libbio-perl-perl 1.7.2-2 / usr / share / perl5 / Bio / DB / MeSH.pm

#
# BioPerl module for Bio::DB::MeSH
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::DB::MeSH - Term retrieval from a Web MeSH database

=head1 SYNOPSIS

 my $mesh = Bio::DB::MeSH->new();
 my $term = $mesh->get_exact_term('Butter');
 print $term->description;

=head1 DESCRIPTION

This class retrieves a term from the Medical Subject Headings database
by the National Library of Medicine of USA. See
L<http://www.nlm.nih.gov/mesh/meshhome.html>. It uses the latest
data available (updates happen on weekdays). If it fails, an archive
cgi scripts accessing older data from previous year is used.

This class implements L<Bio::SimpleAnalysisI> and wraps its methods under
L<get_exact_term>.

By default, web access uses L<WWW::Mechanize>, but in its absence
falls back to bioperl module L<Bio::WebAgent> which is a subclass of
L<LWP::UserAgent>.

=head1 SEE ALSO

L<Bio::Phenotype::MeSH::Term>

=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 lists Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut


# Let the code begin...


package Bio::DB::MeSH;
use strict;

use Bio::Phenotype::MeSH::Term;
use Bio::Phenotype::MeSH::Twig;

use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);


my $URL = 'http://www.nlm.nih.gov/mesh/MBrowser.html';

my $ANALYSIS_SPEC= {name => 'MeSH term retrival',
                    type => 'Entry retrieval'};
my $INPUT_SPEC = [
                  {mandatory=>'true',
                   type => 'scalar',
                   'name'=> 'value',
                  },
                 ];

my  $RESULT_SPEC =
    {
     '' => 'Bio::Phenotype::MeSH::Term',
     raw => 'raw output',
    };


sub _init {
    # Note: Base URL is now set in _webmodule(), depending on which is selected
    my $self = shift;
    $self->{'_ANALYSIS_SPEC'} = $ANALYSIS_SPEC;
    $self->{'_INPUT_SPEC'}    = $INPUT_SPEC;
    $self->{'_RESULT_SPEC'}   = $RESULT_SPEC;
    $self->{'_ANALYSIS_NAME'} = $ANALYSIS_SPEC->{'name'};
    $self->_webmodule;
    return $self;
}


sub _webmodule {
    my ($self) = shift;
    $self->{'_webmodule'} = '';

    # Prefer WWW::Mechanize if available and use $URL
    eval {
        require WWW::Mechanize;
    };
    unless ($@) {
        $self->{'_webmodule'} = 'WWW::Mechanize';
        $self->url($URL);
        return;
    }

    # Bio::WebAgent uses cgi alternative URL
    $self->_set_cgi_base_url;

    # Use Bio::WebAgent alternative
    eval {
        require LWP::UserAgent;
    };
    unless ($@) {
        $self->{'_webmodule'} = 'Bio::WebAgent';
        return;
    }

    $self->throw("Bio::DB::MeSH needs either WWW::Mechanize or Bio::WebAgent");
}


sub _set_cgi_base_url {
    my ($self) = shift;

    # Try to get webpage corresponding to current year.
    # If it fails, try to get previous years until success or 2003
    my $year = 1900 + (localtime)[5];
    my $pass = 0;
    while ($pass == 0 and $year > 2003) {
        my $response;
        eval {
            $response = $self->get( "http://www.nlm.nih.gov/cgi/mesh/$year/MB_cgi" )
        };
        # Note: error 404 is acceptable because it can mean that webpage is not yet
        # implemented for current year. Absence of internet generates error 500.
        if ($@ or $response->{'_rc'} > 404) {
            $self->warn("Could not connect to the server\n") and return;
        }
        # Success closes the loop, fail makes it try with the another year
        if ($response->is_success) {
            $pass = 1;
        }
        else {
            $year -= 1;
        }
    }
    $self->url("http://www.nlm.nih.gov/cgi/mesh/$year/MB_cgi");
}

=head2 get_exact_term

  Title   : get_exact_term
  Usage   : $s = $db->get_exact_term($value);
  Function: Retrieve a single MeSH term using a unique ID or exact name.
  Example :
  Returns : a Bio::Phenotype::MeSH::Term object
  Args    : scalar, UID or name of a MeSH term

The returned term object contains information about the immediate
vincinity of the term in the terminology hierarchy. See
L<Bio::Phenotype::MeSH::Twig>.

=cut


sub get_exact_term {
    my ($self, $value) = @_;
    $self->{'_term'} = undef;
    $self->run($value) if $value;
    $self->throw("Could not connect to the server")
        unless $self->status eq 'COMPLETED';
    return $self->result;
}


sub run {
    my ($self, $value) = @_;

    # check input
    $self->throw("Need a MeSH name or ID  as an input [$value]") if ref $value;

    # internal run()
    $self->_run($value);
}


sub _cgi_url {
    my($self, $field, $term) = @_;

    # we don't bother to URI::Escape $field and $term as this is an untainted private sub
    my $base_url = $self->url;
    return "$base_url?field=$field&term=$term";
}


sub  _run {
    my ($self, $value)  = @_;
    $self->throw('Need a value [$value]')
        unless $value;;
    # delay repeated calls by default by 3 sec, set delay() to change
#    $self->sleep;

    $self->status('TERMINATED_BY_ERROR');

    if ($self->{'_webmodule'} eq 'WWW::Mechanize') {
        $self->debug("using WWW::Mechanize...\n");
        my $agent = WWW::Mechanize->new();
        $agent->get($self->url);
        $agent->status == 200
            or $self->warn("Could not connect to the server\n") and return;

        $agent->form_name('MB');

        $agent->field("term", $value);
        if ($value =~ /\w\d{6}/) {
            $agent->field("field", 'uid');
        } else {
            $agent->field("field", 'entry');
        }
        $agent->click("exact");

        $self->{'_content'} = $agent->content();
        $self->status('COMPLETED');
        return;
    }
    elsif ($self->{'_webmodule'} eq 'Bio::WebAgent') {
        $self->debug("using LWP::UserAgent...\n");
        my $response;
        if ($value =~ /\w\d{6}/) {
            $self->{'_content'} =
                $response = eval {
                    $self->get( $self->_cgi_url('uid', $value) )
                };
            $self->warn("Could not connect to the server\n") and return
                if $@;
        } else {
            $self->{'_content'} =
                eval {
                    $response = $self->get( $self->_cgi_url('entry', $value) )
                };
            $self->warn("Could not connect to the server\n") and return
                if $@;
        }
        if ($response->is_success) {
            $self->{'_content'} =  $response->content;
            $self->status('COMPLETED');
        }
        return;
    }
}


sub result {
    my ($self,$value) = @_;

    $self->throw("Could not retrieve results") unless $self->status('COMPLETED');

    # no processing
    return $self->{'_content'} if $value && $value eq 'raw';


    # create a MeSH::Term object
    $_ = $self->{'_content'};
    $self->debug( substr($_, 0, 100) . "\n");
    my ($id)   = m|Unique \s+ ID </TH>
                   <TD (?: \s+ [^>]+ )? >
                   (.*?)                    # id
                   </TD> |ix;
    my ($name) = m|MeSH \s+ Heading </TH>
                   <TD (?: \s+ [^>]+ )? >
                   (.*?)                    # name
                   </TD> |ix;
    my ($desc) = m|Scope \s+ Note </TH>
                   <TD (?: \s+ [^>]+ )? >
                   (.*?)                    # desc
                   </TD>|isx;
    $self->throw("No description returned: $_") unless defined $desc;
    $desc =~ s/<.*?>//sg;
    $desc =~ s/(?:\r)?\n/ /g;
    $desc =~ s/\( +/\(/g;
    $desc =~ s/ {2,}/ /g;

    my $term = Bio::Phenotype::MeSH::Term->new(-id => $id,
                                               -name => $name,
                                               -description => $desc
                                              );
    my ($trees) = $self->{'_content'} =~ /MeSH Tree Structures(.*)/s;

    while (m|Entry Term</TH><TD(?: [^>]+)?>(.*?)</TD>|ig) {
        $term->add_synonym($1);
        $self->debug("Synonym: |$1|\n");
    }

    foreach (split /<HR>/i, $trees ) {
        next unless /$name/;
        s/<TD.*?>/ /sgi;
        s/<.*?>//sg;
        s/&nbsp;/ /sg;
        #print "|$_|";
        my ($treeno) = /$name \[([^]]+)]/;
        my ($parent_treeno) = $treeno =~ /(.*)\.\d{3}/;
        my ($parent) =  /\n +(\w.+) \[$parent_treeno\]/;

        my $twig = Bio::Phenotype::MeSH::Twig->new(-parent => $parent);
        $term->add_twig($twig);

        $self->debug("Parent: |$parent|\n");
        while (/\n +(\w.+) \[$treeno\./g ) {
            $twig->add_child($1);
            $self->debug("Child: |$1|\n");
        }

        while (/\n +(\w.+) \[$parent_treeno\./g ) {
            next if $name eq $1;
            $twig->add_sister($1);
            $self->debug("Sister: |$1|\n");
        }
    }
    return $term;
}

1;