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[protege-discussion] WebProtege Installation

Tania Tudorache tudorache at stanford.edu
Tue Apr 21 18:14:48 PDT 2009


Hi Ahmed,

Thank you for sending the files. I did not find in them anything related 
to webprotege, only one entry that it was undeployed.

There is probably something wrong with the configuration. A few question:
>
> I could manage to connect to Protege Server via Protege Client by 
> using webprotege username and password.  So I think the first linkthat 
> you have provided me it working fine.

Did you also open a project, or just logged in? You should try to open a 
project, like Pizza or another.

Can you please send a screenshot of the metaproject folder in the 
Protege installation directory, and a screenshot of the metaproject 
folder in tomcat? They should be the exactly the same.

I noticed that you are using Java 1.6, that is not yet officially 
supported by Protege, but it should work.

What version of Windows and Tomcat are you using?

I just did the test with Tomcat 5.5. and it worked fine. If you use 
Tomcat 6, can you please install Tomcat 5.5 and give it a try?

I've also attached a log file, catalina.out, so that you have an idea 
how the logs look like if WebProtege is working.

Tania



>
> I checked the logs and I attached 1. All the logs from tomcat 2. all 
> the logs from protege folder logs 3. metaproject file that I am using 
> in webprotege 4. a screenshot of my webprotege.
>
> I checked the groups and I have two groups world and admin group. I 
> think webprotege is under word group and it has Read and Write 
> permission (I am not sure but this is what I understood).
>
> Best Regards,
> Ahmed
>
> > Date: Mon, 20 Apr 2009 14:34:49 -0700
> > From: tudorache at stanford.edu
> > To: protege-discussion at lists.stanford.edu
> > Subject: Re: [protege-discussion] WebProtege Installation
> >
> > Sorry for the late reply. Thanks a lot, Ron for your excellent advice!
> >
> > Ahmed, so I unders tand 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 th e
> > > 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 r un_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: contex tDestroyed()
> > > 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 Pr otégé 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 cata lina.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.TCP Endpoint.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
> &g t; > 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.
> > >
> > >
> > >
> &g t; > 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
> > >
> > > 
> ------------------------------------------------------------------------
> > >
> > > See all the ways you can stay connected to friends and family
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> > >
> > >
> > >
> > > 
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