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[protege-discussion] Frozen Instance editor window

Bo De Lange bodelange at gmail.com
Tue Jul 3 09:58:39 PDT 2007


dear Tania,


On 03/07/07, Tania Tudorache <tudorache at stanford.edu> wrote:
>
> Hi Bo,
>
> It looks like you are using the multi-user Protege client, right? And it
> looks like the Prompt plugin is activated. In the current version,
> Prompt has not been tested in multi-user mode. We recommend that you use
> Prompt in the stand-alone mode. You can use Prompt on the server
> projects, but starting Protege in stand-alone mode on the server side.
> We will fix this limitation in the future releases.



We shall deactivate the Prompt plugin

There is also another error that should not be there:
>
> java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
>
> Are you using a database project? If so, did you add the database driver
> as driver.jar in the Protege installation directory?
>
> In order to debug this, I need the client and server logs for when the
> problem occurred. The logs are located in the logs folder of the Protege
> installation directory. The logs are overwritten each time you start
> Protege, so please send me the client and server logs before restarting
> Protege.



I'll get back to you on this one. We are experimenting with an sql database
project, but this particular problem occurred when not working on that
project. In order to fix the problem, the only solution was to restart
Protege, so the required log files will have been overwritten. I shall copy
them next time the error occurs.

Did you you have ChangesTab or Collaborative Protege activated, when the
> error occurred?



Nope

Thanks,
> Tania



HTH,

 Bo



Bo De Lange wrote:
> > Hi there,
> >
> > it just happened again, with a colleague. She was working in the
> > Instances tab and had just deleted an instance. The instance
> > disappeared from the middele window frame (Instance Browser), but not
> > from the right window frame (Instance editor). The Instance editor
> > frame was frozen, i.e. she could click through classes and instances,
> > but the frame was not updated.
> >
> > Here's what I grabbed from the Protege.exe terminal window:
> >
> > cwd: C:\Program Files\Protege_3.3_beta\
> > cmd: "C:\Program Files\Protege_3.3_beta\jre\bin\java.exe"
> > -Xms100000000 -Xmx3000
> > 00000 -classpath "C:\Program
> > Files\Protege_3.3_beta\protege.jar;C:\Program Files
> > \Protege_3.3_beta\looks-2.1.3.jar;C:\Program
> > Files\Protege_3.3_beta\unicode_pane
> > l.jar;C:\Program Files\Protege_3.3_beta\driver.jar;C:\Program
> > Files\Protege_3.3_
> > beta\driver0.jar;C:\Program
> > Files\Protege_3.3_beta\driver1.jar;C:\Program Files\
> > Protege_3.3_beta\driver2.jar;C:\Program
> > Files\Protege_3.3_beta\plugins\edu.stanf
> > ord.smi.protegex.changes\change-model.jar;C:\Program
> > Files\Protege_3.3_beta\lax.
> > jar;" com.zerog.lax.LAX "C:/Program
> > Files/Protege_3.3_beta/Protege.lax" "C:/Docu
> > ments and Settings/Lyna/Local Settings/Temp/laxB.tmp"
> > CONFIG: Protege 3.3 Build 409, JVM 1.5.0_11-b03, memory=299M, Windows
> > XP, encodi
> > ng=UTF-8, language=nl, country=NL
> > CONFIG: Loaded plugin ceres
> > CONFIG: Loaded plugin edu.stanford.smi.protege.script - Script Plugin
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.standard_extensions -
> > Graph Widg
> > et, Table Widget
> > CONFIG: Loaded plugin edu.stanford.smi.protege.stringsearch - String
> > Search Tab
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.chatPlugin
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.datamaster -
> > DataMaster Tab
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.facets_tab
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.instance_tree
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF
> Backend
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.psm - PSM Librarian
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab
> > CONFIG: Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
> > CONFIG: Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
> > CONFIG: Preloading frame values
> > CONFIG: Preloading frame values
> > WARNING: Missing map instance: FSD_2_0_0_0_ProjectKB_Instance_227038
> > -- Property
> > MapUtil.getMap()
> > WARNING: null -- WidgetUtilities.isSuitableExport()
> > WARNING: null -- WidgetUtilities.isSuitableExport()
> > CONFIG: PROMPT: Loaded plugin ca.uvic.cs.cogz.PromptUIPlugin - CogZ
> > CONFIG: PROMPT: Loaded plugin
> > edu.stanford.smi.protegex.promptx.foam.FoamPlugin
> > - FOAM Plugin for Prompt
> > CONFIG: PROMPT: Loaded plugin
> > edu.stanford.smi.protegex.promptx.mappingDomainPSM
> > .MappingDomainPSM - Store mappings using the Domain_PSM ontology
> > CONFIG: PROMPT: Loaded plugin
> > edu.stanford.smi.protegex.promptx.simpleMappingSto
> > rage.SimpleMappingStorage - Store mapping using a simple mapping
> ontology
> > CONFIG: PROMPT: Loaded plugin
> > edu.stanford.smi.protegex.promptx.synonyms.Synonym
> > Plugin - Lexical matching with synonyms
> > CONFIG: PROMPT: Loaded plugin
> > edu.stanford.smi.protegex.promptx.umls.UMLSPlugin
> > - Using UMLS concept identifiers for matching
> > INFO: Prompt version 3.0
> > INFO: Prompt version date: August 8, 2006
> > java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
> > INFO: UI display time = 81 sec
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> > WARNING: Exception caught during event dispatch - see the log for
> > details - java
> > .lang.NullPointerException -- EventDispatchFrameStore.dispatchEvents()
> >
> >
> > Bo
> >
> >
> > On 02/07/07, *Tania Tudorache* <tudorache at stanford.edu
> > <mailto:tudorache at stanford.edu>> wrote:
> >
> >     Hi Bo,
> >
> >     Thanks for the bug report. What version of Protege are you using?
> >
> >     From the stack trace it looks like the browser text of an instance
> was
> >     changed, and either the type of the instance became null (which
> should
> >     never happen) or the browser pattern of the instance type could
> >     not be
> >     found.
> >
> >     Do you have some steps to reproduce this behavior? I am sure this
> >     bug is
> >     easy to be fixed, if we can reproduce it.
> >
> >     Thanks,
> >     Tania
> >
> >
> >
> >     Bo De Lange wrote:
> >     > Hi,
> >     >
> >     > we're having recurrent problems with a frozen Instance editor
> >     window.
> >     > Whilst in the Instances tab and clicking through the instances of
> a
> >     > class, the editor window on the right is not updated.
> >     > Only restarting Protege seems to help to fix the problem.
> >     >
> >     > This is what I captured from the logfile:
> >     >
> >     > 2007.06.21 16:08:51.692 CEST WARNING: Exception caught during
> event
> >     > dispatch - see the log for details -
> >     java.lang.NullPointerException --
> >     > EventDispatchFrameStore.dispatchEvents()
> >     > 2007.06.21 16:08:51.708 CEST FINE: Exception caught --
> >     > java.lang.NullPointerException
> >     >  at edu.stanford.smi.protege.ui.FrameRenderer.appendType(Unknown
> >     Source)
> >     >  at edu.stanford.smi.protege.ui.FrameRenderer.loadInstance
> >     (Unknown Source)
> >     >  at edu.stanford.smi.protege.ui.FrameRenderer.load(Unknown Source)
> >     >  at edu.stanford.smi.protege.util.DefaultRenderer.setup(Unknown
> >     Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.util.DefaultRenderer.getListCellRendererComponent
> >     (Unknown
> >     > Source)
> >     >  at javax.swing.plaf.basic.BasicListUI.updateLayoutState(Unknown
> >     Source)
> >     >  at
> >     javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(Unknown
> >     > Source)
> >     >  at javax.swing.plaf.basic.BasicListUI$Handler.valueChanged(Unknown
> >     > Source)
> >     >  at
> >     javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown
> Source)
> >     >  at
> >     javax.swing.DefaultListSelectionModel.fireValueChanged(Unknown
> Source)
> >     >  at javax.swing.DefaultListSelectionModel.fireValueChanged
> >     (Unknown Source)
> >     >  at
> >     javax.swing.DefaultListSelectionModel.insertIndexInterval(Unknown
> >     > Source)
> >     >  at javax.swing.plaf.basic.BasicListUI$Handler.intervalAdded
> (Unknown
> >     > Source)
> >     >  at javax.swing.AbstractListModel.fireIntervalAdded (Unknown
> Source)
> >     >  at edu.stanford.smi.protege.util.SimpleListModel.setValues
> (Unknown
> >     > Source)
> >     >  at edu.stanford.smi.protege.ui.DirectInstancesList.sort(Unknown
> >     Source)
> >     >  at
> >     >
> >     edu.stanford.smi.protege.ui.DirectInstancesList$3.browserTextChanged
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dispatchFrameEvent
> (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dispatchEvent
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dispatchEvents
> (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dispatchEvents
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.dispatchEvents
> (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.EventDispatchFrameStore.commitTransaction
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.ArgumentCheckingFrameStore.commitTransaction
> (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.ChangeMonitorFrameStore.commitTransaction
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.commitTransaction
> (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.FrameStoreAdapter.commitTransaction
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.framestore.DeleteSimplificationFrameStore.deleteSimpleInstance
> (Unknown
> >     > Source)
> >     >  at
> >     >
> >
> edu.stanford.smi.protege.model.DefaultKnowledgeBase.deleteSimpleInstance
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >     edu.stanford.smi.protege.model.DefaultKnowledgeBase.deleteFrame
> (Unknown
> >     > Source)
> >     >  at
> >     >
> >     edu.stanford.smi.protege.action.DeleteInstancesAction.deleteInstance
> >     (Unknown
> >     > Source)
> >     >  at
> >     >
> >     edu.stanford.smi.protege.action.DeleteInstancesAction.onDelete
> (Unknown
> >     > Source)
> >     >  at edu.stanford.smi.protege.util.DeleteAction.onDelete(Unknown
> >     Source)
> >     >  at edu.stanford.smi.protege.util.DeleteAction.onDelete(Unknown
> >     Source)
> >     >  at
> >     edu.stanford.smi.protege.util.DeleteAction.actionPerformed(Unknown
> >     > Source)
> >     >  at javax.swing.AbstractButton.fireActionPerformed (Unknown
> Source)
> >     >  at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
> >     Source)
> >     >  at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
> >     Source)
> >     >  at javax.swing.DefaultButtonModel.setPressed (Unknown Source)
> >     >  at javax.swing.plaf.basic.BasicButtonListener.mouseReleased
> (Unknown
> >     > Source)
> >     >  at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
> >     >  at java.awt.Component.processMouseEvent (Unknown Source)
> >     >  at javax.swing.JComponent.processMouseEvent(Unknown Source)
> >     >  at java.awt.Component.processEvent(Unknown Source)
> >     >  at java.awt.Container.processEvent(Unknown Source)
> >     >  at java.awt.Component.dispatchEventImpl (Unknown Source)
> >     >  at java.awt.Container.dispatchEventImpl(Unknown Source)
> >     >  at java.awt.Component.dispatchEvent(Unknown Source)
> >     >  at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
> >     Source)
> >     >  at java.awt.LightweightDispatcher.processMouseEvent(Unknown
> Source)
> >     >  at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
> >     >  at java.awt.Container.dispatchEventImpl(Unknown Source)
> >     >  at java.awt.Window.dispatchEventImpl(Unknown Source)
> >     >  at java.awt.Component.dispatchEvent(Unknown Source)
> >     >  at java.awt.EventQueue.dispatchEvent(Unknown Source)
> >     >  at java.awt.EventDispatchThread.pumpOneEventForHierarchy
> >     (Unknown Source)
> >     >  at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
> >     Source)
> >     >  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> >     >  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> >     >  at java.awt.EventDispatchThread.run(Unknown Source)
> >     >
> >     >
> >     > Any clues?
> >     >
> >     > Thanks,
> >     >
> >     >
> >     >
> >     > Bo
> >     >
> >
> ------------------------------------------------------------------------
> >
> >     >
> >     > _______________________________________________
> >     > protege-discussion mailing list
> >     > protege-discussion at lists.stanford.edu
> >     <mailto: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
> >     <http://protege.stanford.edu/doc/faq.html#01a.03>
> >     >
> >
> >     _______________________________________________
> >     protege-discussion mailing list
> >     protege-discussion at lists.stanford.edu
> >     <mailto: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
> >
> >
> >
> >
> > --
> > RPJ de Lange, PhD
> > Emotional Brain BV
> > Louis Armstrongweg 78
> > 1311 RL  Almere
> >
> > tel        :  +31 (0)36 - 546 83 46
> > fax       :  +31 (0)36 - 549 71 86
> > e-mail  :   b.delange at emotionalbrain.nl
> > <mailto:b.delange at emotionalbrain.nl>
> > web     :  http://www.emotionalbrain.nl
>
> _______________________________________________
> 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
>



-- 
RPJ de Lange, PhD
Emotional Brain BV
Louis Armstrongweg 78
1311 RL  Almere

tel        :  +31 (0)36 - 546 83 46
fax       :  +31 (0)36 - 549 71 86
e-mail  :  b.delange at emotionalbrain.nl
web     :  http://www.emotionalbrain.nl
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