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[protege-discussion] WebProtege Installation

Tania Tudorache tudorache at stanford.edu
Wed Apr 22 12:58:21 PDT 2009


Ron Schultz wrote:
> 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.
>   
If the server and the webprotege (client) are different builds, then we 
should have seen a serialization exception. But from Ahmed's log I have 
the impression that WebProtege was not even deployed correctly. It's 
curios that I don't see any protege related message in the logs.



> 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
> --------------------------------
>
>   
I intentionally forgot to copy the metaproject in the tomcat folder, to 
see what message I would get in the log, and this is it :) And the 
result was that I got the initial window of webprotege with an empty 
list of ontologies (just like Ahmed did).

After that I copied the metaproject and you can see in the log messages 
like:

INFO: Found project def in metaproject: Newspaper at:
examples/newspaper/newspaper.pprj

These are the good signs :)

My suggestion to Ahmed is to install Tomcat 5.5 (nothing else) and then 
deploy the war file as described on the wiki page. I did a fresh install 
of everything and followed the steps and it worked fine. I have reports 
from other people who have tried the step without any problem. So, there 
might be something in the environment of Ahmed that is different and 
that causes problems. A clean install would solve this mystery.

Tania


> 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.
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>>>>
>>>>
>>>>         
>> ----------------------------------------------------------------------
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>>     
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>>>>         
>> ----------------------------------------------
>>     
>>>> See all the ways you can stay connected to friends and family 
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>>>>
>>>>         
>> ----------------------------------------------------------------------
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>>     
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