pubmed2ref documentation.

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__

}

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
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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
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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
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

_load_instance	No description	Code
convert	No description	Code