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[protege-discussion] WebProtege Installation

Ron Schultz rcaschultz at
Fri Apr 17 11:55:46 PDT 2009



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

INFO: Loading project Requirements from Protege server

Apr 17, 2009 1:39:55 PM edu.stanford.smi.protege.server.RemoteProjectManager

SEVERE: java.rmi.ConnectException: Connection refused to host:;
nested exception is: 

       Connection refused: connect

                at sun.rmi.transport.tcp.TCPEndpoint.newSocket(Unknown

                at sun.rmi.transport.tcp.TCPChannel.createConnection(Unknown

                at sun.rmi.transport.tcp.TCPChannel.newConnection(Unknown


When I attempt to run WebProtege and the Protégé server is not running.




From: protege-discussion-bounces at
[mailto:protege-discussion-bounces at] On Behalf Of Firedrop
Sent: Friday, April 17, 2009 12:04 PM
To: protege-discussion at
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, 


From: firedrop84 at
To: protege-discussion at
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
Please help. The deadline is very soon and I dont know how to fix it.
Best Regards, 


From: rcaschultz at
To: protege-discussion at
Date: Mon, 13 Apr 2009 10:36:09 -0500
Subject: Re: [protege-discussion] WebProtege Installation



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).




From: protege-discussion-bounces at
[mailto:protege-discussion-bounces at] On Behalf Of Firedrop
Sent: Sunday, April 12, 2009 4:31 AM
To: protege-discussion at
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
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 pro tege
Anyone can help me with this problem.
Best Regards, 


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