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[protege-discussion] Exporting from Protege Database to OWL

Tania Tudorache tudorache at stanford.edu
Wed Apr 30 17:24:13 PDT 2008


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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