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

Natsuda Kasisopha gift8201 at gmail.com
Mon Sep 28 20:40:53 PDT 2009


Hello Jenifer,

Sorry to get back to you so late. I have check with the Server admin about
the location of the project. The Server admin move the "webapps" folder to
"/srv/www/webapps/" but he created a shortcut icon in "/usr/local/tomcat5"
to go to "/srv/www/webapps/". It should work the same. Please refer to the
screen shot picture attachment file.

Regards,
Natsuda



2009/9/26 Jennifer Vendetti <vendetti at stanford.edu>

>  Hello Nat,
>
> You mention below that you running WebProtege from
> "/srv/www/webapps/webprotege".  But, in your log file it says that
> WebProtege is running from this directory:
>
> INFO: WebProtege running in: /usr/local/tomcat5/webapps/webprotege/
>
> In addition, it looks like the project objects in your metaproject are
> using relative paths, i.e.:
>
> INFO: Found project def in metaproject: Newspaper at:
> projects/newspaper/newspaper.pprj
>
> So, WebProtege is looking for projects in this path (I'm using the
> newspaper project as an example here):
>
> /usr/local/tomcat5/webapps/webprotege/projects/newspaper/newspaper.pprj
>
> Can you confirm that this is where your projects are physically located?
>
> Jennifer
>
>
> Natsuda Kasisopha wrote:
>
> 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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