Bio::Biblio::IO medlinexml
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Summary
Bio::Biblio::IO::medlinexml - A converter of XML files with MEDLINE citations
Package variables
No package variables defined.
Included modules
XML::Parser
Inherit
Bio::Biblio::IO
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 $io = Bio::Biblio::IO->new(-format => 'medlinexml');
Description
This object reads bibliographic citations in XML/MEDLINE format and
converts them into Bio::Biblio::RefI objects. It is an
implementation of methods defined in Bio::Biblio::IO.
Methods
_initialize
No description
Code
_parse
No description
Code
next_bibref
No description
Code
handle_doc_start
No description
Code
handle_doc_end
No description
Code
handle_char
No description
Code
handle_start
No description
Code
handle_end
No description
Code
_process_citation
No description
Code
_add_element
No description
Code
_data2obj
No description
Code
_obj2obj
No description
Code
_eq_hash_elem
No description
Code
_debug_object_stack
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ($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'} || 'medline2ref'; $result = "\L$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)) { $Convert = "Bio::Biblio::IO::$result"->new (@args); } } # create an instance of the XML parser
# (unless it is already there...)
$self->{'_xml_parser'} = new XML::Parser (Handlers => {Init =>\& handle_doc_start, Start =>\& handle_start, End =>\& handle_end, Char =>\& handle_char, Final =>\& handle_doc_end}) unless $self->{'_xml_parser'}; # if there is an argument '-callback' then start parsing at once -
# the registered event handlers will use 'callback' to report
# back after each citation
#
# we need to remember this situation also in a global variable
# because the event handler subroutines know nothing about this
# object (unfortunately)
if ($Callback = $self->{'_callback'}) { $self->_parse; } } # -----------------------------------------------------------------------------
}
_parsedescriptionprevnextTop
sub _parse {
    my ($self) = shift;


    if (defined $self->{'_file'}) {
	$self->{'_xml_parser'}->parsefile ($self->{'_file'});
    } elsif (defined $self->{'_fh'}) {
	my $fh = $self->{'_fh'};
	if (ref ($fh) and UNIVERSAL::isa ($fh, 'IO::Handler')) {
	    $self->{'_xml_parser'}->parse ($fh);
	} else {
	    my $data;
	    $data .= $_ while <$fh>;
	    $self->{'_xml_parser'}->parse ($data);
	}
    } elsif ($self->{'_data'}) {
	$self->{'_xml_parser'}->parse ($self->{'_data'});
    } else {
	$self->throw ("XML source to be parsed is unknown. Should be given in the new().");
    }

    # when parsing is done all citations have already been delivered
# to the caller using her callbacks - and nothing to be stored
# here, or parser put all citations into global @Cittaions where
# we want to copy there into this instance - so any caller can
# start parsing other XML input without overwriting already read
# citations from the first parser
if (@Citations) { $self->{'_citations'} = []; foreach my $cit (@Citations) { push (@{ $self->{'_citations'} }, $cit); undef $cit; } undef @Citations; } } # ---------------------------------------------------------------------
#
# Here is an implementation of Bio::Biblio::IO methods
#
# ---------------------------------------------------------------------
# global variables used by the XML event handlers
# TBD: make them accessible at least ONLY from this module...
@Citations = (); $Callback = undef; $Convert = undef; @ObjectStack = (); # it has Hash-Ref elements
@PCDataStack = (); # it has String elements
}
next_bibrefdescriptionprevnextTop
sub next_bibref {
   my ($self) = @_;
   $self->throw ("Method 'next_bibref' should not be called when a '-callback' argument given.")
       if $self->{'_callback'};

   # parse the whole input into memory (global @Citations)
# and then copy it into this object
$self->_parse unless $self->{'_citations'}; # return the next citation (and forget it here)
shift (@{ $self->{'_citations'} }); } # ---------------------------------------------------------------------
#
# 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 = ( 'AbstractText' => 1, 'AccessionNumber' => 1, 'Acronym' => 1, 'Affiliation' => 1, 'Agency' => 1, 'ArticleTitle' => 1, 'CASRegistryNumber' => 1, 'CitationSubset' => 1, 'Coden' => 1, 'CollectionTitle' => 1, 'CollectiveName' => 1, 'CopyrightInformation' => 1, 'Country' => 1, 'DataBankName' => 1, 'DateOfElectronicPublication' => 1, 'Day' => 1, 'Descriptor' => 1, 'DescriptorName' => 1, 'EndPage' => 1, 'FirstName' => 1, 'ForeName' => 1, 'GeneralNote' => 1, 'GeneSymbol' => 1, 'GrantID' => 1, 'Hour' => 1, 'ISOAbbreviation' => 1, 'ISSN' => 1, 'Initials' => 1, 'Issue' => 1, 'Keyword' => 1, 'Language' => 1, 'LastName' => 1, 'MedlineCode' => 1, 'MedlineDate' => 1, 'MedlineID' => 1, 'MedlinePgn' => 1, 'MedlineTA' => 1, 'MiddleName' => 1, 'Minute' => 1, 'Month' => 1, 'NameOfSubstance' => 1, 'NlmUniqueID' => 1, 'Note' => 1, 'NumberOfReferences' => 1, 'OtherID' => 1, 'PMID' => 1, 'PublicationType' => 1, 'Publisher' => 1, 'QualifierName' => 1, 'RefSource' => 1, 'RegistryNumber' => 1, 'Season' => 1, 'Second' => 1, 'SpaceFlightMission' => 1, 'StartPage' => 1, 'SubHeading' => 1, 'Suffix' => 1, 'Title' => 1, 'VernacularTitle' => 1, 'Volume' => 1, 'Year' => 1, ); %SIMPLE_TREATMENT = ( 'MeshHeading' => 1, 'Author' => 1, 'Article' => 1, 'Book' => 1, 'Investigator' => 1, 'Chemical' => 1, 'Pagination' => 1, 'MedlineJournalInfo' => 1, 'JournalIssue' => 1, 'Journal' => 1, 'DateCreated' => 1, 'DateCompleted' => 1, 'DateRevised' => 1, 'PubDate' => 1, 'Abstract' => 1, 'Grant' => 1, 'CommentsCorrections' => 1, 'CommentOn' => 1, 'CommentIn' => 1, 'ErratumFor' => 1, 'ErratumIn' => 1, 'OriginalReportIn' => 1, 'RepublishedFrom' => 1, 'RepublishedIn' => 1, 'RetractionOf' => 1, 'RetractionIn' => 1, 'SummaryForPatientsIn' => 1, 'UpdateIn' => 1, 'UpdateOf' => 1, 'DataBank' => 1, 'KeywordList' => 1, 'DeleteCitation' => 1, ); %POP_DATA_AND_PEEK_OBJ = ( 'Descriptor' => 1, 'DescriptorName' => 1, 'Year' => 1, 'Month' => 1, 'Day' => 1, 'LastName' => 1, 'Initials' => 1, 'FirstName' => 1, 'ForeName' => 1, 'NameOfSubstance' => 1, 'RegistryNumber' => 1, 'CASRegistryNumber' => 1, 'MiddleName' => 1, 'NlmUniqueID' => 1, 'MedlineTA' => 1, 'MedlinePgn' => 1, 'MedlineCode' => 1, 'Country' => 1, 'ISSN' => 1, 'ArticleTitle' => 1, 'Issue' => 1, 'AbstractText' => 1, 'VernacularTitle' => 1, 'GrantID' => 1, 'Agency' => 1, 'Acronym' => 1, 'MedlineDate' => 1, 'NumberOfReferences' => 1, 'RefSource' => 1, 'DataBankName' => 1, 'CopyrightInformation' => 1, 'Suffix' => 1, 'Note' => 1, 'CollectiveName' => 1, 'Hour' => 1, 'Minute' => 1, 'Second' => 1, 'Season' => 1, 'Coden' => 1, 'ISOAbbreviation' => 1, 'Publisher' => 1, 'CollectionTitle' => 1, 'DateOfElectronicPublication' => 1, 'StartPage' => 1, 'EndPage' => 1, 'Volume' => 1, 'Title' => 1, ); %POP_OBJ_AND_PEEK_OBJ = ( 'Pagination' => 1, 'JournalIssue' => 1, 'Journal' => 1, 'DateCreated' => 1, 'Article' => 1, 'DateCompleted' => 1, 'DateRevised' => 1, 'CommentsCorrections' => 1, 'Book' => 1, 'PubDate' => 1, 'Abstract' => 1, ); %POP_AND_ADD_DATA_ELEMENT = ( 'Keyword' => 'keywords', 'PublicationType' => 'publicationTypes', 'CitationSubset' => 'citationSubsets', 'Language' => 'languages', 'AccessionNumber' => 'accessionNumbers', 'GeneSymbol' => 'geneSymbols', 'SpaceFlightMission' => 'spaceFlightMissions', ); %POP_AND_ADD_ELEMENT = ( 'OtherAbstract' => 'otherAbstracts', 'Chemical' => 'chemicals', 'KeywordList' => 'keywordLists', 'Grant' => 'grants', 'UpdateIn' => 'updateIns', 'CommentOn' => 'commentOns', 'CommentIn' => 'commentIns', 'DataBank' => 'dataBanks', 'PersonalNameSubject' => 'personalNameSubjects', 'ErratumFor' => 'erratumFors', 'ErratumIn' => 'erratumIns', 'RepublishedFrom' => 'republishedFroms', 'RepublishedIn' => 'republishedIns', 'RetractionOf' => 'retractionOfs', 'RetractionIn' => 'retractionIns', 'UpdateOf' => 'updateOfs', 'OriginalReportIn' => 'originalReportIns', 'SummaryForPatientsIn' => 'summaryForPatientsIns', 'MeshHeading' => 'meshHeadings', );
}
handle_doc_startdescriptionprevnextTop
sub handle_doc_start {
    @Citations = ();
    @ObjectStack = ();
    @PCDataStack = ();
}
handle_doc_enddescriptionprevnextTop
sub handle_doc_end {
    undef @ObjectStack;
    undef @PCDataStack;
}
handle_chardescriptionprevnextTop
sub handle_char {
    my ($expat, $str) = @_;

    # this may happen with whitespaces between tags;
# but because I have not created an entry for data on the stack
# I can also ignore such data, can't I
return if $#PCDataStack < 0; $PCDataStack [$#PCDataStack] .= $str;
}
handle_startdescriptionprevnextTop
sub handle_start {
    my ($expat, $e, %attrs) = @_; 
#    &_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 'QualifierName' or $e eq 'SubHeading') { my %p = (); $p{'majorTopic'} = $attrs{'MajorTopicYN'} if $attrs{'MajorTopicYN'}; push (@ObjectStack,\% p); } if ($e eq 'GeneralNote') { my %p = (); $p{'owner'} = $attrs{'Owner'} if $attrs{'Owner'}; push (@ObjectStack,\% p); } if ($e eq 'OtherID') { my %p = (); $p{'source'} = $attrs{'Source'}; push (@ObjectStack,\% p); } #
# A special treatment is for attributes for personal name.
# Because there is no XML element 'PersonalName' I need to
# to put yet another object on @ObjectStack unless there is
# already one.
#
if ($e eq 'LastName' or $e eq 'FirstName' or $e eq 'MidleName' or $e eq 'Initials' or $e eq 'ForeName' or $e eq 'Suffix') { my $peek = $ObjectStack[$#ObjectStack]; push (@ObjectStack, {'type' => 'PersonalName'}) unless (ref $peek and &_eq_hash_elem ($peek, 'type', 'PersonalName')); } #
# Then we have #PCDATA elements without an attribute list.
# For them I create an entry on @PCDataStack.
#
if (exists $PCDATA_NAMES{$e}) { push (@PCDataStack, ''); #
# And finally, all non-PCDATA elements go to the objectStack
#
} elsif (exists $SIMPLE_TREATMENT{$e}) { push (@ObjectStack, {}); } elsif ($e eq 'PersonalNameSubject') { push (@ObjectStack, {'type' => 'PersonalName'}); } elsif ($e eq 'DescriptorName' or $e eq 'Descriptor') { if (&_eq_hash_elem (\%attrs, 'MajorTopicYN', "Y")) { my $peek = $ObjectStack[$#ObjectStack]; $$peek{'descriptorMajorTopic'} = "Y"; } } elsif ($e eq 'MedlineCitation' || $e eq 'NCBIArticle') { my %p = ( 'type' => 'MedlineCitation' ); $p{'owner'} = $attrs{'Owner'} if $attrs{'Owner'}; $p{'status'} = $attrs{'Status'} if $attrs{'Status'}; push (@ObjectStack,\% p); } elsif ($e eq 'GrantList') { if (&_eq_hash_elem (\%attrs, 'CompleteYN', "N")) { my $peek = $ObjectStack[$#ObjectStack]; $$peek{'grantListComplete'} = "N"; } } elsif ($e eq 'DataBankList') { if (&_eq_hash_elem (\%attrs, 'CompleteYN', "N")) { my $peek = $ObjectStack[$#ObjectStack]; $$peek{'dataBankListComplete'} = "N"; } } elsif ($e eq 'AuthorList') { if (&_eq_hash_elem (\%attrs, 'CompleteYN', "N")) { my $peek = $ObjectStack[$#ObjectStack]; $$peek{'authorListComplete'} = "N"; } } elsif ($e eq 'OtherAbstract') { my %p = (); $p{'type'} = $attrs{'Type'} if $attrs{'Type'}; push (@ObjectStack,\% p); # push (@ObjectStack, { 'type' => 'Abstract' });
}
}
handle_enddescriptionprevnextTop
sub handle_end {
    my ($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 'QualifierName' or $e eq 'SubHeading') { my $p = pop @ObjectStack; # pSubHeading
$$p{'subHeading'} = pop @PCDataStack; &_add_element ('subHeadings', $p); # adding to pMeshHeadings
# &_debug_object_stack ("END", $e);
return; } elsif ($e eq 'GeneralNote') { my $p = pop @ObjectStack; # pGeneralNote
$$p{'generalNote'} = pop @PCDataStack; &_add_element ('generalNotes', $p); # adding to pMedlineCitation
# &_debug_object_stack ("END", $e);
return; } elsif ($e eq 'OtherID') { my $p = pop @ObjectStack; # pOtherID
$$p{'otherID'} = pop @PCDataStack; &_add_element ('otherIDs', $p); # adding to pMedlineCitation
# &_debug_object_stack ("END", $e);
return; } #
# both object and pcdata stacks elements mixed here together
# (the element names appear in the order of frequency in the
# medline data set)
#
if (exists $POP_DATA_AND_PEEK_OBJ{$e}) { &_data2obj ("\l$e"); } elsif (exists $POP_OBJ_AND_PEEK_OBJ{$e}) { &_obj2obj ("\l$e"); } elsif (exists $POP_AND_ADD_ELEMENT{$e}) { &_add_element ($POP_AND_ADD_ELEMENT{$e}, pop @ObjectStack); } elsif (exists $POP_AND_ADD_DATA_ELEMENT{$e}) { &_add_element ($POP_AND_ADD_DATA_ELEMENT{$e}); } elsif ($e eq 'Author' or $e eq 'Investigator') { my $pAuthor; my $p = pop @ObjectStack; # pPersonalName or pAuthor
if (&_eq_hash_elem ($p, 'type', 'PersonalName')) { $pAuthor = pop @ObjectStack; $$pAuthor{'personalName'} = $p; } else { $pAuthor = $p; } my $peek = $ObjectStack[$#ObjectStack]; # pMedlineCitation, pArticle or pBook
if (&_eq_hash_elem ($peek, 'type', 'MedlineCitation')) { &_add_element ('investigators', $pAuthor); } else { &_add_element ('authors', $pAuthor); } } elsif ($e eq 'MedlineJournalInfo') { &_obj2obj ('journalInfo'); } elsif ($e eq 'PMID') { my $peek = $ObjectStack[$#ObjectStack]; # pMedlineCitation, pReference or pDeleteCitation
if (&_eq_hash_elem ($peek, 'type', 'DeleteCitation')) { &_add_element ('PMIDs'); } else { $$peek{'PMID'} = pop @PCDataStack; } } elsif ($e eq 'MedlineID') { my $peek = $ObjectStack[$#ObjectStack]; # pMedlineCitation, pReference or pDeleteCitation
if (&_eq_hash_elem ($peek, 'type', 'DeleteCitation')) { &_add_element ('MedlineIDs'); } else { $$peek{'medlineID'} = pop @PCDataStack; } # } elsif ($e eq 'OtherAbstract') {
# my $pAbstract = pop @ObjectStack;
# my $pOtherAbstract = pop @ObjectStack;
# $$pOtherAbstract{'abstract'} = $pAbstract
# &_add_element ('otherAbstracts', $pOtherAbstract);
} elsif ($e eq 'Affiliation') { my $peek = $ObjectStack[$#ObjectStack]; if (&_eq_hash_elem ($peek, 'type', 'PersonalName')) { my $peek2 = $ObjectStack[$#ObjectStack - 1]; $$peek2{'affiliation'} = pop @PCDataStack; } else { $$peek{'affiliation'} = pop @PCDataStack; } } elsif ($e eq 'DeleteCitation') { pop @ObjectStack; ### warn ("'DeleteCitation' tag found. Not known what to do with it."); # silently ignored
} elsif ($e eq 'MedlineCitation') { #
# Here we finally have the whole citation ready.
#
&_process_citation (pop @ObjectStack); #
# ERROR: if we are here, there was an unexpected element
#
} elsif (exists $PCDATA_NAMES{$e}) { pop @PCDataStack; warn ("An unexpected element found: $e"); } # &_debug_object_stack ("END", $e);
} # what to do when we have the whole $citation ready
}
_process_citationdescriptionprevnextTop
sub _process_citation {
    my ($citation) = @_;
    $citation = $Convert->convert ($citation) if defined $Convert;

    if ($Callback) {
	&$Callback ($citation);
    } else {
	push (@Citations, $citation);
    }
}

# add $element into an array named $key to the top object at @ObjectStack;
# if $element is empty, take it from @PCDataStack
}
_add_elementdescriptionprevnextTop
sub _add_element {
    my ($key, $element) = @_;
    my $peek = $ObjectStack[$#ObjectStack];
    $$peek{$key} = [] unless $$peek{$key};
    push (@{ $$peek{$key} }, (defined $element ? $element : pop @PCDataStack));
}

# remove top of @PCDataStack and put it into top object at @ObjectStack under name $key
}
_data2objdescriptionprevnextTop
sub _data2obj {
    my ($key) = @_;
    my $peek = $ObjectStack[$#ObjectStack];
    $$peek{$key} = pop @PCDataStack;
}

# remove top of @ObjectStack and put it into now-top at @ObjectStack under name $key
}
_obj2objdescriptionprevnextTop
sub _obj2obj {
    my ($key) = @_;
    my $p = pop @ObjectStack;
    my $peek = $ObjectStack[$#ObjectStack];
    $$peek{$key} = $p;
}

# check if a $key exists in a ref-hash $rh and if it is equal to $value
}
_eq_hash_elemdescriptionprevnextTop
sub _eq_hash_elem {
    my ($rh, $key, $value) = @_;
    return (defined $$rh{$key} and $$rh{$key} eq $value);
}

#
# --- only for debugging
#
use vars qw(%DEBUGSTACK); %DEBUGSTACK = ();
}
_debug_object_stackdescriptionprevnextTop
sub _debug_object_stack {
    my ($action, $element) = @_;
    if ($action =~ /^START/o) {
	$DEBUGSTACK{$element} = (@ObjectStack+0);
    } else {
	return if $element eq 'LastName';
	print "Element $element starts on " .
	    $DEBUGSTACK{$element} . 'and ends on ' . (@ObjectStack+0) . "\n"
		if $DEBUGSTACK{$element} != (@ObjectStack+0);
    }
}

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::medlinexml::VERSION;
print $Bio::Biblio::IO::medlinexml::Revision;