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SPARQL Query tab not initializing properly when loading some ontologies #625

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samsontu opened this issue Mar 16, 2017 · 3 comments

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@samsontu
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@samsontu samsontu commented Mar 16, 2017

Protege 5.2.0 (not present in Protege 5.1.0)

Steps to reproduce:

  1. Start Protege 5.2.0
  2. Add SPARQL Query tab
  3. Load http://www.w3.org/ns/prov-o

The SPARQL Query tab is blank
Log:
ERROR: 15:12:47 Uncaught Exception in thread 'AWT-EventQuery-0' (see log file for more details)
Log file:

...
2017-03-16 15:12:44.839 [AWT-EventQueue-0] INFO TabbedWorkspace Disposed of 'DL Query' tab
2017-03-16 15:12:44.840 [AWT-EventQueue-0] INFO TabbedWorkspace Disposed of workspace
2017-03-16 15:12:44.842 [AWT-EventQueue-0] INFO OWLEditorKit
2017-03-16 15:12:47.276 [AWT-EventQueue-0] ERROR ProtegeApplication Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V
at org.protege.owl.rdf.impl.RDFTranslator.(RDFTranslator.java:91) ~[na:na]
at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]
at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]
at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]
at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]
at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:44) ~[na:na]
at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:34) ~[na:na]
at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]
at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]
at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]
at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]
at java.awt.Component.processHierarchyEvent(Component.java:6692) ~[na:1.8.0_40]
at java.awt.Component.processEvent(Component.java:6311) ~[na:1.8.0_40]
at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]
at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]
at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]
at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
at java.awt.Component.createHierarchyEvents(Component.java:5541) ~[na:1.8.0_40]
at java.awt.Container.createHierarchyEvents(Container.java:1443) ~[na:1.8.0_40]
at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
at java.awt.Container.createHierarchyEvents(Container.java:1439) ~[na:1.8.0_40]
at java.awt.Component.show(Component.java:1622) ~[na:1.8.0_40]
at java.awt.Component.show(Component.java:1654) ~[na:1.8.0_40]
at java.awt.Component.setVisible(Component.java:1606) ~[na:1.8.0_40]
at javax.swing.JComponent.setVisible(JComponent.java:2644) ~[na:1.8.0_40]
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:394) ~[na:1.8.0_40]
at javax.swing.JTabbedPane$ModelListener.stateChanged(JTabbedPane.java:270) ~[na:1.8.0_40]
at javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:132) ~[na:1.8.0_40]
at javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67) ~[na:1.8.0_40]
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616) ~[na:1.8.0_40]
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591) ~[na:1.8.0_40]
at javax.swing.plaf.basic.BasicTabbedPaneUI$Handler.mousePressed(BasicTabbedPaneUI.java:3647) ~[na:1.8.0_40]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) ~[na:1.8.0_40]
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279) ~[na:1.8.0_40]
at java.awt.Component.processMouseEvent(Component.java:6522) ~[na:1.8.0_40]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_40]
at java.awt.Component.processEvent(Component.java:6290) ~[na:1.8.0_40]
at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]
at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]
at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]
at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) ~[na:1.8.0_40]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4530) ~[na:1.8.0_40]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) ~[na:1.8.0_40]
at java.awt.Container.dispatchEventImpl(Container.java:2278) ~[na:1.8.0_40]
at java.awt.Window.dispatchEventImpl(Window.java:2750) ~[na:1.8.0_40]
at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751) ~[na:1.8.0_40]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_40]
at java.awt.EventQueue$3.run(EventQueue.java:702) ~[na:1.8.0_40]
at java.awt.EventQueue$3.run(EventQueue.java:696) ~[na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) ~[na:1.8.0_40]
at java.awt.EventQueue$4.run(EventQueue.java:724) ~[na:1.8.0_40]
at java.awt.EventQueue$4.run(EventQueue.java:722) ~[na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:721) ~[na:1.8.0_40]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]

@matthewhorridge

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@matthewhorridge matthewhorridge commented Mar 17, 2017

Looks like this is due to some internal changes in the OWL API (this SPARQL tab relies on non-public constructors and classes). It needs updating.

@csnyulas

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@csnyulas csnyulas commented Apr 11, 2017

This has been fixed with new release of rdf-library and sparql-query-plugin.

To get the fix update the the "OWLAPI RDF Library" and "Protege SPARQL Plugin" to the latest version with the auto-update mechanism (which appears when starting up Protege or can be activated through the File -> Check for plugins... menu):

protege_update_sparql_plugin_to_v2 0 3

@csnyulas csnyulas closed this Apr 11, 2017
@ying6991

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@ying6991 ying6991 commented Feb 7, 2018

@csnyulas
After following the above steps, the SPARQL Query tab is still not working. But I copy all the files of Protégé 5.2 to other computers, it is able to show. Do you know how to solve that? Thanks.
The following screen shots are showing the versions of all the plugins installed and a SPARQL query tab.

1

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3

4

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