#!/usr/bin/perl

use strict; use warnings;
use NEURO4 qw(load_project print_help populate check_or_make);

my $cfile = 'bids/conversion.json';
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-c/) { $cfile = shift; chomp($cfile);}
    if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/bulk2bids.hlp'; exit;}
}
my $proj  = shift;
unless ($proj) { print_help $ENV{'PIPEDIR'}.'/doc/bulk2bids.hlp'; exit;}
my %std = load_project($proj);
my $src_dir = $std{'SRC'};
my $proj_file = $std{'DATA'}.'/'.$proj.'_mri.csv';
my %guys = populate('^(\d{4});(.*)$', $proj_file);
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);
foreach my $subject (sort keys %guys) {
        my $order = 'dcm2bids -d '.$std{'SRC'}.'/'.$guys{$subject}.'/ -p '.$subject.' -c '.$std{'DATA'}.'/'.$cfile.' -o '.$std{'DATA'}.'/bids/';
        #print "$order\n";
        my $orderfile = $outdir.'/'.$subject.'dcm2bids.sh';
        open ORD, ">$orderfile";
        print ORD '#!/bin/bash'."\n";
        print ORD '#SBATCH -J dcm2bids_'.$proj."\n";
        print ORD '#SBATCH --time=2:0:0'."\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.'/dcm2bids'.$subject.'-%j'."\n";
        print ORD "srun $order\n";
        close ORD;
        system("sbatch $orderfile");
}
my $orderfile = $outdir.'/dcm2bids_end.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J dcm2bids_'.$proj."\n";
print ORD '#SBATCH --mail-type=END'."\n"; #email cuando termine o falle
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -o '.$outdir.'/dmc2bids_end-%j'."\n";
print ORD ":\n";
close ORD;
my $xorder = 'sbatch --dependency=singleton'.' '.$orderfile;
exec($xorder);