Eclipse - Tomcat 7 - java.lang.IndexOutOfBoundsException on publish

eclipse maven tomcat7
4_y picture 4_y · Nov 22, 2013 · Viewed 46k times · Source

I have a Webproject using maven and when I try to deploy it to Tomcat 7, I get the following message:

Publishing failed
Could not publish to the server.
java.lang.IndexOutOfBoundsException
Could not publish server configuration: myworkspace\.metadata\.plugins\org.eclipse.wst.server.core\tmp0\conf\server.xml (The system cannot find the path specified.). 
myworkspace\.metadata\.plugins\org.eclipse.wst.server.core\tmp0\conf\server.xml (The system cannot find the path specified.)

When I look at the log file of tomcat in 'myworkpace.metadata.logs' I see the following:

!ENTRY org.eclipse.wst.server.core 4 0 2013-11-22 13:36:40.128
!MESSAGE Publishing failed
!SUBENTRY 1 org.eclipse.wst.server.core 4 0 2013-11-22 13:36:40.128
!MESSAGE Could not publish to the server.
!STACK 0
java.lang.IndexOutOfBoundsException
    at java.io.BufferedInputStream.read(BufferedInputStream.java:338)
    at org.eclipse.jdt.internal.compiler.util.Util.getInputStreamAsByteArray(Util.java:498)
    at org.eclipse.jdt.core.ToolFactory.createDefaultClassFileReader(ToolFactory.java:269)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.isEJBArchive(JavaEEArchiveUtilities.java:900)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.refineForJavaEE(JavaEEArchiveUtilities.java:606)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.openArchive(JavaEEArchiveUtilities.java:370)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.openBinaryArchive(JavaEEArchiveUtilities.java:290)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper$ArchiveCache.openArchive(JavaEEBinaryComponentHelper.java:612)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.openArchive(JavaEEBinaryComponentHelper.java:470)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.getUniqueArchive(JavaEEBinaryComponentHelper.java:422)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.getArchive(JavaEEBinaryComponentHelper.java:415)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.getJavaEEQuickPeek(JavaEEBinaryComponentHelper.java:98)
    at org.eclipse.jst.j2ee.project.JavaEEProjectUtilities.getJ2EEComponentType(JavaEEProjectUtilities.java:273)
    at org.eclipse.jst.j2ee.internal.common.exportmodel.JEEHeirarchyExportParticipant.isChildModule(JEEHeirarchyExportParticipant.java:42)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.isChildModule(FlatVirtualComponent.java:367)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.addUsedReferences(FlatVirtualComponent.java:305)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.treeWalk(FlatVirtualComponent.java:235)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.cacheResources(FlatVirtualComponent.java:188)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.fetchResources(FlatVirtualComponent.java:118)
    at org.eclipse.wst.web.internal.deployables.FlatComponentDeployable.members(FlatComponentDeployable.java:227)
    at org.eclipse.jst.j2ee.internal.deployables.J2EEFlexProjDeployable.members(J2EEFlexProjDeployable.java:267)
    at org.eclipse.wst.server.core.internal.ModulePublishInfo.getDelta(ModulePublishInfo.java:407)
    at org.eclipse.wst.server.core.internal.ServerPublishInfo.getDelta(ServerPublishInfo.java:366)
    at org.eclipse.wst.server.core.internal.Server.getPublishedResourceDelta(Server.java:1574)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.getPublishedResourceDelta(ServerBehaviourDelegate.java:698)
    at org.eclipse.jst.server.tomcat.core.internal.TomcatServerBehaviour.getPublishedResourceDelta(TomcatServerBehaviour.java:958)
    at org.eclipse.jst.server.tomcat.core.internal.PublishOperation2.publishDir(PublishOperation2.java:137)
    at org.eclipse.jst.server.tomcat.core.internal.PublishOperation2.execute(PublishOperation2.java:82)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.performTasks(ServerBehaviourDelegate.java:1335)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:954)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:774)
    at org.eclipse.wst.server.core.internal.Server.publishImpl(Server.java:3153)
    at org.eclipse.wst.server.core.internal.Server$PublishJob.run(Server.java:345)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53)
!SUBENTRY 1 org.eclipse.jst.server.tomcat.core 4 0 2013-11-22 13:36:40.128
!MESSAGE Could not publish server configuration: C:\IBM\workspace\.metadata\.plugins\org.eclipse.wst.server.core\tmp0\conf\server.xml (The system cannot find the path specified.).
!STACK 0
java.io.FileNotFoundException: myworkspace\.metadata\.plugins\org.eclipse.wst.server.core\tmp0\conf\server.xml (The system cannot find the path specified.)
    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(FileInputStream.java:149)
    at org.eclipse.jst.server.tomcat.core.internal.TomcatVersionHelper.publishCatalinaContextConfig(TomcatVersionHelper.java:499)
    at org.eclipse.jst.server.tomcat.core.internal.Tomcat70Configuration.publishContextConfig(Tomcat70Configuration.java:674)
    at org.eclipse.jst.server.tomcat.core.internal.TomcatServerBehaviour.publishFinish(TomcatServerBehaviour.java:462)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:1011)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:774)
    at org.eclipse.wst.server.core.internal.Server.publishImpl(Server.java:3153)
    at org.eclipse.wst.server.core.internal.Server$PublishJob.run(Server.java:345)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53)

If I try to publish again, I only get the first error:

Could not publish to the server.
java.lang.IndexOutOfBoundsException

and in the logs:

!ENTRY org.eclipse.wst.server.core 4 0 2013-11-22 13:41:18.645
!MESSAGE Could not publish to the server.
!STACK 0
java.lang.IndexOutOfBoundsException
    at java.io.BufferedInputStream.read(BufferedInputStream.java:338)
    at org.eclipse.jdt.internal.compiler.util.Util.getInputStreamAsByteArray(Util.java:498)
    at org.eclipse.jdt.core.ToolFactory.createDefaultClassFileReader(ToolFactory.java:269)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.isEJBArchive(JavaEEArchiveUtilities.java:900)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.refineForJavaEE(JavaEEArchiveUtilities.java:606)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.openArchive(JavaEEArchiveUtilities.java:370)
    at org.eclipse.jst.j2ee.internal.archive.JavaEEArchiveUtilities.openBinaryArchive(JavaEEArchiveUtilities.java:290)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper$ArchiveCache.openArchive(JavaEEBinaryComponentHelper.java:612)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.openArchive(JavaEEBinaryComponentHelper.java:470)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.getUniqueArchive(JavaEEBinaryComponentHelper.java:422)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.getArchive(JavaEEBinaryComponentHelper.java:415)
    at org.eclipse.jst.j2ee.internal.componentcore.JavaEEBinaryComponentHelper.getJavaEEQuickPeek(JavaEEBinaryComponentHelper.java:98)
    at org.eclipse.jst.j2ee.project.JavaEEProjectUtilities.getJ2EEComponentType(JavaEEProjectUtilities.java:273)
    at org.eclipse.jst.j2ee.internal.common.exportmodel.JEEHeirarchyExportParticipant.isChildModule(JEEHeirarchyExportParticipant.java:42)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.isChildModule(FlatVirtualComponent.java:367)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.addUsedReferences(FlatVirtualComponent.java:305)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.treeWalk(FlatVirtualComponent.java:235)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.cacheResources(FlatVirtualComponent.java:188)
    at org.eclipse.wst.common.componentcore.internal.flat.FlatVirtualComponent.fetchResources(FlatVirtualComponent.java:118)
    at org.eclipse.wst.web.internal.deployables.FlatComponentDeployable.members(FlatComponentDeployable.java:227)
    at org.eclipse.jst.j2ee.internal.deployables.J2EEFlexProjDeployable.members(J2EEFlexProjDeployable.java:267)
    at org.eclipse.wst.server.core.internal.ModulePublishInfo.fillCache(ModulePublishInfo.java:314)
    at org.eclipse.wst.server.core.internal.ModulePublishInfo.getDelta(ModulePublishInfo.java:396)
    at org.eclipse.wst.server.core.internal.ServerPublishInfo.getDelta(ServerPublishInfo.java:366)
    at org.eclipse.wst.server.core.internal.Server.getPublishedResourceDelta(Server.java:1574)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.getPublishedResourceDelta(ServerBehaviourDelegate.java:698)
    at org.eclipse.jst.server.tomcat.core.internal.TomcatServerBehaviour.getPublishedResourceDelta(TomcatServerBehaviour.java:958)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.computeDelta(ServerBehaviourDelegate.java:874)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:909)
    at org.eclipse.wst.server.core.model.ServerBehaviourDelegate.publish(ServerBehaviourDelegate.java:774)
    at org.eclipse.wst.server.core.internal.Server.publishImpl(Server.java:3153)
    at org.eclipse.wst.server.core.internal.Server$PublishJob.run(Server.java:345)
    at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53)

I tried starting from a clean installation (clean eclipse, clean tomcat and clean workspace), imported the code from CVS, but still the same problem

Anyone got any ideas as to what may be incorrect (or how I could locate the problem)?

EDIT

When I build the project into a WAR-file on another computer and deploy this war file directly to tomcat via the management console, it works.

My guess is that the build must be different somehow...

EDIT2

I removed the complete maven repository. Afer this, I was able to build the project correctly and run it on Tomcat using the exported war-file.

However, I still get the IndexOutOfBoundsException when I try to publish directly from eclipse

EDIT3

After removing the Maven repository a few times, I was able to build and run the project. It seems Maven sometimes gets corrupted.

If others should have this problem, delete the complete Maven directory and run a maven update on each of the projects in the workspace.

Answer

4_y picture 4_y · Dec 3, 2013

The maven repository can be corrupt. It is best to remove the complete repository and update all projects in the workspace.

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