Error when refactoring ontology

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Error when refactoring ontology

Matthew Lange
We are trying to refactor an ontology that was created "incorrectly" with labels where the IRI identifiers. When using the command 'Convert entity URIs to labels' we receive the error below. Please help as the prospect of refactoring this ontology with thousands of entities by hand sure seems daunting.
Kind regards,
~Matthew

Error 12 Logged at Wed Feb 21 12:29:05 PST 2018
StringIndexOutOfBoundsException: String index out of range: -1
    java.lang.String.substring(Unknown Source)
    org.protege.editor.owl.model.refactor.ontology.OWLEntityIRIRegenerator.getBaseIRI(OWLEntityIRIRegenerator.java:93)
    org.protege.editor.owl.model.refactor.ontology.OWLEntityIRIRegenerator.generateNewIRI(OWLEntityIRIRegenerator.java:68)
    org.protege.editor.owl.model.refactor.ontology.ConvertEntityURIsToIdentifierPattern.buildNewIRIMap(ConvertEntityURIsToIdentifierPattern.java:124)
    org.protege.editor.owl.model.refactor.ontology.ConvertEntityURIsToIdentifierPattern.performConversion(ConvertEntityURIsToIdentifierPattern.java:56)
    org.protege.editor.owl.ui.action.ConvertEntityURIsToLabels.performConversion(ConvertEntityURIsToLabels.java:87)
    org.protege.editor.owl.ui.action.ConvertEntityURIsToLabels.actionPerformed(ConvertEntityURIsToLabels.java:75)
    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    javax.swing.AbstractButton.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)
---------------------------------------------------------------------------------------------------



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Re: Error when refactoring ontology

Csongor Nyulas
Administrator
Can we see the ontology? It impossible to tell what the problem is without seeing the ontology.

Csongor


On 02/21/2018 12:47 PM, Matthew Lange wrote:
We are trying to refactor an ontology that was created "incorrectly" with labels where the IRI identifiers. When using the command 'Convert entity URIs to labels' we receive the error below. Please help as the prospect of refactoring this ontology with thousands of entities by hand sure seems daunting.
Kind regards,
~Matthew

Error 12 Logged at Wed Feb 21 12:29:05 PST 2018
StringIndexOutOfBoundsException: String index out of range: -1
    java.lang.String.substring(Unknown Source)
    org.protege.editor.owl.model.refactor.ontology.OWLEntityIRIRegenerator.getBaseIRI(OWLEntityIRIRegenerator.java:93)
    org.protege.editor.owl.model.refactor.ontology.OWLEntityIRIRegenerator.generateNewIRI(OWLEntityIRIRegenerator.java:68)
    org.protege.editor.owl.model.refactor.ontology.ConvertEntityURIsToIdentifierPattern.buildNewIRIMap(ConvertEntityURIsToIdentifierPattern.java:124)
    org.protege.editor.owl.model.refactor.ontology.ConvertEntityURIsToIdentifierPattern.performConversion(ConvertEntityURIsToIdentifierPattern.java:56)
    org.protege.editor.owl.ui.action.ConvertEntityURIsToLabels.performConversion(ConvertEntityURIsToLabels.java:87)
    org.protege.editor.owl.ui.action.ConvertEntityURIsToLabels.actionPerformed(ConvertEntityURIsToLabels.java:75)
    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    javax.swing.AbstractButton.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)
---------------------------------------------------------------------------------------------------




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Re: Error when refactoring ontology

Matthew Horridge-2
Administrator
Hi Matthew,

If you could share the ontology with us that would be great.

Cheers,

Matthew


On 21 Feb 2018, at 14:38, Csongor Nyulas <[hidden email]> wrote:

Can we see the ontology? It impossible to tell what the problem is without seeing the ontology.

Csongor


On 02/21/2018 12:47 PM, Matthew Lange wrote:
We are trying to refactor an ontology that was created "incorrectly" with labels where the IRI identifiers. When using the command 'Convert entity URIs to labels' we receive the error below. Please help as the prospect of refactoring this ontology with thousands of entities by hand sure seems daunting.
Kind regards,
~Matthew

Error 12 Logged at Wed Feb 21 12:29:05 PST 2018
StringIndexOutOfBoundsException: String index out of range: -1
    java.lang.String.substring(Unknown Source)
    org.protege.editor.owl.model.refactor.ontology.OWLEntityIRIRegenerator.getBaseIRI(OWLEntityIRIRegenerator.java:93)
    org.protege.editor.owl.model.refactor.ontology.OWLEntityIRIRegenerator.generateNewIRI(OWLEntityIRIRegenerator.java:68)
    org.protege.editor.owl.model.refactor.ontology.ConvertEntityURIsToIdentifierPattern.buildNewIRIMap(ConvertEntityURIsToIdentifierPattern.java:124)
    org.protege.editor.owl.model.refactor.ontology.ConvertEntityURIsToIdentifierPattern.performConversion(ConvertEntityURIsToIdentifierPattern.java:56)
    org.protege.editor.owl.ui.action.ConvertEntityURIsToLabels.performConversion(ConvertEntityURIsToLabels.java:87)
    org.protege.editor.owl.ui.action.ConvertEntityURIsToLabels.actionPerformed(ConvertEntityURIsToLabels.java:75)
    javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    javax.swing.AbstractButton.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
    java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)
---------------------------------------------------------------------------------------------------




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protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
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[hidden email]
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