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

Natsuda Kasisopha gift8201 at gmail.com
Thu Sep 24 23:48:05 PDT 2009


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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