Upgraded to 5.6.0

Subscription tests fail ...

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

@@ -29,16 +29,6 @@ public class Application extends SpringBootServletInitializer {
 
   public static void main(String[] args) {
 
-  	 /*
-  	 * https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/246
-  	 * This will be allowed for a short period until we know how MDM should be configured
-  	 * or don't have multiple equal bean instantiations.
-  	 *
-  	 * This will require changes in the main project as stated in the Github comment
-  	 * */
-  	 System.setProperty("spring.main.allow-bean-definition-overriding","true");
-
-    System.setProperty("spring.batch.job.enabled", "false");
     SpringApplication.run(Application.class, args);
 
     //Server is now accessible at eg. http://localhost:8080/fhir/metadata

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

@@ -14,6 +14,7 @@ import org.hibernate.search.engine.cfg.BackendSettings;
 import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames;
 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.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy;
 import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy;
 import org.springframework.core.env.CompositePropertySource;
@@ -25,7 +26,8 @@ import java.util.*;
 
 public class EnvironmentHelper {
 
-	public static Properties getHibernateProperties(ConfigurableEnvironment environment) {
+	public static Properties getHibernateProperties(ConfigurableEnvironment environment,
+		ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
 		Properties properties = new Properties();
 		Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties");
 		for (Map.Entry<String, Object> entry : jpaProps.entrySet()) {
@@ -41,7 +43,7 @@ public class EnvironmentHelper {
 		//properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
 
 		//hapi-fhir-jpaserver-base "sensible defaults"
-		Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean().getJpaPropertyMap();
+		Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory).getJpaPropertyMap();
 		hapiJpaPropertyMap.forEach(properties::putIfAbsent);
 
 		//hapi-fhir-jpaserver-starter defaults
@@ -73,7 +75,7 @@ public class EnvironmentHelper {
 				ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
 				IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
 				builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW));
-				builder.setRestUrl(getElasticsearchServerUrl(environment));
+				builder.setHosts(getElasticsearchServerUrl(environment));
 				builder.setUsername(getElasticsearchServerUsername(environment));
 				builder.setPassword(getElasticsearchServerPassword(environment));
 				builder.setProtocol(getElasticsearchServerProtocol(environment));

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

@@ -8,8 +8,9 @@ import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings.CrossPartitionReferenceMode;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory;
+import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
 import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
-import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
+import ca.uhn.fhir.rest.server.mail.MailConfig;
 import com.google.common.base.Strings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.springframework.boot.env.YamlPropertySourceLoader;
@@ -207,22 +208,21 @@ public class FhirServerConfigCommon {
   @Bean()
   public IEmailSender emailSender(AppProperties appProperties, Optional<SubscriptionDeliveryHandlerFactory> subscriptionDeliveryHandlerFactory) {
     if (appProperties.getSubscription() != null && appProperties.getSubscription().getEmail() != null) {
-      JavaMailEmailSender retVal = new JavaMailEmailSender();
+		 MailConfig mailConfig = new MailConfig();
 
       AppProperties.Subscription.Email email = appProperties.getSubscription().getEmail();
-      retVal.setSmtpServerHostname(email.getHost());
-      retVal.setSmtpServerPort(email.getPort());
-      retVal.setSmtpServerUsername(email.getUsername());
-      retVal.setSmtpServerPassword(email.getPassword());
-      retVal.setAuth(email.getAuth());
-      retVal.setStartTlsEnable(email.getStartTlsEnable());
-      retVal.setStartTlsRequired(email.getStartTlsRequired());
-      retVal.setQuitWait(email.getQuitWait());
+      mailConfig.setSmtpHostname(email.getHost());
+      mailConfig.setSmtpPort(email.getPort());
+      mailConfig.setSmtpUsername(email.getUsername());
+      mailConfig.setSmtpPassword(email.getPassword());
+      mailConfig.setSmtpUseStartTLS(email.getStartTlsEnable());
+
+		 IEmailSender emailSender = new EmailSenderImpl(mailConfig);
 
       if(subscriptionDeliveryHandlerFactory.isPresent())
-       subscriptionDeliveryHandlerFactory.get().setEmailSender(retVal);
+       subscriptionDeliveryHandlerFactory.get().setEmailSender(emailSender);
 
-      return retVal;
+      return emailSender;
     }
 
     return null;

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

@@ -5,6 +5,7 @@ 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;
@@ -58,8 +59,9 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
 
   @Override
   @Bean()
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
+	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
     retVal.setPersistenceUnitName("HAPI_PU");
 
     try {
@@ -67,7 +69,7 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
     } catch (Exception e) {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment, myConfigurableListableBeanFactory));
     return retVal;
   }
 

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

@@ -10,6 +10,7 @@ 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;
@@ -62,8 +63,9 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
   
   @Override
   @Bean
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
+	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
     retVal.setPersistenceUnitName("HAPI_PU");
 
     try {
@@ -72,7 +74,8 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment,
+		 myConfigurableListableBeanFactory));
     return retVal;
   }
 
@@ -96,8 +99,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
       }
       String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
       String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
-      int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));
-      return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
+      return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
     } else {
       return null;
     }

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

@@ -7,6 +7,7 @@ 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 org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.*;
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
@@ -58,8 +59,9 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
   @Override
   @Bean()
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
+	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
     retVal.setPersistenceUnitName("HAPI_PU");
 
     try {
@@ -68,7 +70,8 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment,
+		 myConfigurableListableBeanFactory));
     return retVal;
   }
 
@@ -93,8 +96,7 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
       String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
       String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
-      int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));
-      return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
+      return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
     } else {
       return null;
     }

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

@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
 import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
 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;
@@ -59,8 +60,9 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
 
   @Override
   @Bean()
-  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory(
+	  ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(myConfigurableListableBeanFactory);
     retVal.setPersistenceUnitName("HAPI_PU");
 
     try {
@@ -69,7 +71,8 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
       throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
-    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment,
+		 myConfigurableListableBeanFactory));
     return retVal;
   }
 
@@ -93,8 +96,7 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
       }
       String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
       String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
-      int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));
-      return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword);
+      return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchUsername, elasticsearchPassword);
     } else {
       return null;
     }

src/main/resources/application.yaml

@@ -10,6 +10,8 @@ spring:
     # database connection pool size
     hikari:
       maximum-pool-size: 10
+  flyway:
+    check-location: false
   jpa:
     properties:
       hibernate.format_sql: false
@@ -31,9 +33,6 @@ spring:
   batch:
     job:
       enabled: false
-  main:
-#    TODO 5.6.0 -> Prevent duplicate bean definitions in the Spring batch config in HAPI: see:
-    allow-bean-definition-overriding: true
 hapi:
   fhir:
     ### This enables the swagger-ui at /fhir/swagger-ui/index.html as well as the /fhir/api-docs (see https://hapifhir.io/hapi-fhir/docs/server_plain/openapi.html)