Raw content of Bio::DB::Registry
<![CDATA[# POD documentation - main docs before the code
# $Id: Registry.pm,v 1.12.2.2 2003/06/26 11:07:10 heikki Exp $
=head1 NAME
Bio::DB::Registry - Access to the Open Bio Database Access registry scheme
=head1 SYNOPSIS
use Bio::DB::Registry();
$registry = new Bio::DB::Registry();
@available_services = $registry->services;
$db = $registry->get_database('embl');
# $db is a Bio::DB::SeqI implementing class
$seq = $db->get_Seq_by_acc("J02231");
=head1 DESCRIPTION
This module provides access to the Open Bio Database Access scheme,
which provides a cross language and cross platform specification of how
to get to databases.
If the user or system administrator has not installed the default init
file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics
then creating the first Registry object copies the default settings from
the net. The Registry object will attempt to store these settings in
${HOME}/.bioinformatics/seqdatabase.ini.
Users can specify one or more custom locations for the init file by
setting $OBDA_SEARCH_PATH to those directories, where multiple
directories should be separated by ';'.
=head1 CONTACT
Ewan Birney originally wrote this class.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::Registry;
use vars qw(@ISA $VERSION $OBDA_SPEC_VERSION $OBDA_SEARCH_PATH);
use strict;
use Bio::Root::Root;
@ISA = qw(Bio::Root::Root);
use Bio::DB::Failover;
use Bio::Root::HTTPget;
$VERSION = '1.2';
BEGIN {
$OBDA_SPEC_VERSION = 1.0;
if (defined $ENV{OBDA_SEARCH_PATH}) {
$OBDA_SEARCH_PATH = $ENV{OBDA_SEARCH_PATH} || '';
}
}
my %implement = (
'biocorba' => 'Bio::CorbaClient::SeqDB',
'flat' => 'Bio::DB::Flat',
'biosql' => 'Bio::DB::BioSQL::BioDatabaseAdaptor',
'biofetch' => 'Bio::DB::BioFetch'
);
my $fallbackRegistryURL = 'http://www.open-bio.org/registry/seqdatabase.ini';
sub new {
my ($class,@args) = shift;
my $self = $class->SUPER::new(@args);
# open files in order
$self->{'_dbs'} = {};
$self->_load_registry();
return $self;
}
sub _load_registry {
my ($self) = @_;
my $home = (getpwuid($>))[7];
my $f;
if ( $OBDA_SEARCH_PATH ) {
foreach ( split /;/,$OBDA_SEARCH_PATH ) {
next unless -e $_;
open(F,"$OBDA_SEARCH_PATH/seqdatabase.ini");
$f = \*F;
last;
}
}
elsif( -e "$home/.bioinformatics/seqdatabase.ini" ) {
open(F,"$home/.bioinformatics/seqdatabase.ini");
$f = \*F;
} elsif ( -e "/etc/bioinformatics/seqdatabase.ini" ) {
open(F,"/etc/bioinformatics/seqdatabase.ini");
$f = \*F;
} else {
# waiting for information
$self->warn("No seqdatabase.ini file found in ~/.bioinformatics/ \nor in /etc/bioinformatics/.\nor in directory specified by $OBDA_SEARCH_PATH".
"Using web to get database registry from \n$fallbackRegistryURL");
# Last gasp. Try to use HTTPget module to retrieve the registry from
# the web...
$f = Bio::Root::HTTPget::getFH($fallbackRegistryURL);
# store the default registry file
mkdir "$home/.bioinformatics" unless -e "$home/.bioinformatics";
open(F,">$home/.bioinformatics/seqdatabase.ini");
print F while (<$f>);
close F;
$self->warn("Stored the default registry configuration into:\n".
" $home/.bioinformatics/seqdatabase.ini");
open(F,"$home/.bioinformatics/seqdatabase.ini");
$f = \*F;
}
while( <$f> ) {
/^VERSION=([\d\.]+)/;
$self->throw("Do not know about this version [$1] > $OBDA_SPEC_VERSION")
if $1 > $OBDA_SPEC_VERSION or !$1;
last;
}
while( <$f> ) {
if( /^#/ ) {
next;
}
if( /^\s/ ) {
next;
}
if( /\[(\w+)\]/ ) {
my $db = $1;
my $hash = {};
while( <$f> ) {
chomp();
/^#/ && next;
/^$/ && last;
my ($tag,$value) = split('=',$_);
$value =~ s/\s//g;
$tag =~ s/\s//g;
$hash->{"\L$tag"} = lc $value;
}
if( !exists $self->{'_dbs'}->{$db} ) {
my $failover = Bio::DB::Failover->new();
$self->{'_dbs'}->{$db}=$failover;
}
my $class;
if (defined $implement{$hash->{'protocol'}}) {
$class = $implement{$hash->{'protocol'}};
}
else {
$self->warn("Registry does not support protocol ".$hash->{'protocol'});
next;
}
eval "require $class";
if ($@) {
$self->verbose && $self->warn("Couldn't load $class");
next;
}
else {
eval {
my $randi = $class->new_from_registry(%$hash);
$self->{'_dbs'}->{$db}->add_database($randi); };
if ($@) {
$self->warn("Couldn't call new_from_registry on [$class]\n$@");
}
}
next; # back to main loop
}
$self->warn("Uninterpretable line in registry, $_");
}
}
=head2 get_database
Title : get_database
Usage : my $db = $registry->get_database($dbname);
Function: Retrieve a Database object which implements Bio::DB::SeqI interface
Returns : Bio::DB::SeqI object
Args : string describing the name of the database
=cut
sub get_database {
my ($self,$dbname) = @_;
$dbname = lc $dbname;
if( !defined $dbname ) {
$self->warn("must get_database with a database name");
return undef;
}
if( !exists $self->{'_dbs'}->{$dbname} ) {
$self->warn("No database in with $dbname in registry");
return undef;
}
return $self->{'_dbs'}->{$dbname};
}
=head2 services
Title : services
Usage : my @available = $registry->services();
Function: returns list of possible services
Returns : list of strings
Args : none
=cut
sub services{
my ($self) = @_;
return () unless ( defined $self->{'_dbs'} &&
ref( $self->{'_dbs'} ) =~ /HASH/i);
return keys %{$self->{'_dbs'}};
}
## End of Package
1;
__END__
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