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lib/Bio/Biblio/IO/pubmedxml.pm  view on Meta::CPAN

    (
     'PubMedPubDate' => 'pubDates',
     'History' => 'histories',
     );


sub handle_start {
    my ($expat, $e, %attrs) = @_;
#    &Bio::Biblio::IO::medlinexml::_debug_object_stack ("START", $e);

    #
    # The #PCDATA elements which have an attribute list must
    # be first here - because for them I create entries both on
    # the @PCDataStack _and_ on @ObjectStack.
    #
    if ($e eq 'ArticleId') {
        my %p = ();
        $p{'idType'} = (defined $attrs{'IdType'} ? $attrs{'IdType'} : 'pubmed');
        push (@Bio::Biblio::IO::medlinexml::ObjectStack, \%p);
    }

    if ($e eq 'URL') {
        my %p = ();
        $p{'type'} = $attrs{'type'} if $attrs{'type'};
        $p{'lang'} = $attrs{'lang'} if $attrs{'lang'};
        push (@Bio::Biblio::IO::medlinexml::ObjectStack, \%p);
    }

    #
    # Then we have #PCDATA elements without an attribute list.
    # For them I create an entry on @PCDataStack.
    #
    if (exists $PCDATA_NAMES{$e}) {
        push (@Bio::Biblio::IO::medlinexml::PCDataStack, '');

    #
    # And finally, all non-PCDATA elements go to the objectStack
    #
    } elsif (exists $SIMPLE_TREATMENT{$e}) {
        push (@Bio::Biblio::IO::medlinexml::ObjectStack, {});

    } elsif ($e eq 'ArticleIdList') {
        ;

    } elsif ($e eq 'PubMedPubDate') {
        my %p = ();
        $p{'pubStatus'} = $attrs{'PubStatus'} if $attrs{'PubStatus'};
        push (@Bio::Biblio::IO::medlinexml::ObjectStack, \%p);

    } else {
        &Bio::Biblio::IO::medlinexml::handle_start ($expat, $e, %attrs);
    }
}


sub handle_end {
    my ($expat, $e) = @_;

    #
    # First I have to deal with those elements which are both PCDATA
    # (and therefore they are on the pcdataStack) and which have an
    # attribute list (therefore they are also known as a separate
    # p-object on the objectStack.
    #
    if ($e eq 'ArticleId') {
        &Bio::Biblio::IO::medlinexml::_data2obj ('id');
        &Bio::Biblio::IO::medlinexml::_add_element ('pubmedArticleIds', pop @Bio::Biblio::IO::medlinexml::ObjectStack);
#       &Bio::Biblio::IO::medlinexml::_debug_object_stack ("END", $e);
        return;
    }

    if ($e eq 'URL') {
        &Bio::Biblio::IO::medlinexml::_data2obj ('URL');
        &Bio::Biblio::IO::medlinexml::_add_element ('pubmedURLs', pop @Bio::Biblio::IO::medlinexml::ObjectStack);
#       &Bio::Biblio::IO::medlinexml::_debug_object_stack ("END", $e);
        return;
    }


    #
    # both object and pcdata stacks elements mixed here together
    #

    if (exists $POP_DATA_AND_PEEK_OBJ{$e}) {
        &Bio::Biblio::IO::medlinexml::_data2obj ("\l$e");

    } elsif (exists $POP_AND_ADD_DATA_ELEMENT{$e}) {
        &Bio::Biblio::IO::medlinexml::_add_element ($POP_AND_ADD_DATA_ELEMENT{$e}, pop @Bio::Biblio::IO::medlinexml::ObjectStack);

    } elsif ($e eq 'MedlineCitation' ||
             $e eq 'NCBIArticle') {
        &Bio::Biblio::IO::medlinexml::_obj2obj ('Citation');

    } elsif ($e eq 'PubmedData') {
        &Bio::Biblio::IO::medlinexml::_obj2obj ('PubmedData');

    } elsif ($e eq 'PubMedArticle' ||
             $e eq 'PubmedArticle') {

        #
        # Here we finally have the whole citation ready.
        #
        &Bio::Biblio::IO::medlinexml::_process_citation (pop @Bio::Biblio::IO::medlinexml::ObjectStack);

    } else {
        &Bio::Biblio::IO::medlinexml::handle_end ($expat, $e);
    }

#    &Bio::Biblio::IO::medlinexml::_debug_object_stack ("END", $e);

}

1;

__END__
=pod

=encoding utf-8

=head1 NAME

Bio::Biblio::IO::pubmedxml - a converter of XML files with PUBMED citations

=head1 VERSION

version 1.70

=head1 SYNOPSIS

Do not use this object directly, it is recommended to access it and use
it through the I<Bio::Biblio::IO> module:

  use Bio::Biblio::IO;
  my $io = Bio::Biblio::IO->new(-format => 'pubmedxml');

=head1 DESCRIPTION

This object reads bibliographic citations in XML/MEDLINE format and
converts them into I<Bio::Biblio::RefI> objects. It is an
implementation of methods defined in I<Bio::Biblio::IO>.