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[protege-owl] An OWL Database Backend BUG!

Congmin min marlonmin at gmail.com
Tue Sep 5 12:11:10 PDT 2006


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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