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

Firedrop 84 firedrop84 at hotmail.com
Fri Sep 25 08:10:48 PDT 2009


hi nat, 

 

please let me know when you are free. I might be able to come to your office and try to fix it. 

 

I never crossed through this error but we might play around and be able to fix it. Thanks.

 

I am sure someone from this mailing list will be advise you better than me as I am not WebProtege exppert.

 

Best Regards, 

Ahmed

 


 


Date: Fri, 25 Sep 2009 14:48:05 +0800
From: gift8201 at gmail.com
To: protege-discussion at lists.stanford.edu
Subject: Re: [protege-discussion] Server problem and Ontology list won't display

Thanks for helping.

I tried change the folder name but it still didn't work. The full path of directory is "/srv/www/webapps/webprotege".

and there is no Error on the server now. Please find the attachment file for the server log. 

Regards,
Nat


2009/9/25 Jennifer Vendetti <vendetti at stanford.edu>

Hello Nat,

In your log file, there is an error that indicates that WebProtege was not deployed correctly:


"The module path requested, /webprotege/, is not in the same web application as this servlet, /natsuda."

When you drop the WebProtege WAR file into your Servlet Container, it should unpack to a path that looks like this (I'm using Tomcat as an example here):

<your-tomcat-installation-directory>/webapps/webprotege/

Instead, it seems you've somehow deployed to:

<your-tomcat-installation-directory>/webapps/natsuda/

This will break WebProtege because the location of the servlets no longer matches the content of the url-pattern elements in the WEB-INF/web.xml file.

I suggest that you re-deploy WebProtege and when it unpacks into your Servlet Container, do not change the webprotege directory to another name.

Jennifer


Natsuda Kasisopha wrote:




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) 



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