramValues = ArrayListMultimap.create();
 
@@ -519,7 +554,6 @@ public abstract class BaseTransactionProcessor {
 
 				Validate.isTrue(method instanceof BaseResourceReturningMethodBinding, "Unable to handle GET {}", url);
 				try {
-
 					BaseResourceReturningMethodBinding methodBinding = (BaseResourceReturningMethodBinding) method;
 					requestDetails.setRestOperationType(methodBinding.getRestOperationType());
 
@@ -536,23 +570,9 @@ public abstract class BaseTransactionProcessor {
 					myVersionAdapter.setResponseStatus(nextRespEntry, toStatusString(e.getStatusCode()));
 					populateEntryWithOperationOutcome(e, nextRespEntry);
 				}
-
 			}
-		transactionStopWatch.endCurrentTask();
+			theTransactionStopWatch.endCurrentTask();
-
-		// Interceptor broadcast: JPA_PERFTRACE_INFO
-		if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.JPA_PERFTRACE_INFO, myInterceptorBroadcaster, theRequestDetails)) {
-			String taskDurations = transactionStopWatch.formatTaskDurations();
-			StorageProcessingMessage message = new StorageProcessingMessage();
-			message.setMessage("Transaction timing:\n" + taskDurations);
-			HookParams params = new HookParams()
-				.add(RequestDetails.class, theRequestDetails)
-				.addIfMatchesType(ServletRequestDetails.class, theRequestDetails)
-				.add(StorageProcessingMessage.class, message);
-			CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.JPA_PERFTRACE_INFO, params);
 		}
-
-		return response;
 	}
 
 	/**
@@ -564,7 +584,10 @@ public abstract class BaseTransactionProcessor {
 	 * heavy load with lots of concurrent transactions using all available
 	 * database connections.
 	 */
-	private void doTransactionWriteOperations(RequestDetails theRequestDetails, String theActionName, TransactionDetails theTransactionDetails, StopWatch theTransactionStopWatch, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries) {
+	private void doTransactionWriteOperations(RequestDetails theRequestDetails, String theActionName,
+															TransactionDetails theTransactionDetails, StopWatch theTransactionStopWatch,
+															IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder,
+															List<IBase> theEntries) {
 		TransactionWriteOperationsDetails writeOperationsDetails = null;
 		if (CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, myInterceptorBroadcaster, theRequestDetails) ||
 			CompositeInterceptorBroadcaster.hasHooks(Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_POST, myInterceptorBroadcaster, theRequestDetails)) {
@@ -593,14 +616,18 @@ public abstract class BaseTransactionProcessor {
 				.add(TransactionDetails.class, theTransactionDetails)
 				.add(TransactionWriteOperationsDetails.class, writeOperationsDetails);
 			CompositeInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, theRequestDetails, Pointcut.STORAGE_TRANSACTION_WRITE_OPERATIONS_PRE, params);
-
 		}
 
 		TransactionCallback<Map<IBase, IIdType>> txCallback = status -> {
 			final Set<IIdType> allIds = new LinkedHashSet<>();
 			final Map<IIdType, IIdType> idSubstitutions = new HashMap<>();
 			final Map<IIdType, DaoMethodOutcome> idToPersistedOutcome = new HashMap<>();
-			Map<IBase, IIdType> retVal = doTransactionWriteOperations(theRequestDetails, theActionName, theTransactionDetails, allIds, idSubstitutions, idToPersistedOutcome, theResponse, theOriginalRequestOrder, theEntries, theTransactionStopWatch);
+
+			Map<IBase, IIdType> retVal = doTransactionWriteOperations(theRequestDetails, theActionName,
+				theTransactionDetails, allIds,
+				idSubstitutions, idToPersistedOutcome,
+				theResponse, theOriginalRequestOrder,
+				theEntries, theTransactionStopWatch);
 
 			theTransactionStopWatch.startTask("Commit writes to database");
 			return retVal;
@@ -609,7 +636,8 @@ public abstract class BaseTransactionProcessor {
 
 		try {
 			entriesToProcess = myHapiTransactionService.execute(theRequestDetails, theTransactionDetails, txCallback);
-		} finally {
+		}
+		finally {
 			if (writeOperationsDetails != null) {
 				HookParams params = new HookParams()
 					.add(TransactionDetails.class, theTransactionDetails)
@@ -664,27 +692,12 @@ public abstract class BaseTransactionProcessor {
 		myModelConfig = theModelConfig;
 	}
 
-	protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName, TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
+	/**
-																				  Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder, List<IBase> theEntries, StopWatch theTransactionStopWatch) {
+	 * Searches for duplicate conditional creates and consolidates them.
-
+	 *
-		theTransactionDetails.beginAcceptingDeferredInterceptorBroadcasts(
+	 * @param theEntries
-			Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED,
-			Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED,
-			Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED
-		);
-		try {
-
-			Set<String> deletedResources = new HashSet<>();
-			DeleteConflictList deleteConflicts = new DeleteConflictList();
-			Map<IBase, IIdType> entriesToProcess = new IdentityHashMap<>();
-			Set<IIdType> nonUpdatedEntities = new HashSet<>();
-			Set<IBasePersistedResource> updatedEntities = new HashSet<>();
-			List<IBaseResource> updatedResources = new ArrayList<>();
-			Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
-
-			/*
-			 * Look for duplicate conditional creates and consolidate them
 	 */
+	private void consolidateDuplicateConditionals(List<IBase> theEntries) {
 		final HashMap<String, String> keyToUuid = new HashMap<>();
 		for (int index = 0, originalIndex = 0; index < theEntries.size(); index++, originalIndex++) {
 			IBase nextReqEntry = theEntries.get(index);
@@ -743,26 +756,23 @@ public abstract class BaseTransactionProcessor {
 				}
 			}
 		}
-
-
-			/*
-			 * Loop through the request and process any entries of type
-			 * PUT, POST or DELETE
-			 */
-			for (int i = 0; i < theEntries.size(); i++) {
-
-				if (i % 250 == 0) {
-					ourLog.debug("Processed {} non-GET entries out of {} in transaction", i, theEntries.size());
 	}
 
-				IBase nextReqEntry = theEntries.get(i);
+	/**
-				IBaseResource res = myVersionAdapter.getResource(nextReqEntry);
+	 * Retrieves the next resource id (IIdType) from the base resource and next request entry.
+	 * @param theBaseResource - base resource
+	 * @param theNextReqEntry - next request entry
+	 * @param theAllIds - set of all IIdType values
+	 * @return
+	 */
+	private IIdType getNextResourceIdFromBaseResource(IBaseResource theBaseResource,
+													  IBase theNextReqEntry,
+													  Set<IIdType> theAllIds) {
 		IIdType nextResourceId = null;
-				if (res != null) {
+		if (theBaseResource != null) {
+			nextResourceId = theBaseResource.getIdElement();
 
-					nextResourceId = res.getIdElement();
+			String fullUrl = myVersionAdapter.getFullUrl(theNextReqEntry);
-
-					String fullUrl = myVersionAdapter.getFullUrl(nextReqEntry);
 			if (isNotBlank(fullUrl)) {
 				IIdType fullUrlIdType = newIdType(fullUrl);
 				if (isPlaceholder(fullUrlIdType)) {
@@ -777,8 +787,8 @@ public abstract class BaseTransactionProcessor {
 			}
 
 			if (nextResourceId.hasIdPart() && !nextResourceId.hasResourceType() && !isPlaceholder(nextResourceId)) {
-						nextResourceId = newIdType(toResourceName(res.getClass()), nextResourceId.getIdPart());
+				nextResourceId = newIdType(toResourceName(theBaseResource.getClass()), nextResourceId.getIdPart());
-						res.setId(nextResourceId);
+				theBaseResource.setId(nextResourceId);
 			}
 
 			/*
@@ -797,6 +807,47 @@ public abstract class BaseTransactionProcessor {
 
 		}
 
+		return nextResourceId;
+	}
+
+	protected Map<IBase, IIdType> doTransactionWriteOperations(final RequestDetails theRequest, String theActionName,
+																				  TransactionDetails theTransactionDetails, Set<IIdType> theAllIds,
+																				  Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
+																				  IBaseBundle theResponse, IdentityHashMap<IBase, Integer> theOriginalRequestOrder,
+																				  List<IBase> theEntries, StopWatch theTransactionStopWatch) {
+
+		theTransactionDetails.beginAcceptingDeferredInterceptorBroadcasts(
+			Pointcut.STORAGE_PRECOMMIT_RESOURCE_CREATED,
+			Pointcut.STORAGE_PRECOMMIT_RESOURCE_UPDATED,
+			Pointcut.STORAGE_PRECOMMIT_RESOURCE_DELETED
+		);
+		try {
+			Set<String> deletedResources = new HashSet<>();
+			DeleteConflictList deleteConflicts = new DeleteConflictList();
+			Map<IBase, IIdType> entriesToProcess = new IdentityHashMap<>();
+			Set<IIdType> nonUpdatedEntities = new HashSet<>();
+			Set<IBasePersistedResource> updatedEntities = new HashSet<>();
+			List<IBaseResource> updatedResources = new ArrayList<>();
+			Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
+
+			/*
+			 * Look for duplicate conditional creates and consolidate them
+			 */
+			 consolidateDuplicateConditionals(theEntries);
+
+			/*
+			 * Loop through the request and process any entries of type
+			 * PUT, POST or DELETE
+			 */
+			for (int i = 0; i < theEntries.size(); i++) {
+				if (i % 250 == 0) {
+					ourLog.debug("Processed {} non-GET entries out of {} in transaction", i, theEntries.size());
+				}
+
+				IBase nextReqEntry = theEntries.get(i);
+				IBaseResource res = myVersionAdapter.getResource(nextReqEntry);
+				IIdType nextResourceId = getNextResourceIdFromBaseResource(res, nextReqEntry, theAllIds);
+
 				String verb = myVersionAdapter.getEntryRequestVerb(myContext, nextReqEntry);
 				String resourceType = res != null ? myContext.getResourceType(res) : null;
 				Integer order = theOriginalRequestOrder.get(nextReqEntry);
@@ -904,7 +955,8 @@ public abstract class BaseTransactionProcessor {
 							}
 						}
 
-						handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId, outcome, nextRespEntry, resourceType, res, theRequest);
+						handleTransactionCreateOrUpdateOutcome(theIdSubstitutions, theIdToPersistedOutcome, nextResourceId,
+							outcome, nextRespEntry, resourceType, res, theRequest);
 						entriesToProcess.put(nextRespEntry, outcome.getId());
 						break;
 					}
@@ -971,52 +1023,24 @@ public abstract class BaseTransactionProcessor {
 			 * was also deleted as a part of this transaction, which is why we check this now at the
 			 * end.
 			 */
-			for (Iterator<DeleteConflict> iter = deleteConflicts.iterator(); iter.hasNext(); ) {
+			checkForDeleteConflicts(deleteConflicts, deletedResources, updatedResources);
-				DeleteConflict nextDeleteConflict = iter.next();
 
-				/*
+			theIdToPersistedOutcome.entrySet().forEach(idAndOutcome -> {
-				 * If we have a conflict, it means we can't delete Resource/A because
+				theTransactionDetails.addResolvedResourceId(idAndOutcome.getKey(), idAndOutcome.getValue().getPersistentId());
-				 * Resource/B has a reference to it. We'll ignore that conflict though
+			});
-				 * if it turns out we're also deleting Resource/B in this transaction.
-				 */
-				if (deletedResources.contains(nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue())) {
-					iter.remove();
-					continue;
-				}
-
-				/*
-				 * And then, this is kind of a last ditch check. It's also ok to delete
-				 * Resource/A if Resource/B isn't being deleted, but it is being UPDATED
-				 * in this transaction, and the updated version of it has no references
-				 * to Resource/A any more.
-				 */
-				String sourceId = nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue();
-				String targetId = nextDeleteConflict.getTargetId().toUnqualifiedVersionless().getValue();
-				Optional<IBaseResource> updatedSource = updatedResources
-					.stream()
-					.filter(t -> sourceId.equals(t.getIdElement().toUnqualifiedVersionless().getValue()))
-					.findFirst();
-				if (updatedSource.isPresent()) {
-					List<ResourceReferenceInfo> referencesInSource = myContext.newTerser().getAllResourceReferences(updatedSource.get());
-					boolean sourceStillReferencesTarget = referencesInSource
-						.stream()
-						.anyMatch(t -> targetId.equals(t.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue()));
-					if (!sourceStillReferencesTarget) {
-						iter.remove();
-					}
-				}
-			}
-			DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(myContext, deleteConflicts);
-
-			theIdToPersistedOutcome.entrySet().forEach(t -> theTransactionDetails.addResolvedResourceId(t.getKey(), t.getValue().getPersistentId()));
 
 			/*
 			 * Perform ID substitutions and then index each resource we have saved
 			 */
 
-			resolveReferencesThenSaveAndIndexResources(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, theTransactionStopWatch, entriesToProcess, nonUpdatedEntities, updatedEntities);
+			resolveReferencesThenSaveAndIndexResources(theRequest, theTransactionDetails,
+				theIdSubstitutions, theIdToPersistedOutcome,
+				theTransactionStopWatch, entriesToProcess,
+				nonUpdatedEntities, updatedEntities);
 
 			theTransactionStopWatch.endCurrentTask();
+
+			// flush writes to db
 			theTransactionStopWatch.startTask("Flush writes to database");
 
 			flushSession(theIdToPersistedOutcome);
@@ -1070,6 +1094,53 @@ public abstract class BaseTransactionProcessor {
 		}
 	}
 
+	/**
+	 * Checks for any delete conflicts.
+	 * @param theDeleteConflicts - set of delete conflicts
+	 * @param theDeletedResources - set of deleted resources
+	 * @param theUpdatedResources - list of updated resources
+	 */
+	private void checkForDeleteConflicts(DeleteConflictList theDeleteConflicts,
+										 Set<String> theDeletedResources,
+										 List<IBaseResource> theUpdatedResources) {
+		for (Iterator<DeleteConflict> iter = theDeleteConflicts.iterator(); iter.hasNext(); ) {
+			DeleteConflict nextDeleteConflict = iter.next();
+
+			/*
+			 * If we have a conflict, it means we can't delete Resource/A because
+			 * Resource/B has a reference to it. We'll ignore that conflict though
+			 * if it turns out we're also deleting Resource/B in this transaction.
+			 */
+			if (theDeletedResources.contains(nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue())) {
+				iter.remove();
+				continue;
+			}
+
+			/*
+			 * And then, this is kind of a last ditch check. It's also ok to delete
+			 * Resource/A if Resource/B isn't being deleted, but it is being UPDATED
+			 * in this transaction, and the updated version of it has no references
+			 * to Resource/A any more.
+			 */
+			String sourceId = nextDeleteConflict.getSourceId().toUnqualifiedVersionless().getValue();
+			String targetId = nextDeleteConflict.getTargetId().toUnqualifiedVersionless().getValue();
+			Optional<IBaseResource> updatedSource = theUpdatedResources
+				.stream()
+				.filter(t -> sourceId.equals(t.getIdElement().toUnqualifiedVersionless().getValue()))
+				.findFirst();
+			if (updatedSource.isPresent()) {
+				List<ResourceReferenceInfo> referencesInSource = myContext.newTerser().getAllResourceReferences(updatedSource.get());
+				boolean sourceStillReferencesTarget = referencesInSource
+					.stream()
+					.anyMatch(t -> targetId.equals(t.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue()));
+				if (!sourceStillReferencesTarget) {
+					iter.remove();
+				}
+			}
+		}
+		DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(myContext, theDeleteConflicts);
+	}
+
 	/**
 	 * This method replaces any placeholder references in the
 	 * source transaction Bundle with their actual targets, then stores the resource contents and indexes
@@ -1092,7 +1163,10 @@ public abstract class BaseTransactionProcessor {
 	 * pass because it's too complex to try and insert the auto-versioned references and still
 	 * account for NOPs, so we block NOPs in that pass.
 	 */
-	private void resolveReferencesThenSaveAndIndexResources(RequestDetails theRequest, TransactionDetails theTransactionDetails, Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, StopWatch theTransactionStopWatch, Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities) {
+	private void resolveReferencesThenSaveAndIndexResources(RequestDetails theRequest, TransactionDetails theTransactionDetails,
+																			  Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
+																			  StopWatch theTransactionStopWatch, Map<IBase, IIdType> entriesToProcess,
+																			  Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities) {
 		FhirTerser terser = myContext.newTerser();
 		theTransactionStopWatch.startTask("Index " + theIdToPersistedOutcome.size() + " resources");
 		IdentityHashMap<DaoMethodOutcome, Set<IBaseReference>> deferredIndexesForAutoVersioning = null;
@@ -1114,8 +1188,15 @@ public abstract class BaseTransactionProcessor {
 
 			Set<IBaseReference> referencesToAutoVersion = BaseStorageDao.extractReferencesToAutoVersion(myContext, myModelConfig, nextResource);
 			if (referencesToAutoVersion.isEmpty()) {
-				resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, entriesToProcess, nonUpdatedEntities, updatedEntities, terser, nextOutcome, nextResource, referencesToAutoVersion);
+				// no references to autoversion - we can do the resolve and save now
+				resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails,
+					theIdSubstitutions, theIdToPersistedOutcome,
+					entriesToProcess, nonUpdatedEntities,
+					updatedEntities, terser,
+					nextOutcome, nextResource,
+					referencesToAutoVersion); // this is empty
 			} else {
+				// we have autoversioned things to defer until later
 				if (deferredIndexesForAutoVersioning == null) {
 					deferredIndexesForAutoVersioning = new IdentityHashMap<>();
 				}
@@ -1129,12 +1210,24 @@ public abstract class BaseTransactionProcessor {
 				DaoMethodOutcome nextOutcome = nextEntry.getKey();
 				Set<IBaseReference> referencesToAutoVersion = nextEntry.getValue();
 				IBaseResource nextResource = nextOutcome.getResource();
-				resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails, theIdSubstitutions, theIdToPersistedOutcome, entriesToProcess, nonUpdatedEntities, updatedEntities, terser, nextOutcome, nextResource, referencesToAutoVersion);
+
+
+				resolveReferencesThenSaveAndIndexResource(theRequest, theTransactionDetails,
+					theIdSubstitutions, theIdToPersistedOutcome,
+					entriesToProcess, nonUpdatedEntities,
+					updatedEntities, terser,
+					nextOutcome, nextResource,
+					referencesToAutoVersion);
 			}
 		}
 	}
 
-	private void resolveReferencesThenSaveAndIndexResource(RequestDetails theRequest, TransactionDetails theTransactionDetails, Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome, Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities, Set<IBasePersistedResource> updatedEntities, FhirTerser terser, DaoMethodOutcome nextOutcome, IBaseResource nextResource, Set<IBaseReference> theReferencesToAutoVersion) {
+	private void resolveReferencesThenSaveAndIndexResource(RequestDetails theRequest, TransactionDetails theTransactionDetails,
+																			 Map<IIdType, IIdType> theIdSubstitutions, Map<IIdType, DaoMethodOutcome> theIdToPersistedOutcome,
+																			 Map<IBase, IIdType> entriesToProcess, Set<IIdType> nonUpdatedEntities,
+																			 Set<IBasePersistedResource> updatedEntities, FhirTerser terser,
+																			 DaoMethodOutcome nextOutcome, IBaseResource nextResource,
+																			 Set<IBaseReference> theReferencesToAutoVersion) {
 		// References
 		List<ResourceReferenceInfo> allRefs = terser.getAllResourceReferences(nextResource);
 		for (ResourceReferenceInfo nextRef : allRefs) {
@@ -1175,9 +1268,34 @@ public abstract class BaseTransactionProcessor {
 			} else if (nextId.getValue().startsWith("urn:")) {
 				throw new InvalidRequestException("Unable to satisfy placeholder ID " + nextId.getValue() + " found in element named '" + nextRef.getName() + "' within resource of type: " + nextResource.getIdElement().getResourceType());
 			} else {
+				// get a map of
+				// existing ids -> PID (for resources that exist in the DB)
+				// should this be allPartitions?
+				ResourcePersistentIdMap resourceVersionMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
+					theReferencesToAutoVersion.stream()
+						.map(IBaseReference::getReferenceElement).collect(Collectors.toList()));
+
+				for (IBaseReference baseRef : theReferencesToAutoVersion) {
+					IIdType id = baseRef.getReferenceElement();
+					if (!resourceVersionMap.containsKey(id)
+						&& myDaoConfig.isAutoCreatePlaceholderReferenceTargets()) {
+						// not in the db, but autocreateplaceholders is true
+						// so the version we'll set is "1" (since it will be
+						// created later)
+						String newRef = id.withVersion("1").getValue();
+						id.setValue(newRef);
+					} else {
+						// we will add the looked up info to the transaction
+						// for later
+						theTransactionDetails.addResolvedResourceId(id,
+							resourceVersionMap.getResourcePersistentId(id));
+					}
+				}
+
 				if (theReferencesToAutoVersion.contains(resourceReference)) {
 					DaoMethodOutcome outcome = theIdToPersistedOutcome.get(nextId);
-					if (!outcome.isNop() && !Boolean.TRUE.equals(outcome.getCreated())) {
+
+					if (outcome != null && !outcome.isNop() && !Boolean.TRUE.equals(outcome.getCreated())) {
 						addRollbackReferenceRestore(theTransactionDetails, resourceReference);
 						resourceReference.setReference(nextId.getValue());
 						resourceReference.setResource(null);
@@ -1565,30 +1683,29 @@ public abstract class BaseTransactionProcessor {
 		return theStatusCode + " " + defaultString(Constants.HTTP_STATUS_NAMES.get(theStatusCode));
 	}
 
-	public class BundleTask implements Runnable {
+	public class RetriableBundleTask implements Runnable {
 
-		private CountDownLatch myCompletedLatch;
+		private final CountDownLatch myCompletedLatch;
-		private RequestDetails myRequestDetails;
+		private final RequestDetails myRequestDetails;
-		private IBase myNextReqEntry;
+		private final IBase myNextReqEntry;
-		private Map<Integer, Object> myResponseMap;
+		private final Map<Integer, Object> myResponseMap;
-		private int myResponseOrder;
+		private final int myResponseOrder;
-		private boolean myNestedMode;
+		private final boolean myNestedMode;
+		private BaseServerResponseException myLastSeenException;
 
-		protected BundleTask(CountDownLatch theCompletedLatch, RequestDetails theRequestDetails, Map<Integer, Object> theResponseMap, int theResponseOrder, IBase theNextReqEntry, boolean theNestedMode) {
+		protected RetriableBundleTask(CountDownLatch theCompletedLatch, RequestDetails theRequestDetails, Map<Integer, Object> theResponseMap, int theResponseOrder, IBase theNextReqEntry, boolean theNestedMode) {
 			this.myCompletedLatch = theCompletedLatch;
 			this.myRequestDetails = theRequestDetails;
 			this.myNextReqEntry = theNextReqEntry;
 			this.myResponseMap = theResponseMap;
 			this.myResponseOrder = theResponseOrder;
 			this.myNestedMode = theNestedMode;
+			this.myLastSeenException = null;
 		}
 
-		@Override
+		private void processBatchEntry() {
-		public void run() {
-			BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
-			try {
 			IBaseBundle subRequestBundle = myVersionAdapter.createBundle(org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION.toCode());
-				myVersionAdapter.addEntry(subRequestBundle, (IBase) myNextReqEntry);
+			myVersionAdapter.addEntry(subRequestBundle, myNextReqEntry);
 
 			IBaseBundle nextResponseBundle = processTransactionAsSubRequest(myRequestDetails, subRequestBundle, "Batch sub-request", myNestedMode);
 
@@ -1602,22 +1719,45 @@ public abstract class BaseTransactionProcessor {
 				IBase nextResponseBundleFirstEntry = (IBase) myVersionAdapter.getEntries(nextResponseBundle).get(0);
 				myResponseMap.put(myResponseOrder, nextResponseBundleFirstEntry);
 			}
-
+		}
+		private boolean processBatchEntryWithRetry() {
+			int maxAttempts =3;
+			for (int attempt = 1;; attempt++) {
+				try {
+					processBatchEntry();
+					return true;
 				} catch (BaseServerResponseException e) {
-				caughtEx.setException(e);
+					//If we catch a known and structured exception from HAPI, just fail.
+					myLastSeenException = e;
+					return false;
 				} catch (Throwable t) {
+					myLastSeenException = new InternalErrorException(t);
+					//If we have caught a non-tag-storage failure we are unfamiliar with, or we have exceeded max attempts, exit.
+					if (!DaoFailureUtil.isTagStorageFailure(t) || attempt >= maxAttempts) {
 						ourLog.error("Failure during BATCH sub transaction processing", t);
-				caughtEx.setException(new InternalErrorException(t));
+						return false;
+					}
+				}
+			}
 		}
 
-			if (caughtEx.getException() != null) {
+		@Override
-				// add exception to the response map
+		public void run() {
-				myResponseMap.put(myResponseOrder, caughtEx);
+			boolean success = processBatchEntryWithRetry();
+			if (!success) {
+				populateResponseMapWithLastSeenException();
 			}
 
 			// checking for the parallelism
-			ourLog.debug("processing bacth for {} is completed", myVersionAdapter.getEntryRequestUrl((IBase)myNextReqEntry));
+			ourLog.debug("processing batch for {} is completed", myVersionAdapter.getEntryRequestUrl(myNextReqEntry));
 			myCompletedLatch.countDown();
 		}
+
+		private void populateResponseMapWithLastSeenException() {
+			BaseServerResponseExceptionHolder caughtEx = new BaseServerResponseExceptionHolder();
+			caughtEx.setException(myLastSeenException);
+			myResponseMap.put(myResponseOrder, caughtEx);
+		}
+
 	}
 }

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

@@ -0,0 +1,18 @@
+package ca.uhn.fhir.jpa.dao;
+
+import org.apache.commons.lang3.StringUtils;
+
+/**
+ * Utility class to help identify classes of failure.
+ */
+public class DaoFailureUtil {
+
+	public static boolean isTagStorageFailure(Throwable t) {
+		if (StringUtils.isBlank(t.getMessage())) {
+			return false;
+		} else {
+			String msg = t.getMessage().toLowerCase();
+			return msg.contains("hfj_tag_def") || msg.contains("hfj_res_tag");
+		}
+	}
+}

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

@@ -100,6 +100,16 @@ public interface IResourceTableDao extends JpaRepository<ResourceTable, Long> {
 	@Query("SELECT t.myVersion FROM ResourceTable t WHERE t.myId = :pid")
 	Long findCurrentVersionByPid(@Param("pid") Long thePid);
 
+	/**
+	 * This query will return rows with the following values:
+	 * Id (resource pid - long), ResourceType (Patient, etc), version (long)
+	 * Order matters!
+	 * @param pid - list of pids to get versions for
+	 * @return
+	 */
+	@Query("SELECT t.myId, t.myResourceType, t.myVersion FROM ResourceTable t WHERE t.myId IN ( :pid )")
+	Collection<Object[]> getResourceVersionsForPid(@Param("pid") List<Long> pid);
+
 	@Query("SELECT t FROM ResourceTable t LEFT JOIN FETCH t.myForcedId WHERE t.myPartitionId.myPartitionId IS NULL AND t.myId = :pid")
 	Optional<ResourceTable> readByPartitionIdNull(@Param("pid") Long theResourceId);
 

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

@@ -94,7 +94,6 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
 				throw new InvalidRequestException("Resource " + resName + "/" + idPart + " not found, specified in path: " + theSourcePath);
 
 			}
-
 			resolvedResource = createdTableOpt.get();
 		}
 

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

@@ -309,7 +309,7 @@ public class IdHelperService {
 		if (forcedId.isPresent()) {
 			retVal.setValue(theResourceType + '/' + forcedId.get());
 		} else {
-			retVal.setValue(theResourceType + '/' + theId.toString());
+			retVal.setValue(theResourceType + '/' + theId);
 		}
 
 		return retVal;

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

@@ -25,6 +25,7 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.api.model.ResourceVersionConflictResolutionStrategy;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.DaoFailureUtil;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -93,10 +94,9 @@ public class HapiTransactionService {
 		 		 * known to the system already, they'll both try to create a row in HFJ_TAG_DEF,
 		 		 * which is the tag definition table. In that case, a constraint error will be
 		 		 * thrown by one of the client threads, so we auto-retry in order to avoid
-		 		 * annopying spurious failures for the client.
+		 		 * annoying spurious failures for the client.
 		 		 */
-				if (e.getMessage().contains("HFJ_TAG_DEF") || e.getMessage().contains("hfj_tag_def") ||
+				if (DaoFailureUtil.isTagStorageFailure(e)) {
-					 e.getMessage().contains("HFJ_RES_TAG") || e.getMessage().contains("hfj_res_tag")) {
 					maxRetries = 3;
 				}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java

@@ -1087,7 +1087,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				ourLog.trace("Performing count");
 				ISearchBuilder sb = newSearchBuilder();
 				Iterator<Long> countIterator = sb.createCountQuery(myParams, mySearch.getUuid(), myRequest, myRequestPartitionId);
-				Long count = countIterator.hasNext() ? countIterator.next() : 0;
+				Long count = countIterator.hasNext() ? countIterator.next() : 0L;
 				ourLog.trace("Got count {}", count);
 
 				TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java

@@ -729,7 +729,7 @@ public class QueryStack {
 		return predicateBuilder.createPredicate(theRequest, theResourceName, theParamName, theList, theOperation, theRequestPartitionId);
 	}
 
-	private Condition createPredicateReferenceForContainedResource(@Nullable DbColumn theSourceJoinColumn,
+	public Condition createPredicateReferenceForContainedResource(@Nullable DbColumn theSourceJoinColumn,
 																					  String theResourceName, String theParamName, RuntimeSearchParam theSearchParam,
 																					  List<? extends IQueryParameterType> theList, SearchFilterParser.CompareOperation theOperation,
 																					  RequestDetails theRequest, RequestPartitionId theRequestPartitionId) {
@@ -794,31 +794,31 @@ public class QueryStack {
 
 		switch (targetParamDefinition.getParamType()) {
 			case DATE:
-				containedCondition = createPredicateDate(null, theResourceName, spnamePrefix, targetParamDefinition,
+				containedCondition = createPredicateDate(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
 					orValues, theOperation, theRequestPartitionId);
 				break;
 			case NUMBER:
-				containedCondition = createPredicateNumber(null, theResourceName, spnamePrefix, targetParamDefinition,
+				containedCondition = createPredicateNumber(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
 					orValues, theOperation, theRequestPartitionId);
 				break;
 			case QUANTITY:
-				containedCondition = createPredicateQuantity(null, theResourceName, spnamePrefix, targetParamDefinition,
+				containedCondition = createPredicateQuantity(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
 					orValues, theOperation, theRequestPartitionId);
 				break;
 			case STRING:
-				containedCondition = createPredicateString(null, theResourceName, spnamePrefix, targetParamDefinition,
+				containedCondition = createPredicateString(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
 					orValues, theOperation, theRequestPartitionId);
 				break;
 			case TOKEN:
-				containedCondition = createPredicateToken(null, theResourceName, spnamePrefix, targetParamDefinition,
+				containedCondition = createPredicateToken(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
 					orValues, theOperation, theRequestPartitionId);
 				break;
 			case COMPOSITE:
-				containedCondition = createPredicateComposite(null, theResourceName, spnamePrefix, targetParamDefinition,
+				containedCondition = createPredicateComposite(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
 					orValues, theRequestPartitionId);
 				break;
 			case URI:
-				containedCondition = createPredicateUri(null, theResourceName, spnamePrefix, targetParamDefinition,
+				containedCondition = createPredicateUri(theSourceJoinColumn, theResourceName, spnamePrefix, targetParamDefinition,
 					orValues, theOperation, theRequest, theRequestPartitionId);
 				break;
 			case HAS:
@@ -1162,11 +1162,25 @@ public class QueryStack {
 					break;
 				case REFERENCE:
 					for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
-						if (theSearchContainedMode.equals(SearchContainedModeEnum.TRUE))
+						if (theSearchContainedMode.equals(SearchContainedModeEnum.TRUE)) {
-							andPredicates.add(createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, theParamName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId));
+							// TODO: The _contained parameter is not intended to control search chain interpretation like this.
-						else
+							//   See SMILE-2898 for details.
+							//   For now, leave the incorrect implementation alone, just in case someone is relying on it,
+							//   until the complete fix is available.
+							andPredicates.add(createPredicateReferenceForContainedResource(null, theResourceName, theParamName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId));
+						} else if (isEligibleForContainedResourceSearch(nextAnd)) {
+							// TODO for now, restrict contained reference traversal to the last reference in the chain
+							//   We don't seem to be indexing the outbound references of a contained resource, so we can't
+							//   include them in search chains.
+							//   It would be nice to eventually relax this constraint, but no client seems to be asking for it.
+							andPredicates.add(toOrPredicate(
+								createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, nextAnd, null, theRequest, theRequestPartitionId),
+								createPredicateReferenceForContainedResource(theSourceJoinColumn, theResourceName, theParamName, nextParamDef, nextAnd, null, theRequest, theRequestPartitionId)
+							));
+						} else {
 							andPredicates.add(createPredicateReference(theSourceJoinColumn, theResourceName, theParamName, nextAnd, null, theRequest, theRequestPartitionId));
 						}
+					}
 					break;
 				case STRING:
 					for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
@@ -1243,6 +1257,14 @@ public class QueryStack {
 		return toAndPredicate(andPredicates);
 	}
 
+	private boolean isEligibleForContainedResourceSearch(List<? extends IQueryParameterType> nextAnd) {
+		return myModelConfig.isIndexOnContainedResources() &&
+			nextAnd.stream()
+				.filter(t -> t instanceof ReferenceParam)
+				.map(t -> (ReferenceParam) t)
+				.noneMatch(t -> t.getChain().contains("."));
+	}
+
 	public void addPredicateCompositeUnique(String theIndexString, RequestPartitionId theRequestPartitionId) {
 		ComboUniqueSearchParameterPredicateBuilder predicateBuilder = mySqlBuilder.addComboUniquePredicateBuilder();
 		Condition predicate = predicateBuilder.createPredicateIndexString(theRequestPartitionId, theIndexString);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java

@@ -377,7 +377,7 @@ public class SearchBuilder implements ISearchBuilder {
 		SearchQueryBuilder sqlBuilder = new SearchQueryBuilder(myContext, myDaoConfig.getModelConfig(), myPartitionSettings, myRequestPartitionId, sqlBuilderResourceName, mySqlBuilderFactory, myDialectProvider, theCount);
 		QueryStack queryStack3 = new QueryStack(theParams, myDaoConfig, myDaoConfig.getModelConfig(), myContext, sqlBuilder, mySearchParamRegistry, myPartitionSettings);
 
-		if (theParams.keySet().size() > 1 || theParams.getSort() != null || theParams.keySet().contains(Constants.PARAM_HAS)) {
+		if (theParams.keySet().size() > 1 || theParams.getSort() != null || theParams.keySet().contains(Constants.PARAM_HAS) || isPotentiallyContainedReferenceParameterExistsAtRoot(theParams)) {
 			List<RuntimeSearchParam> activeComboParams = mySearchParamRegistry.getActiveComboSearchParams(myResourceName, theParams.keySet());
 			if (activeComboParams.isEmpty()) {
 				sqlBuilder.setNeedResourceTableRoot(true);
@@ -487,6 +487,13 @@ public class SearchBuilder implements ISearchBuilder {
 		return Optional.of(executor);
 	}
 
+	private boolean isPotentiallyContainedReferenceParameterExistsAtRoot(SearchParameterMap theParams) {
+		return myModelConfig.isIndexOnContainedResources() && theParams.values().stream()
+			.flatMap(Collection::stream)
+			.flatMap(Collection::stream)
+			.anyMatch(t -> t instanceof ReferenceParam);
+	}
+
 	private List<Long> normalizeIdListForLastNInClause(List<Long> lastnResourceIds) {
 		/*
 			The following is a workaround to a known issue involving Hibernate. If queries are used with "in" clauses with large and varying

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java

@@ -38,20 +38,18 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderReference;
 import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
-import ca.uhn.fhir.jpa.search.builder.QueryStack;
 import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
+import ca.uhn.fhir.jpa.search.builder.QueryStack;
 import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
 import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
 import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
-import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
-import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
-import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
 import ca.uhn.fhir.rest.param.CompositeParam;
@@ -66,6 +64,8 @@ import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import com.google.common.collect.Lists;
 import com.healthmarketscience.sqlbuilder.BinaryCondition;
 import com.healthmarketscience.sqlbuilder.ComboCondition;
@@ -341,7 +341,7 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 		List<Condition> orPredicates = new ArrayList<>();
 		boolean paramInverted = false;
 		QueryStack childQueryFactory = myQueryStack.newChildQueryFactoryWithFullBuilderReuse();
-		for (String nextType : resourceTypes) {
+
 		String chain = theReferenceParam.getChain();
 
 		String remainingChain = null;
@@ -351,15 +351,6 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 			chain = chain.substring(0, chainDotIndex);
 		}
 
-			RuntimeResourceDefinition typeDef = getFhirContext().getResourceDefinition(nextType);
-			String subResourceName = typeDef.getName();
-
-			IDao dao = myDaoRegistry.getResourceDao(nextType);
-			if (dao == null) {
-				ourLog.debug("Don't have a DAO for type {}", nextType);
-				continue;
-			}
-
 		int qualifierIndex = chain.indexOf(':');
 		String qualifier = null;
 		if (qualifierIndex != -1) {
@@ -368,6 +359,18 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 		}
 
 		boolean isMeta = ResourceMetaParams.RESOURCE_META_PARAMS.containsKey(chain);
+
+		for (String nextType : resourceTypes) {
+
+			RuntimeResourceDefinition typeDef = getFhirContext().getResourceDefinition(nextType);
+			String subResourceName = typeDef.getName();
+
+			IDao dao = myDaoRegistry.getResourceDao(nextType);
+			if (dao == null) {
+				ourLog.debug("Don't have a DAO for type {}", nextType);
+				continue;
+			}
+
 			RuntimeSearchParam param = null;
 			if (!isMeta) {
 				param = mySearchParamRegistry.getActiveSearchParam(nextType, chain);
@@ -408,7 +411,6 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
 			andPredicates.add(childQueryFactory.searchForIdsWithAndOr(myColumnTargetResourceId, subResourceName, chain, chainParamValues, theRequest, theRequestPartitionId, SearchContainedModeEnum.FALSE));
 
 			orPredicates.add(toAndPredicate(andPredicates));
-
 		}
 
 		if (candidateTargetTypes.isEmpty()) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchHibernatePropertiesBuilder.java

@@ -37,6 +37,7 @@ import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings
 import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
 import org.slf4j.Logger;
 
+import javax.annotation.Nullable;
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Properties;
@@ -52,10 +53,10 @@ public class ElasticsearchHibernatePropertiesBuilder {
 	private static final Logger ourLog = getLogger(ElasticsearchHibernatePropertiesBuilder.class);
 
 
-	private IndexStatus myRequiredIndexStatus = IndexStatus.YELLOW.YELLOW;
+	private IndexStatus myRequiredIndexStatus = IndexStatus.YELLOW;
 	private SchemaManagementStrategyName myIndexSchemaManagementStrategy = SchemaManagementStrategyName.CREATE;
 
-	private String myRestUrl;
+	private String myHosts;
 	private String myUsername;
 	private String myPassword;
 	private long myIndexManagementWaitTimeoutMillis = 10000L;
@@ -77,11 +78,8 @@ public class ElasticsearchHibernatePropertiesBuilder {
 
 		// the below properties are used for ElasticSearch integration
 		theProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "elasticsearch");
-
-
 		theProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.ANALYSIS_CONFIGURER), HapiElasticsearchAnalysisConfigurer.class.getName());
-
+		theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), myHosts);
-		theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), myRestUrl);
 		theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.PROTOCOL), myProtocol);
 
 		if (StringUtils.isNotBlank(myUsername)) {
@@ -99,8 +97,10 @@ public class ElasticsearchHibernatePropertiesBuilder {
 		theProperties.put(HibernateOrmMapperSettings.AUTOMATIC_INDEXING_SYNCHRONIZATION_STRATEGY, myDebugSyncStrategy);
 		theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LOG_JSON_PRETTY_PRINTING), Boolean.toString(myDebugPrettyPrintJsonLog));
 
-		injectStartupTemplate(myProtocol, myRestUrl, myUsername, myPassword);
+		//This tells elasticsearch to use our custom index naming strategy.
+		theProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LAYOUT_STRATEGY), IndexNamePrefixLayoutStrategy.class.getName());
 
+		injectStartupTemplate(myProtocol, myHosts, myUsername, myPassword);
 	}
 
 	public ElasticsearchHibernatePropertiesBuilder setRequiredIndexStatus(IndexStatus theRequiredIndexStatus) {
@@ -108,11 +108,8 @@ public class ElasticsearchHibernatePropertiesBuilder {
 		return this;
 	}
 
-	public ElasticsearchHibernatePropertiesBuilder setRestUrl(String theRestUrl) {
+	public ElasticsearchHibernatePropertiesBuilder setHosts(String hosts) {
-		if (theRestUrl.contains("://")) {
+		myHosts = hosts;
-			throw new ConfigurationException("Elasticsearch URL cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.");
-		}
-		myRestUrl = theRestUrl;
 		return this;
 	}
 
@@ -147,18 +144,13 @@ public class ElasticsearchHibernatePropertiesBuilder {
 	 * TODO GGG HS: In HS6.1, we should have a native way of performing index settings manipulation at bootstrap time, so this should
 	 * eventually be removed in favour of whatever solution they come up with.
 	 */
-	void injectStartupTemplate(String theProtocol, String theHostAndPort, String theUsername, String thePassword) {
+	void injectStartupTemplate(String theProtocol, String theHosts, @Nullable String theUsername, @Nullable String thePassword) {
 		PutIndexTemplateRequest ngramTemplate = new PutIndexTemplateRequest("ngram-template")
-			.patterns(Arrays.asList("resourcetable-*", "termconcept-*"))
+			.patterns(Arrays.asList("*resourcetable-*", "*termconcept-*"))
 			.settings(Settings.builder().put("index.max_ngram_diff", 50));
 
-		int colonIndex = theHostAndPort.indexOf(":");
-		String host = theHostAndPort.substring(0, colonIndex);
-		Integer port = Integer.valueOf(theHostAndPort.substring(colonIndex + 1));
-		String qualifiedHost = theProtocol + "://" + host;
-
 		try {
-			RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(qualifiedHost, port, theUsername, thePassword);
+			RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theProtocol, theHosts, theUsername, thePassword);
 			ourLog.info("Adding starter template for large ngram diffs");
 			AcknowledgedResponse acknowledgedResponse = elasticsearchHighLevelRestClient.indices().putTemplate(ngramTemplate, RequestOptions.DEFAULT);
 			assert acknowledgedResponse.isAcknowledged();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/elastic/IndexNamePrefixLayoutStrategy.java

@@ -0,0 +1,99 @@
+package ca.uhn.fhir.jpa.search.elastic;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 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.ConfigurationException;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import org.apache.commons.lang3.StringUtils;
+import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
+import org.hibernate.search.backend.elasticsearch.logging.impl.Log;
+import org.hibernate.search.util.common.logging.impl.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.lang.invoke.MethodHandles;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * This class instructs hibernate search on how to create index names for indexed entities.
+ * In our case, we use this class to add an optional prefix to all indices which are created, which can be controlled via
+ * {@link DaoConfig#setElasticSearchIndexPrefix(String)}.
+ */
+@Service
+public class IndexNamePrefixLayoutStrategy implements IndexLayoutStrategy {
+
+	@Autowired
+	private DaoConfig myDaoConfig;
+
+	static final Log log = LoggerFactory.make(Log.class, MethodHandles.lookup());
+	public static final String NAME = "prefix";
+	public static final Pattern UNIQUE_KEY_EXTRACTION_PATTERN = Pattern.compile("(.*)-\\d{6}");
+
+	public String createInitialElasticsearchIndexName(String hibernateSearchIndexName) {
+		return addPrefixIfNecessary(hibernateSearchIndexName + "-000001");
+	}
+
+	public String createWriteAlias(String hibernateSearchIndexName) {
+		return addPrefixIfNecessary(hibernateSearchIndexName +"-write");
+	}
+
+	public String createReadAlias(String hibernateSearchIndexName) {
+		return addPrefixIfNecessary(hibernateSearchIndexName + "-read");
+	}
+
+	private String addPrefixIfNecessary(String theCandidateName) {
+		validateDaoConfigIsPresent();
+		if (!StringUtils.isBlank(myDaoConfig.getElasticSearchIndexPrefix())) {
+			return myDaoConfig.getElasticSearchIndexPrefix() + "-" + theCandidateName;
+		} else {
+			return theCandidateName;
+		}
+	}
+
+	public String extractUniqueKeyFromHibernateSearchIndexName(String hibernateSearchIndexName) {
+		return hibernateSearchIndexName;
+	}
+
+	public String extractUniqueKeyFromElasticsearchIndexName(String elasticsearchIndexName) {
+		Matcher matcher = UNIQUE_KEY_EXTRACTION_PATTERN.matcher(elasticsearchIndexName);
+		if (!matcher.matches()) {
+			throw log.invalidIndexPrimaryName(elasticsearchIndexName, UNIQUE_KEY_EXTRACTION_PATTERN);
+		} else {
+			String candidateUniqueKey= matcher.group(1);
+			return removePrefixIfNecessary(candidateUniqueKey);
+		}
+	}
+
+	private String removePrefixIfNecessary(String theCandidateUniqueKey) {
+		validateDaoConfigIsPresent();
+		if (!StringUtils.isBlank(myDaoConfig.getElasticSearchIndexPrefix())) {
+			return theCandidateUniqueKey.replace(myDaoConfig.getElasticSearchIndexPrefix() + "-", "");
+		} else {
+			return theCandidateUniqueKey;
+		}
+	}
+	private void validateDaoConfigIsPresent() {
+		if (myDaoConfig == null) {
+			throw new ConfigurationException("While attempting to boot HAPI FHIR, the Hibernate Search bootstrapper failed to find the DaoConfig. This probably means Hibernate Search has been recently upgraded, or somebody modified HapiFhirLocalContainerEntityManagerFactoryBean.");
+		}
+	}
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchRestClientFactory.java

@@ -20,6 +20,8 @@ package ca.uhn.fhir.jpa.search.lastn;
  * #L%
  */
 
+import ca.uhn.fhir.context.ConfigurationException;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.http.Header;
 import org.apache.http.HttpHost;
 import org.apache.http.auth.AuthScope;
@@ -27,41 +29,47 @@ import org.apache.http.auth.UsernamePasswordCredentials;
 import org.apache.http.client.CredentialsProvider;
 import org.apache.http.impl.client.BasicCredentialsProvider;
 import org.apache.http.message.BasicHeader;
+import org.elasticsearch.client.Node;
 import org.elasticsearch.client.RestClient;
 import org.elasticsearch.client.RestClientBuilder;
 import org.elasticsearch.client.RestHighLevelClient;
 
+import javax.annotation.Nullable;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
 public class ElasticsearchRestClientFactory {
 
 
-	private static String determineScheme(String theHostname) {
+	static public RestHighLevelClient createElasticsearchHighLevelRestClient(
-		int schemeIdx = theHostname.indexOf("://");
+		String protocol, String hosts, @Nullable String theUsername, @Nullable String thePassword) {
-		if (schemeIdx > 0) {
+
-			return theHostname.substring(0, schemeIdx);
+		if (hosts.contains("://")) {
-		} else {
+			throw new ConfigurationException("Elasticsearch URLs cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.");
-			return "http";
 		}
+		String[] hostArray = hosts.split(",");
+		List<Node> clientNodes = Arrays.stream(hostArray)
+			.map(String::trim)
+			.filter(s -> s.contains(":"))
+			.map(h -> {
+				int colonIndex = h.indexOf(":");
+				String host = h.substring(0, colonIndex);
+				int port = Integer.parseInt(h.substring(colonIndex + 1));
+				return new Node(new HttpHost(host, port, protocol));
+			})
+			.collect(Collectors.toList());
+		if (hostArray.length != clientNodes.size()) {
+			throw new ConfigurationException("Elasticsearch URLs have to contain ':' as a host:port separator. Example: localhost:9200,localhost:9201,localhost:9202");
 		}
 
-	private static String stripHostOfScheme(String theHostname) {
+		RestClientBuilder clientBuilder = RestClient.builder(clientNodes.toArray(new Node[0]));
-		int schemeIdx = theHostname.indexOf("://");
+		if (StringUtils.isNotBlank(theUsername) && StringUtils.isNotBlank(thePassword)) {
-		if (schemeIdx > 0) {
+			final CredentialsProvider credentialsProvider = new BasicCredentialsProvider();
-			return theHostname.substring(schemeIdx + 3);
+			credentialsProvider.setCredentials(AuthScope.ANY, new UsernamePasswordCredentials(theUsername, thePassword));
-		} else {
+			clientBuilder.setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
-			return theHostname;
-		}
-	}
-
-    static public RestHighLevelClient createElasticsearchHighLevelRestClient(String theHostname, int thePort, String theUsername, String thePassword) {
-        final CredentialsProvider credentialsProvider =
-                new BasicCredentialsProvider();
-        credentialsProvider.setCredentials(AuthScope.ANY,
-                new UsernamePasswordCredentials(theUsername, thePassword));
-        RestClientBuilder clientBuilder = RestClient.builder(
-                new HttpHost(stripHostOfScheme(theHostname), thePort, determineScheme(theHostname)))
-                .setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
 				.setDefaultCredentialsProvider(credentialsProvider));
-
+		}
 		Header[] defaultHeaders = new Header[]{new BasicHeader("Content-Type", "application/json")};
 		clientBuilder.setDefaultHeaders(defaultHeaders);
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchSvcImpl.java

@@ -68,11 +68,11 @@ import org.elasticsearch.search.aggregations.bucket.terms.ParsedTerms;
 import org.elasticsearch.search.aggregations.bucket.terms.Terms;
 import org.elasticsearch.search.aggregations.bucket.terms.TermsAggregationBuilder;
 import org.elasticsearch.search.aggregations.metrics.ParsedTopHits;
-import org.elasticsearch.search.aggregations.support.ValueType;
 import org.elasticsearch.search.builder.SearchSourceBuilder;
 import org.elasticsearch.search.sort.SortOrder;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import javax.annotation.Nullable;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -125,13 +125,13 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
 	private PartitionSettings myPartitionSettings;
 
 	//This constructor used to inject a dummy partitionsettings in test.
-	public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theHostname, int thePort, String theUsername, String thePassword) {
+	public ElasticsearchSvcImpl(PartitionSettings thePartitionSetings, String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
-		this(theHostname, thePort, theUsername, thePassword);
+		this(theHostname, theUsername, thePassword);
 		this.myPartitionSettings = thePartitionSetings;
 	}
 
-	public ElasticsearchSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) {
+	public ElasticsearchSvcImpl(String theHostname, @Nullable String theUsername, @Nullable String thePassword) {
-		myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(theHostname, thePort, theUsername, thePassword);
+		myRestHighLevelClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http", theHostname, theUsername, thePassword);
 
 		try {
 			createObservationIndexIfMissing();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/SqlQuery.java

@@ -126,5 +126,8 @@ public class SqlQuery {
 
 	}
 
-
+	@Override
+	public String toString() {
+		return getSql(true, true);
+	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/cache/ResourceVersionCacheSvcTest.java

@@ -21,12 +21,12 @@ public class ResourceVersionCacheSvcTest extends BaseJpaR4Test {
 		IIdType patientId = myPatientDao.create(patient).getId();
 		ResourceVersionMap versionMap = myResourceVersionCacheSvc.getVersionMap("Patient", SearchParameterMap.newSynchronous());
 		assertEquals(1, versionMap.size());
-		assertEquals("1", versionMap.getVersion(patientId));
+		assertEquals(1L, versionMap.getVersion(patientId));
 
 		patient.setGender(Enumerations.AdministrativeGender.MALE);
 		myPatientDao.update(patient);
 		versionMap = myResourceVersionCacheSvc.getVersionMap("Patient", SearchParameterMap.newSynchronous());
 		assertEquals(1, versionMap.size());
-		assertEquals("2", versionMap.getVersion(patientId));
+		assertEquals(2L, versionMap.getVersion(patientId));
 	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/ElasticsearchWithPrefixConfig.java

@@ -0,0 +1,147 @@
+package ca.uhn.fhir.jpa.config;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.config.BlockLargeNumbersOfParamsListener;
+import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
+import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
+import ca.uhn.fhir.jpa.dao.r4.ElasticsearchPrefixTest;
+import ca.uhn.fhir.jpa.search.elastic.HapiElasticsearchAnalysisConfigurer;
+import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
+import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
+import ca.uhn.fhir.jpa.search.lastn.config.TestElasticsearchContainerHelper;
+import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
+import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
+import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
+import org.apache.commons.dbcp2.BasicDataSource;
+import org.elasticsearch.action.support.master.AcknowledgedResponse;
+import org.elasticsearch.client.RequestOptions;
+import org.elasticsearch.client.RestHighLevelClient;
+import org.elasticsearch.client.indices.PutIndexTemplateRequest;
+import org.elasticsearch.common.settings.Settings;
+import org.hibernate.dialect.H2Dialect;
+import org.hibernate.jpa.HibernatePersistenceProvider;
+import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchBackendSettings;
+import org.hibernate.search.backend.elasticsearch.cfg.ElasticsearchIndexSettings;
+import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
+import org.hibernate.search.engine.cfg.BackendSettings;
+import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
+import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.testcontainers.elasticsearch.ElasticsearchContainer;
+
+import javax.sql.DataSource;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Properties;
+import java.util.concurrent.TimeUnit;
+
+/**
+ * The only reason this is its own class is so that we can set a dao config setting before the whole test framework comes online.
+ * We need to do this as it is during bean creation that HS bootstrapping occurs.
+ */
+@Configuration
+public class ElasticsearchWithPrefixConfig {
+
+	@Bean
+	public DaoConfig daoConfig() {
+		DaoConfig daoConfig = new DaoConfig();
+		daoConfig.setElasticSearchIndexPrefix(ElasticsearchPrefixTest.ELASTIC_PREFIX);
+		return daoConfig;
+	}
+
+	@Bean
+	public IndexNamePrefixLayoutStrategy indexNamePrefixLayoutStrategy() {
+		return new IndexNamePrefixLayoutStrategy();
+	}
+	@Bean
+	public FhirContext fhirContext() {
+		return FhirContext.forR4();
+	}
+
+	@Bean
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
+		LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(theConfigurableListableBeanFactory);
+		retVal.setJpaDialect(new HapiFhirHibernateJpaDialect(fhirContext().getLocalizer()));
+		retVal.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");
+		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
+		retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
+		retVal.setDataSource(dataSource());
+		retVal.setJpaProperties(jpaProperties());
+		return retVal;
+	}
+	@Bean
+	public DataSource dataSource() {
+		BasicDataSource retVal = new BasicDataSource();
+		retVal.setDriver(new org.h2.Driver());
+		retVal.setUrl("jdbc:h2:mem:testdb_r4");
+		retVal.setMaxWaitMillis(30000);
+		retVal.setUsername("");
+		retVal.setPassword("");
+		retVal.setMaxTotal(5);
+
+		SLF4JLogLevel level = SLF4JLogLevel.INFO;
+		DataSource dataSource = ProxyDataSourceBuilder
+			.create(retVal)
+			.logSlowQueryBySlf4j(10, TimeUnit.SECONDS, level)
+			.beforeQuery(new BlockLargeNumbersOfParamsListener())
+			.afterQuery(new CurrentThreadCaptureQueriesListener())
+			.build();
+
+		return dataSource;
+	}
+
+	@Bean
+	public Properties jpaProperties() {
+		Properties extraProperties = new Properties();
+		extraProperties.put("hibernate.format_sql", "false");
+		extraProperties.put("hibernate.show_sql", "false");
+		extraProperties.put("hibernate.hbm2ddl.auto", "update");
+		extraProperties.put("hibernate.dialect", H2Dialect.class.getName());
+		//Override default lucene settings
+		// Force elasticsearch to start first
+		int httpPort = elasticContainer().getMappedPort(9200);//9200 is the HTTP port
+		String host = elasticContainer().getHost();
+		// the below properties are used for ElasticSearch integration
+		extraProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "elasticsearch");
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.ANALYSIS_CONFIGURER), HapiElasticsearchAnalysisConfigurer.class.getName());
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS), host + ":" + httpPort);
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.PROTOCOL), "http");
+		extraProperties.put(HibernateOrmMapperSettings.SCHEMA_MANAGEMENT_STRATEGY, SchemaManagementStrategyName.CREATE.externalRepresentation());
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.SCHEMA_MANAGEMENT_MINIMAL_REQUIRED_STATUS_WAIT_TIMEOUT), Long.toString(10000));
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.SCHEMA_MANAGEMENT_MINIMAL_REQUIRED_STATUS), IndexStatus.YELLOW.externalRepresentation());
+		// Need the mapping to be dynamic because of terminology indexes.
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchIndexSettings.DYNAMIC_MAPPING), "true");
+		// Only for unit tests
+		extraProperties.put(HibernateOrmMapperSettings.AUTOMATIC_INDEXING_SYNCHRONIZATION_STRATEGY, "read-sync");
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LOG_JSON_PRETTY_PRINTING), Boolean.toString(true));
+
+		//This tells elasticsearch to use our custom index naming strategy.
+		extraProperties.put(BackendSettings.backendKey(ElasticsearchBackendSettings.LAYOUT_STRATEGY), IndexNamePrefixLayoutStrategy.class.getName());
+
+		PutIndexTemplateRequest ngramTemplate = new PutIndexTemplateRequest("ngram-template")
+			.patterns(Arrays.asList("*resourcetable-*", "*termconcept-*"))
+			.settings(Settings.builder().put("index.max_ngram_diff", 50));
+
+		try {
+			RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient("http", host + ":" + httpPort, "", "");
+			AcknowledgedResponse acknowledgedResponse = elasticsearchHighLevelRestClient.indices().putTemplate(ngramTemplate, RequestOptions.DEFAULT);
+			assert acknowledgedResponse.isAcknowledged();
+		} catch (IOException theE) {
+			theE.printStackTrace();
+			throw new ConfigurationException("Couldn't connect to the elasticsearch server to create necessary templates. Ensure the Elasticsearch user has permissions to create templates.");
+		}
+		return extraProperties;
+	}
+
+	@Bean
+	public ElasticsearchContainer elasticContainer() {
+		ElasticsearchContainer embeddedElasticSearch = TestElasticsearchContainerHelper.getEmbeddedElasticSearch();
+		embeddedElasticSearch.start();
+		return embeddedElasticSearch;
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java

@@ -16,6 +16,7 @@ import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -134,8 +135,8 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu2");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -15,6 +15,7 @@ import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
 import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -138,8 +139,8 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java

@@ -3,12 +3,14 @@ package ca.uhn.fhir.jpa.config;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
 import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.match.deliver.resthook.SubscriptionDeliveringRestHookSubscriber;
 import ca.uhn.fhir.jpa.subscription.submit.config.SubscriptionSubmitterConfig;
 import ca.uhn.fhir.test.utilities.BatchJobHelper;
+import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
 import org.springframework.batch.core.explore.JobExplorer;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.config;
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
 import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
 import ca.uhn.fhir.jpa.batch.svc.BatchJobSubmitterImpl;
@@ -14,6 +15,8 @@ import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.hibernate.dialect.H2Dialect;
+import org.hibernate.jpa.HibernatePersistenceProvider;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -138,10 +141,15 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		return new SingleQueryCountHolder();
 	}
 
+
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(theConfigurableListableBeanFactory);
+		configureEntityManagerFactory(retVal, fhirContext());
+		retVal.setJpaDialect(new HapiFhirHibernateJpaDialect(fhirContext().getLocalizer()));
+		retVal.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");
+		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticSearch.java

@@ -1,13 +1,19 @@
 package ca.uhn.fhir.jpa.config;
 
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
+import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
 import ca.uhn.fhir.jpa.search.lastn.config.TestElasticsearchContainerHelper;
+import org.h2.index.Index;
 import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
+import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
 import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.DependsOn;
 import org.testcontainers.elasticsearch.ElasticsearchContainer;
 
 import javax.annotation.PreDestroy;
@@ -35,7 +41,7 @@ public class TestR4ConfigWithElasticSearch extends TestR4Config {
 			.setIndexSchemaManagementStrategy(SchemaManagementStrategyName.CREATE)
 			.setIndexManagementWaitTimeoutMillis(10000)
 			.setRequiredIndexStatus(IndexStatus.YELLOW)
-			.setRestUrl(host+ ":" + httpPort)
+			.setHosts(host + ":" + httpPort)
 			.setProtocol("http")
 			.setUsername("")
 			.setPassword("")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4ConfigWithElasticsearchClient.java

@@ -21,7 +21,7 @@ public class TestR4ConfigWithElasticsearchClient extends TestR4ConfigWithElastic
 	public ElasticsearchSvcImpl myElasticsearchSvc() {
 		int elasticsearchPort = elasticContainer().getMappedPort(9200);
 		String host = elasticContainer().getHost();
-		return new ElasticsearchSvcImpl(host, elasticsearchPort, "", "");
+		return new ElasticsearchSvcImpl(host + ":" + elasticsearchPort, null, null);
 	}
 
 	@PreDestroy

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4WithLuceneDisabledConfig.java

@@ -3,9 +3,11 @@ package ca.uhn.fhir.jpa.config;
 import java.util.Properties;
 
 import org.hibernate.dialect.H2Dialect;
+import org.hibernate.search.backend.elasticsearch.index.layout.IndexLayoutStrategy;
 import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -27,8 +29,8 @@ public class TestR4WithLuceneDisabledConfig extends TestR4Config {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR5Config.java

@@ -16,6 +16,7 @@ import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -138,8 +139,8 @@ public class TestR5Config extends BaseJavaConfigR5 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaR5");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDaoTest.java

@@ -13,6 +13,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.fail;
 
 class BaseHapiFhirResourceDaoTest {
+
 	TestResourceDao mySvc = new TestResourceDao();
 
 	@Test

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java

@@ -721,6 +721,4 @@ public abstract class BaseJpaTest extends BaseTest {
 		}
 		Thread.sleep(500);
 	}
-
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java

@@ -5,6 +5,7 @@ import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.interceptor.executor.InterceptorService;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
 import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
@@ -70,6 +71,8 @@ public class TransactionProcessorTest {
 	private MatchUrlService myMatchUrlService;
 	@MockBean
 	private IRequestPartitionHelperSvc myRequestPartitionHelperSvc;
+	@MockBean
+	private IResourceVersionSvc myResourceVersionSvc;
 
 	@MockBean(answer = Answers.RETURNS_DEEP_STUBS)
 	private SessionImpl mySession;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/index/IdHelperServiceTest.java

@@ -1,35 +0,0 @@
-package ca.uhn.fhir.jpa.dao.index;
-
-import ca.uhn.fhir.interceptor.model.RequestPartitionId;
-import ca.uhn.fhir.jpa.model.config.PartitionSettings;
-import org.junit.jupiter.api.Test;
-
-import static org.junit.jupiter.api.Assertions.*;
-
-public class IdHelperServiceTest {
-
-	@Test
-	public void testReplaceDefault_AllPartitions() {
-
-		IdHelperService svc = new IdHelperService();
-		PartitionSettings partitionSettings = new PartitionSettings();
-		partitionSettings.setDefaultPartitionId(1);
-		svc.setPartitionSettingsForUnitTest(partitionSettings);
-
-		RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.allPartitions());
-		assertSame(RequestPartitionId.allPartitions(), outcome);
-	}
-
-	@Test
-	public void testReplaceDefault_DefaultPartition() {
-
-		IdHelperService svc = new IdHelperService();
-		PartitionSettings partitionSettings = new PartitionSettings();
-		partitionSettings.setDefaultPartitionId(1);
-		svc.setPartitionSettingsForUnitTest(partitionSettings);
-
-		RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.defaultPartition());
-		assertEquals(1, outcome.getPartitionIds().get(0));
-	}
-
-}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/index/ResourceVersionSvcTest.java

@@ -0,0 +1,209 @@
+package ca.uhn.fhir.jpa.dao.index;
+
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
+import ca.uhn.fhir.jpa.cache.ResourceVersionSvcDaoImpl;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
+import ca.uhn.fhir.jpa.model.config.PartitionSettings;
+import ca.uhn.fhir.jpa.model.entity.ForcedId;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.Mockito;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import javax.persistence.TypedQuery;
+import javax.persistence.criteria.CriteriaBuilder;
+import javax.persistence.criteria.CriteriaQuery;
+import javax.persistence.criteria.Path;
+import javax.persistence.criteria.Root;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertSame;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+public class ResourceVersionSvcTest {
+
+	// helper class to package up data for helper methods
+	private class ResourceIdPackage {
+		public IIdType MyResourceId;
+		public ResourcePersistentId MyPid;
+		public Long MyVersion;
+
+		public ResourceIdPackage(IIdType id,
+										 ResourcePersistentId pid,
+										 Long version) {
+			MyResourceId = id;
+			MyPid = pid;
+			MyVersion = version;
+		}
+	}
+
+	@Mock
+	DaoRegistry myDaoRegistry;
+	@Mock
+	IResourceTableDao myResourceTableDao;
+	@Mock
+	IdHelperService myIdHelperService;
+
+	// TODO KHS move the methods that use this out to a separate test class
+	@InjectMocks
+	private ResourceVersionSvcDaoImpl myResourceVersionSvc;
+
+	/**
+	 * Gets a ResourceTable record for getResourceVersionsForPid
+	 * Order matters!
+	 * @param resourceType
+	 * @param pid
+	 * @param version
+	 * @return
+	 */
+	private Object[] getResourceTableRecordForResourceTypeAndPid(String resourceType, long pid, long version) {
+		return new Object[] {
+			pid, // long
+			resourceType, // string
+			version // long
+		};
+	}
+
+	/**
+	 * Helper function to mock out resolveResourcePersistentIdsWithCache
+	 * to return empty lists (as if no resources were found).
+	 */
+	private void mock_resolveResourcePersistentIdsWithCache_toReturnNothing() {
+		CriteriaBuilder cb = Mockito.mock(CriteriaBuilder.class);
+		CriteriaQuery<ForcedId> criteriaQuery = Mockito.mock(CriteriaQuery.class);
+		Root<ForcedId> from = Mockito.mock(Root.class);
+		Path path = Mockito.mock(Path.class);
+
+		TypedQuery<ForcedId> queryMock = Mockito.mock(TypedQuery.class);
+	}
+
+	/**
+	 * Helper function to mock out getIdsOfExistingResources
+	 * to return the matches and resources matching those provided
+	 * by parameters.
+	 * @param theResourcePacks
+	 */
+	private void mockReturnsFor_getIdsOfExistingResources(ResourceIdPackage... theResourcePacks) {
+		List<ResourcePersistentId> resourcePersistentIds = new ArrayList<>();
+		List<Object[]> matches = new ArrayList<>();
+
+		for (ResourceIdPackage pack : theResourcePacks) {
+			resourcePersistentIds.add(pack.MyPid);
+
+			matches.add(getResourceTableRecordForResourceTypeAndPid(
+				pack.MyResourceId.getResourceType(),
+				pack.MyPid.getIdAsLong(),
+				pack.MyVersion
+			));
+		}
+
+		ResourcePersistentId first = resourcePersistentIds.remove(0);
+		if (resourcePersistentIds.isEmpty()) {
+			when(myIdHelperService.resolveResourcePersistentIdsWithCache(any(), any())).thenReturn(Collections.singletonList(first));
+		}
+		else {
+			when(myIdHelperService.resolveResourcePersistentIdsWithCache(any(), any())).thenReturn(resourcePersistentIds);
+		}
+	}
+
+	@Test
+	public void getLatestVersionIdsForResourceIds_whenResourceExists_returnsMapWithPIDAndVersion() {
+		IIdType type = new IdDt("Patient/RED");
+		ResourcePersistentId pid = new ResourcePersistentId(1L);
+		pid.setAssociatedResourceId(type);
+		HashMap<IIdType, ResourcePersistentId> map = new HashMap<>();
+		map.put(type, pid);
+		ResourceIdPackage pack = new ResourceIdPackage(type, pid, 2L);
+
+		// when
+		mockReturnsFor_getIdsOfExistingResources(pack);
+
+		// test
+		ResourcePersistentIdMap retMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
+			Collections.singletonList(type));
+
+		Assertions.assertTrue(retMap.containsKey(type));
+		Assertions.assertEquals(pid.getVersion(), map.get(type).getVersion());
+	}
+
+	@Test
+	public void getLatestVersionIdsForResourceIds_whenResourceDoesNotExist_returnsEmptyMap() {
+		IIdType type = new IdDt("Patient/RED");
+
+		// when
+		mock_resolveResourcePersistentIdsWithCache_toReturnNothing();
+
+		// test
+		ResourcePersistentIdMap retMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(RequestPartitionId.allPartitions(),
+			Collections.singletonList(type));
+
+		Assertions.assertTrue(retMap.isEmpty());
+	}
+
+	@Test
+	public void getLatestVersionIdsForResourceIds_whenSomeResourcesDoNotExist_returnsOnlyExistingElements() {
+		// resource to be found
+		IIdType type = new IdDt("Patient/RED");
+		ResourcePersistentId pid = new ResourcePersistentId(1L);
+		pid.setAssociatedResourceId(type);
+		ResourceIdPackage pack = new ResourceIdPackage(type, pid, 2L);
+
+		// resource that won't be found
+		IIdType type2 = new IdDt("Patient/BLUE");
+
+		// when
+		mock_resolveResourcePersistentIdsWithCache_toReturnNothing();
+		mockReturnsFor_getIdsOfExistingResources(pack);
+
+		// test
+		ResourcePersistentIdMap retMap = myResourceVersionSvc.getLatestVersionIdsForResourceIds(
+			RequestPartitionId.allPartitions(),
+			Arrays.asList(type, type2)
+		);
+
+		// verify
+		Assertions.assertEquals(1, retMap.size());
+		Assertions.assertTrue(retMap.containsKey(type));
+		Assertions.assertFalse(retMap.containsKey(type2));
+	}
+
+	@Test
+	public void testReplaceDefault_AllPartitions() {
+
+		IdHelperService svc = new IdHelperService();
+		PartitionSettings partitionSettings = new PartitionSettings();
+		partitionSettings.setDefaultPartitionId(1);
+		svc.setPartitionSettingsForUnitTest(partitionSettings);
+
+		RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.allPartitions());
+		assertSame(RequestPartitionId.allPartitions(), outcome);
+	}
+
+	@Test
+	public void testReplaceDefault_DefaultPartition() {
+
+		IdHelperService svc = new IdHelperService();
+		PartitionSettings partitionSettings = new PartitionSettings();
+		partitionSettings.setDefaultPartitionId(1);
+		svc.setPartitionSettingsForUnitTest(partitionSettings);
+
+		RequestPartitionId outcome = svc.replaceDefault(RequestPartitionId.defaultPartition());
+		assertEquals(1, outcome.getPartitionIds().get(0));
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/ChainingR4SearchTest.java

@@ -0,0 +1,388 @@
+package ca.uhn.fhir.jpa.dao.r4;
+
+import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
+import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.parser.StrictErrorHandler;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.IdType;
+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.StringType;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.contains;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+
+public class ChainingR4SearchTest extends BaseJpaR4Test {
+
+	@Autowired
+	MatchUrlService myMatchUrlService;
+
+	@AfterEach
+	public void after() throws Exception {
+
+		myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
+		myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
+		myDaoConfig.setReuseCachedSearchResultsForMillis(new DaoConfig().getReuseCachedSearchResultsForMillis());
+		myDaoConfig.setCountSearchResultsUpTo(new DaoConfig().getCountSearchResultsUpTo());
+		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
+		myDaoConfig.setAllowContainsSearches(new DaoConfig().isAllowContainsSearches());
+		myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
+
+		myModelConfig.setIndexOnContainedResources(false);
+		myModelConfig.setIndexOnContainedResources(new ModelConfig().isIndexOnContainedResources());
+	}
+
+	@BeforeEach
+	public void before() throws Exception {
+		myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
+
+		myDaoConfig.setAllowMultipleDelete(true);
+		myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());
+		myModelConfig.setIndexOnContainedResources(true);
+		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
+	}
+
+	@Test
+	public void testShouldResolveATwoLinkChainWithStandAloneResources() throws Exception {
+
+		// setup
+		IIdType oid1;
+
+		{
+			Patient p = new Patient();
+			p.setId(IdType.newRandomUuid());
+			p.addName().setFamily("Smith").addGiven("John");
+			myPatientDao.create(p, mySrd);
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference(p.getId());
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject.name=Smith";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	public void testShouldResolveATwoLinkChainWithAContainedResource() throws Exception {
+		// setup
+		IIdType oid1;
+
+		{
+			Patient p = new Patient();
+			p.setId("pat");
+			p.addName().setFamily("Smith").addGiven("John");
+
+			Observation obs = new Observation();
+			obs.getContained().add(p);
+			obs.getCode().setText("Observation 1");
+			obs.setValue(new StringType("Test"));
+			obs.getSubject().setReference("#pat");
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject.name=Smith";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	public void testShouldResolveAThreeLinkChainWhereAllResourcesStandAlone() throws Exception {
+
+		// setup
+		IIdType oid1;
+
+		{
+			Organization org = new Organization();
+			org.setId(IdType.newRandomUuid());
+			org.setName("HealthCo");
+			myOrganizationDao.create(org, mySrd);
+
+			Patient p = new Patient();
+			p.setId(IdType.newRandomUuid());
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getManagingOrganization().setReference(org.getId());
+			myPatientDao.create(p, mySrd);
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference(p.getId());
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject.organization.name=HealthCo";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	public void testShouldResolveAThreeLinkChainWithAContainedResourceAtTheEndOfTheChain() throws Exception {
+		// This is the case that is most relevant to SMILE-2899
+
+		// setup
+		IIdType oid1;
+
+		{
+			Organization org = new Organization();
+			org.setId("org");
+			org.setName("HealthCo");
+
+			Patient p = new Patient();
+			p.setId(IdType.newRandomUuid());
+			p.getContained().add(org);
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getManagingOrganization().setReference("#org");
+			myPatientDao.create(p, mySrd);
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference(p.getId());
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject.organization.name=HealthCo";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	@Disabled
+	public void testShouldResolveAThreeLinkChainWithAContainedResourceAtTheBeginningOfTheChain() throws Exception {
+		// We do not currently support this case - we may not be indexing the references of contained resources
+
+		// setup
+		IIdType oid1;
+
+		{
+			Organization org = new Organization();
+			org.setId(IdType.newRandomUuid());
+			org.setName("HealthCo");
+			myOrganizationDao.create(org, mySrd);
+
+			Patient p = new Patient();
+			p.setId("pat");
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getManagingOrganization().setReference(org.getId());
+
+			Observation obs = new Observation();
+			obs.getContained().add(p);
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference("#pat");
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject.organization.name=HealthCo";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	public void testShouldResolveAThreeLinkChainWithQualifiersWhereAllResourcesStandAlone() throws Exception {
+
+		// setup
+		IIdType oid1;
+
+		{
+			Organization org = new Organization();
+			org.setId(IdType.newRandomUuid());
+			org.setName("HealthCo");
+			myOrganizationDao.create(org, mySrd);
+
+			Patient p = new Patient();
+			p.setId(IdType.newRandomUuid());
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getManagingOrganization().setReference(org.getId());
+			myPatientDao.create(p, mySrd);
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference(p.getId());
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject:Patient.organization:Organization.name=HealthCo";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	public void testShouldResolveAThreeLinkChainWithQualifiersWithAContainedResourceAtTheEndOfTheChain() throws Exception {
+		// This is the case that is most relevant to SMILE-2899
+
+		// setup
+		IIdType oid1;
+
+		{
+			Organization org = new Organization();
+			org.setId("org");
+			org.setName("HealthCo");
+
+			Patient p = new Patient();
+			p.setId(IdType.newRandomUuid());
+			p.getContained().add(org);
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getManagingOrganization().setReference("#org");
+			myPatientDao.create(p, mySrd);
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference(p.getId());
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject:Patient.organization:Organization.name=HealthCo";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	public void testShouldResolveAFourLinkChainWhereAllResourcesStandAlone() throws Exception {
+
+		// setup
+		IIdType oid1;
+
+		{
+			Organization org = new Organization();
+			org.setId(IdType.newRandomUuid());
+			org.setName("HealthCo");
+			myOrganizationDao.create(org, mySrd);
+
+			Organization partOfOrg = new Organization();
+			partOfOrg.setId(IdType.newRandomUuid());
+			partOfOrg.getPartOf().setReference(org.getId());
+			myOrganizationDao.create(partOfOrg, mySrd);
+
+			Patient p = new Patient();
+			p.setId(IdType.newRandomUuid());
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getManagingOrganization().setReference(partOfOrg.getId());
+			myPatientDao.create(p, mySrd);
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference(p.getId());
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject.organization.partof.name=HealthCo";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	@Test
+	public void testShouldResolveAFourLinkChainWhereTheLastReferenceIsContained() throws Exception {
+
+		// setup
+		IIdType oid1;
+
+		{
+			Organization org = new Organization();
+			org.setId("parent");
+			org.setName("HealthCo");
+
+			Organization partOfOrg = new Organization();
+			partOfOrg.setId(IdType.newRandomUuid());
+			partOfOrg.getContained().add(org);
+			partOfOrg.getPartOf().setReference("#parent");
+			myOrganizationDao.create(partOfOrg, mySrd);
+
+			Patient p = new Patient();
+			p.setId(IdType.newRandomUuid());
+			p.addName().setFamily("Smith").addGiven("John");
+			p.getManagingOrganization().setReference(partOfOrg.getId());
+			myPatientDao.create(p, mySrd);
+
+			Observation obs = new Observation();
+			obs.getCode().setText("Observation 1");
+			obs.getSubject().setReference(p.getId());
+
+			oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		String url = "/Observation?subject.organization.partof.name=HealthCo";
+
+		// execute
+		List<String> oids = searchAndReturnUnqualifiedVersionlessIdValues(url);
+
+		// validate
+		assertEquals(1L, oids.size());
+		assertThat(oids, contains(oid1.getIdPart()));
+	}
+
+	private List<String> searchAndReturnUnqualifiedVersionlessIdValues(String theUrl) throws IOException {
+		List<String> ids = new ArrayList<>();
+
+		ResourceSearch search = myMatchUrlService.getResourceSearch(theUrl);
+		SearchParameterMap map = search.getSearchParameterMap();
+		map.setLoadSynchronous(true);
+		IBundleProvider result = myObservationDao.search(map);
+		return result.getAllResourceIds();
+	}
+
+}

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

@@ -0,0 +1,49 @@
+package ca.uhn.fhir.jpa.dao.r4;
+
+import ca.uhn.fhir.jpa.config.ElasticsearchWithPrefixConfig;
+import ca.uhn.fhir.jpa.search.lastn.ElasticsearchRestClientFactory;
+import ca.uhn.fhir.test.utilities.docker.RequiresDocker;
+import org.apache.http.util.EntityUtils;
+import org.elasticsearch.client.Request;
+import org.elasticsearch.client.Response;
+import org.elasticsearch.client.RestClient;
+import org.elasticsearch.client.RestHighLevelClient;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+import org.testcontainers.elasticsearch.ElasticsearchContainer;
+
+import java.io.IOException;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsString;
+
+@RequiresDocker
+@ExtendWith(SpringExtension.class)
+@ContextConfiguration(classes = {ElasticsearchWithPrefixConfig.class})
+public class ElasticsearchPrefixTest {
+
+	@Autowired
+	ElasticsearchContainer elasticsearchContainer;
+
+	public static String ELASTIC_PREFIX = "hapi-fhir";
+	@Test
+	public void test() throws IOException {
+		//Given
+		RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
+			"http", elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), "", "");
+
+		//When
+		RestClient lowLevelClient = elasticsearchHighLevelRestClient.getLowLevelClient();
+		Response get = lowLevelClient.performRequest(new Request("GET", "/_cat/indices"));
+		String catIndexes = EntityUtils.toString(get.getEntity());
+
+		//Then
+		assertThat(catIndexes, containsString(ELASTIC_PREFIX + "-resourcetable-000001"));
+		assertThat(catIndexes, containsString(ELASTIC_PREFIX + "-termconcept-000001"));
+
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java

@@ -1,17 +1,22 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.util.BundleBuilder;
 import ca.uhn.fhir.util.HapiExtensions;
 import com.google.common.collect.Sets;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.AuditEvent;
 import org.hl7.fhir.r4.model.BooleanType;
+import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Extension;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Identifier;
@@ -21,6 +26,7 @@ import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Task;
 import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
 import java.util.List;
@@ -48,12 +54,11 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		myDaoConfig.setResourceClientIdStrategy(new DaoConfig().getResourceClientIdStrategy());
 		myDaoConfig.setPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets(new DaoConfig().isPopulateIdentifierInAutoCreatedPlaceholderReferenceTargets());
 		myDaoConfig.setBundleTypesAllowedForStorage(new DaoConfig().getBundleTypesAllowedForStorage());
-
+		myModelConfig.setAutoVersionReferenceAtPaths(new ModelConfig().getAutoVersionReferenceAtPaths());
 	}
 
 	@Test
 	public void testCreateWithBadReferenceFails() {
-
 		Observation o = new Observation();
 		o.setStatus(ObservationStatus.FINAL);
 		o.getSubject().setReference("Patient/FOO");
@@ -97,27 +102,23 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		params.add(Task.SP_PART_OF, new ReferenceParam("Task/AAA"));
 		List<String> found = toUnqualifiedVersionlessIdValues(myTaskDao.search(params));
 		assertThat(found, contains(id.getValue()));
-
-
 	}
 
 	@Test
 	public void testUpdateWithBadReferenceFails() {
+		Observation o1 = new Observation();
+		o1.setStatus(ObservationStatus.FINAL);
+		IIdType id = myObservationDao.create(o1, mySrd).getId();
 
 		Observation o = new Observation();
-		o.setStatus(ObservationStatus.FINAL);
-		IIdType id = myObservationDao.create(o, mySrd).getId();
-
-		o = new Observation();
 		o.setId(id);
 		o.setStatus(ObservationStatus.FINAL);
 		o.getSubject().setReference("Patient/FOO");
-		try {
+
+		Exception ex = Assertions.assertThrows(InvalidRequestException.class, () -> {
 			myObservationDao.update(o, mySrd);
-			fail();
+		});
-		} catch (InvalidRequestException e) {
+		assertThat(ex.getMessage(), startsWith("Resource Patient/FOO not found, specified in path: Observation.subject"));
-			assertThat(e.getMessage(), startsWith("Resource Patient/FOO not found, specified in path: Observation.subject"));
-		}
 	}
 
 	@Test
@@ -450,8 +451,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		ourLog.info("\nObservation read after Patient update:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
 		assertEquals(createdObs.getSubject().getReference(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
 		assertEquals(placeholderPatId.toUnqualifiedVersionless().getValueAsString(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
-
-
 	}
 
 	@Test
@@ -540,7 +539,6 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 
 		AuditEvent createdEvent = myAuditEventDao.read(id);
 		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEvent));
-
 	}
 
 	@Test
@@ -560,11 +558,96 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
 		IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
 
 		Observation createdObs = myObservationDao.read(id);
-		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
 		assertEquals("Patient/ABC", createdObs.getSubject().getReference());
+	}
 
+	@Test
+	public void testAutocreatePlaceholderTest() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+
+		Observation obs = new Observation();
+		obs.setId("Observation/DEF");
+		Reference patientRef = new Reference("Patient/RED");
+		obs.setSubject(patientRef);
+		BundleBuilder builder = new BundleBuilder(myFhirCtx);
+		builder.addTransactionUpdateEntry(obs);
+
+		mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
+
+		// verify subresource is created
+		Patient returned = myPatientDao.read(patientRef.getReferenceElement());
+		assertNotNull(returned);
 	}
 
 
+	@Test
+	public void testAutocreatePlaceholderWithTargetExistingAlreadyTest() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+		myModelConfig.setAutoVersionReferenceAtPaths("Observation.subject");
+
+		String patientId = "Patient/RED";
+
+		// create
+		Patient patient = new Patient();
+		patient.setIdElement(new IdType(patientId));
+		myPatientDao.update(patient); // use update to use forcedid
+
+		// update
+		patient.setActive(true);
+		myPatientDao.update(patient);
+
+		// observation (with version 2)
+		Observation obs = new Observation();
+		obs.setId("Observation/DEF");
+		Reference patientRef = new Reference(patientId);
+		obs.setSubject(patientRef);
+		BundleBuilder builder = new BundleBuilder(myFhirCtx);
+		builder.addTransactionUpdateEntry(obs);
+
+		Bundle transaction = mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
+
+		Patient returned = myPatientDao.read(patientRef.getReferenceElement());
+		assertNotNull(returned);
+		Assertions.assertTrue(returned.getActive());
+		Assertions.assertEquals(2, returned.getIdElement().getVersionIdPartAsLong());
+
+		Observation retObservation = myObservationDao.read(obs.getIdElement());
+		assertNotNull(retObservation);
+	}
+
+	/**
+	 * This test is the same as above, except it uses the serverid (instead of forcedid)
+	 */
+	@Test
+	public void testAutocreatePlaceholderWithExistingTargetWithServerAssignedIdTest() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+		myModelConfig.setAutoVersionReferenceAtPaths("Observation.subject");
+
+		// create
+		Patient patient = new Patient();
+		patient.setIdElement(new IdType("Patient"));
+		DaoMethodOutcome ret = myPatientDao.create(patient); // use create to use server id
+
+		// update - to update our version
+		patient.setActive(true);
+		myPatientDao.update(patient);
+
+		// observation (with version 2)
+		Observation obs = new Observation();
+		obs.setId("Observation/DEF");
+		Reference patientRef = new Reference("Patient/" + ret.getId().getIdPart());
+		obs.setSubject(patientRef);
+		BundleBuilder builder = new BundleBuilder(myFhirCtx);
+		builder.addTransactionUpdateEntry(obs);
+
+		Bundle transaction = mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
+
+		Patient returned = myPatientDao.read(patientRef.getReferenceElement());
+		assertNotNull(returned);
+		Assertions.assertEquals(2, returned.getIdElement().getVersionIdPartAsLong());
+
+		Observation retObservation = myObservationDao.read(obs.getIdElement());
+		assertNotNull(retObservation);
+	}
 
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ContainedTest.java

@@ -1,10 +1,10 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import static org.hamcrest.MatcherAssert.assertThat;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import static org.hamcrest.Matchers.containsInAnyOrder;
+import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import static org.junit.jupiter.api.Assertions.fail;
+import ca.uhn.fhir.rest.param.ReferenceParam;
-
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Address;
 import org.hl7.fhir.r4.model.Address.AddressUse;
@@ -26,15 +26,13 @@ import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
-import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
-import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.param.ReferenceParam;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-
-import java.util.stream.Collector;
 import java.util.stream.Collectors;
 
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.fail;
+
 public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ContainedTest.class);
 
@@ -80,7 +78,6 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
 		map = new SearchParameterMap();
 		map.add("subject", new ReferenceParam("name", "Smith"));
 		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
-		
 		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id)));
 	}
 	
@@ -116,8 +113,10 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
 		map = new SearchParameterMap();
 		map.add("subject", new ReferenceParam("name", "Smith"));
 		map.setSearchContainedMode(SearchContainedModeEnum.TRUE);
+		map.setLoadSynchronous(true);
 
 		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id)));
+
 	}
 	
 	

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java

@@ -9,11 +9,15 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Properties;
 import java.util.stream.Collectors;
 
 import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
+import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
 import ca.uhn.fhir.test.utilities.docker.RequiresDocker;
 import org.hamcrest.Matchers;
+import org.hibernate.search.backend.elasticsearch.index.IndexStatus;
+import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CodeSystem;
@@ -28,6 +32,8 @@ import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
@@ -341,6 +347,4 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 
 	}
 
-
-
 }

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

@@ -1,9 +1,11 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.util.BundleBuilder;
@@ -20,8 +22,11 @@ import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Task;
 import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.DisplayName;
 import org.junit.jupiter.api.Test;
 
+import java.io.InputStreamReader;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.HashSet;
@@ -30,9 +35,12 @@ import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
 
+import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.matchesPattern;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
@@ -90,7 +98,6 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		assertEquals("Patient/A/_history/1", eob2.getPatient().getReference());
 	}
 
-
 	@Test
 	public void testCreateAndUpdateVersionedReferencesInTransaction_VersionedReferenceToVersionedReferenceToUpsertWithNop() {
 		myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
@@ -283,7 +290,7 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		myObservationDao.update(observation);
 
 		// Make sure we're not introducing any extra DB operations
-		assertEquals(5, myCaptureQueriesListener.logSelectQueries().size());
+		assertEquals(6, myCaptureQueriesListener.logSelectQueries().size());
 
 		// Read back and verify that reference is now versioned
 		observation = myObservationDao.read(observationId);
@@ -295,7 +302,6 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
 		myModelConfig.setAutoVersionReferenceAtPaths("Observation.subject");
 
-
 		BundleBuilder builder = new BundleBuilder(myFhirCtx);
 
 		Patient patient = new Patient();
@@ -326,7 +332,6 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		observation = myObservationDao.read(observationId);
 		assertEquals(patientId.getValue(), observation.getSubject().getReference());
 		assertEquals(encounterId.toVersionless().getValue(), observation.getEncounter().getReference());
-
 	}
 
 	@Test
@@ -389,7 +394,6 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		assertEquals(patientId.getValue(), observation.getSubject().getReference());
 		assertEquals("2", observation.getSubject().getReferenceElement().getVersionIdPart());
 		assertEquals(encounterId.toVersionless().getValue(), observation.getEncounter().getReference());
-
 	}
 
 
@@ -409,7 +413,6 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 			// Update patient to make a second version
 			patient.setActive(false);
 			myPatientDao.update(patient);
-
 		}
 
 		BundleBuilder builder = new BundleBuilder(myFhirCtx);
@@ -458,7 +461,6 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 			// Update patient to make a second version
 			patient.setActive(false);
 			myPatientDao.update(patient);
-
 		}
 
 		BundleBuilder builder = new BundleBuilder(myFhirCtx);
@@ -491,10 +493,8 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 		// Read back and verify that reference is now versioned
 		observation = myObservationDao.read(observationId);
 		assertEquals(patientId.getValue(), observation.getSubject().getReference());
-
 	}
 
-
 	@Test
 	public void testSearchAndIncludeVersionedReference_Asynchronous() {
 		myFhirCtx.getParserOptions().setStripVersionsFromReferences(false);
@@ -780,4 +780,120 @@ public class FhirResourceDaoR4VersionedReferenceTest extends BaseJpaR4Test {
 			assertEquals(patientId.withVersion("2").getValue(), resources.get(1).getIdElement().getValue());
 		}
 	}
+
+	@Test
+	public void testNoNpeOnEoBBundle() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+		List<String> strings = Arrays.asList(
+			"ExplanationOfBenefit.patient",
+			"ExplanationOfBenefit.insurer",
+			"ExplanationOfBenefit.provider",
+			"ExplanationOfBenefit.careTeam.provider",
+			"ExplanationOfBenefit.insurance.coverage",
+			"ExplanationOfBenefit.payee.party"
+		);
+		myModelConfig.setAutoVersionReferenceAtPaths(new HashSet<>(strings));
+
+		Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class,
+			new InputStreamReader(
+				FhirResourceDaoR4VersionedReferenceTest.class.getResourceAsStream("/npe-causing-bundle.json")));
+
+		Bundle transaction = mySystemDao.transaction(new SystemRequestDetails(), bundle);
+
+		assertNotNull(transaction);
+	}
+
+	@Test
+	public void testAutoVersionPathsWithAutoCreatePlaceholders() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+
+		Observation obs = new Observation();
+		obs.setId("Observation/CDE");
+		obs.setSubject(new Reference("Patient/ABC"));
+		DaoMethodOutcome update = myObservationDao.create(obs);
+		Observation resource = (Observation)update.getResource();
+		String versionedPatientReference = resource.getSubject().getReference();
+		assertThat(versionedPatientReference, is(equalTo("Patient/ABC")));
+
+		Patient p = myPatientDao.read(new IdDt("Patient/ABC"));
+		Assertions.assertNotNull(p);
+
+		myModelConfig.setAutoVersionReferenceAtPaths("Observation.subject");
+
+		obs = new Observation();
+		obs.setId("Observation/DEF");
+		obs.setSubject(new Reference("Patient/RED"));
+		update = myObservationDao.create(obs);
+		resource = (Observation)update.getResource();
+		versionedPatientReference = resource.getSubject().getReference();
+
+		assertThat(versionedPatientReference, is(equalTo("Patient/RED/_history/1")));
+	}
+
+
+	@Test
+	@DisplayName("Bundle transaction with AutoVersionReferenceAtPath on and with existing Patient resource should create")
+	public void bundleTransaction_autoreferenceAtPathWithPreexistingPatientReference_shouldCreate() {
+		myModelConfig.setAutoVersionReferenceAtPaths("Observation.subject");
+
+		String patientId = "Patient/RED";
+		IIdType idType = new IdDt(patientId);
+
+		// create patient ahead of time
+		Patient patient = new Patient();
+		patient.setId(patientId);
+		DaoMethodOutcome outcome = myPatientDao.update(patient);
+		assertThat(outcome.getResource().getIdElement().getValue(), is(equalTo(patientId + "/_history/1")));
+
+		Patient returned = myPatientDao.read(idType);
+		Assertions.assertNotNull(returned);
+		assertThat(returned.getId(), is(equalTo(patientId + "/_history/1")));
+
+		// update to change version
+		patient.setActive(true);
+		myPatientDao.update(patient);
+
+		Observation obs = new Observation();
+		obs.setId("Observation/DEF");
+		Reference patientRef = new Reference(patientId);
+		obs.setSubject(patientRef);
+		BundleBuilder builder = new BundleBuilder(myFhirCtx);
+		builder.addTransactionUpdateEntry(obs);
+
+		Bundle submitted = (Bundle)builder.getBundle();
+
+		Bundle returnedTr = mySystemDao.transaction(new SystemRequestDetails(), submitted);
+
+		Assertions.assertNotNull(returnedTr);
+
+		// some verification
+		Observation obRet = myObservationDao.read(obs.getIdElement());
+		Assertions.assertNotNull(obRet);
+	}
+
+	@Test
+	@DisplayName("GH-2901 Test no NPE is thrown on autoversioned references")
+	public void testNoNpeMinimal() {
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
+		myModelConfig.setAutoVersionReferenceAtPaths("Observation.subject");
+
+		Observation obs = new Observation();
+		obs.setId("Observation/DEF");
+		Reference patientRef = new Reference("Patient/RED");
+		obs.setSubject(patientRef);
+		BundleBuilder builder = new BundleBuilder(myFhirCtx);
+		builder.addTransactionUpdateEntry(obs);
+
+		Bundle submitted = (Bundle)builder.getBundle();
+
+		Bundle returnedTr = mySystemDao.transaction(new SystemRequestDetails(), submitted);
+
+		Assertions.assertNotNull(returnedTr);
+
+		// some verification
+		Observation obRet = myObservationDao.read(obs.getIdElement());
+		Assertions.assertNotNull(obRet);
+		Patient returned = myPatientDao.read(patientRef.getReferenceElement());
+		Assertions.assertNotNull(returned);
+	}
 }

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

@@ -1,8 +1,8 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
 import ca.uhn.fhir.jpa.model.entity.ResourceEncodingEnum;
 import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
@@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.entity.ResourceTag;
 import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.provider.SystemProviderDstu2Test;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@@ -119,6 +120,8 @@ public class FhirSystemDaoR4Test extends BaseJpaR4SystemTest {
 		myModelConfig.setNormalizedQuantitySearchLevel(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED);
 		myDaoConfig.setBundleBatchPoolSize(new DaoConfig().getBundleBatchPoolSize());
 		myDaoConfig.setBundleBatchMaxPoolSize(new DaoConfig().getBundleBatchMaxPoolSize());
+		myDaoConfig.setAutoCreatePlaceholderReferenceTargets(new DaoConfig().isAutoCreatePlaceholderReferenceTargets());
+		myModelConfig.setAutoVersionReferenceAtPaths(new ModelConfig().getAutoVersionReferenceAtPaths());
 	}
 
 	@BeforeEach

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4BundleTest.java

@@ -250,6 +250,45 @@ public class ResourceProviderR4BundleTest extends BaseResourceProviderR4Test {
 
 	}
 
+	@Test
+	public void testTagCacheWorksWithBatchMode() {
+		Bundle input = new Bundle();
+		input.setType(BundleType.BATCH);
+
+		Patient p = new Patient();
+		p.setId("100");
+		p.setGender(AdministrativeGender.MALE);
+		p.addIdentifier().setSystem("urn:foo").setValue("A");
+		p.addName().setFamily("Smith");
+		p.getMeta().addTag().setSystem("mysystem").setCode("mycode");
+		input.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST);
+
+		Patient p2 = new Patient();
+		p2.setId("200");
+		p2.setGender(AdministrativeGender.MALE);
+		p2.addIdentifier().setSystem("urn:foo").setValue("A");
+		p2.addName().setFamily("Smith");
+		p2.getMeta().addTag().setSystem("mysystem").setCode("mycode");
+		input.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST);
+
+		Patient p3 = new Patient();
+		p3.setId("pat-300");
+		p3.setGender(AdministrativeGender.MALE);
+		p3.addIdentifier().setSystem("urn:foo").setValue("A");
+		p3.addName().setFamily("Smith");
+		p3.getMeta().addTag().setSystem("mysystem").setCode("mycode");
+		input.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.PUT).setUrl("Patient/pat-300");
+
+		Bundle output = myClient.transaction().withBundle(input).execute();
+		output.getEntry().stream()
+			.map(BundleEntryComponent::getResponse)
+			.map(Bundle.BundleEntryResponseComponent::getStatus)
+			.forEach(statusCode -> {
+				assertEquals(statusCode, "201 Created");
+			});
+	}
+
+	
 	private List<String> createPatients(int count) {
 		List<String> ids = new ArrayList<String>();
 		for (int i = 0; i < count; i++) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/elastic/ElasticsearchHibernatePropertiesBuilderTest.java

@@ -23,17 +23,11 @@ class ElasticsearchHibernatePropertiesBuilderTest {
 
 	ElasticsearchHibernatePropertiesBuilder myPropertiesBuilder = spy(ElasticsearchHibernatePropertiesBuilder.class);
 
-	@BeforeEach
-	public void prepMocks() {
-		//ensures we don't try to reach out to a real ES server on apply.
-		doNothing().when(myPropertiesBuilder).injectStartupTemplate(any(), any(), any(), any());
-	}
-
 	@Test
-	public void testRestUrlCannotContainProtocol() {
+	public void testHostsCannotContainProtocol() {
 		String host = "localhost:9200";
 		String protocolHost = "https://" + host;
-		String failureMessage = "Elasticsearch URL cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.";
+		String failureMessage = "Elasticsearch URLs cannot include a protocol, that is a separate property. Remove http:// or https:// from this URL.";
 
 		myPropertiesBuilder
 			.setProtocol("https")
@@ -42,19 +36,42 @@ class ElasticsearchHibernatePropertiesBuilderTest {
 
 		//SUT
 		try {
-			myPropertiesBuilder.setRestUrl(protocolHost);
+			myPropertiesBuilder.setHosts(protocolHost)
+				.apply(new Properties());
 			fail();
 		} catch (ConfigurationException e ) {
 			assertThat(e.getMessage(), is(equalTo(failureMessage)));
 		}
 
+		doNothing().when(myPropertiesBuilder).injectStartupTemplate(any(), any(), any(), any());
 		Properties properties = new Properties();
 		myPropertiesBuilder
-			.setRestUrl(host)
+			.setHosts(host)
 			.apply(properties);
 
 		assertThat(properties.getProperty(BackendSettings.backendKey(ElasticsearchBackendSettings.HOSTS)), is(equalTo(host)));
 
 	}
 
+	@Test
+	public void testHostsValueValidation() {
+		String host = "localhost_9200,localhost:9201,localhost:9202";
+		String failureMessage = "Elasticsearch URLs have to contain ':' as a host:port separator. Example: localhost:9200,localhost:9201,localhost:9202";
+
+		myPropertiesBuilder
+			.setProtocol("https")
+			.setHosts(host)
+			.setUsername("whatever")
+			.setPassword("whatever");
+
+		//SUT
+		try {
+			myPropertiesBuilder
+				.apply(new Properties());
+			fail();
+		} catch (ConfigurationException e ) {
+			assertThat(e.getMessage(), is(equalTo(failureMessage)));
+		}
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsIT.java

@@ -68,7 +68,7 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
 	public void before() throws IOException {
 		PartitionSettings partitionSettings = new PartitionSettings();
 		partitionSettings.setPartitioningEnabled(false);
-		elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost(), elasticsearchContainer.getMappedPort(9200), "", "");
+		elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), null, null);
 
 		if (!indexLoaded) {
 			createMultiplePatientsAndObservations();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcSingleObservationIT.java

@@ -97,7 +97,7 @@ public class LastNElasticsearchSvcSingleObservationIT {
 	public void before() {
 		PartitionSettings partitionSettings = new PartitionSettings();
 		partitionSettings.setPartitioningEnabled(false);
-		elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost(), elasticsearchContainer.getMappedPort(9200), "", "");
+		elasticsearchSvc = new ElasticsearchSvcImpl(partitionSettings, elasticsearchContainer.getHost() + ":" + elasticsearchContainer.getMappedPort(9200), "", "");
 	}
 
 	@AfterEach

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/stresstest/GiantTransactionPerfTest.java

@@ -14,6 +14,7 @@ import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCache;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheFactory;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheRefresherImpl;
 import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryImpl;
+import ca.uhn.fhir.jpa.cache.ResourcePersistentIdMap;
 import ca.uhn.fhir.jpa.cache.ResourceVersionMap;
 import ca.uhn.fhir.jpa.dao.JpaResourceDao;
 import ca.uhn.fhir.jpa.dao.TransactionProcessor;
@@ -45,6 +46,7 @@ import com.google.common.collect.Lists;
 import org.hamcrest.Matchers;
 import org.hibernate.internal.SessionImpl;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.ExplanationOfBenefit;
 import org.junit.jupiter.api.AfterEach;
@@ -323,10 +325,15 @@ public class GiantTransactionPerfTest {
 
 		@Nonnull
 		@Override
-		public ResourceVersionMap getVersionMap(String theResourceName, SearchParameterMap theSearchParamMap) {
+		public ResourceVersionMap getVersionMap(RequestPartitionId theRequestPartitionId, String theResourceName, SearchParameterMap theSearchParamMap) {
 			myGetVersionMap++;
 			return ResourceVersionMap.fromResources(Lists.newArrayList());
 		}
+
+		@Override
+		public ResourcePersistentIdMap getLatestVersionIdsForResourceIds(RequestPartitionId thePartition, List<IIdType> theIds) {
+			return null;
+		}
 	}
 
 	private class MockResourceHistoryTableDao implements IResourceHistoryTableDao {

hapi-fhir-jpaserver-base/src/test/resources/npe-causing-bundle.json

@@ -0,0 +1,402 @@
+{
+	"resourceType": "Bundle",
+	"type": "transaction",
+	"entry": [ {
+		"resource": {
+			"resourceType": "ExplanationOfBenefit",
+			"id": "26d4cebd-95c6-39ea-855c-dc819bc68d08",
+			"meta": {
+				"lastUpdated": "2016-01-01T00:56:00.000-05:00",
+				"profile": [ "http://hl7.org/fhir/us/carin-bb/StructureDefinition/C4BB-ExplanationOfBenefit-Inpatient-Institutional" ]
+			},
+			"identifier": [ {
+				"type": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBIdentifierType",
+						"code": "uc"
+					} ]
+				},
+				"system": "fhir/CodeSystem/sid/eob-inpatient-claim-id",
+				"value": "20550047"
+			} ],
+			"status": "active",
+			"type": {
+				"coding": [ {
+					"system": "http://terminology.hl7.org/CodeSystem/claim-type",
+					"code": "institutional"
+				} ]
+			},
+			"use": "claim",
+			"patient": {
+				"reference": "Patient/ABC"
+			},
+			"billablePeriod": {
+				"start": "2015-12-14T00:00:00-05:00"
+			},
+			"created": "2021-08-16T13:54:10-04:00",
+			"insurer": {
+				"reference": "Organization/A"
+			},
+			"provider": {
+				"reference": "Organization/b9d22776-1ee9-3843-bc48-b4bf67861483"
+			},
+			"outcome": "complete",
+			"careTeam": [ {
+				"sequence": 1,
+				"provider": {
+					"reference": "Practitioner/H"
+				},
+				"role": {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole",
+						"code": "primary"
+					} ]
+				}
+			}, {
+				"sequence": 2,
+				"provider": {
+					"reference": "Practitioner/I"
+				},
+				"role": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBClaimCareTeamRole",
+						"code": "attending"
+					} ]
+				}
+			}, {
+				"sequence": 3,
+				"provider": {
+					"reference": "Practitioner/J"
+				},
+				"role": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBClaimCareTeamRole",
+						"code": "performing"
+					} ]
+				}
+			} ],
+			"supportingInfo": [ {
+				"sequence": 1,
+				"category": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBSupportingInfoType",
+						"code": "admissionperiod"
+					} ]
+				},
+				"timingPeriod": {
+					"start": "2015-12-14T00:00:00-05:00",
+					"end": "2016-01-11T14:11:00-05:00"
+				}
+			}, {
+				"sequence": 2,
+				"category": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBSupportingInfoType",
+						"code": "clmrecvddate"
+					} ]
+				},
+				"timingDate": "2018-12-23"
+			}, {
+				"sequence": 3,
+				"category": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBSupportingInfoType",
+						"code": "admtype"
+					} ]
+				},
+				"code": {
+					"coding": [ {
+						"system": "https://www.nubc.org/CodeSystem/PriorityTypeOfAdmitOrVisit",
+						"code": "4"
+					} ]
+				}
+			} ],
+			"diagnosis": [ {
+				"sequence": 1,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "Z38.00"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			} ],
+			"insurance": [ {
+				"focal": true,
+				"coverage": {
+					"reference": "Coverage/G"
+				}
+			} ],
+			"total": [ {
+				"category": {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/adjudication",
+						"code": "benefit"
+					} ]
+				},
+				"amount": {
+					"value": 1039.28
+				}
+			}, {
+				"category": {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/adjudication",
+						"code": "submitted"
+					} ]
+				},
+				"amount": {
+					"value": 2011
+				}
+			} ]
+		},
+		"request": {
+			"method": "PUT",
+			"url": "ExplanationOfBenefit/26d4cebd-95c6-39ea-855c-dc819bc68d08"
+		}
+	}, {
+		"resource": {
+			"resourceType": "ExplanationOfBenefit",
+			"id": "a25f1c3a-09b9-3f17-8f1b-0fbbf6391fce",
+			"meta": {
+				"lastUpdated": "2016-01-01T00:58:00.000-05:00",
+				"profile": [ "http://hl7.org/fhir/us/carin-bb/StructureDefinition/C4BB-ExplanationOfBenefit-Inpatient-Institutional" ]
+			},
+			"identifier": [ {
+				"type": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBIdentifierType",
+						"code": "uc"
+					} ]
+				},
+				"system": "fhir/CodeSystem/sid/eob-inpatient-claim-id",
+				"value": "20586901"
+			} ],
+			"status": "active",
+			"type": {
+				"coding": [ {
+					"system": "http://terminology.hl7.org/CodeSystem/claim-type",
+					"code": "institutional"
+				} ]
+			},
+			"use": "claim",
+			"patient": {
+				"reference": "Patient/ABC"
+			},
+			"billablePeriod": {
+				"start": "2015-12-18T00:00:00-05:00"
+			},
+			"created": "2021-08-16T13:54:10-04:00",
+			"insurer": {
+				"reference": "Organization/A"
+			},
+			"provider": {
+				"reference": "Organization/d10823cf-ee15-3a0e-a12e-1509cd18cda4"
+			},
+			"outcome": "complete",
+			"careTeam": [ {
+				"sequence": 1,
+				"provider": {
+					"reference": "Practitioner/D"
+				},
+				"role": {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole",
+						"code": "primary"
+					} ]
+				}
+			}, {
+				"sequence": 2,
+				"provider": {
+					"reference": "Practitioner/E"
+				},
+				"role": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBClaimCareTeamRole",
+						"code": "attending"
+					} ]
+				}
+			}, {
+				"sequence": 3,
+				"provider": {
+					"reference": "Practitioner/F"
+				},
+				"role": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBClaimCareTeamRole",
+						"code": "performing"
+					} ]
+				}
+			} ],
+			"supportingInfo": [ {
+				"sequence": 1,
+				"category": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBSupportingInfoType",
+						"code": "admissionperiod"
+					} ]
+				},
+				"timingPeriod": {
+					"start": "2015-12-18T00:00:00-05:00",
+					"end": "2016-01-11T14:12:00-05:00"
+				}
+			}, {
+				"sequence": 2,
+				"category": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBSupportingInfoType",
+						"code": "clmrecvddate"
+					} ]
+				},
+				"timingDate": "2018-12-29"
+			}, {
+				"sequence": 3,
+				"category": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/us/carin-bb/CodeSystem/C4BBSupportingInfoType",
+						"code": "admtype"
+					} ]
+				},
+				"code": {
+					"coding": [ {
+						"system": "https://www.nubc.org/CodeSystem/PriorityTypeOfAdmitOrVisit",
+						"code": "4"
+					} ]
+				}
+			} ],
+			"diagnosis": [ {
+				"sequence": 1,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "Z38.00"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			}, {
+				"sequence": 2,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "P96.89"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			}, {
+				"sequence": 3,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "R25.8"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			}, {
+				"sequence": 4,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "P08.21"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			}, {
+				"sequence": 5,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "P92.5"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			}, {
+				"sequence": 6,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "P92.6"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			}, {
+				"sequence": 7,
+				"diagnosisCodeableConcept": {
+					"coding": [ {
+						"system": "http://hl7.org/fhir/sid/icd-10-cm",
+						"code": "Z23"
+					} ]
+				},
+				"type": [ {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype",
+						"code": "principal"
+					} ]
+				} ]
+			} ],
+			"insurance": [ {
+				"focal": true,
+				"coverage": {
+					"reference": "Coverage/G"
+				}
+			} ],
+			"total": [ {
+				"category": {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/adjudication",
+						"code": "benefit"
+					} ]
+				},
+				"amount": {
+					"value": 1421.31
+				}
+			}, {
+				"category": {
+					"coding": [ {
+						"system": "http://terminology.hl7.org/CodeSystem/adjudication",
+						"code": "submitted"
+					} ]
+				},
+				"amount": {
+					"value": 2336
+				}
+			} ]
+		},
+		"request": {
+			"method": "PUT",
+			"url": "ExplanationOfBenefit/a25f1c3a-09b9-3f17-8f1b-0fbbf6391fce"
+		}
+	} ] }

hapi-fhir-jpaserver-batch/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-cql/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-mdm/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-migrate/pom.xml

@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-searchparam/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/cache/IResourceVersionSvc.java

@@ -20,9 +20,12 @@ package ca.uhn.fhir.jpa.cache;
  * #L%
  */
 
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import org.hl7.fhir.instance.model.api.IIdType;
 
 import javax.annotation.Nonnull;
+import java.util.List;
 
 /**
  * This interface is used by the {@link IResourceChangeListenerCacheRefresher} to read resources matching the provided
@@ -30,5 +33,12 @@ import javax.annotation.Nonnull;
  */
 public interface IResourceVersionSvc {
 	@Nonnull
-	ResourceVersionMap getVersionMap(String theResourceName, SearchParameterMap theSearchParamMap);
+	ResourceVersionMap getVersionMap(RequestPartitionId theRequestPartitionId, String theResourceName, SearchParameterMap theSearchParamMap);
+
+	@Nonnull
+	default ResourceVersionMap getVersionMap(String theResourceName, SearchParameterMap theSearchParamMap) {
+		return getVersionMap(RequestPartitionId.allPartitions(), theResourceName, theSearchParamMap);
+	}
+
+	ResourcePersistentIdMap getLatestVersionIdsForResourceIds(RequestPartitionId thePartition, List<IIdType> theIds);
 }

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/cache/ResourceChangeListenerCacheRefresherImpl.java

@@ -173,8 +173,8 @@ public class ResourceChangeListenerCacheRefresherImpl implements IResourceChange
 		List<IIdType> updatedIds = new ArrayList<>();
 
 		for (IIdType id : theNewResourceVersionMap.keySet()) {
-			String previousValue = theOldResourceVersionCache.put(id, theNewResourceVersionMap.get(id));
+			Long previousValue = theOldResourceVersionCache.put(id, theNewResourceVersionMap.get(id));
-			IIdType newId = id.withVersion(theNewResourceVersionMap.get(id));
+			IIdType newId = id.withVersion(theNewResourceVersionMap.get(id).toString());
 			if (previousValue == null) {
 				createdIds.add(newId);
 			} else if (!theNewResourceVersionMap.get(id).equals(previousValue)) {

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/cache/ResourcePersistentIdMap.java

@@ -0,0 +1,67 @@
+package ca.uhn.fhir.jpa.cache;
+
+/*-
+ * #%L
+ * HAPI FHIR Search Parameters
+ * %%
+ * Copyright (C) 2014 - 2021 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.storage.ResourcePersistentId;
+import org.hl7.fhir.instance.model.api.IIdType;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ResourcePersistentIdMap {
+	private final Map<IIdType, ResourcePersistentId> myMap = new HashMap<>();
+
+	public static ResourcePersistentIdMap fromResourcePersistentIds(List<ResourcePersistentId> theResourcePersistentIds) {
+		ResourcePersistentIdMap retval = new ResourcePersistentIdMap();
+		theResourcePersistentIds.forEach(retval::add);
+		return retval;
+	}
+
+	private void add(ResourcePersistentId theResourcePersistentId) {
+		IIdType id = theResourcePersistentId.getAssociatedResourceId();
+		myMap.put(id.toUnqualifiedVersionless(), theResourcePersistentId);
+	}
+
+	public boolean containsKey(IIdType theId) {
+		return myMap.containsKey(theId.toUnqualifiedVersionless());
+	}
+
+	public ResourcePersistentId getResourcePersistentId(IIdType theId) {
+		return myMap.get(theId.toUnqualifiedVersionless());
+	}
+
+	public boolean isEmpty() {
+		return myMap.isEmpty();
+	}
+
+	public int size() {
+		return myMap.size();
+	}
+
+	public void put(IIdType theId, ResourcePersistentId thePid) {
+		myMap.put(theId, thePid);
+	}
+
+	public void putAll(ResourcePersistentIdMap theIdAndPID) {
+		myMap.putAll(theIdAndPID.myMap);
+	}
+}

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/cache/ResourceVersionCache.java

@@ -32,7 +32,7 @@ import java.util.Set;
  * detect resources that were modified on remote servers in our cluster.
  */
 public class ResourceVersionCache {
-	private final Map<IIdType, String> myVersionMap = new HashMap<>();
+	private final Map<IIdType, Long> myVersionMap = new HashMap<>();
 
 	public void clear() {
 		myVersionMap.clear();
@@ -43,15 +43,15 @@ public class ResourceVersionCache {
 	 * @param theVersion
 	 * @return previous value
 	 */
-	public String put(IIdType theResourceId, String theVersion) {
+	public Long put(IIdType theResourceId, Long theVersion) {
 		return myVersionMap.put(new IdDt(theResourceId).toVersionless(), theVersion);
 	}
 
-	public String getVersionForResourceId(IIdType theResourceId) {
+	public Long getVersionForResourceId(IIdType theResourceId) {
 		return myVersionMap.get(new IdDt(theResourceId));
 	}
 
-	public String removeResourceId(IIdType theResourceId) {
+	public Long removeResourceId(IIdType theResourceId) {
 		return myVersionMap.remove(new IdDt(theResourceId));
 	}
 

hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/cache/ResourceVersionMap.java

@@ -24,6 +24,8 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.model.primitive.IdDt;
 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 java.util.Collections;
 import java.util.HashMap;
@@ -36,8 +38,10 @@ import java.util.Set;
  * This immutable map holds a copy of current resource versions read from the repository.
  */
 public class ResourceVersionMap {
+	private static final Logger ourLog = LoggerFactory.getLogger(ResourceVersionMap.class);
 	private final Set<IIdType> mySourceIds = new HashSet<>();
-	private final Map<IIdType, String> myMap = new HashMap<>();
+	// Key versionless id, value version
+	private final Map<IIdType, Long> myMap = new HashMap<>();
 	private ResourceVersionMap() {}
 
 	public static ResourceVersionMap fromResourceTableEntities(List<ResourceTable> theEntities) {
@@ -57,13 +61,17 @@ public class ResourceVersionMap {
 	}
 
 	private void add(IIdType theId) {
+		if (theId.getVersionIdPart() == null) {
+			ourLog.warn("Not storing {} in ResourceVersionMap because it does not have a version.", theId);
+			return;
+		}
 		IdDt id = new IdDt(theId);
 		mySourceIds.add(id);
-		myMap.put(id.toUnqualifiedVersionless(), id.getVersionIdPart());
+		myMap.put(id.toUnqualifiedVersionless(), id.getVersionIdPartAsLong());
 	}
 
-	public String getVersion(IIdType theResourceId) {
+	public Long getVersion(IIdType theResourceId) {
-		return myMap.get(new IdDt(theResourceId.toUnqualifiedVersionless()));
+		return get(theResourceId);
 	}
 
 	public int size() {
@@ -78,11 +86,15 @@ public class ResourceVersionMap {
 		return Collections.unmodifiableSet(mySourceIds);
 	}
 
-	public String get(IIdType theId) {
+	public Long get(IIdType theId) {
 		return myMap.get(new IdDt(theId.toUnqualifiedVersionless()));
 	}
 
 	public boolean containsKey(IIdType theId) {
 		return myMap.containsKey(new IdDt(theId.toUnqualifiedVersionless()));
 	}
+
+	public boolean isEmpty() {
+		return myMap.isEmpty();
+	}
 }

hapi-fhir-jpaserver-subscription/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-utilities/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaDstu3Config.java

@@ -41,6 +41,7 @@ import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Lazy;
@@ -94,8 +95,8 @@ public class TestJpaDstu3Config extends BaseJavaConfigDstu3 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaR4Config.java

@@ -41,6 +41,7 @@ import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Lazy;
@@ -94,8 +95,8 @@ public class TestJpaR4Config extends BaseJavaConfigR4 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-fhir</artifactId>
-		<version>5.6.0-PRE3-SNAPSHOT</version>
+		<version>5.6.0-PRE4-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -23,6 +23,7 @@ import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
@@ -134,8 +135,8 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 
 	@Override
 	@Bean
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
-		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu2");
 		retVal.setDataSource(dataSource());
 		retVal.setJpaProperties(jpaProperties());