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Websphere with Oracle DB deployment Error NosuchMethod

I am trying to deploy war file on websphere 8.5.5.13. which is connected to oracle(11g) db and even i had created data sources connection on websphere.
The application is getting installed but when i try to start the application gives me the following error:
[29/10/18 15:00:49:733 IST] 000001e1 SystemErr R Caused by: com.ibm.ws.webcontainer.exception.WebAppNotLoadedException: Failed to load webapp: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaAutoConfiguration.class]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: javax/persistence/Table.indexes()[Ljavax/persistence/Index; (loaded from file:/C:/Program Files (x86)/IBM/WebSphere/AppServer/plugins/javax.j2ee.persistence.jar by org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader#180c62e2) called from class org.hibernate.cfg.annotations.EntityBinder (loaded from file:/C:/Program%20Files%20(x86)/IBM/WebSphere/AppServer/profiles/DefaultAppServer/installedApps/AntivirusServerNode01Cell/cream_war.ear/cream.war/WEB-INF/lib/hibernate-core-5.0.12.Final.jar by
[29/10/18 15:00:49:733 IST] 000001e1 SystemErr R Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaAutoConfiguration.class]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: javax/persistence/Table.indexes()[Ljavax/persistence/Index; (loaded from file:/C:/Program Files (x86)/IBM/WebSphere/AppServer/plugins/javax.j2ee.persistence.jar by org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader#180c62e2) called from class org.hibernate.cfg.annotations.EntityBinder (loaded from file:/C:/Program%20Files%20(x86)/IBM/WebSphere/AppServer/profiles/DefaultAppServer/installedApps/AntivirusServerNode01Cell/cream_war.ear/cream.war/WEB-INF/lib/hibernate-core-5.0.12.Final.jar by
I also tried changing the version of hibernate and jpa but that too didnt work.
But when i deploy application without using oracle db (using h2 or derby) it runs properly.
Please help me out with this error.
Not able to find the path

The NoSuchMethodError indicates that Hibernate is trying to call a method on javax.persistence.Table that doesn't exist. The Table class has been loaded from file:/C:/Program Files (x86)/IBM/WebSphere/AppServer/plugins/javax.j2ee.persistence.jar so it's WAS itself that's providing the incompatible class.
By default, WAS 8.5.5 uses JPA 2.0 but it is possible to use JPA 2.1 by following the steps described here. You've already done most of the steps described in "Embedding a third-party persistence provider within an application". The one remaining step is to configure your application's class loader order so that it will prefer classes bundled with your application to those provided by the application server.

ClassLoader classcastexception with activemq client

I have been struggling with this problem for a while now, decided to ask the community, hoping to get some hints/answers.
I am using tomcat 7.0.54 as my J2EE container which has a WAR deployed with dependency on activemq-all.
Along with the above, I'm also placing a jar in the classpath to register a listener programmatically, by implementing the ServletContainerInitializer interface. This initializes a simple implementation of an active mq client, JvmMessageProducerImpl (I have activemq-client as a dependency in the pom).
With the above setup, when i try to start tomcat, i get the below exception. It seems that instead of loading the classes independently, the listener which is called when the web application starts, is finding an existing instance of TcpTransportFactory and throwing the ClassCastException. I have read the classloader manual for tomcat multiple times, and my understanding is that each of the war files should have independent Class loaders - but dont completely understand why the exception is being thrown?
javax.jms.JMSException: Could not create Transport. Reason: java.io.IOException: Transport scheme NOT recognized: [tcp]
at org.apache.activemq.util.JMSExceptionSupport.create(JMSExceptionSupport.java:36)
at org.apache.activemq.ActiveMQConnectionFactory.createTransport(ActiveMQConnectionFactory.java:317)
at org.apache.activemq.ActiveMQConnectionFactory.createActiveMQConnection(ActiveMQConnectionFactory.java:330)
at org.apache.activemq.ActiveMQConnectionFactory.createConnection(ActiveMQConnectionFactory.java:251)
at com.monitoreverywhere.jvmmon.mq.JvmMessageProducerImpl.setup(JvmMessageProducerImpl.java:66)
at com.monitoreverywhere.jvmmon.mq.JvmMessageProducerImpl$Runner.run(JvmMessageProducerImpl.java:163)
at java.lang.Thread.run(Thread.java:744)
Caused by: java.io.IOException: Transport scheme NOT recognized: [tcp]
at org.apache.activemq.util.IOExceptionSupport.create(IOExceptionSupport.java:27)
at org.apache.activemq.transport.TransportFactory.findTransportFactory(TransportFactory.java:181)
at org.apache.activemq.transport.TransportFactory.connect(TransportFactory.java:63)
at org.apache.activemq.ActiveMQConnectionFactory.createTransport(ActiveMQConnectionFactory.java:315)
... 5 more
Caused by: java.lang.ClassCastException: org.apache.activemq.transport.tcp.TcpTransportFactory cannot be cast to org.apache.activemq.transport.TransportFactory
at org.apache.activemq.transport.TransportFactory.findTransportFactory(TransportFactory.java:178)
... 7 more

Is there a way to log out classes that Java attempts to load, but aren't found on the classpath?

I'm trying to support an old version of a Java web app that I don't have the source to. When I run this program, the log shows the following:
SEVERE: StandardWrapper.Throwable
org.springframework.beans.factory.BeanDefinitionStoreException: Error registering bean with name 'Censored' defined in ServletContext resource [
/WEB-INF/censored.xml]: Class that bean class [com.censored.Censored] depends on not found; nested exception is java.lang.NoClassDefFoundError
java.lang.NoClassDefFoundError
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
...
So I can see what class is throwing the error, but I can't see what dependency it feels is missing. Is there an argument that I can throw into Java somewhere to log out when a class is attempted to be loaded that doesn't really exist?

You could try starting the JVM using the -verbose:class option. That will log all class loading to the console. Maybe that gives you more information.

Jars in my grails project not being picked up when deployed to tomcat 5.5

I am running a grails test run-app all day with my application and it is fine. I type "grails prod war" to get a war, and dump it in the webapps folder of my tomcat install. Now i get the message like so:
11.11.2010 16:35:11 *ERROR* GrailsExceptionResolver: Executing action [index] of controller [ResumeController] caused e
xception: java.lang.NoClassDefFoundError: Could not initialize class org.docx4j.jaxb.Context (GrailsExceptionResolver.ja
va, line 72)
org.codehaus.groovy.grails.web.servlet.mvc.exceptions.ControllerExecutionException: Executing action [index] of controll
er [ResumeController] caused exception: java.lang.NoClassDefFoundError: Could not initialize class org.docx4j.jaxb.Cont
ext
at org.jsecurity.web.servlet.JSecurityFilter.doFilterInternal(JSecurityFilter.java:382)
at org.jsecurity.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:180)
at java.lang.Thread.run(Unknown Source)
Caused by: org.codehaus.groovy.runtime.InvokerInvocationException: java.lang.NoClassDefFoundError: Could not initialize
class org.docx4j.jaxb.Context
... 3 more
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.docx4j.jaxb.Context
at org.docx4j.openpackaging.contenttype.ContentTypeManager.parseContentTypesFile(ContentTypeManager.java:599)
at org.docx4j.openpackaging.io.LoadFromZipNG.process(LoadFromZipNG.java:199)
at org.docx4j.openpackaging.io.LoadFromZipNG.get(LoadFromZipNG.java:188)
at org.docx4j.openpackaging.packages.OpcPackage.load(OpcPackage.java:188)
at org.docx4j.openpackaging.packages.WordprocessingMLPackage.load(WordprocessingMLPackage.java:169)
at com.iai.skillsdb.DocxHelpers.DocxParser.openDocx4j(DocxParser.java:70)
at ResumeController$_closure8.doCall(ResumeController.groovy:164)
at ResumeController$_closure8.doCall(ResumeController.groovy)
at ResumeController.invokeMethod(ResumeController.groovy)
at ResumeController$_closure1.doCall(ResumeController.groovy:41)
at ResumeController$_closure1.doCall(ResumeController.groovy)
... 3 more
What is causing this? I have the docx4j jar in my WAR for sure, and it is there in the web-inf lib folder as well.

You're getting a java.lang.NoClassDefFoundError, not a java.lang.ClassNotFoundException. The class is being loaded, but a class that it depends on (directly or indirectly via another class) isn't there. You're most likely missing a jar that docx4j requires as a dependency.

Make sure that you have the correct version of docx4j and that there is absolutely no other version of docx4j in your classpath, there may be a version of this lib that did not have the 'Content' class implemented.

Using Jersey Client inside EJB 3 stateless session bean on Weblogic

I am using Jersey client inside a EJB 3 stateless session bean. I can deploy the EJB project on Weblogic 11g. But when I try to look up the bean from a JSP, I get the following error
javax.ejb.EJBException: EJB Exception: ; nested exception is:
java.lang.NoClassDefFoundError: com/sun/jersey/api/client/Client; nested exception is: java.rmi.RemoteException: EJB Exception: ; nested exception is:
java.lang.NoClassDefFoundError: com/sun/jersey/api/client/Client
at weblogic.ejb.container.internal.RemoteBusinessIntfProxy.unwrapRemoteException(RemoteBusinessIntfProxy.java:112)
at weblogic.ejb.container.internal.RemoteBusinessIntfProxy.invoke(RemoteBusinessIntfProxy.java:91)
at $Proxy66.sayHelloFromServiceBean(Unknown Source)
at jsp_servlet.__yelpin._jspService(__yelpin.java:92)
at weblogic.servlet.jsp.JspBase.service(JspBase.java:34)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:227)
at weblogic.servlet.internal.StubSecurityHelper.invokeServlet(StubSecurityHelper.java:125)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:292)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:175)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.run(WebAppServletContext.java:3594)
at weblogic.security.acl.internal.AuthenticatedSubject.doAs(AuthenticatedSubject.java:321)
at weblogic.security.service.SecurityManager.runAs(SecurityManager.java:121)
at weblogic.servlet.internal.WebAppServletContext.securedExecute(WebAppServletContext.java:2202)
at weblogic.servlet.internal.WebAppServletContext.execute(WebAppServletContext.java:2108)
at weblogic.servlet.internal.ServletRequestImpl.run(ServletRequestImpl.java:1432)
at weblogic.work.ExecuteThread.execute(ExecuteThread.java:201)
at weblogic.work.ExecuteThread.run(ExecuteThread.java:173)
Caused by: java.rmi.RemoteException: EJB Exception: ; nested exception is:
java.lang.NoClassDefFoundError: com/sun/jersey/api/client/Client
at weblogic.rmi.internal.ServerRequest.sendReceive(ServerRequest.java:205)
at weblogic.rmi.cluster.ClusterableRemoteRef.invoke(ClusterableRemoteRef.java:345)
at weblogic.rmi.cluster.ClusterableRemoteRef.invoke(ClusterableRemoteRef.java:259)
at com.yelpin.ABCD_xruy6c_ABCDRemoteImpl_1032_WLStub.sayHelloFromServiceBean(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at weblogic.ejb.container.internal.RemoteBusinessIntfProxy.invoke(RemoteBusinessIntfProxy.java:73)
... 15 more
Caused by: java.lang.NoClassDefFoundError: com/sun/jersey/api/client/Client
at com.yelpin.ABCD.sayHelloFromServiceBean(ABCD.java:26)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.bea.core.repackaged.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:310)
at com.bea.core.repackaged.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
at com.bea.core.repackaged.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
at com.bea.core.repackaged.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131)
at com.bea.core.repackaged.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119)
at com.bea.core.repackaged.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
at com.bea.core.repackaged.springframework.jee.spi.MethodInvocationVisitorImpl.visit(MethodInvocationVisitorImpl.java:37)
at weblogic.ejb.container.injection.EnvironmentInterceptorCallbackImpl.callback(EnvironmentInterceptorCallbackImpl.java:55)
at com.bea.core.repackaged.springframework.jee.spi.EnvironmentInterceptor.invoke(EnvironmentInterceptor.java:50)
at com.bea.core.repackaged.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
at com.bea.core.repackaged.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:89)
at com.bea.core.repackaged.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
at com.bea.core.repackaged.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131)
at com.bea.core.repackaged.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119)
at com.bea.core.repackaged.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
at com.bea.core.repackaged.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at $Proxy67.sayHelloFromServiceBean(Unknown Source)
at com.yelpin.ABCD_xruy6c_ABCDRemoteImpl.sayHelloFromServiceBean(ABCD_xruy6c_ABCDRemoteImpl.java:61)
at com.yelpin.ABCD_xruy6c_ABCDRemoteImpl_WLSkel.invoke(Unknown Source)
at weblogic.rmi.internal.ServerRequest.sendReceive(ServerRequest.java:174)
... 23 more
I am new to EJB 3, Jersey and Weblogic. What I understand is that, the stateless session bean is unable to find the Jersey Client class. Can anyone help me with this ?
I have two projects in OEPE (Oracle Enterprise Pack for Eclipse). One is a EJB 3.0 project which contains the stateless session bean. The other is a dynamic web project which contains the JSP from which I do a JNDI look up to get the stateless session bean. I am using Jersey Client class inside one of the methods in the stateless session bean. This method is invoked from the JSP.
When I check the deployments on the server using Administrator console, there are two deployments. One is an EAR auto generated by OEPE. This EAR corresponds to the dynamic web project. The other deployment is of type EJB.
I also tried adding the jersey jar files to the lib folder under the server and restarted the server. But still, I get the same error.

Indeed, the NoClassDefFoundError means that the definition of the Jersey Client class can't be found and loaded at runtime (it was there at compile time though). So this is very likely a classpath or packaging issue.
Put your Jersey jar in the APP-INF/lib directory of the EAR and try again (if it doesn't work, please update your question with the structure of your EAR).
See http://download.oracle.com/docs/cd/E12839_01/web.1111/e13706/libraries.htm#sthref135 and http://download.oracle.com/docs/cd/E12839_01/web.1111/e13706/classloading.htm for more details.
Update: JARs should go in EarContent/APP-INF/lib that should have been automatically created but I'm not using OEPE so I can't confirm. Note that according to this very recent thread, there might be a bug in the OEPE publisher that is under investigation (at least under Linux).