Raw content of BioMart::Configuration::RegistryDBPointer
<![CDATA[# $Id:
#
# BioMart module for BioMart::Configuration::RegistryDBPointer
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
BioMart::Configuration::RegistryDBPointer
=head1 SYNOPSIS
A Location that represents the configuration for a mart database accessed
directly from the DB server
=head1 DESCRIPTION
=head1 AUTHOR - Arek Kasprzyk, Damian Smedley
=head1 CONTACT
This module is part of the BioMart project http://www.biomart.org
Questions can be posted to the mart-dev mailing list:
mart-dev@ebi.ac.uk
=head1 METHODS
=cut
package BioMart::Configuration::RegistryDBPointer;
use base qw(BioMart::Configuration::DBLocation);
use strict;
use warnings;
=head2 _new
Usage : see Usage for BioMart::Configuration::Location.
Description: creates a new MartDBLocation object which ...
Returntype : BioMart::Configuration::MartDBLocation
Exceptions : none
Caller : general
=cut
sub _new {
my ($self, @param) = @_;
$self->SUPER::_new(@param);
}
sub getRegistryXML {
my $self=shift;
my $dbh=$self->dbh();
my $dsn=$self->dsn();
unless ($dbh) {
warn("\n\nWARNING: Could not load Registry from database $dsn, SKIPPING\n\n");
return undef;
}
# stops XML too long bug
$dbh->{'LongTruncOk'} = 1;
$dbh->{'LongReadLen'} = 20000;
my $sql = "SELECT compressed_xml FROM ".$self->schema.".meta_registry";
my $sth = $dbh->prepare($sql);
unless ($sth) {
my $err = $dbh->errstr;
$dbh->disconnect;
BioMart::Exception::Database->throw("Could not prepare statement handle for registry fetch for db $dsn: $err");
}
my $executed = $sth->execute;
unless ($executed) {
my $err = $dbh->errstr;
$sth->finish;
$dbh->disconnect;
BioMart::Exception::Database->throw("Could not execute sql for $dsn: $err");
}
my $row = $sth->fetchrow_arrayref;
my $xml = Compress::Zlib::memGunzip($row->[0]) ;
$sth->finish;
$dbh->disconnect;
return $xml;
}
1;
]]>