Raw content of Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
<![CDATA[#
# BioPerl module for DBSQL::Obj
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
=head1 SYNOPSIS
$db = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(
-user => 'root',
-host => 'caldy',
-dbname => 'pog',
-species => 'Multi',
);
$db = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(
-url => 'mysql://user:pass@host:port/db_name');
=head1 DESCRIPTION
This object represents the handle for a comparative DNA alignment database
=head1 CONTACT
Post questions the the EnsEMBL developer list: <ensembl-dev@ebi.ac.uk>
=cut
# Let the code begin...
package Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::DBLoader;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::Argument;
@ISA = qw( Bio::EnsEMBL::DBSQL::DBAdaptor );
=head2 new
Arg [..] : list of named arguments. See Bio::EnsEMBL::DBConnection.
[-CONF_FILE] optional name of a file containing configuration
information for compara genome databases. An example of the conf file
can be found in ensembl-compara/modules/Bio/EnsEMBL/Compara/Compara.conf.example
*** WARNING *** -CONF_FILE is now deprecated. Compara now uses the more generic
Bio::EnsEMBL::Registry configuration file.
[-URL mysql://user:pass@host:port/db_name] alternative way to specify the
connection parameters. Pass and port are optional. If none is speciefied,
the species name will be equal to the db_name.
[-GROUP] This option is *always* set to "compara". Use another DBAdaptor
for other groups.
Example : $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
-user => 'root',
-pass => 'secret',
-host => 'caldy',
-port => 3306,
-dbname => 'ensembl_compara',
-species => 'Multi');
Example : $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
-url => 'mysql://root:secret@caldy:3306/ensembl_compara'
-species => 'Multi');
Description: Creates a new instance of a DBAdaptor for the compara database.
Returntype : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor
Exceptions : none
Caller : general
=cut
sub new {
my ($class, @args) = @_;
my ($conf_file, $url, $species) = rearrange(['CONF_FILE', 'URL', 'SPECIES'], @args);
if ($url and $url =~ /mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?\/(.+)/) {
my $user_pass = $1;
my $host = $2;
my $port = $3;
my $dbname = $4;
$user_pass =~ s/\@$//;
my ($user, $pass) = $user_pass =~ m/([^\:]+)(\:.+)?/;
$pass =~ s/^\:// if ($pass);
$port =~ s/^\:// if ($port);
push(@args, "-user" => $user) if ($user);
push(@args, "-pass" => $pass) if ($pass);
push(@args, "-port" => $port) if ($port);
push(@args, "-host" => $host);
push(@args, "-dbname" => $dbname);
if (!$species) {
push(@args, "-species" => $dbname);
}
}
my $self = $class->SUPER::new(@args);
if(defined($conf_file) and $conf_file ne "") {
deprecate("Compara.conf file is deprecated. Compara is now using the\n" .
"more generic Bio::EnsEMBL::Registry configuration file\n");
#read configuration file from disk
my @conf = @{do $conf_file};
foreach my $genome (@conf) {
my ($species, $assembly, $db_hash) = @$genome;
my $db;
my $module = $db_hash->{'module'};
my $mod = $module;
eval {
# require needs /'s rather than colons
if ( $mod =~ /::/ ) {
$mod =~ s/::/\//g;
}
require "${mod}.pm";
$db = $module->new(-dbname => $db_hash->{'dbname'},
-host => $db_hash->{'host'},
-user => $db_hash->{'user'},
-pass => $db_hash->{'pass'},
-port => $db_hash->{'port'},
-driver => $db_hash->{'driver'},
-disconnect_when_inactive => $db_hash->{'disconnect_when_inactive'});
};
if($@) {
throw("could not load module specified in configuration file:$@");
}
unless($db && ref $db && $db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
throw("[$db] specified in conf file is not a " .
"Bio::EnsEMBL::DBSQL::DBAdaptor");
}
if (defined $db) {
# The core db connection will be cached in the genomeDB object, which is itself
# cached in GenomeDBAdaptor.
my $gdb = $self->get_GenomeDBAdaptor->fetch_by_name_assembly($species,$assembly);
$gdb->db_adaptor($db);
}
}
}
return $self;
}
=head2 add_db_adaptor [DEPRECATED]
Arg [1] : Bio::EnsEMBL::DBSQL::DBConnection
Example : $compara_db->add_db_adaptor($homo_sapiens_db);
Description: Adds a genome-containing database to compara. This database
can be used by compara to obtain sequence for a genome on
on which comparative analysis has been performed. The database
adaptor argument must define the get_MetaContainer argument
so that species name and assembly type information can be
extracted from the database.
DEPRECATED: see Bio::EnsEMBL::Registry module.
Returntype : 1 if success 0 otherwise
Exceptions : Thrown if the argument is not a Bio::EnsEMBL::DBConnection
or if the argument does not implement a get_MetaContainer
method.
Caller : general
=cut
sub add_db_adaptor {
my ($self, $dba) = @_;
deprecate("add_db_adaptor is deprecated. Correct method is to call\n" .
"dba->get_GenomeDBAdaptor->fetch_by_name_assembly(<name>,<assembly>)->db_adaptor(<coreDBA>)\n".
"Or to use add_DBAdaptor using the Bio::EnsEMBL::Registry\n");
unless($dba && ref $dba && $dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
$self->throw("dba argument must be a Bio::EnsEMBL::DBSQL::DBAdaptor\n" .
"not a [$dba]");
}
my $mc = $dba->get_MetaContainer;
my $csa = $dba->get_CoordSystemAdaptor;
my $species = $mc->get_Species->binomial;
my ($cs) = @{$csa->fetch_all};
my $assembly = $cs ? $cs->version : '';
my $gdb;
try {
$gdb = $self->get_GenomeDBAdaptor->fetch_by_name_assembly($species,$assembly);
} catch {
warning("Catched an exception, no GenomeDb defined\n$_\n");
};
return 0 unless (defined $gdb);
$gdb->db_adaptor($dba);
return 1;
}
=head2 get_db_adaptor [DEPRECATED]
Arg [1] : string $species
the name of the species to obtain a genome DBAdaptor for.
Arg [2] : string $assembly
the name of the assembly to obtain a genome DBAdaptor for.
Example : $hs_db = $db->get_db_adaptor('Homo sapiens','NCBI_30');
Description: Obtains a DBAdaptor for the requested genome if it has been
specified in the configuration file passed into this objects
constructor, or subsequently added using the add_db_adaptor
method. If the DBAdaptor is not available (i.e. has not
been specified by one of the abbove methods) undef is returned.
DEPRECATED: see Bio::EnsEMBL::Registry module.
Returntype : Bio::EnsEMBL::DBSQL::DBConnection or undef
Exceptions : none
Caller : Bio::EnsEMBL::Compara::GenomeDBAdaptor
=cut
sub get_db_adaptor {
my ($self, $species, $assembly) = @_;
deprecate("get_db_adaptor is deprecated. Correct method is to call\n".
"dba->get_GenomeDBAdaptor->fetch_by_name_assembly(<name>,<assembly>)->db_adaptor\n".
"Or to use get_DBAdaptor using the Bio::EnsEMBL::Registry\n");
unless($species && $assembly) {
throw("species and assembly arguments are required\n");
}
my $gdb;
eval {
$gdb = $self->get_GenomeDBAdaptor->fetch_by_name_assembly($species, $assembly);
};
if ($@) {
warning("Catched an exception, here is the exception message\n$@\n");
return undef;
}
return $gdb->db_adaptor;
}
sub get_available_adaptors {
my %pairs = (
"MetaContainer" => "Bio::EnsEMBL::DBSQL::MetaContainer",
"MethodLinkSpeciesSet" => "Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor",
"SyntenyRegion" => "Bio::EnsEMBL::Compara::DBSQL::SyntenyRegionAdaptor",
"DnaAlignFeature" => "Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor",
"GenomeDB" => "Bio::EnsEMBL::Compara::DBSQL::GenomeDBAdaptor",
"DnaFrag" => "Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor",
"DnaFragRegion" => "Bio::EnsEMBL::Compara::DBSQL::DnaFragRegionAdaptor",
"GenomicAlignBlock" => "Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor",
"GenomicAlign" => "Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor",
"GenomicAlignGroup" => "Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor",
"GenomicAlignTree" => "Bio::EnsEMBL::Compara::DBSQL::GenomicAlignTreeAdaptor",
"AlignSlice" => "Bio::EnsEMBL::Compara::DBSQL::AlignSliceAdaptor",
"Homology" => "Bio::EnsEMBL::Compara::DBSQL::HomologyAdaptor",
"Family" => "Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor",
"Domain" => "Bio::EnsEMBL::Compara::DBSQL::DomainAdaptor",
"Subset" => "Bio::EnsEMBL::Compara::DBSQL::SubsetAdaptor",
"Member" => "Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor",
"Attribute" => "Bio::EnsEMBL::Compara::DBSQL::AttributeAdaptor",
"Taxon" => "Bio::EnsEMBL::Compara::DBSQL::TaxonAdaptor",
"NCBITaxon" => "Bio::EnsEMBL::Compara::DBSQL::NCBITaxonAdaptor",
"PeptideAlignFeature" => "Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor",
"Sequence" => "Bio::EnsEMBL::Compara::DBSQL::SequenceAdaptor",
"NestedSet" => "Bio::EnsEMBL::Compara::DBSQL::NestedSetAdaptor",
"ProteinTree" => "Bio::EnsEMBL::Compara::DBSQL::ProteinTreeAdaptor",
"Analysis" => "Bio::EnsEMBL::DBSQL::AnalysisAdaptor",
"ConservationScore" => "Bio::EnsEMBL::Compara::DBSQL::ConservationScoreAdaptor",
"ConstrainedElement" => "Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor",
"SitewiseOmega" => "Bio::EnsEMBL::Compara::DBSQL::SitewiseOmegaAdaptor"
);
return (\%pairs);
}
1;
]]>