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Summary

Bio::DB::Registry - Access to the Open Bio Database Access registry scheme

Package variables

Included modules

Inherit

Bio::Root::Root

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");

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 ';'.

Methods

Methods description

 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

 Title   : services
 Usage   : my @available = $registry->services();
 Function: returns list of possible services 
 Returns : list of strings
 Args    : none

Methods code

BEGIN {

    $OBDA_SPEC_VERSION = 1.0;
    if (defined $ENV{OBDA_SEARCH_PATH}) {
        $OBDA_SEARCH_PATH = $ENV{OBDA_SEARCH_PATH} || '';

}

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/\n or 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, $_");
    }

}

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};

}

sub new {

    my ($class,@args) = shift;
    my $self = $class->SUPER::new(@args);

    # open files in order
    $self->{'_dbs'} = {};
    $self->_load_registry();
    return $self;

}

sub services {

    my ($self) = @_;
    return () unless ( defined $self->{'_dbs'} &&
		       ref( $self->{'_dbs'} ) =~ /HASH/i);
    return keys %{$self->{'_dbs'}};
}


## End of Package

1;

__END__

}

General documentation

Ewan Birney originally wrote this class.

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/

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _