Bio::DB Registry
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Summary
Bio::DB::Registry - Access to the Open Bio Database Access registry scheme
Package variables
Privates (from "my" definitions)
%implement = ('flat' => 'Bio::DB::Flat', 'biosql' => 'Bio::DB::BioSQL::OBDA', 'biofetch' => 'Bio::DB::BioFetch' )
Included modules
Bio::DB::Failover
Bio::Root::HTTPget
Inherit
Bio::Root::Root
Synopsis
    use Bio::DB::Registry();
$registry = Bio::DB::Registry->new(); @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 (OBDA)
scheme, which provides a single cross-language and cross-platform
specification of how to get to databases. These databases may be
accessible through the Web, they may be BioSQL databases, or
they may be local, indexed flatfile 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 www.open-bio.org. The Registry object will attempt to store these
settings in a new file, ${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 ';'.
Please see the OBDA Access HOWTO for more information
(http://bioperl.open-bio.org/wiki/HOWTO:OBDA). Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible. Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
Methods
BEGIN Code
new
No description
Code
_load_registryDescriptionCode
get_databaseDescriptionCode
servicesDescriptionCode
_get_ini_filesDescriptionCode
_make_private_registryDescriptionCode
Methods description
_load_registrycode    nextTop
 Title   : _load_registry
Usage :
Function: Looks for seqdatabase.ini files in the expected locations and
in the directories specified by $OBDA_SEARCH_PATH. If no files
are found download a default file from www.open-bio.org
Returns : nothing
Args : none
get_databasecodeprevnextTop
 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
servicescodeprevnextTop
 Title   : services
Usage : my @available = $registry->services();
Function: returns list of possible services
Returns : list of strings
Args : none
_get_ini_filescodeprevnextTop
 Title   : _get_ini_files
Usage : my @files = $self->_get_ini_files
Function: To find all the seqdatabase.ini files
Returns : list of seqdatabase.ini paths
Args : None
_make_private_registrycodeprevnextTop
 Title   : _make_private_registry
Usage :
Function: Make private registry in file in $HOME
Returns : Path to private registry file
Args : None
Methods code
BEGINTop
BEGIN {
   $OBDA_SPEC_VERSION = 1.0;
	$HOME = $ENV{HOME} if (defined $ENV{HOME});
	if (defined $ENV{OBDA_SEARCH_PATH}) {
		$OBDA_SEARCH_PATH = $ENV{OBDA_SEARCH_PATH} || '';
}
newdescriptionprevnextTop
sub new {
    my ($class,@args) = shift;
    my $self = $class->SUPER::new(@args);
    # open files in order
$self->{'_dbs'} = {}; $self->_load_registry(); return $self;
}
_load_registrydescriptionprevnextTop
sub _load_registry {
   my $self = shift;
	eval { $HOME = (getpwuid($>))[7]; } unless $HOME;
	if ($@) {
		$self->warn("This Perl doesn't implement function getpwuid(), no\$ HOME");
	}
	my @ini_files = $self->_get_ini_files();

	@ini_files = $self->_make_private_registry() unless (@ini_files);

   my ($db,$hash) = ();
   for my $file (@ini_files) {
      open my $FH,"$file";
      while( <$FH> ) {
			if (/^VERSION=([\d\.]+)/) {
				if ($1 > $OBDA_SPEC_VERSION or !$1) {
					$self->throw("Do not know about this version [$1] > $OBDA_SPEC_VERSION");
					last;
				}
				next;
         }
			next if( /^#/ );
			next if( /^\s/ );
			if ( /^\[(\S+)\]/ ) {
				$db = $1;
				next;
			}
			my ($tag,$value) = split('=',$_);
			$value =~ s/\s//g;
			$tag =~ s/\s//g;
			$hash->{$db}->{"\L$tag"} = $value;
      }
   }

   for my $db ( keys %{$hash} ) {
      if ( !exists $self->{'_dbs'}->{$db} ) {
			my $failover = Bio::DB::Failover->new();
			$self->{'_dbs'}->{$db} = $failover;
      }
      my $class;
      if (defined $implement{$hash->{$db}->{'protocol'}}) {
			$class = $implement{$hash->{$db}->{'protocol'}};
      } else {
			$self->warn("Registry does not support protocol " .
							$hash->{$db}->{'protocol'});
			next;
      }
      eval "require $class";
      if ($@) {
			$self->warn("Couldn't load $class");
			next;
      } else {
			eval {
				my $randi = $class->new_from_registry( %{$hash->{$db}} );
				$self->{'_dbs'}->{$db}->add_database($randi); 
			};
			if ($@) {
				$self->warn("Couldn't call new_from_registry() on [$class]\n$@");
			}
      }
   }
}
get_databasedescriptionprevnextTop
sub get_database {
	my ($self,$dbname) = @_;

	$dbname = lc $dbname;
	if( !defined $dbname ) {
		$self->warn("must get_database with a database name");
		return;
	}
	if( !exists $self->{'_dbs'}->{$dbname} ) {
		$self->warn("No database with name $dbname in Registry");
		return;
	}
	return $self->{'_dbs'}->{$dbname};
}
servicesdescriptionprevnextTop
sub services {
    my ($self) = @_;
    return () unless ( defined $self->{'_dbs'} &&
		       ref( $self->{'_dbs'} ) =~ /HASH/i);
    return keys %{$self->{'_dbs'}};
}
_get_ini_filesdescriptionprevnextTop
sub _get_ini_files {
	my $self = shift;
   my @ini_files = ();
   if ( $OBDA_SEARCH_PATH ) {
      foreach my $dir ( split /;/, $OBDA_SEARCH_PATH ) {
			my $file = $dir . "/" . $REGISTRY;
			next unless -e $file;
			push @ini_files,$file;
      }
   }
   push @ini_files,"$HOME/$PRIVATE_DIR/$REGISTRY" 
     if ( $HOME && -e "$HOME/$PRIVATE_DIR/$REGISTRY" );
   push @ini_files, "$PUBLIC_DIR/$REGISTRY"
     if ( -e "$PUBLIC_DIR/$REGISTRY" );
   @ini_files;
}
_make_private_registrydescriptionprevnextTop
sub _make_private_registry {
	my $self = shift;
   my @ini_file;

	my $nor_in = $OBDA_SEARCH_PATH ? 
	  "nor in directory specified by\n$OBDA_SEARCH_PATH" : 
	  "and environment variable OBDA_SEARCH_PATH wasn't set";

	$self->warn("No $REGISTRY file found in $HOME/$PRIVATE_DIR/\n" . 
					"nor in $PUBLIC_DIR $nor_in.\n" .
					"Using web to get registry from\n$FALLBACK_REGISTRY");

	# Last gasp. Try to use HTTPget module to retrieve the registry from
# the web...
my $f = Bio::Root::HTTPget::getFH($FALLBACK_REGISTRY); # store the default registry file
eval { mkdir "$HOME/$PRIVATE_DIR" unless -e "$HOME/$PRIVATE_DIR"; }; $self->throw("Could not make directory $HOME/$PRIVATE_DIR, " . "no $REGISTRY file available") if $@; open(my $F,">$HOME/$PRIVATE_DIR/$REGISTRY"); print $F while (<$F>); close $F; $self->warn("Stored $REGISTRY file in $HOME/$PRIVATE_DIR"); push @ini_file,"$HOME/$PRIVATE_DIR/$REGISTRY"; @ini_file; } 1; __END__
}
General documentation
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _