#!/usr/bin/perl 

=head1 NAME

getSemanticRelation.pl - This program returns a concepts semantic relation(s) 
between two semantic types

=head1 SYNOPSIS

This program takes two semantic types in the abbreviation form and returns 
their semantic relation. 

=head1 USAGE

Usage: getSemanticRelation.pl [OPTIONS] [ST1] [ST2]

=head1 INPUT

=head2 Required Arguments:

=head3 [ST1] [ST2]

The semantic types in their abbreviation form. For example, the 
semantic type of ahnd is Body Part, Organ, or Organ Component. Its 
abbreviation form (which is more commonly used - at least by us - 
is pboc <- this is the form that you should entir. 

=head2 Optional Arguments:

=head3 --infile FILE

A file containing a list of concepts or terms. The format requires 
two semantic types per line. For example:
  
  st1<>st2
  st3<>st4
  ...

=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) 2007-2011,

 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", "infile=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;
}

# At least 1 term or cui  should be given on the command line.
# unless the infile option was specified
if( !(defined $opt_infile) and (scalar(@ARGV) < 2) ) {
    print STDERR "At least 2 semantic types should be given on the ";
    print STDERR "command line or use the --infile option\n";
    &minimalUsageNotes();
    exit;
}

my $umls = "";
my %option_hash = ();

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;
}

$option_hash{"t"} = 1;
$umls = UMLS::Interface->new(\%option_hash); 
die "Unable to create UMLS::Interface object.\n" if(!$umls);
    
my @pairs = ();
if(defined $opt_infile) { 
    open(INFILE, $opt_infile) || die "Could not open infile ($opt_infile)\n";
    while(<INFILE>) { 
	chomp;
	push @typespairs, $_;
    } close INFILE;
}
else {
    my $input1 = shift;
    my $input2 = shift;
    push @pairs, "$input1<>$input2";
}

foreach my $input (@pairs) {
    my ($st1, $st2) = split/<>/, $input;
    
    my $relations = $umls->getSemanticRelation($st1, $st2);
	
    if($#{$relations} < 0) {
	print "There are no semantic relations between $st1 and $st2\n";
    }
    else {
	print "The semantic relations between $st1 and $st2:\n";
	foreach my $rel (@{$relations}) {
	    print "  $rel\n";
	}
    }
}

##############################################################################
#  function to output minimal usage notes
##############################################################################
sub minimalUsageNotes {
    
    print "Usage: getSemanticRelation.pl [OPTIONS] [ST1] [ST2] \n";
    &askHelp();
    exit;
}

##############################################################################
#  function to output help messages for this program
##############################################################################
sub showHelp() {

        
    print "This is a utility that takes as input two semantic types in their\n";
    print "abbreviation form and returns all of its semantic relations.\n\n";
  
    print "Usage: getSemanticRelation.pl [OPTIONS] [ST1] [ST2]\n\n";

    print "Options:\n\n";
    
    print "--infile FILE            A file containing a list of semantic type\n";
    print "                         pairs.\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: getSemanticRelation.pl,v 1.3 2011/08/29 16:37:03 btmcinnes Exp $';
    print "\nCopyright (c) 2011, Ted Pedersen & Bridget McInnes\n";
}

##############################################################################
#  function to output "ask for help" message when user's goofed
##############################################################################
sub askHelp {
    print STDERR "Type getSemanticRelation.pl --help for help.\n";
}