# # Ensembl module for Registry # # Copyright EMBL/EBI ## # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::EnsEMBL::Registry =head1 SYNOPSIS Bio::EnsEMBL::Registry->load_all("configuration_file"); $gene_adaptor = Bio::EnsEMBL::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 CONTACT Post questions to the Ensembl developer list: =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 = 51; =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 db connection will not be cleared, if 0 or if not set the db connections will be cleared (this is the default). 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 ) = @_; $config_file ||= $ENV{ENSEMBL_REGISTRY} || $ENV{HOME} . "/.ensembl_init"; $verbose ||= 0; $no_clear ||= 0; if ( !defined($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 ) { # This is a map from group names to Ensembl DB adaptors. 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' ); 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, $parameter ); } if ($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 @ret; my ($species, $group) = rearrange([qw(SPECIES GROUP)], @args); if(defined($species)){ $species = $class->get_alias($species); } 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, $dba; } } } return \@ret; } =head2 get_all_DBAdaptors_by_connection Arg [1] :dbconnection to use to find DBAdaptors Returntype : reference to list of DBAdaptors Exceptions : none. Example : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors_by_connection($dbc); Status : Stable =cut sub get_all_DBAdaptors_by_connection{ my ($self, $dbc_orig) = @_; my @return; foreach my $dba ( @{$registry_register{'_DBA'}}){ my $dbc = $dba->dbc; if($dbc && $dbc->can('equals') && $dbc->equals($dbc_orig)){ 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); 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 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) = @_; # 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'); } # 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 $current_db = $self->get_DBAdaptor($alias, $group); if(! defined $current_db){ throw("There is not current registry DB for:\t${alias}\t${group}"); } $host ||= $current_db->dbc->host; $port ||= $current_db->dbc->port; $user ||= $current_db->dbc->username; $pass ||= $current_db->dbc->password; my $class = ref($current_db); $self->remove_DBAdaptor($alias, $group); my @adaptors = @{$self->get_all_adaptors}; # ConfigRegistry should automatically add this to the Registry my $db = $class->new( -user => $user, -host => $host, -port => $port, -pass => $pass, -dbname => $dbname, -species => $alias, -group => $group, ); return $db; } # # DNA Adaptors # =head2 add_DNAAdaptor Arg [1] : name of the species to add the adaptor to in the registry. Arg [2] : name of the group to add the adaptor to in the registry. Arg [3] : name of the species to get the dna from Arg [4] : name of the group to get the dna from Example : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "estgene", "Human", "core"); Returntype : none Exceptions : none Status : Stable =cut sub add_DNAAdaptor{ my ($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); } else { 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 = qw(sequence 1 assemblymapper 1 karyotypeband 1 repeatfeature 1 coordsystem 1 assemblyexceptionfeature 1 ); 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)){ # 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 $ret; } =head2 get_all_adaptors Arg [SPECIES] : (optional) string species name to get adaptors for Arg [GROUP] : (optional) string group name to get adaptors for Arg [TYPE] : (optional) string type to get adaptors for Example : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()}; Returntype : ref to list of adaptors Exceptions : none Status : Stable =cut sub get_all_adaptors{ my ($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 $url Example : load_registry_from_url("mysql://anonymous@ensembldb.ensembl.org:3306"); Description: Will load the correct versions of the ensembl databases for the software release it can find on a database instance into the registry. Also adds a set of standard aliases. The url format is: mysql://[[username][:password]@]hostname[:port]. You can also request a specific version for the databases by adding a slash and the version number but your script may crash as the API version won't match the DB version. Exceptions : None. Status : Stable =cut sub load_registry_from_url { my ($self, $url, $verbose) = @_; if ($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); } else { throw("Only MySQL URLs are accepted at the moment"); } } =head2 load_registry_from_db Arg [HOST] : 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] : int The port to use when connecting to the database Arg [VERBOSE]: (optional) Wether to print database messages Arg [DB_VERSION]: (optional) 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. 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 ) = rearrange( [qw(HOST PORT USER PASS VERBOSE DB_VERSION WAIT_TIMEOUT )], @args ); my $go_version = 0; my $compara_version =0; my $ancestral_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 =~ /^([a-z]+)_collection_core_(\w+)/ ) { # NEEDS TO BE FIRST if ( $2 eq $software_version ) { $temp{$1} = 'collection_core_' . $2; } } elsif ( $db =~ /^([a-z]+_[a-z]+_[a-z]+)_(\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_ancestral_(\d+)/ ) { if ( $1 eq $software_version ) { $ancestral_version = $1; } } elsif ( $db =~ /^ensembl_go_(\d+)/ ) { if ( $1 eq $software_version ) { $go_version = $1; } } } ## 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+_/ } @dbnames; foreach my $coredb (@core_dbs) { next if ($coredb =~ /collection/); # Skip multi-species databases my ( $species, $num ) = ( $coredb =~ /(^[a-z]+_[a-z]+)_core_(\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 ); ( my $sp = $species ) =~ s/_/ /g; $self->add_alias( $species, $sp ); if ($verbose) { printf( "Species '%s' loaded from database '%s'\n", $species, $coredb ); } } # Register multi-species databases my @multi_dbs = grep { /^[a-z]+_collection_core_\w+$/ } @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, -host => $host, -user => $user, -pass => $pass, -port => $port, -dbname => $multidb, -wait_timeout => $wait_timeout ); ( 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+_/ } @dbnames; for my $cdnadb (@cdna_dbs) { my ( $species, $num ) = ( $cdnadb =~ /(^[a-z]+_[a-z]+)_cdna_(\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 ); ( my $sp = $species ) =~ s/_/ /g; $self->add_alias( $species, $sp ); print $cdnadb. " loaded\n" if ($verbose); } 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 ); ( my $sp = $species ) =~ s/_/ /g; $self->add_alias( $species, $sp ); print $vegadb. " loaded\n" if ($verbose); } # Otherfeatures my @other_dbs = grep { /^[a-z]+_[a-z]+_otherfeatures_\d+_/ } @dbnames; for my $other_db (@other_dbs) { my ( $species, $num ) = ( $other_db =~ /(^[a-z]+_[a-z]+)_otherfeatures_(\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 ); ( my $sp = $species ) =~ s/_/ /g; $self->add_alias( $species, $sp ); print $other_db. " loaded\n" if ($verbose); } # 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 ); (my $sp = $species ) =~ s/_/ /g; $self->add_alias( $species, $sp ); print $userupload_db." loaded\n" if ($verbose); } # Variation eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor"; if ($@) { # Ignore variations as code required not there for this print "Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation databases will be ignored if found\n" if ($verbose); } else { my @variation_dbs = grep { /^[a-z]+_[a-z]+_variation_\d+_/ } @dbnames; for my $variation_db (@variation_dbs) { my ( $species, $num ) = ( $variation_db =~ /(^[a-z]+_[a-z]+)_variation_(\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 ); print $variation_db. " loaded\n" if ($verbose); } } eval "require Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor"; if ($@) { #ignore funcgen DBs as code required not there for this print "Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor module not found so functional genomics databases will be ignored if found\n" if ($verbose); } else { my @funcgen_dbs = grep { /^[a-z]+_[a-z]+_funcgen_\d+_/ } @dbnames; for my $funcgen_db (@funcgen_dbs) { my ( $species, $num ) = ( $funcgen_db =~ /(^[a-z]+_[a-z]+)_funcgen_(\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 ); print $funcgen_db. " loaded\n" if ($verbose); } } # Compara if ($compara_version) { eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor"; if ($@) { # 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 ); } } 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 => $compara_db ); if ($verbose) { printf( "%s loaded\n", $compara_db ); } } } elsif ($verbose) { print("No Compara database 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 ); print $ancestral_db. " loaded\n" if ($verbose); } else { print "No Ancestral database found" if ($verbose); } # GO if ($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 ensemb_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 ); print $go_db. " loaded\n" if ($verbose); } } elsif ($verbose) { print("No GO 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' ] ); @aliases = ('compara'); Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => "multi", -alias => \@aliases ); @aliases = ('go'); Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => "multi", -alias => \@aliases ); } ## end sub load_registry_from_db # # 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 = $1; } else{ warn("No database version for database ".$dba->dbc->dbname().". You must be using a pre version 34 database with version 34 or later code. You need to update your database or use the appropriate ensembl software release to ensure your script does not crash\n"); } } if($database_version != $API_VERSION){ warn("For ".$dba->dbc->dbname()." there is a difference in the software release (".$API_VERSION.") and the database release (".$database_version."). You should change one of these to ensure your script does not crash.\n"); return 0; } else { return 1; } } =head2 get_species_and_object_type get the species and ensembl type (Gene, Transcript or Translation) 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, $type) = Bio::EnsEMBL::Registry->get_species_and_object_type(ENST00000326632); Returntype : array. consisting of the species name and ensembl type. undef, undef returned if not found Exceptions : none Status : At Risk. =cut sub get_species_and_object_type{ my ($self, $stable_id, $force) = @_; my %type; $type{T} = "transcript"; $type{G} = "gene"; $type{P} = "translation"; # Do each in turn in order of the usual suspects. This should increase speed on average. if($stable_id =~ /^ENS([GTP])000/){ # HUMAN NOTE 000 needed else other species will match return "Homo_sapiens", $type{$1}; } elsif($stable_id =~ /^ENSRNO([GTP])/){ #RAT return "Rattus_norvegicus", $type{$1}; } elsif($stable_id =~ /^ENSMUS([GTP])/){ #MOUSE return "Mus_musculus", $type{$1}; } elsif($stable_id =~ /^ENSGAL([GTP])/){ #CHICKEN return "Gallus_gallus", $type{$1}; } elsif($stable_id =~ /^ENSBTA([GTP])/){ #COW return "Bos_taurus", $type{$1}; } elsif($stable_id =~ /^ENSDAR([GTP])/){ #ZEBRAFISH return "Danio_rerio", $type{$1}; } elsif($stable_id =~ /^ENSCAF([GTP])/){ #DOG return "Canis_familiaris", $type{$1}; } elsif($stable_id =~ /^ENSPTR([GTP])/){ #CHIMP return "Pan_troglodytes", $type{$1}; } # Rest done alphabetically elsif($stable_id =~ /^AAEL/){ # if($stable_id =~ /-R\w$/){ return "aedes_aegypti", "Transcript"; } elsif($stable_id =~ /-P\w$/){ return "Aedes_aegypti", "Translation"; } return "Aedes_aegypti", "Gene"; } elsif($stable_id =~ /^AGAP/){ # if($stable_id =~ /-R\w$/){ return "Anopheles_gambiae", "Transcript"; } elsif($stable_id =~ /-P\w$/){ return "Anopheles_gambiae", "Translation"; } return "Anopheles_gambiae", "Gene"; } elsif($stable_id =~ /ENSCPO([GTP])/){ # return "Cavia_porcellus", $type{$1}; } elsif($stable_id =~ /ENSCIN([GTP])/){ # return "Ciona_intestinalis", $type{$1}; } elsif($stable_id =~ /ENSCSAV([GTP])/){ # return "Ciona_savignyi", $type{$1}; } elsif($stable_id =~ /ENSDNO([GTP])/){ # return "Dasypus_novemcinctus", $type{$1}; } elsif($stable_id =~ /ENSETE([GTP])/){ # return "Echinops_telfairi", $type{$1}; } elsif($stable_id =~ /ENSEEU([GTP])/){ # return "Erinaceus_europaeus", $type{$1}; } elsif($stable_id =~ /ENSFCA([GTP])/){ # return "Felis_catus", $type{$1}; } elsif($stable_id =~ /ENSGAC([GTP])/){ # return "Gasterosteus_aculeatus", $type{$1}; } elsif($stable_id =~ /ENSLAF([GTP])/){ # return "Loxodonta_africana", $type{$1}; } elsif($stable_id =~ /ENSMMU([GTP])/){ # return "Macaca_mulatta", $type{$1}; } elsif($stable_id =~ /ENSMOD([GTP])/){ # return "Monodelphis_domestica", $type{$1}; } elsif($stable_id =~ /ENSMLU([GTP])/){ # return "Myotis_lucifugus", $type{$1}; } elsif($stable_id =~ /ENSOAN([GTP])/){ # return "Ornithorhynchus_anatinus", $type{$1}; } elsif($stable_id =~ /ENSOCU([GTP])/){ # return "Oryctolagus_cuniculus", $type{$1}; } elsif($stable_id =~ /ENSORL([GTP])/){ # return "Oryzias_latipes", $type{$1}; } elsif($stable_id =~ /ENSSAR([GTP])/){ # return "Otolemur_garnettii", $type{$1}; } elsif($stable_id =~ /ENSSTO([GTP])/){ # return "Spermophilus_tridecemlineatus", $type{$1}; } elsif($stable_id =~ /ENSTBE([GTP])/){ # return "Tupaia_belangeri", $type{$1}; } elsif($stable_id =~ /SINFRU([GTP])/){ # return "Takifugu_rubripes", $type{$1}; } elsif($stable_id =~ /ENSXET([GTP])/){ # return "Xenopus_tropicalis", $type{$1}; } elsif(defined($force) and $force){ #have to try and find the ones for species with no recognisable pattern foreach my $species (qw(saccharomyces_cerevisiae tetraodon_nigroviridis drosophila_melanogaster caenorhabditis_elegans)){ foreach my $type (qw(Transcript Gene Translation)){ my $adaptor = $self->get_adaptor($species, "core", $type); if(defined($adaptor)){ my $entity = $adaptor->fetch_by_stable_id($stable_id); if(defined($entity)){ return $species, $type; } } } } } return undef,undef; } 1;