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Getting Servlet: "AxisServlet" failed to preload on startup in Web application java.lang.StackOverflowError in Weblogic 12c

I am getting below error while deploying application on WLS 12c
<Jun 8, 2020 11:02:03,120 AM IST> <Error> <HTTP> <BEA-101216> <Servlet: "AxisServlet" failed to
preload on startup in Web application: "MyApplication1.0.war".
java.lang.StackOverflowError
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader$3.next(URLClassLoader.java:601)
at java.net.URLClassLoader$3.hasMoreElements(URLClassLoader.java:626)
at sun.misc.CompoundEnumeration.next(CompoundEnumeration.java:45)
at sun.misc.CompoundEnumeration.hasMoreElements(CompoundEnumeration.java:54)
Truncated. see log file for complete stacktrace
>
<Jun 8, 2020 11:02:08,698 AM IST> <Error> <Deployer> <BEA-149231> <Unable to set the activation state
to true for the application "MyApplication1.0".
weblogic.application.ModuleException: java.lang.StackOverflowError
at weblogic.application.internal.ExtensibleModuleWrapper.start(ExtensibleModuleWrapper.java:140)
at weblogic.application.internal.flow.ModuleListenerInvoker.start(ModuleListenerInvoker.java:124)
at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:233)
at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:228)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
Truncated. see log file for complete stacktrace
Caused By: java.lang.StackOverflowError
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader$3.next(URLClassLoader.java:601)
at java.net.URLClassLoader$3.hasMoreElements(URLClassLoader.java:626)
at sun.misc.CompoundEnumeration.next(CompoundEnumeration.java:45)
at sun.misc.CompoundEnumeration.hasMoreElements(CompoundEnumeration.java:54)
Truncated. see log file for complete stacktrace
Below is my project structure
Same project is working fine with Weblogic 11G

I was able to resolve issue.
For people having similar issue.
Add weblogic.xml with following content in tag.
<container-descriptor>
<prefer-web-inf-classes>true</prefer-web-inf-classes>
</container-descriptor>
This step will remove stackoverflow error.
Later you might get some dependency error which can be resolved as required.

Apache Camel stax2 NoSuchMethodError

I'm getting very weird behavior from the Apache Camel application. I'm deploying the EAR on WebLogic 12.2.1.3 server on our test environment, and everything works fine. The EAR contains all the dependencies used by the application.
However, when I deploy the same EAR to production (it deploys fine), it gives the following runtime exception during message handling:
Exception occurred during execution on the exchange: Exchange[ID-napoli-34361-1518770862962-0-99], StackTrace: org.apache.camel.CamelExecutionException: Exception occurred during execution on the exchange: Exchange[ID-napoli-34361-1518770862962-0-99]
at org.apache.camel.util.ObjectHelper.wrapCamelExecutionException(ObjectHelper.java:1790)
at org.apache.camel.impl.DefaultExchange.setException(DefaultExchange.java:350)
at org.apache.camel.component.cxf.CxfProducer.process(CxfProducer.java:141)
at org.apache.camel.processor.SendProcessor.process(SendProcessor.java:145)
at org.apache.camel.management.InstrumentationProcessor.process(InstrumentationProcessor.java:77)
at org.apache.camel.processor.RedeliveryErrorHandler.process(RedeliveryErrorHandler.java:541)
at org.apache.camel.processor.CamelInternalProcessor.process(CamelInternalProcessor.java:198)
at org.apache.camel.processor.Pipeline.process(Pipeline.java:120)
at org.apache.camel.processor.Pipeline.process(Pipeline.java:83)
at org.apache.camel.processor.CamelInternalProcessor.process(CamelInternalProcessor.java:198)
at org.apache.camel.processor.DelegateAsyncProcessor.process(DelegateAsyncProcessor.java:97)
at org.apache.camel.component.cxf.CxfConsumer$CxfConsumerInvoker.syncInvoke(CxfConsumer.java:220)
at org.apache.camel.component.cxf.CxfConsumer$CxfConsumerInvoker.invoke(CxfConsumer.java:147)
at org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:59)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.cxf.interceptor.ServiceInvokerInterceptor$2.run(ServiceInvokerInterceptor.java:126)
at org.apache.cxf.workqueue.SynchronousExecutor.execute(SynchronousExecutor.java:37)
at org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:131)
at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:308)
at org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121)
at org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:267)
at org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:234)
at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:208)
at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:160)
at org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:191)
at org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:301)
at org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPost(AbstractHTTPServlet.java:220)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:276)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:286)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:260)
at weblogic.servlet.internal.StubSecurityHelper.invokeServlet(StubSecurityHelper.java:137)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:350)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:247)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.wrapRun(WebAppServletContext.java:3697)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.run(WebAppServletContext.java:3667)
at weblogic.security.acl.internal.AuthenticatedSubject.doAs(AuthenticatedSubject.java:326)
at weblogic.security.service.SecurityManager.runAsForUserCode(SecurityManager.java:197)
at weblogic.servlet.provider.WlsSecurityProvider.runAsForUserCode(WlsSecurityProvider.java:203)
at weblogic.servlet.provider.WlsSubjectHandle.run(WlsSubjectHandle.java:71)
at weblogic.servlet.internal.WebAppServletContext.doSecuredExecute(WebAppServletContext.java:2443)
at weblogic.servlet.internal.WebAppServletContext.securedExecute(WebAppServletContext.java:2291)
at weblogic.servlet.internal.WebAppServletContext.execute(WebAppServletContext.java:2269)
at weblogic.servlet.internal.ServletRequestImpl.runInternal(ServletRequestImpl.java:1703)
at weblogic.servlet.internal.ServletRequestImpl.run(ServletRequestImpl.java:1663)
at weblogic.servlet.provider.ContainerSupportProviderImpl$WlsRequestExecutor.run(ContainerSupportProviderImpl.java:272)
at weblogic.invocation.ComponentInvocationContextManager._runAs(ComponentInvocationContextManager.java:352)
at weblogic.invocation.ComponentInvocationContextManager.runAs(ComponentInvocationContextManager.java:337)
at weblogic.work.LivePartitionUtility.doRunWorkUnderContext(LivePartitionUtility.java:57)
at weblogic.work.PartitionUtility.runWorkUnderContext(PartitionUtility.java:41)
at weblogic.work.SelfTuningWorkManagerImpl.runWorkUnderContext(SelfTuningWorkManagerImpl.java:644)
at weblogic.work.ExecuteThread.execute(ExecuteThread.java:415)
at weblogic.work.ExecuteThread.run(ExecuteThread.java:355)
Caused by: java.lang.NoSuchMethodError: org.codehaus.stax2.ri.EmptyIterator.getInstance()Lorg/codehaus/stax2/ri/EmptyIterator;
at com.ctc.wstx.sw.OutputElementBase.getPrefixes(OutputElementBase.java:358)
at org.apache.cxf.staxutils.StaxUtils.writeStartElement(StaxUtils.java:811)
at org.apache.cxf.staxutils.StaxUtils.copy(StaxUtils.java:758)
at org.apache.cxf.staxutils.StaxUtils.copy(StaxUtils.java:722)
at org.apache.cxf.binding.soap.saaj.SAAJOutInterceptor$SAAJOutEndingInterceptor.handleMessage(SAAJOutInterceptor.java:214)
at org.apache.cxf.binding.soap.saaj.SAAJOutInterceptor$SAAJOutEndingInterceptor.handleMessage(SAAJOutInterceptor.java:174)
at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:308)
at org.apache.cxf.endpoint.ClientImpl.doInvoke(ClientImpl.java:516)
at org.apache.cxf.endpoint.ClientImpl.invoke(ClientImpl.java:418)
at org.apache.camel.component.cxf.CxfProducer.process(CxfProducer.java:133)
... 51 more
, Out: null: ]
The camel route success all the way to the cxf component, which tries to call external web service, failing for some reason and causing the exception.
It's the same package with same dependencies on both environments, and in the production environment weblogic I can not see any external libraries installed, which could conflict with the EAR package. So, how do I trace what is causing the problem?

This seems to be a compatibility issue between Stax and Woodstox.
See this issue and try to fix your dependencies:
https://github.com/FasterXML/woodstox/issues/10

The problem was weblogic providing the following library
oracle_common/modules/org.codehaus.woodstox.stax2-api.jar
The different version of same library was also packaged within the EAR. The problem was solved by setting prefer-application-packages in the deployment descriptor.
It is still unknown, why the application worked in our environment without the prefer-application-packages attribute. Shouldn't it have loaded the weblogic-one in our environment too? What causes the seemingly random behavior in this case?

Failure when processing annotations for application.The error is Conflict found while merging web fragment

I am having an application which works fine with version prior to
WebLogic-12.2.1.2 but once I upgrade to WebLogic 12.2.1.2 It throws the following exception.
<Error> <HTTP> <BEA-101371> <There was a failure when processing annotations for application. Ensure that the annotations are valid. The error is Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version>
<Aug 28, 2017, 3:49:13,275 PM IST> <Error> <Deployer> <BEA-149265> <Failure occurred in the execution of deployment request with ID "881239794681866" for task "3" on [partition-name: DOMAIN]. Error is: "weblogic.application.ModuleException: weblogic.servlet.internal.fragment.MergeException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version"
weblogic.application.ModuleException: weblogic.servlet.internal.fragment.MergeException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version
at weblogic.application.internal.ExtensibleModuleWrapper.prepare(ExtensibleModuleWrapper.java:114)
at weblogic.application.internal.flow.ModuleListenerInvoker.prepare(ModuleListenerInvoker.java:100)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:192)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:187)
at weblogic.application.utils.StateMachineDriver$ParallelChange.run(StateMachineDriver.java:83)
Truncated. see log file for complete stacktrace
Caused By: weblogic.servlet.internal.fragment.MergeException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version
at weblogic.servlet.internal.fragment.GeneralRuleMerger.handleChangeEvent(GeneralRuleMerger.java:58)
at weblogic.servlet.internal.fragment.AbstractMerger.merge(AbstractMerger.java:15)
at weblogic.servlet.internal.fragment.WebFragmentMergeDispatcher.merge(WebFragmentMergeDispatcher.java:61)
at weblogic.servlet.internal.fragment.WebFragmentManager.mergeFragment(WebFragmentManager.java:245)
at weblogic.servlet.internal.AnnotationProcessingManager.processAnnotations(AnnotationProcessingManager.java:122)
Truncated. see log file for complete stacktrace
>
<Aug 28, 2017, 3:49:13,296 PM IST> <Warning> <Deployer> <BEA-149004> <Failures were detected while initiating deploy task for application "***".>
<Aug 28, 2017, 3:49:13,296 PM IST> <Warning> <Deployer> <BEA-149078> <Stack trace for message 149004
weblogic.application.ModuleException: weblogic.servlet.internal.fragment.MergeException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version
at weblogic.application.internal.ExtensibleModuleWrapper.prepare(ExtensibleModuleWrapper.java:114)
at weblogic.application.internal.flow.ModuleListenerInvoker.prepare(ModuleListenerInvoker.java:100)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:192)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:187)
at weblogic.application.utils.StateMachineDriver$ParallelChange.run(StateMachineDriver.java:83)
Truncated. see log file for complete stacktrace
Caused By: weblogic.servlet.internal.fragment.MergeException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version
at weblogic.servlet.internal.fragment.GeneralRuleMerger.handleChangeEvent(GeneralRuleMerger.java:58)
at weblogic.servlet.internal.fragment.AbstractMerger.merge(AbstractMerger.java:15)
at weblogic.servlet.internal.fragment.WebFragmentMergeDispatcher.merge(WebFragmentMergeDispatcher.java:61)
at weblogic.servlet.internal.fragment.WebFragmentManager.mergeFragment(WebFragmentManager.java:245)
at weblogic.servlet.internal.AnnotationProcessingManager.processAnnotations(AnnotationProcessingManager.java:122)
Truncated. see log file for complete stacktrace
>
<Aug 28, 2017, 3:49:13,309 PM IST> <Error> <Console> <BEA-240003> <Administration Console encountered the following error: weblogic.application.ModuleException: weblogic.servlet.internal.fragment.MergeException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version
at weblogic.application.internal.ExtensibleModuleWrapper.prepare(ExtensibleModuleWrapper.java:114)
at weblogic.application.internal.flow.ModuleListenerInvoker.prepare(ModuleListenerInvoker.java:100)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:192)
at weblogic.application.internal.flow.ModuleStateDriver$1.next(ModuleStateDriver.java:187)
at weblogic.application.utils.StateMachineDriver$ParallelChange.run(StateMachineDriver.java:83)
at weblogic.application.utils.StateMachineDriver.nextStateInParallel(StateMachineDriver.java:144)
at weblogic.application.internal.flow.ModuleStateDriver.parallelPrepare(ModuleStateDriver.java:46)
at weblogic.application.internal.flow.DeploymentCallbackFlow.prepare(DeploymentCallbackFlow.java:75)
at weblogic.application.internal.flow.DeploymentCallbackFlow.prepare(DeploymentCallbackFlow.java:55)
at weblogic.application.internal.BaseDeployment$1.next(BaseDeployment.java:727)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
at weblogic.application.internal.BaseDeployment.prepare(BaseDeployment.java:239)
at weblogic.application.internal.SingleModuleDeployment.prepare(SingleModuleDeployment.java:52)
at weblogic.application.internal.DeploymentStateChecker.prepare(DeploymentStateChecker.java:158)
at weblogic.deploy.internal.targetserver.AppContainerInvoker.prepare(AppContainerInvoker.java:65)
at weblogic.deploy.internal.targetserver.operations.ActivateOperation.createAndPrepareContainer(ActivateOperation.java:229)
at weblogic.deploy.internal.targetserver.operations.ActivateOperation.doPrepare(ActivateOperation.java:103)
at weblogic.deploy.internal.targetserver.operations.AbstractOperation.prepare(AbstractOperation.java:241)
at weblogic.deploy.internal.targetserver.DeploymentManager.handleDeploymentPrepare(DeploymentManager.java:794)
at weblogic.deploy.internal.targetserver.DeploymentManager.prepareDeploymentList(DeploymentManager.java:1340)
at weblogic.deploy.internal.targetserver.DeploymentManager.handlePrepare(DeploymentManager.java:267)
at weblogic.deploy.internal.targetserver.DeploymentServiceDispatcher.prepare(DeploymentServiceDispatcher.java:177)
at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer.doPrepareCallback(DeploymentReceiverCallbackDeliverer.java:186)
at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer.access$000(DeploymentReceiverCallbackDeliverer.java:14)
at weblogic.deploy.service.internal.targetserver.DeploymentReceiverCallbackDeliverer$1.run(DeploymentReceiverCallbackDeliverer.java:47)
at weblogic.work.SelfTuningWorkManagerImpl$WorkAdapterImpl.run(SelfTuningWorkManagerImpl.java:666)
at weblogic.invocation.ComponentInvocationContextManager._runAs(ComponentInvocationContextManager.java:348)
at weblogic.invocation.ComponentInvocationContextManager.runAs(ComponentInvocationContextManager.java:333)
at weblogic.work.LivePartitionUtility.doRunWorkUnderContext(LivePartitionUtility.java:54)
at weblogic.work.PartitionUtility.runWorkUnderContext(PartitionUtility.java:41)
at weblogic.work.SelfTuningWorkManagerImpl.runWorkUnderContext(SelfTuningWorkManagerImpl.java:640)
at weblogic.work.ExecuteThread.execute(ExecuteThread.java:406)
at weblogic.work.ExecuteThread.run(ExecuteThread.java:346)
Caused by: weblogic.servlet.internal.fragment.MergeException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7740fbd5() : Version
at weblogic.servlet.internal.fragment.GeneralRuleMerger.handleChangeEvent(GeneralRuleMerger.java:58)
at weblogic.servlet.internal.fragment.AbstractMerger.merge(AbstractMerger.java:15)
at weblogic.servlet.internal.fragment.WebFragmentMergeDispatcher.merge(WebFragmentMergeDispatcher.java:61)
at weblogic.servlet.internal.fragment.WebFragmentManager.mergeFragment(WebFragmentManager.java:245)
at weblogic.servlet.internal.AnnotationProcessingManager.processAnnotations(AnnotationProcessingManager.java:122)
at weblogic.servlet.internal.AnnotationProcessingManager.processAnnotations(AnnotationProcessingManager.java:105)
at weblogic.servlet.internal.WebAppModule.processAnnotations(WebAppModule.java:1975)
at weblogic.servlet.internal.WebAppModule.processAnnotations(WebAppModule.java:1937)
at weblogic.servlet.internal.WebAppModule.prepare(WebAppModule.java:800)
at weblogic.application.internal.ExtensibleModuleWrapper$PrepareStateChange.next(ExtensibleModuleWrapper.java:295)
at weblogic.application.internal.ExtensibleModuleWrapper$PrepareStateChange.next(ExtensibleModuleWrapper.java:285)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
at weblogic.application.internal.ExtensibleModuleWrapper.prepare(ExtensibleModuleWrapper.java:109)
>
<Aug 28, 2017, 3:49:13,475 PM IST> <Warning> <Munger> <BEA-2156203> <A version attribute was not found in element "web-app" in the deployment descriptor /u01/***/***/webapps/***/WEB-INF/web.xml. A version attribute is required, but this version of the WebLogic Server will assume that the latest version is used. Future versions of WebLogic Server will reject descriptors that do not specify the Java EE version. To eliminate this warning, add an appropriate "version=" to element "web-app" in the deployment descriptor.>
<Aug 28, 2017, 3:49:13,617 PM IST> <Error> <J2EE> <BEA-160228> <AppMerge failed to merge your application. If you are running AppMerge on the command-line, merge again with the -verbose option for more details. See the error message(s) below.>
weblogic.utils.compiler.ToolFailureException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7b55af1f() : Version
at weblogic.servlet.tools.WARModule.processAnnotations(WARModule.java:504)
at weblogic.servlet.tools.WARModule.processAnnotations(WARModule.java:589)
at weblogic.servlet.tools.WARModule.merge(WARModule.java:537)
at weblogic.application.compiler.ToolsModuleWrapper.merge(ToolsModuleWrapper.java:96)
at weblogic.application.utils.CustomModuleManager.merge(CustomModuleManager.java:78)
at weblogic.application.compiler.flow.SingleModuleMergeFlow.proecessModule(SingleModuleMergeFlow.java:27)
at weblogic.application.compiler.flow.SingleModuleFlow.compile(SingleModuleFlow.java:64)
at weblogic.application.compiler.FlowDriver$FlowStateChange.next(FlowDriver.java:70)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
at weblogic.application.compiler.FlowDriver.nextState(FlowDriver.java:37)
at weblogic.application.compiler.BaseMerger.merge(BaseMerger.java:20)
at weblogic.application.compiler.flow.AppMergerFlow.mergeInput(AppMergerFlow.java:75)
at weblogic.application.compiler.flow.AppMergerFlow.compile(AppMergerFlow.java:40)
at weblogic.application.compiler.FlowDriver$FlowStateChange.next(FlowDriver.java:70)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
at weblogic.application.compiler.FlowDriver.nextState(FlowDriver.java:37)
at weblogic.application.compiler.AppMerge.runBody(AppMerge.java:146)
at weblogic.utils.compiler.Tool.run(Tool.java:159)
at weblogic.utils.compiler.Tool.run(Tool.java:116)
at weblogic.application.compiler.AppMerge.merge(AppMerge.java:158)
at weblogic.deploy.api.internal.utils.AppMerger.merge(AppMerger.java:94)
at weblogic.deploy.api.internal.utils.AppMerger.getMergedApp(AppMerger.java:58)
at weblogic.deploy.api.model.internal.WebLogicDeployableObjectFactoryImpl.createDeployableObject(WebLogicDeployableObjectFactoryImpl.java:186)
at weblogic.deploy.api.model.internal.WebLogicDeployableObjectFactoryImpl.createDeployableObject(WebLogicDeployableObjectFactoryImpl.java:167)
at weblogic.deploy.api.tools.SessionHelper.initialize(SessionHelper.java:847)
at weblogic.deploy.api.tools.SessionHelper.initializeConfiguration(SessionHelper.java:668)
at weblogic.deploy.api.tools.SessionHelper.initializeConfiguration(SessionHelper.java:656)
at weblogic.deploy.api.tools.SessionHelper.initializeConfiguration(SessionHelper.java:739)
at com.bea.console.utils.DeploymentConfigurationHelper$1.execute(DeploymentConfigurationHelper.java:860)
at com.bea.console.utils.DeploymentUtils.runDeploymentAction(DeploymentUtils.java:5646)
at com.bea.console.utils.DeploymentConfigurationHelper.initDeploymentConfiguration(DeploymentConfigurationHelper.java:848)
at com.bea.console.utils.DeploymentConfigurationHelper.completeInitialization(DeploymentConfigurationHelper.java:444)
at com.bea.console.utils.DeploymentConfigurationManager.getDeploymentConfiguration(DeploymentConfigurationManager.java:151)
at com.bea.console.utils.DeploymentConfigurationManager.getDeploymentConfiguration(DeploymentConfigurationManager.java:104)
at com.bea.console.utils.DeploymentConfigurationManager.getDeploymentConfiguration(DeploymentConfigurationManager.java:65)
at com.bea.console.utils.PersistenceUtils.getPersistenceUnitNames(PersistenceUtils.java:76)
at com.bea.console.utils.PersistenceUtils.hasPersistenceUnits(PersistenceUtils.java:52)
at com.bea.console.utils.AppDeploymentBackingFile.preRender(AppDeploymentBackingFile.java:131)
at com.bea.netuix.servlets.controls.Backable$Impl.preRender(Backable.java:191)
at com.bea.netuix.servlets.controls.AdministeredBackableControl.preRender(AdministeredBackableControl.java:104)
at com.bea.netuix.servlets.controls.window.Window.preRender(Window.java:445)
at com.bea.netuix.servlets.controls.page.Page.preRender(Page.java:239)
at com.bea.netuix.nf.ControlLifecycle$6.visit(ControlLifecycle.java:428)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:727)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walk(ControlTreeWalker.java:146)
at com.bea.netuix.nf.Lifecycle.processLifecycles(Lifecycle.java:399)
at com.bea.netuix.nf.Lifecycle.processLifecycles(Lifecycle.java:361)
at com.bea.netuix.nf.Lifecycle.runOutbound(Lifecycle.java:208)
at com.bea.netuix.nf.Lifecycle.run(Lifecycle.java:162)
at com.bea.netuix.servlets.manager.UIServlet.runLifecycle(UIServlet.java:465)
at com.bea.netuix.servlets.manager.UIServlet.doPost(UIServlet.java:291)
at com.bea.netuix.servlets.manager.UIServlet.doGet(UIServlet.java:231)
at com.bea.netuix.servlets.manager.UIServlet.service(UIServlet.java:216)
at com.bea.netuix.servlets.manager.SingleFileServlet.service(SingleFileServlet.java:275)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at com.bea.console.utils.MBeanUtilsInitSingleFileServlet.service(MBeanUtilsInitSingleFileServlet.java:64)
at weblogic.servlet.AsyncInitServlet.service(AsyncInitServlet.java:125)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:286)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:260)
at weblogic.servlet.internal.StubSecurityHelper.invokeServlet(StubSecurityHelper.java:137)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:350)
at weblogic.servlet.internal.TailFilter.doFilter(TailFilter.java:25)
at weblogic.servlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:78)
at com.bea.console.internal.ParamFilter.doFilter(ParamFilter.java:38)
at weblogic.servlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:78)
at weblogic.servlet.internal.RequestEventsFilter.doFilter(RequestEventsFilter.java:32)
at weblogic.servlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:78)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.wrapRun(WebAppServletContext.java:3683)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.run(WebAppServletContext.java:3649)
at weblogic.security.acl.internal.AuthenticatedSubject.doAs(AuthenticatedSubject.java:326)
at weblogic.security.service.SecurityManager.runAsForUserCode(SecurityManager.java:197)
at weblogic.servlet.provider.WlsSecurityProvider.runAsForUserCode(WlsSecurityProvider.java:203)
at weblogic.servlet.provider.WlsSubjectHandle.run(WlsSubjectHandle.java:71)
at weblogic.servlet.internal.WebAppServletContext.doSecuredExecute(WebAppServletContext.java:2433)
at weblogic.servlet.internal.WebAppServletContext.securedExecute(WebAppServletContext.java:2281)
at weblogic.servlet.internal.WebAppServletContext.execute(WebAppServletContext.java:2259)
at weblogic.servlet.internal.ServletRequestImpl.runInternal(ServletRequestImpl.java:1691)
at weblogic.servlet.internal.ServletRequestImpl.run(ServletRequestImpl.java:1651)
at weblogic.servlet.provider.ContainerSupportProviderImpl$WlsRequestExecutor.run(ContainerSupportProviderImpl.java:270)
at weblogic.invocation.ComponentInvocationContextManager._runAs(ComponentInvocationContextManager.java:348)
at weblogic.invocation.ComponentInvocationContextManager.runAs(ComponentInvocationContextManager.java:333)
at weblogic.work.LivePartitionUtility.doRunWorkUnderContext(LivePartitionUtility.java:54)
at weblogic.work.PartitionUtility.runWorkUnderContext(PartitionUtility.java:41)
at weblogic.work.SelfTuningWorkManagerImpl.runWorkUnderContext(SelfTuningWorkManagerImpl.java:640)
at weblogic.work.ExecuteThread.execute(ExecuteThread.java:406)
at weblogic.work.ExecuteThread.run(ExecuteThread.java:346)
<Aug 28, 2017, 3:49:13,621 PM IST> <Error> <Console> <BEA-240003> <Administration Console encountered the following error: java.io.IOException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7b55af1f() : Version
at weblogic.deploy.api.internal.utils.AppMerger.getMergedApp(AppMerger.java:65)
at weblogic.deploy.api.model.internal.WebLogicDeployableObjectFactoryImpl.createDeployableObject(WebLogicDeployableObjectFactoryImpl.java:186)
at weblogic.deploy.api.model.internal.WebLogicDeployableObjectFactoryImpl.createDeployableObject(WebLogicDeployableObjectFactoryImpl.java:167)
at weblogic.deploy.api.tools.SessionHelper.initialize(SessionHelper.java:847)
at weblogic.deploy.api.tools.SessionHelper.initializeConfiguration(SessionHelper.java:668)
at weblogic.deploy.api.tools.SessionHelper.initializeConfiguration(SessionHelper.java:656)
at weblogic.deploy.api.tools.SessionHelper.initializeConfiguration(SessionHelper.java:739)
at com.bea.console.utils.DeploymentConfigurationHelper$1.execute(DeploymentConfigurationHelper.java:860)
at com.bea.console.utils.DeploymentUtils.runDeploymentAction(DeploymentUtils.java:5646)
at com.bea.console.utils.DeploymentConfigurationHelper.initDeploymentConfiguration(DeploymentConfigurationHelper.java:848)
at com.bea.console.utils.DeploymentConfigurationHelper.completeInitialization(DeploymentConfigurationHelper.java:444)
at com.bea.console.utils.DeploymentConfigurationManager.getDeploymentConfiguration(DeploymentConfigurationManager.java:151)
at com.bea.console.utils.DeploymentConfigurationManager.getDeploymentConfiguration(DeploymentConfigurationManager.java:104)
at com.bea.console.utils.DeploymentConfigurationManager.getDeploymentConfiguration(DeploymentConfigurationManager.java:65)
at com.bea.console.utils.PersistenceUtils.getPersistenceUnitNames(PersistenceUtils.java:76)
at com.bea.console.utils.PersistenceUtils.hasPersistenceUnits(PersistenceUtils.java:52)
at com.bea.console.utils.AppDeploymentBackingFile.preRender(AppDeploymentBackingFile.java:131)
at com.bea.netuix.servlets.controls.Backable$Impl.preRender(Backable.java:191)
at com.bea.netuix.servlets.controls.AdministeredBackableControl.preRender(AdministeredBackableControl.java:104)
at com.bea.netuix.servlets.controls.window.Window.preRender(Window.java:445)
at com.bea.netuix.servlets.controls.page.Page.preRender(Page.java:239)
at com.bea.netuix.nf.ControlLifecycle$6.visit(ControlLifecycle.java:428)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:727)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walkRecursivePreRender(ControlTreeWalker.java:739)
at com.bea.netuix.nf.ControlTreeWalker.walk(ControlTreeWalker.java:146)
at com.bea.netuix.nf.Lifecycle.processLifecycles(Lifecycle.java:399)
at com.bea.netuix.nf.Lifecycle.processLifecycles(Lifecycle.java:361)
at com.bea.netuix.nf.Lifecycle.runOutbound(Lifecycle.java:208)
at com.bea.netuix.nf.Lifecycle.run(Lifecycle.java:162)
at com.bea.netuix.servlets.manager.UIServlet.runLifecycle(UIServlet.java:465)
at com.bea.netuix.servlets.manager.UIServlet.doPost(UIServlet.java:291)
at com.bea.netuix.servlets.manager.UIServlet.doGet(UIServlet.java:231)
at com.bea.netuix.servlets.manager.UIServlet.service(UIServlet.java:216)
at com.bea.netuix.servlets.manager.SingleFileServlet.service(SingleFileServlet.java:275)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at com.bea.console.utils.MBeanUtilsInitSingleFileServlet.service(MBeanUtilsInitSingleFileServlet.java:64)
at weblogic.servlet.AsyncInitServlet.service(AsyncInitServlet.java:125)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:286)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:260)
at weblogic.servlet.internal.StubSecurityHelper.invokeServlet(StubSecurityHelper.java:137)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:350)
at weblogic.servlet.internal.TailFilter.doFilter(TailFilter.java:25)
at weblogic.servlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:78)
at com.bea.console.internal.ParamFilter.doFilter(ParamFilter.java:38)
at weblogic.servlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:78)
at weblogic.servlet.internal.RequestEventsFilter.doFilter(RequestEventsFilter.java:32)
at weblogic.servlet.internal.FilterChainImpl.doFilter(FilterChainImpl.java:78)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.wrapRun(WebAppServletContext.java:3683)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.run(WebAppServletContext.java:3649)
at weblogic.security.acl.internal.AuthenticatedSubject.doAs(AuthenticatedSubject.java:326)
at weblogic.security.service.SecurityManager.runAsForUserCode(SecurityManager.java:197)
at weblogic.servlet.provider.WlsSecurityProvider.runAsForUserCode(WlsSecurityProvider.java:203)
at weblogic.servlet.provider.WlsSubjectHandle.run(WlsSubjectHandle.java:71)
at weblogic.servlet.internal.WebAppServletContext.doSecuredExecute(WebAppServletContext.java:2433)
at weblogic.servlet.internal.WebAppServletContext.securedExecute(WebAppServletContext.java:2281)
at weblogic.servlet.internal.WebAppServletContext.execute(WebAppServletContext.java:2259)
at weblogic.servlet.internal.ServletRequestImpl.runInternal(ServletRequestImpl.java:1691)
at weblogic.servlet.internal.ServletRequestImpl.run(ServletRequestImpl.java:1651)
at weblogic.servlet.provider.ContainerSupportProviderImpl$WlsRequestExecutor.run(ContainerSupportProviderImpl.java:270)
at weblogic.invocation.ComponentInvocationContextManager._runAs(ComponentInvocationContextManager.java:348)
at weblogic.invocation.ComponentInvocationContextManager.runAs(ComponentInvocationContextManager.java:333)
at weblogic.work.LivePartitionUtility.doRunWorkUnderContext(LivePartitionUtility.java:54)
at weblogic.work.PartitionUtility.runWorkUnderContext(PartitionUtility.java:41)
at weblogic.work.SelfTuningWorkManagerImpl.runWorkUnderContext(SelfTuningWorkManagerImpl.java:640)
at weblogic.work.ExecuteThread.execute(ExecuteThread.java:406)
at weblogic.work.ExecuteThread.run(ExecuteThread.java:346)
Caused by: weblogic.utils.compiler.ToolFailureException: Conflict found while merging web fragment, weblogic.j2ee.descriptor.WebFragmentBeanImpl#7b55af1f() : Version
at weblogic.servlet.tools.WARModule.processAnnotations(WARModule.java:504)
at weblogic.servlet.tools.WARModule.processAnnotations(WARModule.java:589)
at weblogic.servlet.tools.WARModule.merge(WARModule.java:537)
at weblogic.application.compiler.ToolsModuleWrapper.merge(ToolsModuleWrapper.java:96)
at weblogic.application.utils.CustomModuleManager.merge(CustomModuleManager.java:78)
at weblogic.application.compiler.flow.SingleModuleMergeFlow.proecessModule(SingleModuleMergeFlow.java:27)
at weblogic.application.compiler.flow.SingleModuleFlow.compile(SingleModuleFlow.java:64)
at weblogic.application.compiler.FlowDriver$FlowStateChange.next(FlowDriver.java:70)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
at weblogic.application.compiler.FlowDriver.nextState(FlowDriver.java:37)
at weblogic.application.compiler.BaseMerger.merge(BaseMerger.java:20)
at weblogic.application.compiler.flow.AppMergerFlow.mergeInput(AppMergerFlow.java:75)
at weblogic.application.compiler.flow.AppMergerFlow.compile(AppMergerFlow.java:40)
at weblogic.application.compiler.FlowDriver$FlowStateChange.next(FlowDriver.java:70)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
at weblogic.application.compiler.FlowDriver.nextState(FlowDriver.java:37)
at weblogic.application.compiler.AppMerge.runBody(AppMerge.java:146)
at weblogic.utils.compiler.Tool.run(Tool.java:159)
at weblogic.utils.compiler.Tool.run(Tool.java:116)
at weblogic.application.compiler.AppMerge.merge(AppMerge.java:158)
at weblogic.deploy.api.internal.utils.AppMerger.merge(AppMerger.java:94)
at weblogic.deploy.api.internal.utils.AppMerger.getMergedApp(AppMerger.java:58)
... 78 more
>
I actually include a project in my application which uses servlet-api 3.0(to use some functionality of Async servlet) and I am using servlet-api 2.4 in my application. Also the application doesn't have any web-fragment concept.
Can there be any conflicts because of this? Any help would be much appreciated.

Weblogic 12c onwards, the jars are scanned for presence of web fragments and then merged with the application's web.xml.If your application web.xml or other jars web-fragment.xml have diferent DTD version then this issue will come.Need to make all DTD version quals.

Unable to deploy CXF3.x JAX-RS service in Weblogic 12c (12.2.1)

After upgrading a JAX-RS service built with CXF3.x from weblogic 12.1.3 to 12.2.1 I am facing the following weird issue
<03-ago-2017, 3:22:38,789 PM CEST> <Error> <HTTP> <BEA-101216> <Servlet: "JAX-RS/Jersey#1" failed to preload on startup in Web application: "sife".
A MultiException has 1 exceptions. They are:
1. java.lang.LinkageError: ClassCastException: attempting to castzip:C:/Oracle/Middleware/Oracle_Home/user_projects/domains/base_domain/servers/AdminServer/tmp/_WL_user/sife/845176/war/WEB-INF/lib/javax.ws.rs-api-2.0.1.jar!/javax/ws/rs/ext/RuntimeDelegate.class to jar:file:/C:/Oracle/Middleware/Oracle_Home/oracle_common/modules/javax.ws.rs.javax.ws.rs-api.jar!/javax/ws/rs/ext/RuntimeDelegate.class
at org.jvnet.hk2.internal.Utilities.justCreate(Utilities.java:1007)
at org.jvnet.hk2.internal.ServiceLocatorImpl.create(ServiceLocatorImpl.java:962)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:1054)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:1046)
at org.glassfish.jersey.model.internal.CommonConfig.configureFeatures(CommonConfig.java:696)
Truncated. see log file for complete stacktrace
Note that I am using CXF, not Jersey, but seems Weblogic is trying to use it (it does not happen with 12.1.3). I disabled it in configuration files following this recommendations: https://jerometambo.github.io/blog/2016/12/13/How-to-use-CXF-3x-implementation-of-JAX-RS-20-REST-with-Weblogic-12c.html
With default configuration, Weblogic wants to use its internal implementation (JAX-RS 2.0 and serialization) to deploy the REST web services (Error 500):
META-INF/weblogic-application.xml
<weblogic-application xmlns:wls="http://xmlns.oracle.com/weblogic/weblogic-application"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://xmlns.oracle.com/weblogic/weblogic-application
http://xmlns.oracle.com/weblogic/weblogic-application/1.8/weblogic-application.xsd">
<prefer-application-packages>
<package-name>javax.ws.rs.*</package-name>
<package-name>com.fasterxml.jackson.*</package-name>
<package-name>weblogic.jaxrs.api.client.*</package-name>
<package-name>weblogic.jaxrs.internal.api.*</package-name>
<package-name>weblogic.jaxrs.dispatch.*</package-name>
<package-name>weblogic.jaxrs.monitoring.util.*</package-name>
</prefer-application-packages>
</weblogic-application>
WEB-INF/weblogic.xml
<weblogic-web-app
xmlns="http://xmlns.oracle.com/weblogic/weblogic-web-app"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd http://xmlns.oracle.com/weblogic/weblogic-web-app http://xmlns.oracle.com/weblogic/weblogic-web-app/1.0/weblogic-web-app.xsd">
<container-descriptor>
<prefer-application-packages>
<package-name>javax.ws.rs.*</package-name>
<package-name>com.fasterxml.jackson.*</package-name>
</prefer-application-packages>
</container-descriptor>
</weblogic-web-app>
I do not know if this is a specific problem of my project or it is a weblogic issue. I have found similar issues like this and this, and I tried to use them.
These are my dependencies (IVY syntax)
<dependency org="org.apache.cxf" name="cxf-rt-frontend-jaxrs" rev="3.1.10" conf="default" />
<dependency org="org.apache.cxf" name="cxf-rt-rs-extension-providers" rev="3.1.10" conf="default" />
<dependency org="org.apache.cxf" name="cxf-rt-transports-http" rev="3.1.10" conf="default" />
<dependency org="com.fasterxml.jackson.jaxrs" name="jackson-jaxrs-json-provider" rev="2.6.6" conf="default" />
And the full stack trace
<03-ago-2017, 3:32:03,645 PM CEST> <Warning> <JAXRSIntegration> <BEA-2192510> <Cannot add Jersey servlet for application class org.apache.cxf.jaxrs.servlet.CXFNonSpringJaxrsServlet$ApplicationImpl because ApplicationPath annotation is not set on it.>
<03-ago-2017, 3:32:03,737 PM CEST> <Warning> <JAXRSIntegration> <BEA-2192511> <The list of resource packages: com.fasterxml.jackson.jaxrs.base;org.apache.cxf.jaxrs.provider;com.fasterxml.jackson.jaxrs.json;org.apache.cxf.jaxrs.provider.aegis;es.aragon.sife.server.filter;org.apache.cxf.jaxrs.provider.jsrjsonp;es.aragon.sife.keystore.api;es.aragon.sife.server.account.api;org.apache.cxf.jaxrs.provider.xmlbeans;org.apache.cxf.jaxrs.validation;es.aragon.sife.server.task.api;org.apache.cxf.jaxrs.provider.json;org.apache.cxf.jaxrs.provider.atom;es.aragon.sife.server.config.api>
ago 03, 2017 3:32:16 PM es.gob.afirma.signers.xml.Utils installXmlDSigProvider
<03-ago-2017, 3:32:20,581 PM CEST> <Error> <HTTP> <BEA-101216> <Servlet: "JAX-RS/Jersey#1" failed to preload on startup in Web application: "sife".
A MultiException has 1 exceptions. They are:
1. java.lang.LinkageError: ClassCastException: attempting to castzip:C:/Oracle/Middleware/Oracle_Home/user_projects/domains/base_domain/servers/AdminServer/tmp/_WL_user/sife/845176/war/WEB-INF/lib/javax.ws.rs-api-2.0.1.jar!/javax/ws/rs/ext/RuntimeDelegate.class to jar:file:/C:/Oracle/Middleware/Oracle_Home/oracle_common/modules/javax.ws.rs.javax.ws.rs-api.jar!/javax/ws/rs/ext/RuntimeDelegate.class
at org.jvnet.hk2.internal.Utilities.justCreate(Utilities.java:1007)
at org.jvnet.hk2.internal.ServiceLocatorImpl.create(ServiceLocatorImpl.java:962)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:1054)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:1046)
at org.glassfish.jersey.model.internal.CommonConfig.configureFeatures(CommonConfig.java:696)
Truncated. see log file for complete stacktrace
Caused By: java.lang.LinkageError: ClassCastException: attempting to castzip:C:/Oracle/Middleware/Oracle_Home/user_projects/domains/base_domain/servers/AdminServer/tmp/_WL_user/sife/845176/war/WEB-INF/lib/javax.ws.rs-api-2.0.1.jar!/javax/ws/rs/ext/RuntimeDelegate.class to jar:file:/C:/Oracle/Middleware/Oracle_Home/oracle_common/modules/javax.ws.rs.javax.ws.rs-api.jar!/javax/ws/rs/ext/RuntimeDelegate.class
at javax.ws.rs.ext.RuntimeDelegate.findDelegate(RuntimeDelegate.java:146)
at javax.ws.rs.ext.RuntimeDelegate.getInstance(RuntimeDelegate.java:120)
at javax.ws.rs.core.MediaType.valueOf(MediaType.java:179)
at org.glassfish.jersey.media.sse.SseFeature.<clinit>(SseFeature.java:62)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
Truncated. see log file for complete stacktrace
>
<03-ago-2017, 3:32:20,696 PM CEST> <Error> <Deployer> <BEA-149231> <Unable to set the activation state to true for the application "sife".
weblogic.application.ModuleException: java.lang.LinkageError: ClassCastException: attempting to castzip:C:/Oracle/Middleware/Oracle_Home/user_projects/domains/base_domain/servers/AdminServer/tmp/_WL_user/sife/845176/war/WEB-INF/lib/javax.ws.rs-api-2.0.1.jar!/javax/ws/rs/ext/RuntimeDelegate.class to jar:file:/C:/Oracle/Middleware/Oracle_Home/oracle_common/modules/javax.ws.rs.javax.ws.rs-api.jar!/javax/ws/rs/ext/RuntimeDelegate.class
at weblogic.application.internal.ExtensibleModuleWrapper.start(ExtensibleModuleWrapper.java:140)
at weblogic.application.internal.flow.ModuleListenerInvoker.start(ModuleListenerInvoker.java:124)
at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:233)
at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:228)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
Truncated. see log file for complete stacktrace
Caused By: java.lang.LinkageError: ClassCastException: attempting to castzip:C:/Oracle/Middleware/Oracle_Home/user_projects/domains/base_domain/servers/AdminServer/tmp/_WL_user/sife/845176/war/WEB-INF/lib/javax.ws.rs-api-2.0.1.jar!/javax/ws/rs/ext/RuntimeDelegate.class to jar:file:/C:/Oracle/Middleware/Oracle_Home/oracle_common/modules/javax.ws.rs.javax.ws.rs-api.jar!/javax/ws/rs/ext/RuntimeDelegate.class
at javax.ws.rs.ext.RuntimeDelegate.findDelegate(RuntimeDelegate.java:146)
at javax.ws.rs.ext.RuntimeDelegate.getInstance(RuntimeDelegate.java:120)
at javax.ws.rs.core.MediaType.valueOf(MediaType.java:179)
at org.glassfish.jersey.media.sse.SseFeature.<clinit>(SseFeature.java:62)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
Truncated. see log file for complete stacktrace
>
<03-ago-2017, 3:32:20,762 PM CEST> <Notice> <Log Management> <BEA-170027> <The server has successfully established a connection with the Domain level Diagnostic Service.>
<03-ago-2017, 3:32:20,931 PM CEST> <Notice> <WebLogicServer> <BEA-000365> <Server state changed to ADMIN.>
<03-ago-2017, 3:32:21,46 PM CEST> <Notice> <WebLogicServer> <BEA-000365> <Server state changed to RESUMING.>
<03-ago-2017, 3:32:21,174 PM CEST> <Notice> <WebLogicServer> <BEA-000360> <The server started in RUNNING mode.>
<03-ago-2017, 3:32:21,186 PM CEST> <Notice> <WebLogicServer> <BEA-000365> <Server state changed to RUNNING.>
<03-ago-2017, 3:32:22,710 PM CEST> <Error> <HTTP> <BEA-101216> <Servlet: "weblogic.management.rest.Application" failed to preload on startup in Web application: "wls-management-services.war".
A MultiException has 1 exceptions. They are:
1. java.lang.NoClassDefFoundError: Could not initialize class org.glassfish.jersey.media.sse.SseFeature
at org.jvnet.hk2.internal.Utilities.justCreate(Utilities.java:1007)
at org.jvnet.hk2.internal.ServiceLocatorImpl.create(ServiceLocatorImpl.java:962)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:1054)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:1046)
at org.glassfish.jersey.model.internal.CommonConfig.configureFeatures(CommonConfig.java:696)
Truncated. see log file for complete stacktrace
Caused By: java.lang.NoClassDefFoundError: Could not initialize class org.glassfish.jersey.media.sse.SseFeature
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.glassfish.hk2.utilities.reflection.ReflectionHelper.makeMe(ReflectionHelper.java:1350)
Truncated. see log file for complete stacktrace
>
<03-ago-2017, 3:32:22,747 PM CEST> <Error> <J2EE> <BEA-160001> <Error deploying Internal Application: weblogic.application.ModuleException: java.lang.NoClassDefFoundError: Could not initialize class org.glassfish.jersey.media.sse.SseFeature
weblogic.application.utils.StateChangeException: weblogic.application.ModuleException: java.lang.NoClassDefFoundError: Could not initialize class org.glassfish.jersey.media.sse.SseFeature
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:58)
at weblogic.application.services.BackgroundDeploymentManagerService$BackgroundDeployAction.run(BackgroundDeploymentManagerService.java:396)
at weblogic.work.SelfTuningWorkManagerImpl$WorkAdapterImpl.run(SelfTuningWorkManagerImpl.java:666)
at weblogic.invocation.ComponentInvocationContextManager._runAs(ComponentInvocationContextManager.java:348)
at weblogic.invocation.ComponentInvocationContextManager.runAs(ComponentInvocationContextManager.java:333)
Truncated. see log file for complete stacktrace
Caused By: weblogic.application.ModuleException: java.lang.NoClassDefFoundError: Could not initialize class org.glassfish.jersey.media.sse.SseFeature
at weblogic.application.internal.ExtensibleModuleWrapper.start(ExtensibleModuleWrapper.java:140)
at weblogic.application.internal.flow.ModuleListenerInvoker.start(ModuleListenerInvoker.java:124)
at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:233)
at weblogic.application.internal.flow.ModuleStateDriver$3.next(ModuleStateDriver.java:228)
at weblogic.application.utils.StateMachineDriver.nextState(StateMachineDriver.java:45)
Truncated. see log file for complete stacktrace
Caused By: java.lang.NoClassDefFoundError: Could not initialize class org.glassfish.jersey.media.sse.SseFeature
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.glassfish.hk2.utilities.reflection.ReflectionHelper.makeMe(ReflectionHelper.java:1350)
Truncated. see log file for complete stacktrace
WORKAROUND
It works if I deploy previously other CXF module using the default JAX-RS implementation and removing WEB-INF/lib/javax.ws.rs-api-2.0.1.jar. Maybe weblogic does some kind of internal initialization.
myapp.ear
init.war (JAX-RS with CXF and removing javax.ws.rs-api-2.0.1.jar)
myapp.war (JAX-RS with CXF and weblogic configuration)

#pedrofb, this may not fully answer your question, however, I once had a similar issue with Tomcat. The symptoms are similar, the problem was not really due to the presense of different class present in different jars i.e. jar shadowing. It was due to classloader shadowing. In Tomcat, classloading is actually inverted, not the usual 'ask-your-parent-classloader-first' kind of model, if an application classloader can find a class (where it only loads from WEB-INF/lib or classes) then the classloader loads the class. Now, in your case, I think, since the JAX-RS jars are present in your WEB-INF/lib, it is getting loaded from there at web application level. However, when the same object is being passed to the container, it is trying to cast it to the same class but at container level loaded by a different classloader. Classes loaded by different classloaders are considered different; this would be the cause for ClassCastException.
This would also explain why there is no ClassCastException when you remove the JAX-RS jar from WEB-INF/lib. The workaround here are limited, either you remove the JAX-RS jar from your WEb-INF/lib as you have done. (This could be potentially problematic but you could experiment in non production server), replace the container JAX-RS jar with the one that you want.
As I said, this will probably not solve your problem completely but may point in a direction to where the problem is coming from. [As I noticed some years back, Weblogic uses tomcat as its web container core (not sure if it is still the same) with changed package names like com.bea.weblogic.org.apache.tomcat ...].
Hope this helps.

Eclipselink error 3002

I am doing a simple migration from Toplink 10g to native Eclipselink v2.6.4 by following the instructions here (particularly task 3 and 4). Everything compiles ok but when I try to run my app I get the error below.
I tried using the old mapping file (which is still compatible) as well as a new one generated from Eclipselink workbench by importing my old Toplink workbench project.
Note that I'm only doing a migration from Toplink to native Eclispelink. There is no JPA involved.
Any ideas on what`s wrong? It seems like it's trying to improperly using String instead of my actual class, but not sure.
Also, my app has never had a persistence.xml file. Do I need one now?
2017-02-20 14:55:52 ERROR - Presentation - Local Exception Stack:
Exception [EclipseLink-3002] (Eclipse Persistence Services - 2.6.4.v20160829-44060b6): org.eclipse.persistence.exceptions.ConversionException
Exception Description: The object [ca.ncams.wisor.refdata.AccessTandem], of class [class java.lang.String], from mapping [org.eclipse.persistence.oxm.mappings.XMLDirectMapping[javaClass-->class/text()]] with descriptor [XMLDescriptor(org.eclipse.persistence.descriptors.ClassDescriptor --> [DatabaseTable(class-mapping-descriptor)])], could not be converted to [class java.lang.Class].
Internal Exception: java.lang.ClassNotFoundException: ca.ncams.wisor.refdata.AccessTandem
at org.eclipse.persistence.exceptions.ConversionException.couldNotBeConvertedToClass(ConversionException.java:98)
at org.eclipse.persistence.internal.helper.ConversionManager.convertObjectToClass(ConversionManager.java:451)
at org.eclipse.persistence.internal.helper.ConversionManager.convertObject(ConversionManager.java:146)
at org.eclipse.persistence.internal.oxm.XMLConversionManager.convertObject(XMLConversionManager.java:197)
at org.eclipse.persistence.internal.databaseaccess.DatasourcePlatform.convertObject(DatasourcePlatform.java:179)
at org.eclipse.persistence.oxm.mappings.XMLDirectMapping.getAttributeValue(XMLDirectMapping.java:301)
at org.eclipse.persistence.oxm.mappings.XMLDirectMapping.valueFromRow(XMLDirectMapping.java:364)
at org.eclipse.persistence.mappings.DatabaseMapping.readFromRowIntoObject(DatabaseMapping.java:1539)
at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildAttributesIntoObject(ObjectBuilder.java:462)
at org.eclipse.persistence.internal.oxm.XMLObjectBuilder.buildAttributesIntoObject(XMLObjectBuilder.java:378)
at org.eclipse.persistence.internal.oxm.XMLObjectBuilder.buildObject(XMLObjectBuilder.java:291)
at org.eclipse.persistence.oxm.mappings.XMLCompositeCollectionMapping.buildCompositeObject(XMLCompositeCollectionMapping.java:380)
at org.eclipse.persistence.oxm.mappings.XMLCompositeCollectionMapping.buildObjectFromNestedRow(XMLCompositeCollectionMapping.java:587)
at org.eclipse.persistence.oxm.mappings.XMLCompositeCollectionMapping.valueFromRow(XMLCompositeCollectionMapping.java:511)
at org.eclipse.persistence.mappings.DatabaseMapping.readFromRowIntoObject(DatabaseMapping.java:1539)
at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildAttributesIntoObject(ObjectBuilder.java:462)
at org.eclipse.persistence.internal.oxm.XMLObjectBuilder.buildAttributesIntoObject(XMLObjectBuilder.java:378)
at org.eclipse.persistence.internal.oxm.XMLObjectBuilder.buildObject(XMLObjectBuilder.java:291)
at org.eclipse.persistence.internal.oxm.record.DOMUnmarshaller.xmlToObject(DOMUnmarshaller.java:469)
at org.eclipse.persistence.internal.oxm.record.DOMUnmarshaller.unmarshal(DOMUnmarshaller.java:267)
at org.eclipse.persistence.internal.oxm.record.DOMUnmarshaller.unmarshal(DOMUnmarshaller.java:246)
at org.eclipse.persistence.internal.oxm.XMLUnmarshaller.unmarshal(XMLUnmarshaller.java:530)
at org.eclipse.persistence.sessions.factories.XMLProjectReader.readObjectPersistenceRuntimeFormat(XMLProjectReader.java:293)
at org.eclipse.persistence.sessions.factories.XMLProjectReader.read(XMLProjectReader.java:186)
at org.eclipse.persistence.sessions.factories.XMLProjectReader.read(XMLProjectReader.java:242)
at org.eclipse.persistence.sessions.factories.XMLProjectReader.read(XMLProjectReader.java:100)
at ca.ncams.wisor.persistence.toplink.PersistenceManager.initializeTopLink(PersistenceManager.java:491)
at ca.ncams.wisor.persistence.toplink.PersistenceManager.<init>(PersistenceManager.java:83)
at ca.ncams.wisor.persistence.toplink.PersistenceManager.getInstance(PersistenceManager.java:96)
at ca.ncams.wisor.persistence.toplink.AutoRollbackFilter.doFilter(AutoRollbackFilter.java:57)
at ca.ncams.wisor.filter.FilterChainImpl.doFilter(FilterChainImpl.java:124)
at ca.ncams.wisor.presentation.filters.CatchAllFilter.doFilter(CatchAllFilter.java:60)
at ca.ncams.wisor.filter.FilterChainImpl.doFilter(FilterChainImpl.java:124)
at ca.ncams.wisor.presentation.filters.NoCacheFilter.doFilter(NoCacheFilter.java:47)
at ca.ncams.wisor.filter.FilterChainImpl.doFilter(FilterChainImpl.java:124)
at ca.ncams.wisor.filter.FilterJspBase.service(FilterJspBase.java:111)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:286)
at weblogic.servlet.internal.StubSecurityHelper$ServletServiceAction.run(StubSecurityHelper.java:260)
at weblogic.servlet.internal.StubSecurityHelper.invokeServlet(StubSecurityHelper.java:137)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:350)
at weblogic.servlet.internal.ServletStubImpl.onAddToMapException(ServletStubImpl.java:489)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:376)
at weblogic.servlet.internal.ServletStubImpl.execute(ServletStubImpl.java:247)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.wrapRun(WebAppServletContext.java:3679)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.__run(WebAppServletContext.java:3649)
at weblogic.servlet.internal.WebAppServletContext$ServletInvocationAction.run(WebAppServletContext.java)
at weblogic.security.acl.internal.AuthenticatedSubject.doAs(AuthenticatedSubject.java:326)
at weblogic.security.service.SecurityManager.runAsForUserCode(SecurityManager.java:197)
at weblogic.servlet.provider.WlsSecurityProvider.runAsForUserCode(WlsSecurityProvider.java:203)
at weblogic.servlet.provider.WlsSubjectHandle.run(WlsSubjectHandle.java:71)
at weblogic.servlet.internal.WebAppServletContext.doSecuredExecute(WebAppServletContext.java:2433)
at weblogic.servlet.internal.WebAppServletContext.securedExecute(WebAppServletContext.java:2281)
at weblogic.servlet.internal.WebAppServletContext.execute(WebAppServletContext.java:2259)
at weblogic.servlet.internal.ServletRequestImpl.runInternal(ServletRequestImpl.java:1691)
at weblogic.servlet.internal.ServletRequestImpl.run(ServletRequestImpl.java:1651)
at weblogic.servlet.provider.ContainerSupportProviderImpl$WlsRequestExecutor.run(ContainerSupportProviderImpl.java:270)
at weblogic.invocation.ComponentInvocationContextManager._runAs(ComponentInvocationContextManager.java:348)
at weblogic.invocation.ComponentInvocationContextManager.runAs(ComponentInvocationContextManager.java:333)
at weblogic.work.LivePartitionUtility.doRunWorkUnderContext(LivePartitionUtility.java:54)
at weblogic.work.PartitionUtility.runWorkUnderContext(PartitionUtility.java:41)
at weblogic.work.SelfTuningWorkManagerImpl.runWorkUnderContext(SelfTuningWorkManagerImpl.java:640)
at weblogic.work.ExecuteThread.execute(ExecuteThread.java:406)
at weblogic.work.ExecuteThread.run(ExecuteThread.java:346)
Caused by: java.lang.ClassNotFoundException: ca.ncams.wisor.refdata.AccessTandem
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.eclipse.persistence.internal.helper.ConversionManager.convertObjectToClass(ConversionManager.java:448)
... 61 more

Here's what I ended up doing:
Add Eclipselink 2.6.4 dependency to pom (compile instead of provided)
Add to weblogic.xml:
<wls:container-descriptor>
<wls:prefer-application-packages>
<wls:package-name>org.eclipse.persistence</wls:package-name>
</wls:prefer-application-packages>
</wls:container-descriptor>
Now Eclipselink finds my classes and boots up.
Note that my code was only passing in the mapping file and not a classloader to XMLProjectReader.read(); so I guess was using the default classloader.
If anyone knows of how to pass in a classloader I'd still be curious to know (where do I get it from?).