[MOBY-l] registering Scored_string object...

[Michael Jensen]

Thanks again for Ken and his examples to get me this far...

I want to register this object, but as it is my first one I may need 
some assistance. Some output of my service may be:

<Collection>
<Simple>
<Scored_string namespace="" id="">
         <String namespace="Global_keyword" id="" 
articleName="acronym">MAPK</String>
         <Object namespace="Global_keyword" id="mitogen-activated 
protein kinase" articleName="string_component"/>
         <Long namespace="" id="" 
articleName="score">0.90884572798250385</Long>
</Scored_string>
</Simple>
<Simple>
<Scored_string namespace="" id="">
         <String namespace="Global_keyword" id="" articleName="acronym"/>
         <Object namespace="Global_keyword" id="MAPK" 
articleName="string_component"/>
         <Long namespace="" id="" articleName="score">1</Long>
</Scored_string>
</Simple>
<Simple>
<Scored_string namespace="" id="">
         <String namespace="Global_keyword" id="" articleName="acronym"/>
         <Object namespace="Global_keyword" id="increase" 
articleName="string_component"/>
         <Long namespace="" id="" 
articleName="score">0.06212914418525689</Long>
</Scored_string>
</Simple>
</Collection>


Starting with Ken's object registration example script, I put the 
following together. On the ISA and HASA I am assuming below the first 
value is what the tag is, like String, Object, or Long, unless it is a 
ISA, then it is just what type it is. Then I assume the second value is 
what the articleName is, and can be blank if there is none.

Is this correct? Will what I have below register the object for the XML 
output above?

------------------------
#!/usr/local/bin/perl5.6.1
use warnings 'all';
use strict;

# Register a new data object called Scored_string

use lib '/usr/home/jonhar/Apps/moby-live/Perl';
use MOBY::Client::Central;
use MOBY::Client::Service;

my $Central = MOBY::Client::Central->new();

my $reg = $Central->registerObjectClass(
   objectType => "Scored_string",
   description => "Any text with a score or ranking associated, with a 
possible acronym for the keyword",
   contactEmail => 'michael at inblosam.com',
   authURI => "www.inblosam.com",
   Relationships => {
     ISA => [
       ['Object', ''],
     ],
     HASA => [
       ['String', 'acronym'],
       ['Object', 'string_component'],
       ['Long', 'score'],
     ]
   }
);

print STDERR "registerObjectClass failed: ", $reg->message, "\n"
   unless $reg->success;
-----------------------

And one more question: In the MOBYClientCentral test file 
(testMOBYClientCentral_v05.pl) on the site, it has the following 
snippet of code. As I will have a collection as my output, do I just 
use it like I have it below (below the test one)?


TEST($C->registerService(
     serviceName  => "myfirstservice2",
     serviceType  => "Retrieval",
     authURI      => "www.illuminae.com",
     contactEmail => 'your at mail.address',
     description => "this is my first service",
     category  =>  "moby",
     URL    =>  "http://illuminae/cgi-bin/service.pl",
	input =>[
#        ['articleName1', [[Object => ['UglyNamespace']]]], # Collection
	        ['articleName1', [Object => ['UglyNamespace']]], # Simple
	        ],
	output =>[
         ['articleName2', [String => ['UglyNamespace']]], # Simple
	         ],
	), 20, 1);



sub register_service {
   my $C = shift;
   my $reg = $C->registerService(
     serviceName  => 'extractGeneProteinNames',
     authURI      => $authURI,
     contactEmail => $email,
     description  => "Takes any text (abstract, full text article, etc.) 
and extr
acts names and abbreviations of genes and proteins, with a score (0-1, 
with 1 be
ing highest).",
     URL          => $url,
     input        => [ ['', ["text-plain" => []]], ],
     output       => [ ['', [["Scored_string" => []]]], ],
     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";
   }
}

I am not sure the "text-plain" is right for the input either, but all I 
expect is something like this.

<?xml version='1.0' encoding='UTF-8'?>
<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>
<moby:Query>
<moby:queryInput moby:articleName=''>
<moby:Simple>
<moby:Text namespace=''>
<moby:String namespace='' id='' articleName='text'>We observed an 
increase in mitogen-activated protein kinase (MAPK) 
activity.</moby:String>
</moby:Text>
</moby:Simple>
</moby:queryInput>
</moby:Query>
</moby:MOBY>

Thanks for all your help with all of my questions!!

-Michael Jensen
michael at inblosam.com