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[protege-discussion] question on color

hhuang hui-min.huang at nist.gov
Mon Feb 25 08:15:34 PST 2008


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:
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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
> > _______________________________________
> >
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> >
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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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>
>
>------------------------------
>
>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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> >
>
>
>
>------------------------------
>
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>End of protege-discussion Digest, Vol 19, Issue 26
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