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###################################################
#                                                 #
#             SUBROUTINES BELOW                   #
#             -----------------                   #
#                                                 #
###################################################

############################ SUBROUTINE 1 #######################################################
#This subroutine prints the program details at start-up.
sub start_up {
	
	print color ("yellow"),"  
#######################################################################
#                                                                     #
#                easyDifferentialGeneCoexpressionWrapper v1.00        #
#                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~        #
#                                                                     #
#                Author:  Abbas Alameer, Kuwait University            #
#                         abbas.alameer\@ku.edu.kw                     #
#                                                                     #
#                                                                     #
#                       Developed in February 2022                    #
#                     and released under GPLv2 license                #
#                                                                     #
#######################################################################\n\n\n" , color("reset");
}
############################ SUBROUTINE 2 #######################################################
#various checks done before program's run execution.
sub initial_checks {
	
	#check 1 - check that the script is installed on the system.
	#Prompt user to install it, if not found in the $PATH.
	my $which_path	  	= qx{which easyDifferentialGeneCoexpressionWrapper};
	$run_subdir			= "/easyDifferentialGeneCoexpressionWrapper_files";
	$rscript_subdir 	= "$run_subdir/Rscript/";
	$csv_file_subdir 	= "$run_subdir/data/";
	$results_subdir		= "$run_subdir/results/";

	unless ($which_path) {
		
		print color ("red"), "easyDifferentialGeneCoexpressionWrapper is not installed on this system...\n", color("reset");
		print color ("red"), "See \"README\" for installation instructions.\n", color("reset");
		exit;
	} 

	else {
		
		my $home_dir  = File::HomeDir -> my_home;
		$rscript_path = $home_dir . $rscript_subdir;
		$data_path	  = $home_dir . $csv_file_subdir;
		$results_path = $home_dir . $results_subdir;
		
		#create main directories - ignore if already present
		system("mkdir -p $rscript_path $data_path $results_path");
	}
	
	#check 2 - check for the presence of curl binary in the $PATH. 
	#if not found, install on Ubuntu-based systems. 
	#if system is not Ubuntu-based systems, prompt user to install it manually.
	my $check_curl = qx{which curl};
	#check if current system is Ubuntu-based
	my $ubuntu = qx{uname -a};
	
	if (!$check_curl) {
			
		if ($ubuntu=~ /.+ubuntu.+/ig) {
			
			print color ("red"), "curl binary was not found: follow onscreen instructions/input your password for its installation...\n\n", color("reset");
			system("sudo apt -y install curl"); #install curl
			print "done\n";	
		} 
			
		else { 
				
			print color ("red"), "curl binary was not found: install it on your system.\n", color("reset");
			exit; 
		}
	}	
	
	#check 3 - check for presence of easyDifferentialGeneCoexpressionInputParameters.r and its auxiliary file && .csv file(s)
	$RscriptFile 	 = "$rscript_path" . "easyDifferentialGeneCoexpressionInputParameters.r";
	
	unless (-e $RscriptFile) {

			#The script downloads the two R scripts if they do not exist in the current folder
			print color ("red"), "\"$RscriptFile\" & \"installPackages.r\" files are missing and will be downloaded...\n\n", color("reset");
			system ("cd $rscript_path && { curl -O -C - https://raw.githubusercontent.com/davidechicco/easyDifferentialGeneCoexpression/main/bin/easyDifferentialGeneCoexpressionInputParameters.r ; }");
			#make sure to download installPackages.r an auxiliary script used for installing/loading CRAN packages by the main R script.
			system ("cd $rscript_path && { curl -O -C - https://raw.githubusercontent.com/davidechicco/easyDifferentialGeneCoexpression/main/bin/installPackages.r ; }");

	}
	
}
############################ SUBROUTINE 3 #######################################################
#get the current date and time.
sub date_time {
	
    my ($sec, $min, $hour, $mday, $mon, $yr, $wday, $yday, $isdst) = localtime();
    my $ctime = localtime();
    my $time_hour;
    my $time_minutes; 
                                       #hour  #minutes
    if ($ctime =~ m/^\w+\s+\w+\s+\d+\s+(\d+)\:(\d+)\:\d+\s+\d+/) {
		
		$time_hour = $1;
		$time_minutes = $2;
	}
	
    my $month    = $mon + 1;
    my $year     = $yr + 1900;
    return "$year-0$month-$mday\_h$time_hour$time_minutes";
}
############################ SUBROUTINE 4 #######################################################
#This subroutine checks all command line input switches and arguments (including optional ones).
#It warns user if mandatory command line input switches and arguments are missing.
sub input_parameters_check {


	my $help_message1  = "Usage: easyDifferentialGeneCoexpressionWrapper -h [-a PROBESETS_OR_GENE_SYMBOLS] [-f INPUT_FILE] [-d GEO_DATASET_CODE] [-v FEATURE_NAME] [-v1 CONDITION_1] [-v2 CONDITION_2] [-o OUTPUT_DIRECTORY]";