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

Jennifer Vendetti vendetti at stanford.edu
Thu Sep 24 14:36:24 PDT 2009 

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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