=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] EMBL-European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =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 environment 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 warnings; our $NEW_EVAL = 0; use Bio::EnsEMBL::DBSQL::DBAdaptor; use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor; use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning ); use Bio::EnsEMBL::Utils::Argument qw(rearrange); use Bio::EnsEMBL::Utils::ConfigRegistry; use Bio::EnsEMBL::ApiVersion; use Bio::EnsEMBL::Utils::URI qw/parse_uri/; use DBI qw(:sql_types); use Scalar::Util qw/blessed/; use vars qw(%registry_register); # This is a map from group names to Ensembl DB adaptors. Used by # load_all() and reset_DBAdaptor(). my %group2adaptor = ( 'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor', 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'estgene' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'funcgen' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor', 'gene2phenotype' => 'Bio::EnsEMBL::G2P::DBSQL::DBAdaptor', 'regulation' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor', 'hive' => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor', 'metadata' => 'Bio::EnsEMBL::MetaData::DBSQL::MetaDataDBAdaptor', 'ontology' => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor', 'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'pipeline' => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor', 'production' => 'Bio::EnsEMBL::Production::DBSQL::DBAdaptor', 'stable_ids' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'taxonomy' => 'Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyDBAdaptor', 'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor', 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'vega_update' => '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 environment 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 the developer mailing list. Arg [5]: (optional) boolean This option will make load_all() throw if the configuration file is missing and cannot be guessed from the environment Example : Bio::EnsEMBL::Registry->load_all(); Returntype : Int count of the DBAdaptor instances which can be found in the registry due to this method being called. Will never be negative Exceptions : Throws if $throw_if_missing is set and ($config_file is missing and cannot be guessed from the environment Status : Stable =cut sub load_all { my ($class, $config_file, $verbose, $no_clear, $no_cache, $throw_if_missing ) = @_; if ( !defined($config_file) ) { if ( defined( $ENV{ENSEMBL_REGISTRY} ) ) { if (-e $ENV{ENSEMBL_REGISTRY}) { $config_file = $ENV{ENSEMBL_REGISTRY}; } else { warning("\$ENV{ENSEMBL_REGISTRY} points to a file ('$ENV{ENSEMBL_REGISTRY}') that does not exist.\n"); } } elsif ( defined( $ENV{HOME} ) ) { if (-e ($ENV{HOME} . "/.ensembl_init")) { $config_file = $ENV{HOME} . "/.ensembl_init"; } } if ($throw_if_missing and !defined($config_file) ) { throw("No registry configuration to load, and no default could be guessed.\n"); } } elsif ($throw_if_missing and !(-e $config_file)) { throw(printf("Configuration file '%s' does not exist. Registry configuration not loaded.\n", $config_file )); } $verbose ||= 0; $no_clear ||= 0; $no_cache ||= 0; my $original_count = $class->get_DBAdaptor_count(); if ( !defined($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; my $test_eval = eval { require Config::IniFiles }; if ($@ or (!$test_eval)) { # The user does not have the 'Config::IniFiles' module. if ($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 ); } my $test_eval = eval "require $adaptor"; ## no critic if ($@ or (!$test_eval)) { die($@) } $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. my $test_eval; if($NEW_EVAL) { require Bio::EnsEMBL::Utils::IO; my $contents = Bio::EnsEMBL::Utils::IO::slurp($config_file); $test_eval = eval $contents; ## no critic } else { $test_eval = eval { require($config_file) }; # To make the web code avoid doing this again we delete first delete $INC{$config_file}; } #Now raise the exception just in case something above is #catching this if ($@ or (!$test_eval)) { die($@) } } } ## end else [ if ( !defined($config_file... my $count = $class->get_DBAdaptor_count() - $original_count; return $count >= 0 ? $count : 0; } ## end sub load_all =head2 clear Will clear the registry and disconnect from all databases. Example : Bio::EnsEMBL::Registry->clear(); Returntype : none Exceptions : none Status : Stable =cut sub clear{ my ($self); foreach my $dba (@{$registry_register{'_DBA'}}){ if($dba->dbc->connected){ $dba->dbc->db_handle->disconnect(); } } %registry_register = (); return; } # # db adaptors. (for backwards compatibility) # =head2 add_db Arg [1] : db (DBAdaptor) to add adaptor to. Arg [2] : name of the name to add the adaptor to in the registry. Arg [3] : The adaptor to be added to the registry. Example : Bio::EnsEMBL::Registry->add_db($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 ) = @_; #No warnings brought in due to some overzelous webcode triggering a lot of warnings. no warnings 'uninitialized'; if ( lc( $db->species() ) ne lc( $adap->species ) ) { $registry_register{_SPECIES}{ lc( $db->species() ) } { lc( $db->group() ) }{'_special'}{ lc($name) } = $adap; } return; } =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{_SPECIES}{ lc( $db->species() ) } { lc( $db->group() ) }{'_special'}{ lc($name) }; $registry_register{_SPECIES}{ 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 : See get_DBAdaptor() 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{_SPECIES}{ 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{_SPECIES} { $class->get_alias( $db->species() ) }{ lc( $db->group() ) } {'_special'} } ) { $ret{$key} = $registry_register{_SPECIES} { $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] : DBAdaptor 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, $adap ) = @_; if ( !defined($species) ) { throw('Species not defined.'); } if ( !( $class->alias_exists($species) ) ) { $class->add_alias( $species, $species ); } $species = $class->get_alias($species); $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'} = $adap; if ( !defined( $registry_register{'_DBA'} ) ) { $registry_register{'_DBA'} = [$adap]; } else { push( @{ $registry_register{'_DBA'} }, $adap ); } return; } =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. Arg [3] : if set will not give warnings when looking for alias. Example : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core"); Returntype : DBAdaptor Exceptions : If $species is not defined and if no valid internal name could be found for $species. If thrown check your API and DB version Status : Stable =cut sub get_DBAdaptor { my ( $class, $species, $group, $no_alias_check ) = @_; if ( !defined($species) ) { throw('Species not defined.'); } my $ispecies = $class->get_alias( $species, $no_alias_check ); if ($group eq 'regulation') { $group = 'funcgen'; } if ( !defined($ispecies) ) { if(! $no_alias_check) { throw("Can not find internal name for species '$species'"); } } else { $species = $ispecies } return $registry_register{_SPECIES}{$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) && !defined($group) ) { return $registry_register{'_DBA'} || []; } if ( defined($species) ) { $species = $class->get_alias($species); return [] unless $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 $registry_register{_SPECIES}{$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 = $i; last; } } # Now remove from _DBA cache if ( defined($index) ) { splice( @{ $registry_register{'_DBA'} }, $index, 1 ); } return; } ## end sub remove_DBAdaptor =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 ); # 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 { $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA'} = $dnadb_group; $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA2'} = $dnadb_species; } return; } =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 = $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA'}; my $new_species = $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA2'}; if ( defined $new_group ) { return $class->get_DBAdaptor( $new_species, $new_group ); } return; } # # 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 DBAdaptor to be added to the registry. Arg [5] : (optional) Set to allow overwrites of existing adaptors. 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); my $lc_group = lc($group); my $lc_type = lc($type); # 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 RESET THE HASH VALUE NO MORE PROCESSING NEEDED $registry_register{_SPECIES}{$species}{ $lc_group }{ $lc_type } = $adap; return; } if ( defined( $registry_register{_SPECIES}{$species}{ $lc_group }{ $lc_type } ) ) { # print STDERR ( # "Overwriting Adaptor in Registry for $species $group $type\n"); $registry_register{_SPECIES}{$species}{ $lc_group }{ $lc_type } = $adap; return; } $registry_register{_SPECIES}{$species}{ $lc_group }{ $lc_type } = $adap; if ( !defined( $registry_register{_SPECIES}{$species}{'list'} ) ) { $registry_register{_SPECIES}{$species}{'list'} = [$type]; } else { push( @{ $registry_register{_SPECIES}{$species}{'list'} }, $type ); } return; } ## end sub add_adaptor =head2 add_switchable_adaptor Arg [1] : String name of the species to add its switchable adaptor into the registry Arg [2] : String name of the group to add its switchable adaptor into the registry Arg [3] : String name of the type to add its switchable adaptor into the registry Arg [4] : Reference switchable adaptor to insert Arg [5] : Boolean override any existing switchable adaptor Example : Bio::EnsEMBL::Registry->add_switchable_adaptor("Human", "core", "Gene", $my_other_source); Returntype : None Exceptions : Thrown if a valid internal name cannot be found for the given name. If thrown check your API and DB version. Also thrown if no type, group or switchable adaptor instance was given =cut sub add_switchable_adaptor { my ($class, $species, $group, $adaptor_type, $instance, $override) = @_; my $ispecies = $class->get_alias($species); throw "Cannot decode given species ${species} to an internal registry name" if ! $species; throw "No group given" if ! $group; throw "No adaptor type given" if ! $adaptor_type; throw "No switchable adaptor given" if ! $instance; throw "Switchable adaptor was not a blessed reference" if ! blessed($instance); $group = lc($group); $adaptor_type = lc($adaptor_type); if($override) { $registry_register{_SWITCHABLE}{$species}{$group}{$adaptor_type} = $instance; return; } if(exists $registry_register{_SWITCHABLE}{$species}{$group}{$adaptor_type}) { my $existing_ref = ref($registry_register{_SWITCHABLE}{$species}{$group}{$adaptor_type}); throw "Cannot switch adaptors for ${species}, ${group} and ${adaptor_type} because one is already set ($existing_ref). Use the override flag or revert_switchable_adaptor"; } $registry_register{_SWITCHABLE}{$species}{$group}{$adaptor_type} = $instance; return; } =head2 has_switchable_adaptor Arg [1] : String name of the species to add its switchable adaptor into the registry Arg [2] : String name of the group to add its switchable adaptor into the registry Arg [3] : String name of the type to add its switchable adaptor into the registry Example : Bio::EnsEMBL::Registry->has_switchable_adaptor("Human", "core", "Gene"); Returntype : Boolean indicating if a switchable adaptor is available for your submitted combination Exceptions : Thrown if a valid internal name cannot be found for the given name. If thrown check your API and DB version. Also thrown if no type, group or switchable adaptor instance was given =cut sub has_switchable_adaptor { my ($class, $species, $group, $adaptor_type) = @_; my $ispecies = $class->get_alias($species); throw "Cannot decode given species ${species} to an internal registry name" if ! $species; throw "No group given" if ! $group; throw "No adaptor type given" if ! $adaptor_type; $group = lc($group); $adaptor_type = lc($adaptor_type); return (defined $registry_register{_SWITCHABLE}{$species}{$group}{$adaptor_type}) ? 1 : 0; } =head2 remove_switchable_adaptor Arg [1] : name of the species to remove its switchable adaptor from the registry Arg [2] : name of the group to remove its switchable adaptor from the registry Arg [3] : name of the type to remove its switchable adaptor from the registry Example : $adap = Bio::EnsEMBL::Registry->remove_switchable_adaptor("Human", "core", "Gene"); Returntype : The removed adaptor if one was removed. Otherwise undef Exceptions : Thrown if a valid internal name cannot be found for the given name. If thrown check your API and DB version. Also thrown if no type or group was given =cut sub remove_switchable_adaptor { my ($class, $species, $group, $adaptor_type) = @_; my $ispecies = $class->get_alias($species); throw "Cannot decode given species ${species} to an internal registry name" if ! $species; throw "No group given" if ! $group; throw "No adaptor type given" if ! $adaptor_type; $group = lc($group); $adaptor_type = lc($adaptor_type); if(defined $registry_register{_SWITCHABLE}{$ispecies}{$group}{$adaptor_type}) { my $adaptor = $registry_register{_SWITCHABLE}{$ispecies}{$group}{$adaptor_type}; delete $registry_register{_SWITCHABLE}{$ispecies}{$group}{$adaptor_type}; return $adaptor; } return; } =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"); Description : Finds and returns the specified adaptor. This method will also check if the species, group and adaptor combination satisfy a DNADB condition (and will return that DNADB's implementation). Also we check for any available switchable adaptors and will return that if available. Returntype : adaptor Exceptions : Thrown if a valid internal name cannot be found for the given name. If thrown check your API and DB version. Also thrown if no type or group was given Status : Stable =cut sub get_adaptor { my ( $class, $species, $group, $type ) = @_; my $ispecies = $class->get_alias($species); if ( !defined($ispecies) ) { throw("Can not find internal name for species '$species'"); } else { $species = $ispecies } throw 'No adaptor group given' if ! defined $group; throw 'No adaptor type given' if ! defined $type; $group = lc($group); my $lc_type = lc($type); if($type =~ /Adaptor$/i) { warning("Detected additional Adaptor string in given the type '$type'. Removing it to avoid possible issues. Alter your type to stop this message"); $type =~ s/Adaptor$//i; } # For historical reasons, allow use of group 'regulation' to refer to # group 'funcgen'. if ( $group eq 'regulation' ) { $group = 'funcgen' } my %dnadb_adaptors = ( 'sequence' => 1, 'assemblymapper' => 1, 'karyotypeband' => 1, 'repeatfeature' => 1, 'coordsystem' => 1, 'assemblyexceptionfeature' => 1 ); #Before looking for DNA adaptors we need to see if we have a switchable adaptor since they take preference if(defined $registry_register{_SWITCHABLE}{$species}{$group}{$lc_type}) { return $registry_register{_SWITCHABLE}{$species}{$group}{$lc_type}; } # Look for a possible DNADB group alongside the species hash my $dnadb_group = $registry_register{_SPECIES}{$species}{ $group }{'_DNA'}; # If we found one & this is an adaptor we should be replaced by a DNADB then # look up the species to use and replace the current group with the DNADB group # (groups are held in _DNA, species are in _DNA2) if ( defined($dnadb_group) && defined( $dnadb_adaptors{ $lc_type } ) ) { $species = $registry_register{_SPECIES}{$species}{ $group }{'_DNA2'}; $group = $dnadb_group; # Once we have switched to the possibility of a DNADB call now check again for # a switchable adaptor if(defined $registry_register{_SWITCHABLE}{$species}{$group}{$lc_type}) { return $registry_register{_SWITCHABLE}{$species}{$group}{$lc_type}; } } # No switchable adaptor? Ok then continue with the normal logic my $ret = $registry_register{_SPECIES}{$species}{ $group }{ $lc_type }; if ( !defined($ret) ) { return } if ( ref($ret) ) { return $ret } # Not instantiated yet my $dba = $registry_register{_SPECIES}{$species}{ $group }{'_DB'}; my $module = $ret; my $test_eval = eval "require $module"; ## no critic if ($@ or (!$test_eval)) { warning("'$module' cannot be found.\nException $@\n"); return; } if ( !defined( $registry_register{_SPECIES}{$species}{ $group }{'CHECKED'} ) ) { $registry_register{_SPECIES}{$species}{ $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{_SPECIES}{ 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($species); return; } =head2 remove_alias Arg [1] : name of the species to remove alias for Arg [2] : name of the alias Example : Bio::EnsEMBL::Registry->remove_alias("Homo Sapiens","Human"); Description: remove alternative name for the species. Returntype : none Exceptions : none Status : Stable =cut sub remove_alias{ my ($class, $species,$key) = @_; delete $registry_register{'_ALIAS'}{lc($key)}; return; } =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, $no_warn ) = @_; if ( !defined( $registry_register{'_ALIAS'}{ lc($key) } ) ) { if ( ( !defined( $registry_register{_SPECIES}{ lc($key) } ) ) and ( !defined( $registry_register{_ALIAS}{ lc($key) } ) ) ) { if ( ( !defined($no_warn) ) or ( !$no_warn ) ) { warning( "$key is not a valid species name " . "(check DB and API version)" ); } return; } else { return $key } } return $registry_register{'_ALIAS'}{ lc($key) }; } =head2 get_all_aliases Arg [1] : Species name to retrieve aliases for (may be an alias as well). Example : Bio::EnsEMBL::Registry->get_all_aliases('Homo sapiens'); Description: Returns all known aliases for a given species (but not the species name/alias that was given). Returntype : ArrayRef of all known aliases Exceptions : none Status : Development =cut sub get_all_aliases { my ( $class, $key ) = @_; my $species = $registry_register{_ALIAS}{ lc($key) }; my @aliases; if ( defined($species) ) { foreach my $alias ( keys( %{ $registry_register{_ALIAS} } ) ) { if ( $species ne $alias && $species eq $registry_register{_ALIAS}{ lc($alias) } ) { push( @aliases, $alias ); } } } return \@aliases; } =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 ) = @_; return defined( $registry_register{'_ALIAS'}{ lc($key) } ); } =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); } return; } =head2 set_reconnect_when_lost Example : Bio::EnsEMBL::Registry->set_reconnect_when_lost(); Description: Set the flag to make sure that the database connection is not lost before it's used. This is useful for long running jobs (over 8hrs). Returntype : none Exceptions : none Status : Stable =cut sub set_reconnect_when_lost{ foreach my $dba ( @{get_all_DBAdaptors()}){ my $dbc = $dba->dbc; $dbc->reconnect_when_lost(1); } return; } =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 $dbc->connected(); } return; } =head get_DBAdaptor_count Example : Bio::EnsEMBL::Registry->get_DBAdaptor_count(); Description : Returns the count of database adaptors currently held by the registry Returntype : Int count of database adaptors currently known Exceptions : None =cut sub get_DBAdaptor_count { return scalar(@{$registry_register{'_DBA'}}) if(defined $registry_register{'_DBA'}); return 0; } =head2 change_access Will change the username and password for a set of databases. if host,user or database names are missing then these are not checked. So for example if you do not specify a database then ALL databases on the specified host and port will be changed. Arg [1] : name of the host to change access on Arg [2] : port number to change access on Arg [3] : name of the user to change access on Arg [4] : name of the database to change access on Arg [5] : name of the new user Arg [6] : new password Example : Bio::EnsEMBL::Registry->get_alias("Human"); Description: change username and password on one or more databases Returntype : none Exceptions : none Status : Stable =cut sub change_access{ my ($self, $host,$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); } } return; } =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 the developer mailing list. Example : load_registry_from_url( 'mysql://anonymous@ensembldb.ensembl.org:3306'); load_registry_from_url( 'mysql://anonymous@ensembldb.ensembl.org:3306/homo_sapiens_core_65_37?group=core&species=homo_sapiens' ); load_registry_from_url( 'mysql://anonymous@ensembldb.ensembl.org:3306/homo_sapiens_core_65_37?group=core' ); 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. You can also specify a database name which will cause the loading of a single DBAdaptor instance. Parameters are mapped from a normal URL parameter set to their DBAdaptor equivalent. Group must be defined. Returntype : Int count of the DBAdaptor instances which can be found in the registry Exceptions : Thrown if the given URL does not parse according to the above scheme and if the specified database cannot be connected to (see L for more information) Status : Stable =cut sub load_registry_from_url { my ( $self, $url, $verbose, $no_cache ) = @_; if ( $url =~ /^mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?\/?$/x ) { my $user_pass = $1; my $host = $2; my $port = $3; my $version = $4; $user_pass =~ s/\@$//; my ( $user, $pass ) = $user_pass =~ m/([^\:]+)(\:.+)?/x; $pass =~ s/^\://x if ($pass); $port =~ s/^\://x if ($port); $version =~ s/^\///x if ($version); return $self->load_registry_from_db( -host => $host, -user => $user, -pass => $pass, -port => $port, -db_version => $version, -verbose => $verbose, -no_cache => $no_cache ); } my $uri = parse_uri($url); if($uri) { if($uri->scheme() eq 'mysql') { my %params = $uri->generate_dbsql_params(); if($params{-DBNAME}) { $params{-SPECIES} = $params{-DBNAME} unless $params{-SPECIES}; $params{-NO_CACHE} = 1 if $no_cache; my $group = $params{-GROUP}; my $class = $self->_group_to_adaptor_class($group); if($verbose) { printf("Loading database '%s' from group '%s' with DBAdaptor class '%s' from url %s\n", $params{-DBNAME}, $group, $class, $url); } $class->new(%params); return 1; } } } throw("Only MySQL URLs are accepted. Given URL was '${url}'"); } ## end sub load_registry_from_url =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. This includes a listing of all available species & databases. Arg [SPECIES]: (optional) string By default, all databases that are found on the server and that corresponds to the correct release are probed for aliases etc. For some people, depending on where they are in the world, this might be a slow operation. With the '-species' argument, one may reduce the startup time by restricting the set of databases that are probed to those of a particular species. Note that the latin name of the species is required, e.g., 'homo sapiens', 'gallus gallus', 'callithrix jacchus' etc. It may be the whole species name, or only the first part of the name, e.g. 'homo', 'gallus', or 'callithrix'. This will be used in matching against the name of the databases. Arg [DB_VERSION]: (optional) integer By default, only databases corresponding to the current API version are loaded. This argument allows the script to use databases from another version although it might not work properly. This argument 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) 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 the developer mailing list. Arg [SPECIES_SUFFIX]: (optional) string This option will append the string to the species name in the registry for all databases found on this server. Example : $registry->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. Returntype : Int count of the DBAdaptor instances which can be found in the registry due to this method call. Exceptions : Thrown if the given MySQL database cannot be connected to or there is any error whilst querying the database. Status : Stable =cut sub load_registry_from_db { my ( $self, @args ) = @_; my ( $host, $port, $user, $pass, $verbose, $db_version, $wait_timeout, $no_cache, $species, $species_suffix, $db_prefix ) = rearrange( [ 'HOST', 'PORT', 'USER', 'PASS', 'VERBOSE', 'DB_VERSION', 'WAIT_TIMEOUT', 'NO_CACHE', 'SPECIES', 'SPECIES_SUFFIX', 'DB_PREFIX' ], @args ); my $ignore_multi = 0; if ( defined($species) ) { $species = lc($species); $species =~ tr/ -/__/; $ignore_multi = 1; } if (!defined($species_suffix)) { $species_suffix = ""; } if (defined($db_prefix)) { $db_prefix = $db_prefix . '_'; } else { $db_prefix = ''; } if(! defined $db_version) { # Do checking for the -DB_VERSION flag which can be mis-spelt. Regex assembled using: # perl -MRegexp::Assemble -e '$r=Regexp::Assemble->new(); $r->add($_) for ("-dbversion","-version","-verion","-verison"); print $r->re, "\n";' my %hashed_args = @args; my ($possible_key) = grep { $_ =~ /(?-xism:-(?:ver(?:is?|si)|dbversi)on)/xism } keys %hashed_args; if($possible_key) { my $msg = sprintf(q{Detected no -DB_VERSION flag but found '%s'; assuming a mis-spelling. Please fix}, $possible_key); warning($msg); $db_version = $hashed_args{$possible_key}; } } my $ontology_db; my $ontology_version; my $taxonomy_db; my $ensembl_metadata_db; my $ensembl_metadata_db_versioned; my $production_dba_ok = eval { require Bio::EnsEMBL::Production::DBSQL::DBAdaptor; 1 }; my $production_db; my $production_version; my $stable_ids_db; my $stable_ids_version; $user ||= "anonymous"; if ( !defined($port) ) { $port = 3306; if ( $host eq "ensembldb.ensembl.org" && defined($db_version) && $db_version < 48 ) { $port = 4306; } } $wait_timeout ||= 0; my $original_count = $self->get_DBAdaptor_count(); my $err_pattern = 'Cannot %s to the Ensembl MySQL server at %s:%d; check your settings & DBI error message: %s'; my $dbh = DBI->connect( "DBI:mysql:host=$host;port=$port", $user, $pass ) or throw(sprintf($err_pattern, 'connect', $host, $port, $DBI::errstr)); $dbh->ping() or throw(sprintf($err_pattern, 'ping', $host, $port, $DBI::errstr)); my $res = $dbh->selectall_arrayref('SHOW DATABASES'); my @dbnames = map { $_->[0] } @$res; my %temp; my $software_version = software_version(); if ( defined($db_version) ) { $software_version = $db_version; } if ($verbose) { printf( "Will only load v%d databases\n", $software_version ); } # From the list of all the databses create a tempory hash of those we # are interested in for my $db (@dbnames) { if ( $db =~ /^(\w+_collection_\w+(?:_\d+)?)_((\d+)_\w+)/ ) { # NEEDS TO BE FIRST TO PICK UP COLLECTION DBS if ( $3 eq $software_version ) { $temp{$1} = $2; } } elsif ( $db =~ /^(.+)_(userdata)$/x ) { $temp{$1} = $2; } elsif ( $db =~ /^(ensembl_compara # compara database (?:_\w+)*?) # optional ensembl genomes bit _ (\d+)$/x ) { # db version if ( $2 eq $software_version ) { $temp{$1} = $2; } } elsif ( $db =~ /^(ensembl_ancestral(?:_\w+?)*?)_(\d+)$/x ) { if ( $2 eq $software_version ) { $temp{$1} = $2; } } elsif ( $db =~ /^ensembl(?:genomes)?_ontology_(?:\d+_)?(\d+)/x ) { if ( $1 eq $software_version ) { $ontology_db = $db; $ontology_version = $1; } } elsif ( $db =~ /^ncbi_taxonomy$/ ) { $taxonomy_db = $db; } elsif ( $db =~ /^ensembl_metadata$/ ) { $ensembl_metadata_db = $db; } elsif ( $db =~ m{ \A ensembl_metadata_(\d+) \z }msx ) { if ( $1 eq $software_version ) { $ensembl_metadata_db_versioned = $db; } } elsif ( $production_dba_ok and $db =~ /^ensembl(?:genomes)?_production(_\d+)?/x ) { # production db can come with no version (i.e. that on ens-staging1), # but it's backed up with a release number my $version = $1; if ($version) { $version =~ s/_//; if ($software_version and $version eq $software_version) { $production_db = $db; $production_version = $version; } } else { # this is the default choice $production_db = $db if $db =~ /^ensembl(?:genomes)?_production$/; } } elsif ( $db =~ /^ensembl(?:genomes)?_stable_ids_(?:\d+_)?(\d+)/x ) { if ( $1 eq $software_version ) { $stable_ids_db = $db; $stable_ids_version = $1; } } elsif ( $db =~ /^(?:$db_prefix)([a-z]+_[a-z0-9]+(?:_[a-z0-9]+)? # species name e.g. homo_sapiens or canis_lupus_familiaris _ [a-z]+ # db type (?:_\d+)?) # optional end bit for ensembl genomes databases _ (\d+) # database release _ (\w+)$ # assembly number can have letters too e.g 37c /x ) { # Species specific databases (core, cdna, vega etc.) my ( $sp_name, $db_rel, $assem ) = ( $1, $2, $3 ); if ($db_prefix) { $sp_name = $db_prefix . $sp_name; } if ( !defined($species) || $sp_name =~ /^$species/ ) { if ( $db_rel eq $software_version ) { $temp{$sp_name} = $db_rel . "_" . $assem; } } } 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 like databases my $core_like_dbs_found = 0; foreach my $type (qw(core cdna vega vega_update otherfeatures rnaseq ccds)) { my @dbs = grep { /^(?:$db_prefix)[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)? # species name _ $type # the database type _ (?:\d+_)? # optional end bit for ensembl genomes \d+ # database release _ /x } @dbnames; if(@dbs) { $core_like_dbs_found = 1; } foreach my $database (@dbs) { if ( index( $database, 'collection' ) != -1 ) { # Skip multi-species databases. next; } my ( $prefix, $species, $num ) = ( $database =~ /(^$db_prefix)([a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?) # species name _ $type # type _ (?:\d+_)? # optional endbit for ensembl genomes (\d+) # databases release _ /x ); if(!defined($species)){ warn "Cannot extract species name from database '$database'"; } my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( -group => $type, -species => $species.$species_suffix, -host => $host, -user => $user, -pass => $pass, -port => $port, -dbname => $database, -wait_timeout => $wait_timeout, -no_cache => $no_cache ); if ($verbose) { printf( "Species '%s' loaded from database '%s'\n", $species, $database ); } } } # Register multi-species databases my @multi_dbs = grep { /^\w+_collection_core_\w+$/ } @dbnames; if (!$ignore_multi) { foreach my $multidb (@multi_dbs) { my $sth = $dbh->prepare( sprintf( "SELECT species_id, meta_value FROM %s.meta " . "WHERE meta_key = 'species.db_name'", $dbh->quote_identifier($multidb) ) ); $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_suffix, -species_id => $species_id, -multispecies_db => 1, -host => $host, -user => $user, -pass => $pass, -port => $port, -dbname => $multidb, -wait_timeout => $wait_timeout, -no_cache => $no_cache ); if ($verbose) { printf( "Species '%s' (id:%d) loaded from database '%s'\n", $species, $species_id, $multidb ); } } } ## end foreach my $multidb (@multi_dbs) } if(!$core_like_dbs_found && $verbose) { print("No core-like databases found. Check your DB_VERSION (used '$software_version')\n"); } # User upload DBs my @userupload_dbs = grep { /_userdata$/ } @dbnames; if (!$ignore_multi) { for my $userupload_db (@userupload_dbs) { if ( index( $userupload_db, 'collection' ) != -1 ) { # Skip multi-species databases. next; } my ($species) = ( $userupload_db =~ /(^.+)_userdata$/ ); my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( -group => "userupload", -species => $species.$species_suffix, -host => $host, -user => $user, -pass => $pass, -port => $port, -wait_timeout => $wait_timeout, -dbname => $userupload_db, -no_cache => $no_cache ); if ($verbose) { printf( "%s loaded\n", $userupload_db ); } } } # Register multi-species userupload databases. my @userdata_multidbs = grep { /^.+_collection_userdata$/ } @dbnames; if (!$ignore_multi) { foreach my $multidb (@userdata_multidbs) { my $sth = $dbh->prepare( sprintf( "SELECT species_id, meta_value FROM %s.meta " . "WHERE meta_key = 'species.db_name'", $dbh->quote_identifier($multidb) ) ); $sth->execute(); my ( $species_id, $species ); $sth->bind_columns( \( $species_id, $species ) ); while ( $sth->fetch() ) { my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( -group => "userupload", -species => $species.$species_suffix, -species_id => $species_id, -multispecies_db => 1, -host => $host, -user => $user, -pass => $pass, -port => $port, -dbname => $multidb, -wait_timeout => $wait_timeout, -no_cache => $no_cache ); if ($verbose) { printf( "Species '%s' (id:%d) loaded from database '%s'\n", $species, $species_id, $multidb ); } } } ## end foreach my $multidb (@userdata_multidbs) } # Variation my $test_eval = eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor"; ## no critic if ($@or (!$test_eval)) { # Ignore variations as code required not there for this if ($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-z0-9]+(?:_[a-z0-9]+)?_variation_(?:\d+_)?\d+_/ } @dbnames; if(! @variation_dbs && $verbose) { print("No variation databases found\n"); } for my $variation_db (@variation_dbs) { if ( index( $variation_db, 'collection' ) != -1 ) { # Skip multi-species databases. next; } my ( $species, $num ) = ( $variation_db =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?)_variation_(?:\d+_)?(\d+)_/ ); my $dba = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new( -group => "variation", -species => $species.$species_suffix, -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", $variation_db ); } } # Register variation multispecies databases my @variation_multidbs = grep { /^\w+_collection_variation_\w+$/ } @dbnames; if (!$ignore_multi) { foreach my $multidb (@variation_multidbs) { 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::Variation::DBSQL::DBAdaptor->new( -group => 'variation', -species => $species.$species_suffix, -species_id => $species_id, -multispecies_db => 1, -host => $host, -user => $user, -pass => $pass, -port => $port, -dbname => $multidb, -wait_timeout => $wait_timeout, -no_cache => $no_cache ); if ($verbose) { printf( "Species '%s' (id:%d) loaded from database '%s'\n", $species, $species_id, $multidb ); } } } ## end foreach my $multidb (@variation_multidbs) } } my $func_eval = eval "require Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor"; ## no critic if ($@ or (!$func_eval)) { if ($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-z0-9]+(?:_[a-z0-9]+)?_funcgen_(?:\d+_)?\d+_/ } @dbnames; if(! @funcgen_dbs && $verbose) { print("No funcgen databases found\n"); } for my $funcgen_db (@funcgen_dbs) { if ( index( $funcgen_db, 'collection' ) != -1 ) { # Skip multi-species databases. next; } my ( $species, $num ) = ( $funcgen_db =~ /(^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?)_funcgen_(?:\d+_)?(\d+)_/ ); my $dba = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new( -group => "funcgen", -species => $species.$species_suffix, -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", $funcgen_db ); } } # Register functional genomics multispecies databases my @funcgen_multidbs = grep { /^\w+_collection_funcgen_\w+$/ } @dbnames; if (!$ignore_multi) { foreach my $multidb (@funcgen_multidbs) { 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::Funcgen::DBSQL::DBAdaptor->new( -group => 'funcgen', -species => $species.$species_suffix, -species_id => $species_id, -multispecies_db => 1, -host => $host, -user => $user, -pass => $pass, -port => $port, -dbname => $multidb, -wait_timeout => $wait_timeout, -no_cache => $no_cache ); if ($verbose) { printf( "Species '%s' (id:%d) loaded from database '%s'\n", $species, $species_id, $multidb ); } } } ## end foreach my $multidb (@funcgen_multidbs) } } ## end else [ if ($@) ] # Compara my @compara_dbs = grep { /^ensembl_compara/ } @dbnames; if (!$ignore_multi) { if (@compara_dbs) { my $comp_eval = eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor"; ## no critic if ($@ or (!$comp_eval)) { # Ignore Compara as code required not there for this if ($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 => $species.$species_suffix, -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 ($verbose) { print("No Compara databases found\n"); } } # Ancestral sequences my @ancestral_dbs = sort grep { /^ensembl_ancestral/ } @dbnames; if (@ancestral_dbs && !$ignore_multi) { my $ancestral_db = shift @ancestral_dbs; my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( -group => 'core', -species => 'Ancestral sequences'.$species_suffix, -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"); } # Ontology if ( defined($ontology_version) && $ontology_version != 0 && !$ignore_multi) { require Bio::EnsEMBL::DBSQL::OntologyDBAdaptor; my $dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new( '-species' => 'multi' . $species_suffix, '-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"); } # Taxonomy if ( defined $taxonomy_db) { my $has_taxonomy = eval {require Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyDBAdaptor}; if($@ or (!defined $has_taxonomy)) { if($verbose) { print "ensembl_taxonomy API not found - ignoring $taxonomy_db\n"; } } else { my $dba = Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyDBAdaptor->new( '-species' => 'multi' . $species_suffix, '-group' => 'taxonomy', '-host' => $host, '-port' => $port, '-user' => $user, '-pass' => $pass, '-dbname' => $taxonomy_db, ); if ($verbose) { printf( "%s loaded\n", $taxonomy_db ); } } } elsif ($verbose) { print("No taxonomy database found\n"); } # ensembl_metadata if ( ( defined $ensembl_metadata_db ) || ( defined $ensembl_metadata_db_versioned ) ) { my $has_metadata = eval {require Bio::EnsEMBL::MetaData::DBSQL::MetaDataDBAdaptor}; if($@ or (!defined $has_metadata)) { if($verbose) { print "ensembl_metadata API not found - ignoring $ensembl_metadata_db\n"; } } else { my $metadata_dbname; # Versioned database has priority over unversioned one. if ( defined $ensembl_metadata_db_versioned ) { $metadata_dbname = $ensembl_metadata_db_versioned; } else { $metadata_dbname = $ensembl_metadata_db; } my $dba = Bio::EnsEMBL::MetaData::DBSQL::MetaDataDBAdaptor->new( '-species' => 'multi' . $species_suffix, '-group' => 'metadata', '-host' => $host, '-port' => $port, '-user' => $user, '-pass' => $pass, '-dbname' => $metadata_dbname, ); if ($verbose) { printf( "%s loaded\n", $metadata_dbname ); } } } elsif ($verbose) { print("No ensembl_metadata database found\n"); } # Production if ( $production_dba_ok and defined($production_db) && !$ignore_multi) { # require Bio::EnsEMBL::Production::DBSQL::DBAdaptor; my $dba = Bio::EnsEMBL::Production::DBSQL::DBAdaptor->new( '-species' => 'multi' . $species_suffix, '-group' => 'production', '-host' => $host, '-port' => $port, '-user' => $user, '-pass' => $pass, '-dbname' => $production_db, ); if ($verbose) { printf( "%s loaded\n", $production_db ); } } elsif ($verbose) { print("No production database or adaptor found\n"); } # Stable IDs if ( defined($stable_ids_db) && $stable_ids_version != 0 && !$ignore_multi) { my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( '-species' => 'multi' . $species_suffix, '-group' => 'stable_ids', '-host' => $host, '-port' => $port, '-user' => $user, '-pass' => $pass, '-dbname' => $stable_ids_db, ); if ($verbose) { printf( "%s loaded\n", $stable_ids_db ); } } Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => 'multi'.$species_suffix, -alias => ['compara'.$species_suffix] ); Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => 'multi'.$species_suffix, -alias => ['ontology'.$species_suffix] ); $production_dba_ok and Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => 'multi'.$species_suffix, -alias => ['production'.$species_suffix] ); Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => 'multi'.$species_suffix, -alias => ['stable_ids'.$species_suffix] ); Bio::EnsEMBL::Utils::ConfigRegistry->add_alias( -species => 'Ancestral sequences'.$species_suffix, -alias => ['ancestral_sequences'.$species_suffix] ); # Register aliases as found in adaptor meta tables. $self->find_and_add_aliases( '-handle' => $dbh, '-species_suffix' => $species_suffix ); $dbh->disconnect(); my $count = $self->get_DBAdaptor_count() - $original_count; return $count >= 0 ? $count : 0; } ## end sub load_registry_from_db =head2 _group_to_adaptor_class Arg [1] : The group you wish to decode to an adaptor class Example : Bio::EnsEMBL::Registry->_group_to_adaptor_class('core'); Description : Has an internal lookup of groups to their adaptor classes Returntype : String Exceptions : Thrown if the group is unknown Status : Stable =cut sub _group_to_adaptor_class { my ($self, $group) = @_; my $class = { core => 'Bio::EnsEMBL::DBSQL::DBAdaptor', cdna => 'Bio::EnsEMBL::DBSQL::DBAdaptor', otherfeatures => 'Bio::EnsEMBL::DBSQL::DBAdaptor', rnaseq => 'Bio::EnsEMBL::DBSQL::DBAdaptor', vega => 'Bio::EnsEMBL::DBSQL::DBAdaptor', variation => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor', funcgen => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor', compara => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor', }->{$group}; throw "Group '${group}' is unknown" if ! $class; return $class; } =head2 find_and_add_aliases 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. Arg [SPECIES_SUFFIX]: (optional) string This option will append the string to the species name in the registry for all databases. 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 : Throws if an alias is found in more than one species. Status : Stable =cut sub find_and_add_aliases { my $class = shift ; my ($adaptor, $group, $dbh, $species_suffix ) = rearrange( [ 'ADAPTOR', 'GROUP', 'HANDLE', 'SPECIES_SUFFIX' ], @_ ); #Can be undef; needs to be something to avoid warnings $species_suffix ||= q{}; my @dbas; if ( defined($adaptor) ) { @dbas = ($adaptor); } elsif ( defined($dbh) ) { if ( length($species_suffix) > 0 ) { my @full = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) }; foreach my $db (@full) { if ( $db->species =~ /$species_suffix/ ) { push( @dbas, $db ); } } } else { @dbas = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) }; } } else { @dbas = @{ $class->get_all_DBAdaptors( '-GROUP' => $group ) }; } my $aliases_for_dbc = {}; foreach my $dba (@dbas) { my @aliases; my $species = $dba->species(); if ( defined($dbh) ) { my $dbname = $dba->dbc()->dbname(); if (!defined $aliases_for_dbc->{$dbname}) { my $sth = $dbh->prepare(sprintf("SELECT species_id,meta_value FROM %s.meta " . "WHERE meta_key = 'species.alias' ", $dbh->quote_identifier($dbname)) ); # Execute, and don't care about errors (there will be errors for # databases without a 'meta' table. $sth->{'PrintError'} = 0; $sth->{'RaiseError'} = 0; if (!$sth->execute()) { next } $sth->{'PrintError'} = $dbh->{'PrintError'}; $sth->{'RaiseError'} = $dbh->{'RaiseError'}; my $alias; my $species_id; $sth->bind_columns(\$species_id, \$alias); while ($sth->fetch()) { push(@{$aliases_for_dbc->{$dbname}{$species_id}}, $alias); } } @aliases = @{$aliases_for_dbc->{$dbname}{$dba->species_id()}||[]} } else { my $meta_container = eval { $dba->get_MetaContainer() }; if ( defined($meta_container) ) { push( @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) { my $alias_suffix = $alias.$species_suffix; #Lowercase because stored aliases are lowercased my $lc_species = lc($species); my $lc_alias_suffix = lc($alias_suffix); if ( !$class->alias_exists( $alias_suffix ) && $lc_species ne $lc_alias_suffix ) { $class->add_alias( $species, $alias_suffix ); } elsif ( $lc_species ne $class->get_alias( $alias_suffix ) ) { $class->remove_alias( $species, $alias_suffix ); } } } ## end foreach my $dba (@dbas) return; } ## end sub find_and_add_aliases =head2 load_registry_from_multiple_dbs Arg [1] : Array of hashes, each hash being a set of arguments to load_registry_from_db() (see above). Example : $registry->load_registry_from_multiple_dbs( { '-host' => 'ensembldb.ensembl.org', '-user' => 'anonymous', '-verbose' => '1' }, { '-host' => 'server.example.com', '-user' => 'anonymouse', '-password' => 'cheese', '-verbose' => '1' } ); Description: Will call load_registry_from_db() (see above) multiple times and merge the resulting registries into one, effectively allowing a user to connect to databases on multiple database servers from within one program. If a database is found on more than one server, the first found instance of that database will be used. Returntype : Int count of the DBAdaptor instances which can be found in the registry =cut sub load_registry_from_multiple_dbs { my ( $self, @args ) = @_; my $original_count = $self->get_DBAdaptor_count(); my %merged_register = %registry_register; foreach my $arg (@args) { local %registry_register = (); my $verbose; ($verbose) = rearrange( ['VERBOSE'], %{$arg} ); $self->load_registry_from_db( %{$arg} ); # # Merge the localized %registry_register into %merged_register. # # Merge the _SPECIES and _ALIAS sections of %registry_register. foreach my $section ( 'Species', 'Alias' ) { my $section_key = '_' . uc($section); while ( my ( $key, $value ) = each( %{ $registry_register{$section_key} } ) ) { if ( !exists( $merged_register{$section_key}{$key} ) ) { $merged_register{$section_key}{$key} = $value; } elsif ($verbose) { printf( "%s '%s' found on multiple servers, " . "using first found\n", $section, $key ); } } } } ## end foreach my $arg (@args) # Add the DBAs from the _SPECIES section into the _DBA section. foreach my $species_hash ( values( %{ $merged_register{_SPECIES} } ) ) { foreach my $group_hash ( values( %{$species_hash} ) ) { if ( ref($group_hash) eq 'HASH' && exists( $group_hash->{_DB} ) ) { push( @{ $merged_register{_DBA} }, $group_hash->{_DB} ); } } } %registry_register = %merged_register; my $count = $self->get_DBAdaptor_count() - $original_count; return $count >= 0 ? $count : 0; } ## end sub load_registry_from_multiple_dbs # # Web specific routines # =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; return; } =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 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 $registry_register{'_no_version_check'}; } =head2 no_cache_warnings Arg[0] : boolean for turning the flag on and off Description : Turns off any warnings about not using caching in all available adaptors. Returntype : boolean Current status Exceptions : None =cut sub no_cache_warnings { my ($self, $arg) = @_; if(defined $arg) { $Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::SILENCE_CACHE_WARNINGS = $arg; } return $Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::SILENCE_CACHE_WARNINGS; } =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_/x ) { return 1; } if ( $dba->dbc()->dbname() =~ /ensembl_metadata/x ) { return 1; } if ( $dba->dbc()->dbname() =~ /(\d+)_\S+$/x ) { $database_version = $1; } elsif ( $dba->dbc()->dbname() =~ /ensembl_compara_(\d+)/x ) { $database_version = $1; } elsif ( $dba->dbc()->dbname() =~ /ensembl_help_(\d+)/x ) { $database_version = $1; } elsif ( $dba->dbc()->dbname() =~ /ensembl_ontology_(\d+)/x ) { $database_version = $1; } elsif ( $dba->dbc()->dbname() =~ /ensembl_stable_ids_(\d+)/x ) { $database_version = $1; } else { warn( sprintf( "No database version for database %s " . ". You must be using a post 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 != software_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", $dba->dbc()->dbname()."@".$dba->dbc()->host, software_version(), $database_version ) ); return 0; } return 1; # Ok } ## end sub version_check =head2 get_all_species Arg [1] : String group type, such as core, or otherfeatures Description: Method for getting all valid species names found in available databases. This excludes the ancestral sequence databases, and any species from a non-core database. Specifying a group allows the list to apply to non-core database types. Example : my @species_names = @{ $reg->get_all_species() }; Returntype : Listref of species names =cut sub get_all_species { my ($self,$group) = @_; $group ||= 'core'; my @species; foreach my $name (keys %{$registry_register{_SPECIES}}) { push @species, $name if ( # limit species names to given db group and no ancestral dbs $registry_register{_SPECIES}->{$name}->{$group} && $name !~ /^ancestral/i ); } return \@species; } =head2 get_species_and_object_type Description: Get the species name, object type (gene, transcript, translation, or exon etc.), and database type for a stable ID. Arg [1] : String stable_id The stable ID to find species and object type for. Arg [2] : String known_type (optional) The type of the stable ID, if it is known. Arg [3] : String known_species (optional) The species, if known Arg [4] : String known_db_type (optional) The database type, if known Example : my $stable_id = 'ENST00000326632'; my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type($stable_id); my $adaptor = $registry->get_adaptor( $species, $db_type, $object_type ); my $object = $adaptor->fetch_by_stable_id($stable_id); Return type: Array consisting of the species name, object type, and database type. The array may be empty if no match is found. Exceptions : none Status : At Risk. =cut my %stable_id_stmts = ( gene => 'SELECT m.meta_value ' . 'FROM %1$s.gene ' . 'JOIN %1$s.seq_region USING (seq_region_id) ' . 'JOIN %1$s.coord_system USING (coord_system_id) ' . 'JOIN %1$s.meta m USING (species_id) ' . 'WHERE stable_id = ? ' . 'AND m.meta_key = "species.production_name"', transcript => 'SELECT m.meta_value ' . 'FROM %1$s.transcript ' . 'JOIN %1$s.seq_region USING (seq_region_id) ' . 'JOIN %1$s.coord_system USING (coord_system_id) ' . 'JOIN %1$s.meta m USING (species_id) ' . 'WHERE stable_id = ? ' . 'AND m.meta_key = "species.production_name"', exon => 'SELECT m.meta_value ' . 'FROM %1$s.exon ' . 'JOIN %1$s.seq_region USING (seq_region_id) ' . 'JOIN %1$s.coord_system USING (coord_system_id) ' . 'JOIN %1$s.meta m USING (species_id) ' . 'WHERE stable_id = ? ' . 'AND m.meta_key = "species.production_name"', translation => 'SELECT m.meta_value ' . 'FROM %1$s.translation tl ' . 'JOIN %1$s.transcript USING (transcript_id) ' . 'JOIN %1$s.seq_region USING (seq_region_id) ' . 'JOIN %1$s.coord_system USING (coord_system_id) ' . 'JOIN %1$s.meta m USING (species_id) ' . 'WHERE tl.stable_id = ? ' . 'AND m.meta_key = "species.production_name"', operon => 'SELECT m.meta_value ' . 'FROM %1$s.operon ' . 'JOIN %1$s.seq_region USING (seq_region_id) ' . 'JOIN %1$s.coord_system USING (coord_system_id) ' . 'JOIN %1$s.meta m USING (species_id) ' . 'WHERE stable_id = ? ' . 'AND m.meta_key = "species.production_name"', operontranscript => 'SELECT m.meta_value ' . 'FROM %1$s.operon_transcript ' . 'JOIN %1$s.seq_region USING (seq_region_id) ' . 'JOIN %1$s.coord_system USING (coord_system_id) ' . 'JOIN %1$s.meta m USING (species_id) ' . 'WHERE stable_id = ? ' . 'AND m.meta_key = "species.production_name"', ); my %compara_stable_id_stmts = ( genetree => 'SELECT 1 FROM %1$s.gene_tree_root WHERE stable_id =?', family => 'SELECT 1 from %1$s.family where stable_id = ?', ); sub get_species_and_object_type { my ($self, $stable_id, $known_type, $known_species, $known_db_type, $force_long_lookup, $use_archive) = @_; #get the stable_id lookup database adaptor my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1); if ($stable_ids_dba && ! $force_long_lookup) { return $self->_lookup_db_get_species_and_object_type($stable_id, $known_type, $known_species, $known_db_type, $use_archive); } else { if(defined $known_type) { my $lc_known_type = lc $known_type; if(!exists $stable_id_stmts{$lc_known_type} && ! exists $compara_stable_id_stmts{$lc_known_type}) { return; } } $known_db_type = 'core' if ! $known_db_type; my %get_adaptors_args = ('-GROUP' => $known_db_type); $get_adaptors_args{'-species'} = $known_species if $known_species; my @dbas = sort { $a->dbc->host cmp $b->dbc->host || $a->dbc->port <=> $b->dbc->port } grep { $_->dbc->dbname ne 'ncbi_taxonomy' && $_->dbc->dbname ne 'ensembl_metadata' } @{$self->get_all_DBAdaptors(%get_adaptors_args)}; foreach my $dba (@dbas) { my @results; my $dba_adaptor_type = $group2adaptor{$dba->group()}; if($dba_adaptor_type eq 'Bio::EnsEMBL::DBSQL::DBAdaptor') { @results = $self->_core_get_species_and_object_type($stable_id, $known_type, $dba); } elsif($dba_adaptor_type eq 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') { @results = $self->_compara_get_species_and_object_type($stable_id, $known_type, $dba); } return @results if scalar(@results) > 0; } ## end foreach my $dba ( sort { $a...}) } return; } ## end sub get_species_and_object_type sub _lookup_db_get_species_and_object_type { my ($self, $stable_id, $known_type, $known_species, $known_db_type, $use_archive) = @_; my $retired; my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1); my ($species, $type, $db_type) = $self->stable_id_lookup($stable_id, $known_type, $known_species, $known_db_type); if (!$species && $use_archive) { ($species, $type, $db_type) = $self->archive_id_lookup($stable_id, $known_type, $known_species, $known_db_type); $retired = 1 if $species; } return ($species ,$type, $db_type, $retired); } ## end sub _lookup_db_get_species_and_object_type sub stable_id_lookup { my ($self, $stable_id, $known_type, $known_species, $known_db_type) = @_; my $retired; my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1); my $statement = 'SELECT name, object_type, db_type FROM stable_id_lookup join species using(species_id) WHERE stable_id = ?'; if ($known_species) { $statement .= ' AND name = ?'; } if ($known_db_type) { $statement .= ' AND db_type = ?'; } if ($known_type) { $statement .= ' AND object_type = ?'; } my $sth = $stable_ids_dba->dbc()->prepare($statement); $sth->bind_param(1, $stable_id, SQL_VARCHAR); my $param_count = 1; if ($known_species) { $known_species = $self->get_alias($known_species); $param_count++; $sth->bind_param($param_count, $known_species, SQL_VARCHAR); } if ($known_db_type) { $param_count++; $sth->bind_param($param_count, $known_db_type, SQL_VARCHAR); } if ($known_type) { $param_count++; $sth->bind_param($param_count, $known_type, SQL_VARCHAR); } $sth->execute(); my ($species, $type, $db_type) = $sth->fetchrow_array(); $sth->finish(); return ($species ,$type, $db_type); } sub archive_id_lookup { my ($self, $stable_id, $known_type, $known_species, $known_db_type) = @_; my $retired; my $stable_ids_dba = $self->get_DBAdaptor("multi", "stable_ids", 1); my $archive_statement = 'SELECT name, object_type, db_type FROM archive_id_lookup join species using(species_id) WHERE archive_id = ?'; if ($known_species) { $archive_statement .= ' AND name = ?'; } if ($known_db_type) { $archive_statement .= ' AND db_type = ?'; } if ($known_type) { $archive_statement .= ' AND object_type = ?'; } my $archive_sth = $stable_ids_dba->dbc()->prepare($archive_statement); $archive_sth->bind_param(1, $stable_id, SQL_VARCHAR); my $param_count = 1; if ($known_species) { $known_species = $self->get_alias($known_species); $param_count++; $archive_sth->bind_param($param_count, $known_species, SQL_VARCHAR); } if ($known_db_type) { $param_count++; $archive_sth->bind_param($param_count, $known_db_type, SQL_VARCHAR); } if ($known_type) { $param_count++; $archive_sth->bind_param($param_count, $known_type, SQL_VARCHAR); } $archive_sth->execute(); my ($species, $type, $db_type) = $archive_sth->fetchrow_array(); $archive_sth->finish(); return ($species ,$type, $db_type); } # A level of abstraction because we need to test the stable_id as-is and then # try to chop off a version id if nothing is return, and try again sub _core_get_species_and_object_type { my ($self, $stable_id, $known_type, $dba) = @_; # Try looking up the species with the stable_is, as-is my @results = $self->_core_get_species_and_object_type_worker($stable_id, $known_type, $dba); if(@results) { return @results; } elsif(my $vindex = rindex($stable_id, '.')) { return $self->_core_get_species_and_object_type_worker(substr($stable_id,0,$vindex), $known_type, $dba) if(substr($stable_id,$vindex+1) =~ /^\d+$/); } return; } # Loop over a known set of object types for a core DB until we find a hit sub _core_get_species_and_object_type_worker { my ($self, $stable_id, $known_type, $dba) = @_; my @types = defined $known_type ? ($known_type) : ('Gene', 'Transcript', 'Translation', 'Exon', 'Operon', 'OperonTranscript'); my ($species, $final_type, $final_db_type); foreach my $type (@types) { my $statement = sprintf $stable_id_stmts{lc $type}, $dba->dbc->dbname; my $sth = $dba->dbc()->prepare($statement); $sth->bind_param(1, $stable_id, SQL_VARCHAR); $sth->execute; $species = $sth->fetchall_arrayref->[0][0]; $sth->finish; if(defined $species) { $final_type = $type; $final_db_type = $dba->group(); last; } } $dba->dbc->disconnect_if_idle(); # always disconnect after lookup return ($species, $final_type, $final_db_type) if defined $species; return; } # A level of abstraction because we need to test the stable_id as-is and then # try to chop off a version id if nothing is return, and try again sub _compara_get_species_and_object_type { my ($self, $stable_id, $known_type, $dba) = @_; # Try looking up the species with the stable_is, as-is my @results = $self->_compara_get_species_and_object_type_worker($stable_id, $known_type, $dba); if(@results) { return @results; } elsif(my $vindex = rindex($stable_id, '.')) { return $self->_compara_get_species_and_object_type_worker(substr($stable_id,0,$vindex), $known_type, $dba) if(substr($stable_id,$vindex+1) =~ /^\d+$/); } return; } # Loop over a known set of object types for a compara DB until we find a hit sub _compara_get_species_and_object_type_worker { my ($self, $stable_id, $known_type, $dba) = @_; my @types = defined $known_type ? ($known_type) : ('GeneTree'); my ($species, $final_type, $final_db_type); foreach my $type (@types) { my $statement = sprintf $compara_stable_id_stmts{lc $type}, $dba->dbc->dbname; my $sth = $dba->dbc()->prepare($statement); $sth->bind_param(1, $stable_id, SQL_VARCHAR); $sth->execute; my $found = $sth->fetchall_arrayref->[0][0]; $sth->finish; if(defined $found) { $species = $dba->species(); $final_type = $type; $final_db_type = $dba->group(); last; } } $dba->dbc->disconnect_if_idle(); # always disconnect after lookup return ($species, $final_type, $final_db_type) if defined $species; return; } 1;