Commit 8c36d61c authored by Patrick Meidl's avatar Patrick Meidl
Browse files

added get_dbconnection()

parent 4403a9a3
......@@ -52,6 +52,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use FindBin qw($Bin $Script);
use POSIX qw(strftime);
use Cwd qw(abs_path);
use DBI;
=head2 new
......@@ -139,7 +140,7 @@ sub parse_common_options {
$self->param($name, $val);
}
$self->param('conffile', $conffile);
} else {
} elsif ($conffile) {
warning("Unable to open configuration file $conffile for reading: $!");
}
......@@ -651,6 +652,59 @@ sub get_database {
return $self->{'_dba'}->{$database};
}
=head2 get_dbconnection
Arg[1] : (optional) String $prefix - the prefix used for retrieving the
connection settings from the configuration
Example : my $dbh = $self->get_dbconnection;
Description : Connects to the database server specified. You don't have to
specify a database name (this is useful for running commands
like $dbh->do('show databases')).
Return type : DBI database handle
Exceptions : thrown if connection fails
Caller : general
Status : At Risk
=cut
sub get_dbconnection {
my $self = shift;
my $prefix = shift;
$self->check_required_params(
"${prefix}host",
"${prefix}port",
"${prefix}user",
);
my $dsn = "DBI:" . ($self->param('driver')||'mysql') .
":host=" . $self->param("${prefix}host") .
";port=" . $self->param("${prefix}port");
if ($self->param("${prefix}dbname")) {
$dsn .= ";dbname=".$self->param("${prefix}dbname");
}
my $dbh;
eval{
$dbh = DBI->connect($dsn, $self->param("${prefix}user"),
$self->param("${prefix}pass"), {'RaiseError' => 1, 'PrintError' => 0});
};
if (!$dbh || $@ || !$dbh->ping) {
$self->log_error("Could not connect to db server as user ".
$self->param("${prefix}user") .
" using [$dsn] as a locator:\n" . $DBI::errstr);
}
$self->{'_dbh'} = $dbh;
return $self->{'_dbh'};
}
=head2 get_glovar_database
Example : my $dba = $support->get_glovar_database;
......@@ -1294,7 +1348,7 @@ sub init_log {
sub finish_log {
my $self = shift;
$self->log("All done. ".$self->warnings." warnings. ");
$self->log("\nAll done. ".$self->warnings." warnings. ");
if ($self->{'_start_time'}) {
$self->log("Runtime ");
my $diff = time - $self->{'_start_time'};
......
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