Raw content of Bio::EnsEMBL::Pipeline::AnaSubmission
<![CDATA[#!/usr/local/bin/perl5.6.1 -w
package Bio::EnsEMBL::Pipeline::AnaSubmission;
use strict;
use DBI;
use Carp;
use Time::Local qw( timelocal );
use Exporter;
use vars qw( @ISA @EXPORT_OK );
use Hum::Submission qw{ get_user };
use Hum::SubmissionConf;
@ISA = ('Exporter');
@EXPORT_OK = qw(
set_db_args
sub_db
prepare_statement
get_db
);
=pod
=head2 ref_from_query( SQL )
Returns a reference to an array of anonymous
arrays containing the results from running the
B<SQL> query on the database.
=cut
##
##sub ref_from_query {
## my( $query ) = @_;
##
##my $dbh = sub_db();
## my $sth = $dbh->prepare( $query );
## $sth->execute;
## return $sth->fetchall_arrayref;
##}
##
##sub_db returns the database handle
{
my ($user , $dbname , $host, $port);
my( $db );
sub set_db_args{
## take in user name password port etc, and use them to connect to the db
my %args_hash = @_;
$user = $args_hash{user} ;
$dbname = $args_hash{db_name};
$host = $args_hash{host};
$port = $args_hash{port};
}
sub sub_db{
unless ($db) {
# go to default values unless given already
unless ($user) { $user= get_user();};
unless ($dbname) { $dbname = 'submissions'} ;
unless (defined $host && defined $port){
($host, $port)=Hum::SubmissionConf::localisation();
}
if (my $test = $ENV{'SUBMISSION_TEST_DB'}) {
# Legal formats:
#
# submissions_test
# submissions_test:3306
# submissions_test@ecs2b
# submissions_test@ecs2b:3306
if ($test =~ /^([\w_\$]+)(?:\@([\w\-\.]+))?(?::(\d+))?$/) {
$dbname = $1;
$host = $2 if $2;
$port = $3 if $3;
} else {
confess "Can't parse SUBMISSION_TEST_DB environment variable '$test'";
}
}
# warn "DBI:mysql:host=$host;port=$port;database=$dbname:", $user;
# Make the database connection
$db = DBI->connect("DBI:mysql:host=$host;port=$port;database=$dbname",
$user, undef, {RaiseError => 1, PrintError => 0})
or die "Can't connect to submissions database as '$user' ",
DBI::errstr();
}
return $db;
}
my( @active_statement_handles );
sub prepare_statement {
my( $text ) = @_;
my $sth = sub_db()->prepare($text);
push(@active_statement_handles, $sth);
return $sth;
}
sub get_db{
if ($db){
return $db;
}else{
warn "Not returning a db;";
return;
}
}
}
1;
__END__
=head1 NAME - Submission
=head1 AUTHOR
James Gilbert B<email> jgrg@sanger.ac.uk
]]>