#!/usr/bin/perl
# Copyright 2019 O. Sotolongo <asqwerty@gmail.com>
use strict; use warnings;
 
use File::Find::Rule;
use NEURO qw(print_help get_pair load_study achtung shit_done get_lut check_or_make centiloid_fbb);
use Data::Dump qw(dump);
use File::Remove 'remove';
use File::Basename qw(basename);

my $cpac_img = '/nas/software/cpac-latest.simg';
my $pipe_conf = 'cpac_pipeline_config.yml';
my $lib_conf = $ENV{'PIPEDIR'}.'/lib/'.$pipe_conf;
my $cfile;

@ARGV = ("-h") unless @ARGV;

while (@ARGV and $ARGV[0] =~ /^-/) {
    $_ = shift;
    last if /^--$/;
    if (/^-cut/) { $cfile = shift; chomp($cfile);}
    if (/^-h$/) { print_help $ENV{'PIPEDIR'}.'/doc/cpac.hlp'; exit;}
}
my $study = shift;
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/cpac.hlp'; exit;}
my %std = load_study($study);
my $w_dir = $std{'WORKING'};
my $data_dir = $std{'DATA'};
my $bids_dir = $data_dir.'/bids';
my $fmriout_dir = $data_dir.'/cpac_out';
check_or_make($fmriout_dir);
my $outdir = "$std{'DATA'}/slurm";
check_or_make($outdir);
my $tmpdir = "$std{'DATA'}/ctmp";
check_or_make($tmpdir);
my $proj_conf = $data_dir.'/'.$pipe_conf;
system("cp $lib_conf $proj_conf") unless (-e $proj_conf);
my @subjects;
if($cfile){
	open DBF, $cfile or die "No such file\n";
	while(<DBF>) {
		chomp;
		push @subjects, $_;
	}
	close DBF;
}else{
	opendir DBD, $bids_dir or die "Cold not open dir\n";
	while (my $thing = readdir DBD){
		if ($thing eq '.' or $thing eq '..') {
			next;
		}
		if ($thing =~ /sub-*/) {
			push @subjects, $thing;
		}
	}
	closedir DBD;
}
foreach my $subject (@subjects) {
	my $orderfile = $outdir.'/'.$subject.'_cpac.sh';
	open ORD, ">$orderfile";
	print ORD '#!/bin/bash'."\n";
	print ORD '#SBATCH -J cpac_'.$study."\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 -o '.$outdir.'/cpac-%j'."\n";
	print ORD '#SBATCH -c 20'."\n";
	print ORD '#SBATCH -p fast'."\n";
	print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
	print ORD 'srun singularity run --cleanenv -B '.$data_dir.':/project -B '.$bids_dir.':/bids_dataset -B '.$fmriout_dir.':/outputs -B '.$tmpdir.':/scratch '.$cpac_img.' --pipeline_file /project/'.$pipe_conf.' /bids_dataset /outputs participant --participant_label '.$subject."\n";
	close ORD;
	system("sbatch $orderfile");
	sleep(20);
}
my $orderfile = $outdir.'/cpac_end.sh';
open ORD, ">$orderfile";
print ORD '#!/bin/bash'."\n";
print ORD '#SBATCH -J cpac_'.$study."\n";
print ORD '#SBATCH --mail-type=END'."\n"; #email cuando termine
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";
print ORD '#SBATCH -p fast'."\n";
print ORD '#SBATCH -o '.$outdir.'/cpac_end-%j'."\n";
print ORD ":\n";
close ORD;
my $order = 'sbatch --dependency=singleton '.$orderfile;
exec($order);