#!/usr/bin/env perl

use strict;
use warnings;
use diagnostics;
use autodie;
use feature qw(say);

use Storable;
use Expect;
use Term::ReadKey;

# my $data_dir = $ENV{'DATA_DIR'};
my $job_index  = $ENV{'LSB_JOBINDEX'};
my $user       = $ENV{'USER'};
my $password   = $ENV{'SANG_PASS'};
my $output_dir = $ARGV[1];

my @filenames = split /,/, $ARGV[0];

my $filename = $filenames[ $job_index - 1 ];
my ($parent_dir) = split /_/, $filename;

# deal with iRODS initialisation
my $session = Expect->spawn('kinit') or die $!;

if ( $session->expect( 5, "Password for $user\@INTERNAL.SANGER.AC.UK:" ) ) {
    print $session "$password\r";
}
else {
    say STDERR 'kinit failed';
}

$session->soft_close();

# run actual download command
my $iget_cmd
    = 'iget -K /seq/' . $parent_dir . '/' . $filename . ' ' . $output_dir;

# say $iget_cmd;

my $exit_code = system($iget_cmd);
if ( $exit_code != 0 ) {
    say STDERR 'This system call has failed: ' . $iget_cmd;
}