[MOBY] [MOBY-l] New example service

[Ken Steube]

You can link to the FASTA example, but I have a whole MOBY education site
at

  http://plantgenome.sdsc.edu/mobyed2/learn.html

and you should provide a link to it. BTW I'm very open to any suggestions
about how to improve my ed. program. If you or anyone else wants to look
it over and offer comments that would be very welcome.

getMobySimples does overlap with CommonSubs a little. I didn't want to
create competing software but it kind of went in that direction.  It
returns a list of MobyXmlObject objects.  If that belongs in CommonSubs
then let's put it in there and I'll add MobyXmlObject to the CVS tree.

As for MobyXmlObject I will add soon:

  method getMobyCollections
  ability to set values in object and write it as XML
  method getMobyGenericSequence (a convenience method)
  capability to deal with secondary articles and CRIB/PIB

Ken

On Mon, 3 Nov 2003, Mark Wilkinson wrote:

> hey Ken!
>
> that is fantastic!  Can I put a link to that on the BioMOBY website?  I
> need to set up a page for links to tutorials like this one, and the one
> that Catherine set up last month.
>
> One comment - I like the 'getMobySimples' routine in your MobyXMLObject
> module, but I'd prefer it if you could somehow roll that code into the
> CommonSubs module instead, since the two modules are now working in
> opposition to each other; i.e. in CommonSubs you call "getInputArticles"
> using the $query, which handles all types of potential MOBY inputs
> (single-simple, multiple-simple, single-collection, multiple-collection,
> and combinations of these) whereas your module assumes that all services
> consume single-simples (as far as I can tell).
>
> What do you think?
>
> M
>
> On Fri, 2003-10-31 at 11:31, Ken Steube wrote:
> > Hey there,
> >
> > I just created a new example service to give to aspiring MOBY'ers.
> > It's not really a useful service but it's OK for an example of how to
> > write services:  it takes a GenericSequence or better and returns a
> > String containing a FASTA formatted sequence.
> >
> >   http://plantgenome.sdsc.edu/mobyed2/Fasta_Service
> >
> > XML parsing: I finally got around to doing this better, but still within
> > the limitations of XML::DOM. I created a perl module MobyXmlObject.pm that
> > stores any MOBY data object and gives easy access to all the data and all
> > the included MOBY objects.
> >
> > The best part:  it also has a script that allows you to debug it at
> > the command line without going through a SOAP connection.
> >
> > Comments welcome...could use some help to make sure I'm providing a good
> > example! It comes with detailed instructions on how to set it up and run
> > it.
> >
> > Ken
> >
> > -------------------------------------
> > Ken Steube            steube at sdsc.edu
> > San Diego Supercomputer Center @ UCSD
> > San Diego, California             USA
> >
> >
> >
> > _______________________________________________
> > moby-l mailing list
> > moby-l at biomoby.org
> > http://biomoby.org/mailman/listinfo/moby-l
>

-- 
-------------------------------------
Ken Steube            steube at sdsc.edu
San Diego Supercomputer Center @ UCSD
San Diego, California             USA