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sub GetNeighbors::read_object which reads hash reference object passed to this
sub and fetches the required Neighbors' information.

sub GetNeighbors::format_object calls appropriate functions like format_homogenous_hash,
format_scalar, format_homogenous_array depending on the object reference it is called with.
format_homogenous_hash,format_scalar and format_homogenous_array are subroutines which 
read the objects they are called with and fetch the desired information.

=item package ConnectUMLS

sub ConnectUMLS::get_pt to get the proxy ticket using a web service.

sub ConnectUMLS::connect_umls to connect to UMLS by sending username 
and password and getting back a proxy ticket.

=item package ValidateTerm

sub ValidateTerm::validateTerm to accepts an input and validates it 
for as valid or invalid CUI or a term.

=item package GetUserData

sub GetUserData::getUserDetails to get username and password from the user.

=item package Query

sub Query::runQuery which takes method name, service and other parameters as argument and calls the web service. 
It also displays the information received from the web service and other error messages. 

=item package FormGraph

sub FormGraph::form_graph forms graph using standard BFS algorithm and creates a graph
using the concepts and their neighbor concepts. It finds shortest path between two
input concepts and displays the path. 

=back

=cut

#---------------------------------------------------------------------------------------------------------------------------

#------------------------------PERLDOC ENDS HERE------------------------------------------------------------------------------


###############################################################################
##########  CODE STARTS HERE  #################################################

#use lib "/home/mugdha/UMLS-HSO/UMLS-HSO/WebService-UMLSKS-Similarity/lib";

use strict;
use warnings;
use SOAP::Lite;
use Term::ReadKey;
use WebService::UMLSKS::GetUserData;
use WebService::UMLSKS::ValidateTerm;
use WebService::UMLSKS::Query;
use WebService::UMLSKS::ConnectUMLS;
use WebService::UMLSKS::Similarity;
use WebService::UMLSKS::GetCUIs;
use WebService::UMLSKS::FormGraph;
use Log::Message::Simple qw[msg error debug];

#use get_all_associatedCUIs;
use Getopt::Long;
#use SOAP::Lite +trace => 'debug';
no warnings qw/redefine/;


#Program that returns the shortest path between two concepts using UMLS database.

# Author :			 Mugdha
# Reference:         Program provided by Olivier B., NLM.



my $verbose = '';
my $log_file = '';
my $patterns_file = '';
my $sources = '';
my $relations = '';
my $directions = '';
my $similarity;
my $config_file = '';
my $login_file = '';
my $test_file = '';
my $input1 = '';
my $input2 = '';
my $chd_threshold = '';
my $sib_threshold = '';


GetOptions( 'verbose:i' => \$verbose , 'sources=s' => \$sources , 'rels=s' =>\$relations, 'dirs=s' =>\$directions,
 'config=s' =>\$config_file, 'log=s' => \$log_file, 'login=s' => \$login_file ,'patterns=s' => \$patterns_file, 
 'testfile=s' => \$test_file, 'input1=s' => \$input1, 'input2=s'=>\$input2,'chd_threshold=s' => \$chd_threshold, 'sib_threshold=s'=>\$sib_threshold);

# Reference for use of Log package
# http://perldoc.perl.org/Log/Message/Simple.html#msg(%22message-string%22-%5b%2cVERBOSE%5d)


if($log_file ne '' && $verbose eq 1){

open (LOG , '>>', $log_file);


$Log::Message::Simple::MSG_FH     = \*LOG;
$Log::Message::Simple::ERROR_FH   = \*LOG;
$Log::Message::Simple::DEBUG_FH   = \*LOG;

# Following code to print time and date in readable form is taken from following source 
#http://perl.about.com/od/perltutorials/a/perllocaltime_2.htm

my @months = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec);
my @weekDays = qw(Sun Mon Tue Wed Thu Fri Sat Sun);
my ($second, $minute, $hour, $dayOfMonth, $month, $yearOffset, $dayOfWeek, $dayOfYear, $daylightSavings) = localtime();
my $year = 1900 + $yearOffset;
my $theTime = "$hour:$minute:$second, $weekDays[$dayOfWeek] $months[$month] $dayOfMonth, $year";

# Code from source ends here

debug("\n*********************************\n Log written on :
$theTime\n************************************", $verbose); 

}

if($log_file ne '' && $verbose eq '')
{
	print "\nPlease set verbose option to true to see the log\n";
	exit;
}

if(defined $config_file && $config_file ne "")
{
	 $similarity = WebService::UMLSKS::Similarity->new({"config" => $config_file});
	# print "\n creating  object of similarity with config file";
	msg("\n creating  object of similarity with config file", $verbose);
}

else
{
	if($sources eq "" && $relations eq "" && $directions eq "")
	{
		# use default things
		msg("\n creating default object of similarity", $verbose);
		 $similarity = WebService::UMLSKS::Similarity->new();
	}
	else{
		
		if( $sources ne "" && $relations ne "" && $directions ne "")
		{
			# user specified sources through command line
			my @source_list = split ("," , $sources);
			my @relation_list = split ("," , $relations);
			my @direction_list = split ("," , $directions);
			 $similarity = WebService::UMLSKS::Similarity->new({"sources" =>  \@source_list,
														    	 "rels"   =>  \@relation_list,
														    	 "dirs"   =>  \@direction_list }	);
			msg("\n creating  object of similarity with sources, rels and dirs", $verbose);
			#$ConfigurationParameters{"SAB"} = \@sources_list;
		}
		else{
		
			if($relations ne "" && $directions ne "")
			{
				# user specified rels through command line
				my @relation_list = split ("," , $relations);
				my @direction_list = split ("," , $directions);
				 $similarity = WebService::UMLSKS::Similarity->new({ "rels"   =>  \@relation_list,