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[protege-discussion] Problems when using WebProtege: java.rmi.UnmarshalException: error unmarshalling return;

Zarko Acimovic zacimovi at cisco.com
Fri Jul 31 01:33:58 PDT 2009


Hi all,

 

I have a problem when I want to load Protégé projects through WebProtege.

I tried both Protégé 3.4 release + 0.5 alpha, build 102  and Protégé 3.4
beta, build 513 + 0.5 alpha, build 101

I use Apache Tomcat 5.5 on Ubuntu 9, and Tomcate uses Protégé’s Java

Below is the catalina.out for Protégé 3.4 release + 0.5 alpha, build 102  

 

Thanks,

Zarko

 

 

Jul 30, 2009 9:23:13 PM org.apache.catalina.core.AprLifecycleListener
lifecycleEvent

INFO: The Apache Tomcat Native library which allows optimal performance in
production environments was not found on the java.library.path:
/home/zareac/Protege_3.4.1/jre/lib/i386/client:/home/zareac/Protege_3.4.1/jr
e/lib/i386:/home/zareac/Protege_3.4.1/jre/../lib/i386

Jul 30, 2009 9:23:13 PM org.apache.coyote.http11.Http11BaseProtocol init

INFO: Initializing Coyote HTTP/1.1 on http-8080

Jul 30, 2009 9:23:13 PM org.apache.catalina.startup.Catalina load

INFO: Initialization processed in 927 ms

Jul 30, 2009 9:23:13 PM org.apache.catalina.core.StandardService start

INFO: Starting service Catalina

Jul 30, 2009 9:23:13 PM org.apache.catalina.core.StandardEngine start

INFO: Starting Servlet Engine: Apache Tomcat/5.5.27

Jul 30, 2009 9:23:13 PM org.apache.catalina.core.StandardHost start

INFO: XML validation disabled

Jul 30, 2009 9:23:14 PM org.apache.coyote.http11.Http11BaseProtocol start

INFO: Starting Coyote HTTP/1.1 on http-8080

Jul 30, 2009 9:23:15 PM org.apache.jk.common.ChannelSocket init

INFO: JK: ajp13 listening on /0.0.0.0:8009

Jul 30, 2009 9:23:15 PM org.apache.jk.server.JkMain start

INFO: Jk running ID=0 time=0/38  config=null

Jul 30, 2009 9:23:15 PM org.apache.catalina.storeconfig.StoreLoader load

INFO: Find registry server-registry.xml at classpath resource

Jul 30, 2009 9:23:15 PM org.apache.catalina.startup.Catalina start

INFO: Server startup in 2164 ms

Jul 30, 2009 9:23:24 PM
edu.stanford.bmir.protege.web.server.AdminServiceImpl init

INFO: In AdminServiceImpl -- init

Jul 30, 2009 9:23:24 PM edu.stanford.smi.protege.plugin.PluginUtilities
findPluginsDirectory

WARNING: Plugins directory not found:
/home/zareac/apache-tomcat-5.5.27/bin/plugins

Jul 30, 2009 9:23:26 PM edu.stanford.smi.protege.plugin.PluginUtilities
isLoadableClass

WARNING: java.lang.NoClassDefFoundError: com/nwoods/jgo/JGoViewListener

Jul 30, 2009 9:23:26 PM edu.stanford.smi.protege.resource.BundleHelper
<init>

WARNING: missing bundle: standard_extensions_text

Jul 30, 2009 9:23:26 PM edu.stanford.smi.protege.resource.BundleHelper
internalGetText

WARNING: no resource bundle: tab.queries

Jul 30, 2009 9:23:26 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getMetaprojectURI

INFO: Path to Metaproject:
/home/zareac/apache-tomcat-5.5.27/webapps/webprotege/projects/metaproject/me
taproject.pprj

Jul 30, 2009 9:23:28 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Collaborative Newspaper at:
examples/collaborativeNewspaper/collaborativeNewspaper.pprj

Jul 30, 2009 9:23:28 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Newspaper at:
examples/newspaper/newspaper.pprj

Jul 30, 2009 9:23:28 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Wines at: examples/wines/wines.pprj

Jul 30, 2009 9:23:28 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Pizza at:
examples/pizza/pizza.owl.pprj

Jul 30, 2009 9:23:28 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Collaborative Pizza at:
examples/collaborativePizza/collaborativePizza.owl.pprj

Jul 30, 2009 9:23:31 PM
edu.stanford.bmir.protege.web.server.OntologyServiceImpl init

INFO: In init of OntologyServiceImp

Jul 30, 2009 9:23:31 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getMetaprojectURI

INFO: Path to Metaproject:
/home/zareac/apache-tomcat-5.5.27/webapps/webprotege/projects/metaproject/me
taproject.pprj

Jul 30, 2009 9:23:31 PM edu.stanford.bmir.protege.web.server.ProjectManager
openProjectRemote

INFO: Loading project Collaborative Newspaper from Protege server localhost

Jul 30, 2009 9:23:33 PM edu.stanford.smi.protege.server.RemoteProjectManager
getProject

SEVERE: java.lang.RuntimeException: java.rmi.UnmarshalException: error
unmarshalling return; nested exception is: 

      java.io.InvalidClassException:
edu.stanford.smi.protege.server.update.ValueUpdate; local class
incompatible: stream classdesc serialVersionUID = -7753881900765528485,
local class serialVersionUID = -4059275656078639103

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.convertExc
eption(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.getFrame(U
nknown Source)

      at
edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrame(Un
known Source)

      at
edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.getFram
e(Unknown Source)

      at
edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrame(Un
known Source)

      at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrame(Unknown
Source)

      at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrame(Unknown
Source)

      at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrame(Unknown
Source)

      at
edu.stanford.smi.protege.model.DefaultKnowledgeBase.getFrame(Unknown Source)

      at
edu.stanford.smi.protege.model.DefaultKnowledgeBase.getFrameOfType(Unknown
Source)

      at edu.stanford.smi.protege.model.DefaultKnowledgeBase.getCls(Unknown
Source)

      at edu.stanford.smi.protege.model.Project.getProjectInstance(Unknown
Source)

      at edu.stanford.smi.protege.server.RemoteClientProject.copyKb(Unknown
Source)

      at edu.stanford.smi.protege.server.RemoteClientProject.<init>(Unknown
Source)

      at
edu.stanford.smi.protege.server.RemoteClientProject.createProject(Unknown
Source)

      at
edu.stanford.smi.protege.server.RemoteProjectManager.getProject(Unknown
Source)

      at
edu.stanford.bmir.protege.web.server.ProjectManager.openProjectRemote(Unknow
n Source)

      at
edu.stanford.bmir.protege.web.server.ProjectManager.ensureProjectOpen(Unknow
n Source)

      at
edu.stanford.bmir.protege.web.server.ProjectManager.getServerProject(Unknown
Source)

      at
edu.stanford.bmir.protege.web.server.OntologyServiceImpl.loadProject(Unknown
Source)

      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

      at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

      at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

      at java.lang.reflect.Method.invoke(Unknown Source)

      at
com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:527)

      at
com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServic
eServlet.java:164)

      at
com.google.gwt.user.server.rpc.RemoteServiceServlet.doPost(RemoteServiceServ
let.java:86)

      at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

      at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)

      at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application
FilterChain.java:269)

      at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh
ain.java:188)

      at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.ja
va:213)

      at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.ja
va:172)

      at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127
)

      at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117
)

      at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java
:108)

      at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)

      at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875)

      at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processC
onnection(Http11BaseProtocol.java:665)

      at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.jav
a:528)

      at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWo
rkerThread.java:81)

      at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.jav
a:689)

      at java.lang.Thread.run(Unknown Source)

Caused by: java.rmi.UnmarshalException: error unmarshalling return; nested
exception is: 

      java.io.InvalidClassException:
edu.stanford.smi.protege.server.update.ValueUpdate; local class
incompatible: stream classdesc serialVersionUID = -7753881900765528485,
local class serialVersionUID = -4059275656078639103

      at sun.rmi.server.UnicastRef.invoke(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.ServerFrameStore_Stub.getFrame(Un
known Source)

      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

      at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

      at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

      at java.lang.reflect.Method.invoke(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore$2.invoke(U
nknown Source)

      at $Proxy1.getFrame(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.getFrame(U
nknown Source)

      ... 41 more

Caused by: java.io.InvalidClassException:
edu.stanford.smi.protege.server.update.ValueUpdate; local class
incompatible: stream classdesc serialVersionUID = -7753881900765528485,
local class serialVersionUID = -4059275656078639103

      at java.io.ObjectStreamClass.initNonProxy(Unknown Source)

      at java.io.ObjectInputStream.readNonProxyDesc(Unknown Source)

      at java.io.ObjectInputStream.readClassDesc(Unknown Source)

      at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

      at java.io.ObjectInputStream.readObject0(Unknown Source)

      at java.io.ObjectInputStream.readObject(Unknown Source)

      at java.util.ArrayList.readObject(Unknown Source)

      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

      at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

      at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

      at java.lang.reflect.Method.invoke(Unknown Source)

      at java.io.ObjectStreamClass.invokeReadObject(Unknown Source)

      at java.io.ObjectInputStream.readSerialData(Unknown Source)

      at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

      at java.io.ObjectInputStream.readObject0(Unknown Source)

      at java.io.ObjectInputStream.defaultReadFields(Unknown Source)

      at java.io.ObjectInputStream.readSerialData(Unknown Source)

      at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

      at java.io.ObjectInputStream.readObject0(Unknown Source)

      at java.io.ObjectInputStream.readObject(Unknown Source)

      at sun.rmi.server.UnicastRef.unmarshalValue(Unknown Source)

      ... 50 more

 

Jul 30, 2009 9:29:26 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Collaborative Newspaper at:
examples/collaborativeNewspaper/collaborativeNewspaper.pprj

Jul 30, 2009 9:29:26 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Newspaper at:
examples/newspaper/newspaper.pprj

Jul 30, 2009 9:29:26 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Wines at: examples/wines/wines.pprj

Jul 30, 2009 9:29:26 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Pizza at:
examples/pizza/pizza.owl.pprj

Jul 30, 2009 9:29:26 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getLocalProjectsData

INFO: Found project def in metaproject: Collaborative Pizza at:
examples/collaborativePizza/collaborativePizza.owl.pprj

Jul 30, 2009 9:29:29 PM edu.stanford.bmir.protege.web.server.ProjectManager
openProjectRemote

INFO: Loading project Collaborative Pizza from Protege server localhost

Jul 30, 2009 9:29:30 PM
edu.stanford.smi.protegex.owl.repository.impl.LocalFolderRepository update

WARNING: [Local Folder Repository] The specified file must be a directory.
(/home/zareac/apache-tomcat-5.5.27/bin/plugins/edu.stanford.smi.protegex.owl
)

Jul 30, 2009 9:29:31 PM edu.stanford.smi.protege.server.RemoteProjectManager
getProject

SEVERE: java.lang.RuntimeException: java.rmi.UnmarshalException: error
unmarshalling return; nested exception is: 

      java.io.InvalidClassException:
edu.stanford.smi.protege.server.update.ValueUpdate; local class
incompatible: stream classdesc serialVersionUID = -7753881900765528485,
local class serialVersionUID = -4059275656078639103

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.convertExc
eption(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.getFrame(U
nknown Source)

      at
edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrame(Un
known Source)

      at
edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.getFram
e(Unknown Source)

      at
edu.stanford.smi.protege.model.framestore.ModificationFrameStore.getFrame(Un
known Source)

      at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrame(Unknown
Source)

      at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrame(Unknown
Source)

      at
edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.getFrame(Unknown
Source)

      at
edu.stanford.smi.protege.model.DefaultKnowledgeBase.getFrame(Unknown Source)

      at
edu.stanford.smi.protege.model.DefaultKnowledgeBase.getFrameOfType(Unknown
Source)

      at edu.stanford.smi.protege.model.DefaultKnowledgeBase.getCls(Unknown
Source)

      at edu.stanford.smi.protege.model.Project.getProjectInstance(Unknown
Source)

      at edu.stanford.smi.protege.server.RemoteClientProject.copyKb(Unknown
Source)

      at edu.stanford.smi.protege.server.RemoteClientProject.<init>(Unknown
Source)

      at
edu.stanford.smi.protege.server.RemoteClientProject.createProject(Unknown
Source)

      at
edu.stanford.smi.protege.server.RemoteProjectManager.getProject(Unknown
Source)

      at
edu.stanford.bmir.protege.web.server.ProjectManager.openProjectRemote(Unknow
n Source)

      at
edu.stanford.bmir.protege.web.server.ProjectManager.ensureProjectOpen(Unknow
n Source)

      at
edu.stanford.bmir.protege.web.server.ProjectManager.getServerProject(Unknown
Source)

      at
edu.stanford.bmir.protege.web.server.OntologyServiceImpl.loadProject(Unknown
Source)

      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

      at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

      at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

      at java.lang.reflect.Method.invoke(Unknown Source)

      at
com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:527)

      at
com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServic
eServlet.java:164)

      at
com.google.gwt.user.server.rpc.RemoteServiceServlet.doPost(RemoteServiceServ
let.java:86)

      at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

      at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)

      at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application
FilterChain.java:269)

      at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh
ain.java:188)

      at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.ja
va:213)

      at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.ja
va:172)

      at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127
)

      at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117
)

      at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java
:108)

      at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)

      at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875)

      at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processC
onnection(Http11BaseProtocol.java:665)

      at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.jav
a:528)

      at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWo
rkerThread.java:81)

      at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.jav
a:689)

      at java.lang.Thread.run(Unknown Source)

Caused by: java.rmi.UnmarshalException: error unmarshalling return; nested
exception is: 

      java.io.InvalidClassException:
edu.stanford.smi.protege.server.update.ValueUpdate; local class
incompatible: stream classdesc serialVersionUID = -7753881900765528485,
local class serialVersionUID = -4059275656078639103

      at sun.rmi.server.UnicastRef.invoke(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.ServerFrameStore_Stub.getFrame(Un
known Source)

      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

      at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

      at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

      at java.lang.reflect.Method.invoke(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore$2.invoke(U
nknown Source)

      at $Proxy1.getFrame(Unknown Source)

      at
edu.stanford.smi.protege.server.framestore.RemoteClientFrameStore.getFrame(U
nknown Source)

      ... 41 more

Caused by: java.io.InvalidClassException:
edu.stanford.smi.protege.server.update.ValueUpdate; local class
incompatible: stream classdesc serialVersionUID = -7753881900765528485,
local class serialVersionUID = -4059275656078639103

      at java.io.ObjectStreamClass.initNonProxy(Unknown Source)

      at java.io.ObjectInputStream.readNonProxyDesc(Unknown Source)

      at java.io.ObjectInputStream.readClassDesc(Unknown Source)

      at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

      at java.io.ObjectInputStream.readObject0(Unknown Source)

      at java.io.ObjectInputStream.readObject(Unknown Source)

      at java.util.ArrayList.readObject(Unknown Source)

      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

      at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)

      at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)

      at java.lang.reflect.Method.invoke(Unknown Source)

      at java.io.ObjectStreamClass.invokeReadObject(Unknown Source)

      at java.io.ObjectInputStream.readSerialData(Unknown Source)

      at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

      at java.io.ObjectInputStream.readObject0(Unknown Source)

      at java.io.ObjectInputStream.defaultReadFields(Unknown Source)

      at java.io.ObjectInputStream.readSerialData(Unknown Source)

      at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

      at java.io.ObjectInputStream.readObject0(Unknown Source)

      at java.io.ObjectInputStream.readObject(Unknown Source)

      at sun.rmi.server.UnicastRef.unmarshalValue(Unknown Source)

      ... 50 more

 

 

 

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