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[protege-discussion] question on color

Tania Tudorache tudorache at stanford.edu
Mon Feb 25 15:05:37 PST 2008


Hui,

A red border around a slot widget usually indicates that the values of 
that slot are invalid. Usually there is also a tool tip that indicates 
the problem. For example, if a slot is required (so it has a cardinality 
at least one), and you have no values for that slot at an instance, you 
will see a red border around the slot widget for that slot.

In Ontoviz, you can configure the colors used in the graph by clicking 
on the "Op" button and going to the "colors" tab.

Tania

hhuang wrote:
> Hi,
>
> Does red color always indicate errors, in all Protoge facilities, 
> particularly in ontoviz graphs?
>
> Thanks,
>
> Hui
>
> At 03:06 PM 2/23/2008, you wrote:
>   
>> Send protege-discussion mailing list submissions to
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>> When replying, please edit your Subject line so it is more specific
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>>
>> Today's Topics:
>>
>>    1. Re: Protege Server lost connection to MySQL       database
>>       (Timothy Redmond)
>>    2. Re: Project->Archive Project when using Protege Database
>>       (Tania Tudorache)
>>    3. Re: Pluging Protege on top of Jena. (Tania Tudorache)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 22 Feb 2008 12:27:38 -0800
>> From: Timothy Redmond <tredmond at stanford.edu>
>> Subject: Re: [protege-discussion] Protege Server lost connection to
>>         MySQL   database
>> To: User support for Core Protege and the Protege-Frames editor
>>         <protege-discussion at lists.stanford.edu>
>> Message-ID: <3A3E37BB-B6BA-4E82-A18B-D730DFF4C714 at stanford.edu>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>>
>> On Feb 21, 2008, at 2:54 AM, Jonathan Carter wrote:
>>
>>     
>>> Hi,
>>>
>>> Has anyone else had a similar exception from Protege Server -
>>> connection lost to database?
>>> I'm using MySQL 5.051 Community edition and my server had been
>>> running for about 1.5 days with possibly more than 8 hours idle time
>>> over night.
>>> When the server received the database connection loss, it seemed to
>>> go into a funny state, locking up a Protege Client that was
>>> connected at the time. The only way forward was to restart the
>>> Protege server.
>>>       
>> Yes this is a known bug.  The database is closing the connection and
>> the client does not know.  Sometimes there are ways to correct the
>> problem which a new session but it is awkward.  For some time I was
>> unclear on how to fix this.
>>
>> The good news is that it is fixed in the release coming in March
>> thanks to a suggestion by Bob Dionne.  I did not find a good way to
>> determine that a connection has been closed.  So what the new version
>> of Protege does is to have a timeout on idle connections so that it
>> can close the connection on its side.  Then when the user tries to
>> access the knowledge base again protege automatically sets up a new
>> connection with the database.  The idle timeout can be set with a flag
>> (and should be longer than any single database operation).
>>
>>     
>>>  I've done some digging and losing connections to MySQL 5 appears to
>>> be something that others (in the wider Java community) have seen and
>>> it sounds like when MySQL shuts down idle connections, any
>>> connection pools don't seem to get notified of this.
>>>
>>> Has anyone had a similar experience?
>>> Does the Protege Server attempt to reconnect explicitly (rather than
>>> relying on the connection pool) with MySQL?
>>> Are there any recommended settings on MySQL that have been used to
>>> avoid this? e.g. I've found a suggestion to up the wait-timeout in
>>> MySQL from default of 8 hours to much more to stop MySQL culling
>>> idle connections. I'm going to try putting this to 36 hours and see
>>> how that affects things.
>>>       
>> NCI is using this setting and it is working for them.  I believe that
>> the code has been fixed on their branch though.
>>
>> -Timothy
>>
>>
>>     
>>> Thanks
>>>
>>> Jonathan
>>> _______________________________________
>>>
>>> Jonathan Carter - Head of Technical Architecture
>>> Enterprise Architecture Solutions Ltd
>>>
>>> Mobile: +44 (0) 7904 198295
>>> Email: jonathan.carter at e-asolutions.com
>>> Web: www.enterprise-architecture.com
>>> _______________________________________
>>>
>>> Assess your EA maturity at:
>>> www.enterprise-architecture.com/EAvaluator
>>> _______________________________________
>>>
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>> http://protege.stanford.edu/doc/faq.html#01a.03
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>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 22 Feb 2008 21:28:34 -0800
>> From: Tania Tudorache <tudorache at stanford.edu>
>> Subject: Re: [protege-discussion] Project->Archive Project when using
>>         Protege Database
>> To: User support for Core Protege and the Protege-Frames editor
>>         <protege-discussion at lists.stanford.edu>
>> Message-ID: <47BFAF02.1040000 at stanford.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi Jonathan,
>>
>> Currently, the archive function works only for file projects. We have
>> recently implemented the archiving of database projects, too. We are
>> currently testing it and if everything goes well, we will integrate this
>> functionality in the next beta release.
>>
>> Tania
>>
>>
>> Jonathan Carter wrote:
>>     
>>> Hi everyone,
>>>
>>> I really like the Archive and Restore features of the Project.
>>> However, when I archive a project that has been converted to a Protege
>>> Database format, it seems that the archive only archives the PPRJ file
>>> (the project) but does not archive the Ontology and Instances that are
>>> held in the relational database - e.g. in MySQL.
>>>
>>> Is this what I should expect to see or am I missing something?
>>> Thanks very much for your help
>>>
>>> Regards
>>>
>>> Jonathan
>>>
>>> _______________________________________
>>>
>>> Jonathan Carter - Head of Technical Architecture
>>> Enterprise Architecture Solutions Ltd
>>>
>>> Mobile: +44 (0) 7904 198295
>>> Email: jonathan.carter at e-asolutions.com
>>> <mailto:jonathan.carter at e-asolutions.com>
>>> Web: www.enterprise-architecture.com
>>> <http://www.enterprise-architecture.com/>
>>> ------------------------------------------------------------------------
>>>
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>> http://protege.stanford.edu/doc/faq.html#01a.03
>>     
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 22 Feb 2008 21:48:08 -0800
>> From: Tania Tudorache <tudorache at stanford.edu>
>> Subject: Re: [protege-discussion] Pluging Protege on top of Jena.
>> To: User support for Core Protege and the Protege-Frames editor
>>         <protege-discussion at lists.stanford.edu>
>> Message-ID: <47BFB398.6000503 at stanford.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Olivier,
>>
>> Please note that we have a separate mailing list for posting Protege-OWL
>> related questions:
>>
>> http://protege.stanford.edu/community/lists.html
>>
>> I did not understand exactly what you are trying to do. Protege has its
>> own API which is used to built plug-ins or applications on top of
>> Protege. For more documentation about the Protege APIs, both frames and
>> OWL, please see [1].
>>
>> Protege API is not built on top of Jena API. There are ways of obtaining
>> a Jena model out of a Protege OWL model, which are documented here [2].
>>
>> The KnowledgeBase, Cls and Slot classes are part of the Protege frames
>> API. The Protege OWL API is built on top of it. However, if you want to
>> develop a plugin or an application in OWL, you should not use the frames
>> API, but the Protege-OWL API [3].
>>
>> Please ask in future OWL related questions on the Protege-OWL mailing list.
>>
>> Thanks,
>> Tania
>>
>>
>> [1]: http://protege.stanford.edu/doc/dev.html
>> [2]: http://protege.cim3.net/cgi-bin/wiki.pl?ProtegeJenaIntegration
>> [3]: http://protege.stanford.edu/plugins/owl/api/guide.html
>>
>>
>> Olivier Rossel wrote:
>>     
>>> Hello.
>>> I am trying to see the difficulty of pluging some Protege components
>>> on top of Jena.
>>> Basically, when browsing the sources, I am always sent back to
>>> KnowledgeBase.class.
>>> Even Cls and Slot are delagates of KnowledgeBase.class.
>>>
>>> Does it mean that achieving my goal is as simple as coding a
>>> JenaBasedKnowledgeBase.class?
>>> And injecting it into a JenaBasedProject.class ?
>>>
>>> I would appreciate any comment about that idea (especially from people
>>> used to Protege internals).
>>>
>>> PS: The point is to propose editing facilities for any project that
>>> has chosen Jena as its internal API.
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>> http://protege.stanford.edu/doc/faq.html#01a.03
>>     
>>>       
>>
>> ------------------------------
>>
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>>
>> End of protege-discussion Digest, Vol 19, Issue 26
>> **************************************************
>>     
>
>
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