#!/usr/bin/perl

use strict; use warnings;
use File::Basename qw(basename);
use Data::Dump qw(dump);

use NEURO4 qw(populate check_subj load_project print_help check_or_make get_subjects get_list);

my $ifile;

@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-i/) { $ifile = shift; chomp($ifile);}
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/longitudinal.hlp'; exit;}
}

my $study = shift;
unless ($ifile && $study) { print_help $ENV{'PIPEDIR'}.'/doc/longitudinal.hlp'; exit;}
my $debug = 1;
my %lsubjects;

open ILF, "<$ifile" or die "Could not open input data file\n";
while(<ILF>){
        my @long_list = split /;/, $_;
        my $lindex = $long_list[0];
        splice(@long_list,0,1);
        $lsubjects{$lindex} = [ @long_list ];
}
close ILF;
my %std = load_project($study);
my $data_dir=$std{'DATA'};
#open debug file
my $logfile = "$std{'DATA'}/.debug.controlled.log";
$debug ? open DBG, ">$logfile" :0;
#open slurm file
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);
foreach my $lsubject (sort keys %lsubjects){
        my $sub_check_dir = $ENV{'SUBJECTS_DIR'}.'/'.$lsubjects{$lsubject}[0];
        if( -e $sub_check_dir && -d $sub_check_dir){
                my $subol = join ' -tp ', @{$lsubjects{$lsubject}};
                chomp $subol;
                my $order = "recon-all -base ".$lsubject." -tp ".$subol." -all";
                my $orderfile = $outdir.'/'.$lsubject.'_fs_long_base.sh';
                open ORD, ">$orderfile";
                print ORD '#!/bin/bash'."\n";
                print ORD '#SBATCH -J fs_long_'.$study."\n";
                print ORD '#SBATCH --time=48:0:0'."\n"; #si no ha terminado en X horas matalo
                print ORD '#SBATCH --mail-type=FAIL,TIME_LIMIT,STAGE_OUT'."\n"; #no quieres que te mande email de todo
                print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
                print ORD '#SBATCH -p fast'."\n";
                print ORD '#SBATCH -c 4'."\n";
                print ORD '#SBATCH --mem-per-cpu=4G'."\n";
                print ORD '#SBATCH -o '.$outdir.'/fs_long_base-slurm-'.$lsubject.'-%j'."\n";
                print ORD "srun $order\n";
                close ORD;
                my $jobid = `sbatch $orderfile`;
                $jobid = ( split ' ', $jobid )[ -1 ];
                foreach my $ind_subject (sort @{$lsubjects{$lsubject}}){
                        chomp $ind_subject;
                        my $order = "recon-all -long ".$ind_subject." ".$lsubject." -all";
                        my $orderfile = $outdir.'/'.$lsubject.'_'.$ind_subject.'_fs_long_base.sh';
                        open IORD, ">$orderfile";
                        print IORD '#!/bin/bash'."\n";
                        print IORD '#SBATCH -J fs_long_'.$study."\n";
                        print IORD '#SBATCH --time=48:0:0'."\n"; #si no ha terminado en X horas matalo
                        print IORD '#SBATCH --mail-type=FAIL,TIME_LIMIT,STAGE_OUT'."\n"; #no quieres que te mande email de todo
                        print IORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
                        print IORD '#SBATCH -p fast'."\n";
                        print IORD '#SBATCH -c 4'."\n";
                        print IORD '#SBATCH --mem-per-cpu=4G'."\n";
                        print IORD '#SBATCH -o '.$outdir.'/fs_long_ind-slurm-'.$lsubject.'_'.$ind_subject.'-%j'."\n";
                        print IORD "srun $order\n";
                        close IORD;
                        system("sbatch --dependency=afterok:$jobid $orderfile");
                }
                sleep(2);
        }
}

$debug ? close DBG:0;
my $orderfile = $outdir.'/fs_long_end.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J fs_long_'.$study."\n";
print ORD '#SBATCH --mail-type=END'."\n"; #email cuando termine
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -o '.$outdir.'/fs_long_end-%j'."\n";
print ORD ":\n";
close ORD;
my $order = 'sbatch --dependency=singleton '.$orderfile;
exec($order);