diff variant_effect_predictor/Bio/Biblio/IO/pubmedxml.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Biblio/IO/pubmedxml.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,309 @@
+# $Id: pubmedxml.pm,v 1.4 2002/10/22 07:45:13 lapp Exp $
+#
+# BioPerl module Bio::Biblio::IO::pubmedxml.pm
+#
+# Cared for by Martin Senger <[e-mail]>
+# For copyright and disclaimer see below.
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Biblio::IO::pubmedxml - A converter of XML files with PUBMED citations
+
+=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 = new Bio::Biblio::IO (-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>.
+
+=head1 FEEDBACK
+
+=head2 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.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR
+
+Martin Senger ([e-mail])
+
+=head1 COPYRIGHT
+
+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.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=head1 APPENDIX
+
+The main documentation details are to be found in
+L<Bio::Biblio::IO>.
+
+Here is the rest of the object methods.  Internal methods are preceded
+with an underscore _.
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Biblio::IO::pubmedxml;
+use vars qw(@ISA $VERSION $Revision);
+use vars qw(%PCDATA_NAMES %SIMPLE_TREATMENT %POP_DATA_AND_PEEK_OBJ %POP_AND_ADD_DATA_ELEMENT);
+
+use strict;
+
+use Bio::Biblio::IO::medlinexml;
+
+@ISA = qw(Bio::Biblio::IO::medlinexml);
+
+BEGIN { 
+    # set the version for version checking
+    $VERSION = do { my @r = (q$Revision: 1.4 $ =~ /\d+/g); sprintf "%d.%-02d", @r };
+    $Revision = q$Id: pubmedxml.pm,v 1.4 2002/10/22 07:45:13 lapp Exp $;
+}
+
+sub _initialize {
+    my ($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',
+     );
+
+
+=head2 VERSION and Revision
+
+ Usage   : print $Bio::Biblio::IO::pubmedxml::VERSION;
+           print $Bio::Biblio::IO::pubmedxml::Revision;
+
+=cut
+
+
+sub handle_start {
+    my ($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__