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[protege-discussion] Exporting from Protege Database to OWL

Cecil O. Lynch, MD, MS clynch at surewest.net
Wed Apr 30 18:11:30 PDT 2008


Tania,

BTW, I just tried using 3.4 build 130 both with and without the native
writer checked and failed on both. You should have the files now. Let me
know if the zip file did not make it through the firewalls and I will rename
and resend.

thanks

Cecil

-----Original Message-----
From: protege-discussion-bounces at mailman.stanford.edu
[mailto:protege-discussion-bounces at mailman.stanford.edu] On Behalf Of Tania
Tudorache
Sent: Wednesday, April 30, 2008 5:24 PM
To: User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] Exporting from Protege Database to OWL

Hi Cecil,

I assume you tried File -> Export to Format -> OWL. Did you try to 
enable the chechbox "Use Protege native writer"?

I have just tried now to export a project from Frames DB to an OWL file 
and I did not reproduce the exception.

Can you send me privately a dump of the ontology that caused this behavior?

Tania


Cecil O. Lynch, MD, MS wrote:
>
> Tania,
>
> I am trying to export a very simple (but moderate size) Protégé 
> database file to OWL and get the following trace:
>
> cwd: C:\Program Files\Protege_3.3.1\
> cmd: "C:\Program Files\Protege_3.3.1\jre\bin\java.exe" -Xms1215098112 
> -Xmx121509
> 8112 -classpath "C:\Program Files\Protege_3.3.1\protege.jar;C:\Program 
> Files\Pro
> tege_3.3.1\looks-2.1.3.jar;C:\Program 
> Files\Protege_3.3.1\unicode_panel.jar;C:\P
> rogram Files\Protege_3.3.1\driver.jar;C:\Program 
> Files\Protege_3.3.1\dbdrivers\m
> ysql-connector-java-5.1.6-bin.jar;C:\Program 
> Files\Protege_3.3.1\driver1.jar;C:\
> Program Files\Protege_3.3.1\driver2.jar;C:\Program 
> Files\Protege_3.3.1\plugins\e
> du.stanford.smi.protegex.changes\change-model.jar;C:\Program 
> Files\Protege_3.3.1
> \lax.jar;" com.zerog.lax.LAX "C:/Program 
> Files/Protege_3.3.1/Protege.lax" "C:/Do
> cuments and Settings/Cecil/Local Settings/Temp/lax98.tmp"
> CONFIG: Protege 3.3.1 Build 430, JVM 1.5.0_11-b03, memory=1207M, 
> Windows XP, enc
> oding=UTF-8, language=en, country=US
> CONFIG: Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
> CONFIG: Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
> CONFIG: Loaded plugin com.ngs - ONTOBaseTab
> WARNING: java.lang.NoClassDefFoundError: 
> edu/stanford/smi/protege/widget/_Abstra
> ctWidget -- PluginUtilities.isLoadableClass()
> WARNING: missing file: doc/index.html -- PluginUtilities.loadURL()
> CONFIG: Loaded plugin dfki.protege.ontoviz
> CONFIG: Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend
> CONFIG: Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
> CONFIG: Loaded plugin edu.stanford.smi.protegex.chatPlugin
> CONFIG: Loaded plugin edu.stanford.smi.protege.collab - Collaborative 
> Protege
> 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.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.prompt - PROMPT Tab
> 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 images
> CONFIG: Loaded plugin OntoReason.DataImport.v2
> CONFIG: Loaded plugin org.algernon - Algernon
> CONFIG: Loaded plugin org.ecoinformatics.seek.growl.protegex - GrOWL View
> CONFIG: Loaded plugin plugins
> CONFIG: Loaded plugin se.liu.ida.JessTab - JessTab Plugin
> CONFIG: Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.debugger
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owldoc
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.owlviz
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic 
> Wizards
> CONFIG: Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL 
> Wizards
> INFO: Load time for file:\C:\Program%20Files\Protege_3.3.1\CHT.pprj 
> <file:%5CC:%5CProgram%20Files%5CProtege_3.3.1%5CCHT.pprj> = 0 sec (pro
> ject) + 1 sec (ui)
> [ProtegeUI]  Warning: No ProjectView registered for project CHT
> [ProtegeUI]  Warning: No ProjectView registered for project CHT
> SEVERE: Exception caught -- java.lang.ClassCastException: 
> edu.stanford.smi.prote
> ge.model.DefaultCls
>         at 
> edu.stanford.smi.protegex.owl.model.impl.AbstractOWLModel.createOWLNa
> medClass(Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.storage.ProtegeSaver.createCls(Unknown
> Source)
>         at 
> edu.stanford.smi.protegex.owl.storage.KnowledgeBaseCopier.getNewCls(U
> nknown Source)
>         at 
> edu.stanford.smi.protegex.owl.storage.ProtegeSaver.getNewCls(Unknown
> Source)
>         at 
> edu.stanford.smi.protegex.owl.storage.KnowledgeBaseCopier.createClses
> (Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.storage.KnowledgeBaseCopier.run(Unknown
>  Source)
>         at 
> edu.stanford.smi.protegex.owl.jena.export.JenaExportPlugin.exportProj
> ect(Unknown Source)
>         at 
> edu.stanford.smi.protegex.owl.jena.export.JenaExportPlugin.handleExpo
> rtRequest(Unknown Source)
>         at 
> edu.stanford.smi.protege.ui.ProjectManager.exportProjectRequest(Unkno
> wn Source)
>         at 
> edu.stanford.smi.protege.action.ExportPluginAction.actionPerformed(Un
> known Source)
>         at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>         at javax.swing.AbstractButton$Handler.actionPerformed(Unknown 
> Source)
>         at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown 
> Source)
>         at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>         at javax.swing.AbstractButton.doClick(Unknown Source)
>         at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>         at 
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.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)
>
> I am using Protégé 3.3.1 Build 430 on an XP platform
>

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