Raw content of Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection
<![CDATA[package Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection;
=head1 NAME
Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection -
Database connection object for a SangerSNP database
=head1 SYNOPSIS
$dbc = Bio::EnsEMBL::DBSQL::DBConnection->new(
-user => 'anonymous',
-dbname => 'snp',
-host => 'ocs4',
-driver => 'Oracle',
-species => 'Homo Sapiens',
-group => 'sangersnp'
);
SQL statements should be created/executed through
this modules prepare() and do() methods.
$sth = $dbc->prepare( "SELECT something FROM yourtable" );
$sth->execute();
# do something with rows returned ...
$sth->finish();
=head1 DESCRIPTION
This class is a wrapper around DBIs datbase handle.
Generally this class will be used through one of the object adaptors or the
Bio::EnsEMBL::Registry and will not be instantiated directly.
=head1 LICENCE
This code is distributed under an Apache style licence:
Please see /code_licence.html for details
=head1 AUTHOR
Steve Searle <searle@sanger.ac.uk>
=head1 CONTACT
Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
=cut
use strict;
use DBI;
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::Utils::Exception qw(throw info warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::DBConnection);
=head2 new
Arg [DBNAME] : string
The name of the database to connect to.
Arg [HOST] : (optional) string
The domain name of the database host to connect to.
'localhost' by default.
Arg [USER] : string
The name of the database user to connect with
Arg [PASS] : (optional) string
The password to be used to connect to the database
Arg [PORT] : int
The port to use when connecting to the database
Arg [DRIVER] : (optional) string
The type of database driver to use to connect to the DB
mysql by default.
Arg [DBCONN] : (optional)
Open another handle to the same database as another connection
If this argument is specified, no other arguments should be
specified.
Example : $dbc = Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection->new
(-user => 'anonymous',
-dbname => 'snp',
-host => 'ocs4',
-driver => 'Oracle');
Description: Constructor for a DatabaseConenction. Any adaptors that require
database connectivity should inherit from this class.
Returntype : Bio::EnsEMBL::ExternalData::SangerSNP::DBConnection
Exceptions : thrown if USER or DBNAME are not specified, or if the database
cannot be connected to.
Caller : Bio::EnsEMBL::::Utils::ConfigRegistry (for newer code using the
registry), Bio::EnsEMBL::DBSQL::DBAdaptor (for old style code)
=cut
sub new {
my $class = shift;
my ($db, $host, $driver, $user, $password, $port, $dbconn) =
rearrange([qw(DBNAME HOST DRIVER USER PASS PORT DBCONN )], @_);
my $self = {};
bless $self, $class;
if($dbconn) {
if($db || $host || $driver || $password || $port) {
throw("Cannot specify other arguments when -DBCONN argument used.");
}
$self->dbname($dbconn->dbname);
$self->username($dbconn->username);
$self->host($dbconn->host);
$self->password($dbconn->password);
$self->port($dbconn->port);
$self->driver($dbconn->driver);
} else {
$db || throw("-DBNAME argument is required.");
$user || throw("-USER argument is required.");
$driver ||= 'Oracle';
$self->username($user);
$self->host($host);
$self->dbname($db);
$self->password($password);
$self->driver($driver);
}
return $self;
}
=head2 connect
Example : $dbc->connect
Description: Connects to the database using the connection attribute
information.
Returntype : none
Exceptions : thrown if it can't connect to database
Caller : $self->new, $self->db_handle
=cut
sub connect {
my $self = shift;
return if($self->connected);
$self->connected(1);
if(defined($self->db_handle) and $self->db_handle->ping) {
warning("unconnected db_handle is still pingable, reseting connected boolean\n");
}
my $dbh;
my $dsn;
if ($self->driver eq 'Oracle') {
$dsn = "DBI:" . $self->driver . ":";
eval {
$dbh = DBI->connect($dsn,
$self->username . "\@" . $self->dbname,
$self->password,
{ 'RaiseError' => 1, 'PrintError' => 0, 'AutoCommit' => 1 });
};
} else {
$dsn = "DBI:" . $self->driver() .
":database=". $self->dbname() .
";host=" . $self->host() .
";port=" . $self->port();
eval{ $dbh = DBI->connect($dsn, $self->username(), $self->password(), {'RaiseError' => 1}); };
}
if(!$dbh || $@ || !$dbh->ping) {
warn("Could not connect to database " . $self->dbname .
" as user " . $self->username .
" using [$dsn] as a locator:\n" . $DBI::errstr);
throw("Could not connect to database " . $self->dbname .
" as user " . $self->username .
" using [$dsn] as a locator:\n" . $DBI::errstr);
}
$self->db_handle($dbh);
}
1;
]]>