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[protege-owl] An OWL Database Backend BUG!

Tania Tudorache tudorache at stanford.edu
Wed Sep 6 10:34:46 PDT 2006


Congmin,

Thank you for reporting this bug. I have added a bugzilla entry for it: 
http://171.65.65.92/bugzilla/show_bug.cgi?id=159

Even if your OWL file is bigger than 50MB, you should try to load it 
into Protege (by increasing the heap size: 
http://protege.cim3.net/cgi-bin/wiki.pl?SettingHeapSize) and then 
convert the Project to OWL DB format.

Tania


Congmin min wrote:

> Hi, is this a protege-owl bug?
>
> I want to use database backend, and I have no problem to converting a 
> owl file ontology into a database ontology. But to do that, I have to 
> first load the owl file into protege and then
> use 'File/convert project to format/owl/rdf database'.
>
> However, my ontology is too large, the file can't be loaded into 
> protege, then I have to use create a new project as follows:
>
> 1) File
> 2) New Project
> 3) OWL/RDF Database (using existing sources)
> 4) OWL File
> ...
>
> After everything is done, I have the following exception (even for 
> very small owl file). Is this a bug? if so, can it be fixed!! I need 
> the database option urgently.
>
> java.lang.IndexOutOfBoundsException: Index: 0
>     at java.util.Collections$EmptyList.get(Collections.java:2923)
>     at 
> edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStoreModel.setHomeTripleStore(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.model.triplestore.impl.AddRDFTypePropertyHandler.handleAdd(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.model.triplestore.impl.AbstractTripleStore.add(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$MyStatementHandler.statement(Unknown 
> Source)
>     at com.hp.hpl.jena.rdf.arp.ARPResource.tripleRes(ARPResource.java:185)
>     at com.hp.hpl.jena.rdf.arp.ARPResource.triple(ARPResource.java:170)
>     at 
> com.hp.hpl.jena.rdf.arp.ARPResource.setPredObject(ARPResource.java:147)
>     at com.hp.hpl.jena.rdf.arp.ARPResource.setType(ARPResource.java:142)
>     at com.hp.hpl.jena.rdf.arp.RDFParser.typedNode(RDFParser.java:961)
>     at com.hp.hpl.jena.rdf.arp.RDFParser.description(RDFParser.java:433)
>     at com.hp.hpl.jena.rdf.arp.RDFParser.obj(RDFParser.java:346)
>     at com.hp.hpl.jena.rdf.arp.RDFParser.rdf(RDFParser.java:326)
>     at com.hp.hpl.jena.rdf.arp.RDFParser.rdfFileSub(RDFParser.java:107)
>     at com.hp.hpl.jena.rdf.arp.RDFParser.rdfFile(RDFParser.java:99)
>     at 
> com.hp.hpl.jena.rdf.arp.SingleThreadedParser.parse(SingleThreadedParser.java:146)
>     at com.hp.hpl.jena.rdf.arp.ARP.load(ARP.java:136)
>     at 
> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$1.invokeARP(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown 
> Source)
>     at 
> edu.stanford.smi.protegex.owl.database.CreateOWLDatabaseFromFileProjectPlugin.buildNewProject(Unknown 
> Source)
>     at 
> edu.stanford.smi.protege.plugin.AbstractCreateProjectPlugin.createProject(Unknown 
> Source)
>     at 
> edu.stanford.smi.protege.plugin.CreateProjectWizard.onFinish(Unknown 
> Source)
>     at edu.stanford.smi.protege.util.Wizard$1.actionPerformed(Unknown 
> Source)
>     at 
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1834)
>     at 
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2152)
>     at 
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
>     at 
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>     at 
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:234)
>     at java.awt.Component.processMouseEvent(Component.java:5463)
>     at javax.swing.JComponent.processMouseEvent(JComponent.java:3052)
>     at java.awt.Component.processEvent(Component.java:5228)
>     at java.awt.Container.processEvent(Container.java:1961)
>     at java.awt.Component.dispatchEventImpl(Component.java:3931)
>     at java.awt.Container.dispatchEventImpl(Container.java:2019)
>     at java.awt.Component.dispatchEvent(Component.java:3779)
>     at 
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4203)
>     at 
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3883)
>     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3813)
>     at java.awt.Container.dispatchEventImpl(Container.java:2005)
>     at java.awt.Window.dispatchEventImpl(Window.java:1757)
>     at java.awt.Component.dispatchEvent(Component.java:3779)
>     at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>     at 
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:234)
>     at 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
>     at 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:153)
>     at java.awt.Dialog+1.run(Dialog.java:514)
>     at java.awt.Dialog.show(Dialog.java:535)
>     at java.awt.Component.show(Component.java:1292)
>     at java.awt.Component.setVisible(Component.java:1247)
>     at edu.stanford.smi.protege.util.Wizard.execute(Unknown Source)
>     at 
> edu.stanford.smi.protege.ui.ProjectManager.createNewProjectRequest(Unknown 
> Source)
>     at 
> edu.stanford.smi.protege.action.CreateProject.actionPerformed(Unknown 
> Source)
>     at 
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1834)
>     at 
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2152)
>     at 
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
>     at 
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>     at javax.swing.AbstractButton.doClick(AbstractButton.java:302)
>     at 
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
>     at 
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1041)
>     at java.awt.Component.processMouseEvent(Component.java:5463)
>     at javax.swing.JComponent.processMouseEvent(JComponent.java:3052)
>     at java.awt.Component.processEvent(Component.java:5228)
>     at java.awt.Container.processEvent(Container.java:1961)
>     at java.awt.Component.dispatchEventImpl(Component.java:3931)
>     at java.awt.Container.dispatchEventImpl(Container.java:2019)
>     at java.awt.Component.dispatchEvent(Component.java:3779)
>     at 
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4203)
>     at 
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3883)
>     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3813)
>     at java.awt.Container.dispatchEventImpl(Container.java:2005)
>     at java.awt.Window.dispatchEventImpl(Window.java:1757)
>     at java.awt.Component.dispatchEvent(Component.java:3779)
>     at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>     at 
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:234)
>     at 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
>     at 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>     at 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>     at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
>
>
>
>------------------------------------------------------------------------
>
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>protege-owl at lists.stanford.edu
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>  
>




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