=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
http://www.ensembl.org/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Registry
=head1 SYNOPSIS
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_all("configuration_file");
$gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
=head1 DESCRIPTION
All Adaptors are stored/registered using this module. This module should
then be used to get the adaptors needed.
The registry can be loaded from a configuration file using the load_all
method.
If a filename is passed to load_all then this is used. Else if the
enviroment variable ENSEMBL_REGISTRY is set to the name on an existing
configuration file, then this is used. Else if the file .ensembl_init
in your home directory exist, it is used.
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm. This
will then be passed on to load_all.
The registry can also be loaded via the method load_registry_from_db
which given a database host will load the latest versions of the Ensembl
databases from it.
The four types of registries are for db adaptors, dba adaptors, dna
adaptors and the standard type.
=head2 db
These are registries for backwards compatibility and enable the
subroutines to add other adaptors to connections.
e.g. get_all_db_adaptors, get_db_adaptor, add_db_adaptor,
remove_db_adaptor are the old DBAdaptor subroutines which are now
redirected to the Registry.
So if before we had
my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
We now want to change this to
my $sfa =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "blast" );
=head2 DBA
These are the stores for the DBAdaptors
The Registry will create all the DBConnections needed now if you set up
the configuration correctly. So instead of the old commands like
my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
my $exon_adaptor = $db->get_ExonAdaptor;
we should now have just
my $exon_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
=head2 DNA
This is an internal Registry and allows the configuration of a dnadb.
An example here is to set the est database to get its dna data from the
core database.
## set the est db to use the core for getting dna data.
# Bio::EnsEMBL::Utils::ConfigRegistry->dnadb_add( "Homo Sapiens",
# "core", "Homo Sapiens", "est" );
=head2 adaptors
This is the registry for all the general types of adaptors like
GeneAdaptor, ExonAdaptor, Slice Adaptor etc.
These are accessed by the get_adaptor subroutine i.e.
my $exon_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
=head1 METHODS
=cut
package Bio::EnsEMBL::Registry;
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::ConfigRegistry;
use DBI;
use vars qw(%registry_register);
my $API_VERSION = 55;
# 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',
'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
'estgene' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
'funcgen' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
'haplotype' => 'Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor',
'hive' => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor',
'lite' => 'Bio::EnsEMBL::Lite::DBAdaptor',
'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
'pipeline' => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
'snp' => 'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
);
=head2 load_all
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.
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.
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 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
Status : Stable
=cut
sub load_all {
my $class = shift;
my ( $config_file, $verbose, $no_clear, $no_cache ) = @_;
$config_file ||= $ENV{ENSEMBL_REGISTRY}
|| $ENV{HOME} . "/.ensembl_init";
$verbose ||= 0;
$no_clear ||= 0;
$no_cache ||= 0;
if ( !defined($config_file) ) {
if ($verbose) {
print( STDERR
"No default registry configuration to load.\n" );
}
} elsif ( !-e $config_file ) {
if ($verbose) {
printf( STDERR "Configuration file '%s' does not exist. "
. "Registry configuration not loaded.\n",
$config_file );
}
} else {
if ( defined( $registry_register{'seen'} ) ) {
if ( !$no_clear ) {
if ($verbose) {
print( STDERR "Clearing previously loaded "
. "registry configuration\n" );
}
$class->clear();
}
}
$registry_register{'seen'} = 1;
if ($verbose) {
printf( STDERR
"Loading registry configuration from '%s'.\n",
$config_file );
}
my $cfg;
eval { require Config::IniFiles };
if ($@) {
# The user does not have the 'Config::IniFiles' module.
if ($verbose) {
print( STDERR "No Config::IniFiles module found, "
. "assuming this is not an ini-file\n" );
}
# If the configuration file *is* an ini-file, we can expect a
# load of compilation errors from the next eval...
} else {
# The user has the 'Config::IniFiles' module installed. See
# if this is an ini-file or not...
$cfg = Config::IniFiles->new( -file => $config_file );
}
if ( defined $cfg ) {
my %default_adaptor_args = ();
if ( $cfg->SectionExists('default') ) {
# The 'default' section is special. It contain default
# values that should be implicit to all other section in
# this configuration file. Aliases are added if there
# is also a 'species' setting.
my $alias = $cfg->val( 'default', 'alias' );
$cfg->delval( 'default', 'alias' );
my $species = $cfg->val( 'default', 'species' );
if ( defined($alias) && defined($species) ) {
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => $species,
-alias => [ split( /\n/, $alias ) ]
);
}
%default_adaptor_args =
map { '-' . $_ => $cfg->val( 'default', $_ ) }
$cfg->Parameters('default');
}
foreach my $section ( $cfg->Sections() ) {
if ( $section eq 'default' )
{ # We have already done the 'default' section.
next;
}
my $group = $cfg->val( $section, 'group' )
|| $cfg->val( 'default', 'group' );
if ( !defined($group) ) {
printf( STDERR "Key 'group' is undefined "
. "for configuration section '%s', "
. "skipping this section.\n",
$section );
next;
}
my $adaptor = $group2adaptor{ lc($group) };
if ( !defined($adaptor) ) {
printf( STDERR "Unknown group '%s' "
. "for configuration section '%s', "
. "skipping this section.\n",
$group, $section );
next;
}
# Handle aliases. A section must have both an 'alias'
# setting and a 'species' setting for aliases to be
# added. The 'species' setting might be inherited from
# the 'default' section.
my $alias = $cfg->val( $section, 'alias' );
$cfg->delval( $section, 'alias' );
my $species = $cfg->val( $section, 'species' )
|| $cfg->val( 'default', 'species' );
if ( defined($alias) && defined($species) ) {
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => $species,
-alias => [ split( /\n/, $alias ) ]
);
}
# Fill in the adaptor initialization arguments.
# 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) {
$adaptor_args{'-no_cache'} = 1;
}
}
if ($verbose) {
printf( "Configuring adaptor '%s' "
. "for configuration section '%s'...\n",
$adaptor, $section );
}
eval "require $adaptor";
if ($@) { die($@) }
$adaptor->new(%adaptor_args);
} ## end foreach my $section ( $cfg->Sections...
} else {
# This is probably no ini-file but an old style piece
# of configuration written in Perl. We need to try to
# require() it.
eval { require($config_file) };
if ($@) { die($@) }
# To make the web code avoid doing this again:
delete $INC{$config_file};
}
} ## end else [ if ( !defined($config_file...
} ## end sub load_all
=head2 clear
Will clear the registry and disconnect from all databases.
Example : Bio::EnsEMBL::Registry->clear();
Returntype : none
Exceptions : none
Status : Stable
=cut
sub clear{
my ($self);
foreach my $dba (@{$registry_register{'_DBA'}}){
if($dba->dbc->connected){
$dba->dbc->db_handle->disconnect();
}
}
%registry_register = ();
}
#
# db adaptors. (for backwards compatibility)
#
=head2 add_db
Arg [1] : db (DBAdaptor) to add adaptor to.
Arg [2] : name of the name to add the adaptor to in the registry.
Arg [3] : The adaptor to be added to the registry.
Example : Bio::EnsEMBL::Registry->add_db($db, "lite", $dba);
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
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;
}
}
=head2 remove_db
Arg [1] : db (DBAdaptor) to remove adaptor from.
Arg [2] : name to remove the adaptor from in the registry.
Example : my $db = Bio::EnsEMBL::Registry->remove_db($db, "lite");
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.
=cut
sub remove_db {
my ( $class, $db, $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;
return $ret;
}
=head2 get_db
Arg [1] : db (DBAdaptor) to get adaptor from.
Arg [2] : name to get the adaptor for in the registry.
Example : my $db = Bio::EnsEMBL::Registry->get_db("Human", "core", "lite");
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.
=cut
sub get_db {
my ( $class, $db, $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) };
}
=head2 get_all_db_adaptors
Arg [1] : db (DBAdaptor) to get all the adaptors from.
Example : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($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");
=cut
sub get_all_db_adaptors {
my ( $class, $db ) = @_;
my %ret = ();
# we now also want to add all the DBAdaptors for the same species.
# as add_db_adaptor does not add if it is from the same species.
foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
if ( lc( $dba->species() ) eq lc( $db->species() ) ) {
$ret{ $dba->group() } = $dba;
}
}
foreach my $key (
keys %{
$registry_register{ $class->get_alias( $db->species() ) }
{ lc( $db->group() ) }{'_special'} } )
{
$ret{$key} =
$registry_register{ $class->get_alias( $db->species() ) }
{ lc( $db->group() ) }{'_special'}{$key};
}
return \%ret;
} ## end sub get_all_db_adaptors
#
# DBAdaptors
#
=head2 add_DBAdaptor
Arg [1] : name of the species to add the adaptor to in the registry.
Arg [2] : name of the group to add the adaptor to in the registry.
Arg [3] : The DBAaptor to be added to the registry.
Example : Bio::EnsEMBL::Registry->add_DBAdaptor("Human", "core", $dba);
Returntype : none
Exceptions : none
caller : internal
Status : Stable
=cut
sub add_DBAdaptor {
my ( $class, $species, $group, $adap ) = @_;
if ( !( $class->alias_exists($species) ) ) {
$class->add_alias( $species, $species );
}
$species = $class->get_alias($species);
$registry_register{$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 );
}
}
=head2 get_DBAdaptor
Arg [1] : name of the species to get the adaptor for in the registry.
Arg [2] : name of the group to get the adaptor for in the registry.
Example : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
Returntype : DBAdaptor
Exceptions : none
Status : Stable
=cut
sub get_DBAdaptor {
my ( $class, $species, $group ) = @_;
$species = $class->get_alias($species);
return $registry_register{$species}{ lc($group) }{'_DB'};
}
=head2 get_all_DBAdaptors
Arg [SPECIES]: (optional) string
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'
) };
Returntype : list of DBAdaptors
Exceptions : none
Status : Stable
=cut
sub get_all_DBAdaptors {
my ( $class, @args ) = @_;
my ( $species, $group ) = rearrange( [qw(SPECIES GROUP)], @args );
if ( defined($species) ) { $species = $class->get_alias($species) }
my @ret;
foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
if ( ( !defined($species) || lc($species) eq lc( $dba->species() ) )
&& ( !defined($group) || lc($group) eq lc( $dba->group() ) ) )
{
push( @ret, $dba );
}
}
return \@ret;
}
=head2 get_all_DBAdaptors_by_connection
Arg [1] : DBConnection used to find DBAdaptors
Returntype : reference to list of DBAdaptors
Exceptions : none
Example : @dba = @{ Bio::EnsEMBL::Registry
->get_all_DBAdaptors_by_connection($dbc) };
Status : Stable
=cut
sub get_all_DBAdaptors_by_connection {
my ( $self, $dbc_orig ) = @_;
my @return;
foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
my $dbc = $dba->dbc();
if ( defined($dbc)
&& $dbc->can('equals')
&& $dbc->equals($dbc_orig) )
{
push( @return, $dba );
}
}
return \@return;
}
=head2 get_all_DBAdaptors_by_dbname
Arg [1] : string, name of database
Returntype : reference to list of DBAdaptors
Exceptions : none
Example : @dba = @{ Bio::EnsEMBL::Registry
->get_all_DBAdaptors_by_dbname($dbname) };
Status : Stable
=cut
sub get_all_DBAdaptors_by_dbname {
my ( $self, $dbname ) = @_;
my @return;
foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
my $dbc = $dba->dbc();
if ( defined($dbc) && $dbc->dbname() eq $dbname ) {
push( @return, $dba );
}
}
return \@return;
}
=head2 remove_DBAdaptor
Arg [1] : name of the species to get the adaptor for in the registry.
Arg [2] : name of the group to get the adaptor for in the registry.
Example : $dba = Bio::EnsEMBL::Registry->remove_DBAdaptor("Human", "core");
Returntype : none
Exceptions : none
Status : At risk
=cut
sub remove_DBAdaptor{
my ($class, $species, $group) = @_;
$species = $class->get_alias($species);
delete $registry_register{$species}{$group};
# This will remove the DBAdaptor and all the other adaptors
# Now remove if from the _DBA array
my $index;
foreach my $i(0..$#{$registry_register{'_DBA'}}){
my $dba = $registry_register{'_DBA'}->[$i];
if(($dba->species eq $species) &&
$dba->group eq $group){
$index = $i;
last;
}
}
# Now remove from _DBA cache
splice(@{$registry_register{'_DBA'}}, $index, 1) if defined $index;
return;
}
=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
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' );
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
=cut
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 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 );
# Get all current defaults if not defined
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 ( !( $host && $user ) ) {
throw("No comparable $alias $group DB present in Registry. "
. "You must pass at least a dbhost and dbuser" );
}
}
$self->remove_DBAdaptor( $alias, $group );
#my @adaptors = @{$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} );
return $db;
} ## end sub reset_DBAdaptor
#
# DNA Adaptors
#
=head2 add_DNAAdaptor
Arg [1] : name of the species to add the adaptor to in the registry.
Arg [2] : name of the group to add the adaptor to in the registry.
Arg [3] : name of the species to get the dna from
Arg [4] : name of the group to get the dna from
Example : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "estgene", "Human", "core");
Returntype : none
Exceptions : none
Status : Stable
=cut
sub add_DNAAdaptor {
my ( $class, $species, $group, $dnadb_species, $dnadb_group ) = @_;
$species = $class->get_alias($species);
$dnadb_species = $class->get_alias($dnadb_species);
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;
}
}
=head2 get_DNAAdaptor
Arg [1] : name of the species to get the adaptor for in the registry.
Arg [2] : name of the group to get the adaptor for in the registry.
Example : $dnaAdap = Bio::EnsEMBL::Registry->get_DNAAdaptor("Human", "core");
Returntype : adaptor
Exceptions : none
Status : Stable
=cut
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 );
}
return undef;
}
#
# General Adaptors
#
=head2 add_adaptor
Arg [1] : name of the species to add the adaptor to in the registry.
Arg [2] : name of the group to add the adaptor to in the registry.
Arg [3] : name of the type to add the adaptor to in the registry.
Arg [4] : The DBAaptor to be added to the registry.
Arg [5] : (optional) if set okay to overwrite.
Example : Bio::EnsEMBL::Registry->add_adaptor("Human", "core", "Gene", $adap);
Returntype : none
Exceptions : none
Caller : internal
Status : Stable
=cut
sub add_adaptor {
my ( $class, $species, $group, $type, $adap, $reset ) = @_;
$species = $class->get_alias($species);
# Since the adaptors are not stored initially, only their class paths
# when the adaptors are obtained, we need to store these instead. It
# is not necessarily an error if the registry is overwritten without
# the reset set but it is an indication that we are overwriting a
# database which should be a warning for now
if ( defined($reset) )
{ # JUST REST THE HASH VALUE NO MORE PROCESSING NEEDED
$registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
return;
}
if (
defined( $registry_register{$species}{ lc($group) }{ lc($type) } ) )
{
# print STDERR (
# "Overwriting Adaptor in Registry for $species $group $type\n");
$registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
return;
}
$registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
if ( !defined( $registry_register{$species}{'list'} ) ) {
$registry_register{$species}{'list'} = [$type];
} else {
push( @{ $registry_register{$species}{'list'} }, $type );
}
if ( !defined( $registry_register{ lc($type) }{$species} ) ) {
$registry_register{ lc($type) }{$species} = [$type];
} else {
push( @{ $registry_register{ lc($type) }{$species} }, $adap );
}
} ## end sub add_adaptor
=head2 get_adaptor
Arg [1] : name of the species to add the adaptor to in the registry.
Arg [2] : name of the group to add the adaptor to in the registry.
Arg [3] : name of the type to add the adaptor to in the registry.
Example : $adap = Bio::EnsEMBL::Registry->get_adaptor("Human", "core", "Gene");
Returntype : adaptor
Exceptions : none
Status : Stable
=cut
sub get_adaptor {
my ( $class, $species, $group, $type ) = @_;
$species = $class->get_alias($species);
my %dnadb_adaptors = (
'sequence' => 1,
'assemblymapper' => 1,
'karyotypeband' => 1,
'repeatfeature' => 1,
'coordsystem' => 1,
'assemblyexceptionfeature' => 1
);
## warn "$species, $group, $type";
$type = lc($type);
my $dnadb_group = $registry_register{$species}{ lc($group) }{'_DNA'};
if ( defined($dnadb_group)
&& defined( $dnadb_adaptors{ lc($type) } ) )
{
$species = $registry_register{$species}{ lc($group) }{'_DNA2'};
$group = $dnadb_group;
}
my $ret = $registry_register{$species}{ lc($group) }{ lc($type) };
if ( !defined($ret) ) { return undef }
if ( ref($ret) ) { return $ret }
# Not instantiated yet
my $dba = $registry_register{$species}{ lc($group) }{'_DB'};
my $module = $ret;
eval "require $module";
if ($@) {
warning("'$module' cannot be found.\nException $@\n");
return undef;
}
if (
!defined( $registry_register{$species}{ lc($group) }{'CHECKED'} ) )
{
$registry_register{$species}{ lc($group) }{'CHECKED'} = 1;
$class->version_check($dba);
}
my $adap = "$module"->new($dba);
Bio::EnsEMBL::Registry->add_adaptor( $species, $group, $type, $adap,
'reset' );
$ret = $adap;
return $ret;
} ## end sub get_adaptor
=head2 get_all_adaptors
Arg [SPECIES] : (optional) string
species name to get adaptors for
Arg [GROUP] : (optional) string
group name to get adaptors for
Arg [TYPE] : (optional) string
type to get adaptors for
Example : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
Returntype : ref to list of adaptors
Exceptions : none
Status : Stable
=cut
sub get_all_adaptors{
my ($class,@args)= @_;
my ($species, $group, $type);
my @ret=();
my (%species_hash, %group_hash, %type_hash);
if(@args == 1){ # Old species only one parameter
warn("-SPECIES argument should now be used to get species adaptors");
$species = $args[0];
}
else{
# new style -SPECIES, -GROUP, -TYPE
($species, $group, $type) =
rearrange([qw(SPECIES GROUP TYPE)], @args);
}
if(defined($species)){
$species_hash{$species} = 1;
}
else{
# get list of species
foreach my $dba (@{$registry_register{'_DBA'}}){
$species_hash{lc($dba->species())} = 1;
}
}
if(defined($group)){
$group_hash{$group} = 1;
}
else{
foreach my $dba (@{$registry_register{'_DBA'}}){
$group_hash{lc($dba->group())} = 1;
}
}
if(defined($type)){
$type_hash{$type} =1;
}
else{
foreach my $dba (@{$registry_register{'_DBA'}}){
foreach my $ty (@{$registry_register{lc($dba->species)}{'list'}}){
$type_hash{lc($ty)} = 1;
}
}
}
### NOW NEED TO INSTANTIATE BY CALLING get_adaptor
foreach my $sp (keys %species_hash){
foreach my $gr (keys %group_hash){
foreach my $ty (keys %type_hash){
my $temp = $class->get_adaptor($sp,$gr,$ty);
if(defined($temp)){
push @ret, $temp;
}
}
}
}
return (\@ret);
}
=head2 add_alias
Arg [1] : name of the species to add alias for
Arg [2] : name of the alias
Example : Bio::EnsEMBL::Registry->add_alias("Homo Sapiens","Human");
Description: add alternative name for the species.
Returntype : none
Exceptions : none
Status : Stable
=cut
sub add_alias{
my ($class, $species,$key) = @_;
$registry_register{'_ALIAS'}{lc($key)} = lc($species);
}
=head2 get_alias
Arg [1] : name of the possible alias to get species for
Example : Bio::EnsEMBL::Registry->get_alias("Human");
Description: get proper species name.
Returntype : species name
Exceptions : none
Status : Stable
=cut
sub get_alias{
my ($class, $key) = @_;
if(!defined($registry_register{'_ALIAS'}{lc($key)})){
return $key;
}
return $registry_register{'_ALIAS'}{lc($key)};
}
=head2 alias_exists
Arg [1] : name of the possible alias to get species for
Example : Bio::EnsEMBL::Registry->alias_exists("Human");
Description: does the species name exist.
Returntype : 1 if exists else 0
Exceptions : none
Status : Stable
=cut
sub alias_exists{
my ($class, $key) = @_;
if(defined($registry_register{'_ALIAS'}{lc($key)})){
return 1;
}
return 0;
}
=head2 set_disconnect_when_inactive
Example : Bio::EnsEMBL::Registry->set_disconnect_when_inactive();
Description: Set the flag to make sure that the database connection is dropped if
not being used on each database.
Returntype : none
Exceptions : none
Status : Stable
=cut
sub set_disconnect_when_inactive{
foreach my $dba ( @{get_all_DBAdaptors()}){
my $dbc = $dba->dbc;
# Disconnect if connected
$dbc->disconnect_if_idle() if $dbc->connected();
$dbc->disconnect_when_inactive(1);
}
}
=head2 disconnect_all
Example : Bio::EnsEMBL::Registry->disconnect_all();
Description: disconnect from all the databases.
Returntype : none
Exceptions : none
Status : Stable
=cut
sub disconnect_all {
foreach my $dba ( @{get_all_DBAdaptors()||[]} ){
my $dbc = $dba->dbc;
next unless $dbc;
# Disconnect if connected
$dbc->disconnect_if_idle() if $dbc->connected();
}
}
=head2 change_access
Will change the username and password for a set of databases.
if host,user or database names are missing then these are not checked.
So for example if you do not specify a database then ALL databases on
the specified host and port will be changed.
Arg [1] : name of the host to change access on
Arg [2] : port number to change access on
Arg [3] : name of the user to change access on
Arg [4] : name of the database to change access on
Arg [5] : name of the new user
Arg [6] : new password
Example : Bio::EnsEMBL::Registry->get_alias("Human");
Description: change username and password on one or more databases
Returntype : none
Exceptions : none
Status : Stable
=cut
sub change_access{
my $self = shift;
my ($host,$port,$user,$dbname,$new_user,$new_pass) = @_;
foreach my $dba ( @{$registry_register{'_DBA'}}){
my $dbc = $dba->dbc;
if((!defined($host) or $host eq $dbc->host) and
(!defined($port) or $port eq $dbc->port) and
(!defined($user) or $user eq $dbc->username) and
(!defined($dbname) or $dbname eq $dbc->dbname)){
if($dbc->connected()){
$dbc->db_handle->disconnect();
$dbc->connected(undef);
}
# over write the username and password
$dbc->username($new_user);
$dbc->password($new_pass);
}
}
}
=head2 load_registry_from_url
Arg [1] : string $url
Arg [2] : (optional) integer
If not 0, will print out all information.
Arg [3] : (optional) integer
This option will turn off caching for slice features,
so, every time a set of features is retrieved, they
will come from the database instead of the cache. This
option is only recommended for advanced users, specially
if you need to store and retrieve features. It might
reduce performance when querying the database if not used
properly. If in doubt, do not use it or ask in ensembl-dev
Example : load_registry_from_url(
'mysql://anonymous@ensembldb.ensembl.org:3306');
Description: Will load the correct versions of the ensembl
databases for the software release it can find on
a database instance into the registry. Also adds
a set of standard aliases. The url format is:
mysql://[[username][:password]@]hostname[:port]. You
can also request a specific version for the databases
by adding a slash and the version number but your
script may crash as the API version won't match the
DB version.
Exceptions : None.
Status : Stable
=cut
sub load_registry_from_url {
my ($self, $url, $verbose, $no_cache) = @_;
if ($url =~ /mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?/) {
my $user_pass = $1;
my $host = $2;
my $port = $3;
my $version = $4;
$user_pass =~ s/\@$//;
my ($user, $pass) = $user_pass =~ m/([^\:]+)(\:.+)?/;
$pass =~ s/^\:// if ($pass);
$port =~ s/^\:// if ($port);
$version =~ s/^\/// if ($version);
$self->load_registry_from_db(
-host=> $host,
-user => $user,
-pass => $pass,
-port => $port,
-db_version => $version,
-verbose => $verbose,
-no_cache => $no_cache);
} else {
throw("Only MySQL URLs are accepted at the moment");
}
}
=head2 load_registry_from_db
Arg [HOST] : string
The domain name of the database host to connect to.
Arg [USER] : string
The name of the database user to connect with.
Arg [PASS] : (optional) string
The password to be used to connect to the database.
Arg [PORT] : (optional) integer
The port to use when connecting to the database.
Arg [VERBOSE]: (optional) boolean
Whether to print database messages.
Arg [DB_VERSION]: (optional) integer
By default, only databases corresponding to this API
version are loaded. This allows the script to use
databases from another version although it might not
work properly. This option should only be used for
production or testing purposes and if you really
know what you are doing.
Arg [WAIT_TIMEOUT]: (optional) integer
Time in seconds for the wait timeout to happen.
Time after which the connection is deleted if not
used. By default this is 28800 (8 hours), so set
this to greater than this if your connection are
getting deleted. Only set this if you are having
problems and know what you are doing.
Arg [-NO_CACHE]: (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.
Example : load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
-verbose => '1'
);
Description: Will load the correct versions of the ensembl
databases for the software release it can find on a
database instance into the registry. Also adds a set
of standard aliases.
Exceptions : None.
Status : Stable
=cut
sub load_registry_from_db {
my ( $self, @args ) = @_;
my ( $host, $port, $user, $pass, $verbose, $db_version, $wait_timeout,
$no_cache )
= rearrange( [
'HOST', 'PORT', 'USER', 'PASS',
'VERBOSE', 'DB_VERSION', 'WAIT_TIMEOUT', 'NO_CACHE'
],
@args
);
my $go_version = 0;
my $ontology_version = 0;
$user ||= "ensro";
if ( !defined($port) ) {
$port = 3306;
if ( $host eq "ensembldb.ensembl.org" ) {
if ( !defined($db_version) or $db_version >= 48 ) {
$port = 5306;
}
}
}
$wait_timeout ||= 0;
my $dbh =
DBI->connect( "DBI:mysql:host=$host;port=$port", $user, $pass );
my $res = $dbh->selectall_arrayref('SHOW DATABASES');
my @dbnames = map { $_->[0] } @$res;
my %temp;
my $software_version = $self->software_version();
if ( defined($db_version) ) {
$software_version = $db_version;
}
if ($verbose) {
printf( "Will only load v%d databases\n", $software_version );
}
for my $db (@dbnames) {
if ( $db =~ /^(\w+)_(collection_core_(?:\d+_)?(\d+)_(\w+))/ )
{ # NEEDS TO BE FIRST
if ( $3 eq $software_version ) {
$temp{$1} = $2;
}
} elsif ( $db =~ /^(.+)_(userdata)$/ ) {
$temp{$1} = $2;
} elsif ( $db =~ /^(ensembl_compara(?:_\w+)*?)_(\d+)$/ ) {
if ( $2 eq $software_version ) {
$temp{$1} = $2;
}
} 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 =~ /^(ensembl_ontology)_(\d+)/ ) {
if ( $2 eq $software_version ) {
$ontology_version = $2;
}
} elsif (
$db =~ /^([a-z]+_[a-z]+_[a-z]+(?:_\d+)?)_(\d+)_(\w+)/ )
{
if ( $2 eq $software_version ) {
$temp{$1} = $2 . "_" . $3;
}
} else {
# warn( sprintf( "Skipping database '%s'\n", $db ) );
}
} ## end for my $db (@dbnames)
@dbnames = ();
foreach my $key ( keys %temp ) {
push @dbnames, $key . "_" . $temp{$key};
}
# Register Core databases
my @core_dbs = grep { /^[a-z]+_[a-z]+_core_(?:\d+_)?\d+_/ } @dbnames;
foreach my $coredb (@core_dbs) {
next if ($coredb =~ /collection/); # Skip multi-species databases
my ( $species, $num ) =
( $coredb =~ /(^[a-z]+_[a-z]+)_core_(?:\d+_)?(\d+)/ );
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "core",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $coredb,
-wait_timeout => $wait_timeout,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
if ($verbose) {
printf( "Species '%s' loaded from database '%s'\n",
$species, $coredb );
}
}
# Register multi-species databases
my @multi_dbs = grep { /^\w+_collection_core_\w+$/ } @dbnames;
foreach my $multidb (@multi_dbs) {
my $sth =
$dbh->prepare(
sprintf( 'SELECT species_id, meta_value FROM %s.meta ',
$dbh->quote_identifier($multidb) )
. "WHERE meta_key = 'species.db_name'" );
$sth->execute();
my ( $species_id, $species );
$sth->bind_columns( \( $species_id, $species ) );
while ( $sth->fetch() ) {
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "core",
-species => $species,
-species_id => $species_id,
-multispecies_db => 1,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $multidb,
-wait_timeout => $wait_timeout,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
if ($verbose) {
printf( "Species '%s' (id:%d) loaded from database '%s'\n",
$species, $species_id, $multidb );
}
}
} ## end foreach my $multidb (@multi_dbs)
# register cdna databases
my @cdna_dbs = grep { /^[a-z]+_[a-z]+_cdna_(?:\d+_)?\d+_/ } @dbnames;
for my $cdnadb (@cdna_dbs) {
my ( $species, $num ) =
( $cdnadb =~ /(^[a-z]+_[a-z]+)_cdna_(?:\d+_)?(\d+)_/ );
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "cdna",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $cdnadb,
-wait_timeout => $wait_timeout,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
if ($verbose) {
printf( "%s loaded\n", $cdnadb );
}
}
my @vega_dbs = grep { /^[a-z]+_[a-z]+_vega_\d+_/ } @dbnames;
for my $vegadb (@vega_dbs) {
my ( $species, $num ) =
( $vegadb =~ /(^[a-z]+_[a-z]+)_vega_(\d+)/ );
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "vega",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $vegadb,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
if ($verbose) {
printf( "%s loaded\n", $vegadb );
}
}
# Otherfeatures
my @other_dbs = grep { /^[a-z]+_[a-z]+_otherfeatures_(?:\d+_)?\d+_/ } @dbnames;
for my $other_db (@other_dbs) {
my ( $species, $num ) =
( $other_db =~ /(^[a-z]+_[a-z]+)_otherfeatures_(?:\d+_)?(\d+)_/ );
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "otherfeatures",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $other_db,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
if ($verbose) {
printf( "%s loaded\n", $other_db );
}
}
# User upload DBs
my @userupload_dbs = grep { /_userdata$/ } @dbnames;
for my $userupload_db (@userupload_dbs) {
my ($species) = ( $userupload_db =~ /(^.+)_userdata$/ );
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-group => "userupload",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $userupload_db,
-no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
if ($verbose) {
printf( "%s loaded\n", $userupload_db );
}
}
# Variation
eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor";
if ($@) {
# Ignore variations as code required not there for this
if ($verbose) {
print(
"Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found "
. "so variation databases will be ignored if found\n" );
}
} else {
my @variation_dbs =
grep { /^[a-z]+_[a-z]+_variation_(?:\d+_)?\d+_/ } @dbnames;
for my $variation_db (@variation_dbs) {
my ( $species, $num ) =
( $variation_db =~ /(^[a-z]+_[a-z]+)_variation_(?:\d+_)?(\d+)_/ );
my $dba =
Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(
-group => "variation",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $variation_db,
-no_cache => $no_cache );
if ($verbose) {
printf( "%s loaded\n", $variation_db );
}
}
}
eval "require Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor";
if ($@) {
if ($verbose) {
# Ignore funcgen DBs as code required not there for this
print( "Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found "
. "so functional genomics databases will be ignored if found\n"
);
}
} else {
my @funcgen_dbs = grep { /^[a-z]+_[a-z]+_funcgen_(?:\d+_)?\d+_/ } @dbnames;
for my $funcgen_db (@funcgen_dbs) {
my ( $species, $num ) =
( $funcgen_db =~ /(^[a-z]+_[a-z]+)_funcgen_(?:\d+_)?(\d+)_/ );
my $dba =
Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(
-group => "funcgen",
-species => $species,
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-wait_timeout => $wait_timeout,
-dbname => $funcgen_db,
-no_cache => $no_cache );
if ($verbose) {
printf( "%s loaded\n", $funcgen_db );
}
}
}
# Compara
my @compara_dbs = grep { /^ensembl_compara/ } @dbnames;
if (@compara_dbs) {
eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
if ($@) {
# Ignore Compara as code required not there for this
if ($verbose) {
printf(
"Bio::EnsEMBL::Compara::DBSQL::DBAdaptor "
. "not found so the following compara "
. "databases will be ignored: %s\n",
join( ', ', @compara_dbs ) );
}
} else {
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 );
}
} ## end foreach my $compara_db (@compara_dbs)
} ## end else [ if ($@)
} elsif ($verbose) {
print("No Compara databases found\n");
}
# Ancestral sequences
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\n");
}
# GO
if ($go_version) {
eval "require Bio::EnsEMBL::ExternalData::GO::GOAdaptor";
if ($@) {
#ignore go as code required not there for this
# print $@;
if ($verbose) {
print "GO software not installed "
. "so GO database ensembl_go_$go_version will be ignored\n";
}
} else {
my $go_db = "ensembl_go_" . $go_version;
my $dba =
Bio::EnsEMBL::ExternalData::GO::GOAdaptor->new(
-group => "go",
-species => "multi",
-host => $host,
-user => $user,
-pass => $pass,
-port => $port,
-dbname => $go_db,
-no_cache => $no_cache
);
if ($verbose) {
printf( "%s loaded\n", $go_db );
}
}
} elsif ($verbose) {
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' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Pan_troglodytes",
-alias => \@aliases
);
@aliases = ( 'elegans', 'worm' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Caenorhabditis_elegans",
-alias => \@aliases
);
@aliases = ('tetraodon');
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tetraodon_nigroviridis",
-alias => \@aliases
);
@aliases = (
'H_Sapiens', 'homo sapiens', 'Homo_Sapiens', 'Homo',
'human', 'Hg17', 'ensHS', '9606'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Homo_sapiens",
-alias => \@aliases
);
@aliases = (
'M_Musculus', 'mus musculus', 'Mus_Musculus', 'Mus',
'mouse', 'Mm5', 'ensMM', '10090'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Mus_musculus",
-alias => \@aliases
);
@aliases = (
'R_Norvegicus', 'rattus norvegicus',
'Rattus_Norvegicus', 'Rattus',
'rat', 'Rn3',
'10116'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Rattus_norvegicus",
-alias => \@aliases
);
@aliases = ( 'T_Rubripes', 'Fugu', 'takifugu' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Takifugu_rubripes",
-alias => \@aliases
);
@aliases = ( 'G_Gallus', 'gallus gallus', 'Chicken', 'GalGal2' );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Gallus_Gallus",
-alias => \@aliases
);
@aliases = (
'D_Rerio', 'danio rerio', 'Danio_Rerio', 'Danio',
'zebrafish', 'zfish'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Danio_rerio",
-alias => \@aliases
);
@aliases = (
'X_Tropicalis', 'xenopus tropicalis',
'Xenopus_tropicalis', 'Xenopus'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Xenopus_tropicalis",
-alias => \@aliases
);
@aliases = (
'A_Gambiae', 'Anopheles Gambiae',
'Anopheles_gambiae', 'Anopheles',
'mosquito'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Anopheles_gambiae",
-alias => \@aliases
);
@aliases = (
'D_Melanogaster', 'drosophila melanogaster',
'Drosophila_melanogaster', 'drosophila',
'fly'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Drosophila_melanogaster",
-alias => \@aliases
);
@aliases = (
'S_Cerevisiae', 'Saccharomyces Cerevisiae',
'Saccharomyces_cerevisiae', 'Saccharomyces',
'yeast'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Saccharomyces_cerevisiae",
-alias => \@aliases
);
@aliases = (
'C_Familiaris', 'Canis Familiaris',
'Canis_familiaris', 'Canis',
'dog'
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Canis_familiaris",
-alias => \@aliases
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Ciona_intestinalis",
-alias => [ 'ciona', 'Ciona intestinalis' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Bos_taurus",
-alias => [ 'cow', 'bos_taurus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Macaca_mulatta",
-alias => [ 'rhesus', 'rhesus_monkey', 'macaque', 'macaca mulatta' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Otolemur_garnettii",
-alias => [ 'bushbaby', 'galago', 'Otolemur garnettii' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Oryctolagus_cuniculus",
-alias => [ 'rabbit', 'Oryctolagus cuniculus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Felis_catus",
-alias => [ 'cat', 'felis catus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Sus_scrofa",
-alias => [ 'pig', 'sus scrofa' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-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' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Myotis_lucifugus",
-alias => [ 'microbat', 'little_brown_bat' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Dasypus_novemcinctus",
-alias => [ 'armadillo', 'arma', 'Dasypus novemcinctu' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-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'
] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Monodelphis_domestica",
-alias => [ 'opossum', 'Monodelphis domestica' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Ornithorhynchus_anatinus",
-alias => [ 'platypus', 'Ornithorhynchus anatinus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Gasterosteus_aculeatus",
-alias => [ 'stickleback', 'Gasterosteus aculeatus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Oryzias_latipes",
-alias => [ 'medaka', 'Oryzias latipes' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Cavia_porcellus",
-alias => [ 'guinea_pig', '"Cavia porcellus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Aedes_aegypti",
-alias => [ 'aedes', 'Aedes aegypti' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Spermophilus_tridecemlineatus",
-alias => [ 'squirrel', 'Spermophilus tridecemlineatus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tupaia_belangeri",
-alias => [ 'tree_shrew', 'Tupaia belangeri' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Culex_pipiens",
-alias => [ 'culex', 'Culex Pipiens' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Ochotona_princeps",
-alias => [ 'pika', 'Ochotona princeps' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Anolis_carolinensis",
-alias => [ 'anolis', 'anolis_lizard', 'Anolis carolinensis' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Microcebus_murinus",
-alias => [ 'mouse_lemur', 'Microcebus murinus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Pongo_pygmaeus",
-alias => [ 'orang', 'orang_utan', 'orangutan', 'Pongo pygmaeus' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Equus_caballus",
-alias => [ 'horse', 'Equuscaballus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tursiops_truncatus",
-alias => [ 'dolphin', 'Tursiopstruncatus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Procavia_capensis",
-alias => [ 'rock_hyrax', 'hyrax', 'Procaviacapensis' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Dipodomys_ordii",
-alias => [ 'kangaroo_rat', 'Dipodomysordii' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Pteropus_vampyrus",
-alias => [ 'megabat', 'Pteropusvampyrus' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Tarsius_syrichta",
-alias => [ 'philippine tarsier', 'tarsier', 'Tarsiussyrichta' ]
);
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-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' ] );
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' ] );
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => "Macropus_eugenii",
-alias =>
[ 'wallaby', 'macropus', 'macropuseugenii' ] );
@aliases = ('compara');
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 => ['ontology'] );
# Register aliases as found in adaptor meta tables.
$self->find_and_add_aliases( '-handle' => $dbh );
$dbh->disconnect();
} ## end 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.
Arg [HANDLE] : (optional) DBI database handle
A connected database handle to use instead of the
database handles stored in the DBAdaptors. Bypasses
the use of MetaContainer.
Example : Bio::EnsEMBL::Registry->find_and_add_aliases(
-ADAPTOR => $dba,
-GROUP => 'core'
);
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. If no MetaContainer
can be returned from a given adaptor then no alias
searching is performed.
Return type : none
Exceptions : none
Status : Stable
=cut
sub find_and_add_aliases {
my $class = shift @_;
my ( $adaptor, $group, $dbh ) =
rearrange( [qw(ADAPTOR GROUP HANDLE)], @_ );
my @dbas;
if ( defined($adaptor) ) {
@dbas = ($adaptor);
} else {
@dbas = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) };
}
foreach my $dba (@dbas) {
my @aliases;
my $species = $dba->species();
if ( defined($dbh) ) {
my $dbname = $dba->dbc()->dbname();
my $sth = $dbh->prepare(
sprintf(
"SELECT meta_value FROM %s.meta "
. "WHERE meta_key = 'species.alias' "
. "AND species_id = ?",
$dbh->quote_identifier($dbname) ) );
# Execute, and don't care about errors (there will be errors for
# databases without a 'meta' table, such as ensembl_ontology_NN).
$sth->{'PrintError'} = 0;
$sth->{'RaiseError'} = 0;
if ( !$sth->execute( $dba->species_id() ) ) { next }
$sth->{'PrintError'} = $dbh->{'PrintError'};
$sth->{'RaiseError'} = $dbh->{'RaiseError'};
my $alias;
$sth->bind_columns( \$alias );
while ( $sth->fetch() ) {
push( @aliases, $alias );
}
} else {
my $meta_container = eval { $dba->get_MetaContainer() };
if ( defined($meta_container) ) {
@aliases =
@{ $meta_container->list_value_by_key('species.alias') };
}
# Need to disconnect so we do not spam the MySQL servers trying to
# get aliases. Can only call disonnect if dbc was defined.
if ( defined( $dba->dbc() ) ) {
$dba->dbc()->disconnect_if_idle();
}
}
foreach my $alias (@aliases) {
$class->add_alias( $species, $alias );
}
} ## end foreach my $dba (@dbas)
} ## end sub find_and_add_aliases
#
# Web specific routines
#
=head2 DEPRECATED load_registry_with_web_adaptors
DEPRECATED: Use load_registry_from_db instead.
=cut
sub load_registry_with_web_adaptors{
my $class = shift;
deprecate('Use the load_registry_from_db instead');
eval{ require SiteDefs };
if ($@){ die "Can't use SiteDefs.pm - $@\n"; }
SiteDefs->import(qw(:ALL));
eval{ require SpeciesDefs };
if ($@){ die "Can't use SpeciesDefs.pm - $@\n"; }
my $conf = new SpeciesDefs();
my %species_alias = %{$SiteDefs::ENSEMBL_SPECIES_ALIASES};
foreach my $spec (keys %species_alias){
Bio::EnsEMBL::Registry->add_alias($species_alias{$spec},$spec);
}
}
=head2 set_default_track
Sets a flag to say that that this species/group are a default track and do not
need to be added as another web track.
Arg [1] : name of the species to get the adaptors for in the registry.
Arg [2] : name of the type to get the adaptors for in the registry.
Example : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
Returntype : none
Exceptions : none
Status : At Risk.
=cut
sub set_default_track{
my ($class, $species, $group) = @_;
$species = get_alias($species);
$registry_register{'def_track'}{$species}{lc($group)} = 1;
}
=head2 default_track
Check flag to see if this is a default track
Arg [1] : name of the species to get the adaptors for in the registry.
Arg [2] : name of the type to get the adaptors for in the registry.
Example : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
Returntype : int
Exceptions : none
Status : At Risk.
=cut
sub default_track{
my ($class, $species, $group) = @_;
$species = get_alias($species);
if(defined($registry_register{'def_track'}{$species}{lc($group)})){
return 1;
}
return 0;
}
=head2 add_new_tracks
Will add new gene tracks to the configuration of the WEB server if they are
not of the type default and the configuration already has genes in the display.
Arg [1] : hash of the default configuration of the web page
Returntype : none
Exceptions : none
Called by : UserConfig.pm
Status : At Risk.
=cut
sub add_new_tracks{
my($class, $conf, $pos) = @_;
my $start = 0;
my $reg = $class;
my $species_reg = $reg->get_alias($conf->{'species'},"nothrow");
my %pars;
# print STDERR "Species $species_reg check for default tracks\n";
if(defined($species_reg)){
foreach my $dba (@{$reg->get_all_DBAdaptors()}){
if(!$reg->default_track($dba->species,$dba->group)){
$pars{'available'} = "species ".$reg->get_alias($dba->species());
$pars{'db_alias'} = $dba->group();
# print STDERR "Adding new track for ".$dba->species."\t".$dba->group."\n";
$conf->add_new_track_generictranscript('',$dba->group(), "black",$pos,%pars);
$pos++;
}
}
}
return $pos;
}
=head2 software_version
get the software version.
Args : none
ReturnType : int
Status : At Risk
=cut
sub software_version{
my ($self) = @_;
return $API_VERSION;
}
=head2 no_version_check
getter/setter for whether to run the version checking
Arg[0] : (optional) int
Returntype : int or undef if not set
Exceptions : none
Status : At Risk.
=cut
sub no_version_check {
my ($self, $arg ) = @_;
( defined $arg ) && ( $registry_register{'_no_version_check'} = $arg );
return $registry_register{'_no_version_check'};
}
=head2 version_check
run the database/API code version check for a DBAdaptor
Arg[0] : DBAdaptor to check
Returntype : int 1 if okay, 0 if not the same
Exceptions : none
Status : At Risk.
=cut
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 ) ) )
{
return 1;
}
my $mca =
$self->get_adaptor( $dba->species(), $dba->group(),
"MetaContainer" );
my $database_version = 0;
if ( defined($mca) ) {
$database_version = $mca->get_schema_version();
}
if ( $database_version == 0 ) {
# Try to work out the version
if ( $dba->dbc()->dbname() =~ /^_test_db_/ ) {
return 1;
}
if ( $dba->dbc()->dbname() =~ /(\d+)_\S+$/ ) {
$database_version = $1;
} elsif ( $dba->dbc()->dbname() =~ /ensembl_compara_(\d+)/ ) {
$database_version = $1;
} elsif ( $dba->dbc()->dbname() =~ /ensembl_go_(\d+)/ ) {
$database_version = $1;
} 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() ) );
}
} ## 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, $database_version
) );
return 0;
}
return 1; # Ok
} ## end sub version_check
=head2 get_species_and_object_type
get the species, ensembl type (Gene, Transcript , Translation or Exon)
and database type (core, vega, otherfeatures) for a given stable_id
Arg[1] : stable_id to find species and ensembl type for.
Arg[2] : (optional) integer. force searching of other databases that do not have a set format
for the stable_id by connecting to the databases and trying to retrieve each of the
ensembl object fetching using the stabke_id.
Example : my ($species, $type, $db_type) = Bio::EnsEMBL::Registry->get_species_and_object_type(ENST00000326632);
Returntype : array. consisting of the species name, ensembl type and database type (core,vega,otherfeatures). undef, undef, undef returned if not found
Exceptions : none
Status : At Risk.
=cut
#hashes containing codes of species and different database types to return
our %ensembl_type = qw(T Transcript G Gene P Translation E Exon);
our %ensembl_species = qw(
ENS Homo_sapiens
ENSRNO Rattus_norvegicus
ENSMUS Mus_musculus
ENSGAL Gallus_gallus
ENSBTA Bos_taurus
ENSDAR Danio_rerio
ENSCAF Canis_familiaris
ENSPTR Pan_troglodytes
ENSCPO Cavia_porcellus
ENSCIN Ciona_intestinalis
ENSCSAV Ciona_savignyi
ENSDNO Dasypus_novemcinctus
ENSETE Echinops_telfairi
ENSEEU Erinaceus_europaeus
ENSFCA Felis_catus
ENSGAC Gasterosteus_aculeatus
ENSLAF Loxodonta_africana
ENSMMU Macaca_mulatta
ENSMOD Monodelphis_domestica
ENSMLU Myotis_lucifugus
ENSOAN Ornithorhynchus_anatinus
ENSOCU Oryctolagus_cuniculus
ENSORL Oryzias_latipes
ENSSAR Otolemur_garnettii
ENSSTO Spermophilus_tridecemlineatus
ENSTBE Tupaia_belangeri
SINFRU Takifugu_rubripes
ENSXET Xenopus_tropicalis
ENSMEU Macropus_eugenii
);
our %vega_species = qw(
OTTHUM Homo_sapiens
OTTMUS Mus_musculus
);
our %ensembl_db_type = qw(EST otherfeatures);
our %vectorbase_species = qw(
AAEL Aedes_aegypti
AGAP Anopheles_gambiae
);
our %vectorbase_type = qw(R Transcript P Translation);
sub get_species_and_object_type{
my ($self, $stable_id, $force) = @_;
## Check for Ensembl/Vega style identifiers...
if( $stable_id =~ /(\w+?)(EST)?([GTPE])\d/ ) {
return $ensembl_species{$1},$ensembl_type{$3}, $ensembl_db_type{$2} ||'core' if $ensembl_species{$1};
return $vega_species{$1}, $ensembl_type{$3}, 'vega' if $vega_species{$1};
}
## Check for Vector base style identifiers
if( $stable_id =~ /^([A-Z]+)\d+-?(RP)?\w?/ && $vectorbase_species{$1} ) {
return $vectorbase_species{$1}, $vectorbase_type{$2}||'Gene','core';
}
if( $stable_id =~ /^([A-Z]+)?(\.e|E)\d+$/ && ($1 eq '' || $vectorbase_species{$1}) ) {
return $vectorbase_species{$1||'AGAP'}, 'Exon', 'core';
}
return unless defined($force) && $force;
## Finally if "force" is passed see if we can find a non-standard string...
foreach my $species (qw(saccharomyces_cerevisiae tetraodon_nigroviridis
drosophila_melanogaster caenorhabditis_elegans)){
foreach my $type (qw(Transcript Gene Translation Exon)){
my $adaptor = $self->get_adaptor($species, 'core', $type);
next unless defined($adaptor);
my $entity = $adaptor->fetch_by_stable_id($stable_id);
return ucfirst( $species ), $type,'core' if defined $entity;
}
}
return;
}
1;