Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations

SYNOPSIS

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 # to be written

DESCRIPTION

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 # to be written

FEEDBACK

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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

Support

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 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/

AUTHOR

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Martin Senger (senger@ebi.ac.uk)

COPYRIGHT

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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.

DISCLAIMER

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This software is provided "as is" without warranty of any kind.

APPENDIX

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Here is the rest of the object methods. Internal methods are preceded with an underscore _.

BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module Bio::Biblio::IO::pubmed2ref.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Martin Senger <senger@ebi.ac.uk>
# For copyright and disclaimer see below.

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Biblio::IO::pubmed2ref;

use strict;

use base qw(Bio::Biblio::IO::medline2ref);


# ---------------------------------------------------------------------
#
#   Here is the core...
#
# ---------------------------------------------------------------------

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;
}

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__