#!/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 $fslic = '/nas/usr/local/opt/freesurfer/.license';                                                                                                                                             
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/cfmriprep.hlp'; exit;}                                                                                                                         
}                                                                                                                                                                                                 
my $study = shift;                                                                                                                                                                                
unless ($study) { print_help $ENV{'PIPEDIR'}.'/doc/cfmriprep.hlp'; exit;}                                                                                                                         
my %std = load_study($study);                                                                                                                                                                     
my $w_dir = $std{'WORKING'};                                                                                                                                                                      
my $data_dir = $std{'DATA'};                                                                                                                                                                      
my $bids_dir = $data_dir.'/bids';                                                                                                                                                                 
my $fmriout_dir = $data_dir.'/fmriprep_out';                                                                                                                                                      
check_or_make($fmriout_dir);                                                                                                                                                                      
my $outdir = "$std{'DATA'}/slurm";                                                                                                                                                                
check_or_make($outdir);                                                                                                                                                                           
                                                                                                                                                                                                  
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.'_fmriprep.sh';                                                                                                                                      
        open ORD, ">$orderfile";                                                                                                                                                                  
        print ORD '#!/bin/bash'."\n";                                                                                                                                                             
        print ORD '#SBATCH -J fmriprep_'.$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 '.$outdir.'/fmriprep-%j'."\n";                                                                                                                                      
        print ORD '#SBATCH -c 20'."\n";                                                                                                                                                           
        print ORD '#SBATCH -p fast'."\n";                                                                                                                                                         
        print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";    
        print ORD 'srun docker run --rm -v '.$fslic.':/opt/freesurfer/license.txt:ro -v '.$bids_dir.':/data:ro -v '.$fmriout_dir.':/out poldracklab/fmriprep:1.5.0 /data /out participant --participant-label '.$subject.' --ignore slicetiming --skip_bids_validation'."\n";                                                                                  
        #print ORD 'srun fmriprep-docker '.$bids_dir.' '.$fmriout_dir.' --participant-label "'.$subject.'" --ignore slicetiming --skip_bids_validation --fs-license-file '.$fslic."\n";            
        close ORD;                                                                                                                                                                                
        system("sbatch $orderfile");                                                                                                                                                              
        sleep(20);                                                                                                                                                                                
}                                                                                                                                                                                                 
my $orderfile = $outdir.'/fmriprep_end.sh';                                                                                                                                                       
open ORD, ">$orderfile";                                                                                                                                                                          
print ORD '#!/bin/bash'."\n";                                                                                                                                                                     
print ORD '#SBATCH -J fmriprep_'.$study."\n";                                                                                                                                                     
print ORD '#SBATCH --mail-type=END'."\n"; #email cuando termine                                                                                                                                   
print ORD '#SBATCH --mail-user='."$ENV{'USER'}\n";                                                                                                                                                
print ORD '#SBATCH -p fast'."\n";                                                                                                                                                                 
print ORD '#SBATCH -o '.$outdir.'/fmriprep_end-%j'."\n";                                                                                                                                          
print ORD ":\n";                                                                                                                                                                                  
close ORD;                                                                                                                                                                                        
my $order = 'sbatch --dependency=singleton '.$orderfile;                                                                                                                                          
exec($order);