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[protege-discussion] JDBC Registry plugin broken?

Victor Mataré matare at lih.rwth-aachen.de
Mon Aug 1 07:41:26 PDT 2011


Ah well, FINALLY!
Compiling org.protege.osgi.jdbc.prefs r23543 did the trick for me. 
Thanks a ton.

But if I'm not severely confused, there's no precompiled .jar for this 
on the web, right? I got the broken one from
http://smi-protege.stanford.edu/protege4/plugins/4.0/org.protege.osgi.jdbc.prefs.jar.
Dunno what that was built from, but maybe it should be updated?

On 01.08.2011 07:10, Timothy Redmond wrote:
>
> I didn't replicate your problem using the org.protege.osgi.jdbc and 
> org.protege.osgi.jdbc.prefs plugins from trunk.  You mentioned before 
> that were building from svn revision 19106 and this might be the 
> problem.  There were some changes sometime before July 2010 involving 
> the class loader.  We have the following logs for the changes:
>
>    [tredmond at Saturn org.protege.osgi.jdbc.prefs]$ svn log -r 19106:head
>    
> ------------------------------------------------------------------------
>    r19573 | tredmond | 2010-07-20 14:58:46 -0700 (Tue, 20 Jul 2010) | 
> 1 line
>
>    added swing
>    
> ------------------------------------------------------------------------
>    r23543 | tredmond | 2011-07-31 19:35:48 -0700 (Sun, 31 Jul 2011) | 
> 1 line
>
>    prevent a null pointer when the jdbc service isn't ready when this 
> plugin starts
>    
> ------------------------------------------------------------------------
>    [tredmond at Saturn org.protege.osgi.jdbc.prefs]$ svn info
>    Path: .
>    URL: 
> http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.osgi.jdbc.prefs/trunk
>    Repository Root: http://smi-protege.stanford.edu/repos/protege
>    Repository UUID: 30a32298-b1ee-0310-87e3-a7336bc3aa68
>    Revision: 23545
>    Node Kind: directory
>    Schedule: normal
>    Last Changed Author: tredmond
>    Last Changed Rev: 23543
>    Last Changed Date: 2011-07-31 19:35:48 -0700 (Sun, 31 Jul 2011)
>
>    [tredmond at Saturn org.protege.osgi.jdbc.prefs]$
>
>
> -Timothy
>
>
> On 07/31/2011 08:05 PM, Victor Mataré wrote:
>> Hm, actually I'm trying to follow this advice:
>> https://babbage.inf.unibz.it/trac/obdapublic/wiki/ObdalibPluginInstallation#JDBCDriversSetup 
>>
>> Which instructs me to find the "JDBC Drivers" tab in the Protege 
>> preference panel, which is nowhere to be seen. I thought this error 
>> might be the cause for that. The symptom is the same with Protege 
>> 4.1, but I get an additional error message when opening the preferences:
>>
>> java.lang.NoClassDefFoundError: javax/swing/JPanel
>>         at java.lang.Class.getDeclaredConstructors0(Native Method)
>>         at 
>> java.lang.Class.privateGetDeclaredConstructors(Class.java:2389)
>>         at java.lang.Class.getConstructor0(Class.java:2699)
>>         at java.lang.Class.newInstance0(Class.java:326)
>>         at java.lang.Class.newInstance(Class.java:308)
>>         at 
>> org.protege.editor.core.plugin.PluginUtilities.getExtensionObject(PluginUtilities.java:131)
>>         at 
>> org.protege.editor.core.plugin.ExtensionInstantiator.instantiate(ExtensionInstantiator.java:74)
>>         at 
>> org.protege.editor.core.plugin.AbstractProtegePlugin.newInstance(AbstractProtegePlugin.java:32)
>>         at 
>> org.protege.editor.core.ui.preferences.PreferencesPanelPluginJPFImpl.newInstance(PreferencesPanelPluginJPFImpl.java:39)
>>         at 
>> org.protege.editor.core.ui.preferences.PreferencesPanelPluginJPFImpl.newInstance(PreferencesPanelPluginJPFImpl.java:18)
>>         at 
>> org.protege.editor.core.ui.preferences.PreferencesDialogPanel.<init>(PreferencesDialogPanel.java:64)
>>         at 
>> org.protege.editor.core.ui.preferences.PreferencesDialogPanel.showPreferencesDialog(PreferencesDialogPanel.java:121)
>>         at 
>> org.protege.editor.core.ui.workspace.Workspace$1.actionPerformed(Workspace.java:165)
>>         at 
>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
>>         at 
>> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
>>         at 
>> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
>>         at 
>> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
>>         at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
>>         at 
>> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
>>         at 
>> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
>>         at java.awt.Component.processMouseEvent(Component.java:6288)
>>         at 
>> javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
>>         at java.awt.Component.processEvent(Component.java:6053)
>>         at java.awt.Container.processEvent(Container.java:2041)
>>         at java.awt.Component.dispatchEventImpl(Component.java:4651)
>>         at java.awt.Container.dispatchEventImpl(Container.java:2099)
>>         at java.awt.Component.dispatchEvent(Component.java:4481)
>>         at 
>> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
>>         at 
>> java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
>>         at 
>> java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
>>         at java.awt.Container.dispatchEventImpl(Container.java:2085)
>>         at java.awt.Window.dispatchEventImpl(Window.java:2478)
>>         at java.awt.Component.dispatchEvent(Component.java:4481)
>>         at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:643)
>>         at java.awt.EventQueue.access$000(EventQueue.java:84)
>>         at java.awt.EventQueue$1.run(EventQueue.java:602)
>>         at java.awt.EventQueue$1.run(EventQueue.java:600)
>>         at java.security.AccessController.doPrivileged(Native Method)
>>         at 
>> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>>         at 
>> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
>>         at java.awt.EventQueue$2.run(EventQueue.java:616)
>>         at java.awt.EventQueue$2.run(EventQueue.java:614)
>>         at java.security.AccessController.doPrivileged(Native Method)
>>         at 
>> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
>>         at java.awt.EventQueue.dispatchEvent(EventQueue.java:613)
>>         at 
>> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>>         at 
>> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>>         at 
>> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>>         at 
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>>         at 
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>>         at 
>> java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>> Caused by: java.lang.ClassNotFoundException: javax.swing.JPanel
>>         at 
>> org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:814)
>>         at 
>> org.apache.felix.framework.ModuleImpl.access$100(ModuleImpl.java:61)
>>         at 
>> org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1733)
>>         at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>>         ... 51 more
>>
>> All in all, I just can't get JDBC to work. Moving to 4.1 is not even 
>> an option since I want to use OBDA to couple the ontology with a 
>> geospatial database, and OBDA so far supports 4.0 only. So any other 
>> idea why the "JDBC Drivers" panel might be missing?
>>
>> thanks so far...
>>
>>
>> On 01.08.2011 04:43, Timothy Redmond wrote:
>>> On 07/31/2011 05:08 PM, Victor Mataré wrote:
>>>> Hello everyone,
>>>>
>>>> I'm trying to use the OBDA plugin 
>>>> (http://obda.inf.unibz.it/protege-plugin/index.html) which requires 
>>>> Protégé 4.0 with JDBC drivers. But the Jdbc Registry Plugin 
>>>> (org.protege.osgi.jdbc.jar) seems broken:
>>>
>>> The no plugin xml is a minor problem and can be ignored.  I fixed it 
>>> in the latest svn.  The exception means that plugin failed. It 
>>> probably only does that in Protege 4.0 but this is sloppy code and I 
>>> fixed this in the latest svn also.
>>>
>>> Let me know if you need me to push an update to the repository.
>>>
>>> -Timothy
>>>
>>>
>>>>
>>>> Starting Protege 4 OWL Editor (Version 4.0.115)
>>>> Platform:
>>>>     Java: JVM 1.6.0_26-b03 Memory: 186M
>>>>     Language: de, Country: DE
>>>>     Framework: Eclipse (1.5.0)
>>>>     OS: Linux (2.6.39)
>>>>     Processor: x86-64
>>>> Installed plugin DL Query Tab
>>>> Installed plugin Protege JDBC Registry Plugin
>>>> Installed plugin owleditor
>>>> Installed plugin Jdbc Registry
>>>> Installed plugin The OWL API
>>>> Installed plugin OWLViz
>>>> Installed plugin Factplusplus Plug-in
>>>> Problem starting plugin Protege JDBC Registry Plugin
>>>> org.osgi.framework.BundleException: Exception in 
>>>> org.protege.osgi.jdbc.prefs.Activator.start() of bundle 
>>>> org.protege.osgi.jdbc.prefs.
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActivator(BundleContextImpl.java:805)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(BundleContextImpl.java:754)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(BundleHost.java:352)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.AbstractBundle.start(AbstractBundle.java:280)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.AbstractBundle.start(AbstractBundle.java:272)
>>>>         at 
>>>> org.protege.editor.core.BundleManager.startPlugins(BundleManager.java:144)
>>>>         at 
>>>> org.protege.editor.core.BundleManager.loadPlugins(BundleManager.java:45) 
>>>>
>>>>         at 
>>>> org.protege.editor.core.ProtegeApplication.loadPlugins(ProtegeApplication.java:263)
>>>>         at 
>>>> org.protege.editor.core.ProtegeApplication.initApplication(ProtegeApplication.java:158)
>>>>         at 
>>>> org.protege.editor.core.ProtegeApplication.start(ProtegeApplication.java:105)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl$1.run(BundleContextImpl.java:782)
>>>>         at java.security.AccessController.doPrivileged(Native Method)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActivator(BundleContextImpl.java:773)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl.start(BundleContextImpl.java:754)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleHost.startWorker(BundleHost.java:352)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.AbstractBundle.resume(AbstractBundle.java:370)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.Framework.resumeBundle(Framework.java:1068)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.StartLevelManager.resumeBundles(StartLevelManager.java:557)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.StartLevelManager.incFWSL(StartLevelManager.java:464)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.StartLevelManager.doSetStartLevel(StartLevelManager.java:248)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.StartLevelManager.dispatchEvent(StartLevelManager.java:445)
>>>>         at 
>>>> org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:220)
>>>>         at 
>>>> org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.run(EventManager.java:330)
>>>> Caused by: java.lang.NullPointerException: A null service reference 
>>>> is not allowed.
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl.getService(BundleContextImpl.java:659)
>>>>         at 
>>>> org.protege.osgi.jdbc.prefs.Activator.start(Activator.java:20)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl$1.run(BundleContextImpl.java:782)
>>>>         at java.security.AccessController.doPrivileged(Native Method)
>>>>         at 
>>>> org.eclipse.osgi.framework.internal.core.BundleContextImpl.startActivator(BundleContextImpl.java:773)
>>>>         ... 22 more
>>>>         Jdbc Registry Plugin has no plugin.xml resource
>>>>
>>>> This happens with both 4.0.2 and 4.1. I've also compiled the latest 
>>>> org.protege.osgi.jdbc.jar from SVN rev 19106, but that's also 
>>>> missing the plugin.xml. This looks a lot like there has never been 
>>>> any plugin.xml, so I assume I'm not understanding the problem. Any 
>>>> help is much appreciated.
>>>>
>>>> regards,
>>>> Victor
>>>>
>>>>
>>>> _______________________________________________
>>>> protege-discussion mailing list
>>>> protege-discussion at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>>
>>>> Instructions for unsubscribing: 
>>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> protege-discussion mailing list
>>> protege-discussion at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>
>>> Instructions for unsubscribing: 
>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>
>
>

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