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usenet | 2 Jul 2007 13:40
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Protege 3.3b411 and Query Results protege_query_results.txt

Hi,
I just found a problem with Protege 3.3 beta 411. I get exceptions when
trying to save Query results.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at java.io.File.<init>(File.java:332)
	at
edu.stanford.smi.protegex.queries_tab.InstancesList$3.actionPerformed(Unknown
Source)
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)

I use a Server-based Protge installation. Looking at the Sourcecode, I
find that the output directory is not configurable and retrieved by deprecated
function getProjectDirectoryFile(). To where does this directory resolve
in a Server mode project? With Protege 3.2.1 it was Protege installation
directory, which is also not a good idea because it might be readonly.

Is there any way we could make the output directory configurable?

Regards,
Jens.

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usenet | 2 Jul 2007 13:45
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Ontoviz Plugin - location of generated dot file?

Hi,
Ontoviz Plugin is nice, but I'd like to get the generated picture outside of
Protege.

On a windows installation, I found out that Ontoviz generates two files with the
name of the Ontology (I use a Server sided) in the root of the Installation
directory. My Protege is in D:\Prog... and I find D:\FooBar.dot and
D:\FooBar.dot-input.

Is there any way to configure the output directory of intermediate dot files?

Regards,
Jens.

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Taylor Cowan | 2 Jul 2007 16:17
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transitive properties

I'm experimenting with an OWL ontology and hoped to demonstrate the power of a transitive property I
labeled "partOf".  Running pellet doesn't insert any new assertions and queries via SPARQL only return
neighbors (ie, there's no transitive closure).  I'm using the DIG integration with a Pellet server and
Protege 3.3.

My expectation would be that if I assert San Jose is part of California and CA is part of US, then there should
be someway of learning that San Jose is part of the US without manually traversing the graph myself.  Given
that OWL provides a transitive property support, how can I demonstrate that using Protege OWL?

Taylor

       
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Jens | 2 Jul 2007 17:43
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collabProtege is fantastic! - trying to convert annotation onto to database

Hi,
these days I upgraded my server based protege installation from 3.2.1 to 3.3
and include collaborative Protege option.

It's amazing! Natasha, Tania and the rest of the protege group did a great
job. It's the long missing feature for a real multi user environment with
change history. Thank's a lot! 

We build some automated interfaces to populate and modify our ontology. Even
those - as they connect to the remote Protege server - are included in the
change history.

There are a few open questions for me:

- Annotation Database Project is file based. On a protege server installation,
this forces me to use the "saveIntervalSec" option to save the file every 120
seconds. I tried to convert this project to a database project as well, but
it doesn't work when starting the server. Protege allows only conversion to
Frames Database project. Why did you choose RDFS File format in favor of a
Database Annotation Project and is there any way to achieve this?

- How about scalability? Tracking any changes to the main ontology causes
one or more instances in the annotation history. The annotation history could
get very big. What impact does it have? Are there any thoughts on housekeeping
e.g. removing very old changes in the change history

Regards,
Jens.

Protege Server side log:
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Jens | 2 Jul 2007 19:59
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Protege 3.3b411 - small problem with collabProtege and Workaround

Hi,
just tried to demonstrate collabProtege annotation/changes to a collegue and it
didn't show any changes! Playing around with protege gui, I found out that 
changes seem to appear only when you activated the ChangeTab and did some
searching in the change tab. After the first change appears in the annotation
tab, then it keeps working. 

Is there a connection or initalization problem in annotation tab, something
which is handled by ChangeTab to get annotation tab changes working?

Workaround works fine so far...

Regards,
jens.

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Tania Tudorache | 2 Jul 2007 20:28
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Re: Frozen Instance editor window

Hi Bo,

Thanks for the bug report. What version of Protege are you using?

 From the stack trace it looks like the browser text of an instance was 
changed, and either the type of the instance became null (which should 
never happen) or the browser pattern of the instance type could not be 
found.

Do you have some steps to reproduce this behavior? I am sure this bug is 
easy to be fixed, if we can reproduce it.

Thanks,
Tania

Bo De Lange wrote:
> Hi,
>
> we're having recurrent problems with a frozen Instance editor window.
> Whilst in the Instances tab and clicking through the instances of a 
> class, the editor window on the right is not updated.
> Only restarting Protege seems to help to fix the problem.
>
> This is what I captured from the logfile:
>
> 2007.06.21 16:08:51.692 CEST WARNING: Exception caught during event 
> dispatch - see the log for details - java.lang.NullPointerException -- 
> EventDispatchFrameStore.dispatchEvents()
> 2007.06.21 16:08:51.708 CEST FINE: Exception caught -- 
> java.lang.NullPointerException
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Tania Tudorache | 2 Jul 2007 23:08
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Re: Protege 3.3b411 and Query Results protege_query_results.txt

Jens,

I have extended the Export functionality, so that the user can choose 
where to save the query results.

In the client-server mode, the query results will be saved on the client 
side, not on the server side. This was a mistake in the previous 
implementation.

Cheers,
Tania

usenet <at> mnet-mail.de wrote:
> Hi,
> I just found a problem with Protege 3.3 beta 411. I get exceptions when
> trying to save Query results.
>
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> 	at java.io.File.<init>(File.java:332)
> 	at
> edu.stanford.smi.protegex.queries_tab.InstancesList$3.actionPerformed(Unknown
> Source)
> 	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)
>
>
> I use a Server-based Protge installation. Looking at the Sourcecode, I
> find that the output directory is not configurable and retrieved by deprecated
> function getProjectDirectoryFile(). To where does this directory resolve
> in a Server mode project? With Protege 3.2.1 it was Protege installation
> directory, which is also not a good idea because it might be readonly.
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Barry Jackson | 3 Jul 2007 00:08
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Re: Ontoviz Plugin - location of generated dot file?

Assuming you are working on a PC and not a Mac you need to check the  
"Save as gif" in the "Ontoviz Global Options" window obtained by  
clicking on the Op tab. A gif file is produced when you next create a  
graph. The file appears in your designated work area.

if it is a Macintosh see my earlier message to this forum.

Barry

On Jul 2, 2007, at 11:45 PM, usenet <at> mnet-mail.de wrote:

> Hi,
> Ontoviz Plugin is nice, but I'd like to get the generated picture  
> outside of
> Protege.
>
> On a windows installation, I found out that Ontoviz generates two  
> files with the
> name of the Ontology (I use a Server sided) in the root of the  
> Installation
> directory. My Protege is in D:\Prog... and I find D:\FooBar.dot and
> D:\FooBar.dot-input.
>
> Is there any way to configure the output directory of intermediate  
> dot files?
>
> Regards,
> Jens.
>
> _______________________________________________
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Tania Tudorache | 3 Jul 2007 00:56
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Re: Ontoviz Plugin - location of generated dot file?

Jens,

The OntoViz plugin does not work correctly in client-server mode. I have 
fixed it. The fix will be available in the next Protege release.

In the multi-user client, the user will be asked where he wants to save 
the OntoViz files (.dot, .dot-input and .gif). A Protege client cannot 
(or actually, it should not) write to the file system of the server.

Cheers,
Tania

usenet <at> mnet-mail.de wrote:
> Hi,
> Ontoviz Plugin is nice, but I'd like to get the generated picture outside of
> Protege.
>
> On a windows installation, I found out that Ontoviz generates two files with the
> name of the Ontology (I use a Server sided) in the root of the Installation
> directory. My Protege is in D:\Prog... and I find D:\FooBar.dot and
> D:\FooBar.dot-input.
>
> Is there any way to configure the output directory of intermediate dot files?
>
> Regards,
> Jens.
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion <at> lists.stanford.edu
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Tania Tudorache | 3 Jul 2007 00:58
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Re: transitive properties

Taylor,

Please post the OWL related questions on the Protege OWL mailing list.

Thanks,
Tania

Taylor Cowan wrote:
> I'm experimenting with an OWL ontology and hoped to demonstrate the power of a transitive property I
labeled "partOf".  Running pellet doesn't insert any new assertions and queries via SPARQL only return
neighbors (ie, there's no transitive closure).  I'm using the DIG integration with a Pellet server and
Protege 3.3.
>
> My expectation would be that if I assert San Jose is part of California and CA is part of US, then there should
be someway of learning that San Jose is part of the US without manually traversing the graph myself.  Given
that OWL provides a transitive property support, how can I demonstrate that using Protege OWL?
>
> Taylor
>
>
>
>        
> ____________________________________________________________________________________
> Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online.
> http://smallbusiness.yahoo.com/webhosting 
> _______________________________________________
> protege-discussion mailing list
> protege-discussion <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
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