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#!/usr/bin/perl 
HideShow 150 lines of Pod
=head1 NAME
getExtendedDef.pl - This program returns the extended definition of a 
concept or a term.
=head1 SYNOPSIS
This program takes in a CUI or a term and returns its extended 
definition consisting of the its definition, the definition of 
its all of its relations. 
=head1 USAGE
Usage: getExtendedDef.pl [OPTIONS] [CUI|TERM]
=head1 INPUT
=head2 Required Arguments:
=head3 [CUI|TERM}
Concept Unique Identifier (CUI) or a term from the Unified Medical 
Language System (UMLS)
=head2 Optional Arguments:
=head3 --config FILE
This is the configuration file. The format of the configuration 
file is as follows:
SABDEF :: <include|exclude> <source1, source2, ... sourceN>
RELDEF :: <include|exclude> <relation1, relation2, ... relationN>
SABDEF refers to the sources in which the definitions can come from.
RELDEF refers to the relations in which the definitions can come from.
The possible relations that can be included in RELDEF are:
  1. all of the possible relations in MRREL such as PAR, CHD, ...
  2. CUI which refers the concepts definition
  3. ST which refers to the concepts semantic types definition
  4. TERM which refers to the concepts associated terms
For example, if we wanted to use the MSH vocabulary and we 
wanted to use the terms, the CUIs definition and the CUIs 
parent definition and its semantic type definition as the 
extended definition the configuration file would be:
SABDEF :: include MSH
RELDEF :: include TERM, CUI, PAR, ST
or 
SABDEF :: include MSH
If you go to the configuration file directory, there will 
be example configuration files for the different runs that 
you have performed.
The default is:
SABDEF :: include UMLS_ALL
RELDEF :: include UMLS_ALL
which uses all of the sources and all of the relations. 
=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
List of CUIs that are associated with the input term
=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) 2007-2009,
 Bridget T. McInnes, University of Minnesota
 bthomson at cs.umn.edu
     
 Ted Pedersen, University of Minnesota Duluth
 tpederse at d.umn.edu
 Siddharth Patwardhan, University of Utah, Salt Lake City
 sidd@cs.utah.edu
  
 Serguei Pakhomov, University of Minnesota Twin Cities
 pakh0002@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", "debug", "username=s", "password=s", "hostname=s", "database=s", "socket=s", "config=s")) 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;
}
#  check the config 
if( defined $opt_config) { 
    checkConfigFile($opt_config);
}
# At least 1 CUI should be given on the command line.
if(scalar(@ARGV) < 1) {
    print STDERR "No term was specified on the command line\n";
    &minimalUsageNotes();
    exit;
}
my $umls = "";
my %option_hash = ();
if(defined $opt_config) {
    $option_hash{"config"} = $opt_config;
}
if(defined $opt_verbose) {
    $option_hash{"verbose"} = $opt_verbose;
}
if(defined $opt_debug) {
    $option_hash{"debug"} = $opt_debug;
}
if(defined $opt_username) {
    $option_hash{"username"} = $opt_username;
}
if(defined $opt_driver) {
    $option_hash{"driver"}   = $opt_driver;
}
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;
}
$umls = UMLS::Interface->new(\%option_hash); 
die "Unable to create UMLS::Interface object.\n" if(!$umls);
my $input = shift;
my $term  = $input;
my $c = undef;
if($input=~/C[0-9]+/) {
    push @{$c}, $input;
    my $terms = $umls->getDefTermList($input);
    $term = shift @{$terms};
}
else {
    $c = $umls->getDefConceptList($input);
}
my $printFlag = 0;
foreach my $cui (@{$c}) {
    my $defs = $umls->getExtendedDefinition($cui); 
    if($#{$defs} >= 0) {
        print "The definition(s) of $term ($cui):\n";
        my $i = 1;
        foreach $def (@{$defs}) {
            print "  $i. $def\n"; $i++;
        }
    }
    else {
        print "There are no definitions for $term ($cui)\n";
    }
    $printFlag = 1;
}
if(! ($printFlag) ) {
    print "There are no definitions for $input\n";
}
                                             
##############################################################################  
#  check to make certain the config file contains the correct parameters        
##############################################################################  
sub checkConfigFile {                                                           
    my $configfile = shift;                                                     
    open(CONFIG, $configfile) || die "Could not open config file ($config)\n";  
    while(<CONFIG>) {                                                           
        chomp;                                                                  
        if($_=~/SAB\s*\:\:/) {                                                      
            print STDERR "SAB not valid parameter for getExtendedDef.pl\n";
            &minimalUsageNotes();                              
            exit;                                                               
        }                                                                       
        if($_=~/REL\s*\:\:/) {                                                      
            print STDERR "REL not valid parameter for getExtendedDef.pl\n";
            &minimalUsageNotes(); 
            exit;                                                               
        }                                                                       
    }            
} 
##############################################################################
#  function to output minimal usage notes
##############################################################################
sub minimalUsageNotes {
     
    print "Usage: getExtendedDef.pl [OPTIONS] [CUI|TERM] \n";
    &askHelp();
    exit;
}
##############################################################################
#  function to output help messages for this program
##############################################################################
sub showHelp() {
         
    print "This is a utility that takes as input a term\n";
    print "or CUI and returns its extended definitions.\n\n";
   
    print "Usage: getExtendedDef.pl [OPTIONS] [CUI|TERM]\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 "--config FILE            Configuration file\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: getExtendedDef.pl,v 1.13 2011/08/29 16:37:03 btmcinnes Exp $';
    print "\nCopyright (c) 2008, Ted Pedersen & Bridget McInnes\n";
}
##############################################################################
#  function to output "ask for help" message when user's goofed
##############################################################################
sub askHelp {
    print STDERR "Type getExtendedDef.pl --help for help.\n";
}