including projects NullPointerException

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including projects NullPointerException

Fred Freitas

HI all,

The instructions on how to include projects on the users' guide are
stale and I could not find any for the newer Protege versions ( I am
using 3.2 build 234). It also looks more complicated than the earlier
versions but seems to provide more functionalities which are not
documented.

I could not include one onto into another. What I did (and got):

- I clicked "project-> manage included projects",
- I selected the projct to be included (NeuralNets),
- the system told me the project would be saved and reloaded
- I got the exceptions listed below.

Has anybody got any idea of what's going on and how to fix it?

In both projects I used a metaclass with two new slots for Synonyms and
keywords, but I also tries it without the metaclass, and received the
same exception.

Any help is appreciated, thanx in advance,

Fred

PS: Below the generated exception

Unable to load project:
file:/C:/Ontologies/ontos/ontos-eunice/Areas-Applications/file:/C:/Ontologies/ontos/ontos-eunice/NeuralNets/NeuralNets.pprj
java.lang.NullPointerException
        at edu.stanford.smi.protege.model.Project.includeDomainKB(Unknown Source)
        at edu.stanford.smi.protege.model.Project.loadIncludedProject(Unknown
Source)
        at edu.stanford.smi.protege.model.Project.loadIncludedProjects(Unknown
Source)
        at
edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown
Source)
        at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
        at edu.stanford.smi.protege.model.Project.<init>(Unknown Source)
        at edu.stanford.smi.protege.model.Project.loadProjectFromURI(Unknown
Source)
        at
edu.stanford.smi.protege.ui.ProjectManager.loadProjectFromURI(Unknown
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.changeIncludedProjectURIsRequest(Unknown
Source)
        at
edu.stanford.smi.protege.action.ManageIncludedProjectsPanel.saveContents(Unknown
Source)
        at edu.stanford.smi.protege.util.ModalDialog.attemptClose(Unknown Source)
        at edu.stanford.smi.protege.util.ModalDialog$1.actionPerformed(Unknown
Source)
        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
        at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
        at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
        at javax.swing.plaf.basic.BasicButtonListener.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.pumpEventsForHierarchy(Unknown Source)
        at java.awt.Dialog$1.run(Unknown Source)
        at java.awt.Dialog.show(Unknown Source)
        at java.awt.Component.show(Unknown Source)
        at java.awt.Component.setVisible(Unknown Source)
        at edu.stanford.smi.protege.util.ModalDialog.init(Unknown Source)
        at edu.stanford.smi.protege.util.ModalDialog.<init>(Unknown Source)
        at edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown Source)
        at edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown Source)
        at edu.stanford.smi.protege.util.ModalDialog.showDialog(Unknown Source)
        at
edu.stanford.smi.protege.action.ManageIncludedProjectsAction.actionPerformed(Unknown
Source)
        at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
        at javax.swing.AbstractButton$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)

--
[]s

Fred Freitas
************
Associate Professor
Centro de Informática - CIn
Universidade Federal de Pernambuco - UFPE - Brazil
Phone: +55 81 2126 8430 r. 4345

Research interests: Ontologies, semantic web, ontology-based text processing


       

       
               
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Re: including projects NullPointerException

Nigam Shah

>I could not include one onto into another. What I did (and got):
>
>- I clicked "project-> manage included projects",
>- I selected the projct to be included (NeuralNets),
>- the system told me the project would be saved and reloaded
>- I got the exceptions listed below.
>
>Has anybody got any idea of what's going on and how to fix it?
>
>In both projects I used a metaclass with two new slots for
>Synonyms and keywords, but I also tries it without the
>metaclass, and received the same exception.
>
>Any help is appreciated, thanx in advance,

Hi Fred,

Once the "save" part is done, quite protégé (just force the command
window to close) and then open the .pprj file in a text editor. Do a
CTRL+F for the name of the project file that you included.

For your example below, it seems it will be called NeuralNets.pprj.
The file path will contain

>file:/C:/Ontologies/ontos/ontos-eunice/Areas-Applications/file:
>/C:/Ontologies/ontos/ontos-eunice/NeuralNets/NeuralNets.pprj

Remove everything before the 'NeuralNets.pprj'. It should look like
this:

        (included_projects
                "NeuralNets.pprj")

Save and close the .pprj file. Now, copy the NeuralNets.pprj (and the
pins and ponts file that go with it) into the directory of the parent
project (I am guessing it will be
C:/Ontologies/ontos/ontos-eunice/Areas-Applications/ ).

Once you have all six files (pprj, pins, pont for the parent and the 3
files for the NeuralNet) in one directory double click on the parent
projects .pprj file and protégé will start up and all will be well.

--Nigam.


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Re: including projects NullPointerException

Timothy Redmond


This is a known bug and I believe that it is getting fixed now...

--------------------------------
Timothy Redmond, PhD
Research Staff
Stanford Medical Informatics
Medical School Office Building X-215
251 Campus Drive
Stanford, CA 94305
[hidden email]



On Feb 2, 2006, at 3:09 PM, Nigam Shah wrote:

>
>> I could not include one onto into another. What I did (and got):
>>
>> - I clicked "project-> manage included projects",
>> - I selected the projct to be included (NeuralNets),
>> - the system told me the project would be saved and reloaded
>> - I got the exceptions listed below.
>>
>> Has anybody got any idea of what's going on and how to fix it?
>>
>> In both projects I used a metaclass with two new slots for
>> Synonyms and keywords, but I also tries it without the
>> metaclass, and received the same exception.
>>
>> Any help is appreciated, thanx in advance,
>
> Hi Fred,
>
> Once the "save" part is done, quite protégé (just force the command
> window to close) and then open the .pprj file in a text editor. Do a
> CTRL+F for the name of the project file that you included.
>
> For your example below, it seems it will be called NeuralNets.pprj.
> The file path will contain
>
>> file:/C:/Ontologies/ontos/ontos-eunice/Areas-Applications/file:
>> /C:/Ontologies/ontos/ontos-eunice/NeuralNets/NeuralNets.pprj
>
> Remove everything before the 'NeuralNets.pprj'. It should look like
> this:
>
> (included_projects
> "NeuralNets.pprj")
>
> Save and close the .pprj file. Now, copy the NeuralNets.pprj (and the
> pins and ponts file that go with it) into the directory of the parent
> project (I am guessing it will be
> C:/Ontologies/ontos/ontos-eunice/Areas-Applications/ ).
>
> Once you have all six files (pprj, pins, pont for the parent and the 3
> files for the NeuralNet) in one directory double click on the parent
> projects .pprj file and protégé will start up and all will be well.
>
> --Nigam.
>
>
> ----------------------------------------------------------------------
> ---
> To unsubscribe go to http://protege.stanford.edu/community/ 
> subscribe.html
>

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Re: including projects NullPointerException

Fred Freitas

NIgam and Timothy,

Thanx a lot for your help! I 'll try out your solution, Nigam.

fred

Redmond escreveu:

>
> This is a known bug and I believe that it is getting fixed now...
>
> --------------------------------
> Timothy Redmond, PhD
> Research Staff
> Stanford Medical Informatics
> Medical School Office Building X-215
> 251 Campus Drive
> Stanford, CA 94305
> [hidden email]
>
>
>
> On Feb 2, 2006, at 3:09 PM, Nigam Shah wrote:
>
>
>>>I could not include one onto into another. What I did (and got):
>>>
>>>- I clicked "project-> manage included projects",
>>>- I selected the projct to be included (NeuralNets),
>>>- the system told me the project would be saved and reloaded
>>>- I got the exceptions listed below.
>>>
>>>Has anybody got any idea of what's going on and how to fix it?
>>>
>>>In both projects I used a metaclass with two new slots for
>>>Synonyms and keywords, but I also tries it without the
>>>metaclass, and received the same exception.
>>>
>>>Any help is appreciated, thanx in advance,
>>
>>Hi Fred,
>>
>>Once the "save" part is done, quite protégé (just force the command
>>window to close) and then open the .pprj file in a text editor. Do a
>>CTRL+F for the name of the project file that you included.
>>
>>For your example below, it seems it will be called NeuralNets.pprj.
>>The file path will contain
>>
>>
>>>file:/C:/Ontologies/ontos/ontos-eunice/Areas-Applications/file:
>>>/C:/Ontologies/ontos/ontos-eunice/NeuralNets/NeuralNets.pprj
>>
>>Remove everything before the 'NeuralNets.pprj'. It should look like
>>this:
>>
>> (included_projects
>> "NeuralNets.pprj")
>>
>>Save and close the .pprj file. Now, copy the NeuralNets.pprj (and the
>>pins and ponts file that go with it) into the directory of the parent
>>project (I am guessing it will be
>>C:/Ontologies/ontos/ontos-eunice/Areas-Applications/ ).
>>
>>Once you have all six files (pprj, pins, pont for the parent and the 3
>>files for the NeuralNet) in one directory double click on the parent
>>projects .pprj file and protégé will start up and all will be well.
>>
>>--Nigam.
>>
>>
>>----------------------------------------------------------------------
>>---
>>To unsubscribe go to http://protege.stanford.edu/community/ 
>>subscribe.html
>>
>
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>
>


--
[]s

Fred Freitas
************
Associate Professor
Centro de Informática - CIn
Universidade Federal de Pernambuco - UFPE - Brazil
Phone: +55 81 2126 8430 r. 4345

Research interests: Ontologies, semantic web, ontology-based text processing


               
_______________________________________________________
Yahoo! Acesso Grátis - Internet rápida e grátis. Instale o discador agora!
http://br.acesso.yahoo.com
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Re: including projects NullPointerException

Tania Tudorache

This is fixed in the next beta.

Tania


Fred Freitas wrote:

> NIgam and Timothy,
>
> Thanx a lot for your help! I 'll try out your solution, Nigam.
>
> fred
>
> Redmond escreveu:
>  
>> This is a known bug and I believe that it is getting fixed now...
>>
>> --------------------------------
>> Timothy Redmond, PhD
>> Research Staff
>> Stanford Medical Informatics
>> Medical School Office Building X-215
>> 251 Campus Drive
>> Stanford, CA 94305
>> [hidden email]
>>
>>
>>
>> On Feb 2, 2006, at 3:09 PM, Nigam Shah wrote:
>>
>>
>>    
>>>> I could not include one onto into another. What I did (and got):
>>>>
>>>> - I clicked "project-> manage included projects",
>>>> - I selected the projct to be included (NeuralNets),
>>>> - the system told me the project would be saved and reloaded
>>>> - I got the exceptions listed below.
>>>>
>>>> Has anybody got any idea of what's going on and how to fix it?
>>>>
>>>> In both projects I used a metaclass with two new slots for
>>>> Synonyms and keywords, but I also tries it without the
>>>> metaclass, and received the same exception.
>>>>
>>>> Any help is appreciated, thanx in advance,
>>>>        
>>> Hi Fred,
>>>
>>> Once the "save" part is done, quite protégé (just force the command
>>> window to close) and then open the .pprj file in a text editor. Do a
>>> CTRL+F for the name of the project file that you included.
>>>
>>> For your example below, it seems it will be called NeuralNets.pprj.
>>> The file path will contain
>>>
>>>
>>>      
>>>> file:/C:/Ontologies/ontos/ontos-eunice/Areas-Applications/file:
>>>> /C:/Ontologies/ontos/ontos-eunice/NeuralNets/NeuralNets.pprj
>>>>        
>>> Remove everything before the 'NeuralNets.pprj'. It should look like
>>> this:
>>>
>>> (included_projects
>>> "NeuralNets.pprj")
>>>
>>> Save and close the .pprj file. Now, copy the NeuralNets.pprj (and the
>>> pins and ponts file that go with it) into the directory of the parent
>>> project (I am guessing it will be
>>> C:/Ontologies/ontos/ontos-eunice/Areas-Applications/ ).
>>>
>>> Once you have all six files (pprj, pins, pont for the parent and the 3
>>> files for the NeuralNet) in one directory double click on the parent
>>> projects .pprj file and protégé will start up and all will be well.
>>>
>>> --Nigam.
>>>
>>>
>>> ----------------------------------------------------------------------
>>> ---
>>> To unsubscribe go to http://protege.stanford.edu/community/ 
>>> subscribe.html
>>>
>>>      
>> -------------------------------------------------------------------------
>> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>>
>>
>>
>>    
>
>
>  

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