[MOBY-l] Re: namespace

[Ken Steube]

I'm not sure I understand the question...I'll try to answer and you can
reply for more info.

An object belongs to a particular namespace
<Object namespace=AGI_LocusCode id=At3g19100/>
belongs to AGI_LocusCode. Sometimes you might see the namespace might being
left blank if it's not important (such as for the Integer object inside
a GenericSequence).

I wouldn't really say a service belongs to a namespace, rather we say it
accepts objects from particular namespaces. Or a service might accept
objects of a certain type from any namespace if the namespace isn't
important (such as BLAST: can accept a DNA seq from any namespace so
the namespace isn't generally critical info for BLAST).

Ken

On Wed, 28 Jan 2004, Ardavan Kanani wrote:

> Ken,
>
> Thanks for responding to my question.  My question is more about an
> object belonging to a namespace or services belonging to a namespace
> and not accepting or outputting objects from a particular namespace.
> Do objects belong to particular namespaces?  If that's the case where
> in the object registration should I declare its namespace?  Since
> services are, sort of, objects too, where do I specify what namespace
> they belong to.  I am trying to create all my objects and services
> under a namespace called "haplotyping_study"  I might be totally
> confused as how the namespaces work on MOBY.  I am coming from an
> object oriented world.  So when I see the disjoint between objects and
> services in MOBY I get confused.
>
> Thanks, Ardavan Kanani
>
> On Jan 28, 2004, at 11:36 AM, Ken Steube wrote:
>
> > On Wed, 28 Jan 2004, Ardavan Kanani wrote:
> >> Mark,
> >> How would I register an object or a service under a particular
> >> namespace?  I looked at the API doc and the signature for
> >> registerObjectClass and registerServiceName/Type does not include a
> >> namespace parameter.
> >
> > Here is the script that registers my plantspGetProtein service to
> > accept an Object from any of the namespaces
> > ['AGI_LocusCode', 'NCBI_gi', 'SDSC_fg'].
> >
> > Ken
> >
> >
> >
> >
> >
> > #!/usr/local/bin/perl5.6.1
> > use warnings 'all';	# Issue warnings about suspicious programming
> > use strict;		# Must declare and initialize all variables
> >
> > #######################################################################
> > ##
> > # This script will register the plantspGetProtein MOBY service
> > #######################################################################
> > ##
> >
> > use MOBY::Client::Central;
> > use MOBY::Client::Service;
> >
> > my $Central = MOBY::Client::Central->new();
> >
> > my $reg = $Central->registerService(
> >   serviceName  => 'plantspGetProtein',
> >   authURI      => 'www.sdsc.edu',
> >   contactEmail => 'steube at sdsc.edu',
> >   description  => "Retrieves a protein sequence from the PlantsP
> > database (proteins related to phosphorylation, transporters and
> > ubiquitin)",
> >   URL          =>
> > 'http://plantsp.sdsc.edu/cgi-bin/MOBY/PlantsP_dispatcher.cgi',
> >   input        => [ ['', ["Object" => ['AGI_LocusCode', 'NCBI_gi',
> > 'SDSC_fg']]], ],
> >   output       => [ ['', ["AminoAcidSequence" => []]], ],
> >   category     => "moby",
> >   serviceType  => "Retrieval",
> > );
> > die "Bad return value from registerService" unless $reg;
> > if ($reg->success == 1){
> >   print "Registration successful\n\n";
> > }
> > else {
> >   print "Registration failed: ", $reg->message, "\n";
> > }
> >
> >
> > --
> > --
> > --
> > Ken Steube
> > San Diego Supercomputer Center
> > University of California, San Diego
> > Mail code 0537, CRB room 207
> > 9500 Gilman Drive
> > San Diego, California, 92093-0537  USA
> > FAX (858) 822-3610
> >
>

-- 
--
--
Ken Steube
San Diego Supercomputer Center
University of California, San Diego
Mail code 0537, CRB room 207
9500 Gilman Drive
San Diego, California, 92093-0537  USA
FAX (858) 822-3610