Raw content of Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild
<![CDATA[#This is to be a baseclass for the genebuild code to have various
#object like methods which genebuild modules want. GeneBuild code
#should ideally inherit from this
package Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild;
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw warning verbose);
use Bio::EnsEMBL::Analysis::Tools::Logger qw(logger_info);
use Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Analysis::Config::Databases qw(DATABASES DNA_DBNAME);
use Bio::EnsEMBL::Analysis::RunnableDB;
use vars qw(@ISA);
@ISA = qw (Bio::EnsEMBL::Analysis::RunnableDB);
#first of all we just need methods to get databases from the
#database config
sub database_hash{
my ($self, $name, $db) = @_;
if(!$self->{'db_hash'}){
$self->{'db_hash'} = {};
}
if($name && $db){
$self->{'db_hash'}->{$name} = $db;
}
return $self->{'db_hash'};
}
=head2 get_dbadaptor
Arg [1] : String - key of database hash
Arg [2] : return a pipeline db adaptor flag
Function : Returns a Bio::EnsEMBL::DBSQL::DBAdaptor for a given hash key.
or a Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor if requested
Requires proper configuration of
Bio::EnsEMBL::Analysis::Config::Databases
Returntype: Bio::EnsEMBL:DBSQL::DBAdaptor or Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor
Exceptions: throw if key can't be found in Databases.pm
=cut
sub get_dbadaptor{
my ($self, $name, $use_pipeline_adaptor) = @_;
my $hash = $self->database_hash;
my $db;
if(!$hash->{$name}){
if (exists $DATABASES->{$name}) {
my $constructor_args = $DATABASES->{$name};
foreach my $arg ( qw ( -user -port -host -dbname) ) {
unless ( $$constructor_args{$arg}){
throw ("Database-connection-details not properly configured : Arguemnt : $arg missing in Databases.pm\n") ;
}
}
if ( $use_pipeline_adaptor ) {
$db = Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor->new(
%$constructor_args,
);
} else {
$db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
%$constructor_args,
);
}
if($name ne $DNA_DBNAME ){
if (length($DNA_DBNAME) ne 0 ){
my $dnadb = $self->get_dbadaptor($DNA_DBNAME);
$db->dnadb($dnadb);
}else{
warning("You haven't defined a DNA_DBNAME in Config/Databases.pm");
}
}
$self->database_hash($name, $db);
} else {
throw("No entry in Config/Databases.pm hash for $name");
}
}else{
$db = $hash->{$name};
}
throw("Unable to find a db with name ".$name) if not $db;
return $db;
}
1;
]]>