package Spiders::LSFQueue;

use strict;
use File::Spec;

sub new {
	my ($class,%arg) = @_;
	my $self = {};
	bless $self, $class;
	return $self;
}

sub submit_job {
	(my $self, my $path, my $name, my $cmd) = @_;
	my $file = File::Spec->catfile($path,"$name.sh");
	open (JOB, ">", $file) or die "Cannot create a job file\n";
	print JOB "#!/bin/bash\n";
	print JOB "#BSUB -P prot\n";
	print JOB "#BSUB -q standard\n";
	print JOB "#BSUB -R \"rusage[mem=20000]\"\n";
	print JOB "#BSUB -eo $path/$name.e\n";
	print JOB "#BSUB -oo $path/$name.o\n";
	print JOB $cmd;
	close (JOB);
	my $command = qq(cd $path && bsub < $name.sh);
	my $job = qx[$command];
	chomp ($job);
	if ($job =~ /Job \<(\d+)\>/) {
		$job = $1;
	} else {
		warn "could not parse bsub output: $job";
	}
	return $job;
}

sub get_running_jobs {
	my ($self, $jobshash) = @_;
	my $command = "bjobs -noheader";
	my $jobStatus = qx[$command];
	my @lines = split(/\n/, $jobStatus);
	my @retval;
	foreach my $l (@lines) {
    	my @toks = split(/\s+/, $l);
    	if (defined($jobshash->{$toks[0]})) {
			push (@retval, $toks[0]);
		}
	}
	return \@retval;
}

1;