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[protege-discussion] WebProtege Installation

Ron Schultz rcaschultz at gmail.com
Tue Apr 21 19:32:51 PDT 2009


Tania,

I agree something environmental is at issue here. It appears that WebProtege
cannot communicate with the Protégé server. The RMI port must be working if
the Protégé client can talk to the server. Is it possible that Ahmed has an
two different builds of Protégé running between Webprotege and the Protégé
server? I do not recall confirming the builds with him and I am not sure if
this would cause the issue he is seeing.

On a side note: The catalina.out file you provided shows a runtime exception
where the metaproject does not load. Not sure your webprotege example is
working as you expect. Note the error below:

-------------------------------
SEVERE: Unable to load project from: file:/work/tools/apache-tomcat-
5.5.27/webapps/webprotege/projects/metaproject/metaproject.pprj
ERROR [http-8080-Processor24] (ApplicationContext.java:678) -
StandardWrapper.Throwable
java.lang.RuntimeException:
edu.stanford.smi.protege.util.MessageError at 366573
--------------------------------

Here is an example catalina.log file, running 64-bit Java 1.6.0_13 and
Tomcat 6.0.18 on Windows-64, from my environment. The log file is very
similar in content to yours, but it does show me logging onto my WebProtege
instance and retrieving the Newspaper project.

Apr 17, 2009 1:35:41 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal
performance in production environments was not found on the
java.library.path:
c:\Tomcat6\bin;.;C:\WINDOWS\Sun\Java\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\W
INDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;c:\jdk\bin;
Apr 17, 2009 1:35:41 PM org.apache.coyote.http11.Http11Protocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Apr 17, 2009 1:35:41 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 581 ms
Apr 17, 2009 1:35:41 PM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Apr 17, 2009 1:35:41 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/6.0.18
Apr 17, 2009 1:35:41 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive webprotege.war
Apr 17, 2009 1:35:41 PM org.apache.catalina.loader.WebappClassLoader
validateJarFile
INFO:
validateJarFile(c:\Tomcat6\webapps\webprotege\WEB-INF\lib\gwt-dev-windows.ja
r) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:
javax/servlet/Servlet.class
Apr 17, 2009 1:35:41 PM org.apache.catalina.loader.WebappClassLoader
validateJarFile
INFO:
validateJarFile(c:\Tomcat6\webapps\webprotege\WEB-INF\lib\gwt-user.jar) -
jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:
javax/servlet/Servlet.class
Apr 17, 2009 1:35:42 PM org.apache.coyote.http11.Http11Protocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Apr 17, 2009 1:35:42 PM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Apr 17, 2009 1:35:42 PM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/63  config=null
Apr 17, 2009 1:35:42 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 941 ms
Apr 17, 2009 1:39:37 PM
edu.stanford.bmir.protege.web.server.AdminServiceImpl init
INFO: In AdminServiceImpl -- init
Apr 17, 2009 1:39:37 PM edu.stanford.smi.protege.plugin.PluginUtilities
findPluginsDirectory
WARNING: Plugins directory not found: c:\Tomcat6\plugins
Apr 17, 2009 1:39:39 PM edu.stanford.smi.protege.resource.BundleHelper
<init>
WARNING: missing bundle: standard_extensions_text
Apr 17, 2009 1:39:39 PM edu.stanford.smi.protege.resource.BundleHelper
internalGetText
WARNING: no resource bundle: tab.queries
Apr 17, 2009 1:39:39 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getMetaprojectURI
INFO: Path to Metaproject:
c:\Tomcat6\webapps\webprotege\projects\metaproject\metaproject.pprj
Apr 17, 2009 1:39:40 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getProjectsData
INFO: Found project def in metaproject: Newspaper at:
examples/newspaper/newspaper.pprj
Apr 17, 2009 1:39:50 PM
edu.stanford.bmir.protege.web.server.AdminServiceImpl validateUser
INFO: User Ron Schultz logged in at: Fri Apr 17 13:39:50 CDT 2009
Apr 17, 2009 1:39:51 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getProjectsData
INFO: Found project def in metaproject: Newspaper at:
examples/newspaper/newspaper.pprj
Apr 17, 2009 1:39:51 PM
edu.stanford.bmir.protege.web.server.MetaProjectManager getProjectsData
INFO: Ron Schultz : AdminGroup, World
---------------------------------- - - - - - - - - - - - - - - - - -

-----Original Message-----
From: protege-discussion-bounces at lists.stanford.edu
[mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of Tania
Tudorache
Sent: Tuesday, April 21, 2009 8:15 PM
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] WebProtege Installation

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_Tutori
> al_Setup#Testing:_Connect_a_Client_to_the_Server
> > [2]:
> > 
> http://protegewiki.stanford.edu/index.php/Protege_Client_Server_Tutori
> al_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 
> > > <http://www.microsoft .com/windows/windowslive/default.aspx>
> > >
> > >
> > >
> > > 
> ----------------------------------------------------------------------
> --
> > >
> > > Invite your mail contacts to join your friends list with Windows 
> > > Live Spaces. It's easy! Try it!
> > > 
> <http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friend
> s.aspx&mkt=en-us>
> > >
> > > 
> ----------------------------------------------------------------------
> --
> > >
> > > Get news, entertainment and everything you care about at Live.com.
> > > Check it out! <http://www.live.com/getstarted.aspx>
> > >
> > >
> > > 
> ----------------------------------------------------------------------
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> > > --------------------------
> ----------------------------------------------
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> > > <http://www.microsoft.com/windows/windowslive/default.aspx>
> > > 
> ----------------------------------------------------------------------
> --
> > >
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> > > https://mailman.stanford.edu/mailman/listinfo/protege-discussion
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