Commit 62b58cec authored by Nathan Johnson's avatar Nathan Johnson
Browse files

added reset_DBAdaptor method

parent 50b40137
......@@ -620,6 +620,67 @@ sub remove_DBAdaptor{
=head2 reset_DBAdaptor
Arg [1]: string - species e.g. homo_sapiens
Arg [2]: string - DB group e.g. core
Arg [3]: string - new dbname
Args [4-7]: string - optional DB parameters, defaults to current db params if omitted
Usage : $reg->reset_registry_db('homo_sapiens', 'core', 'homo_sapiens_core_37_35j');
Description: Resets a DB within the registry.
Exceptions: Throws if mandatory params not supplied
Throws if species name is not already seen by the registry
Throws if no current DB for species/group available
Status : At risk
sub reset_DBAdaptor{
my ($self, $species, $group, $dbname, $host, $port, $user, $pass) = @_;
#Check mandatory params
if(! (defined $species && defined $group && defined $dbname)){
throw('Must provide at least a species, group and dbname parmeter to redefine a DB in the registry');
#validate species here
my $alias = $self->get_alias($species);
throw("Could not find registry alias for species:\t$species") if(! defined $alias);
#Get all current defaults if not defined
my $current_db = $self->get_DBAdaptor($alias, $group);
if(! defined $current_db){
throw("There is not current registry DB for:\t${alias}\t${group}");
$host ||= $current_db->dbc->host;
$port ||= $current_db->dbc->port;
$user ||= $current_db->dbc->username;
$pass ||= $current_db->dbc->password;
my $class = ref($current_db);
$self->remove_DBAdaptor($alias, $group);
#ConfigRegistry should automatically add this to the Registry
my $db = $class->new(
-user => $user,
-host => $host,
-port => $port,
-pass => $pass,
-dbname => $dbname,
-species => $alias,
-group => $group,
return $db;
# DNA Adaptors
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