[MOBY-dev] First (?) MOBY 0.5 service up and running

[Mark Wilkinson]

Hi MOBYers and I3Cers, 

I set up a simple service at mobycentral.cbr.nrc.ca that takes base
objects with GO accessions and returns the GO term/definition.

Attached are:

RegisterGOService.pl - shows how to use the Perl interface to register
objects, namespaces, and services.  How to discover services.  How to
use the MOBY::Client::Service and ServiceInstance modules to connect to
and execute the service (for the moment we are still coding XML by
hand...)

Services.cgi - this is the cgi program at mobycentral that is serving
the service.

BasicLocalServices.pm - this contains the subroutine that is executed in
order to do the ID -> GO_Term transformation.

*** Please do a CVS update before running the script ***

I'm off for the weekend!  Back Monday.  Let me know if this works for
you, 

Cheers all!

Mark



-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae
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package Services::BasicLocalServices;

use lib "/var/www/cgi-bin";
use strict;
use MIME::Base64;
use XML::DOM;
use vars qw(@ISA);
@ISA = qw(SOAP::Server::Parameters);   # uncomment this line if you want access to the SOM as the
                                       # last parameter passed to thh subroutine

sub getGoTerm {

    my $SOM = pop;  
    my ($self, $data) = @_;
    my $response; my @objects;
    my $parser = new XML::DOM::Parser;
    my $doc = $parser->parse($data);
    my $moby = $doc->getDocumentElement();

    my $x = $moby->getElementsByTagName('queryInput');
	unless ($x->item(0)){
		$x = $moby->getElementsByTagName('moby:queryInput');
	}
    my @accessions;
	if ($x->item(0)){
        my @child = $x->item(0)->getChildNodes;
        my $content;
        foreach (@child){
            $content .= $_->toString;
            unless ($content =~ /namespace\s*=\s*['"]GO\/Accession.*?id\s*=\s*['"](GO:\d\d\d\d\d\d\d)/s){
                push @accessions, undef;
                next;
            } else {
				push @accessions, $1;
			}
        }
	}
		
    use DBI;
    use DBD::mysql;
    my $dbh = _dbAccess('go');
    die "can't connecvt to database\n" unless $dbh;
    my $sth = $dbh->prepare(q{select name, term_definition from term, term_definition where term.id = term_definition.term_id and acc=?});
    
    foreach (@accessions){
        $sth->execute($_);        
        my ($term, $def) = $sth->fetchrow_array;
        if ($term){
            $response .= simpleResponse("
                <moby:GO_Term namespace='GO/Accession' id='$_'>
                    <moby:String namespace='' id='' articleName='Term'>$term</String>
                    <moby:String namespace='' id='' articleName='Definition'>$def</String>
                </moby:GO_term>")
        } else {
            $response .= simpleResponse("")
        }
    }

    $response =  responseHeader() . $response . responseFooter();
    my $SOAPResponse = SOAP::Data->type('base64' => $response);
    return $SOAPResponse
    
}
    
sub responseHeader {
    return "<?xml version='1.0' encoding='UTF-8'?>
      <moby:MOBY xmlns:moby='http://www.biomoby.org/moby'>
        <moby:Response moby:authority='http://www.illuminae.com'>
        ";
}

sub responseFooter {
    return "
    </moby:Response>
      </moby:MOBY>\n"
}

sub simpleResponse {
    my ($data, $articleName) = @_;  # articleName optional
    if ($articleName) {
        return "
        <moby:queryResponse>
            <Simple articleName='$articleName'>
                $data
            </Simple>
        </moby:queryResponse>
        ";
    } else {
        return "
        <moby:queryResponse>
            <Simple>
                $data
            </Simple>
        </moby:queryResponse>
        ";
    }
}

sub _dbAccess {
    my ($dbname) = @_;
    return undef unless $dbname;
	my $url = $ENV{MOBY_CENTRAL_URL}; chomp $url;
	my $username = $ENV{MOBY_CENTRAL_DBUSER}; chomp $username;
	my $password = $ENV{MOBY_CENTRAL_DBPASS}; chomp $password;
	my $port = $ENV{MOBY_CENTRAL_DBPORT}; chomp $port;
	
	my ($dsn) = "DBI:mysql:$dbname:$url:$port";
	my $dbh = DBI->connect($dsn, $username, $password, {RaiseError => 1}) or die "can't connect to database";
	
	return ($dbh);
}
    
    
    
    
1;