[MOBY] Re: [MISC] [MOBY-l] Processing MOBY responses:MOBYSHoundGetGenBankff as an example

[Gabriel Berriz]

OK, I'll look over the code and get to it.  Thanks.

G.

At 09:37 AM 4/9/2004 -0700, Mark Wilkinson wrote:
>Ha!  Network is back up :-)
>
>So, the module is described on the following page:
>
>http://plantgenome.sdsc.edu/mobyed2/learn.html
>
>It is called "MobyXmlObject.pm"
>
>The portions that are not fully API compliant (AFAIK) are:
>
>1)  It does not record the queryID when parsing MOBY messages.  This
>will be critical for both client and service-side message parsing.
>
>2)  The latest API change (not yet implemented, since we only decided it
>last weekend) is that the message structure for both request and
>response will be identical.  Thus the moby:Query moby:queryInput,
>moby:Response and moby:queryResponse have been replaced by the two tags
>moby:mobyContent (outer tag) and moby:mobyData (inner tag).  I don't
>know if Ken's parser is parsing messages based on these tags, but it if
>is, it will need to be tweaked to accept both the old and the new for at
>least the transition period.
>
>
>If you are planning to migrate this into the CommonSubs routine (sub
>genericServiceInputParser and sub extractResponseArticles) that would be
>wonderful!
>
>That code (CommonSubs.pm) is quite hairy, though, since it is really
>just in the prototype stages...  I hope it is readable!
>
>M
>
>
>
>
>On Fri, 2004-04-09 at 06:46, Gabriel Berriz wrote:
> > In that case, I'd be happy to try coding it from scratch.  I would need to
> > know the specific API/input-output signature for this sub.  Do you (or
> > anyone else reading this) have it?
> >
> > Regards,
> >
> > G.
> >
> > At 08:29 AM 4/9/2004 -0500, mwilkinson wrote:
> >
> > >Hi Gabriel
> > >
> > >I decided to take advantage of the easter weekend to upgrade my Linux
> > >kernel... It didn't go as well as I had hoped!  I don't have a network at
> > >the moment so I can't point you to Ken's library (I'm responding from my
> > >blackberry)
> > >
> > >If you don't get a response from someone else first, I'll reply as 
> soon as
> > >I get my net back up.
> > >
> > >Thanks for the offer!
> > >
> > >M
> > >
> > >-----Original Message-----
> > >From: Gabriel Berriz <gberriz at hms.harvard.edu>
> > >Date: Fri, 09 Apr 2004 09:30:01
> > >To:markw at illuminae.com
> > >Cc:mobyl <moby-l at biomoby.org>
> > >Subject: Re: [MISC] [MOBY-l] Processing MOBY responses:
> > >         MOBYSHoundGetGenBankff as an example
> > >
> > >At 03:41 PM 4/8/2004 -0700, Mark Wilkinson wrote:
> > > >There is only one ~useful client-side method call "extract response
> > > >articles", that is available in the MOBY::CommonSubs module.
> > > >
> > > >This (unfortunately) returns the individual responses as XML::DOM
> > > >objects, rather than having a MOBY-specific API to access the
> > > >information in these objects.  Ken has some code that does a much nicer
> > > >job of creating Perl objects from MOBY Object XML, but at the moment it
> > > >isn't 100% API compliant. I'm hoping this will one day this will migrate
> > > >into this CommonSubs routine so that all of the libraries are in one
> > > >place...
> > >
> > >Mark,
> > >
> > >I'd be happy to take a crack at it.  Where can I find this code by
> > >Ken?  What's the name of the sub, and what exactly is not API-compliant
> > >about it?  (I assume that the API you are referring to is the one at
> > >http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI ; please correct 
> me if
> > >I'm wrong.)
> > >
> > >Regards,
> > >
> > >Gabriel
> > >
> > >
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> > >
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> > >
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>--
>Mark Wilkinson (mwilkinson at mrl.ubc.ca)
>University of British Columbia iCAPTURE Centre