#!/usr/bin/perl

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

use NEURO qw(populate check_subj load_study print_help achtung shit_done get_pair check_or_make);

my $attach = 0;
my $cfile;

@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-a/) { $attach = 1;} 
    if (/^-cut/) { $cfile = shift; chomp($cfile);}
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/recon.hlp'; exit;}
}

my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/recon.hlp'; exit;}
my $debug = 1;
my $max_processes = 24;                                                                                                                                                  
my $max_gpu = 12;
my $nodes = 3;
my $stage = "-autorecon-all";
y %std = load_study($study);
my $db = $std{'DATABASE'};
my $data_dir=$std{'DATA'};
#open debug file
my $logfile = "$std{'DATA'}/.debug.controlled.log";
$debug ? open DBG, ">$logfile" :0;
#open slurm file
my $orderfile = "$std{'DATA'}/mri_orders.sh";
my $conffile = "$std{'DATA'}/mri_orders.conf";
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);

#get subjects from database or file
my %plist;
my %iplist = populate($db);


if ($cfile){
        my %cuts = get_pair($data_dir."/".$cfile);
        foreach my $cut (keys %cuts){
                if(grep {/$cut/} %iplist){
                        $plist{$cut} = $iplist{$cut};
                }
        }
}else{
        %plist = %iplist;
}
my @jobs_list;
foreach my $pkey (sort keys %plist){
        my $subj = $study."_".$plist{$pkey}.$pkey;
        my $care; my $gpu;
        if(check_subj($subj)){
                $gpu = ""; #because it dont use gpu, YET!
                my $order = "recon-all ".$stage." -subjid ".$subj." ".$gpu;
                my $orderfile = $outdir.'/'.$subj.'fs_orders.sh';
                open ORD, ">$orderfile";
                print ORD '#!/bin/bash'."\n";
                print ORD '#SBATCH -J fs_recon_'.$subj."\n";
                print ORD '#SBATCH --time=72:0:0'."\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='."$ENV{'USER'}\n";
                print ORD '#SBATCH -o '.$outdir.'/fs_recon-slurm-'.$subj.'-%j'."\n";
                print ORD "srun $order\n";
                close ORD;
                my $jobid = `sbatch $orderfile`;
                $jobid = ( split ' ', $jobid )[ -1 ];
                push @jobs_list, $jobid;
                $debug ? print DBG "$order\n" :0;
        }
}
$debug ? close DBG:0;   
my $sjobs = join(',',@jobs_list);
my $orderfile = $outdir.'/fs_recon_end.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J fs_recon_end'."\n";
print ORD '#SBATCH -o '.$outdir.'/fs_recon_end-%j'."\n";
print ORD 'srun -w detritus '.$ENV{'PIPEDIR'}.'/bin/emailme.pl '.$study.' '.basename($ENV{_})."\n";
close ORD;
my $order = 'sbatch --depend=afterany:'.$sjobs.' '.$orderfile;
exec($order);