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[protege-owl] Newbie question get error when trying to upgrade owel editor

John Armstrong johna318 at hotmail.com
Sat Nov 13 12:32:10 PST 2010


Tried to run protégé as administrator and the process died without launching
the app (or at least the gui).  If it wrote a log, I don’t know where it
went.

 

Went back to running as me, tried fiddling some permissions without any
visible effect (including successful update).

 

Tried grabbing the downloaded newer jar and copied it into the Program Files
plugin directory after moving the old version out of the way.

 

Got an exception relating to bundle constraints (something I don’t
understand) but protégé launched and ran.  Didn’t seem like a stable
configuration so I restored the old jar and now the app launches normally.

 

However, it now reports both the old and the new version of the owl editor
jar in the About box, and now thinks it has the latest version and doesn’t
invite me to install it.

 

I believe I’m running Vista in a pretty vanilla way.  I run as a user and
the user has ordinary administrator permissions but I think not special ones
(i.e. I always get prompted when I change anything in Program Files).

 

At this point I’m hoping Protégé will provide a solution or at least a
manual workaround. (If I didn’t say, I’m running Vista 32-bit SP2.)

 

BTW here is the bundle exception – I’m sure it’s not surprising given what I
did:

 

INFO      Framework: Apache Software Foundation (1.5)
org.protege.editor.core.ProtegeApplication[main]

INFO      OS: windowsvista (6.0)
org.protege.editor.core.ProtegeApplication[main]

INFO      Processor: x86  org.protege.editor.core.ProtegeApplication[main]

INFO  Installed plugin Pellet Reasoner Plug-in
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin Browser View (OWLDoc)
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin Dlquery  org.protege.editor.core.BundleManager[main]

INFO  Installed plugin Existential Tree
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin Owlviz Plug-in
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin The Protege 4 OWL Editor
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin The Protege 4 OWL Editor
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin OntoGraf Plug-in
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin HermiT Reasoner
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin The OWL API
org.protege.editor.core.BundleManager[main]

INFO  Installed plugin Factplusplus Plug-in
org.protege.editor.core.BundleManager[main]

WARN  Error logged  org.protege.editor.core.ui.error.ErrorLog[main]

org.osgi.framework.BundleException: Unable to resolve due to constraint
violation.

                at
org.apache.felix.framework.Felix.resolveBundle(Felix.java:3302)

                at
org.apache.felix.framework.Felix.startBundle(Felix.java:1653)

                at
org.apache.felix.framework.BundleImpl.start(BundleImpl.java:905)

                at
org.apache.felix.framework.BundleImpl.start(BundleImpl.java:892)

                at
org.protege.editor.core.BundleManager.startPlugins(BundleManager.java:110)

                at
org.protege.editor.core.BundleManager.loadPlugins(BundleManager.java:41)

                at
org.protege.editor.core.ProtegeApplication.loadPlugins(ProtegeApplication.ja
va:277)

                at
org.protege.editor.core.ProtegeApplication.initApplication(ProtegeApplicatio
n.java:171)

                at
org.protege.editor.core.ProtegeApplication.start(ProtegeApplication.java:113
)

                at
org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.jav
a:661)

                at
org.apache.felix.framework.Felix.activateBundle(Felix.java:1756)

                at
org.apache.felix.framework.Felix.startBundle(Felix.java:1678)

                at
org.apache.felix.framework.BundleImpl.start(BundleImpl.java:905)

                at
org.apache.felix.framework.BundleImpl.start(BundleImpl.java:892)

                at
org.protege.osgi.framework.Launcher.start(Launcher.java:102)

                at
org.protege.osgi.framework.Launcher.main(Launcher.java:120)

WARN  Problem starting plugin The Protege 4 OWL Editor
org.protege.editor.core.BundleManager[main]

INFO  Downloading OWL Editor
org.protege.editor.core.update.PluginInstaller[Installing plugins thread]

INFO  Copying OWL Editor
org.protege.editor.core.update.PluginInstaller[Installing plugins thread]

ERROR Could not safely install new version of the plugin.
org.protege.editor.core.update.PluginInstaller[Installing plugins thread]

ERROR Could not install plugin
org.protege.editor.core.update.PluginInstaller[Installing plugins thread]

INFO  Using OWL API version 3.1.0.20069
org.protege.editor.owl.OWLEditorKit[AWT-EventQueue-0]

INFO  Rebuilding entity indices...
org.protege.editor.owl.model.OWLModelManagerImpl[AWT-EventQueue-0]




 

-- John

 

 

 

From: protege-owl-bounces at lists.stanford.edu
[mailto:protege-owl-bounces at lists.stanford.edu] On Behalf Of John Armstrong
Sent: Friday, November 12, 2010 4:56 PM
To: 'User support for the Protege-OWL editor'
Subject: Re: [protege-owl] Newbie question get error when trying to upgrade
owel editor

 

> This theory is inconsistent with your statement that "I have succeeded in
downloading and installing other plugins, just not the editor".

 

Looks like a permissions issue:

 

C:\Program Files\Protege_4.1_beta>ls -l -d plugins

drwx------+ 1 Administrators None 4096 2010-11-01 14:45 plugins

 

C:\Program Files\Protege_4.1_beta\plugins>ls -l

total 13052

-rwx------+ 1 John           None 2111693 2010-11-09 10:35
com.clarkparsia.protege.plugin.pellet.jar

-rwx------+ 1 John           None  217881 2010-11-09 09:24
org.coode.browser.jar

-rwx------+ 1 Administrators None   25663 2010-11-01 14:45
org.coode.dlquery.jar

-rwx------+ 1 John           None   92256 2010-11-09 10:35
org.coode.existentialtree.jar

-rwx------+ 1 Administrators None  295486 2010-11-01 14:45
org.coode.owlviz.jar

-rwx------+ 1 Administrators None 1789909 2010-11-01 14:45
org.protege.editor.owl.jar

-rwx------+ 1 Administrators None 2206672 2010-11-01 14:45
org.protege.ontograf.jar

-rwx------+ 1 Administrators None 1600299 2010-11-01 14:45
org.semanticweb.HermiT.jar

-rwx------+ 1 Administrators None 2003984 2010-11-01 14:45
org.semanticweb.owl.owlapi.jar

-rwx------+ 1 John           None 2999581 2010-11-12 15:09
uk.ac.manchester.cs.owl.factplusplus.jar

 

Seems like the software originally got installed with owner Administrators
(I see this in Windows Explorer as well) but updates get installed with
owner John.  My regular user John has administrative permission so I never
hit problems with access but it seems the protégé installer can’t overwrite
a file owned by Administrators with one owned by John.  The download per se
of the updated editor file actually succeeded:

 

C:\Users\John\AppData\Local\Temp>ls -l *.jar

-rwx------+ 1 John None 1792246 2010-11-12 15:09 org.protege.editor.owl.jar

-rwx------+ 1 John None 2999581 2010-11-12 15:09
uk.ac.manchester.cs.owl.factplusplus-P4.1-v1.5.0.jar

 

It’s presumably the copy that failed.

 

-- John

 

From: protege-owl-bounces at lists.stanford.edu
[mailto:protege-owl-bounces at lists.stanford.edu] On Behalf Of Timothy Redmond
Sent: Friday, November 12, 2010 2:37 PM
To: protege-owl at lists.stanford.edu
Subject: Re: [protege-owl] Newbie question get error when trying to upgrade
owel editor

 


I just tried this on a 32 bit vista machine and it worked fine.  So I can
think of two things that might be wrong:

1.	The owleditor update was broken for a while but I fixed it.  (Thanks
to Shahim Essaid for debugging this.)  So maybe you just need to try again.
2.	You might have a permissions problem.  Since the Protege_4.1_beta
has been installed in the Program Files directory, you need administrative
privilege to update the owleditor plugin.  You can check this by installing
to the Desktop and seeing if things work there.  Also I think that in
windows there is a way to run a program as administrator.  This theory is
inconsistent with your statement that "I have succeeded in downloading and
installing other plugins, just not the editor".


Let me know if neither of these hints moves us forwards and we will think
about what the next step should be.

-Timothy


On 11/11/2010 11:19 AM, John Armstrong wrote: 

Hi all,

 

I downloaded protégé-owl 4.10 (build 213) a couple days am successfully
using it to view and create owl ontologies.

 

However, each time I start up I get a dialog box inviting me to upgrade the
owl editor and when I accept I get an error in the console window:

 

 

C:\Program Files\Protege_4.1_beta>java -Dlog4j.configuration=file:log4j.xml
<file:///\\log4j.xml>  -Den

tityExpansionLimit=100000000 -Dfile.encoding=utf-8
-Dorg.protege.plugin.dir=plug

ins -classpath bin/felix.jar;bin/ProtegeLauncher.jar
org.protege.osgi.framework.

Launcher

Starting Protege 4 OWL Editor (Version 4.1.0, Build = 213)

Platform:

    Java: JVM 1.6.0-oem-b104 Memory: 66M

    Language: en, Country: US

    Framework: Apache Software Foundation (1.5)

    OS: windowsvista (6.0)

    Processor: x86

Installed plugin Pellet Reasoner Plug-in

Installed plugin Browser View (OWLDoc)

Installed plugin Dlquery

Installed plugin Existential Tree

Installed plugin Owlviz Plug-in

Installed plugin The Protege 4 OWL Editor

Installed plugin OntoGraf Plug-in

Installed plugin HermiT Reasoner

Installed plugin The OWL API

Downloading OWL Editor

Copying OWL Editor

Could not safely install new version of the plugin.

Could not install plugin

Using OWL API version 3.1.0.20069

 

 

I can’t capture the full version ids of the old and new editor versions but
descriptions are:

 

Old: v4.1.0 Build 213 - 26 Oct, 2010 

New:  v4.1.0 Update Build 213 - 4 Nov, 2010

 

I have succeeded in downloading and installing other plugins, just not the
editor.

 

-- John 

 

 
 
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