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[protege-discussion] Fwd: FW: Protege client-server [WAS: Interface)

Tania Tudorache tudorache at stanford.edu
Mon Aug 22 12:40:06 PDT 2011


Hi Karl,

Thank you for the suggestions. Except the CODEBASE (which used to be in 
there), the other arguments should be explained on the wiki.

I added the CODEBASE_URL to the description of the Windows installation. 
Thank you for noticing that it was missing. I think most people use 
Linux or Unix systems to run the server (at least for production 
settings), so this issue did not come up before, or they have figured it 
out somehow :)

Tania


-------- Original Message --------
Subject: 	FW: [protege-discussion] Protege client-server [WAS: Interface)
Date: 	Sat, 20 Aug 2011 07:28:11 -0500
From: 	Schulmeisters, Karl <Karl.Schulmeisters at unisys.com>
To: 	tudorache at stanford.edu <tudorache at stanford.edu>



Sorry about the wrong thread -- I've been so focused on getting this 
project up and running I didn't pay attention

Note that this is a suggestion then for the Windows Documentation.  
Windows Server since the x64 versions have started shipping, will 
typically install Protégé in the "Program Files (x86)" directory instead 
of the "Program Files" directory.  And since the Run_Server.Bat  has an 
explicit "set" statement that assumes it is in "program files" 
directory, this will cause it to commonly break in installations on a 
Windows Server.  At least this should be in the FAQ section

In fact a description of what the Headless, Codebase et. al. environment 
variables are used for, so that appropriate changes can be made, would 
be very useful

*Karl Schulmeisters -- *Director Solutions Architecture.

*From:*protege-discussion-bounces at lists.stanford.edu 
[mailto:protege-discussion-bounces at lists.stanford.edu] *On Behalf Of 
*Tania Tudorache
*Sent:* Friday, August 19, 2011 4:30 PM
*To:* User support for Core Protege and the Protege-Frames editor
*Subject:* Re: [protege-discussion] Protege client-server [WAS: Interface)

On 08/19/2011 04:29 PM, Tania Tudorache wrote:

Ralf,


Sorry about the wrong name!

Karl,



You replied to the wrong thread. Please use your own threads, to make 
the discussion useful also for others. I moved the discussion to this 
new thread.

To fix the exception that you get, you need to edit the 
run_protege_server.bat file and add the right location for the CODEBASE_URL.

Basically, edit this line and fix it to match the path to protege.jar 
from your Protege installation directory (this is a URL, so use forward 
slashes):

set CODEBASE_URL=file:/c:/program%%20files/protege_3.4.7/protege.jar 
<file:///c:%5Cprogram%25%20files%5Cprotege_3.4.7%5Cprotege.jar>

(space is represented as %20, I don't think double % is necessary, but 
you need to try it out)

Related to the other problem, of the clients timing out, see if the 
above fix works for them, too.

If not, you need to configure the server to use the firewall [1], and 
make sure you open on your Windows Firewall (the machine where the 
Protege server is hosted) the two ports used by the Protege server.

If this still fails, then it is something related to your specific 
network setup. In order to help further, we need to know your network 
setup and the Protege server configuration.

Tania

[1]: 
http://protegewiki.stanford.edu/wiki/Protege_Client_Server_Tutorial_Advanced#Working_with_Firewalls



-------- Original Message --------

*Subject: *

	

Re: [protege-discussion] Interface

*Date: *

	

Fri, 19 Aug 2011 09:33:29 -0500

*From: *

	

Schulmeisters, Karl <Karl.Schulmeisters at unisys.com> 
<mailto:Karl.Schulmeisters at unisys.com>

*Reply-To: *

	

User support for Core Protege and the Protege-Frames editor 
<protege-discussion at lists.stanford.edu> 
<mailto:protege-discussion at lists.stanford.edu>

*To: *

	

User support for Core Protege and the Protege-Frames editor 
<protege-discussion at lists.stanford.edu> 
<mailto:protege-discussion at lists.stanford.edu>




Ok I have another problem that I'm simply not well versed enough to sort out.  When I run the Protégé Server on my personal machine -- which has direct connection to the internet via local ISP, it starts up just fine,  BUT users inside of my Corpnet can only see it.  When they try to load a project they end up essentially timing out while waiting for the project to load.  They show up as a session connection, they just never get a loaded project.

  

Otoh if I connect via Localhost, I get connected just fine

  

So I hosted the Protégé server on a BehindThe Firewall VM based Windows server.  Everything installed as expected.  Protégé runs fine in local mode against the database and the metaProject.  Except when I go to load the server  I get a normal startup UNTIL it tries to load the last project.  At which point I get the following error sequence.  Its as though my Jave instance cannot reach the Standford server -- though why it would need to I'm not sure

  

Anyone seen this behavior before?  I'll admit, I'm a Java/Tomcat newbie

  

SEVERE: java.rmi.ServerException: RemoteException occurred in server thread; nes

ted exception is:

         java.rmi.UnmarshalException: error unmarshalling arguments; nested excep

tion is:

         java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server

_Stub

         at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source)

         at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source)

         at sun.rmi.transport.Transport$1.run(Unknown Source)

         at java.security.AccessController.doPrivileged(Native Method)

         at sun.rmi.transport.Transport.serviceCall(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Sour

ce)

         at java.lang.Thread.run(Unknown Source)

         at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(Unknow

n Source)

         at sun.rmi.transport.StreamRemoteCall.executeCall(Unknown Source)

         at sun.rmi.server.UnicastRef.invoke(Unknown Source)

         at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)

         at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)

         at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)

         at edu.stanford.smi.protege.server.Server.main(Unknown Source)

Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested ex

ception is:

         java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server

_Stub

         at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source)

         at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source)

         at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source)

         at sun.rmi.transport.Transport$1.run(Unknown Source)

         at java.security.AccessController.doPrivileged(Native Method)

         at sun.rmi.transport.Transport.serviceCall(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Sour

ce)

         at java.lang.Thread.run(Unknown Source)

Caused by: java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Ser

ver_Stub

         at java.net.URLClassLoader$1.run(Unknown Source)

         at java.security.AccessController.doPrivileged(Native Method)

         at java.net.URLClassLoader.findClass(Unknown Source)

         at java.lang.ClassLoader.loadClass(Unknown Source)

         at java.lang.ClassLoader.loadClass(Unknown Source)

         at java.lang.ClassLoader.loadClassInternal(Unknown Source)

         at java.lang.Class.forName0(Native Method)

         at java.lang.Class.forName(Unknown Source)

         at sun.rmi.server.LoaderHandler.loadClass(Unknown Source)

         at sun.rmi.server.LoaderHandler.loadClass(Unknown Source)

         at java.rmi.server.RMIClassLoader$2.loadClass(Unknown Source)

         at java.rmi.server.RMIClassLoader.loadClass(Unknown Source)

         at sun.rmi.server.MarshalInputStream.resolveClass(Unknown Source)

         at java.io.ObjectInputStream.readNonProxyDesc(Unknown Source)

         at java.io.ObjectInputStream.readClassDesc(Unknown Source)

         at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

         at java.io.ObjectInputStream.readObject0(Unknown Source)

         at java.io.ObjectInputStream.readObject(Unknown Source)

         ... 9 more

  -- Server.bindName()

SEVERE: server startup failed -- java.rmi.ServerException: RemoteException occur

red in server thread; nested exception is:

         java.rmi.UnmarshalException: error unmarshalling arguments; nested excep

tion is:

         java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server

_Stub

         at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source)

         at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source)

         at sun.rmi.transport.Transport$1.run(Unknown Source)

         at java.security.AccessController.doPrivileged(Native Method)

         at sun.rmi.transport.Transport.serviceCall(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Sour

ce)

         at java.lang.Thread.run(Unknown Source)

         at sun.rmi.transport.StreamRemoteCall.exceptionReceivedFromServer(Unknow

n Source)

         at sun.rmi.transport.StreamRemoteCall.executeCall(Unknown Source)

         at sun.rmi.server.UnicastRef.invoke(Unknown Source)

         at sun.rmi.registry.RegistryImpl_Stub.rebind(Unknown Source)

         at edu.stanford.smi.protege.server.Server.bindName(Unknown Source)

         at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)

         at edu.stanford.smi.protege.server.Server.main(Unknown Source)

Caused by: java.rmi.UnmarshalException: error unmarshalling arguments; nested ex

ception is:

         java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Server

_Stub

         at sun.rmi.registry.RegistryImpl_Skel.dispatch(Unknown Source)

         at sun.rmi.server.UnicastServerRef.oldDispatch(Unknown Source)

         at sun.rmi.server.UnicastServerRef.dispatch(Unknown Source)

         at sun.rmi.transport.Transport$1.run(Unknown Source)

         at java.security.AccessController.doPrivileged(Native Method)

         at sun.rmi.transport.Transport.serviceCall(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport.handleMessages(Unknown Source)

         at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(Unknown Sour

ce)

         at java.lang.Thread.run(Unknown Source)

Caused by: java.lang.ClassNotFoundException: edu.stanford.smi.protege.server.Ser

ver_Stub

         at java.net.URLClassLoader$1.run(Unknown Source)

         at java.security.AccessController.doPrivileged(Native Method)

         at java.net.URLClassLoader.findClass(Unknown Source)

         at java.lang.ClassLoader.loadClass(Unknown Source)

         at java.lang.ClassLoader.loadClass(Unknown Source)

         at java.lang.ClassLoader.loadClassInternal(Unknown Source)

         at java.lang.Class.forName0(Native Method)

         at java.lang.Class.forName(Unknown Source)

         at sun.rmi.server.LoaderHandler.loadClass(Unknown Source)

         at sun.rmi.server.LoaderHandler.loadClass(Unknown Source)

         at java.rmi.server.RMIClassLoader$2.loadClass(Unknown Source)

         at java.rmi.server.RMIClassLoader.loadClass(Unknown Source)

         at sun.rmi.server.MarshalInputStream.resolveClass(Unknown Source)

         at java.io.ObjectInputStream.readNonProxyDesc(Unknown Source)

         at java.io.ObjectInputStream.readClassDesc(Unknown Source)

         at java.io.ObjectInputStream.readOrdinaryObject(Unknown Source)

         at java.io.ObjectInputStream.readObject0(Unknown Source)

         at java.io.ObjectInputStream.readObject(Unknown Source)

         ... 9 more

  

  

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