#!/usr/bin/perl 

=head1 NAME

getPropagationCount.pl - This program returns the propagation count of 
    a specified term or concept.

=head1 SYNOPSIS

This program takes in a cui (or term) and returns its propagation count.

=head1 USAGE

Usage: getPropagationCount.pl [OPTIONS] [CUI|TERM]

=head1 INPUT

=head2 Required Arguments:

=head3 [CUI|TERM]

A concept (CUI) or a term from the Unified Medical Language System

=head2 Optional Arguments:

=head3 --propagation FILE

The file containing the frequency counts for propagation

=head3 --infile FILE

A file containing a list of concepts or terms.

=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 children CUIs and their associated terms of the 
given CUI or 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;

GetOptions( "version", "help", "debug", "username=s", "password=s", "hostname=s", "database=s", "socket=s", "config=s", "infile=s", "propagation=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 term should be given on the command line.
if( (scalar(@ARGV) < 1) and !(defined $opt_infile) ){
    print STDERR "No term was specified on the command line\n";
    &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 = "";
my %option_hash = ();

$option_hash{"propagation"} = $opt_propagation;

if(defined $opt_config) {
    $option_hash{"config"} = $opt_config;
}
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_driver) {
    $option_hash{"driver"}   = "mysql";
}
if(defined $opt_database) {
    $option_hash{"database"} = $database;
}
if(defined $opt_password) {
    $option_hash{"password"} = $opt_password;
}
if(defined $opt_hostname) {
    $option_hash{"hostname"} = $hostname;
}
if(defined $opt_socket) {
    $option_hash{"socket"}   = $socket;
}

$umls = UMLS::Interface->new(\%option_hash); 
die "Unable to create UMLS::Interface object.\n" if(!$umls);
($errCode, $errString) = $umls->getError();
die "$errString\n" if($errCode);

&errorCheck($umls);

my $precision = 2;
my $floatformat = join '', '%', '.', $precision, 'f';


my @terms = ();
if(defined $opt_infile) {
    open(FILE, $opt_infile) || die "Could not open file: $file\n";
    while(<FILE>) {
	chomp;
	push @terms, $_;
    }
}
else {
    
    my $input = shift;
    push @terms, $input;
}

foreach my $input (@terms) {
    
    my $term = $input;

    my @c = ();
    if($input=~/C[0-9]+/) {
	push @c, $input;
	($term) = $umls->getTermList($input);
    }
    else {
	@c = $umls->getConceptList($input);
    }
    
    &errorCheck($umls);
    
    my $printFlag = 0;
    
    foreach my $cui (@c) {
	
	if($umls->validCui($cui)) {
	    print STDERR "ERROR: The concept ($cui) is not valid.\n";
	    exit;
	}

	#  make certain cui exists in this view
	if($umls->checkConceptExists($cui) == 0) { next; }	

	my $pcount = sprintf $floatformat, $umls->getPropagationCount($cui); 
	my $ic     = sprintf $floatformat, $umls->getIC($cui);

	&errorCheck($umls);
	
	if($pcount < 0) {
	    print "Input $input does not exist in this view of the UMLS.\n";
	}
	else {
	    print "The propagation count of $term ($cui) is $pcount ($ic). \n";
	}
	$printFlag = 1;
    }
    
    if(! ($printFlag) ) {
	print "Input $input does not exist in this view of the UMLS.\n";
    }
}

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


##############################################################################
#  function to output minimal usage notes
##############################################################################
sub minimalUsageNotes {
    
    print "Usage: getPropagationCount.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 CUI or a term\n";
    print "and returns all of its possible children given\n";
    print "a specified set of sources\n\n";
  
    print "Usage: getPropagationCount.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: getPropagationCount.pl,v 1.2 2010/02/25 19:54:15 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 getPropagationCount.pl --help for help.\n";
}
    
