Merge commit '528d2bc087ae2f5bf49b2fb38d17dba134feda63'

# Conflicts:
#	src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java
#	src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
#	src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java
#	src/main/resources/application.yaml

Preparing for 5.7.0

README.md

@@ -354,10 +354,14 @@ elasticsearch.schema_management_strategy=CREATE
 
 Set `hapi.fhir.lastn_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable the $lastn operation on this server.  Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch.
 
+## Enabling Resource to be stored in Lucene Index
+
+Set `hapi.fhir.store_resource_in_lucene_index_enabled` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable storing of resource json along with Lucene/Elasticsearch index mappings.
+
 ## Changing cached search results time
 
-It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml] is 6000 miliseconds by default.
+It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) is 6000 miliseconds by default.
-Set `reuse_cached_search_results_millis: -1` in the [application.yaml] file to ignore the cache time every search. 
+Set `reuse_cached_search_results_millis: -1` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to ignore the cache time every search. 
 
 ## Build the distroless variant of the image (for lower footprint and improved security)
 

pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-		  <version>5.6.0</version>
+		  <version>5.7.0-PRE9-SNAPSHOT</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -68,13 +68,12 @@
 
         <!-- Needed for Email subscriptions -->
         <dependency>
-            <groupId>com.sun.mail</groupId>
+            <groupId>org.simplejavamail</groupId>
-            <artifactId>javax.mail</artifactId>
+            <artifactId>simple-java-mail</artifactId>
-            <version>1.6.2</version>
             <exclusions>
                 <exclusion>
-                    <groupId>javax.activation</groupId>
+                    <groupId>jakarta.annotation</groupId>
-                    <artifactId>activation</artifactId>
+                    <artifactId>jakarta.annotation-api</artifactId>
                 </exclusion>
             </exclusions>
         </dependency>
@@ -85,6 +84,12 @@
             <artifactId>hapi-fhir-base</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <!-- This dependency includes the EmailSenderImpl we will be using instead of standard javamail.-->
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-jpaserver-subscription</artifactId>
+            <version>${project.version}</version>
+        </dependency>
 
         <!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
         <dependency>

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -11,10 +11,7 @@ import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.context.annotation.Configuration;
 
-import java.util.ArrayList;
+import java.util.*;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
 
 @ConfigurationProperties(prefix = "hapi.fhir")
 @Configuration
@@ -24,6 +21,7 @@ public class AppProperties {
   private Boolean cql_enabled = false;
   private Boolean openapi_enabled = false;
   private Boolean mdm_enabled = false;
+  private boolean advanced_lucene_indexing = false;
   private Boolean allow_cascading_deletes = false;
   private Boolean allow_contains_searches = true;
   private Boolean allow_external_references = false;
@@ -68,6 +66,7 @@ public class AppProperties {
   private Map<String, ImplementationGuide> implementationGuides = null;
 
   private Boolean lastn_enabled = false;
+  private boolean store_resource_in_lucene_index_enabled = false;
   private NormalizedQuantitySearchLevel normalized_quantity_search_level = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED;
 
   private Integer search_coord_core_pool_size = 20;
@@ -76,6 +75,10 @@ public class AppProperties {
   private Boolean use_apache_address_strategy = false;
   private Boolean use_apache_address_strategy_https = false;
 
+  private Integer bundle_batch_pool_size = 20;
+  private Integer bundle_batch_pool_max_size = 100;
+  private List<String> local_base_urls = new ArrayList<>();
+
 	public Boolean getOpenapi_enabled() {
 		return openapi_enabled;
 	}
@@ -196,7 +199,11 @@ public class AppProperties {
     this.supported_resource_types = supported_resource_types;
   }
 
-  public Logger getLogger() {
+	public List<String> getSupported_resource_types(List<String> supported_resource_types) {
+		return this.supported_resource_types;
+	}
+
+	public Logger getLogger() {
     return logger;
   }
 
@@ -213,7 +220,15 @@ public class AppProperties {
     this.client_id_strategy = client_id_strategy;
   }
 
-  public Boolean getAllow_cascading_deletes() {
+	public boolean getAdvanced_lucene_indexing() {
+		return this.advanced_lucene_indexing;
+	}
+
+	public void setAdvanced_lucene_indexing(boolean theAdvanced_lucene_indexing) {
+		advanced_lucene_indexing = theAdvanced_lucene_indexing;
+	}
+
+	public Boolean getAllow_cascading_deletes() {
     return allow_cascading_deletes;
   }
 
@@ -455,7 +470,15 @@ public class AppProperties {
     this.lastn_enabled = lastn_enabled;
   }
 
-  public NormalizedQuantitySearchLevel getNormalized_quantity_search_level() {
+	public boolean getStore_resource_in_lucene_index_enabled() {
+		return store_resource_in_lucene_index_enabled;
+	}
+
+	public void setStore_resource_in_lucene_index_enabled(Boolean store_resource_in_lucene_index_enabled) {
+		this.store_resource_in_lucene_index_enabled = store_resource_in_lucene_index_enabled;
+	}
+
+	public NormalizedQuantitySearchLevel getNormalized_quantity_search_level() {
 	return this.normalized_quantity_search_level;
   }
 
@@ -489,6 +512,26 @@ public class AppProperties {
 		this.install_transitive_ig_dependencies = install_transitive_ig_dependencies;
 	}
 
+	public Integer getBundle_batch_pool_size() {
+		return this.bundle_batch_pool_size;
+	}
+
+	public void setBundle_batch_pool_size(Integer bundle_batch_pool_size) {
+		this.bundle_batch_pool_size = bundle_batch_pool_size;
+	}
+
+	public Integer getBundle_batch_pool_max_size() {
+		return bundle_batch_pool_max_size;
+	}
+
+	public void setBundle_batch_pool_max_size(Integer bundle_batch_pool_max_size) {
+		this.bundle_batch_pool_max_size = bundle_batch_pool_max_size;
+	}
+
+	public List<String> getLocal_base_urls() {
+		return local_base_urls;
+	}
+
 	public static class Cors {
     private Boolean allow_Credentials = true;
     private List<String> allowed_origin = ImmutableList.of("*");

src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

@@ -11,11 +11,11 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
 import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
+import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
 import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
-import ca.uhn.fhir.jpa.provider.GraphQLProvider;
 import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
 import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
 import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
@@ -384,6 +384,9 @@ public class BaseJpaRestfulServer extends RestfulServer {
       daoConfig.setResourceServerIdStrategy(DaoConfig.IdStrategyEnum.UUID);
       daoConfig.setResourceClientIdStrategy(appProperties.getClient_id_strategy());
     }
+    //Parallel Batch GET execution settings
+  	 daoConfig.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_size());
+  	 daoConfig.setBundleBatchPoolSize(appProperties.getBundle_batch_pool_max_size());
 
     if (appProperties.getImplementationGuides() != null) {
       Map<String, AppProperties.ImplementationGuide> guides = appProperties.getImplementationGuides();
@@ -410,8 +413,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
       daoConfig.setLastNEnabled(true);
     }
 
+	 daoConfig.setStoreResourceInLuceneIndex(appProperties.getStore_resource_in_lucene_index_enabled());
     daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
-
+	 daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
-		daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
   }
 }

src/main/java/ca/uhn/fhir/jpa/starter/ElasticsearchConfig.java

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.core.env.ConfigurableEnvironment;
+
+/** Shared configuration for Elasticsearch */
+@Configuration
+public class ElasticsearchConfig {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElasticsearchConfig.class);
+
+	@Autowired
+	private ConfigurableEnvironment configurableEnvironment;
+
+	@Bean()
+	public ElasticsearchSvcImpl elasticsearchSvc() {
+		if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
+			String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
+			if (elasticsearchUrl.startsWith("http")) {
+				elasticsearchUrl =elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3);
+			}
+			String elasticsearchProtocol = EnvironmentHelper.getElasticsearchServerProtocol(configurableEnvironment);
+			String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
+			String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
+			ourLog.info("Configuring elasticsearch {} {}", elasticsearchProtocol, elasticsearchUrl);
+			return new ElasticsearchSvcImpl(elasticsearchProtocol, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
+		} else {
+			return null;
+		}
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java

@@ -11,7 +11,10 @@ import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHan
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
 import ca.uhn.fhir.rest.server.mail.MailConfig;
+import ca.uhn.fhir.rest.server.mail.MailSvc;
 import com.google.common.base.Strings;
+import java.util.HashSet;
+import java.util.Optional;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.springframework.boot.env.YamlPropertySourceLoader;
 import org.springframework.context.annotation.Bean;
@@ -21,8 +24,6 @@ import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import java.util.Optional;
-
 /**
  * This is the primary configuration file for the example server
  */
@@ -117,6 +118,8 @@ public class FhirServerConfigCommon {
     }
 
     retVal.setFilterParameterEnabled(appProperties.getFilter_search_enabled());
+	 retVal.setAdvancedLuceneIndexing(appProperties.getAdvanced_lucene_indexing());
+	 retVal.setTreatBaseUrlsAsLocal(new HashSet<>(appProperties.getLocal_base_urls()));
 
     return retVal;
   }
@@ -152,8 +155,8 @@ public class FhirServerConfigCommon {
   }
 
   @Bean
-  public ModelConfig modelConfig(AppProperties appProperties) {
+  public ModelConfig modelConfig(AppProperties appProperties, DaoConfig daoConfig) {
-    ModelConfig modelConfig = new ModelConfig();
+    ModelConfig modelConfig = daoConfig.getModelConfig();
     modelConfig.setAllowContainsSearches(appProperties.getAllow_contains_searches());
     modelConfig.setAllowExternalReferences(appProperties.getAllow_external_references());
     modelConfig.setDefaultSearchParamsCanBeOverridden(appProperties.getAllow_override_default_search_params());
@@ -217,10 +220,9 @@ public class FhirServerConfigCommon {
       mailConfig.setSmtpPassword(email.getPassword());
       mailConfig.setSmtpUseStartTLS(email.getStartTlsEnable());
 
-		 IEmailSender emailSender = new EmailSenderImpl(mailConfig);
+		IEmailSender emailSender = new EmailSenderImpl(new MailSvc(mailConfig));
 
-      if(subscriptionDeliveryHandlerFactory.isPresent())
+		subscriptionDeliveryHandlerFactory.ifPresent(theSubscriptionDeliveryHandlerFactory -> theSubscriptionDeliveryHandlerFactory.setEmailSender(emailSender));
-       subscriptionDeliveryHandlerFactory.get().setEmailSender(emailSender);
 
       return emailSender;
     }

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java

@@ -2,9 +2,7 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
-import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
-import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
 import ca.uhn.fhir.jpa.starter.cql.StarterCqlDstu3Config;
 import javax.annotation.PostConstruct;
@@ -23,7 +21,7 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
 @Configuration
 @Conditional(OnDSTU3Condition.class)
-@Import(StarterCqlDstu3Config.class)
+@Import({StarterCqlDstu3Config.class, ElasticsearchConfig.class})
 public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
   @Autowired
@@ -77,6 +75,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
     retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment,
 		 myConfigurableListableBeanFactory));
+
     return retVal;
   }
 
@@ -87,23 +86,4 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
     retVal.setEntityManagerFactory(entityManagerFactory);
     return retVal;
   }
-
-  @Bean()
-  public ElasticsearchSvcImpl elasticsearchSvc(PartitionSettings thePartitionSetings) {
-	  if (Boolean.TRUE.equals(EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment))) {
-		  String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
-		  String elasticsearchHost = elasticsearchUrl;
-		  String elasticsearchProtocol = EnvironmentHelper.getElasticsearchServerProtocol(configurableEnvironment);
-		  if (elasticsearchUrl.startsWith("http")) {
-			  elasticsearchProtocol = elasticsearchUrl.split("://")[0];
-			  elasticsearchHost = elasticsearchUrl.split("://")[1];
-		  }
-		  String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
-		  String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
-		  return new ElasticsearchSvcImpl(thePartitionSetings, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
-	  } else {
-		  return null;
-	  }
-  }
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java

@@ -2,25 +2,26 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
-import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
-import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config;
+import javax.annotation.PostConstruct;
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
-import org.springframework.context.annotation.*;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.Primary;
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
-import javax.annotation.PostConstruct;
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-
 @Configuration
 @Conditional(OnR4Condition.class)
-@Import(StarterCqlR4Config.class)
+@Import({StarterCqlR4Config.class, ElasticsearchConfig.class})
 public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
   @Autowired
@@ -84,22 +85,4 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
     return retVal;
   }
 
-  @Bean()
-  public ElasticsearchSvcImpl elasticsearchSvc(PartitionSettings thePartitionSetings) {
-	  if (Boolean.TRUE.equals(EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment))) {
-		  String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
-		  String elasticsearchHost = elasticsearchUrl;
-		  String elasticsearchProtocol = EnvironmentHelper.getElasticsearchServerProtocol(configurableEnvironment);
-		  if (elasticsearchUrl.startsWith("http")) {
-			  elasticsearchProtocol = elasticsearchUrl.split("://")[0];
-			  elasticsearchHost = elasticsearchUrl.split("://")[1];
-		  }
-		  String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
-		  String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
-		  return new ElasticsearchSvcImpl(thePartitionSetings, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
-	  } else {
-		  return null;
-	  }
-  }
-
 }

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java

@@ -2,26 +2,25 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
-import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
-import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
 import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
+import javax.annotation.PostConstruct;
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
 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.Conditional;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
 import org.springframework.context.annotation.Primary;
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
-import javax.annotation.PostConstruct;
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-
 @Configuration
 @Conditional(OnR5Condition.class)
+@Import({ElasticsearchConfig.class})
 public class FhirServerConfigR5 extends BaseJavaConfigR5 {
 
   @Autowired
@@ -85,23 +84,4 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
     return retVal;
   }
 
-  @Bean()
-  public ElasticsearchSvcImpl elasticsearchSvc(PartitionSettings thePartitionSetings) {
-    if (Boolean.TRUE.equals(EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment))) {
-      String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
-      String elasticsearchHost;
-		String elasticsearchProtocol = EnvironmentHelper.getElasticsearchServerProtocol(configurableEnvironment);
-      if (elasticsearchUrl.startsWith("http")) {
-        elasticsearchProtocol = elasticsearchUrl.split("://")[0];
-		  elasticsearchHost = elasticsearchUrl.split("://")[1];
-		}
-      String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
-      String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
-		 return new ElasticsearchSvcImpl(thePartitionSetings, elasticsearchUrl, elasticsearchUsername, elasticsearchPassword);
-    } else {
-      return null;
-    }
-  }
-
-
 }

src/main/resources/application.yaml

@@ -1,4 +1,8 @@
 spring:
+  flyway:
+    enabled: false
+    check-location: false
+    baselineOnMigrate: true
   datasource:
     url: 'jdbc:h2:file:./target/database/h2'
     #url: jdbc:h2:mem:test_mem
@@ -10,9 +14,6 @@ spring:
     # database connection pool size
     hikari:
       maximum-pool-size: 10
-  flyway:
-    check-location: false
-    baselineOnMigrate: true
   jpa:
     properties:
       hibernate.format_sql: false
@@ -77,7 +78,9 @@ hapi:
     #    enable_repository_validating_interceptor: false
     #    enable_index_missing_fields: false
     #    enable_index_contained_resource: false
-    #    enforce_referential_integrity_on_delete: false
+    #    advanced_lucene_indexing: false
+    advanced_lucene_indexing: true
+#    enforce_referential_integrity_on_delete: false
     #    enforce_referential_integrity_on_write: false
     #    etag_support_enabled: true
     #    expunge_enabled: true
@@ -88,6 +91,8 @@ hapi:
     #    graphql_enabled: true
     #    narrative_enabled: true
     #    mdm_enabled: true
+#    local_base_urls:
+#      - https://hapi.fhir.org/baseR4
     #    partitioning:
     #      allow_references_across_partitions: false
     #      partitioning_include_in_search_hashes: false
@@ -102,7 +107,11 @@ hapi:
     search-coord-max-pool-size: 100
     search-coord-queue-capacity: 200
 
-    #    logger:
+    # Threadpool size for BATCH'ed GETs in a bundle.
+#    bundle_batch_pool_size: 10
+#    bundle_batch_pool_max_size: 50
+
+#    logger:
     #      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
     #      format: >-
     #        Path[${servletPath}] Source[${requestHeader.x-forwarded-for}]
@@ -145,6 +154,7 @@ hapi:
 #        startTlsRequired:
 #        quitWait:
 #    lastn_enabled: true
+#    store_resource_in_lucene_index_enabled: true
 ###  This is configuration for normalized quantity serach level default is 0
 ###   0: NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED - default
 ###   1: NORMALIZED_QUANTITY_STORAGE_SUPPORTED

src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java

@@ -42,6 +42,7 @@ import org.testcontainers.elasticsearch.ElasticsearchContainer;
     "spring.datasource.url=jdbc:h2:mem:dbr4",
     "hapi.fhir.fhir_version=r4",
     "hapi.fhir.lastn_enabled=true",
+	 "hapi.fhir.store_resource_in_lucene_index_enabled=true",
     "elasticsearch.enabled=true",
     // Because the port is set randomly, we will set the rest_url using the Initializer.
     // "elasticsearch.rest_url='http://localhost:9200'",

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java

@@ -21,7 +21,6 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
      "spring.batch.job.enabled=false",
      "hapi.fhir.fhir_version=dstu2",
      "spring.datasource.url=jdbc:h2:mem:dbr2",
-	  "spring.main.allow-bean-definition-overriding=true"
   })
 public class ExampleServerDstu2IT {
 

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java

@@ -46,7 +46,6 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
      "hapi.fhir.subscription.websocket_enabled=true",
      "hapi.fhir.allow_external_references=true",
      "hapi.fhir.allow_placeholder_references=true",
-	  "spring.main.allow-bean-definition-overriding=true"
   })
 
 

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -1,9 +1,12 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.CacheControlDirective;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 
@@ -86,6 +89,57 @@ class ExampleServerR4IT {
 		}
 	}
 
+	@Test
+	public void testBatchPutWithIdenticalTags() {
+		String batchPuts = "{\n" +
+			"\t\"resourceType\": \"Bundle\",\n" +
+			"\t\"id\": \"patients\",\n" +
+			"\t\"type\": \"batch\",\n" +
+			"\t\"entry\": [\n" +
+			"\t\t{\n" +
+			"\t\t\t\"request\": {\n" +
+			"\t\t\t\t\"method\": \"PUT\",\n" +
+			"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"resource\": {\n" +
+			"\t\t\t\t\"resourceType\": \"Patient\",\n" +
+			"\t\t\t\t\"id\": \"pat-1\",\n" +
+			"\t\t\t\t\"meta\": {\n" +
+			"\t\t\t\t\t\"tag\": [\n" +
+			"\t\t\t\t\t\t{\n" +
+			"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
+			"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
+			"\t\t\t\t\t\t}\n" +
+			"\t\t\t\t\t]\n" +
+			"\t\t\t\t}\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
+			"\t\t},\n" +
+			"\t\t{\n" +
+			"\t\t\t\"request\": {\n" +
+			"\t\t\t\t\"method\": \"PUT\",\n" +
+			"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"resource\": {\n" +
+			"\t\t\t\t\"resourceType\": \"Patient\",\n" +
+			"\t\t\t\t\"id\": \"pat-2\",\n" +
+			"\t\t\t\t\"meta\": {\n" +
+			"\t\t\t\t\t\"tag\": [\n" +
+			"\t\t\t\t\t\t{\n" +
+			"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
+			"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
+			"\t\t\t\t\t\t}\n" +
+			"\t\t\t\t\t]\n" +
+			"\t\t\t\t}\n" +
+			"\t\t\t},\n" +
+			"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
+			"\t\t}\n" +
+			"\t]\n" +
+			"}";
+		Bundle bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle.class, batchPuts);
+		ourClient.transaction().withBundle(bundle).execute();
+	}
+
 	@Test
 	@Order(1)
 	void testWebsocketSubscription() throws Exception {

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java

@@ -39,7 +39,6 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
      "hapi.fhir.fhir_version=r5",
      "hapi.fhir.subscription.websocket_enabled=true",
 	  "hapi.fhir.subscription.websocket_enabled=true",
-	  "spring.main.allow-bean-definition-overriding=true"
   })
 public class ExampleServerR5IT {
 

src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java

@@ -25,7 +25,6 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
     "hapi.fhir.fhir_version=r4",
     "hapi.fhir.subscription.websocket_enabled=true",
     "hapi.fhir.partitioning.partitioning_include_in_search_hashes=false",
-	  "spring.main.allow-bean-definition-overriding=true"
 
   })
 public class MultitenantServerR4IT {

src/test/resources/application-integrationtest.yaml

@@ -35,6 +35,8 @@ hapi:
 #    fhirpath_interceptor_enabled: false
 #    filter_search_enabled: true
 #    graphql_enabled: true
+#    local_base_urls:
+#      - http://hapi.fhir.org/baseR4
     #partitioning:
     #  cross_partition_reference_mode: true
     #  multitenancy_enabled: true