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

Natsuda Kasisopha gift8201 at gmail.com
Mon Sep 28 21:26:41 PDT 2009


Hi again,

I want to give you additional information. You guys can click on the URI :
http://natsuda.tomcat.debii.curtin.edu.au/ to see the page display. Also you
can access the ontology file directly with URI:
http://natsuda.tomcat.debii.curtin.edu.au/projects/pizza/pizza.owl.

I hope this helps.

Natsuda




2009/9/29 Natsuda Kasisopha <gift8201 at gmail.com>

> 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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>>
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>>
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