#
# BioPerl module Bio::DB::Biblio::eutils.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Allen Day <allenday@ucla.edu>
# For copyright and disclaimer see below.
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::Biblio::eutils - Access to PubMed's bibliographic query service
=head1 SYNOPSIS
Do not use this object directly, it is recommended to access it and use
it through the I<Bio::Biblio> module:
use Bio::Biblio;
use Bio::Biblio::IO;
my $biblio = Bio::Biblio->new( -access => 'eutils' );
$biblio->find("10336996");
my $xml = $biblio->get_next;
my $io = Bio::Biblio::IO->new( -data => $xml,
-format => 'medlinexml' );
my $article = $io->next_bibref();
=head1 DESCRIPTION
This object contains the real implementation of a Bibliographic Query
Service as defined in L<Bio::DB::BiblioI>.
L<Bio::DB::BiblioI> is not implemented as documented in the interface,
particularly the find() method, which is not compatible with PubMed's
query language.
=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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Allen Day E<lt>allenday@ucla.eduE<gt>
=head1 COPYRIGHT
Copyright (c) 2004 Allen Day, University of California, Los Angeles.
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
=item *
More testing and debugging needed to ensure that returned citations
are properly transferred even if they contain foreign characters.
=item *
Maximum record count (MAX_RECORDS) returned currently hard coded to
100K.
=item *
Biblio retrieval methods should be more tightly integrated with
L<Bio::Biblio::Ref> and L<Bio::DB::MeSH>.
=back
=head1 SEE ALSO
Pub Med Help:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
Entrez Utilities:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
Example code:
examples/biblio/biblio-eutils-example.pl
=head1 APPENDIX
The main documentation details are to be found in
L<Bio::DB::BiblioI>.
Here is the rest of the object methods. Interface methods first,
followed by internal methods.
=cut
# Let the code begin...
package Bio::DB::Biblio::eutils;
use vars qw($DEFAULT_URN);
use strict;
use LWP::Simple;
use XML::Twig;
use URI::Escape;
use base qw(Bio::Biblio Bio::DB::BiblioI);
our $EFETCH = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi';
our $ESEARCH = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi';
our $MAX_RECORDS = 100_000;
# -----------------------------------------------------------------------------
=head2 _initialize
Usage : my $obj = Bio::Biblio->new(-access => 'eutils' ...);
(_initialize is internally called from this constructor)
Returns : 1 on success
Args : none
This is an actual new() method (except for the real object creation
and its blessing which is done in the parent class Bio::Root::Root in
method _create_object).
Note that this method is called always as an I<object> method (never as
a I<class> method) - and that the object who calls this method may
already be partly initiated (from Bio::Biblio::new method); so if you
need to do some tricks with the 'class invocation' you need to change
Bio::Biblio::new method, not this one.
=cut
sub _initialize {
my ($self, @args) = @_;
#eutils doesn't need this code, but it doesn't hurt to leave it here... -ad
# make a hashtable from @args
my %param = @args;
@param { map { lc $_ } keys %param } = values %param; # lowercase keys
# copy all @args into this object (overwriting what may already be
# there) - changing '-key' into '_key'
my $new_key;
foreach my $key (keys %param) {
($new_key = $key) =~ s/^-/_/;
$self->{ $new_key } = $param { $key };
}
# set up internal data
$self->twig(XML::Twig->new());
# finally add default values for those keys who have default value
# and who are not yet in the object
#AOK
return 1;
}
=head2 db
Title : db
Usage : $obj->db($newval)
Function: specifies the database to search. valid values are:
pubmed, pmc, journals
it is also possible to add the following, and i will do
so on request:
genome, nucleotide, protein, popset, snp, sequence, taxonomy
pubmed is default.
Returns : value of db (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub db{
my($self,$arg) = @_;
if($arg){
my %ok = map {$_=>1} qw(pubmed pmc journals);
if($ok{lc($arg)}){
$self->{'db'} = lc($arg);
} else {
$self->warn("invalid db $arg, keeping value as ".$self->{'db'} || 'pubmed');
}
}
return $self->{'db'};
}
=head1 Methods implementing Bio::DB::BiblioI interface
=head2 get_collection_id
Title : get_collection_id
Usage : $id = $biblio->get_collection_id();
Function: returns WebEnv value from ESearch
Returns : ESearch WebEnv value as a string
Args : none
=cut
sub get_collection_id {
return shift->collection_id();
}
sub get_count {
return shift->count();
}
sub get_by_id {
my $self = shift;
my $id = shift;
my $db = $self->db || 'pubmed';
$self->throw("must provide valid ID, not undef") unless defined($id);
my $xml = get($EFETCH.'?rettype=abstract&retmode=xml&db='.$db.'&id='.$id);
return $xml;
}
=head2 reset_retrieval
Title : reset_retrieval
Usage : $biblio->reset_retrieval();
Function: reset cursor in id list, see cursor()
Returns : 1
Args : none
=cut
sub reset_retrieval {
shift->cursor(0);
return 1;
}
=head2 get_next
Title : get_next
Usage : $xml = $biblio->get_next();
Function: return next record as xml
Returns : an xml string
Args : none
=cut
sub get_next {
my $self = shift;
return unless $self->has_next;
my $xml = $self->get_by_id( @{ $self->ids }[$self->cursor] );
$self->cursor( $self->cursor + 1 );
return $xml;
}
=head2 get_more
Title : get_more
Usage : $xml = $biblio->get_more($more);
Function: returns next $more records concatenated
Returns : a string containing multiple xml documents
Args : an integer representing how many records to retrieve
=cut
sub get_more {
my ($self,$more) = @_;
my @return = ();
for(1..$more){
my $next = $self->get_next();
last unless $next;
push @return, $next;
}
return \@return;
}
=head2 has_next
Title : has_next
Usage : $has_next = $biblio->has_next();
Function: check to see if there are more items to be retrieved
Returns : 1 on true, undef on false
Args : none
=cut
sub has_next {
my $self = shift;
return ($self->cursor < $self->count) ? 1 : undef;
}
=head2 find
Title : find
Usage : $biblio = $biblio->find($pubmed_query_phrase);
Function: perform a PubMed query using Entrez ESearch
Returns : a reference to the object on which the method was called
Args : a PubMed query phrase. See
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
for help on how to construct a query.
=cut
sub find {
my ($self,$query) = @_;
$query = uri_escape($query);
my $db = $self->db || 'pubmed';
my $url = $ESEARCH."?usehistory=y&db=$db&retmax=$MAX_RECORDS&term=$query";
my $xml = get($url) or $self->throw("couldn't retrieve results from $ESEARCH: $!");
$self->twig->parse($xml);
my @ids = map {$_->text} $self->twig->get_xpath('//IdList//Id');
$self->ids(\@ids);
##
#should we be using the ids, or the count tag?
##
my($count_element) = $self->twig->get_xpath('//Count');
if (defined $count_element) {
my $count = $count_element->text();
$self->count(scalar(@ids));
}
my($retmax_element) = $self->twig->get_xpath('//RetMax');
if (defined $retmax_element) {
my $retmax = $retmax_element->text();
}
my($querykey_element) = $self->twig->get_xpath('//QueryKey');
if (defined $querykey_element) {
$self->query_key($querykey_element->text());
}
my($webenv_element) = $self->twig->get_xpath('//WebEnv');
if (defined $webenv_element) {
$self->collection_id($webenv_element->text());
}
#initialize/reset cursor
$self->cursor(0);
return $self;
}
=head2 get_all_ids
Title : get_all_ids
Usage : @ids = $biblio->get_all_ids();
Function: return a list of PubMed ids resulting from call to find()
Returns : a list of PubMed ids, or an empty list
Args : none
=cut
sub get_all_ids {
my $self = shift;
return $self->ids() if $self->ids();
return ();
}
=head2 get_all
Title : get_all
Usage : $xml = $biblio->get_all();
Function: retrieve all records from query
Returns : return a large concatenated string of PubMed xml documents
Args : none
=cut
sub get_all {
my ($self) = shift;
my $db = $self->db || 'pubmed';
my $xml = get($EFETCH.'?rettype=abstract&retmode=xml&db=pubmed&query_key='.
$self->query_key.'&WebEnv='.$self->collection_id.
'&retstart=1&retmax='.$MAX_RECORDS
);
return $xml;
}
=head2 exists
Title : exists
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
=cut
sub exists {
return;
}
=head2 destroy
Title : destroy
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
=cut
sub destroy {
return;
}
=head2 get_vocabulary_names
Title : get_vocabulary_names
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : empty arrayref
Args : none
=cut
sub get_vocabulary_names {
return [];
}
=head2 contains
Title : contains
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
=cut
sub contains {
return;
}
=head2 get_entry_description
Title : get_entry_description
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
=cut
sub get_entry_description {
return;
}
=head2 get_all_values
Title : get_all_values
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
=cut
sub get_all_values {
return;
}
=head2 get_all_entries
Title : get_all_entries
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
=cut
sub get_all_entries {
return;
}
=head1 Internal methods unrelated to Bio::DB::BiblioI
=head2 cursor
Title : cursor
Usage : $obj->cursor($newval)
Function: holds position in reference collection
Returns : value of cursor (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub cursor {
my $self = shift;
my $arg = shift;
return $self->{'cursor'} = $arg if defined($arg);
return $self->{'cursor'};
}
=head2 twig
Title : twig
Usage : $obj->twig($newval)
Function: holds an XML::Twig instance.
Returns : value of twig (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub twig {
my $self = shift;
return $self->{'twig'} = shift if @_;
return $self->{'twig'};
}
=head2 ids
Title : ids
Usage : $obj->ids($newval)
Function: store pubmed ids resulting from find() query
Returns : value of ids (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub ids {
my $self = shift;
return $self->{'ids'} = shift if @_;
return $self->{'ids'};
}
=head2 collection_id
Title : collection_id
Usage : $obj->collection_id($newval)
Function:
Returns : value of collection_id (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub collection_id {
my $self = shift;
return $self->{'collection_id'} = shift if @_;
return $self->{'collection_id'};
}
=head2 count
Title : count
Usage : $obj->count($newval)
Function:
Returns : value of count (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub count {
my $self = shift;
return $self->{'count'} = shift if @_;
return $self->{'count'};
}
=head2 query_key
Title : query_key
Usage : $obj->query_key($newval)
Function: holds query_key from ESearch document
Returns : value of query_key (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub query_key {
my $self = shift;
return $self->{'query_key'} = shift if @_;
return $self->{'query_key'};
}
1;