Hibernate DuplicateMappingException with beans from different databases - spring

Question

Edit:
I realized this morning that the exception seems to be linked to Spring boot actuator that seems to be run only for production and not when starting the prohect from spring tools suite. (see the exception trace at the end of the post)
I have a spring boot project that I recently upgraded from 1.5 version to 2.2.
In this project we access beans from two different databases.
I followed steps from this article to configure the databases.
The primary database is accessed using jpa and everything about this database is in a specific package.
The other database is used to access legacy beans using directly hibernate. Everything about those legacy beans is in a different package.
Some beans have the same name in the two packages, but as they are configured in two different repositories, I thought it would not be a problem.
When I run the project in Spring Tools Suite (using the embeded tomcat) everything works perfectly.
But If I build a war and deploy it to a standalone tomcat (tried with version 8.5 and 9) I get an exception :
org.hibernate.DuplicateMappingException: The [fr.mycompany.dbconfprimary.MyBean] and [fr.mycomany.dbconfsecondary.MyBean] entities share the same JPA entity name: [MyBean] which is not allowed!
I don't understand why I have this problem with war deployment but not with spring boot embedded tomcat.
Here is the configuration class for the primary database:
package fr.mycompany.dbconfprimary;
...
...
#Configuration
#EnableJpaRepositories(
basePackages = "fr.mycompany.dbconfprimary",
entityManagerFactoryRef = "entityManagerFactory",
transactionManagerRef = "transactionManager",
repositoryBaseClass = BaseRepositoryImpl.class)
public class HibernatePrimaryConfig {
...
...
#Bean
#Primary
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean em
= new LocalContainerEntityManagerFactoryBean();
em.setDataSource(dataSource());
em.setPackagesToScan(
new String[] { "fr.mycompany.dbconfprimary" });
HibernateJpaVendorAdapter vendorAdapter
= new HibernateJpaVendorAdapter();
em.setJpaVendorAdapter(vendorAdapter);
HashMap<String, Object> properties = new HashMap<>();
properties.put("hibernate.hbm2ddl.auto",ddlMode);
properties.put("hibernate.dialect",dialect);
em.setJpaPropertyMap(properties);
return em;
}
#Primary
#Bean
public PlatformTransactionManager transactionManager() {
JpaTransactionManager transactionManager
= new JpaTransactionManager();
transactionManager.setEntityManagerFactory(
entityManagerFactory().getObject());
return transactionManager;
}
#Primary
#Bean("serversDataSource")
public DataSource dataSource() {
DriverManagerDataSource dataSource
= new DriverManagerDataSource();
dataSource.setDriverClassName(driverClassName);
dataSource.setUrl(url);
dataSource.setUsername(username);
dataSource.setPassword(password);
return dataSource;
}
}
And here is the configuration for the secondary database:
package fr.mycompany.dbconfsecondary;
...
...
#Configuration
#EnableJpaRepositories(
basePackages = {"fr.mycompany.dbconfsecondary"},
entityManagerFactoryRef = "secondaryEntityManagerFactory",
transactionManagerRef = "secondaryTransactionManager")
public class HibernateSecondaryConfig {
...
...
#Bean
public LocalContainerEntityManagerFactoryBean secondaryEntityManagerFactory() {
LocalContainerEntityManagerFactoryBean em
= new LocalContainerEntityManagerFactoryBean();
em.setDataSource(secondaryDataSource());
em.setPackagesToScan(
new String[] {"fr.mycompany.dbconfsecondary");
String[] hbmFiles=new String[hibernateHbmResources.length];
for(int i=0;i<hibernateHbmResources.length;i++)
try {
hbmFiles[i]=convertHbmPath(hibernateHbmResources[i].getFile().getAbsolutePath());
} catch (IOException e) {
throw(new RuntimeException(e));
}
em.setMappingResources(hbmFiles);
HibernateJpaVendorAdapter vendorAdapter
= new HibernateJpaVendorAdapter();
em.setJpaVendorAdapter(vendorAdapter);
HashMap<String, Object> properties = new HashMap<>();
properties.put("hibernate.hbm2ddl.auto",ddlMode);
properties.put("hibernate.dialect",dialect);
properties.put("hibernate.current_session_context_class","thread");
em.setJpaPropertyMap(properties);
return em;
}
#Bean
public PlatformTransactionManager secondaryTransactionManager() {
JpaTransactionManager transactionManager
= new JpaTransactionManager();
transactionManager.setEntityManagerFactory(
secondaryEntityManagerFactory().getObject());
return transactionManager;
}
#Bean("secondaryServersDataSource")
public DataSource secondaryDataSource() {
DriverManagerDataSource dataSource
= new DriverManagerDataSource();
dataSource.setDriverClassName(driverClassName);
dataSource.setUrl(url);
dataSource.setUsername(username);
dataSource.setPassword(password);
return dataSource;
}
...
...
}
[Almost]Full Exception trace:
2019-12-11 10:08:39 [main] ERROR
o.s.b.w.e.tomcat.TomcatStarter - Error starting Tomcat context. Exception: org.springframework.beans.factory.BeanCreationException. Message: Error creating bean with name 'servletEndpointRegistrar' defined in class path resource [org/springframework/boot/actuate/autoconfigure/endpoint/web/ServletEndpointManagementContextConfiguration$WebMvcServletEndpointManagementContextConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.endpoint.web.ServletEndpointRegistrar]: Factory method 'servletEndpointRegistrar' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'healthEndpoint' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Unsatisfied dependency expressed through method 'healthEndpoint' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'healthContributorRegistry' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.health.HealthContributorRegistry]: Factory method 'healthContributorRegistry' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'applicationDiskUsage': Unsatisfied dependency expressed through field 'parameterService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
2019-12-11 10:08:39 [main] INFO
o.a.catalina.core.StandardService - Stopping service [Tomcat]
2019-12-11 10:08:39 [main] WARN
o.s.b.w.s.c.AnnotationConfigServletWebServerApplicationContext - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.context.ApplicationContextException: Unable to start web server; nested exception is org.springframework.boot.web.server.WebServerException: Unable to start embedded Tomcat
2019-12-11 10:08:39 [main] INFO
o.s.b.a.l.ConditionEvaluationReportLoggingListener -
Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
2019-12-11 10:08:39 [main] ERROR
o.s.boot.SpringApplication - Application run failed
org.springframework.context.ApplicationContextException: Unable to start web server; nested exception is org.springframework.boot.web.server.WebServerException: Unable to start embedded Tomcat
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:156)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:544)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:141)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:747)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:397)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:315)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1226)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1215)
at fr.mycompany.Application.main(Application.java:41)
Caused by: org.springframework.boot.web.server.WebServerException: Unable to start embedded Tomcat
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.initialize(TomcatWebServer.java:126)
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.<init>(TomcatWebServer.java:88)
at org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory.getTomcatWebServer(TomcatServletWebServerFactory.java:438)
at org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory.getWebServer(TomcatServletWebServerFactory.java:191)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.createWebServer(ServletWebServerApplicationContext.java:180)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:153)
... 8 common frames omitted
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'servletEndpointRegistrar' defined in class path resource [org/springframework/boot/actuate/autoconfigure/endpoint/web/ServletEndpointManagementContextConfiguration$WebMvcServletEndpointManagementContextConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.endpoint.web.ServletEndpointRegistrar]: Factory method 'servletEndpointRegistrar' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'healthEndpoint' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Unsatisfied dependency expressed through method 'healthEndpoint' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'healthContributorRegistry' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.health.HealthContributorRegistry]: Factory method 'healthContributorRegistry' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'applicationDiskUsage': Unsatisfied dependency expressed through field 'parameterService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
at org.springframework.beans.factory.support.ConstructorResolver.instantiate(ConstructorResolver.java:656)
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:636)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1338)
...
... 13 common frames omitted
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.endpoint.web.ServletEndpointRegistrar]: Factory method 'servletEndpointRegistrar' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'healthEndpoint' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Unsatisfied dependency expressed through method 'healthEndpoint' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'healthContributorRegistry' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.health.HealthContributorRegistry]: Factory method 'healthContributorRegistry' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'applicationDiskUsage': Unsatisfied dependency expressed through field 'parameterService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'healthEndpoint' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Unsatisfied dependency expressed through method 'healthEndpoint' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'healthContributorRegistry' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.health.HealthContributorRegistry]: Factory method 'healthContributorRegistry' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'applicationDiskUsage': Unsatisfied dependency expressed through field 'parameterService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'healthContributorRegistry' defined in class path resource [org/springframework/boot/actuate/autoconfigure/health/HealthEndpointConfiguration.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.health.HealthContributorRegistry]: Factory method 'healthContributorRegistry' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'applicationDiskUsage': Unsatisfied dependency expressed through field 'parameterService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.boot.actuate.health.HealthContributorRegistry]: Factory method 'healthContributorRegistry' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'applicationDiskUsage': Unsatisfied dependency expressed through field 'parameterService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'applicationDiskUsage': Unsatisfied dependency expressed through field 'parameterService'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'parameterService': Unsatisfied dependency expressed through field 'paramEnumerationRepo'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'parametrageTypeEnumerationRepo': Cannot create inner bean '(inner bean)#255eadf5' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#255eadf5': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [fr/mycompany/ipolice/server/Hibernatev3Config.class]: Invocation of init method failed; nested exception is org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
Caused by: org.hibernate.DuplicateMappingException: The [fr.mycompany.secondarydb.BeanName] and [fr.mycompany.primarydb.BeanName] entities share the same JPA entity name: [BeanName] which is not allowed!
at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.addEntityBinding(InFlightMetadataCollectorImpl.java:305)
at org.hibernate.cfg.AnnotationBinder.bindClass(AnnotationBinder.java:822)
... 148 common frames omitted

Answer 1

The problem is that you should directly disable the default Spring Data JPA repository initialization.
This can be achieved by specifying the spring.data.jpa.repositories.enabled=false configuration property (either via startup parameter or via application.properties)

Answer 2

Assign names to your secondary beans like #Bean("beanName").
And then, when you want to inject them inside a component you can do it with
#Qualifier("beanName").
If you don't use the qualifier, the primary bean will be selected for injection.

Answer 3

I finally realised that my problem comes from the fact that primary database uses anotated beans and secondary database uses hbm files.
Hbm files seem to be found in the classpath when I build the project and not when the project is launched via Spring Tools Suite.
So my problem is a conflict between beans defined in my primary repository and beans in the hbms that were loaded automatically in the primary repository.
To correct the problem I changed the extension of the hbm files to avoid the automatic detection by the primary configuration and modified the secondary configuration to search for the new extension instead of .hbm.xml.