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Commits (2)
......@@ -2279,29 +2279,43 @@ sub load_registry_from_db {
sort grep { /^ensembl_ancestral/ } @dbnames;
if (@ancestral_dbs && !$ignore_multi) {
my $ancestral_db = shift @ancestral_dbs;
my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => 'core',
-species => 'Ancestral sequences'.$species_suffix,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $ancestral_db,
-no_cache => $no_cache
);
foreach my $ancestral_db (@ancestral_dbs) {
# Looking for Compara's "ancestral" databases.
# ensembl_ancestral_plants_47_100 is registered with the 'plants'
# prefix, while ensembl_ancestral_100 is not given any prefix for
# backwards compatibility.
# Similarly, contrary to the nomenclature, "Ancestral sequences"
# is the species (production) name and "ancestral_sequences" is
# an alias.
my $alias;
my ($division) = $ancestral_db =~ /^ensembl_ancestral_(\w+)(?:_\d+){2}$/xm;
if ($division) {
$species = (ucfirst $division).' Ancestral sequences'.$species_suffix;
$alias = $division.'_ancestral_sequences'.$species_suffix;
} else {
$species = 'Ancestral sequences'.$species_suffix;
$alias = 'ancestral_sequences'.$species_suffix;
}
if ($verbose) {
printf( "%s loaded\n", $ancestral_db );
if (@ancestral_dbs) {
# If we still had some more then report the problem.
printf(
"Multiple ancestral databases found.\n"
. "Ignoring the following: %s\n",
join( ', ', @ancestral_dbs ) );
my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => 'core',
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $ancestral_db,
-no_cache => $no_cache
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => $species,
-alias => [$alias],
);
if ($verbose) {
printf( "%s loaded\n", $ancestral_db );
}
}
} elsif ($verbose) {
......@@ -2468,10 +2482,6 @@ sub load_registry_from_db {
-species => 'multi'.$species_suffix,
-alias => ['stable_ids'.$species_suffix] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'Ancestral sequences'.$species_suffix,
-alias => ['ancestral_sequences'.$species_suffix] );
# Register aliases as found in adaptor meta tables.
$self->find_and_add_aliases( '-handle' => $dbh,
......