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[protege-discussion] WebProtege Installation

Tania Tudorache tudorache at stanford.edu
Mon Apr 20 14:34:49 PDT 2009


Sorry for the late reply. Thanks a lot, Ron for your excellent advice!

Ahmed, so I understand that you have already tried to connect to the 
Protege server using the user name webprotege/webprotege and you opened 
the Pizza project from the server and it works fine in a protege client 
(when you execute Protege.exe, or run_protege.bat). Here is a guide on 
how to test the server installation [1]. Before you proceed, please test 
that this works fine.

Now the Protege server enforces the read and write permissions on 
ontologies on the server. This means that you need to give read 
permission to the user webprotege on the projects that you should see in 
the ontology list in web protege. I will update the documentation to 
reflect that. Here is some documentation about the policiies [2]

In the attached logs I did not see any Protege logs. You should have in 
your tomcat installation folder, a logs subfolder, in which you will 
find catalina.out and protege_x.log. Please attach catalina.out and the 
protege_x.log (where x is the biggest number). If this sounds confusing, 
you can zip all the protege_x.log files and attach them. These logs 
should contain any errors related to the Protege server (if there are any).

I suspect that the issues in your case are related to the permissions.

Please send the log files and then we'll take it from there.

Tania

[1]: 
http://protegewiki.stanford.edu/index.php/Protege_Client_Server_Tutorial_Setup#Testing:_Connect_a_Client_to_the_Server
[2]: 
http://protegewiki.stanford.edu/index.php/Protege_Client_Server_Tutorial_Configuration


Firedrop 84 wrote:
> hi again,
>  
> I noticed what/  think the problem I been have./
> // 
> /When I try to run Protege Server it shows in the another screen the 
> following error /
> // 
> /Could not set up class specifc logging/
> /Exception configuring logger/
> /Could not set logger level/
> /Warning: IO excception getting logger. access denided 
> <java.util.PropertyPermission protege.proprties.in.user.home read>/
> // 
> I think something with the RMI.
>  
> Best Regards,
>  
> Ahmed
>
>  
> ------------------------------------------------------------------------
> From: firedrop84 at hotmail.com
> To: protege-discussion at lists.stanford.edu
> Date: Sat, 18 Apr 2009 11:05:30 +0000
> Subject: Re: [protege-discussion] WebProtege Installation
>
> Ron,
>  
> everything that I installed is on my laptop (Protege, Tomcat, etc).
>  
> When I run the run_protege.bat and it opened the protege application. 
> Does Protege Clients means the application. If so, how can I connect 
> to the server when I run the client.
>  
> I usually run the run_protege_server.bat to run the protege server and 
> it never ask me for any username or password.
>  
> I created a small jsp file just to test tomcat and it worked fine. 
> Then, I checked the file that you told me about under webapps 
> directory (webproteg.jar) but I can't find it there or anywhere in 
> my computer.
>  
> Then, I checked the webprotege folder and I have all the folders such 
> ass css, images, js, etc. Most of the jar files was under lib or 
> WEB-INF\lib but nothing called webprotege.jar.
>  
> Then I checked the log files that you told me to check and I couldn't 
> find errors. This is what I have in t he log files
>  
> catalina.2009-04-18.log
>  
> 18-Apr-2009 00:33:44 org.apache.catalina.startup.HostConfig checkResources
> INFO: Undeploying context [/webprotege]
> 18-Apr-2009 00:44:26 org.apache.coyote.http11.Http11Protocol pause
> INFO: Pausing Coyote HTTP/1.1 on http-8080
> 18-Apr-2009 00:44:27 org.apache.catalina.core.StandardService stop
> INFO: Stopping service Catalina
> 18-Apr-2009 00:44:28 org.apache.coyote.http11.Http11Protocol destroy
> INFO: Stopping Coyote HTTP/1.1 on http-8080
>
>  
> localhost.2009-04-18.log
>  
> 18-Apr-2009 00:44:27 org.apache.catalina.core.ApplicationContext log
> INFO: SessionListe ner: contextDestroyed()
> 18-Apr-2009 00:44:27 org.apache.catalina.core.ApplicationContext log
> INFO: ContextListener: contextDestroyed()
> 18-Apr-2009 00:44:27 org.apache.catalina.core.ApplicationContext log
> INFO: SessionListener: contextDestroyed()
> 18-Apr-2009 00:44:27 org.apache.catalina.core.ApplicationContext log
> INFO: ContextListener: contextDestroyed()
> 18-Apr-2009 00:44:28 org.apache.catalina.core.ApplicationContext log
> INFO: SessionListener: contextDestroyed()
> 18-Apr-2009 00:44:28 org.apache.catalina.core.ApplicationContext log
> INFO: ContextListener: contextDestroyed()
>
>  
> ------------------------------------------------------------------------
> From: rcaschultz at gmail.com
> To: protege-discussion at lists.stanford.edu
> Date: Fri, 17 Apr 2009 13:55:46 -0500
> Subject: Re: [protege-discussion] WebProtege Installation
>
> Ahmed,
>
>  
>
> If your Protégé Server displays: “Protégé server ready to accept 
> connections. . .” then the Protégé server is running fine. You can 
> verify access and firewall rules by running a Protégé client and 
> connecting to the server itself from the same machine you intend to 
> run Tomcat from. Just run run_protege.bat and connect to localhost 
> using the username and password you put into your metaproject.
>
>  
>
> Assuming the Protégé client access works, next look in your 
> Tomcat\webapps directory for webprotege.jar. Is there also a directory 
> named webprotege? Ensure the jar file is expanded into the directory. 
> You should see a number of directories (such as css, images, …) and 
> files (e.g., WebProtege.html) in the webprotege directory.
>
>  
>
> Also look in Tomcat\logs in  the file catalina.2009-04-17.log and 
> localhost.2009-04-17.log and see if Tomcat is reporting errors.
>
>  
>
> For instance – I get this kind of error in the catalina log when I 
> attempt to run WebProtege and the Protégé server is not running.
>
>  
>
> Apr 17, 2009 1:39:54 PM 
> edu.stanford.bmir.protege.web.server.ProjectManager openProjectRemote
>
> INFO: Loading project Requirements from Protege server 75.66.64.68
>
> Apr 17, 2009 1:39:55 PM 
> edu.stanford.smi.protege.server.RemoteProjectManager getProject
>
> SEVERE: java.rmi.ConnectException: Connection refused to host: 
> 75.66.64.68; nested exception is:
>
>                 java.net.ConnectException: Connection refused: connect
>
>                 at sun.rmi.transport.tcp.TCPEndpoint.newSocket(Unknown 
> Source)
>
>                 at 
> sun.rmi.transport.tcp.TCPChannel.createConnection(Unknown Source)
>
>                 at 
> sun.rmi.transport.tcp.TCPChannel.newConnection(Unknown Source)
>
>  
>
> When I attempt to run WebProtege and the Protégé server is not running.
>
>  
>
>  
>
>  
>
> *From:* protege-discussion-bounces at lists.stanford.edu 
> [mailto:protege-discussion-bounces at lists.stanford.edu] *On Behalf Of 
> *Firedrop 84
> *Sent:* Friday, April 17, 2009 12:04 PM
> *To:* protege-discussion at lists.stanford.edu
> *Subject:* Re: [protege-discussion] WebProtege Installation
>
>  
>
> I am checking it more. You might be right ron. Tomcat is working 
> without any problem but I think it must be either from tomcat or 
> protege server.
>  
> The reason I am thinking this way because I am using XAMPP for my PHP 
> part and I added tomcat as an add-on. I will try to install tomcat now 
> spereatly and see how I will go. maybe this will solve the problem.
>  
> I runt he run_protege_server batch file. It's showing me in the last 
> line that Proteger server ready to accept connections...
>  
> Does that mean it's working fine.
>  
> When I open the WebProtege Screen. It's not I can't login. also, I 
> can't see any of the ontologies that shows in the wiki 
> tutorial. That's why I am concentrating on the Protege Server and Tomcat.
>  
> Best Regards,
> Ahmed
>  
>
> ------------------------------------------------------------------------
>
> From: firedrop84 at hotmail.com
> To: protege-discussion at lists.stanford.edu
> Date: Fri, 17 Apr 2009 16:09:22 +0000
> Subject: Re: [protege-discussion] WebProtege Installation
>
> Thanks Ron.
>  
> I have installed PHP, MySQL and Apache for some blog that I will try 
> to link it with Webprotege by just providing hyperlink. I shouldn't 
> mention these as I confused things up in my previous email.
>  
> Tomcat is working perfectly fine.
>  
> I am really getting crazy on how to let it run. I am trying to write a 
> publication and this part is the only part that is left. if it works 
> it means I will have a publication on my topic that the university 
> wiill provide me a ticket to travel to a trip and present my paper in 
> a conference.
>  
> Please help. The deadline is very soon and I dont know how to fix it.
>  
> Best Regards,
> Ahmed
>  < /P>
> ------------------------------------------------------------------------
>
> From: rcaschultz at gmail.com
> To: protege-discussion at lists.stanford.edu
> Date: Mon, 13 Apr 2009 10:36:09 -0500
> Subject: Re: [protege-discussion] WebProtege Installation
>
> Ahmed,
>
>  
>
> Have you first ensured that Tomcat is running? Go to 
> http://localhost:8080 <http://localhost:8080/> and see if the Tomcat 
> administration appears. If not, see if in your Windows Service Manager 
> that the Apache Tomcat service is running. That is at least a starting 
> point.
>
>  
>
> Not sure why you installed PHP and MySQL unless you have some reason 
> beyond Protégé for doing so. Protégé does not require either (although 
> I believe it can use MySQL as a storage backend).
>
>  
>
> Ron
>
>  
>
> *From:* protege-discussion-bounces at lists.stanford.edu 
> [mailto:protege-discussion-bounces at lists.stanford.edu] *On Behalf Of 
> *Firedrop 84
> *Sent:* Sunday, April 12, 2009 4:31 AM
> *To:* protege-discussion at lists.stanford.edu
> *Subject:* [protege-discussion] WebProtege Installation
>
>  
>
> Hi All,
>  
> I am trying to install Web Protege in my PC but it's still not 
> working. when I open WebProtege.html it doesn't show me any ontologies 
> or anything. I can't even login even though I created the users.
>  
> I have installed Apapche, MySQL, PHP, Tomcat, JDK, Protege.
>  
> I followed the steps in that is described in the following link 
> http://protegewiki.stanford.edu/index.php/WebProtegeAdminGuide
>  
> The only step that I didn't do was the step that says
>  
> If a user launches a Protege client, they are presented with a dialog 
> that requires them to enter the host machine name:
>  
> (all the way before it asks to copy the *metaproject*  file in web pr 
> o tege folder.
>  
> Anyone can help me with this problem.
>  
> Best Regards,
> Ahmed
>
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