[MOBY-dev] how to handle errors in a biomoby service?

[Oswaldo Trelles]

----- Original Message ----- 
From: "Oswaldo Trelles" <ots at ac.uma.es>
To: "Core developer announcements" <moby-dev at portal.open-bio.org>; "Moby
Developers" <moby-dev at biomoby.org>
Sent: Thursday, August 11, 2005 12:05 PM
Subject: Re: [MOBY-dev] how to handle errors in a biomoby service?


> Dear all,
>
> We sent a message (July 25) regarding error handling. I am not sure
weather
> the message is in your hands, thus I am re-sending it for discussion.
>
> best regards
>
> Oswaldo
>
>
>
>
>
> --------------
>
>
> ----- Original Message ----- 
> From: "Oswaldo Trelles" <ots at ac.uma.es>
> To: "Eddie Kawas" <ed.kawas at gmail.com>
> Sent: Monday, July 25, 2005 6:43 PM
> Subject: Error handling proposal
>
>
> > Eddie, could you please circulate this message and made the document
> > available following your protocol?
> > thanks in advance
> > Oswaldo
> >
> > Please let me introduce myself. My name is Oswaldo Trelles and I work at
> the
> > Computer architecture Department of the University of Malaga, Spain
(where
> > all of you are invited and welcomed). Our group is in charge of the
> > "Integrated Bioinformatics" aspects at the INB (National Institute of
> > Bioinformatics). As David Gonzáles Pisano informed you at the Vancouver
> > meeting we are developing an integrated platform to deploy general and
> > specific services using BioMOBY as the underlying protocol.
> >
> > Thus we are quite concerned with BM specifications and we would like to
> > contribute in the development, extension and improvements in the
protocol.
> > At this moment Roman has made a preliminary version and description of
> > Theseu project available. Now we would like to put over the table the
> error
> > handling issue. We have prepared a document, which represent an
extension
> of
> > our current implementation. This proposal was discussed during the
> > INB-meeting here in Malaga (July 2005) and now is distributed as an open
> > document for further discussion.
> >
> > Please feel free to comment.
> >
> > best regards, Oswaldo + GNV5 team + INB team
>
>
> ----- Original Message ----- 
> From: "Martin Senger" <senger at ebi.ac.uk>
> To: "Moby Developers" <moby-dev at biomoby.org>
> Sent: Thursday, August 11, 2005 3:10 AM
> Subject: [MOBY-dev] how to handle errors in a biomoby service?
>
>
> > This question is meant primarily for Java-based biomoby services, but a
> > suggestion from Perl people can help me as well.
> >
> > I wonder what are the general rules for handling errors in biomoby
> > services. The API is silent about it, and the only thing I remember from
> > the discussions is that if there is an error the service will return an
> > empty output object (still, of course, wrapped in a biomoby XML
> > envelope). Is this really the only way how to handle all kinds of
> > errors?
> >
> > I understand that this behaviour is reasonable when my input data does
not
> > produce any result (wrong id, non-existing id, etc.). But should I use
the
> > same mechanism for things like:
> >    * the input data does not come as String or base64 type,
> >    * the input XML does not conform to the Biomoby API,
> >    * my service cannot respond because of some limited internal
resources,
> >    * etc.
> >
> > Any advise how you deal with these situations will be appreciated, and I
> > thank you very much.
> >
> >    With regards,
> >    Martin
> >
> > PS. Of course, you noticed that in my main email body above I have not
> > mentioned how dissapointing the Biomoby API is if it does not deal with
> > error handling :-)
> >
> > M.
> >
> >
> > -- 
> > Martin Senger
> >    email: martin.senger at gmail.com
> >    skype: martinsenger
> > International Rice Research Institute
> > Biometrics and Bioinformatics Unit
> > DAPO BOX 7777, Metro Manila
> > Philippines, phone: +63-2-580-5600 (ext.2324)
> >
> > _______________________________________________
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> > MOBY-dev at biomoby.org
> > http://www.biomoby.org/mailman/listinfo/moby-dev
>