Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[protege-discussion] protege-discussion Digest, Vol 46, Issue 25

Tania Tudorache tudorache at stanford.edu
Wed May 26 11:56:41 PDT 2010


Hi Errol,

I noticed several things in your email that could be problematic.

It is not a good idea to have a slot redefined in an included project. 
Especially, if you change its value type completely (e.g. from String to 
Instance or Integer), or even other less prominent changes, then Protege 
will get confused. It is expected that the definition of a Slot stays 
the same across included projects. You can overide the slot at the level 
of classes, that is expected.

The inclusions for all backends are expected to work the same way. The 
XML Backend is still labled "Experimental", and it may well be that the 
inclusion mechanism is not working properly. Normally, it should be 
enough to have the inclusion as: C - B - A, just like for the other 
backends. The XML backend was supposed to become the default backend 
some time ago, but that never happened, and we are not really 
maintaining it at this time.

It is not recommended to use MsAccess, especially with the JDBC-ODBC 
bridge. It is very slow and it is missing several features. I would 
recommend to use MySQL or Postgres, or other relational db engines.

Tania

On 05/22/2010 12:47 AM, Errol Babel wrote:
> Hi Tania,
>
> First of all thanks for your quick reply and enabling us to use Protégé which meets our requirements perfectly.
>
> I have been puzzling all day (and night :-)) trying to solve this issue. In my search I came up with two possible causes .
>
> 1. As you mentioned 'corrupted' slot in one of the included ontologies.
> That is I that a slot with the same name was present in ontology 'C' and in ontology 'A' and/or 'B' only with a slightly different definition.
>
> 2. MS Access back-end requires different inclusion structure than the XML back end
> With the MS Access back end there is probably no need to include all underlying projects explicitly.
> With the Experimental XML as back-end there probably is. Let me try to explain this.
>
> I have at least 3 projects in total, project A, B and C and so forth. The relation between those projects is that project B uses/specialises classes from  project A, and project C uses/specialises classes from  project B, etc.
>
> In protégé,  in case of the MS ACCESS back end,  I only had to include project A in project B and project B in project C. This inclusion structure worked fine. However after converting/saving all my projects to the XML back end I probably should have had to including project A in project C also (even though project A is already included in and via project B). Thus with the XML as back-end it seems like all projects should be included explicitly. The above in example:
>
> My project structure with the MS Access back end of the first 3 projects looked like this
>
> Project	Included projects
> C		B
> B		A
> A		<none>
>
> My project structure with the XML back end looked like this
>
> Project	Included projects
> C		B and A !!!!!!!!!
> B		A
> A		<none>
>
>
> The latter solved my issue without solving the ambiguously defined slot in project C and B or A.
> That brings me to the question: Do the requirements of setting up included projects structures in Protégé differ per back-end type?
>
> And to answer your questions:
> 1. The exception was applicable in CS and in Stand Alone mode.
> 2. I assume I don't have to send you the ontologies/projects. Otherwise, please let me know.
>
>
> Regards, Errol
>
> -----Oorspronkelijk bericht-----
> Van: protege-discussion-bounces at lists.stanford.edu [mailto:protege-discussion-bounces at lists.stanford.edu] Namens protege-discussion-request at lists.stanford.edu
> Verzonden: zaterdag 22 mei 2010 4:01
> Aan: protege-discussion at lists.stanford.edu
> Onderwerp: protege-discussion Digest, Vol 46, Issue 25
>
> Send protege-discussion mailing list submissions to
> 	protege-discussion at lists.stanford.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://mailman.stanford.edu/mailman/listinfo/protege-discussion
> or, via email, send a message with subject or body 'help' to
> 	protege-discussion-request at lists.stanford.edu
>
> You can reach the person managing the list at
> 	protege-discussion-owner at lists.stanford.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of protege-discussion digest..."
>
>
> Today's Topics:
>
>     1. Re: errors loading SlotsTAB (Tania Tudorache)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 21 May 2010 19:00:42 -0700
> From: Tania Tudorache<tudorache at stanford.edu>
> To: User support for Core Protege and the Protege-Frames editor
> 	<protege-discussion at lists.stanford.edu>
> Subject: Re: [protege-discussion] errors loading SlotsTAB
> Message-ID:<4BF73ACA.7010101 at stanford.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> If you are using the Protege standalone (not collaborative, or
> client-server), do you still get this exception? It looks like you might
> have a corrupted slot in one of the included projects.
>
> If you can send me the ontology, I can take a look what the problem is.
>
> Tania
>
> On 05/21/2010 02:11 AM, Errol Babel wrote:
>    
>> Dear All,
>>
>> When Loading a collaborative  Prot?g? Frames (3.4.1) with 2 included
>> projects,  the SlotTab won't show. When removing the included projects
>> the SlotsTab is active again. In the console I receive the error
>> message below. Can somebody tell me how to solve this issue:
>>
>> WARNING: Errors at adding tab edu.stanford.smi.protege.widget.SlotsTab
>> -- java.l
>>
>> ang.AssertionError: type
>>
>>          at edu.stanford.smi.protege.util.Assert.assertNotNull(Unknown
>> Source)
>>
>>          at edu.stanford.smi.protege.model.ValueType.valueOf(Unknown
>> Source)
>>
>>          at
>> edu.stanford.smi.protege.model.ValueTypeConstraint.getType(Unknown So
>>
>> urce)
>>
>>          at
>> edu.stanford.smi.protege.model.DefaultKnowledgeBase.getValueType(Unkn
>>
>> own Source)
>>
>>          at
>> edu.stanford.smi.protege.model.DefaultSlot.getValueType(Unknown Sourc
>>
>> e)
>>
>>          at
>> edu.stanford.smi.protege.widget.SlotValuesWidget.getCurrentType(Unkno
>>
>> wn Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.SlotValuesWidget.updateButtons(Unknow
>>
>> n Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.SlotValuesWidget.setValues(Unknown So
>>
>> urce)
>>
>>          at
>> edu.stanford.smi.protege.widget.AbstractSlotWidget.setWidgetValues(Un
>>
>> known Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.AbstractSlotWidget.loadValues(Unknown
>>
>>   Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.AbstractSlotWidget.setInstance(Unknow
>>
>> n Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.AbstractListWidget.setInstance(Unknow
>>
>> n Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.SlotValuesWidget.setInstance(Unknown
>>
>> Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.FormWidget.propagateSetInstanceToWidg
>>
>> ets(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.FormWidget.setInstance(Unknown Source
>>
>> )
>>
>>          at
>> edu.stanford.smi.protege.model.Project.createRuntimeClsWidget(Unknown
>>
>>   Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.InstanceDisplay.getWidget(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.InstanceDisplay.addRuntimeWidgets(Unknown
>>
>>   Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.InstanceDisplay.setInstance(Unknown Sourc
>>
>> e)
>>
>>          at
>> edu.stanford.smi.protege.ui.InstanceDisplay.setInstance(Unknown Sourc
>>
>> e)
>>
>>          at
>> edu.stanford.smi.protege.widget.SlotsTab.transmitSelection(Unknown So
>>
>> urce)
>>
>>          at edu.stanford.smi.protege.widget.SlotsTab.initialize(Unknown
>> Source)
>>
>>          at
>> edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unkno
>>
>> wn Source)
>>
>>          at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Sour
>>
>> ce)
>>
>>          at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unkn
>>
>> own Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unkn
>>
>> own Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown Source
>>
>> )
>>
>>          at edu.stanford.smi.protege.ui.ProjectManager.reload(Unknown
>> Source)
>>
>>          at
>> edu.stanford.smi.protege.ui.ProjectManager.changeIncludedProjectURIsR
>>
>> equest(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.action.ManageIncludedProjectsPanel.saveConte
>>
>> nts(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.util.ModalDialog.attemptClose(Unknown Source
>>
>> )
>>
>>          at
>> edu.stanford.smi.protege.util.ModalDialog$1.actionPerformed(Unknown S
>>
>> ource)
>>
>>          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>>
>>          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
>> Source)
>>
>>          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
>> Source)
>>
>>          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>
>>          at
>> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Sour
>>
>> ce)
>>
>>          at java.awt.Component.processMouseEvent(Unknown Source)
>>
>>          at javax.swing.JComponent.processMouseEvent(Unknown Source)
>>
>>          at java.awt.Component.processEvent(Unknown Source)
>>
>>          at java.awt.Container.processEvent(Unknown Source)
>>
>>          at java.awt.Component.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Container.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Component.dispatchEvent(Unknown Source)
>>
>>          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
>> Source)
>>
>>          at java.awt.LightweightDispatcher.processMouseEvent(Unknown
>> Source)
>>
>>          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>>
>>          at java.awt.Container.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Window.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Component.dispatchEvent(Unknown Source)
>>
>>          at java.awt.EventQueue.dispatchEvent(Unknown Source)
>>
>>          at
>> java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
>>
>>          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
>> Source)
>>
>>          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
>> Source)
>>
>>          at java.awt.Dialog$1.run(Unknown Source)
>>
>>          at java.awt.Dialog$2.run(Unknown Source)
>>
>>          at java.security.AccessController.doPrivileged(Native Method)
>>
>>          at java.awt.Dialog.show(Unknown Source)
>>
>>          at java.awt.Component.show(Unknown Source)
>>
>>          at java.awt.Component.setVisible(Unknown Source)
>>
>>          at edu.stanford.smi.protege.util.ModalDialog.init(Unknown Source)
>>
>>          at edu.stanford.smi.protege.util.ModalDialog.<init>(Unknown
>> Source)
>>
>>          at
>> edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown Source)
>>
>>          at
>> edu.stanford.smi.protege.action.ManageIncludedProjectsAction.actionPe
>>
>> rformed(Unknown Source)
>>
>>          at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>>
>>          at javax.swing.AbstractButton$Handler.actionPerformed(Unknown
>> Source)
>>
>>          at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
>> Source)
>>
>>          at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>
>>          at javax.swing.AbstractButton.doClick(Unknown Source)
>>
>>          at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>>
>>          at
>> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
>>
>> Source)
>>
>>          at java.awt.Component.processMouseEvent(Unknown Source)
>>
>>          at javax.swing.JComponent.processMouseEvent(Unknown Source)
>>
>>          at java.awt.Component.processEvent(Unknown Source)
>>
>>          at java.awt.Container.processEvent(Unknown Source)
>>
>>          at java.awt.Component.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Container.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Component.dispatchEvent(Unknown Source)
>>
>>          at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown
>> Source)
>>
>>          at java.awt.LightweightDispatcher.processMouseEvent(Unknown
>> Source)
>>
>>          at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>>
>>          at java.awt.Container.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Window.dispatchEventImpl(Unknown Source)
>>
>>          at java.awt.Component.dispatchEvent(Unknown Source)
>>
>>          at java.awt.EventQueue.dispatchEvent(Unknown Source)
>>
>>          at
>> java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
>>
>>          at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
>> Source)
>>
>>          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>>
>>          at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>>
>>          at java.awt.EventDispatchThread.run(Unknown Source)
>>
>> Started Collaborative Protege on Fri May 21 11:05:40 CEST 2010
>>
>> Load time for
>> file:\Z:\Solution\03%20Projectdossier%20MAPP-RZW\05%20Customer%20P
>>
>> roductmodel\02.00%20Protege\CBS\CBS.pprj = 6 sec (project) + 25 sec (ui)
>>
>>
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>      
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:<http://mailman.stanford.edu/pipermail/protege-discussion/attachments/20100521/f4c56eb6/attachment.htm>
>
> ------------------------------
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
>
> End of protege-discussion Digest, Vol 46, Issue 25
> **************************************************
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
>    




More information about the protege-discussion mailing list