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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Utils/ConfigRegistry.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,337 @@
+=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;