SpringBoot META-INF entries are duplicated under BOOT-INF/classes causing "Conflicting persistence unit definitions" error

Hi,

We recently upgraded to Spring Boot 3.2.0 and we are seeing the following error when the service starts up.

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [com/config/EclipseLinkJpaConfiguration.class]: Conflicting persistence unit definitions for name 'persistence-config': nested:/opt/application/service.jar/!BOOT-INF/classes/, file:/opt/application/service.jar

We have the persistence configuration in src/main/resources/META-INF/persistence.xml

Am I right to think this is because of the new Nested Jar Support? It appears the jar file is twice in the error message above, one with nested:... and one without.

If we fallback to the classic loader the service starts up ok.

Comment From: scottfrederick

@rmatec We have fixed several issues in the area of the new loader. Can you test with the latest Spring Boot 3.2.1-SNAPSHOT and see if your use case works without falling back to the classic loader?

Comment From: rmatec

@scottfrederick I tried with the snapshot version but I am getting the same error.

Comment From: philwebb

@rmatec Can you please provide the full stacktrace and if possible a sample application that reproduces the problem.

Comment From: rmatec

Hi @philwebb I created the following repo with a simple example https://github.com/rmatec/nested-jars-issue To reproduce the issue, generate a jar file and run it.

2023-12-20T17:29:22.332Z ERROR 148390 --- [           main] o.s.boot.SpringApplication               : Application run failed

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaConfiguration.class]: Conflicting persistence unit definitions for name 'persistence-config': nested:/home/rmatec/git/nested-jars-issue/build/libs/demo-0.0.1-SNAPSHOT.jar/!BOOT-INF/classes/, file:/home/rmatec/git/nested-jars-issue/build/libs/demo-0.0.1-SNAPSHOT.jar
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1775) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:601) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:523) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1173) ~[spring-context-6.1.1.jar!/:6.1.1]
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:936) ~[spring-context-6.1.1.jar!/:6.1.1]
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:616) ~[spring-context-6.1.1.jar!/:6.1.1]
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:753) ~[spring-boot-3.2.0.jar!/:3.2.0]
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:455) ~[spring-boot-3.2.0.jar!/:3.2.0]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:323) ~[spring-boot-3.2.0.jar!/:3.2.0]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1342) ~[spring-boot-3.2.0.jar!/:3.2.0]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1331) ~[spring-boot-3.2.0.jar!/:3.2.0]
    at com.example.demo.DemoApplication.main(DemoApplication.java:10) ~[!/:0.0.1-SNAPSHOT]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
    at java.base/java.lang.reflect.Method.invoke(Method.java:568) ~[na:na]
    at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:91) ~[demo-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
    at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:53) ~[demo-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
    at org.springframework.boot.loader.launch.JarLauncher.main(JarLauncher.java:58) ~[demo-0.0.1-SNAPSHOT.jar:0.0.1-SNAPSHOT]
Caused by: java.lang.IllegalStateException: Conflicting persistence unit definitions for name 'persistence-config': nested:/home/rmatec/git/nested-jars-issue/build/libs/demo-0.0.1-SNAPSHOT.jar/!BOOT-INF/classes/, file:/home/rmatec/git/nested-jars-issue/build/libs/demo-0.0.1-SNAPSHOT.jar
    at org.springframework.orm.jpa.persistenceunit.DefaultPersistenceUnitManager.preparePersistenceUnitInfos(DefaultPersistenceUnitManager.java:495) ~[spring-orm-6.1.1.jar!/:6.1.1]
    at org.springframework.orm.jpa.persistenceunit.DefaultPersistenceUnitManager.afterPropertiesSet(DefaultPersistenceUnitManager.java:435) ~[spring-orm-6.1.1.jar!/:6.1.1]
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.afterPropertiesSet(LocalContainerEntityManagerFactoryBean.java:339) ~[spring-orm-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1822) ~[spring-beans-6.1.1.jar!/:6.1.1]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1771) ~[spring-beans-6.1.1.jar!/:6.1.1]
    ... 22 common frames omitted

Comment From: rmatec

Thanks @philwebb