Re: ConcurrentModificationException null error on protege-discussion Digest, Vol 82, Issue 13

Dear Samson,

Thanks for the reply.  Read my comments below please.

Yours truly,

André Luiz


On Tue, 2013-05-21 at 11:14 -0700, Samson Tu wrote: 

> I don't have access to a ubuntu environment. On Windows the stack trace 
> appears in the Java console window.


Ok, I found it.  It is below.

andreltr@sigmatech:/opt/Protege_4.2_beta$ ./run.sh
Starting Protege 4 OWL Editor (Version 4.2.0, Build = 278)
Platform:
    Java: JVM 1.6.0_27-b27 Memory: 466M
    Language: en, Country: US
    Framework: Apache Software Foundation (1.5)
    OS: linux (3.8.0-21-generic)
    Processor: x86-64
Plugin: OWL-RDF bridge (1.0.0.2012_07_12_0451)
Plugin: The OWL API (3.2.5.1957)
Plugin: OntoGraf Plug-in (1.0.1.2012_07_12_0451)
Plugin: Factplusplus Plug-in (1.6.1)
Plugin: OWL Diff Tool (1.0.0.2012_07_12_0451)
Plugin: Cajun Visualization Plugin (1.0.0.2012_07_12_0451)
Plugin: OWL Diff Library (1.0.0.2012_07_12_0451)
Plugin: SPARQL Query Plugin (1.0.0.2012_07_12_0451)
Plugin: The Protege 4 OWL Editor (4.2.0.b278_2012_07_12_0450)
Plugin: Dlquery (1.1.0.2012_07_12_0450)
Plugin: Owlviz Plug-in (4.1.1.2012_07_12_0450)
Plugin: Explanation Workbench (1.0.0.2012_07_12_0451)
Plugin: Protege OWL Code Generation (1.0.0.2012_07_12_0451)
Plugin: HermiT Reasoner (1.3.6)
Plugin: ontostep-plugin (1.0.0.beta1)
OWL-RDF bridge Plugin has no plugin.xml resource
Cajun Visualization Plugin Plugin has no plugin.xml resource
Using OWL API version 3.3.1957
Rebuilding entity indices...
... rebuilt in 11 ms
Setting active ontology to
<http://www.semanticweb.org/andreltr/ontologies/2013/4/24/untitled-ontology-75>
Rebuilding entity indices...
... rebuilt in 1 ms
... active ontology changed
Cannot generate ontology catalog for ontology at
http://www.semanticweb.org/andreltr/ontologies/2013/4/24/untitled-ontology-75
log4j:ERROR Could not create an Appender. Reported error follows.
java.lang.ClassNotFoundException:
org.protege.common.log.ProtegeRotatingAppender not found by
gov.nist.msid.ontostep.plugin [23]
at
org.apache.felix.framework.BundleWiringImpl.findClassOrResourceByDelegation(BundleWiringImpl.java:1460)
at org.apache.felix.framework.BundleWiringImpl.access
$400(BundleWiringImpl.java:72)
at org.apache.felix.framework.BundleWiringImpl
$BundleClassLoader.loadClass(BundleWiringImpl.java:1843)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:188)
at org.apache.log4j.helpers.Loader.loadClass(Loader.java:178)
at
org.apache.log4j.xml.DOMConfigurator.parseAppender(DOMConfigurator.java:174)
at
org.apache.log4j.xml.DOMConfigurator.findAppenderByName(DOMConfigurator.java:150)
at
org.apache.log4j.xml.DOMConfigurator.findAppenderByReference(DOMConfigurator.java:163)
at
org.apache.log4j.xml.DOMConfigurator.parseChildrenOfLoggerElement(DOMConfigurator.java:425)
at
org.apache.log4j.xml.DOMConfigurator.parseRoot(DOMConfigurator.java:394)
at org.apache.log4j.xml.DOMConfigurator.parse(DOMConfigurator.java:829)
at
org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:712)
at
org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:618)
at
org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:468)
at org.apache.log4j.LogManager.<clinit>(LogManager.java:122)
at org.apache.log4j.Logger.getLogger(Logger.java:117)
at
gov.nist.msid.ImportP11FileAction.<clinit>(ImportP11FileAction.java:41)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
at java.lang.Class.newInstance0(Class.java:374)
at java.lang.Class.newInstance(Class.java:327)
at
org.protege.editor.core.plugin.PluginUtilities.getExtensionObject(PluginUtilities.java:131)
at
org.protege.editor.core.plugin.ExtensionInstantiator.instantiate(ExtensionInstantiator.java:74)
at
org.protege.editor.core.plugin.AbstractProtegePlugin.newInstance(AbstractProtegePlugin.java:32)
at
org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:148)
at
org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:31)
at
org.protege.editor.core.ui.menu.MenuBuilder.buildInnerMenu(MenuBuilder.java:140)
at
org.protege.editor.core.ui.menu.MenuBuilder.addMenu(MenuBuilder.java:95)
at
org.protege.editor.core.ui.menu.MenuBuilder.buildCompositeMenu(MenuBuilder.java:115)
at
org.protege.editor.core.ui.menu.MenuBuilder.addMenu(MenuBuilder.java:89)
at
org.protege.editor.core.ui.menu.MenuBuilder.buildMenu(MenuBuilder.java:78)
at
org.protege.editor.core.ui.workspace.WorkspaceFrame.createMenuBar(WorkspaceFrame.java:174)
at
org.protege.editor.core.ui.workspace.WorkspaceFrame.createUI(WorkspaceFrame.java:144)
at
org.protege.editor.core.ui.workspace.WorkspaceFrame.<init>(WorkspaceFrame.java:62)
at
org.protege.editor.core.ui.workspace.WorkspaceManager.addWorkspace(WorkspaceManager.java:44)
at
org.protege.editor.core.editorkit.EditorKitManager.addEditorKit(EditorKitManager.java:44)
at
org.protege.editor.core.ProtegeManager.createAndSetupNewEditorKit(ProtegeManager.java:139)
at
org.protege.editor.core.ProtegeApplication.createAndSetupDefaultEditorKit(ProtegeApplication.java:415)
at
org.protege.editor.core.ProtegeApplication.startApplication(ProtegeApplication.java:381)
at
org.protege.editor.core.ProtegeApplication.reallyStart(ProtegeApplication.java:135)
at org.protege.editor.core.ProtegeApplication
$1.frameworkEvent(ProtegeApplication.java:115)
at
org.apache.felix.framework.util.EventDispatcher.invokeFrameworkListenerCallback(EventDispatcher.java:835)
at
org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:785)
at
org.apache.felix.framework.util.EventDispatcher.run(EventDispatcher.java:1088)
at org.apache.felix.framework.util.EventDispatcher.access
$000(EventDispatcher.java:54)
at org.apache.felix.framework.util.EventDispatcher
$1.run(EventDispatcher.java:101)
at java.lang.Thread.run(Thread.java:679)
log4j:ERROR Could not parse url [file:log4j.xml].
java.lang.NullPointerException
at java.util.Hashtable.put(Hashtable.java:411)
at
org.apache.log4j.xml.DOMConfigurator.findAppenderByName(DOMConfigurator.java:151)
at
org.apache.log4j.xml.DOMConfigurator.findAppenderByReference(DOMConfigurator.java:163)
at
org.apache.log4j.xml.DOMConfigurator.parseChildrenOfLoggerElement(DOMConfigurator.java:425)
at
org.apache.log4j.xml.DOMConfigurator.parseRoot(DOMConfigurator.java:394)
at org.apache.log4j.xml.DOMConfigurator.parse(DOMConfigurator.java:829)
at
org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:712)
at
org.apache.log4j.xml.DOMConfigurator.doConfigure(DOMConfigurator.java:618)
at
org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:468)
at org.apache.log4j.LogManager.<clinit>(LogManager.java:122)
at org.apache.log4j.Logger.getLogger(Logger.java:117)
at
gov.nist.msid.ImportP11FileAction.<clinit>(ImportP11FileAction.java:41)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
at java.lang.Class.newInstance0(Class.java:374)
at java.lang.Class.newInstance(Class.java:327)
at
org.protege.editor.core.plugin.PluginUtilities.getExtensionObject(PluginUtilities.java:131)
at
org.protege.editor.core.plugin.ExtensionInstantiator.instantiate(ExtensionInstantiator.java:74)
at
org.protege.editor.core.plugin.AbstractProtegePlugin.newInstance(AbstractProtegePlugin.java:32)
at
org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:148)
at
org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:31)
at
org.protege.editor.core.ui.menu.MenuBuilder.buildInnerMenu(MenuBuilder.java:140)
at
org.protege.editor.core.ui.menu.MenuBuilder.addMenu(MenuBuilder.java:95)
at
org.protege.editor.core.ui.menu.MenuBuilder.buildCompositeMenu(MenuBuilder.java:115)
at
org.protege.editor.core.ui.menu.MenuBuilder.addMenu(MenuBuilder.java:89)
at
org.protege.editor.core.ui.menu.MenuBuilder.buildMenu(MenuBuilder.java:78)
at
org.protege.editor.core.ui.workspace.WorkspaceFrame.createMenuBar(WorkspaceFrame.java:174)
at
org.protege.editor.core.ui.workspace.WorkspaceFrame.createUI(WorkspaceFrame.java:144)
at
org.protege.editor.core.ui.workspace.WorkspaceFrame.<init>(WorkspaceFrame.java:62)
at
org.protege.editor.core.ui.workspace.WorkspaceManager.addWorkspace(WorkspaceManager.java:44)
at
org.protege.editor.core.editorkit.EditorKitManager.addEditorKit(EditorKitManager.java:44)
at
org.protege.editor.core.ProtegeManager.createAndSetupNewEditorKit(ProtegeManager.java:139)
at
org.protege.editor.core.ProtegeApplication.createAndSetupDefaultEditorKit(ProtegeApplication.java:415)
at
org.protege.editor.core.ProtegeApplication.startApplication(ProtegeApplication.java:381)
at
org.protege.editor.core.ProtegeApplication.reallyStart(ProtegeApplication.java:135)
at org.protege.editor.core.ProtegeApplication
$1.frameworkEvent(ProtegeApplication.java:115)
at
org.apache.felix.framework.util.EventDispatcher.invokeFrameworkListenerCallback(EventDispatcher.java:835)
at
org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:785)
at
org.apache.felix.framework.util.EventDispatcher.run(EventDispatcher.java:1088)
at org.apache.felix.framework.util.EventDispatcher.access
$000(EventDispatcher.java:54)
at org.apache.felix.framework.util.EventDispatcher
$1.run(EventDispatcher.java:101)
at java.lang.Thread.run(Thread.java:679)
Setting active ontology to
<http://www.semanticweb.org/andreltr/ontologies/2013/4/24/untitled-ontology-75>
Rebuilding entity indices...
... rebuilt in 1 ms
... active ontology changed


Using OWL API version 3.3.1957
Rebuilding entity indices...
... rebuilt in 3 ms
loading Anonymous-1 from
file:/home/andreltr/Documents/phd/code/dfmontoagent4.1/dfmontologyworkingcopy.owl
Setting active ontology to <http://jade.cselt.it/beangenerator>
Rebuilding entity indices...
... rebuilt in 1 ms
... active ontology changed
Setting active ontology to <http://jade.cselt.it/beangenerator>
Rebuilding entity indices...
... rebuilt in 1 ms
... active ontology changed
Error logged
java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$KeyIterator.next(HashMap.java:845)
at
org.protege.editor.owl.ui.tree.OWLModelManagerTree.autoExpand(OWLModelManagerTree.java:108)
at
org.protege.editor.owl.ui.tree.OWLModelManagerTree.autoExpand(OWLModelManagerTree.java:113)
at
org.protege.editor.owl.ui.tree.OWLModelManagerTree.autoExpand(OWLModelManagerTree.java:113)
at
org.protege.editor.owl.ui.tree.OWLModelManagerTree.autoExpandTree(OWLModelManagerTree.java:93)
at
org.protege.editor.owl.ui.tree.OWLModelManagerTree.reload(OWLModelManagerTree.java:73)
at
org.protege.editor.owl.ui.tree.OWLObjectTree.setOWLObjectComparator(OWLObjectTree.java:312)
at
org.protege.editor.owl.ui.view.AbstractOWLEntityHierarchyViewComponent.initialiseView(AbstractOWLEntityHierarchyViewComponent.java:62)
at
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.initialiseOWLView(AbstractOWLSelectionViewComponent.java:118)
at
org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:61)
at org.protege.editor.core.ui.view.View.createContent(View.java:439)
at org.protege.editor.core.ui.view.View.createUI(View.java:219)
at org.protege.editor.core.ui.view.View
$1.hierarchyChanged(View.java:149)
at java.awt.Component.processHierarchyEvent(Component.java:6455)
at java.awt.Component.processEvent(Component.java:6074)
at java.awt.Container.processEvent(Container.java:2045)
at java.awt.Component.dispatchEventImpl(Component.java:4649)
at java.awt.Container.dispatchEventImpl(Container.java:2103)
at java.awt.Component.dispatchEvent(Component.java:4475)
at java.awt.Component.createHierarchyEvents(Component.java:5304)
at java.awt.Container.createHierarchyEvents(Container.java:1366)
at java.awt.Container.createHierarchyEvents(Container.java:1363)
at java.awt.Container.createHierarchyEvents(Container.java:1363)
at java.awt.Container.createHierarchyEvents(Container.java:1363)
at java.awt.Container.createHierarchyEvents(Container.java:1363)
at java.awt.Container.createHierarchyEvents(Container.java:1363)
at java.awt.Component.show(Component.java:1539)
at java.awt.Component.show(Component.java:1571)
at java.awt.Component.setVisible(Component.java:1523)
at javax.swing.JComponent.setVisible(JComponent.java:2612)
at javax.swing.JTabbedPane.fireStateChanged(JTabbedPane.java:395)
at javax.swing.JTabbedPane
$ModelListener.stateChanged(JTabbedPane.java:270)
at
javax.swing.DefaultSingleSelectionModel.fireStateChanged(DefaultSingleSelectionModel.java:133)
at
javax.swing.DefaultSingleSelectionModel.setSelectedIndex(DefaultSingleSelectionModel.java:67)
at javax.swing.JTabbedPane.setSelectedIndexImpl(JTabbedPane.java:616)
at javax.swing.JTabbedPane.setSelectedIndex(JTabbedPane.java:591)
at javax.swing.plaf.basic.BasicTabbedPaneUI
$Handler.mousePressed(BasicTabbedPaneUI.java:3639)
at java.awt.Component.processMouseEvent(Component.java:6285)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6053)
at java.awt.Container.processEvent(Container.java:2045)
at java.awt.Component.dispatchEventImpl(Component.java:4649)
at java.awt.Container.dispatchEventImpl(Container.java:2103)
at java.awt.Component.dispatchEvent(Component.java:4475)
at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4633)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4294)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4227)
at java.awt.Container.dispatchEventImpl(Container.java:2089)
at java.awt.Window.dispatchEventImpl(Window.java:2587)
at java.awt.Component.dispatchEvent(Component.java:4475)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:675)
at java.awt.EventQueue.access$300(EventQueue.java:96)
at java.awt.EventQueue$2.run(EventQueue.java:634)
at java.awt.EventQueue$2.run(EventQueue.java:632)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext
$1.doIntersectionPrivilege(AccessControlContext.java:105)
at java.security.AccessControlContext
$1.doIntersectionPrivilege(AccessControlContext.java:116)
at java.awt.EventQueue$3.run(EventQueue.java:648)
at java.awt.EventQueue$3.run(EventQueue.java:646)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext
$1.doIntersectionPrivilege(AccessControlContext.java:105)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:645)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)


> 
> BTW, your ontology loads fine in Protege 4.2, but is inconsistent. The 
> reasoner says:
> 
> Reason for inconsistency: Antisymmetric property isDimensionDefinedBy


Really?  How come and how have found that out, please?  I infer the
ontology under v4.2b and nothing shows up under the Nothing class.  Is
there something else that I'm missing?  I did not use Protégé's latest
version because I'm not sure of how compatible two plugins I need
openSTEP and bean generator (JADE agent architecture) are.

Sincerely,

Andre Luiz


> 
> With best regards,
> Samson
> 
> On 5/18/2013 12:45 AM, André Luiz Tietböhl Ramos wrote:
> > Dear Timothy,
> >
> > I do not know how to send, or find out, the stack trace.  Could you
> > explain how to do that, please?  The ontology is attached.  Dear Samson
> > I'm not using version 4.3 because of a plugin, ontoSTEP, which wasn't
> > designed for that version thus I don't know if it is fully compatible
> > with it, even.  The OS is ubuntu 13.04.
> >
> > Sincerely,
> >
> > Andre Luiz
> 



-- 
André Luiz Tietböhl Ramos
http://www.feng.pucrs.br/~andreltr 

“Não se mede o valor de um homem pelas suas roupas ou pelos bens que
possui.  O verdadeiro valor de um homem é seu caráter, suas idéias e a
nobreza de seus ideais.”
Charles Chaplin

"The best way to cheer yourself up is to try to cheer someone else up."
Mark Twain

I want a feeling worth paying for before I say goodbye...
Matt Johnson




-- 
André Luiz Tietböhl Ramos
http://www.feng.pucrs.br/~andreltr 

“Não se mede o valor de um homem pelas suas roupas ou pelos bens que
possui.  O verdadeiro valor de um homem é seu caráter, suas idéias e a
nobreza de seus ideais.”
Charles Chaplin

"The best way to cheer yourself up is to try to cheer someone else up."
Mark Twain

I want a feeling worth paying for before I say goodbye...
Matt Johnson

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