diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 43dab02cf4cf0f51a05b8641e3cfa167d5de8f6b..051dc799dbe3b5cec3936a8b830c549e4bf3e575 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -144,33 +144,39 @@ my %group2adaptor =
=head2 load_all
- Will load the registry with the configuration file which is obtained
- from the first in the following and in that order.
+ Will load the registry with the configuration file which is
+ obtained from the first in the following and in that order.
- 1) If an argument is passed to this method, this is used as the name
- of the configuration file to read.
+ 1) If an argument is passed to this method, this is used as the
+ name of the configuration file to read.
- 2) If the enviroment variable ENSEMBL_REGISTRY is set, this is used as
- the name of the configuration file to read.
+ 2) If the enviroment variable ENSEMBL_REGISTRY is set, this is
+ used as the name of the configuration file to read.
- 3) If the file .ensembl_init exist in the home directory, it is used
- as the configuration file.
+ 3) If the file .ensembl_init exist in the home directory, it is
+ used as the configuration file.
Arg [1] : (optional) string
Name of file to load the registry from.
+
Arg [2] : (optional) integer
If not 0, will print out all information.
+
Arg [3] : (optional) integer
- If not 0, the db connection will not be cleared, if 0 or
- if not set the db connections will be cleared (this is
- the default).
- Arg [4]: (optional) int 1
- This option will turn off caching for slice features, so,
- every time a set of features is retrieved, they will come from
- the database instead of the cache. This option is only recommended
- for advanced users, specially if you need to store and retrieve
- features. It might reduce performance when querying the database if
- not used properly. If in doubt, do not use it or ask in ensembl-dev
+ If not 0, the database connection will not be
+ cleared, if 0 or if not set the database connections
+ will be cleared (this is the default).
+
+ Arg [4]: (optional) boolean
+ This option will turn off caching for slice features,
+ so, every time a set of features is retrieved,
+ they will come from the database instead of the
+ cache. This option is only recommended for advanced
+ users, specially if you need to store and retrieve
+ features. It might reduce performance when querying
+ the database if not used properly. If in doubt, do
+ not use it or ask in ensembl-dev.
+
Example : Bio::EnsEMBL::Registry->load_all();
Returntype : none
Exceptions : none
@@ -309,12 +315,14 @@ sub load_all {
# We trust the user to provide sensible key-value pairs.
my %adaptor_args = %default_adaptor_args;
foreach my $parameter ( $cfg->Parameters($section) ) {
- $adaptor_args{ '-' . $parameter } =
- $cfg->val( $section, $parameter );
- #when set, do not use the feature cache in the different adaptors
- if ($no_cache){
- $adaptor_args{'-no_cache'} = 1;
- }
+ $adaptor_args{ '-' . $parameter } =
+ $cfg->val( $section, $parameter );
+
+ # when set, do not use the feature cache in the
+ # different adaptors
+ if ($no_cache) {
+ $adaptor_args{'-no_cache'} = 1;
+ }
}
if ($verbose) {
@@ -378,18 +386,19 @@ sub clear{
Returntype : none
Exceptions : none
Status : At Risk.
- : This is here for backwards compatibility only and may be removed
- : eventually. Solution is to make sure the db and the adaptor have
- : the same species and the call is then no longer needed.
-
-=cut
+ : This is here for backwards compatibility only and may
+ : be removed eventually. Solution is to make sure the
+ : db and the adaptor have the same species and the call
+ : is then no longer needed.
-sub add_db{
- my ($class, $db, $name, $adap) = @_;
+=cut
+sub add_db {
+ my ( $class, $db, $name, $adap ) = @_;
- if(lc($db->species()) ne lc($adap->species)){
- $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = $adap;
+ if ( lc( $db->species() ) ne lc( $adap->species ) ) {
+ $registry_register{ lc( $db->species() ) }{ lc( $db->group() ) }
+ {'_special'}{ lc($name) } = $adap;
}
}
@@ -401,17 +410,22 @@ sub add_db{
Returntype : adaptor
Exceptions : none
Status : At Risk.
- : This is here for backwards compatibility only and may be removed
- : eventually. Solution is to make sure the db and the adaptor have
- : the same species and the call is then no longer needed.
+ : This is here for backwards compatibility only and may
+ : be removed eventually. Solution is to make sure the
+ : db and the adaptor have the same species and the call
+ : is then no longer needed.
=cut
-sub remove_db{
- my ($class, $db, $name) = @_;
+sub remove_db {
+ my ( $class, $db, $name ) = @_;
+
+ my $ret =
+ $registry_register{ lc( $db->species() ) }{ lc( $db->group() ) }
+ {'_special'}{ lc($name) };
- my $ret = $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
- $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = undef;
+ $registry_register{ lc( $db->species() ) }{ lc( $db->group() ) }
+ {'_special'}{ lc($name) } = undef;
return $ret;
}
@@ -424,21 +438,23 @@ sub remove_db{
Returntype : adaptor
Exceptions : none
Status : At Risk.
- : This is here for backwards compatibility only and may be removed
- : eventually. Solution is to make sure the db and the adaptor have
- : the same species then call get_DBAdaptor instead.
+ : This is here for backwards compatibility only and may
+ : be removed eventually. Solution is to make sure the
+ : db and the adaptor have the same species then call
+ : get_DBAdaptor instead.
=cut
-sub get_db{
- my ($class, $db, $name) = @_;
+sub get_db {
+ my ( $class, $db, $name ) = @_;
- my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor(lc($db->species),lc($name));
+ my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor( lc( $db->species ),
+ lc($name) );
- if(defined($ret)){
- return $ret;
- }
- return $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
+ if ( defined($ret) ) { return $ret }
+
+ return $registry_register{ lc( $db->species() ) }
+ { lc( $db->group() ) }{'_special'}{ lc($name) };
}
=head2 get_all_db_adaptors
@@ -448,9 +464,10 @@ sub get_db{
Returntype : adaptor
Exceptions : none
Status : At Risk.
- : This is here for backwards compatibility only and may be removed
- : eventually. Solution is to make sure the dbs all have
- : the same species then call get_all_DBAdaptors(-species => "human");
+ : This is here for backwards compatibility only and
+ : may be removed eventually. Solution is to make
+ : sure the dbs all have the same species then call
+ : get_all_DBAdaptors(-species => "human");
=cut
@@ -469,9 +486,9 @@ sub get_all_db_adaptors {
}
foreach my $key (
- keys %{
- $registry_register{ $class->get_alias( $db->species() ) }
- { lc( $db->group() ) }{'_special'} } )
+ keys %{
+ $registry_register{ $class->get_alias( $db->species() ) }
+ { lc( $db->group() ) }{'_special'} } )
{
$ret{$key} =
$registry_register{ $class->get_alias( $db->species() ) }
@@ -499,25 +516,23 @@ sub get_all_db_adaptors {
=cut
-sub add_DBAdaptor{
- my ($class, $species, $group, $adap) = @_;
+sub add_DBAdaptor {
+ my ( $class, $species, $group, $adap ) = @_;
- if(!($class->alias_exists($species))){
- $class->add_alias($species,$species);
+ if ( !( $class->alias_exists($species) ) ) {
+ $class->add_alias( $species, $species );
}
-
$species = $class->get_alias($species);
- $registry_register{$species}{lc($group)}{'_DB'} = $adap;
+ $registry_register{$species}{ lc($group) }{'_DB'} = $adap;
- if(!defined($registry_register{'_DBA'})){
- my @list =();
- push(@list,$adap);
- $registry_register{'_DBA'}= \@list;
- }
- else{
- push(@{$registry_register{'_DBA'}},$adap);
+ if ( !defined( $registry_register{'_DBA'} ) ) {
+ my @list = ();
+ push( @list, $adap );
+ $registry_register{'_DBA'} = \@list;
+ } else {
+ push( @{ $registry_register{'_DBA'} }, $adap );
}
}
@@ -535,13 +550,12 @@ sub add_DBAdaptor{
=cut
-sub get_DBAdaptor{
- my ($class, $species, $group) = @_;
+sub get_DBAdaptor {
+ my ( $class, $species, $group ) = @_;
$species = $class->get_alias($species);
- return $registry_register{$species}{lc($group)}{'_DB'};
-
+ return $registry_register{$species}{ lc($group) }{'_DB'};
}
=head2 get_all_DBAdaptors
@@ -550,8 +564,15 @@ sub get_DBAdaptor{
species name to get adaptors for
Arg [GROUP] : (optional) string
group name to get adaptors for
- Example : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors()};
- : @human_dbas = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors(-species => 'human')};
+ Example :
+ @dba =
+ @{ Bio::EnsEMBL::Registry->get_all_DBAdaptors() };
+
+ @human_dbas =
+ @{ Bio::EnsEMBL::Registry->get_all_DBAdaptors(
+ -species => 'human'
+ ) };
+
Returntype : list of DBAdaptors
Exceptions : none
Status : Stable
@@ -561,18 +582,16 @@ sub get_DBAdaptor{
sub get_all_DBAdaptors {
my ( $class, @args ) = @_;
- my @ret;
my ( $species, $group ) = rearrange( [qw(SPECIES GROUP)], @args );
- if ( defined($species) ) {
- $species = $class->get_alias($species);
- }
+ if ( defined($species) ) { $species = $class->get_alias($species) }
+ my @ret;
foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
- if ( !defined($species) || lc($species) eq lc( $dba->species ) ) {
- if ( !defined($group) || lc($group) eq lc( $dba->group ) ) {
- push( @ret, $dba );
- }
+ if ( ( !defined($species) || lc($species) eq lc( $dba->species() ) )
+ && ( !defined($group) || lc($group) eq lc( $dba->group() ) ) )
+ {
+ push( @ret, $dba );
}
}
@@ -687,7 +706,8 @@ sub remove_DBAdaptor{
Arg [3]: string - new dbname
Args [4-7]: string - optional DB parameters, defaults to current db params if omitted
Arg [8]: hashref - Hash ref of additional parameters e.g. eFG dnadb params for auto selecting dnadb
- Usage : $reg->reset_registry_db('homo_sapiens', 'core', 'homo_sapiens_core_37_35j');
+ Usage : $reg->reset_registry_db( 'homo_sapiens', 'core',
+ 'homo_sapiens_core_37_35j' );
Description: Resets a DB within the registry.
Exceptions: Throws if mandatory params not supplied
Throws if species name is not already seen by the registry
@@ -696,67 +716,66 @@ sub remove_DBAdaptor{
=cut
-sub reset_DBAdaptor{
- my ($self, $species, $group, $dbname, $host, $port, $user, $pass, $params) = @_;
+sub reset_DBAdaptor {
+ my (
+ $self, $species, $group, $dbname, $host,
+ $port, $user, $pass, $params
+ ) = @_;
# 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');
+ if ( !( defined $species && defined $group && defined $dbname ) ) {
+ throw(
+ 'Must provide at least a species, group, and dbname parameter '
+ . '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 $alias);
-
+ throw("Could not find registry alias for species:\t$species")
+ if ( !defined $alias );
+
# Get all current defaults if not defined
- my $db = $self->get_DBAdaptor($alias, $group);
+ my $db = $self->get_DBAdaptor( $alias, $group );
my $class;
- if($db){
- $class = ref($db);
- $host ||= $db->dbc->host;
- $port ||= $db->dbc->port;
- $user ||= $db->dbc->username;
- $pass ||= $db->dbc->password;
- }
- else{
- #Now we need to test mandatory params
- $class = $group2adaptor{ lc($group) };
+ if ($db) {
+ $class = ref($db);
+ $host ||= $db->dbc->host;
+ $port ||= $db->dbc->port;
+ $user ||= $db->dbc->username;
+ $pass ||= $db->dbc->password;
+ } else {
+ #Now we need to test mandatory params
+ $class = $group2adaptor{ lc($group) };
- if(! ($host && $user)){
- throw("No comparable $alias $group DB present in Registry. You must pass at least a dbhost and dbuser");
- }
+ if ( !( $host && $user ) ) {
+ throw("No comparable $alias $group DB present in Registry. "
+ . "You must pass at least a dbhost and dbuser" );
+ }
}
-
- $self->remove_DBAdaptor($alias, $group);
+ $self->remove_DBAdaptor( $alias, $group );
-
-
#my @adaptors = @{$self->get_all_adaptors};
#This is causing a loop as it was constantly trying to reset the db
#and never getting there.
#I think this was left over from testing
-
# ConfigRegistry should automatically add this to the Registry
-
$db = $class->new(
- -user => $user,
- -host => $host,
- -port => $port,
- -pass => $pass,
- -dbname => $dbname,
- -species => $alias,
- -group => $group,
- %{$params}
- );
-
+ -user => $user,
+ -host => $host,
+ -port => $port,
+ -pass => $pass,
+ -dbname => $dbname,
+ -species => $alias,
+ -group => $group,
+ %{$params} );
return $db;
-}
+} ## end sub reset_DBAdaptor
#
@@ -776,17 +795,17 @@ sub reset_DBAdaptor{
=cut
-sub add_DNAAdaptor{
- my ($class, $species, $group, $dnadb_species, $dnadb_group) = @_;
+sub add_DNAAdaptor {
+ my ( $class, $species, $group, $dnadb_species, $dnadb_group ) = @_;
- $species = $class->get_alias($species);
+ $species = $class->get_alias($species);
$dnadb_species = $class->get_alias($dnadb_species);
- if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
+ if ( $dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
deprecated("");
- }
- else{
- $registry_register{$species}{lc($group)}{'_DNA'} = $dnadb_group;
- $registry_register{$species}{lc($group)}{'_DNA2'} = $dnadb_species;
+ } else {
+ $registry_register{$species}{ lc($group) }{'_DNA'} = $dnadb_group;
+ $registry_register{$species}{ lc($group) }{'_DNA2'} =
+ $dnadb_species;
}
}
@@ -801,17 +820,18 @@ sub add_DNAAdaptor{
=cut
-sub get_DNAAdaptor{
- my ($class, $species, $group) = @_;
+sub get_DNAAdaptor {
+ my ( $class, $species, $group ) = @_;
$species = $class->get_alias($species);
- my $new_group = $registry_register{$species}{lc($group)}{'_DNA'};
- my $new_species = $registry_register{$species}{lc($group)}{'_DNA2'};
- if( defined $new_group ) {
- return $class->get_DBAdaptor($new_species,$new_group);
- } else {
- return undef;
+ my $new_group = $registry_register{$species}{ lc($group) }{'_DNA'};
+ my $new_species = $registry_register{$species}{ lc($group) }{'_DNA2'};
+
+ if ( defined $new_group ) {
+ return $class->get_DBAdaptor( $new_species, $new_group );
}
+
+ return undef;
}
#
@@ -831,7 +851,6 @@ sub get_DNAAdaptor{
Caller : internal
Status : Stable
-
=cut
sub add_adaptor {
@@ -1294,8 +1313,6 @@ sub load_registry_from_db {
);
my $go_version = 0;
- my $compara_version = 0;
- my $ancestral_version = 0;
$user ||= "ensro";
if ( !defined($port) ) {
@@ -1312,7 +1329,7 @@ sub load_registry_from_db {
my $dbh =
DBI->connect( "DBI:mysql:host=$host;port=$port", $user, $pass );
- my $res = $dbh->selectall_arrayref("show databases");
+ my $res = $dbh->selectall_arrayref('SHOW DATABASES');
my @dbnames = map { $_->[0] } @$res;
my %temp;
@@ -1332,26 +1349,28 @@ sub load_registry_from_db {
if ( $3 eq $software_version ) {
$temp{$1} = $2;
}
- } elsif (
- $db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\d+[a-z]*)/ )
- {
- if ( $2 eq $software_version ) {
- $temp{$1} = $2 . "_" . $3;
- }
} elsif ( $db =~ /^(.+)_(userdata)$/ ) {
$temp{$1} = $2;
- } elsif ( $db =~ /^ensembl_compara_(\d+)/ ) {
- if ( $1 eq $software_version ) {
- $compara_version = $1;
+ } elsif ( $db =~ /^(ensembl_compara(?:_\w+)*?)_(\d+)$/ ) {
+ if ( $2 eq $software_version ) {
+ $temp{$1} = $2;
}
- } elsif ( $db =~ /^ensembl_ancestral_(\d+)/ ) {
- if ( $1 eq $software_version ) {
- $ancestral_version = $1;
+ } elsif ( $db =~ /^(ensembl_ancestral(?:_\w+?)*?)_(\d+)$/ ) {
+ if ( $2 eq $software_version ) {
+ $temp{$1} = $2;
}
} elsif ( $db =~ /^ensembl_go_(\d+)/ ) {
if ( $1 eq $software_version ) {
$go_version = $1;
}
+ } elsif (
+ $db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\d+[a-z]*)/)
+ {
+ if ( $2 eq $software_version ) {
+ $temp{$1} = $2 . "_" . $3;
+ }
+ } else {
+ # warn( sprintf( "Skipping database '%s'\n", $db ) );
}
} ## end for my $db (@dbnames)
@@ -1601,60 +1620,87 @@ sub load_registry_from_db {
# Compara
- if ($compara_version) {
+ my @compara_dbs = grep { /^ensembl_compara/ } @dbnames;
+
+ if (@compara_dbs) {
eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
if ($@) {
# Ignore Compara as code required not there for this
if ($verbose) {
- printf( "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor "
- . "not found so compara database "
- . "ensembl_compara_%d will be ignored\n",
- $compara_version );
+ printf(
+ "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor "
+ . "not found so the following compara "
+ . "databases will be ignored: %s\n",
+ join( ', ', @compara_dbs ) );
}
} else {
- my $compara_db = "ensembl_compara_" . $compara_version;
-
- my $dba =
- Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(
- -group => "compara",
- -species => "multi",
- -host => $host,
- -user => $user,
- -pass => $pass,
- -port => $port,
- -wait_timeout => $wait_timeout,
- -dbname => $compara_db,
- -no_cache => $no_cache );
+ foreach my $compara_db (@compara_dbs) {
+ # Looking for EnsEMBL Genomes Comparas.
+ # ensembl_compara_bacteria_2_53 is registered as
+ # 'bacteria', ensembl_compara_pan_homology_2_53 is
+ # registered as 'pan_homology', ensembl_compara_53 is
+ # registered as 'multi', and the alias 'compara' still
+ # operates.
+
+ my ($species) =
+ $compara_db =~ /^ensembl_compara_(\w+)(?:_\d+){2}$/xm;
+
+ $species ||= 'multi';
+
+ my $dba = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(
+ -group => 'compara',
+ -species => $species,
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -wait_timeout => $wait_timeout,
+ -dbname => $compara_db,
+ -no_cache => $no_cache
+ );
- if ($verbose) {
- printf( "%s loaded\n", $compara_db );
- }
- }
+ if ($verbose) {
+ printf( "%s loaded\n", $compara_db );
+ }
+ } ## end foreach my $compara_db (@compara_dbs)
+ } ## end else [ if ($@)
} elsif ($verbose) {
- print("No Compara database found\n");
+ print("No Compara databases found\n");
}
# Ancestral sequences
- if ($ancestral_version) {
- my $ancestral_db = "ensembl_ancestral_" . $ancestral_version;
- my $dba =
- Bio::EnsEMBL::DBSQL::DBAdaptor->new(
- -group => "core",
- -species => "Ancestral sequences",
- -host => $host,
- -user => $user,
- -pass => $pass,
- -port => $port,
- -wait_timeout => $wait_timeout,
- -dbname => $ancestral_db,
- -no_cache => $no_cache );
+ my @ancestral_dbs =
+ sort grep { /^ensembl_ancestral/ } @dbnames;
+
+ if (@ancestral_dbs) {
+ my $ancestral_db = shift @ancestral_dbs;
+
+ my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+ -group => 'core',
+ -species => 'Ancestral sequences',
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -wait_timeout => $wait_timeout,
+ -dbname => $ancestral_db,
+ -no_cache => $no_cache
+ );
if ($verbose) {
printf( "%s loaded\n", $ancestral_db );
+
+ if (@ancestral_dbs) {
+ # If we still had some more then report the problem.
+ printf(
+ "Multiple ancestral databases found.\n"
+ . "Ignoring the following: %s\n",
+ join( ', ', @ancestral_dbs ) );
+ }
}
} elsif ($verbose) {
- print("No Ancestral database found");
+ print("No ancestral database found\n");
}
# GO
@@ -1694,104 +1740,129 @@ sub load_registry_from_db {
my @aliases = ( 'chimp', 'PanTro1', 'Pan', 'P_troglodytes' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Pan_troglodytes",
- -alias => \@aliases );
+ -species => "Pan_troglodytes",
+ -alias => \@aliases
+ );
@aliases = ( 'elegans', 'worm' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Caenorhabditis_elegans",
- -alias => \@aliases );
+ -species => "Caenorhabditis_elegans",
+ -alias => \@aliases
+ );
@aliases = ('tetraodon');
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Tetraodon_nigroviridis",
- -alias => \@aliases );
+ -species => "Tetraodon_nigroviridis",
+ -alias => \@aliases
+ );
- @aliases = ( 'H_Sapiens', 'homo sapiens',
- 'Homo_Sapiens', 'Homo',
- 'human', 'Hg17',
- 'ensHS', '9606' );
+ @aliases = (
+ 'H_Sapiens', 'homo sapiens', 'Homo_Sapiens', 'Homo',
+ 'human', 'Hg17', 'ensHS', '9606'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Homo_sapiens",
- -alias => \@aliases );
+ -species => "Homo_sapiens",
+ -alias => \@aliases
+ );
- @aliases = ( 'M_Musculus', 'mus musculus',
- 'Mus_Musculus', 'Mus',
- 'mouse', 'Mm5',
- 'ensMM', '10090' );
+ @aliases = (
+ 'M_Musculus', 'mus musculus', 'Mus_Musculus', 'Mus',
+ 'mouse', 'Mm5', 'ensMM', '10090'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Mus_musculus",
- -alias => \@aliases );
+ -species => "Mus_musculus",
+ -alias => \@aliases
+ );
- @aliases = ( 'R_Norvegicus', 'rattus norvegicus',
- 'Rattus_Norvegicus', 'Rattus',
- 'rat', 'Rn3',
- '10116' );
+ @aliases = (
+ 'R_Norvegicus', 'rattus norvegicus',
+ 'Rattus_Norvegicus', 'Rattus',
+ 'rat', 'Rn3',
+ '10116'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Rattus_norvegicus",
- -alias => \@aliases );
+ -species => "Rattus_norvegicus",
+ -alias => \@aliases
+ );
@aliases = ( 'T_Rubripes', 'Fugu', 'takifugu' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Takifugu_rubripes",
- -alias => \@aliases );
+ -species => "Takifugu_rubripes",
+ -alias => \@aliases
+ );
@aliases = ( 'G_Gallus', 'gallus gallus', 'Chicken', 'GalGal2' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Gallus_Gallus",
- -alias => \@aliases );
+ -species => "Gallus_Gallus",
+ -alias => \@aliases
+ );
- @aliases = ( 'D_Rerio', 'danio rerio',
- 'Danio_Rerio', 'Danio',
- 'zebrafish', 'zfish' );
+ @aliases = (
+ 'D_Rerio', 'danio rerio', 'Danio_Rerio', 'Danio',
+ 'zebrafish', 'zfish'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Danio_rerio",
- -alias => \@aliases );
+ -species => "Danio_rerio",
+ -alias => \@aliases
+ );
- @aliases = ( 'X_Tropicalis', 'xenopus tropicalis',
- 'Xenopus_tropicalis', 'Xenopus' );
+ @aliases = (
+ 'X_Tropicalis', 'xenopus tropicalis',
+ 'Xenopus_tropicalis', 'Xenopus'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Xenopus_tropicalis",
- -alias => \@aliases );
+ -species => "Xenopus_tropicalis",
+ -alias => \@aliases
+ );
- @aliases = ( 'A_Gambiae', 'Anopheles Gambiae',
- 'Anopheles_gambiae', 'Anopheles',
- 'mosquito' );
+ @aliases = (
+ 'A_Gambiae', 'Anopheles Gambiae',
+ 'Anopheles_gambiae', 'Anopheles',
+ 'mosquito'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Anopheles_gambiae",
- -alias => \@aliases );
+ -species => "Anopheles_gambiae",
+ -alias => \@aliases
+ );
- @aliases = ( 'D_Melanogaster', 'drosophila melanogaster',
- 'Drosophila_melanogaster', 'drosophila',
- 'fly' );
+ @aliases = (
+ 'D_Melanogaster', 'drosophila melanogaster',
+ 'Drosophila_melanogaster', 'drosophila',
+ 'fly'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Drosophila_melanogaster",
- -alias => \@aliases );
+ -species => "Drosophila_melanogaster",
+ -alias => \@aliases
+ );
- @aliases = ( 'S_Cerevisiae', 'Saccharomyces Cerevisiae',
- 'Saccharomyces_cerevisiae', 'Saccharomyces',
- 'yeast' );
+ @aliases = (
+ 'S_Cerevisiae', 'Saccharomyces Cerevisiae',
+ 'Saccharomyces_cerevisiae', 'Saccharomyces',
+ 'yeast'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Saccharomyces_cerevisiae",
- -alias => \@aliases );
+ -species => "Saccharomyces_cerevisiae",
+ -alias => \@aliases
+ );
- @aliases = ( 'C_Familiaris', 'Canis Familiaris',
- 'Canis_familiaris', 'Canis',
- 'dog' );
+ @aliases = (
+ 'C_Familiaris', 'Canis Familiaris',
+ 'Canis_familiaris', 'Canis',
+ 'dog'
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Canis_familiaris",
- -alias => \@aliases );
+ -species => "Canis_familiaris",
+ -alias => \@aliases
+ );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Ciona_intestinalis",
- -alias => [ 'ciona', 'Ciona intestinalis' ]
- );
+ -species => "Ciona_intestinalis",
+ -alias => [ 'ciona', 'Ciona intestinalis' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Bos_taurus",
- -alias => [ 'cow', 'bos_taurus' ]
- );
+ -species => "Bos_taurus",
+ -alias => [ 'cow', 'bos_taurus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Macaca_mulatta",
@@ -1799,191 +1870,223 @@ sub load_registry_from_db {
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Otolemur_garnettii",
- -alias => [ 'bushbaby', 'galago', 'Otolemur garnettii' ]
- );
+ -species => "Otolemur_garnettii",
+ -alias => [ 'bushbaby', 'galago', 'Otolemur garnettii' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Oryctolagus_cuniculus",
- -alias => [ 'rabbit', 'Oryctolagus cuniculus' ]
- );
+ -species => "Oryctolagus_cuniculus",
+ -alias => [ 'rabbit', 'Oryctolagus cuniculus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Felis_catus",
- -alias => [ 'cat', 'felis catus' ]
- );
+ -species => "Felis_catus",
+ -alias => [ 'cat', 'felis catus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Sus_scrofa",
- -alias => [ 'pig', 'sus scrofa' ]
- );
+ -species => "Sus_scrofa",
+ -alias => [ 'pig', 'sus scrofa' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Sorex_araneus",
- -alias =>
- [ 'shrew', 'ground_shrew', 'european_shrew', 'Sorex araneus' ]
- );
+ -species => "Sorex_araneus",
+ -alias =>
+ [ 'shrew', 'ground_shrew', 'european_shrew', 'Sorex araneus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Erinaceus_europaeus",
- -alias => [ 'western_european_hedgehog', 'Erinaceus europaeus' ]
+ -species => "Erinaceus_europaeus",
+ -alias => [ 'western_european_hedgehog', 'Erinaceus europaeus' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Myotis_lucifugus",
- -alias => [ 'microbat', 'little_brown_bat' ]
- );
+ -species => "Myotis_lucifugus",
+ -alias => [ 'microbat', 'little_brown_bat' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Dasypus_novemcinctus",
- -alias => [ 'armadillo', 'arma', 'Dasypus novemcinctu' ]
- );
+ -species => "Dasypus_novemcinctus",
+ -alias => [ 'armadillo', 'arma', 'Dasypus novemcinctu' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Loxodonta_africana",
- -alias => [ 'african_elephant', 'elephant', 'Loxodonta africana' ]
+ -species => "Loxodonta_africana",
+ -alias => [ 'african_elephant', 'elephant', 'Loxodonta africana' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Echinops_telfairi",
- -alias => [
- 'tenrec', 'madagascar_hedgehog',
- 'lesser_hedgehog', 'Echinops telfairi'
- ] );
+ -species => "Echinops_telfairi",
+ -alias => [
+ 'tenrec', 'madagascar_hedgehog',
+ 'lesser_hedgehog', 'Echinops telfairi'
+ ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Monodelphis_domestica",
- -alias => [ 'opossum', 'Monodelphis domestica' ]
- );
+ -species => "Monodelphis_domestica",
+ -alias => [ 'opossum', 'Monodelphis domestica' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Ornithorhynchus_anatinus",
- -alias => [ 'platypus', 'Ornithorhynchus anatinus' ]
- );
+ -species => "Ornithorhynchus_anatinus",
+ -alias => [ 'platypus', 'Ornithorhynchus anatinus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Gasterosteus_aculeatus",
- -alias => [ 'stickleback', 'Gasterosteus aculeatus' ]
- );
+ -species => "Gasterosteus_aculeatus",
+ -alias => [ 'stickleback', 'Gasterosteus aculeatus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Oryzias_latipes",
- -alias => [ 'medaka', 'Oryzias latipes' ]
- );
+ -species => "Oryzias_latipes",
+ -alias => [ 'medaka', 'Oryzias latipes' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Cavia_porcellus",
- -alias => [ 'guinea_pig', '"Cavia porcellus' ]
- );
+ -species => "Cavia_porcellus",
+ -alias => [ 'guinea_pig', '"Cavia porcellus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Aedes_aegypti",
- -alias => [ 'aedes', 'Aedes aegypti' ]
- );
+ -species => "Aedes_aegypti",
+ -alias => [ 'aedes', 'Aedes aegypti' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Spermophilus_tridecemlineatus",
- -alias => [ 'squirrel', 'Spermophilus tridecemlineatus' ]
- );
+ -species => "Spermophilus_tridecemlineatus",
+ -alias => [ 'squirrel', 'Spermophilus tridecemlineatus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Tupaia_belangeri",
- -alias => [ 'tree_shrew', 'Tupaia belangeri' ]
- );
+ -species => "Tupaia_belangeri",
+ -alias => [ 'tree_shrew', 'Tupaia belangeri' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Culex_pipiens",
- -alias => [ 'culex', 'Culex Pipiens' ]
- );
+ -species => "Culex_pipiens",
+ -alias => [ 'culex', 'Culex Pipiens' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Ochotona_princeps",
- -alias => [ 'pika', 'Ochotona princeps' ]
- );
+ -species => "Ochotona_princeps",
+ -alias => [ 'pika', 'Ochotona princeps' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Anolis_carolinensis",
- -alias => [ 'anolis', 'anolis_lizard', 'Anolis carolinensis' ]
- );
+ -species => "Anolis_carolinensis",
+ -alias => [ 'anolis', 'anolis_lizard', 'Anolis carolinensis' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Microcebus_murinus",
- -alias => [ 'mouse_lemur', 'Microcebus murinus' ]
- );
+ -species => "Microcebus_murinus",
+ -alias => [ 'mouse_lemur', 'Microcebus murinus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Pongo_pygmaeus",
- -alias => [ 'orang', 'orang_utan', 'orangutan', 'Pongo pygmaeus' ]
+ -species => "Pongo_pygmaeus",
+ -alias => [ 'orang', 'orang_utan', 'orangutan', 'Pongo pygmaeus' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Equus_caballus",
- -alias => [ 'horse', 'Equuscaballus' ]
- );
+ -species => "Equus_caballus",
+ -alias => [ 'horse', 'Equuscaballus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Tursiops_truncatus",
- -alias => [ 'dolphin', 'Tursiopstruncatus' ]
- );
+ -species => "Tursiops_truncatus",
+ -alias => [ 'dolphin', 'Tursiopstruncatus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Procavia_capensis",
- -alias => [ 'rock_hyrax', 'hyrax', 'Procaviacapensis' ]
- );
+ -species => "Procavia_capensis",
+ -alias => [ 'rock_hyrax', 'hyrax', 'Procaviacapensis' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Dipodomys_ordii",
- -alias => [ 'kangaroo_rat', 'Dipodomysordii' ]
- );
+ -species => "Dipodomys_ordii",
+ -alias => [ 'kangaroo_rat', 'Dipodomysordii' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Pteropus_vampyrus",
- -alias => [ 'megabat', 'Pteropusvampyrus' ]
- );
+ -species => "Pteropus_vampyrus",
+ -alias => [ 'megabat', 'Pteropusvampyrus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Tarsius_syrichta",
- -alias => [ 'philippine tarsier', 'tarsier', 'Tarsiussyrichta' ]
+ -species => "Tarsius_syrichta",
+ -alias => [ 'philippine tarsier', 'tarsier', 'Tarsiussyrichta' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Vicugna_pacos",
- -alias => [ 'alpaca', 'vicugnapacos' ]
- );
+ -species => "Vicugna_pacos",
+ -alias => [ 'alpaca', 'vicugnapacos' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Gorilla_gorilla",
- -alias => [ 'gorilla', 'gorillagorilla' ]
- );
-
- Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Anolis_carolinensis",
- -alias => [ 'anolis', 'anoliscarolinensis' ]
- );
+ -species => "Gorilla_gorilla",
+ -alias => [ 'gorilla', 'gorillagorilla' ] );
- Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Choloepus_hoffmanni",
- -alias => [ 'sloth', 'choloepus', 'choloepushoffmanni' ]
- );
+ Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+ -species => "Anolis_carolinensis",
+ -alias => [ 'anolis', 'anoliscarolinensis' ] );
- Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
- -species => "Taeniopygia_guttata",
- -alias => [ 'finch', 'zebrafinch', 'taeniopygia', 'taeniopygiaguttata' ]
- );
+ Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+ -species => "Choloepus_hoffmanni",
+ -alias => [ 'sloth', 'choloepus', 'choloepushoffmanni' ] );
+ Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+ -species => "Taeniopygia_guttata",
+ -alias =>
+ [ 'finch', 'zebrafinch', 'taeniopygia', 'taeniopygiaguttata' ] );
@aliases = ('compara');
- Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => "multi",
- -alias => \@aliases
+ Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+ -species => "multi",
+ -alias => \@aliases
);
@aliases = ('go');
-
- Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => "multi",
- -alias => \@aliases
+ Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
+ -species => "multi",
+ -alias => \@aliases
);
+
+ # Register aliases as found in adaptor meta tables.
+ $self->find_and_add_aliases();
+
} ## end sub load_registry_from_db
+=head2 find_and_add_aliases
+
+ 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.
+
+ Example : Bio::EnsEMBL::Registry->find_and_add_aliases(
+ -GROUP => 'core',
+ -ADAPTOR => $dba
+ );
+
+ Description : Looks in the meta container for each database for
+ an entry called "species.alias". If any are found
+ then the species adaptor is registered to that
+ set of aliases. This can work across any adaptor
+ which has a MetaContainer.
+
+ Return type : none
+ Exceptions : none
+ Status : Stable
+
+=cut
+
+sub find_and_add_aliases {
+ my $class = shift @_;
+
+ my ( $group, $adaptor ) = rearrange( [qw(GROUP ADAPTOR)], @_ );
+
+ my @dbas;
+ if ( defined($adaptor) ) {
+ @dbas = ($adaptor);
+ } else {
+ @dbas = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) };
+ }
+
+ foreach my $dba (@dbas) {
+ my $species = $dba->species();
+ my $meta_container = $dba->get_MetaContainer();
+
+ my @aliases =
+ @{ $meta_container->list_value_by_key('species.alias') };
+
+ # Need to disconnect so we do not spam the MySQL servers trying to
+ # get aliases.
+ $dba->dbc()->disconnect_if_idle();
+
+ foreach my $alias (@aliases) {
+ $class->add_alias( $species, $alias );
+ }
+ }
+
+} ## end sub find_and_add_aliases
+
#
# Web specific routines