cellLabelChanged Intercepted

[Joseph-Zalewski]

After editing for a few minutes, I double clicked on a class to change its name (its name was still "Class" since it had just been created.) The text in the cell shifted up and to the left a little as if it were selected, but was not highlighted as usual. I could not edit it, and could move the cell but not delete it. When this happened, all other text labels started showing the same behavior - as the log is probably showing, I tried double-clicking on many of them.

INFO 13:13:23 ------------------------------------ Protege -----------------------------------
INFO 13:13:23 Protege Desktop
INFO 13:13:23 Version 5.5.0, Build
INFO 13:13:23
INFO 13:13:23
INFO 13:13:23 ----------------------------------- Platform -----------------------------------
INFO 13:13:23 Java: JVM 1.8.0_121-b13 Memory: 466M
INFO 13:13:23 Language: en, Country: US
INFO 13:13:23 Framework: Apache Software Foundation (1.8)
INFO 13:13:23 OS: windows8 (6.3)
INFO 13:13:23 Processor: x86-64

INFO 13:13:23
INFO 13:13:23 ------------------------------------ Plugins -----------------------------------
INFO 13:13:23 Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)
INFO 13:13:23 Plugin: OWL Code Generation Plug-in (2.0.0)
INFO 13:13:23 Plugin: CoModIDE (1.1.1)
INFO 13:13:23 Plugin: Existential Query (2.0.0)
INFO 13:13:23 Plugin: Explanation Workbench (3.0.0)
INFO 13:13:23 Plugin: OntoGraf (2.0.3)
INFO 13:13:23 Plugin: OPLa Annotator Protege 5.0+ Plugin (1.0.0)
INFO 13:13:23 Plugin: DL Query (4.0.1)
INFO 13:13:23 Plugin: HermiT Reasoner (1.4.3.456)
INFO 13:13:23 Plugin: OWLAx Protege 5.0+ Plugin (1.2.0)
INFO 13:13:23 Plugin: Browser View (OWLDoc) (3.0.3)
INFO 13:13:23 Plugin: OWLViz (5.0.3)
INFO 13:13:23 Plugin: OWLAPI RDF Library (3.0.0)
INFO 13:13:23 Plugin: SPARQL Query Plugin (3.0.0)
INFO 13:13:23 Plugin: SWRLTab Protege 5.0+ Plugin (2.0.6)
INFO 13:13:23
INFO 13:13:23 Creating and setting up empty (default) editor kit
INFO 13:13:24 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 13:13:25 [OplaController] Starting Update.
INFO 13:13:25 [OplaController] Update Completed.
WARN 13:13:25 [OplaTab] Abort Update: no active ontology.
INFO 13:13:25 Cannot generate ontology catalog for ontology at http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-58. URI scheme is not "file"
INFO 13:13:25 [OplaController] Starting Update.
INFO 13:13:25 [OplaController] Active Ontology items updated.
INFO 13:13:25 [OplaController] Update Completed.
INFO 13:13:25 [OplaController] Starting Update.
INFO 13:13:25 [OplaController] 'opla' namespace already present.
INFO 13:13:25 [OplaController] Active Ontology items updated.
INFO 13:13:25 [OplaController] Update Completed.
INFO 13:13:26 ------------------------------- Auto-update Check ------------------------------
INFO 13:13:26 Auto-update last performed: Tue Jul 20 12:40:44 CDT 2021
INFO 13:13:26 Auto-update has been performed today. Not performing it again.
INFO 13:13:26
INFO 13:13:32 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 13:13:32 [OplaController] Starting Update.
INFO 13:13:32 [OplaController] Update Completed.
WARN 13:13:32 [OplaTab] Abort Update: no active ontology.
INFO 13:13:32 ------------------------------- Loading Ontology -------------------------------
INFO 13:13:32 Loading ontology from file:/C:/Users/Joseph/Desktop/Test3.owl
INFO 13:13:32 Finished loading file:/C:/Users/Joseph/Desktop/Test3.owl
INFO 13:13:32 [OplaController] Starting Update.
INFO 13:13:32 [OplaController] 'opla' namespace already present.
INFO 13:13:32 [OplaController] Active Ontology items updated.
INFO 13:13:32 [OplaController] Update Completed.
INFO 13:13:32 [OplaController] Starting Update.
INFO 13:13:32 [OplaController] 'opla' namespace already present.
INFO 13:13:32 [OplaController] Active Ontology items updated.
INFO 13:13:32 [OplaController] Update Completed.
INFO 13:13:32 Loading for ontology and imports closure successfully completed in 225 ms
INFO 13:13:32
INFO 13:13:32 [OplaController] Starting Update.
INFO 13:13:32 [OplaController] 'opla' namespace already present.
INFO 13:13:32 [OplaController] Active Ontology items updated.
INFO 13:13:32 [OplaController] Update Completed.
INFO 13:13:32 ---------------------------- Disposing of Workspace ----------------------------
INFO 13:13:32 Saved tab state for 'Data properties' tab
INFO 13:13:32 Saved tab state for 'CoModIDE' tab
INFO 13:13:32 Saved tab state for 'Individuals by class' tab
INFO 13:13:32 Saved tab state for 'OWLAx' tab
INFO 13:13:32 Saved tab state for 'Entities' tab
INFO 13:13:32 Saved tab state for 'OPLa' tab
INFO 13:13:32 Saved workspace
INFO 13:13:32 Disposed of 'Data properties' tab
INFO 13:13:32 Disposed of 'CoModIDE' tab
INFO 13:13:32 Disposed of 'Individuals by class' tab
INFO 13:13:32 Disposed of 'OWLAx' tab
INFO 13:13:32 Disposed of 'Entities' tab
INFO 13:13:32 Disposed of 'OPLa' tab
INFO 13:13:32 Disposed of workspace
INFO 13:13:33
INFO 13:13:34 Cannot generate ontology catalog for ontology at file://null/C:/Users/Joseph/Desktop/Test3-comodide-metadata.owl. URI has an authority component
INFO 13:13:34 [CoModIDE:OPLaAnnotationManager] successfully initialized.
INFO 13:13:34 [CoModIDE:SchemaDiagram] Successfully initialized.
INFO 13:13:34 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#Incident_Complex
INFO 13:13:34 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#abc
INFO 13:13:34 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#abc
INFO 13:13:34 [CoModIDE:SchemaDiagram] Adding OWL Classhttp://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#Incident_Complex
INFO 13:13:34 [CoModIDE:SchemaDiagram] Adding OWL Property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#xsd_colon_property
WARN 13:13:34 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyDomain(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#xsd_colon_property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#abc)
WARN 13:13:34 [CoModIDE:UFOH] Unsupported AddAxiom: ObjectPropertyRange(http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#xsd_colon_property http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-56#Incident_Complex)
INFO 13:13:34 [CoModIDE:SDConnectionHandler] SDConnectionHandler Initialized.
INFO 13:13:34 [CoModIDE:SchemaDiagramComponent] succesfully initialized.
INFO 13:13:34 [CoModIDE:RenderingView] Successfully initialized
INFO 13:13:35 Pattern Selector view initialized
INFO 13:13:35 Configuration view initialized
INFO 13:13:54 [OplaController] Starting Update.
INFO 13:13:54 [OplaController] Active Ontology items updated.
INFO 13:13:54 [OplaController] Update Completed.
INFO 13:13:54 Cannot generate ontology catalog for ontology at http://www.semanticweb.org/joseph/ontologies/2021/6/untitled-ontology-59. URI scheme is not "file"
ERROR 13:13:54 Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.IllegalArgumentException: URI has an authority component
at java.io.File.(File.java:423) ~[na:1.8.0_121]
at org.protege.editor.owl.model.io.OntologySourcesManager.getTimestampOfUri(OntologySourcesManager.java:111) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.getChangedOntologies(OntologySourcesManager.java:71) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.checkSources(OntologySourcesManager.java:54) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI.handleWindowActivated(OntologySourcesChangedHandlerUI.java:170) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI$1$1.windowActivated(OntologySourcesChangedHandlerUI.java:62) ~[na:na]
at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:390) ~[na:1.8.0_121]
at java.awt.Window.processWindowEvent(Window.java:2066) ~[na:1.8.0_121]
at javax.swing.JFrame.processWindowEvent(JFrame.java:305) ~[na:1.8.0_121]
at java.awt.Window.processEvent(Window.java:2013) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:995) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:488) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SentEvent.dispatch(SentEvent.java:70) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch(DefaultKeyboardFocusManager.java:217) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.sendMessage(DefaultKeyboardFocusManager.java:244) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:366) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SequencedEvent.dispatch(SequencedEvent.java:128) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
ERROR 13:14:17 Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.IllegalArgumentException: URI has an authority component
at java.io.File.(File.java:423) ~[na:1.8.0_121]
at org.protege.editor.owl.model.io.OntologySourcesManager.getTimestampOfUri(OntologySourcesManager.java:111) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.getChangedOntologies(OntologySourcesManager.java:71) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.checkSources(OntologySourcesManager.java:54) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI.handleWindowActivated(OntologySourcesChangedHandlerUI.java:170) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI$1$1.windowActivated(OntologySourcesChangedHandlerUI.java:62) ~[na:na]
at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:390) ~[na:1.8.0_121]
at java.awt.Window.processWindowEvent(Window.java:2066) ~[na:1.8.0_121]
at javax.swing.JFrame.processWindowEvent(JFrame.java:305) ~[na:1.8.0_121]
at java.awt.Window.processEvent(Window.java:2013) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:995) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:488) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SentEvent.dispatch(SentEvent.java:70) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch(DefaultKeyboardFocusManager.java:217) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.sendMessage(DefaultKeyboardFocusManager.java:244) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:366) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SequencedEvent.dispatch(SequencedEvent.java:128) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
INFO 13:14:40 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:14:48 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:14:58 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:15:05 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:15:11 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:15:31 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:15:56 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:16:08 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:16:20 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:16:44 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
ERROR 13:17:03 Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.IllegalArgumentException: URI has an authority component
at java.io.File.(File.java:423) ~[na:1.8.0_121]
at org.protege.editor.owl.model.io.OntologySourcesManager.getTimestampOfUri(OntologySourcesManager.java:111) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.getChangedOntologies(OntologySourcesManager.java:71) ~[na:na]
at org.protege.editor.owl.model.io.OntologySourcesManager.checkSources(OntologySourcesManager.java:54) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI.handleWindowActivated(OntologySourcesChangedHandlerUI.java:170) ~[na:na]
at org.protege.editor.owl.ui.ontology.OntologySourcesChangedHandlerUI$1$1.windowActivated(OntologySourcesChangedHandlerUI.java:62) ~[na:na]
at java.awt.AWTEventMulticaster.windowActivated(AWTEventMulticaster.java:390) ~[na:1.8.0_121]
at java.awt.Window.processWindowEvent(Window.java:2066) ~[na:1.8.0_121]
at javax.swing.JFrame.processWindowEvent(JFrame.java:305) ~[na:1.8.0_121]
at java.awt.Window.processEvent(Window.java:2013) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:995) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:488) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SentEvent.dispatch(SentEvent.java:70) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch(DefaultKeyboardFocusManager.java:217) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.sendMessage(DefaultKeyboardFocusManager.java:244) ~[na:1.8.0_121]
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:366) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4760) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.SequencedEvent.dispatch(SequencedEvent.java:128) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
INFO 13:17:13 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:17 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:23 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:25 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:27 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:31 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:36 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:38 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:43 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:51 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:17:54 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:18:04 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:18:05 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:18:08 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.
INFO 13:18:43 [CoModIDE:SchemaDiagram] cellLabelChanged intercepted.

[cogan-shimizu]

so after digging into the log, something really weird seemed to have happened in Protégé before CoModIDE even started up. It looks like something happened during loading. I have not been able to replicate. In any weird chance, do you have the ontology file referenced in the log?