view variant_effect_predictor/Bio/EnsEMBL/Utils/ConfigRegistry.pm @ 0:1f6dce3d34e0

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=head1 LICENSE

  Copyright (c) 1999-2012 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 <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=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);



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' || $dba->group eq 'vega_update' ) {
      $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, $dba->group, 1 );
    if ( defined($db_reg) ) {
      if ( $dba->dbc->equals( $db_reg->dbc ) ) { return $db_reg }
      else {
        my $msg =
          sprintf( 'WARN: Species (%s) and group (%s) '
            . 'same for two seperate databases',
          $dba->species(), $dba->group() );

        warn "${msg}\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;
} ## end sub gen_load



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' );
}


=head2 load_core
  Arg [1]    : DBAdaptor with DBConnection already attached
  Returntype : DBAdaptor
  Exceptions : none
=cut
sub load_core      { load_adaptors(@_) }


#
# 1) core. no need to add dnadb
# 2) not core add dnadb
# 3) 
#

=head2 load_compara
  Arg [1]    : DBAdaptor with DBConnection already attached
  Returntype : DBAdaptor
  Exceptions : none
=cut
sub load_compara   { load_adaptors(@_) }

=head2 load_hive
  Arg [1]    : DBAdaptor with DBConnection already attached
  Returntype : DBAdaptor
  Exceptions : none
=cut
sub load_hive      { load_adaptors(@_) }

=head2 load_pipeline
  Arg [1]    : DBAdaptor with DBConnection already attached
  Returntype : DBAdaptor
  Exceptions : none
=cut
sub load_pipeline  { load_adaptors(@_) }

=head2 load_SNP
  Arg [1]    : DBAdaptor with DBConnection already attached
  Returntype : DBAdaptor
  Exceptions : none
=cut
sub load_SNP       { load_adaptors(@_) }

sub load_haplotype { load_adaptors(@_) }

sub load_ontology  { load_adaptors(@_) }


# these that need to attach to the core to get the sequence data

sub load_estgene       { load_and_attach_dnadb_to_core(@_) }

sub load_variation { load_and_attach_dnadb_to_core(@_) }

sub load_funcgen   { load_and_attach_dnadb_to_core(@_) }

=head2 load_otherfeatures
  Arg [1]    : DBAdaptor with DBConnection alredy attached
  Returntype : DBAdaptor
  Exceptions : none

=cut
sub load_otherfeatures { load_and_attach_dnadb_to_core(@_) }

=head2 load_vega
  Arg [1]    : DBAdaptor with DBConnection already attached
  Returntype : DBAdaptor
  Exceptions : none
=cut
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;