#!/usr/bin/perl
=head1 NAME
getDUI.pl - This program returns the DUI of a CUI (if in MSH)
=head1 SYNOPSIS
This program takes in a cui as input and returns its associated dui
=head1 USAGE
Usage: getDUI.pl [OPTIONS] [CUI|TERM]
=head1 INPUT
=head2 Required Arguments:
=head3 [CUI|TERM]
A concept (CUI) from the Unified Medical Language System
=head2 Optional Arguments:
=head3 --debug
Sets the debug flag for testing
=head3 --username STRING
Username is required to access the umls database on MySql
unless it was specified in the my.cnf file at installation
=head3 --password STRING
Password is required to access the umls database on MySql
unless it was specified in the my.cnf file at installation
=head3 --hostname STRING
Hostname where mysql is located. DEFAULT: localhost
=head3 --socket STRING
The socket your mysql is using. DEFAULT: /tmp/mysql.sock
=head3 --database STRING
Database contain UMLS DEFAULT: umls
=head4 --help
Displays the quick summary of program options.
=head4 --version
Displays the version information.
=head1 OUTPUT
DUI of a given CUI
=head1 SYSTEM REQUIREMENTS
=over
=item * Perl (version 5.8.5 or better) - http://www.perl.org
=back
=head1 AUTHOR
Bridget T. McInnes, University of Minnesota
=head1 COPYRIGHT
Copyright (c) 2016
Bridget T. McInnes, Virginia Commonwealth University
btmcinnes at vcu.edu
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation; either version 2 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program; if not, write to:
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
=cut
###############################################################################
# THE CODE STARTS HERE
###############################################################################
# ================================
# COMMAND LINE OPTIONS AND USAGE
# ================================
use UMLS::Interface;
use Getopt::Long;
eval(GetOptions( "version", "help", "username=s", "password=s", "hostname=s", "database=s", "socket=s", "verbose=s", "debug")) or die ("Please check the above mentioned option(s).\n");
# if help is defined, print out help
if( defined $opt_help ) {
$opt_help = 1;
&showHelp();
exit;
}
# if version is requested, show version
if( defined $opt_version ) {
$opt_version = 1;
&showVersion();
exit;
}
# At least 1 term should be given on the command line.
if(scalar(@ARGV) < 1) {
print STDERR "No CUI was specified on the command line\n";
&minimalUsageNotes();
exit;
}
my $umls = "";
my %option_hash = ();
if(defined $opt_verbose) {
$option_hash{"verbose"} = $opt_verbose;
}
if(defined $opt_username) {
$option_hash{"username"} = $opt_username;
}
if(defined $opt_debug) {
$option_hash{"debug"} = $opt_debug;
}
if(defined $opt_database) {
$option_hash{"database"} = $opt_database;
}
if(defined $opt_password) {
$option_hash{"password"} = $opt_password;
}
if(defined $opt_hostname) {
$option_hash{"hostname"} = $opt_hostname;
}
if(defined $opt_socket) {
$option_hash{"socket"} = $opt_socket;
}
$umls = UMLS::Interface->new(\%option_hash);
if(!$umls) {
print STDERR "Unable to create UMLS::Interface object.\n";
exit;
}
my $concept = shift;
my $dui = $umls->getDUI($concept);
if($dui=~/^\s*$/) {
print "There is no DUI associated with $concept\n";
}
else {
print "The DUI for $concept is $dui\n";
}
##############################################################################
# function to output minimal usage notes
##############################################################################
sub minimalUsageNotes {
print "Usage: getDUI.pl [OPTIONS] [CUI]\n";
&askHelp();
exit;
}
##############################################################################
# function to output help messages for this program
##############################################################################
sub showHelp() {
print "This is a utility that takes as input a CUI \n";
print "and returns its associated MSH DUI\n\n";
print "Usage: getDUI.pl [OPTIONS] [CUI]\n\n";
print "Options:\n\n";
print "--debug Sets the debug flag for testing\n\n";
print "--username STRING Username required to access mysql\n\n";
print "--password STRING Password required to access mysql\n\n";
print "--hostname STRING Hostname for mysql (DEFAULT: localhost)\n\n";
print "--database STRING Database contain UMLS (DEFAULT: umls)\n\n";
print "--socket STRING Socket used by mysql (DEFAULT: /tmp.mysql.sock)\n\n";
print "--version Prints the version number\n\n";
print "--help Prints this help message.\n\n";
}
##############################################################################
# function to output the version number
##############################################################################
sub showVersion {
print '$Id: getDUI.pl,v 1.1 2016/01/07 22:50:15 btmcinnes Exp $';
print "\nCopyright (c) 2016, Ted Pedersen & Bridget McInnes\n";
}
##############################################################################
# function to output "ask for help" message when user's goofed
##############################################################################
sub askHelp {
print STDERR "Type getDUI.pl --help for help.\n";
}