#! /usr/local/bin/perl 
#!/usr/bin/perl 

=head1 NAME

getCuiDef.pl - this program returns the definition of a concept.

=head1 SYNOPSIS

This program takes in a CUI and returns its definitions

=head1 USAGE

Usage: getCuiDef.pl [OPTIONS] CUI

=head1 INPUT

=head2 Required Arguments:

=head3 CUI

Concept Unique Identifier (CUI) from the Unified Medical 
Language System (UMLS)

=head2 Optional Arguments:

=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) 2007-2008,

 Bridget T. McInnes, University of Minnesota
 bthomson at cs.umn.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;

GetOptions( "version", "help", "username=s", "password=s", "hostname=s", "database=s", "socket=s", "config=s" );


#  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 CUI should be given on the command line.
if(scalar(@ARGV) < 1) {
    print STDERR "No term was specified on the command line";
    &minimalUsageNotes();
    exit;
}

my $database = "umls";
if(defined $opt_database) { $database = $opt_database; }
my $hostname = "localhost";
if(defined $opt_hostname) { $hostname = $opt_hostname; }
my $socket   = "/tmp/mysql.sock";
if(defined $opt_socket)   { $socket   = $opt_socket;   }

my $umls = "";

if(defined $opt_username and defined $opt_password and defined $opt_config) {
    $umls = UMLS::Interface->new({"driver" => "mysql", 
				  "database" => "$database", 
				  "username" => "$opt_username",  
				  "password" => "$opt_password", 
				  "hostname" => "$hostname", 
				  "socket"   => "$socket",
			          "config"   => "$opt_config"}); 
    die "Unable to create UMLS::Interface object.\n" if(!$umls);
    ($errCode, $errString) = $umls->getError();
    die "$errString\n" if($errCode);
}
elsif(defined $opt_username and defined $opt_password) {    
    $umls = UMLS::Interface->new({"driver" => "mysql", 
				  "database" => "$database", 
				  "username" => "$opt_username",  
				  "password" => "$opt_password", 
				  "hostname" => "$hostname", 
				  "socket"   => "$socket"}); 
    die "Unable to create UMLS::Interface object.\n" if(!$umls);
    ($errCode, $errString) = $umls->getError();
    die "$errString\n" if($errCode);
}
elsif(defined $opt_config) {
    $umls = UMLS::Interface->new({"config" => "$opt_config"});
    die "Unable to create UMLS::Interface object.\n" if(!$umls);
    ($errCode, $errString) = $umls->getError();
    die "$errString\n" if($errCode);
}
else {
    $umls = UMLS::Interface->new(); 
    die "Unable to create UMLS::Interface object.\n" if(!$umls);
    ($errCode, $errString) = $umls->getError();
    die "$errString\n" if($errCode);
}

&errorCheck($umls);

my $cui = shift;

if($umls->validCui($cui)) {
    print STDERR "ERROR: The concept ($cui) is not valid.\n";
    exit;
}

my @defs = $umls->getCuiDef($cui); 

&errorCheck($umls);

print "The definition(s) of $cui:\n";
my $i = 1;
foreach $def (@defs) {
    print "$i. $def\n"; $i++;
}

sub errorCheck
{
    my $obj = shift;
    ($errCode, $errString) = $obj->getError();
    print "ERRORCHECK: $errCode ($errString)\n";
    print STDERR "$errString\n" if($errCode);
    exit if($errCode > 1);
}


##############################################################################
#  function to output minimal usage notes
##############################################################################
sub minimalUsageNotes {
    
    print "Usage: queryCui.pl [OPTIONS] CUI \n\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 all of its definitions.\n\n";
  
    print "Usage: getCuiDef.pl [OPTIONS] CUI\n\n";

    print "Options:\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";

    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: getCuiDef.pl,v 1.4 2009/01/12 19:58:45 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 queryCui.pl --help for help.\n";
}
    
