Bio::Biblio::IO pubmedxml
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Summary
Bio::Biblio::IO::pubmedxml - A converter of XML files with PUBMED citations
Package variables
No package variables defined.
Inherit
Bio::Biblio::IO::medlinexml
Synopsis
Do not use this object directly, it is recommended to access it and use
it through the Bio::Biblio::IO module:
  use Bio::Biblio::IO;
my $io = Bio::Biblio::IO->new(-format => 'pubmedxml');
Description
This object reads bibliographic citations in XML/MEDLINE format and
converts them into Bio::Biblio::RefI objects. It is an
implementation of methods defined in Bio::Biblio::IO.
Methods
_initialize
No description
Code
handle_start
No description
Code
handle_end
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ($self, @args) = @_;
    
    # 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', and making keys lowercase
my $new_key; foreach my $key (keys %param) { ($new_key = $key) =~ s/^-/_/; $self->{ lc $new_key } = $param { $key }; } # find the format for output - and put it into a global $Convert
# because it will be used by the event handler who knows nothing
# about this object
my $result = $self->{'_result'} || 'pubmed2ref'; $result = "\L$result"; # normalize capitalization to lower case
# a special case is 'raw' when no converting module is loaded
# and citations will be returned as a hashtable (the one which
# is created during parsing XML file/stream)
unless ($result eq 'raw') { # load module with output converter - as defined in $result
if (defined &Bio::Biblio::IO::_load_format_module ($result)) { $Bio::Biblio::IO::medlinexml::Convert = "Bio::Biblio::IO::$result"->new (@args); } } # create an instance of the XML parser
# (unless it is already there...)
$self->{'_xml_parser'} = new XML::Parser (Handlers => {Init =>\& Bio::Biblio::IO::medlinexml::handle_doc_start, Start =>\& handle_start, End =>\& handle_end, Char =>\& Bio::Biblio::IO::medlinexml::handle_char, Final =>\& Bio::Biblio::IO::medlinexml::handle_doc_end}) unless $self->{'_xml_parser'}; # if there is an argument '-callback' then start parsing at once -
# the registered event handlers will use 'callback' to report
# back after each citation
#
# we need to remember this situation also in a global variable
# because the event handler subroutines know nothing about this
# object (unfortunately)
if ($SUPER::Callback = $self->{'_callback'}) { $self->_parse; } } # ---------------------------------------------------------------------
#
# Here are the event handlers (they do the real job!)
#
# Note that these methods do not know anything about the object they
# are part of - they are called as subroutines. not as methods.
# It also means that they need to use global variables to store and
# exchnage intermediate results.
#
# ---------------------------------------------------------------------
#
# This is a list of #PCDATA elements.
#
%PCDATA_NAMES = ( 'PublicationStatus' => 1, 'ProviderId' => 1, 'ArticleId' => 1, 'URL' => 1, ); %SIMPLE_TREATMENT = ( 'History' => 1, 'PubMedArticle' => 1, 'PubmedArticle' => 1, 'PubmedData' => 1, ); %POP_DATA_AND_PEEK_OBJ = ( 'Year' => 1, 'Month' => 1, 'Day' => 1, 'Hour' => 1, 'Minute' => 1, 'Second' => 1, 'ProviderId' => 1, 'PublicationStatus' => 1, ); %POP_AND_ADD_DATA_ELEMENT = ( 'PubMedPubDate' => 'pubDates', 'History' => 'histories', );
}
handle_startdescriptionprevnextTop
sub handle_start {
    my ($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, $e, %attrs); }
}
handle_enddescriptionprevnextTop
sub handle_end {
    my ($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__
}
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
The main documentation details are to be found in
Bio::Biblio::IO.
Here is the rest of the object methods. Internal methods are preceded
with an underscore _.
VERSION and RevisionTop
 Usage   : print $Bio::Biblio::IO::pubmedxml::VERSION;
print $Bio::Biblio::IO::pubmedxml::Revision;