Bio::Biblio::IO pubmed2ref
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Summary
Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations
Package variables
No package variables defined.
Inherit
Bio::Biblio::IO::medline2ref
Synopsis
 # to be written
Description
 # to be written
Methods
_load_instance
No description
Code
convert
No description
Code
Methods description
None available.
Methods code
_load_instancedescriptionprevnextTop
sub _load_instance {
    my ($self, $source) = @_;

    my $result;
    my $article = $$source{'article'};
    if (defined $article) {
	if (defined $$article{'journal'}) {
	    $result = $self->_new_instance ('Bio::Biblio::PubmedJournalArticle');
	    $result->type ('JournalArticle');
	} elsif (defined $$article{'book'}) {
	    $result = $self->_new_instance ('Bio::Biblio::PubmedBookArticle');
	    $result->type ('BookArticle');
	} else {
	    $result->type ('PubmedArticle');
	}
    }
    $result = $self->_new_instance ('Bio::Biblio::Ref') unless defined $result;
    return $result;
}
convertdescriptionprevnextTop
sub convert {
    my ($self, $source) = @_;
    my $result = $self->SUPER::convert ($source->{'Citation'});	

    # here we do PUBMED's specific stuff
my $pubmed_data = $$source{'PubmedData'}; if (defined $pubmed_data) { # ... just take it (perhaps rename it)
$result->pubmed_status ($$pubmed_data{'publicationStatus'}) if defined $$pubmed_data{'publicationStatus'}; $result->pubmed_provider_id ($$pubmed_data{'providerId'}) if defined $$pubmed_data{'providerId'}; $result->pubmed_article_id_list ($$pubmed_data{'pubmedArticleIds'}) if defined $$pubmed_data{'pubmedArticleIds'}; $result->pubmed_url_list ($$pubmed_data{'pubmedURLs'}) if defined $$pubmed_data{'pubmedURLs'}; # ... put all dates from all 'histories' into one array
if (defined $$pubmed_data{'histories'}) { my @history_list; foreach my $history ( @{ $$pubmed_data{'histories'} } ) { my $ra_pub_dates = $$history{'pubDates'}; foreach my $pub_date ( @{ $ra_pub_dates } ) { my %history = (); my $converted_date = &Bio::Biblio::IO::medline2ref::_convert_date ($pub_date); $history{'date'} = $converted_date if defined $converted_date; $history{'pub_status'} = $$pub_date{'pubStatus'} if defined $$pub_date{'pubStatus'}; push (@history_list,\% history); } } $result->pubmed_history_list (\@history_list); } } # Done!
return $result; } 1; __END__
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHORTop
Martin Senger (senger@ebi.ac.uk)
COPYRIGHTTop
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.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
APPENDIXTop
Here is the rest of the object methods. Internal methods are preceded
with an underscore _.