Merge pull request #372 from hapifhir/rel_6_0_0_mergeback

Rel 6 0 0 mergeback

.github/workflows/maven.yml

@@ -17,9 +17,9 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up JDK 11
+    - name: Set up JDK 17
       uses: actions/setup-java@v1
       with:
-        java-version: 11
+        java-version: 17
     - name: Build with Maven
       run: mvn -B package --file pom.xml

pom.xml

@@ -14,13 +14,13 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-		  <version>5.7.2</version>
+		  <version>6.0.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
 
     <properties>
-        <java.version>8</java.version>
+        <java.version>11</java.version>
     </properties>
 
     <prerequisites>
@@ -405,7 +405,7 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.8.1</version>
                 <configuration>
-                    <release>8</release>
+                    <release>11</release>
                 </configuration>
             </plugin>
 

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

@@ -11,7 +11,10 @@ import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.context.annotation.Configuration;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
 
 @ConfigurationProperties(prefix = "hapi.fhir")
 @Configuration
@@ -71,9 +74,6 @@ public class AppProperties {
   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;
-  private Integer search_coord_max_pool_size = 100;
-  private Integer search_coord_queue_capacity = 200;
   private Boolean use_apache_address_strategy = false;
   private Boolean use_apache_address_strategy_https = false;
 
@@ -496,24 +496,6 @@ public class AppProperties {
 	this.normalized_quantity_search_level = normalized_quantity_search_level;
   }
 
-  public Integer getSearch_coord_core_pool_size() { return search_coord_core_pool_size; }
-
-  public void setSearch_coord_core_pool_size(Integer search_coord_core_pool_size) {
-    this.search_coord_core_pool_size = search_coord_core_pool_size;
-  }
-
-  public Integer getSearch_coord_max_pool_size() { return search_coord_max_pool_size; }
-
-  public void setSearch_coord_max_pool_size(Integer search_coord_max_pool_size) {
-    this.search_coord_max_pool_size = search_coord_max_pool_size;
-  }
-
-  public Integer getSearch_coord_queue_capacity() { return search_coord_queue_capacity; }
-
-  public void setSearch_coord_queue_capacity(Integer search_coord_queue_capacity) {
-  	 this.search_coord_queue_capacity = search_coord_queue_capacity;
-  }
-
 	public boolean getInstall_transitive_ig_dependencies() {
 		return install_transitive_ig_dependencies;
 	}

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

@@ -1,7 +1,7 @@
 package ca.uhn.fhir.jpa.starter;
 
-import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
 import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
+import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
 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.config.WebsocketDispatcherConfig;

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

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.starter;
 
+import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.support.IValidationSupport;
@@ -9,20 +10,15 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 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.binary.interceptor.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.IJpaSystemProvider;
+import ca.uhn.fhir.jpa.provider.*;
-import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
-import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
-import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
-import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
-import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.mdm.provider.MdmProviderLoader;
@@ -30,19 +26,9 @@ import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
 import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
-import ca.uhn.fhir.rest.server.ApacheProxyAddressStrategy;
+import ca.uhn.fhir.rest.server.*;
-import ca.uhn.fhir.rest.server.ETagSupportEnum;
+import ca.uhn.fhir.rest.server.interceptor.*;
-import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
-import ca.uhn.fhir.rest.server.IncomingRequestAddressStrategy;
-import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
-import ca.uhn.fhir.rest.server.provider.ReindexProvider;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
@@ -50,19 +36,16 @@ import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import com.google.common.base.Strings;
 import com.google.common.collect.ImmutableList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-import java.util.stream.Collectors;
-import javax.servlet.ServletException;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
 import org.springframework.http.HttpHeaders;
 import org.springframework.web.cors.CorsConfiguration;
 
+import javax.servlet.ServletException;
+import java.util.*;
+import java.util.stream.Collectors;
+
 public class BaseJpaRestfulServer extends RestfulServer {
   private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaRestfulServer.class);
 
@@ -80,6 +63,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
   @Autowired
   IJpaSystemProvider jpaSystemProvider;
   @Autowired
+  ValueSetOperationProvider myValueSetOperationProvider;
+  @Autowired
   IInterceptorBroadcaster interceptorBroadcaster;
   @Autowired
   DatabaseBackedPagingProvider databaseBackedPagingProvider;
@@ -93,8 +78,9 @@ public class BaseJpaRestfulServer extends RestfulServer {
   BulkDataExportProvider bulkDataExportProvider;
   @Autowired
   PartitionManagementProvider partitionManagementProvider;
-  @Autowired
+	//TODO GGG RE-ADD ONCE FIXED IN HAPI-FHIR
-  ValueSetOperationProvider valueSetOperationProvider;
+//	@Autowired
+//  ValueSetOperationProvider valueSetOperationProvider;
    @Autowired
 	ReindexProvider reindexProvider;
   @Autowired
@@ -149,7 +135,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
 
     registerProviders(resourceProviderFactory.createProviders());
     registerProvider(jpaSystemProvider);
-
+	 //TODO GGG RE-ADD ONCE FIXED IN HAPI-FHIR
+//	 registerProvider(myValueSetOperationProvider);
     /*
      * The conformance provider exports the supported resources, search parameters, etc for
      * this server. The JPA version adds resourceProviders counts to the exported statement, so it
@@ -376,7 +363,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
     }
 
     // valueSet Operations i.e $expand
-    registerProvider(valueSetOperationProvider);
+	  //TODO GGG RE-ADD ONCE FIXED IN HAPI-FHIR
+//	 registerProvider(myValueSetOperationProvider);
 
 	 //reindex Provider $reindex
 	 registerProvider(reindexProvider);

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

@@ -14,7 +14,7 @@ public class ElasticsearchConfig {
 	@Autowired
 	private ConfigurableEnvironment configurableEnvironment;
 
-	@Bean()
+	@Bean
 	public ElasticsearchSvcImpl elasticsearchSvc() {
 		if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
 			String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);

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

@@ -22,7 +22,10 @@ import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.core.env.EnumerablePropertySource;
 import org.springframework.core.env.PropertySource;
 
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
 
 public class EnvironmentHelper {
 

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

@@ -1,8 +1,8 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.binary.api.IBinaryStorageSvc;
 import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
-import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
 import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings.CrossPartitionReferenceMode;
@@ -14,8 +14,6 @@ import ca.uhn.fhir.rest.server.mail.IMailSvc;
 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;
@@ -25,6 +23,9 @@ import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
+import java.util.HashSet;
+import java.util.Optional;
+
 /**
  * This is the primary configuration file for the example server
  */
@@ -75,7 +76,7 @@ public class FhirServerConfigCommon {
   /**
    * Configure FHIR properties around the the JPA server via this bean
    */
-  @Bean()
+  @Bean
   public DaoConfig daoConfig(AppProperties appProperties) {
     DaoConfig retVal = new DaoConfig();
 
@@ -212,7 +213,7 @@ public class FhirServerConfigCommon {
     return binaryStorageSvc;
   }
 
-  @Bean()
+  @Bean
   public IEmailSender emailSender(AppProperties appProperties, Optional<SubscriptionDeliveryHandlerFactory> subscriptionDeliveryHandlerFactory) {
     if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
 		 MailConfig mailConfig = new MailConfig();

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java

@@ -1,85 +1,16 @@
 package ca.uhn.fhir.jpa.starter;
 
-import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.jpa.config.JpaDstu2Config;
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
-import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition;
-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.Primary;
+import org.springframework.context.annotation.Import;
-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(OnDSTU2Condition.class)
-public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
+@Import({
-
+	StarterJpaConfig.class,
-  @Autowired
+	JpaDstu2Config.class
-  private DataSource myDataSource;
+})
-
+public class FhirServerConfigDstu2 {
-  /**
-   * We override the paging provider definition so that we can customize
-   * the default/max page sizes for search results. You can set these however
-   * you want, although very large page sizes will require a lot of RAM.
-   */
-  @Autowired
-  AppProperties appProperties;
-
-  @PostConstruct
-  public void initSettings() {
-    if(appProperties.getSearch_coord_core_pool_size() != null) {
-		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
-	 }
-	  if(appProperties.getSearch_coord_max_pool_size() != null) {
-		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
-	  }
-	  if(appProperties.getSearch_coord_queue_capacity() != null) {
-		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
-	  }
-  }
-
-  @Override
-  public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
-    DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
-    return pagingProvider;
-  }
-
-  @Autowired
-  private ConfigurableEnvironment configurableEnvironment;
-
-  @Override
-  @Bean()
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
-	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
-    retVal.setPersistenceUnitName("HAPI_PU");
-
-    try {
-      retVal.setDataSource(myDataSource);
-    } catch (Exception e) {
-      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
-    }
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
-    return retVal;
-  }
-
-  @Bean
-  @Primary
-  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-    JpaTransactionManager retVal = new JpaTransactionManager();
-    retVal.setEntityManagerFactory(entityManagerFactory);
-    return retVal;
-  }
-
-
 }

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

@@ -1,89 +1,19 @@
 package ca.uhn.fhir.jpa.starter;
 
-import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
-import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
 import ca.uhn.fhir.jpa.starter.cql.StarterCqlDstu3Config;
-import javax.annotation.PostConstruct;
+import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
-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;
 
 @Configuration
 @Conditional(OnDSTU3Condition.class)
-@Import({StarterCqlDstu3Config.class, ElasticsearchConfig.class})
+@Import({
-public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
+	StarterJpaConfig.class,
-
+	JpaDstu3Config.class,
-  @Autowired
+	StarterCqlDstu3Config.class,
-  private DataSource myDataSource;
+	ElasticsearchConfig.class})
-
+public class FhirServerConfigDstu3 {
-  /**
-   * We override the paging provider definition so that we can customize
-   * the default/max page sizes for search results. You can set these however
-   * you want, although very large page sizes will require a lot of RAM.
-   */
-  @Autowired
-  AppProperties appProperties;
-
-  @PostConstruct
-  public void initSettings() {
-    if(appProperties.getSearch_coord_core_pool_size() != null) {
-		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
-	 }
-	  if(appProperties.getSearch_coord_max_pool_size() != null) {
-		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
-	  }
-	  if(appProperties.getSearch_coord_queue_capacity() != null) {
-		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
-	  }
-  }
-
-
-  @Override
-  public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
-    DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
-    return pagingProvider;
-  }
-
-  @Autowired
-  private ConfigurableEnvironment configurableEnvironment;
-  
-  @Override
-  @Bean
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
-	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
-    retVal.setPersistenceUnitName("HAPI_PU");
-
-    try {
-      retVal.setDataSource(myDataSource);
-    } catch (Exception e) {
-      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
-    }
-
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment,
-		 myConfigurableListableBeanFactory));
-
-    return retVal;
-  }
-
-  @Bean
-  @Primary
-  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-    JpaTransactionManager retVal = new JpaTransactionManager();
-    retVal.setEntityManagerFactory(entityManagerFactory);
-    return retVal;
-  }
 }

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

@@ -1,88 +1,20 @@
 package ca.uhn.fhir.jpa.starter;
 
-import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
-import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
-import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import ca.uhn.fhir.jpa.starter.cql.StarterCqlR4Config;
-import javax.annotation.PostConstruct;
+import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
-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;
 
 @Configuration
 @Conditional(OnR4Condition.class)
-@Import({StarterCqlR4Config.class, ElasticsearchConfig.class})
+@Import({
-public class FhirServerConfigR4 extends BaseJavaConfigR4 {
+	StarterJpaConfig.class,
-
+	JpaR4Config.class,
-  @Autowired
+	StarterCqlR4Config.class,
-  private DataSource myDataSource;
+	ElasticsearchConfig.class
-
+})
-  /**
+public class FhirServerConfigR4 {
-   * We override the paging provider definition so that we can customize
-   * the default/max page sizes for search results. You can set these however
-   * you want, although very large page sizes will require a lot of RAM.
-   */
-  @Autowired
-  AppProperties appProperties;
-
-  @PostConstruct
-  public void initSettings() {
-    if(appProperties.getSearch_coord_core_pool_size() != null) {
-		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
-	 }
-	  if(appProperties.getSearch_coord_max_pool_size() != null) {
-		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
-	  }
-	  if(appProperties.getSearch_coord_queue_capacity() != null) {
-		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
-	  }
-  }
-
-  @Override
-  public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
-    DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
-    return pagingProvider;
-  }
-
-  @Autowired
-  private ConfigurableEnvironment configurableEnvironment;
-
-  @Override
-  @Bean()
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
-	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
-    retVal.setPersistenceUnitName("HAPI_PU");
-
-    try {
-      retVal.setDataSource(myDataSource);
-    } catch (Exception e) {
-      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
-    }
-
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment,
-		 myConfigurableListableBeanFactory));
-    return retVal;
-  }
-
-  @Bean
-  @Primary
-  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-    JpaTransactionManager retVal = new JpaTransactionManager();
-    retVal.setEntityManagerFactory(entityManagerFactory);
-    return retVal;
-  }
-
 }

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

@@ -1,87 +1,17 @@
 package ca.uhn.fhir.jpa.starter;
 
-import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.jpa.config.r5.JpaR5Config;
-import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
-import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 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;
 
 @Configuration
 @Conditional(OnR5Condition.class)
-@Import({ElasticsearchConfig.class})
+@Import({
-public class FhirServerConfigR5 extends BaseJavaConfigR5 {
+	StarterJpaConfig.class,
-
+	JpaR5Config.class,
-  @Autowired
+	ElasticsearchConfig.class
-  private DataSource myDataSource;
+})
-
+public class FhirServerConfigR5 {
-  /**
-   * We override the paging provider definition so that we can customize
-   * the default/max page sizes for search results. You can set these however
-   * you want, although very large page sizes will require a lot of RAM.
-   */
-  @Autowired
-  AppProperties appProperties;
-
-  @PostConstruct
-  public void initSettings() {
-    if(appProperties.getSearch_coord_core_pool_size() != null) {
-		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
-	 }
-	  if(appProperties.getSearch_coord_max_pool_size() != null) {
-		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
-	  }
-	  if(appProperties.getSearch_coord_queue_capacity() != null) {
-		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
-	  }
-  }
-
-  @Override
-  public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
-    DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
-    return pagingProvider;
-  }
-
-  @Autowired
-  private ConfigurableEnvironment configurableEnvironment;
-
-  @Override
-  @Bean()
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
-	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
-    retVal.setPersistenceUnitName("HAPI_PU");
-
-    try {
-      retVal.setDataSource(myDataSource);
-    } catch (Exception e) {
-      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
-    }
-
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment,
-		 myConfigurableListableBeanFactory));
-    return retVal;
-  }
-
-  @Bean
-  @Primary
-  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-    JpaTransactionManager retVal = new JpaTransactionManager();
-    retVal.setEntityManagerFactory(entityManagerFactory);
-    return retVal;
-  }
-
 }

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

@@ -0,0 +1,109 @@
+package ca.uhn.fhir.jpa.starter;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.api.IDaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
+import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
+import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
+import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
+import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
+import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.provider.DaoRegistryResourceSupportedSvc;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
+import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
+import ca.uhn.fhir.jpa.util.ResourceCountCache;
+import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
+import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
+import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
+import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
+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.Primary;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.orm.jpa.JpaTransactionManager;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+
+@Configuration
+public class StarterJpaConfig {
+	@Bean
+	public IFulltextSearchSvc fullTextSearchSvc() {
+		return new FulltextSearchSvcImpl();
+	}
+
+	@Bean
+	public IStaleSearchDeletingSvc staleSearchDeletingSvc() {
+		return new StaleSearchDeletingSvcImpl();
+	}
+
+	@Primary
+	@Bean
+	public CachingValidationSupport validationSupportChain(JpaValidationSupportChain theJpaValidationSupportChain) {
+		return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
+	}
+
+	@Bean
+	public BatchConfigurer batchConfigurer() {
+		return new NonPersistedBatchConfigurer();
+	}
+
+	@Autowired
+	AppProperties appProperties;
+	@Autowired
+	private DataSource myDataSource;
+	@Autowired
+	private ConfigurableEnvironment configurableEnvironment;
+
+	/**
+	 * Customize the default/max page sizes for search results. You can set these however
+	 * you want, although very large page sizes will require a lot of RAM.
+	 */
+	@Bean
+	public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
+		DatabaseBackedPagingProvider pagingProvider = new DatabaseBackedPagingProvider();
+		pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
+		pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
+		return pagingProvider;
+	}
+
+	@Bean
+	public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
+		return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
+	}
+
+	@Bean(name = "myResourceCountsCache")
+	public ResourceCountCache resourceCountsCache(IFhirSystemDao<?, ?> theSystemDao) {
+		return ResourceCountCacheUtil.newResourceCountCache(theSystemDao);
+	}
+
+	@Primary
+	@Bean
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory(
+		ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
+		LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
+		retVal.setPersistenceUnitName("HAPI_PU");
+
+		try {
+			retVal.setDataSource(myDataSource);
+		} catch (Exception e) {
+			throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
+		}
+		retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
+		return retVal;
+	}
+
+	@Bean
+	@Primary
+	public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
+		JpaTransactionManager retVal = new JpaTransactionManager();
+		retVal.setEntityManagerFactory(entityManagerFactory);
+		return retVal;
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/mdm/MdmConfig.java

@@ -1,15 +1,12 @@
 package ca.uhn.fhir.jpa.starter.mdm;
 
-import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.mdm.config.MdmConsumerConfig;
 import ca.uhn.fhir.jpa.mdm.config.MdmSubmitterConfig;
 import ca.uhn.fhir.jpa.starter.AppProperties;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
 import ca.uhn.fhir.mdm.rules.config.MdmSettings;
-import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import com.google.common.base.Charsets;
-import java.io.IOException;
 import org.apache.commons.io.IOUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
@@ -19,6 +16,8 @@ import org.springframework.context.annotation.Import;
 import org.springframework.core.io.DefaultResourceLoader;
 import org.springframework.core.io.Resource;
 
+import java.io.IOException;
+
 @Configuration
 @Conditional(MdmConfigCondition.class)
 @Import({MdmConsumerConfig.class, MdmSubmitterConfig.class})

src/main/resources/application.yaml

@@ -95,7 +95,9 @@ hapi:
     #    enable_index_contained_resource: false
     ###  !!Extended Lucene/Elasticsearch Indexing is still a experimental feature, expect some features (e.g. _total=accurate) to not work as expected!!
     ###  more information here: https://hapifhir.io/hapi-fhir/docs/server_jpa/elastic.html
-    #    advanced_lucene_indexing: false
+    advanced_lucene_indexing: false
+    #    enforce_referential_integrity_on_delete: false
+    # This is an experimental feature, and does not fully support _total and other FHIR features.
 #    enforce_referential_integrity_on_delete: false
     #    enforce_referential_integrity_on_write: false
     #    etag_support_enabled: true
@@ -109,6 +111,7 @@ hapi:
     #    mdm_enabled: true
 #    local_base_urls:
 #      - https://hapi.fhir.org/baseR4
+    mdm_enabled: false
     #    partitioning:
     #      allow_references_across_partitions: false
     #      partitioning_include_in_search_hashes: false

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

@@ -43,13 +43,18 @@ import org.testcontainers.elasticsearch.ElasticsearchContainer;
     "hapi.fhir.fhir_version=r4",
     "hapi.fhir.lastn_enabled=true",
 	 "hapi.fhir.store_resource_in_lucene_index_enabled=true",
+	 "hapi.fhir.advanced_lucene_indexing=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'",
     "elasticsearch.username=SomeUsername",
     "elasticsearch.password=SomePassword",
+    "elasticsearch.debug.refresh_after_write=true",
 	 "elasticsearch.protocol=http",
-	  "spring.main.allow-bean-definition-overriding=true"
+	  "spring.main.allow-bean-definition-overriding=true",
+	  "spring.jpa.properties.hibernate.search.enabled=true",
+	  "spring.jpa.properties.hibernate.search.backend.type=elasticsearch",
+	  "spring.jpa.properties.hibernate.search.backend.analysis.configurer=ca.uhn.fhir.jpa.search.elastic.HapiElasticsearchAnalysisConfigurer"
   })
 @ContextConfiguration(initializers = ElasticsearchLastNR4IT.Initializer.class)
 public class ElasticsearchLastNR4IT {
@@ -57,9 +62,8 @@ public class ElasticsearchLastNR4IT {
   private IGenericClient ourClient;
   private FhirContext ourCtx;
 
-  private static final String ELASTIC_VERSION = "7.10.2";
+  private static final String ELASTIC_VERSION = "7.16.3";
   private static final String ELASTIC_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTIC_VERSION;
-
   private static ElasticsearchContainer embeddedElastic;
 
   @Autowired
@@ -80,7 +84,8 @@ public class ElasticsearchLastNR4IT {
   private int port;
 
   @Test
-  void testLastN() throws IOException {
+  void testLastN() throws IOException, InterruptedException {
+	  Thread.sleep(2000);
 
     Patient pt = new Patient();
     pt.addName().setFamily("Lastn").addGiven("Arthur");
@@ -90,8 +95,10 @@ public class ElasticsearchLastNR4IT {
     obs.getSubject().setReferenceElement(id);
     String observationCode = "testobservationcode";
     String codeSystem = "http://testobservationcodesystem";
+
     obs.getCode().addCoding().setCode(observationCode).setSystem(codeSystem);
     obs.setValue(new StringType(observationCode));
+
     Date effectiveDtm = new GregorianCalendar().getTime();
     obs.setEffective(new DateTimeType(effectiveDtm));
     obs.getCategoryFirstRep().addCoding().setCode("testcategorycode").setSystem("http://testcategorycodesystem");