diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index ae6beea380adbd674a28164f3977a325cfb0b27d..76f4eabfa3bcf3649250a5dc722ca1a27e9aeecb 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -131,8 +131,8 @@ use vars qw(%registry_register);
my $API_VERSION = 54;
-# This is a map from group names to Ensembl DB adaptors.
-#Used by load_all and reset_DBAdaptor
+# This is a map from group names to Ensembl DB adaptors. Used by
+# load_all() and reset_DBAdaptor().
my %group2adaptor =
(
'blast' => 'Bio::EnsEMBL::External::BlastAdaptor',
@@ -1322,7 +1322,8 @@ sub load_registry_from_db {
@args
);
- my $go_version = 0;
+ my $go_version = 0;
+ my $ontology_version = 0;
$user ||= "ensro";
if ( !defined($port) ) {
@@ -1373,8 +1374,12 @@ sub load_registry_from_db {
if ( $1 eq $software_version ) {
$go_version = $1;
}
+ } elsif ( $db =~ /^(ensembl_ontology)_(\d+)/ ) {
+ if ( $2 eq $software_version ) {
+ $ontology_version = $2;
+ }
} elsif (
- $db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\d+[a-z]*)/)
+ $db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\d+[a-z]*)/ )
{
if ( $2 eq $software_version ) {
$temp{$1} = $2 . "_" . $3;
@@ -1746,6 +1751,31 @@ sub load_registry_from_db {
print("No GO database found\n");
}
+ # Ontology
+
+ if ( $ontology_version != 0 ) {
+ require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
+
+ my $ontology_db =
+ sprintf( "ensembl_ontology_%d", $ontology_version );
+
+ my $dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
+ '-species' => 'multi',
+ '-group' => 'ontology',
+ '-host' => $host,
+ '-port' => $port,
+ '-user' => $user,
+ '-pass' => $pass,
+ '-dbname' => $ontology_db,
+ );
+
+ if ($verbose) {
+ printf( "%s loaded\n", $ontology_db );
+ }
+ } elsif ($verbose) {
+ print("No ontology database found\n");
+ }
+
# Hard coded aliases for the different species
my @aliases = ( 'chimp', 'PanTro1', 'Pan', 'P_troglodytes' );
@@ -2036,6 +2066,10 @@ sub load_registry_from_db {
-alias => \@aliases
);
+ Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+ -species => 'multi',
+ -alias => ['ontology'] );
+
# Register aliases as found in adaptor meta tables.
$self->find_and_add_aliases( '-handle' => $dbh );
$dbh->disconnect();
@@ -2044,12 +2078,17 @@ sub load_registry_from_db {
=head2 find_and_add_aliases
+ Arg [DBH] : (optional) DBI handle
+ A connected DBI database handle. Used instead
+ of the database handles stored in the DBAdaptor
+ objects. Bypasses the use of MetaContainer.
+
Arg [ADAPTOR] : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor
The adaptor to use to retrieve aliases from.
Arg [GROUP] : (optional) string
- The group you want to find aliases for. If not given
- assumes all types.
+ The group you want to find aliases for. If not
+ given assumes all types.
Arg [HANDLE] : (optional) DBI database handle
A connected database handle to use instead of the
@@ -2127,7 +2166,6 @@ sub find_and_add_aliases {
if ( defined( $dba->dbc() ) ) {
$dba->dbc()->disconnect_if_idle();
}
-
}
foreach my $alias (@aliases) {
@@ -2297,50 +2335,73 @@ sub no_version_check {
=cut
-sub version_check{
- my ($self, $dba) = @_;
-
+sub version_check {
+ my ( $self, $dba ) = @_;
+
# Check the datbase and versions match
# give warning if they do not.
my $check = no_version_check();
- if( (defined($ENV{HOME}) and (-e $ENV{HOME}."/.ensemblapi_no_version_check"))
- or (defined($check) and ($check != 0))){
+
+ if ( (
+ defined( $ENV{HOME} )
+ and ( -e $ENV{HOME} . "/.ensemblapi_no_version_check" ) )
+ or ( defined($check) and ( $check != 0 ) ) )
+ {
return 1;
}
- my $mca = $self->get_adaptor($dba->species(),$dba->group(),"MetaContainer");
+
+ my $mca =
+ $self->get_adaptor( $dba->species(), $dba->group(),
+ "MetaContainer" );
+
my $database_version = 0;
- if(defined($mca)){
+ if ( defined($mca) ) {
$database_version = $mca->get_schema_version();
}
- if($database_version == 0){
+
+ if ( $database_version == 0 ) {
# Try to work out the version
- if($dba->dbc->dbname() =~ /^_test_db_/){
+ if ( $dba->dbc()->dbname() =~ /^_test_db_/ ) {
return 1;
}
- if($dba->dbc->dbname() =~ /(\d+)_\S+$/){
+ if ( $dba->dbc()->dbname() =~ /(\d+)_\S+$/ ) {
$database_version = $1;
- }
- elsif($dba->dbc->dbname() =~ /ensembl_compara_(\d+)/){
+ } elsif ( $dba->dbc()->dbname() =~ /ensembl_compara_(\d+)/ ) {
$database_version = $1;
- }
- elsif($dba->dbc->dbname() =~ /ensembl_go_(\d+)/){
+ } elsif ( $dba->dbc()->dbname() =~ /ensembl_go_(\d+)/ ) {
$database_version = $1;
- }
- elsif($dba->dbc->dbname() =~ /ensembl_help_(\d+)/){
+ } elsif ( $dba->dbc()->dbname() =~ /ensembl_help_(\d+)/ ) {
$database_version = $1;
+ } elsif ( $dba->dbc()->dbname() =~ /ensembl_ontology_(\d+)/ ) {
+ $database_version = $1;
+ } else {
+ warn(
+ sprintf(
+ "No database version for database %s "
+ . ". You must be using a pre version 34 database "
+ . "with version 34 or later code.\n"
+ . "You need to update your database "
+ . "or use the appropriate Ensembl software release "
+ . "to ensure your script does not crash\n",
+ $dba->dbc()->dbname() ) );
}
- else{
- warn("No database version for database ".$dba->dbc->dbname().". You must be using a pre version 34 database with version 34 or later code. You need to update your database or use the appropriate ensembl software release to ensure your script does not crash\n");
- }
- }
- if($database_version != $API_VERSION){
- warn("For ".$dba->dbc->dbname()." there is a difference in the software release (".$API_VERSION.") and the database release (".$database_version."). You should change one of these to ensure your script does not crash.\n");
+ } ## end if ( $database_version...
+
+ if ( $database_version != $API_VERSION ) {
+ warn(
+ sprintf(
+ "For %s there is a difference in the software release (%s) "
+ . "and the database release (%s). "
+ . "You should update one of these to ensure that your script "
+ . "does not crash.\n",
+ $dba->dbc()->dbname(),
+ $API_VERSION, $database_version
+ ) );
return 0;
}
- else {
- return 1;
- }
-}
+
+ return 1; # Ok
+} ## end sub version_check
=head2 get_species_and_object_type
diff --git a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
index 66bd1d37522c9d4d2d873a29eb5cb0fb85cbd095..f3ca596e06592fb6c70fa3ff2e00ef4511009ef3 100644
--- a/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
+++ b/modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm
@@ -125,6 +125,12 @@ sub gen_load{
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen;
}
+ elsif ( $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) {
+ if ( !defined( $dba->group() ) ) {
+ $dba->group('ontology');
+ }
+ $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_ontology;
+ }
elsif($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
#vega uses the core DBAdaptor so test if vega is in the dbname
if(!defined($dba->group())){
@@ -192,37 +198,37 @@ sub gen_load{
-sub find_unique_species{
- my ($species, $group) = @_;
+sub find_unique_species {
+ my ( $species, $group ) = @_;
- $reg->add_alias($species,$species);
+ $reg->add_alias( $species, $species );
- my $i = 0;
- my $free =0;
- while(!$free){
- if($i == 0){
- if(!defined($reg->get_DBAdaptor($species, $group))){
- $free =1;
- $i ="";
+ my $i = 0;
+ my $free = 0;
+
+ while ( !$free ) {
+ if ( $i == 0 ) {
+ if ( !defined( $reg->get_DBAdaptor( $species, $group ) ) ) {
+ $free = 1;
+ $i = "";
+ } else {
+ $i = 1;
}
- else{
- $i = 1;
- }
- }
- else{
- $reg->add_alias($species.$i,$species.$i); #set needed self alias
- if(!defined($reg->get_DBAdaptor($species.$i, $group))){
- $free =1;
- }
- else{
- $i++;
+ } else {
+ # set needed self alias
+ $reg->add_alias( $species . $i, $species . $i );
+
+ if ( !defined( $reg->get_DBAdaptor( $species . $i, $group ) ) ) {
+ $free = 1;
+ } else {
+ $i++;
}
}
}
-
+
$species .= $i;
return ($species);
-}
+} ## end sub find_unique_species
@@ -231,9 +237,9 @@ sub load_adaptors {
my %pairs = %{ $dba->get_available_adaptors() };
- foreach my $key ( keys %pairs ) {
- Bio::EnsEMBL::Registry->add_adaptor( $dba->species, $dba->group,
- $key, $pairs{$key} );
+ while ( my ( $key, $value ) = each(%pairs) ) {
+ Bio::EnsEMBL::Registry->add_adaptor( $dba->species(), $dba->group(),
+ $key, $value );
}
}
@@ -241,9 +247,8 @@ sub load_and_attach_dnadb_to_core {
my ($dba) = @_;
load_adaptors($dba);
-
- $reg->add_DNAAdaptor( $dba->species, $dba->group,
- $dba->species, "core" );
+ $reg->add_DNAAdaptor( $dba->species(), $dba->group(), $dba->species(),
+ 'core' );
}
@@ -256,6 +261,7 @@ sub load_SNP { load_adaptors(@_) }
sub load_variation { load_and_attach_dnadb_to_core(@_) }
sub load_funcgen { load_and_attach_dnadb_to_core(@_) }
sub load_haplotype { load_adaptors(@_) }
+sub load_ontology { load_adaptors(@_) }
# these that need to attach to the core to get the sequense data
@@ -265,20 +271,21 @@ sub load_otherfeatures { load_and_attach_dnadb_to_core(@_) }
sub load_vega { load_and_attach_dnadb_to_core(@_) }
-sub add_alias{
- my ($class, @args) = @_;
- my ($species, $aliases) = rearrange([qw(SPECIES ALIAS)],@args);
+sub add_alias {
+ my ( $class, @args ) = @_;
- #make sure it exists itself
- Bio::EnsEMBL::Registry->add_alias($species,$species);
+ my ( $species, $aliases ) = rearrange( [qw(SPECIES ALIAS)], @args );
- if($aliases){
- foreach my $ali (@$aliases){
- Bio::EnsEMBL::Registry->add_alias($species,$ali);
+ # Make sure it exists itself
+ Bio::EnsEMBL::Registry->add_alias( $species, $species );
+
+ if ( defined($aliases) ) {
+ foreach my $ali (@$aliases) {
+ Bio::EnsEMBL::Registry->add_alias( $species, $ali );
}
}
-
}
+
#
# overwrite/load new types. Done this way to enable no changes to CVS for
# external users. External users should add there own "GROUPS" in the file