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[protege-discussion] installation problem, cannot load the list of ontologies, cannot login

Tania Tudorache tudorache at
Thu May 21 18:28:06 PDT 2009


I'm developing WebProtege using also Ubuntu and Tomcat 5.5 and there is 
no problem with the configuration, it runs well.

It seems that this is a file access problem. The log kind of already 
says what the problem is:

"INFO: Illegal access: this web application instance has been stopped 
already.  Could not load"

Looks like tomcat tries to load the from:

I am not sure why it tries to load it from the classes folder..

I'm not an expert in tomcat, but it seems that you need to configure the 
tomcat policy file. Here is the solution for a similar case:

Another thing that was suspicious in one of your log files was:

May 19, 2009 7:37:45 PM 
edu.stanford.bmir.protege.web.server.ProjectManager getServer
SEVERE: Could not connect to server: localhost

This means that you did not start the Protege server, or that WebProtege 
could not connect to it. Make sure that the Protege server is running, 
and that you can connect to it from the Protege rich client, using u/p: 

If you still have problems, please send also the protege.log files from 

I hope that the tomcat policy file will fix the problem.


Michal Trna wrote:
> Hello Jennifer,
> Jennifer Vendetti escribió:
>> Hello Michal,
>> Michal Trna wrote:
>>> I have installed Webprotege according to instructions [1] on Ubuntu 
>>> machine in these two configurations:
>>> Tomcat 5.5, Protege 3.4 release, WebProtege 0.5 alpha, build 102.
>>> Tomcat 6, Protege 3.4 release, WebProtege 0.5 alpha, build 102.
>> We have not tested WebProtege with Tomcat 6.  Only with 5.5.
>>> To both of them it is possible to connect through Protege Client. Both 
>>> also fail when I try to connect via WebProtege. For both cases, 
>>> WebProtege screen shows all the control elements like the frames and 
>>> buttons, but the list of ontologies is empty and it is not possible to 
>>> log in.
>>> My log files look like:
>>> Tomcat 5.5, catalina.log:
>>> May 19, 2009 7:29:19 PM org.apache.commons.modeler.Registry 
>>> registerComponent
>>> SEVERE: Error registering 
>>> Catalina:type=Valve,name=StandardContextValve,path=/webprotege,host=localhost 
>>> Cannot instantiate ModelMBean of 
>>> class org.apache.commons.modeler.BaseModelMBean
>>>    at 
>>> org.apache.commons.modeler.ManagedBean.createMBean(
>>>    at 
>>> org.apache.commons.modeler.Registry.registerComponent(
>>> ...
>>> Caused by: access denied 
>>> ( 
>>> /var/lib/tomcat5.5/webapps/webprotege/WEB-INF/classes/ 
>>> read)
>> I notice in the exception above that you are getting an access denied error:
>> /var/lib/tomcat5.5/webapps/webprotege/WEB-INF/classes/ 
>> read
>> Did you check that you have the proper access permissions for this file?
> the file originaly didn't exist. The error didn't dissapear after I 
> have created the file and set read/write permissions to everybody to 
> everything in the webprotege folder in webapps.
> (In my windows version, the file doesn't exist either and there is no 
> problem)
>> Jennifer
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at
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> Thanks,
> Michal
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