[protege-discussion] Server problem and Ontology list won't display

[Natsuda Kasisopha]

Hi Every body,

I had upload the Web Protege up on the server, the web page are 
displaying but the ontology list (example ontologies) are not 
displaying. Also I check the server log, there were errors (as email 
below). How can I fix these problem?

I actually tried to run the Web Protege on my laptop with Tomcat 6. It 
run with Ontology list and no problem at all, except it's the local host 
which other people can't access it.

P.S. I'm not the server administrator, so I don't know much of the 
server stuff but I'll try have the hang of it though.

Cheers,
Nat

------------------------------------------------------------------------

Subject:
From:
Christopher Jones <thejonesyboy at gmail.com>
Date:
Tue, 22 Sep 2009 16:45:58 +0800

To:
Natsuda Kasisopha <gift8201 at gmail.com>


22-Sep-2009 16:16:46 
edu.stanford.bmir.protege.web.server.AdminServiceImpl init
INFO: WebProtege running in: /usr/local/tomcat5/webapps/natsuda/
22-Sep-2009 16:16:46 edu.stanford.smi.protege.plugin.PluginUtilities 
findPluginsDirectory
WARNING: Plugins directory not found: 
/usr/local/tomcat5/webapps/natsuda/plugins
22-Sep-2009 16:16:47 edu.stanford.smi.protege.resource.BundleHelper <init>
WARNING: missing bundle: standard_extensions_text
22-Sep-2009 16:16:47 edu.stanford.smi.protege.resource.BundleHelper 
internalGetText
WARNING: no resource bundle: tab.queries
22-Sep-2009 16:16:47 edu.stanford.smi.protege.plugin.PluginUtilities 
isLoadableClass
WARNING: java.lang.NoClassDefFoundError: com/nwoods/jgo/JGoView
22-Sep-2009 16:16:47 
edu.stanford.bmir.protege.web.server.ApplicationProperties 
getLocalMetaprojectURI
INFO: Path to local metaproject: 
/usr/local/tomcat5/webapps/natsuda/projects/metaproject/metaproject.pprj
22-Sep-2009 16:16:48 edu.stanford.bmir.protege.web.server.ProjectManager 
<init>
INFO: WebProtege server running with local projects
ERROR [http-8080-Processor19] (ApplicationContext.java:676) - 
AdminServiceImpl: ERROR: The module path requested, /webprotege/, is not 
in the same web application as this servlet, /natsuda.  Your module may 
not be properly configured or your client and server code maybe out of date.
ERROR [http-8080-Processor19] (ApplicationContext.java:676) - 
AdminServiceImpl: WARNING: Failed to get the SerializationPolicy 
'896FFE7CA6A53292BD812834C3B4032E' for module 
'http://natsuda.tomcat.debii.curtin.edu.au/webprotege/'; a legacy, 1.3.3 
compatible, serialization policy will be used.  You may experience 
SerializationExceptions as a result.
22-Sep-2009 16:16:48 
edu.stanford.bmir.protege.web.server.LocalMetaProjectManager getProjectsData
INFO: Found project def in metaproject: Newspaper at: 
projects/newspaper/newspaper.pprj
22-Sep-2009 16:16:48 
edu.stanford.bmir.protege.web.server.LocalMetaProjectManager getProjectsData
INFO: Found project def in metaproject: Collaborative Pizza at: 
projects/collaborativePizza/collaborativePizza.owl.pprj
22-Sep-2009 16:16:48 
edu.stanford.bmir.protege.web.server.LocalMetaProjectManager getProjectsData
INFO: Found project def in metaproject: specificOnto at: 
projects/specificOnto/specificOnto.owl.pprj
22-Sep-2009 16:16:48 
edu.stanford.bmir.protege.web.server.LocalMetaProjectManager getProjectsData
INFO: Found project def in metaproject: Collaborative Newspaper at: 
projects/collaborativeNewspaper/collaborativeNewspaper.pprj
22-Sep-2009 16:16:48 
edu.stanford.bmir.protege.web.server.LocalMetaProjectManager getProjectsData
INFO: Found project def in metaproject: Wines at: projects/wines/wines.pprj
22-Sep-2009 16:16:48 
edu.stanford.bmir.protege.web.server.LocalMetaProjectManager getProjectsData
INFO: Found project def in metaproject: genericOnto at: 
projects/genericOnto/genericOnto.owl.pprj
22-Sep-2009 16:16:48 
edu.stanford.bmir.protege.web.server.LocalMetaProjectManager getProjectsData
INFO: Found project def in metaproject: Pizza at: 
projects/pizza/pizza.owl.pprj
ERROR [http-8080-Processor19] (ApplicationContext.java:676) - Exception 
while dispatching incoming RPC call
com.google.gwt.user.client.rpc.SerializationException: 
java.lang.reflect.InvocationTargetException
    at 
com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeWithCustomSerializer(ServerSerializationStreamWriter.java:696)
    at 
com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeImpl(ServerSerializationStreamWriter.java:659)
    at 
com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serialize(ServerSerializationStreamWriter.java:593)
    at 
com.google.gwt.user.client.rpc.impl.AbstractSerializationStreamWriter.writeObject(AbstractSerializationStreamWriter.java:129)
    at 
com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter$ValueWriter$8.write(ServerSerializationStreamWriter.java:146)
    at 
com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeValue(ServerSerializationStreamWriter.java:530)
    at com.google.gwt.user.server.rpc.RPC.encodeResponse(RPC.java:573)
    at 
com.google.gwt.user.server.rpc.RPC.encodeResponseForSuccess(RPC.java:441)
    at 
com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:529)
    at 
com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:166)
    at 
com.google.gwt.user.server.rpc.RemoteServiceServlet.doPost(RemoteServiceServlet.java:86)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
    at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
    at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
    at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
    at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
    at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
    at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
    at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
    at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:874)
    at 
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
    at 
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
    at 
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
    at 
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
    at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at 
com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeWithCustomSerializer(ServerSerializationStreamWriter.java:678)
    ... 26 more
Caused by: com.google.gwt.user.client.rpc.SerializationException: Type 
'edu.stanford.bmir.protege.web.client.rpc.data.ProjectData' was not 
assignable to 'com.google.gwt.user.client.rpc.IsSerializable' and did 
not have a custom field serializer.  For security purposes, this type 
will not be serialized.
    at 
com.google.gwt.user.server.rpc.impl.LegacySerializationPolicy.validateSerialize(LegacySerializationPolicy.java:140)
    at 
com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serialize(ServerSerializationStreamWriter.java:591)
    at 
com.google.gwt.user.client.rpc.impl.AbstractSerializationStreamWriter.writeObject(AbstractSerializationStreamWriter.java:129)
    at 
com.google.gwt.user.client.rpc.core.java.util.Collection_CustomFieldSerializerBase.serialize(Collection_CustomFieldSerializerBase.java:43)
    at 
com.google.gwt.user.client.rpc.core.java.util.ArrayList_CustomFieldSerializer.serialize(ArrayList_CustomFieldSerializer.java:36)