[protege-owl] Problem loading & saving with latest build on MacOS X 1.4/Java 5.0 r3

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[protege-owl] Problem loading & saving with latest build on MacOS X 1.4/Java 5.0 r3

Rinke Hoekstra-3
Hi all,

I'm experiencing some problems in loading an ontology from file using
the latest build + latest (available) Java on Tiger (all set up properly).
When I create a new project from existing sources, and select the owl
file using the file browser, the location is not properly understood by
Protege (see the first exception below). When I add a 'file://' prefix
to the path, the file loads flawlessly.

Furthermore, an exception is thrown when I try to save the project. For
some reason there's a problem in adding the file to the most recently
used projects list (see Exception 2). When I then try to prefix the save
location of the project with 'file://' as well, the exception gets
slightly more informative (Exception 3). In both cases, the file is not
saved at all.

Straaaange.

Cheers,

        Rinke


===========
Exception 1
===========
java.net.MalformedURLException: no protocol:
/Users/breuker/Documents/tekst/ontologies/owl:protege/lricore-nieuw/lricore-stable.owl
     at java.net.URL.<init>(URL.java:567)
     at java.net.URL.<init>(URL.java:464)
     at java.net.URL.<init>(URL.java:413)
     at
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLParser.java:136)
     at
edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:230)
     at
edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:254)
     at
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(JenaKnowledgeBaseFactory.java:165)
     at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown Source)
     at
edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
Source)
     at
edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProject2(OWLFilesCreateProjectPlugin.java:157)
     at
edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProject(OWLFilesCreateProjectPlugin.java:135)
     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$1.actionPerformed(Unknown
Source)
     at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
     at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
     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:5554)
     at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
     at java.awt.Component.processEvent(Component.java:5319)
     at java.awt.Container.processEvent(Container.java:2010)
     at java.awt.Component.dispatchEventImpl(Component.java:4021)
     at java.awt.Container.dispatchEventImpl(Container.java:2068)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
     at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
     at java.awt.Container.dispatchEventImpl(Container.java:2054)
     at java.awt.Window.dispatchEventImpl(Window.java:1774)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
     at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:275)
     at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:196)
     at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:186)
     at java.awt.Dialog$1.run(Dialog.java:515)
     at java.awt.Dialog.show(Dialog.java:536)
     at java.awt.Component.show(Component.java:1300)
     at java.awt.Component.setVisible(Component.java:1253)
     at edu.stanford.smi.protege.util.Wizard.execute(Unknown Source)
     at
edu.stanford.smi.protege.ui.ProjectManager.createNewProjectRequest(Unknown
Source)
     at
edu.stanford.smi.protege.action.CreateProject.actionPerformed(Unknown
Source)
     at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
     at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
     at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
     at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
     at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
     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:5554)
     at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
     at java.awt.Component.processEvent(Component.java:5319)
     at java.awt.Container.processEvent(Container.java:2010)
     at java.awt.Component.dispatchEventImpl(Component.java:4021)
     at java.awt.Container.dispatchEventImpl(Container.java:2068)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
     at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
     at java.awt.Container.dispatchEventImpl(Container.java:2054)
     at java.awt.Window.dispatchEventImpl(Window.java:1774)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
     at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:275)
     at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:196)
     at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
     at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
     at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

Please consider running the file through an RDF or OWL validation
service such as
   - RDF Validator: http://www.w3.org/RDF/Validator
   - OWL Validator: http://phoebus.cs.man.ac.uk:9999/OWL/Validator



===========
Exception 2
===========

java.lang.NullPointerException
     at
edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unknown
Source)
     at
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBase(JenaKnowledgeBaseFactory.java:191)
     at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown Source)
     at edu.stanford.smi.protege.model.Project.save(Unknown Source)
     at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
     at
edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
Source)
     at
edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
Source)
     at
edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
Source)
     at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
     at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
     at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
     at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
     at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
     at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
     at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1041)
     at java.awt.Component.processMouseEvent(Component.java:5554)
     at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
     at java.awt.Component.processEvent(Component.java:5319)
     at java.awt.Container.processEvent(Container.java:2010)
     at java.awt.Component.dispatchEventImpl(Component.java:4021)
     at java.awt.Container.dispatchEventImpl(Container.java:2068)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
     at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
     at java.awt.Container.dispatchEventImpl(Container.java:2054)
     at java.awt.Window.dispatchEventImpl(Window.java:1774)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
     at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:275)
     at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:196)
     at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
     at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
     at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)


===========
Exception 3
===========

Failed to use Protege2Jena: java.lang.IllegalArgumentException: URI is
not absolute
Please see Java console for error details and possibly
report this error to [hidden email]
java.lang.NullPointerException
     at
edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unknown
Source)
     at
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBase(JenaKnowledgeBaseFactory.java:191)
     at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown Source)
     at edu.stanford.smi.protege.model.Project.save(Unknown Source)
     at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
     at
edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
Source)
     at
edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
Source)
     at
edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
Source)
     at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
     at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
     at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
     at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
     at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
     at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
     at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1041)
     at java.awt.Component.processMouseEvent(Component.java:5554)
     at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
     at java.awt.Component.processEvent(Component.java:5319)
     at java.awt.Container.processEvent(Container.java:2010)
     at java.awt.Component.dispatchEventImpl(Component.java:4021)
     at java.awt.Container.dispatchEventImpl(Container.java:2068)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
     at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
     at java.awt.Container.dispatchEventImpl(Container.java:2054)
     at java.awt.Window.dispatchEventImpl(Window.java:1774)
     at java.awt.Component.dispatchEvent(Component.java:3869)
     at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
     at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:275)
     at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:196)
     at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
     at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
     at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

--
--------------------------------------
Rinke Hoekstra         [hidden email]
T: +31-20-5253499    F: +31-20-5253495
Leibniz Center for Law,    Law Faculty
University of Amsterdam,   PO Box 1030
1000 BA  Amsterdam,    The Netherlands
--------------------------------------

-------------------------------------------------------------------------
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[protege-owl] Re: Problem loading & saving with latest build on MacOS X 1.4/Java 5.0 r3

Ronnie Valkky
Hi Rinke,

Exception 1: see
http://java.sun.com/j2se/1.5.0/docs/api/java/net/MalformedURLException.html
i.e. specifying the "file:///" for the protocol in URL is needed to access
local files, that's why you got it to work.
I think the latest build should be able convert file path to legal URL
without you having to do it.

Exception 2: referring to my earlier emails in list I have not been able to
save my projects without problems.
Instead I close Protege (which save project), Open Protege and continue
working.

Exception3: looks to me as the URI, which Protege2Jena gets as argument from
Protege is not OK.

I have suggested that in future URI (URL is a valid URI) would be handled as
URI class, see
http://java.sun.com/j2se/1.5.0/docs/api/java/net/URI.html .
Now it is String. But naturally not an easy task & requires similar
processing in many programs.

I believe developers will fix above challenges.

Cheers,
Ronnie


----- Original Message -----
From: "Rinke Hoekstra" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, February 07, 2006 3:40 PM
Subject: [protege-owl] Problem loading & saving with latest build on MacOS X
1.4/Java 5.0 r3


> Hi all,
>
> I'm experiencing some problems in loading an ontology from file using
> the latest build + latest (available) Java on Tiger (all set up properly).
> When I create a new project from existing sources, and select the owl
> file using the file browser, the location is not properly understood by
> Protege (see the first exception below). When I add a 'file://' prefix
> to the path, the file loads flawlessly.
>
> Furthermore, an exception is thrown when I try to save the project. For
> some reason there's a problem in adding the file to the most recently
> used projects list (see Exception 2). When I then try to prefix the save
> location of the project with 'file://' as well, the exception gets
> slightly more informative (Exception 3). In both cases, the file is not
> saved at all.
>
> Straaaange.
>
> Cheers,
>
> Rinke
>
>
> ===========
> Exception 1
> ===========
> java.net.MalformedURLException: no protocol:
>
/Users/breuker/Documents/tekst/ontologies/owl:protege/lricore-nieuw/lricore-
stable.owl
>      at java.net.URL.<init>(URL.java:567)
>      at java.net.URL.<init>(URL.java:464)
>      at java.net.URL.<init>(URL.java:413)
>      at
>
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLPar
ser.java:136)
>      at
>
edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:230)
>      at
>
edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:254)
>      at
>
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBas
e(JenaKnowledgeBaseFactory.java:165)
>      at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown
Source)
>      at
> edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
> Source)
>      at
>
edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProje
ct2(OWLFilesCreateProjectPlugin.java:157)
>      at
>
edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProje
ct(OWLFilesCreateProjectPlugin.java:135)
>      at
>
edu.stanford.smi.protege.plugin.AbstractCreateProjectPlugin.createProject(Un
known
> Source)
>      at
> edu.stanford.smi.protege.plugin.CreateProjectWizard.onFinish(Unknown
Source)
>      at edu.stanford.smi.protege.util.Wizard$1.actionPerformed(Unknown
> Source)
>      at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>      at
>
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>      at
>
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
20)
>      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:5554)
>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>      at java.awt.Component.processEvent(Component.java:5319)
>      at java.awt.Container.processEvent(Container.java:2010)
>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>      at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>      at
>
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
va:275)
>      at
>
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:196)
>      at
>
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:186)

>      at java.awt.Dialog$1.run(Dialog.java:515)
>      at java.awt.Dialog.show(Dialog.java:536)
>      at java.awt.Component.show(Component.java:1300)
>      at java.awt.Component.setVisible(Component.java:1253)
>      at edu.stanford.smi.protege.util.Wizard.execute(Unknown Source)
>      at
> edu.stanford.smi.protege.ui.ProjectManager.createNewProjectRequest(Unknown
> Source)
>      at
> edu.stanford.smi.protege.action.CreateProject.actionPerformed(Unknown
> Source)
>      at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>      at
>
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>      at
>
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
20)
>      at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
>      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:5554)
>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>      at java.awt.Component.processEvent(Component.java:5319)
>      at java.awt.Container.processEvent(Container.java:2010)
>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>      at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>      at
>
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
va:275)
>      at
>
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:196)

>      at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
>      at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
> Please consider running the file through an RDF or OWL validation
> service such as
>    - RDF Validator: http://www.w3.org/RDF/Validator
>    - OWL Validator: http://phoebus.cs.man.ac.uk:9999/OWL/Validator
>
>
>
> ===========
> Exception 2
> ===========
>
> java.lang.NullPointerException
>      at
>
edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unkn
own
> Source)
>      at
>
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBas
e(JenaKnowledgeBaseFactory.java:191)
>      at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown
Source)

>      at edu.stanford.smi.protege.model.Project.save(Unknown Source)
>      at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
>      at
> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> Source)
>      at
> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> Source)
>      at
> edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
> Source)
>      at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>      at
>
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>      at
>
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
20)
>      at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
>      at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
>      at
>
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI
.java:1041)

>      at java.awt.Component.processMouseEvent(Component.java:5554)
>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>      at java.awt.Component.processEvent(Component.java:5319)
>      at java.awt.Container.processEvent(Container.java:2010)
>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>      at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>      at
>
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
va:275)
>      at
>
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:196)

>      at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
>      at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
>
> ===========
> Exception 3
> ===========
>
> Failed to use Protege2Jena: java.lang.IllegalArgumentException: URI is
> not absolute
> Please see Java console for error details and possibly
> report this error to [hidden email]
> java.lang.NullPointerException
>      at
>
edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unkn
own
> Source)
>      at
>
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBas
e(JenaKnowledgeBaseFactory.java:191)
>      at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown
Source)

>      at edu.stanford.smi.protege.model.Project.save(Unknown Source)
>      at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
>      at
> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> Source)
>      at
> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> Source)
>      at
> edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
> Source)
>      at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>      at
>
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>      at
>
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
20)
>      at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
>      at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
>      at
>
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI
.java:1041)

>      at java.awt.Component.processMouseEvent(Component.java:5554)
>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>      at java.awt.Component.processEvent(Component.java:5319)
>      at java.awt.Container.processEvent(Container.java:2010)
>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>      at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>      at java.awt.Component.dispatchEvent(Component.java:3869)
>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>      at
>
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
va:275)
>      at
>
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
:196)

>      at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
>      at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
> --
> --------------------------------------
> Rinke Hoekstra         [hidden email]
> T: +31-20-5253499    F: +31-20-5253495
> Leibniz Center for Law,    Law Faculty
> University of Amsterdam,   PO Box 1030
> 1000 BA  Amsterdam,    The Netherlands
> --------------------------------------
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>


-------------------------------------------------------------------------
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[protege-owl] Re: Problem loading & saving with latest build on MacOS X 1.4/Java 5.0 r3

Rinke Hoekstra-3
Ronnie Valkky wrote:
> Hi Rinke,
>
> Exception 1: see
> http://java.sun.com/j2se/1.5.0/docs/api/java/net/MalformedURLException.html
> i.e. specifying the "file:///" for the protocol in URL is needed to access
> local files, that's why you got it to work.
> I think the latest build should be able convert file path to legal URL
> without you having to do it.

Hmm... That line of reasoning shows a striking resemblance to the reason
I had for filing the bug report in the first place ;)

>
> Exception 2: referring to my earlier emails in list I have not been able to
> save my projects without problems.
> Instead I close Protege (which save project), Open Protege and continue
> working.

How can you continue working if you cannot save the project? Does
Protege only save the file 'on exit', and not when you select 'Save'
from the file menu?
I will try that..

>
> Exception3: looks to me as the URI, which Protege2Jena gets as argument from
> Protege is not OK.
>
> I have suggested that in future URI (URL is a valid URI) would be handled as
> URI class, see
> http://java.sun.com/j2se/1.5.0/docs/api/java/net/URI.html .
> Now it is String. But naturally not an easy task & requires similar
> processing in many programs.

Yes, right, but the thing is... a quick peek at the Protege2Jena source
file shows that the save methods require a URI (as in java.net.URI) as
argument. And the methods are called using URI's as well, because
otherwise the source would not compile.

>
> I believe developers will fix above challenges.

I hope so ;)

        -Rinke

>
> Cheers,
> Ronnie
>
>
> ----- Original Message -----
> From: "Rinke Hoekstra" <[hidden email]>
> To: <[hidden email]>
> Sent: Tuesday, February 07, 2006 3:40 PM
> Subject: [protege-owl] Problem loading & saving with latest build on MacOS X
> 1.4/Java 5.0 r3
>
>
>> Hi all,
>>
>> I'm experiencing some problems in loading an ontology from file using
>> the latest build + latest (available) Java on Tiger (all set up properly).
>> When I create a new project from existing sources, and select the owl
>> file using the file browser, the location is not properly understood by
>> Protege (see the first exception below). When I add a 'file://' prefix
>> to the path, the file loads flawlessly.
>>
>> Furthermore, an exception is thrown when I try to save the project. For
>> some reason there's a problem in adding the file to the most recently
>> used projects list (see Exception 2). When I then try to prefix the save
>> location of the project with 'file://' as well, the exception gets
>> slightly more informative (Exception 3). In both cases, the file is not
>> saved at all.
>>
>> Straaaange.
>>
>> Cheers,
>>
>> Rinke
>>
>>
>> ===========
>> Exception 1
>> ===========
>> java.net.MalformedURLException: no protocol:
>>
> /Users/breuker/Documents/tekst/ontologies/owl:protege/lricore-nieuw/lricore-
> stable.owl
>>      at java.net.URL.<init>(URL.java:567)
>>      at java.net.URL.<init>(URL.java:464)
>>      at java.net.URL.<init>(URL.java:413)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLPar
> ser.java:136)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:230)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:254)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBas
> e(JenaKnowledgeBaseFactory.java:165)
>>      at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown
> Source)
>>      at
>> edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
>> Source)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProje
> ct2(OWLFilesCreateProjectPlugin.java:157)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProje
> ct(OWLFilesCreateProjectPlugin.java:135)
>>      at
>>
> edu.stanford.smi.protege.plugin.AbstractCreateProjectPlugin.createProject(Un
> known
>> Source)
>>      at
>> edu.stanford.smi.protege.plugin.CreateProjectWizard.onFinish(Unknown
> Source)
>>      at edu.stanford.smi.protege.util.Wizard$1.actionPerformed(Unknown
>> Source)
>>      at
>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>>      at
>>
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>>      at
>>
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> 20)
>>      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:5554)
>>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>>      at java.awt.Component.processEvent(Component.java:5319)
>>      at java.awt.Container.processEvent(Container.java:2010)
>>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at
>> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>>      at
>> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>>      at
>>
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> va:275)
>>      at
>>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
> :196)
>>      at
>>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
> :186)
>>      at java.awt.Dialog$1.run(Dialog.java:515)
>>      at java.awt.Dialog.show(Dialog.java:536)
>>      at java.awt.Component.show(Component.java:1300)
>>      at java.awt.Component.setVisible(Component.java:1253)
>>      at edu.stanford.smi.protege.util.Wizard.execute(Unknown Source)
>>      at
>> edu.stanford.smi.protege.ui.ProjectManager.createNewProjectRequest(Unknown
>> Source)
>>      at
>> edu.stanford.smi.protege.action.CreateProject.actionPerformed(Unknown
>> Source)
>>      at
>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>>      at
>>
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>>      at
>>
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> 20)
>>      at
>> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
>>      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:5554)
>>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>>      at java.awt.Component.processEvent(Component.java:5319)
>>      at java.awt.Container.processEvent(Container.java:2010)
>>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at
>> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>>      at
>> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>>      at
>>
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> va:275)
>>      at
>>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
> :196)
>>      at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
>>      at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
>>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>>
>> Please consider running the file through an RDF or OWL validation
>> service such as
>>    - RDF Validator: http://www.w3.org/RDF/Validator
>>    - OWL Validator: http://phoebus.cs.man.ac.uk:9999/OWL/Validator
>>
>>
>>
>> ===========
>> Exception 2
>> ===========
>>
>> java.lang.NullPointerException
>>      at
>>
> edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unkn
> own
>> Source)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBas
> e(JenaKnowledgeBaseFactory.java:191)
>>      at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown
> Source)
>>      at edu.stanford.smi.protege.model.Project.save(Unknown Source)
>>      at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
>>      at
>> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
>> Source)
>>      at
>> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
>> Source)
>>      at
>> edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
>> Source)
>>      at
>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>>      at
>>
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>>      at
>>
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> 20)
>>      at
>> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
>>      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:5554)
>>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>>      at java.awt.Component.processEvent(Component.java:5319)
>>      at java.awt.Container.processEvent(Container.java:2010)
>>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at
>> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>>      at
>> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>>      at
>>
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> va:275)
>>      at
>>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
> :196)
>>      at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
>>      at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
>>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>>
>>
>> ===========
>> Exception 3
>> ===========
>>
>> Failed to use Protege2Jena: java.lang.IllegalArgumentException: URI is
>> not absolute
>> Please see Java console for error details and possibly
>> report this error to [hidden email]
>> java.lang.NullPointerException
>>      at
>>
> edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unkn
> own
>> Source)
>>      at
>>
> edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBas
> e(JenaKnowledgeBaseFactory.java:191)
>>      at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown
> Source)
>>      at edu.stanford.smi.protege.model.Project.save(Unknown Source)
>>      at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
>>      at
>> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
>> Source)
>>      at
>> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
>> Source)
>>      at
>> edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
>> Source)
>>      at
>> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>>      at
>>
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>>      at
>>
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> 20)
>>      at
>> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
>>      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:5554)
>>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
>>      at java.awt.Component.processEvent(Component.java:5319)
>>      at java.awt.Container.processEvent(Container.java:2010)
>>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at
>> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>>      at
>> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>>      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
>>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
>>      at java.awt.Component.dispatchEvent(Component.java:3869)
>>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>>      at
>>
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> va:275)
>>      at
>>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
> :196)
>>      at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
>>      at
>> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
>>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>>
>> --
>> --------------------------------------
>> Rinke Hoekstra         [hidden email]
>> T: +31-20-5253499    F: +31-20-5253495
>> Leibniz Center for Law,    Law Faculty
>> University of Amsterdam,   PO Box 1030
>> 1000 BA  Amsterdam,    The Netherlands
>> --------------------------------------
>>
>> -------------------------------------------------------------------------
>> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>>
>>
>
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>


--
--------------------------------------
Rinke Hoekstra         [hidden email]
T: +31-20-5253499    F: +31-20-5253495
Leibniz Center for Law,    Law Faculty
University of Amsterdam,   PO Box 1030
1000 BA  Amsterdam,    The Netherlands
--------------------------------------

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[protege-owl] Re: Problem loading & saving with latest build on MacOS X 1.4/Java 5.0 r3

Ronnie Valkky
Hi Rinke,

At the moment the following paths works for me:
Path I:
1. start Protege
2. open project
3. do my work
4. close +  for "Do you want to save changes" Yes
5. I go to 2, , if I want to continue

Path II:
1. start Protege
2. open project
3. do my work
4. exit Protege  + "Do you want to save changes" Yes
5. I go to 1, if I want to continue

SAVE does NOT save changes for me, so I don't use it.

Cheers
Ronnie


----- Original Message -----
From: "Rinke Hoekstra" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, February 07, 2006 9:53 PM
Subject: [protege-owl] Re: Problem loading & saving with latest build on
MacOS X 1.4/Java 5.0 r3


> Ronnie Valkky wrote:
> > Hi Rinke,
> >
> > Exception 1: see
> >
http://java.sun.com/j2se/1.5.0/docs/api/java/net/MalformedURLException.html
> > i.e. specifying the "file:///" for the protocol in URL is needed to
access
> > local files, that's why you got it to work.
> > I think the latest build should be able convert file path to legal URL
> > without you having to do it.
>
> Hmm... That line of reasoning shows a striking resemblance to the reason
> I had for filing the bug report in the first place ;)
>
> >
> > Exception 2: referring to my earlier emails in list I have not been able
to

> > save my projects without problems.
> > Instead I close Protege (which save project), Open Protege and continue
> > working.
>
> How can you continue working if you cannot save the project? Does
> Protege only save the file 'on exit', and not when you select 'Save'
> from the file menu?
> I will try that..
>
> >
> > Exception3: looks to me as the URI, which Protege2Jena gets as argument
from
> > Protege is not OK.
> >
> > I have suggested that in future URI (URL is a valid URI) would be
handled as

> > URI class, see
> > http://java.sun.com/j2se/1.5.0/docs/api/java/net/URI.html .
> > Now it is String. But naturally not an easy task & requires similar
> > processing in many programs.
>
> Yes, right, but the thing is... a quick peek at the Protege2Jena source
> file shows that the save methods require a URI (as in java.net.URI) as
> argument. And the methods are called using URI's as well, because
> otherwise the source would not compile.
>
> >
> > I believe developers will fix above challenges.
>
> I hope so ;)
>
> -Rinke
> >
> > Cheers,
> > Ronnie
> >
> >
> > ----- Original Message -----
> > From: "Rinke Hoekstra" <[hidden email]>
> > To: <[hidden email]>
> > Sent: Tuesday, February 07, 2006 3:40 PM
> > Subject: [protege-owl] Problem loading & saving with latest build on
MacOS X
> > 1.4/Java 5.0 r3
> >
> >
> >> Hi all,
> >>
> >> I'm experiencing some problems in loading an ontology from file using
> >> the latest build + latest (available) Java on Tiger (all set up
properly).
> >> When I create a new project from existing sources, and select the owl
> >> file using the file browser, the location is not properly understood by
> >> Protege (see the first exception below). When I add a 'file://' prefix
> >> to the path, the file loads flawlessly.
> >>
> >> Furthermore, an exception is thrown when I try to save the project. For
> >> some reason there's a problem in adding the file to the most recently
> >> used projects list (see Exception 2). When I then try to prefix the
save

> >> location of the project with 'file://' as well, the exception gets
> >> slightly more informative (Exception 3). In both cases, the file is not
> >> saved at all.
> >>
> >> Straaaange.
> >>
> >> Cheers,
> >>
> >> Rinke
> >>
> >>
> >> ===========
> >> Exception 1
> >> ===========
> >> java.net.MalformedURLException: no protocol:
> >>
> >
/Users/breuker/Documents/tekst/ontologies/owl:protege/lricore-nieuw/lricore-
> > stable.owl
> >>      at java.net.URL.<init>(URL.java:567)
> >>      at java.net.URL.<init>(URL.java:464)
> >>      at java.net.URL.<init>(URL.java:413)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(ProtegeOWLPar
> > ser.java:136)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:230)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.JenaOWLModel.load(JenaOWLModel.java:254)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBas
> > e(JenaKnowledgeBaseFactory.java:165)
> >>      at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown
> > Source)
> >>      at
> >>
edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
> >> Source)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProje
> > ct2(OWLFilesCreateProjectPlugin.java:157)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.OWLFilesCreateProjectPlugin.buildNewProje
> > ct(OWLFilesCreateProjectPlugin.java:135)
> >>      at
> >>
> >
edu.stanford.smi.protege.plugin.AbstractCreateProjectPlugin.createProject(Un
> > known
> >> Source)
> >>      at
> >> edu.stanford.smi.protege.plugin.CreateProjectWizard.onFinish(Unknown
> > Source)
> >>      at edu.stanford.smi.protege.util.Wizard$1.actionPerformed(Unknown
> >> Source)
> >>      at
> >>
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
> >>      at
> >>
> >
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
> >>      at
> >>
> >
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> > 20)
> >>      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:5554)
> >>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
> >>      at java.awt.Component.processEvent(Component.java:5319)
> >>      at java.awt.Container.processEvent(Container.java:2010)
> >>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at
> >> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
> >>      at
> >> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
> >>      at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
> >>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> > va:275)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
> > :196)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java
> > :186)
> >>      at java.awt.Dialog$1.run(Dialog.java:515)
> >>      at java.awt.Dialog.show(Dialog.java:536)
> >>      at java.awt.Component.show(Component.java:1300)
> >>      at java.awt.Component.setVisible(Component.java:1253)
> >>      at edu.stanford.smi.protege.util.Wizard.execute(Unknown Source)
> >>      at
> >>
edu.stanford.smi.protege.ui.ProjectManager.createNewProjectRequest(Unknown
> >> Source)
> >>      at
> >> edu.stanford.smi.protege.action.CreateProject.actionPerformed(Unknown
> >> Source)
> >>      at
> >>
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
> >>      at
> >>
> >
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
> >>      at
> >>
> >
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> > 20)
> >>      at
> >> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
> >>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
> >>      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:5554)
> >>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
> >>      at java.awt.Component.processEvent(Component.java:5319)
> >>      at java.awt.Container.processEvent(Container.java:2010)
> >>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at
> >> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
> >>      at
> >> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
> >>      at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
> >>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> > va:275)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java

> > :196)
> >>      at
> >> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
> >>      at
> >> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
> >>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
> >>
> >> Please consider running the file through an RDF or OWL validation
> >> service such as
> >>    - RDF Validator: http://www.w3.org/RDF/Validator
> >>    - OWL Validator: http://phoebus.cs.man.ac.uk:9999/OWL/Validator
> >>
> >>
> >>
> >> ===========
> >> Exception 2
> >> ===========
> >>
> >> java.lang.NullPointerException
> >>      at
> >>
> >
edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unkn
> > own
> >> Source)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBas

> > e(JenaKnowledgeBaseFactory.java:191)
> >>      at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown
> > Source)
> >>      at edu.stanford.smi.protege.model.Project.save(Unknown Source)
> >>      at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
> >>      at
> >> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> >> Source)
> >>      at
> >> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> >> Source)
> >>      at
> >> edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
> >> Source)
> >>      at
> >>
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
> >>      at
> >>
> >
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
> >>      at
> >>
> >
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> > 20)
> >>      at
> >> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
> >>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
> >>      at
> >>
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
> >>      at
> >>
> >
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI

> > .java:1041)
> >>      at java.awt.Component.processMouseEvent(Component.java:5554)
> >>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
> >>      at java.awt.Component.processEvent(Component.java:5319)
> >>      at java.awt.Container.processEvent(Container.java:2010)
> >>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at
> >> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
> >>      at
> >> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
> >>      at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
> >>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> > va:275)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java

> > :196)
> >>      at
> >> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
> >>      at
> >> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
> >>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
> >>
> >>
> >> ===========
> >> Exception 3
> >> ===========
> >>
> >> Failed to use Protege2Jena: java.lang.IllegalArgumentException: URI is
> >> not absolute
> >> Please see Java console for error details and possibly
> >> report this error to [hidden email]
> >> java.lang.NullPointerException
> >>      at
> >>
> >
edu.stanford.smi.protege.util.ApplicationProperties.addProjectToMRUList(Unkn
> > own
> >> Source)
> >>      at
> >>
> >
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.saveKnowledgeBas

> > e(JenaKnowledgeBaseFactory.java:191)
> >>      at edu.stanford.smi.protege.model.Project.saveDomainKB(Unknown
> > Source)
> >>      at edu.stanford.smi.protege.model.Project.save(Unknown Source)
> >>      at edu.stanford.smi.protege.ui.ProjectManager.save(Unknown Source)
> >>      at
> >> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> >> Source)
> >>      at
> >> edu.stanford.smi.protege.ui.ProjectManager.saveProjectAsRequest(Unknown
> >> Source)
> >>      at
> >> edu.stanford.smi.protege.action.SaveProjectAs.actionPerformed(Unknown
> >> Source)
> >>      at
> >>
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
> >>      at
> >>
> >
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
> >>      at
> >>
> >
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:4
> > 20)
> >>      at
> >> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
> >>      at javax.swing.AbstractButton.doClick(AbstractButton.java:334)
> >>      at
> >>
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)
> >>      at
> >>
> >
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI

> > .java:1041)
> >>      at java.awt.Component.processMouseEvent(Component.java:5554)
> >>      at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
> >>      at java.awt.Component.processEvent(Component.java:5319)
> >>      at java.awt.Container.processEvent(Container.java:2010)
> >>      at java.awt.Component.dispatchEventImpl(Component.java:4021)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2068)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at
> >> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
> >>      at
> >> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
> >>      at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
> >>      at java.awt.Container.dispatchEventImpl(Container.java:2054)
> >>      at java.awt.Window.dispatchEventImpl(Window.java:1774)
> >>      at java.awt.Component.dispatchEvent(Component.java:3869)
> >>      at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.ja
> > va:275)
> >>      at
> >>
> >
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java

> > :196)
> >>      at
> >> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:190)
> >>      at
> >> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:182)
> >>      at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
> >>
> >> --
> >> --------------------------------------
> >> Rinke Hoekstra         [hidden email]
> >> T: +31-20-5253499    F: +31-20-5253495
> >> Leibniz Center for Law,    Law Faculty
> >> University of Amsterdam,   PO Box 1030
> >> 1000 BA  Amsterdam,    The Netherlands
> >> --------------------------------------
> >>
>
>> -------------------------------------------------------------------------
> >> To unsubscribe go to
http://protege.stanford.edu/community/subscribe.html
> >>
> >>
> >
> >
>
> -------------------------------------------------------------------------
> > To unsubscribe go to
http://protege.stanford.edu/community/subscribe.html

> >
> >
>
>
> --
> --------------------------------------
> Rinke Hoekstra         [hidden email]
> T: +31-20-5253499    F: +31-20-5253495
> Leibniz Center for Law,    Law Faculty
> University of Amsterdam,   PO Box 1030
> 1000 BA  Amsterdam,    The Netherlands
> --------------------------------------
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>


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