java - Deploying application using Hibernate JPA 2.1 to IBM WebSphere gives NullPointerException

Question

We are trying to deploy a Java 7 Spring MVC application using Hibernate into an IBM WebSphere 8.5.5.2 server. The application runs fine on a Tomcat server, but we cannot get it running in WebSphere.

The stack trace output is the following:

[3/26/15 13:49:53:552 MDT] 00000066 AutowiredAnno I org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor <init> JSR-330 'javax.inject.Inject' annotation found and supported for autowiring
[3/26/15 13:49:54:299 MDT] 00000066 LocalContaine I org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean createNativeEntityManagerFactory Building JPA container EntityManagerFactory for persistence unit 'default'
[3/26/15 13:49:54:339 MDT] 00000066 LogHelper     Z org.hibernate.jpa.internal.util.LogHelper logPersistenceUnitInformation HHH000204: Processing PersistenceUnitInfo [
    name: default
    ...]
[3/26/15 13:49:54:536 MDT] 00000066 Version       Z org.hibernate.Version logVersion HHH000412: Hibernate Core {4.3.7.Final}
[3/26/15 13:49:54:543 MDT] 00000066 Environment   Z org.hibernate.cfg.Environment <clinit> HHH000206: hibernate.properties not found
[3/26/15 13:49:54:546 MDT] 00000066 Environment   Z org.hibernate.cfg.Environment buildBytecodeProvider HHH000021: Bytecode provider name : javassist
[3/26/15 13:49:54:580 MDT] 00000066 JarInputStrea Z org.hibernate.jpa.boot.archive.internal.JarInputStreamBasedArchiveDescriptor visitArchive HHH015010: Unable to find file (ignored): bundleresource://130.fwk-1163147521/
                                 java.lang.NullPointerException: in is null
    at java.util.zip.ZipInputStream.<init>(ZipInputStream.java:111)
    at java.util.zip.ZipInputStream.<init>(ZipInputStream.java:90)
    at java.util.jar.JarInputStream.<init>(JarInputStream.java:87)
    at java.util.jar.JarInputStream.<init>(JarInputStream.java:73)
    at org.hibernate.jpa.boot.archive.internal.JarInputStreamBasedArchiveDescriptor.visitArchive(JarInputStreamBasedArchiveDescriptor.java:73)
    at org.hibernate.jpa.boot.scan.spi.AbstractScannerImpl.scan(AbstractScannerImpl.java:72)
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.scan(EntityManagerFactoryBuilderImpl.java:725)
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:221)
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:188)
    at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider$1.<init>(SpringHibernateJpaPersistenceProvider.java:49)
    at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:49)
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:343)
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:318)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1627)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1564)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:540)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:229)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:956)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:747)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
    at com.ibm.ws.webcontainer.webapp.WebApp.notifyServletContextCreated(WebApp.java:1686)
    at com.ibm.ws.webcontainer.webapp.WebAppImpl.initialize(WebAppImpl.java:414)
    at com.ibm.ws.webcontainer.webapp.WebGroupImpl.addWebApplication(WebGroupImpl.java:88)
    at com.ibm.ws.webcontainer.VirtualHostImpl.addWebApplication(VirtualHostImpl.java:169)
    at com.ibm.ws.webcontainer.WSWebContainer.addWebApp(WSWebContainer.java:749)
    at com.ibm.ws.webcontainer.WSWebContainer.addWebApplication(WSWebContainer.java:634)
    at com.ibm.ws.webcontainer.component.WebContainerImpl.install(WebContainerImpl.java:426)
    at com.ibm.ws.webcontainer.component.WebContainerImpl.start(WebContainerImpl.java:718)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl.start(ApplicationMgrImpl.java:1177)
    at com.ibm.ws.runtime.component.DeployedApplicationImpl.fireDeployedObjectStart(DeployedApplicationImpl.java:1370)
    at com.ibm.ws.runtime.component.DeployedModuleImpl.start(DeployedModuleImpl.java:639)
    at com.ibm.ws.runtime.component.DeployedApplicationImpl.start(DeployedApplicationImpl.java:968)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl.startApplication(ApplicationMgrImpl.java:776)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl$5.run(ApplicationMgrImpl.java:2195)
    at com.ibm.ws.security.auth.ContextManagerImpl.runAs(ContextManagerImpl.java:5474)
    at com.ibm.ws.security.auth.ContextManagerImpl.runAsSystem(ContextManagerImpl.java:5600)
    at com.ibm.ws.security.core.SecurityContext.runAsSystem(SecurityContext.java:255)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl.start(ApplicationMgrImpl.java:2200)
    at com.ibm.ws.runtime.component.CompositionUnitMgrImpl.start(CompositionUnitMgrImpl.java:446)
    at com.ibm.ws.runtime.component.CompositionUnitImpl.start(CompositionUnitImpl.java:123)
    at com.ibm.ws.runtime.component.CompositionUnitMgrImpl.start(CompositionUnitMgrImpl.java:389)
    at com.ibm.ws.runtime.component.CompositionUnitMgrImpl.access$500(CompositionUnitMgrImpl.java:117)
    at com.ibm.ws.runtime.component.CompositionUnitMgrImpl$CUInitializer.run(CompositionUnitMgrImpl.java:995)
    at com.ibm.wsspi.runtime.component.WsComponentImpl$_AsynchInitializer.run(WsComponentImpl.java:502)
    at com.ibm.ws.util.ThreadPool$Worker.run(ThreadPool.java:1864)

[3/26/15 13:49:54:899 MDT] 00000066 Version       Z org.hibernate.annotations.common.reflection.java.JavaReflectionManager <clinit> HCANN000001: Hibernate Commons Annotations {4.0.5.Final}
[3/26/15 13:49:55:511 MDT] 00000066 Enhance       E   CWWJP9992E: openjpa.Enhance: Error: The identity field defined in the com.company.model.KeyValueMapping Embeddable is not supported. 
[3/26/15 13:49:55:837 MDT] 00000066 Dialect       Z org.hibernate.dialect.Dialect <init> HHH000400: Using dialect: org.hibernate.dialect.SQLServer2008Dialect
[3/26/15 13:49:55:864 MDT] 00000066 LobCreatorBui Z org.hibernate.engine.jdbc.internal.LobCreatorBuilder useContextualLobCreation HHH000423: Disabling contextual LOB creation as JDBC driver reported JDBC version [3] less than 4
[3/26/15 13:49:56:071 MDT] 00000066 AnnotationCon W org.springframework.context.support.AbstractApplicationContext refresh Exception encountered during context initialization - cancelling refresh attempt
                                 org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in com.company.WebConfig: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: javax/persistence/Table.indexes()[Ljavax/persistence/Index;
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1568)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:540)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:229)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:956)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:747)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
    at com.ibm.ws.webcontainer.webapp.WebApp.notifyServletContextCreated(WebApp.java:1686)
    at com.ibm.ws.webcontainer.webapp.WebAppImpl.initialize(WebAppImpl.java:414)
    at com.ibm.ws.webcontainer.webapp.WebGroupImpl.addWebApplication(WebGroupImpl.java:88)
    at com.ibm.ws.webcontainer.VirtualHostImpl.addWebApplication(VirtualHostImpl.java:169)
    at com.ibm.ws.webcontainer.WSWebContainer.addWebApp(WSWebContainer.java:749)
    at com.ibm.ws.webcontainer.WSWebContainer.addWebApplication(WSWebContainer.java:634)
    at com.ibm.ws.webcontainer.component.WebContainerImpl.install(WebContainerImpl.java:426)
    at com.ibm.ws.webcontainer.component.WebContainerImpl.start(WebContainerImpl.java:718)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl.start(ApplicationMgrImpl.java:1177)
    at com.ibm.ws.runtime.component.DeployedApplicationImpl.fireDeployedObjectStart(DeployedApplicationImpl.java:1370)
    at com.ibm.ws.runtime.component.DeployedModuleImpl.start(DeployedModuleImpl.java:639)
    at com.ibm.ws.runtime.component.DeployedApplicationImpl.start(DeployedApplicationImpl.java:968)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl.startApplication(ApplicationMgrImpl.java:776)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl$5.run(ApplicationMgrImpl.java:2195)
    at com.ibm.ws.security.auth.ContextManagerImpl.runAs(ContextManagerImpl.java:5474)
    at com.ibm.ws.security.auth.ContextManagerImpl.runAsSystem(ContextManagerImpl.java:5600)
    at com.ibm.ws.security.core.SecurityContext.runAsSystem(SecurityContext.java:255)
    at com.ibm.ws.runtime.component.ApplicationMgrImpl.start(ApplicationMgrImpl.java:2200)
    at com.ibm.ws.runtime.component.CompositionUnitMgrImpl.start(CompositionUnitMgrImpl.java:446)
    at com.ibm.ws.runtime.component.CompositionUnitImpl.st

Answer 1

I share what worked for me. Me and my team were able to deploy our application with Spring 4.2.4, Hibernate 5.1 and Hibernate JPA 2.1 in Websphere 8.5.5 and Websphere 7.

The key to do this is to extract all the hibernate libraries and put them in a shared library folder in your server, create in your server configuration a new class loader with parent last order and assign to this class loader the shared library containing the hibernate libraries. Then you must change the Default Java Persistence API settings to use the hibernate persistence provider and not the default WebSphere persistence provider. So the steps are the followings:

1. Create a folder in your server and put in it all the hibernate libraries

   

2. Create the shared library in Websphere (Environment / Shared libraries) and set it to the path of the folder you just created on the server

3. On WebSphere click on your server and under Server Infrastructure click on Java and Process Management / Class Loader. Click on New and select the Parent Last option. Save

   

4. Click on the new class loader you just created and click on Shared library references on the right. Here add the shared library containing the Hibernate Libraries

5. Now under the section Container Settings of your server click on Container Services / Default Java Persistence API settings. Here you have to specify an alternate default persistence provider. See the image below.

   

6. Now compile your application and remove from the generated war the Hibernate libraries (see image 1). Then install it in the server.

In my case the application works like a charm also in WebSphere 7. This procedure solves javax/persistence/Table.indexes() error and all the other compilation error caused by libraries conflict between WebSphere and Hibernate.

Reference:

https://www.ibm.com/developerworks/community/wikis/form/anonymous/api/wiki/53181ccd-bcd4-431f-b968-0b5f6d46d652/page/192a432b-28bb-4080-b037-345e5d83da76/attachment/61e74f67-1d60-4120-ba25-ad7264c9f4f6/media/AlternateJPAProviders_TestReport.pdf