Raw content of Bio::EnsEMBL::Utils::ConfigRegistry
<![CDATA[=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
/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::Utils::ConfigRegistry;
=head1 SYNOPSIS
Bio::EnsEMBL::Utils::ConfigRegistry->load_core($dba);
=head1 DESCRIPTION
The ConfigRegistry will "Register" a set of adaptors based on the type
of database that is being loaded.
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::ConfigRegistry;
use strict;
use warnings;
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::DBSQL::DBConnection;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(warning throw deprecate stack_trace_dump);
=head2 load_core, load_otherfeatures, load_vega, load_compara, load_pipeline, load_SNP, load_lite
Arg [1] : DBAdaptor with DBConnection alredy attached
Returntype : DBAdaptor;
Exceptions : none
=cut
#
# 1) core. no need to add dnadb
# 2) not core add dnadb
# 3)
#
sub gen_load{
my ($dba) = @_;
my $config_sub;
# at some point we hope to set the group in the DBadaptor
# hence this long check etc should be simpler
if($dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('compara');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_compara;
}
elsif($dba->isa('Bio::EnsEMBL::Lite::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('lite');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_lite;
}
elsif($dba->isa('Bio::EnsEMBL::External::BlastAdaptor')){
if(!defined($dba->group())){
$dba->group('blast');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_blast;
}
elsif($dba->isa('Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('SNP');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_SNP;
}
elsif($dba->isa('Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('pipeline');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_pipeline;
}
elsif($dba->isa('Bio::EnsEMBL::Hive::DBSQL::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('hive');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_hive;
}
elsif($dba->isa('Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('haplotype');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_haplotype;
}
elsif($dba->isa('Bio::EnsEMBL::Variation::DBSQL::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('variation');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_variation;
}
elsif($dba->isa('Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor')){
if(!defined($dba->group())){
$dba->group('funcgen');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen;
}
elsif ( $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) {
if ( !defined( $dba->group() ) ) {
$dba->group('ontology');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_ontology;
}
elsif($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
#vega uses the core DBAdaptor so test if vega is in the dbname
if(!defined($dba->group())){
$dba->group('core');
}
if($dba->group eq "estgene"){
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_estgene;
}
elsif($dba->group eq "otherfeatures"){
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_otherfeatures;
}
elsif($dba->group eq "vega"){
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_vega;
}
else{
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_core;
}
}
else{
# none standard DBA adaptor
if(!defined($dba->group())){
$dba->group('none_standard');
}
$config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_and_attach_dnadb_to_core;
# throw("Unknown DBAdaptor type $dba\n");
}
# return if the connection and species, group are the same
if(defined($dba->species)){
my $db_reg = $reg->get_DBAdaptor($dba->species,$dba->group);
if(defined($db_reg)){
if($dba->dbc->equals($db_reg->dbc)){
return $db_reg;
}
else{
warn "WARN: Species and group same for two seperate databases\nModify species name for one of these\n";
$dba->species(find_unique_species($dba->species,$dba->group));
}
}
}
else{ # no species
my @db_reg = @{$reg->get_all_DBAdaptors_by_connection($dba->dbc)};
foreach my $db_adaptor (@db_reg){
if($db_adaptor->group eq $dba->group){ # found same db connection and group
return $db_adaptor;
}
}
$dba->species(find_unique_species("DEFAULT",$dba->group));
if($dba->species ne "DEFAULT"){
warn "WARN: For multiple species use species attribute in DBAdaptor->new\n"
}
}
Bio::EnsEMBL::Registry->add_DBAdaptor($dba->species(), $dba->group(), $dba);
#call the loading subroutine. (add the adaptors to the DBAdaptor)
&{$config_sub}($dba);
return $dba;
}
sub find_unique_species {
my ( $species, $group ) = @_;
$reg->add_alias( $species, $species );
my $i = 0;
my $free = 0;
while ( !$free ) {
if ( $i == 0 ) {
if ( !defined( $reg->get_DBAdaptor( $species, $group ) ) ) {
$free = 1;
$i = "";
} else {
$i = 1;
}
} else {
# set needed self alias
$reg->add_alias( $species . $i, $species . $i );
if ( !defined( $reg->get_DBAdaptor( $species . $i, $group ) ) ) {
$free = 1;
} else {
$i++;
}
}
}
$species .= $i;
return ($species);
} ## end sub find_unique_species
sub load_adaptors {
my ($dba) = @_;
my %pairs = %{ $dba->get_available_adaptors() };
while ( my ( $key, $value ) = each(%pairs) ) {
Bio::EnsEMBL::Registry->add_adaptor( $dba->species(), $dba->group(),
$key, $value );
}
}
sub load_and_attach_dnadb_to_core {
my ($dba) = @_;
load_adaptors($dba);
$reg->add_DNAAdaptor( $dba->species(), $dba->group(), $dba->species(),
'core' );
}
sub load_core { load_adaptors(@_) }
sub load_compara { load_adaptors(@_) }
sub load_hive { load_adaptors(@_) }
sub load_pipeline { load_adaptors(@_) }
sub load_lite { load_adaptors(@_) }
sub load_SNP { load_adaptors(@_) }
sub load_variation { load_and_attach_dnadb_to_core(@_) }
sub load_funcgen { load_and_attach_dnadb_to_core(@_) }
sub load_haplotype { load_adaptors(@_) }
sub load_ontology { load_adaptors(@_) }
# these that need to attach to the core to get the sequense data
sub load_estgene { load_and_attach_dnadb_to_core(@_) }
sub load_otherfeatures { load_and_attach_dnadb_to_core(@_) }
sub load_vega { load_and_attach_dnadb_to_core(@_) }
sub add_alias {
my ( $class, @args ) = @_;
my ( $species, $aliases ) = rearrange( [qw(SPECIES ALIAS)], @args );
# Make sure it exists itself
Bio::EnsEMBL::Registry->add_alias( $species, $species );
if ( defined($aliases) ) {
foreach my $ali (@$aliases) {
Bio::EnsEMBL::Registry->add_alias( $species, $ali );
}
}
}
#
# overwrite/load new types. Done this way to enable no changes to CVS for
# external users. External users should add there own "GROUPS" in the file
# User_defined_load.
#
eval{ require Bio::EnsEMBL::Utils::User_defined_load };
1;
]]>