# $Id: biofetch.pm 16123 2009-09-17 12:57:27Z cjfields $
#
# BioPerl module Bio::DB::Biblio::biofetch.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
# For copyright and disclaimer see below.
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::Biblio::biofetch - A BioFetch-based access to a bibliographic
citation retrieval
=head1 SYNOPSIS
Do not use this object directly, only access it through the
I<Bio::Biblio> module:
use Bio::Biblio;
my $biblio = Bio::Biblio->new(-access => 'biofetch');
my $ref = $biblio->get_by_id('20063307'));
my $ids = ['20063307', '98276153'];
my $refio = $biblio->get_all($ids);
while ($ref = $refio->next_bibref) {
print $ref->identifier, "\n";
}
=head1 DESCRIPTION
This class uses BioFetch protocol based service to retrieve Medline
references by their ID.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
=head1 AUTHOR
Heikki Lehvaslaiho (heikki-at-bioperl-dot-org)
=head1 COPYRIGHT
Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=head1 BUGS AND LIMITATIONS
=over 1
=item *
Only method get_by_id() is supported.
=back
=head1 APPENDIX
The main documentation details are to be found in
L<Bio::DB::BiblioI>.
Here is the rest of the object methods. Internal methods are preceded
with an underscore _.
=cut
# Let the code begin...
package Bio::DB::Biblio::biofetch;
use vars qw(%HOSTS %FORMATMAP $DEFAULTFORMAT $DEFAULTRETRIEVAL_TYPE
$DEFAULT_SERVICE $DEFAULT_NAMESPACE);
use strict;
use Bio::Biblio::IO;
use base qw(Bio::DB::DBFetch Bio::Biblio);
BEGIN {
# you can add your own here theoretically.
%HOSTS = (
'dbfetch' => {
baseurl => 'http://%s/cgi-bin/dbfetch?db=medline&style=raw',
hosts => {
'ebi' => 'www.ebi.ac.uk'
}
}
);
%FORMATMAP = ( 'default' => 'medlinexml'
);
$DEFAULTFORMAT = 'medlinexml';
$DEFAULT_SERVICE = 'http://www.ebi.ac.uk/cgi-bin/dbfetch';
$DEFAULTRETRIEVAL_TYPE = 'tempfile';
}
sub new {
my ($class, @args ) = @_;
my $self = $class->SUPER::new(@args);
$self->{ '_hosts' } = {};
$self->{ '_formatmap' } = {};
$self->hosts(\%HOSTS);
$self->formatmap(\%FORMATMAP);
$self->retrieval_type($DEFAULTRETRIEVAL_TYPE);
$self->{'_default_format'} = $DEFAULTFORMAT;
return $self;
}
=head2 get_by_id
Title : get_by_id
Usage : $entry = $db->get__by_id('20063307')
Function: Gets a Bio::Biblio::RefI object by its name
Returns : a Bio::Biblio::Medline object
Args : the id (as a string) of the reference
=cut
sub get_by_id {
my ($self,$id) = @_;
my $io = $self->get_Stream_by_id([$id]);
$self->throw("id does not exist") if( !defined $io ) ;
return $io->next_bibref();
}
=head2 get_all
Title : get_all
Usage : $seq = $db->get_all($ref);
Function: Retrieves reference objects from the server 'en masse',
rather than one at a time. For large numbers of sequences,
this is far superior than get_by_id().
Example :
Returns : a stream of Bio::Biblio::Medline objects
Args : $ref : either an array reference, a filename, or a filehandle
from which to get the list of unique ids/accession numbers.
=cut
sub get_all {
my ($self, $ids) = @_;
return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single');
}
=head2 get_seq_stream
Title : get_seq_stream
Usage : my $seqio = $self->get_seq_stream(%qualifiers)
Function: builds a url and queries a web db
Returns : a Bio::SeqIO stream capable of producing sequence
Args : %qualifiers = a hash qualifiers that the implementing class
will process to make a url suitable for web querying
=cut
sub get_seq_stream {
my ($self, %qualifiers) = @_;
my ($rformat, $ioformat) = $self->request_format();
my $seen = 0;
foreach my $key ( keys %qualifiers ) {
if( $key =~ /format/i ) {
$rformat = $qualifiers{$key};
$seen = 1;
}
}
$qualifiers{'-format'} = $rformat if( !$seen);
($rformat, $ioformat) = $self->request_format($rformat);
my $request = $self->get_request(%qualifiers);
my ($stream,$resp);
if ( $self->retrieval_type =~ /temp/i ) {
my $dir = $self->io()->tempdir( CLEANUP => 1);
my ( $fh, $tmpfile) = $self->io()->tempfile( DIR => $dir );
close $fh;
my ($resp) = $self->_request($request, $tmpfile);
if( ! -e $tmpfile || -z $tmpfile || ! $resp->is_success() ) {
$self->throw("WebDBSeqI Error - check query sequences!\n");
}
$self->postprocess_data('type' => 'file',
'location' => $tmpfile);
# this may get reset when requesting batch mode
($rformat,$ioformat) = $self->request_format();
if ( $self->verbose > 0 ) {
open(my $ERR, "<", $tmpfile);
while(<$ERR>) { $self->debug($_);}
}
$stream = Bio::Biblio::IO->new('-format' => $ioformat,
'-file' => $tmpfile);
} elsif ( $self->retrieval_type =~ /io_string/i ) {
my ($resp) = $self->_request($request);
my $content = $resp->content_ref;
$self->debug( "content is $$content\n");
if( ! $resp->is_success() || length(${$resp->content_ref()}) == 0 ) {
$self->throw("WebDBSeqI Error - check query sequences!\n");
}
($rformat,$ioformat) = $self->request_format();
$self->postprocess_data('type'=> 'string',
'location' => $content);
$stream = Bio::Biblio::IO->new('-format' => $ioformat,
# '-data' => "<tag>". $$content. "</tag>");
'-data' => $$content
);
} else {
$self->throw("retrieval type " . $self->retrieval_type .
" unsupported\n");
}
return $stream;
}
=head2 postprocess_data
Title : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr);
Function: process downloaded data before loading into a Bio::SeqIO
Returns : void
Args : hash with two keys - 'type' can be 'string' or 'file'
- 'location' either file location or string
reference containing data
=cut
# the default method, works for genbank/genpept, other classes should
# override it with their own method.
sub postprocess_data {
my ($self, %args) = @_;
my ($data, $TMP);
my $type = uc $args{'type'};
my $location = $args{'location'};
if( !defined $type || $type eq '' || !defined $location) {
return;
} elsif( $type eq 'STRING' ) {
$data = $$location;
} elsif ( $type eq 'FILE' ) {
open($TMP, "<", $location) or $self->throw("could not open file $location");
my @in = <$TMP>;
$data = join("", @in);
}
if( $type eq 'FILE' ) {
open($TMP, ">", $location) or $self->throw("could overwrite file $location");
print $TMP $data;
} elsif ( $type eq 'STRING' ) {
${$args{'location'}} = $data;
}
$self->debug("format is ". $self->request_format(). " data is $data\n");
}
=head2 VERSION and Revision
Usage : print $Bio::DB::Biblio::biofetch::VERSION;
print $Bio::DB::Biblio::biofetch::Revision;
=cut
=head2 Defaults
Usage : print $Bio::DB::Biblio::biofetch::DEFAULT_SERVICE;
=cut
1;
__END__