File Coverage

lib/Bio/Roary/JobRunner/Role.pm

Criterion	Covered	Total	%
statement	28	29	96.5
branch	4	6	66.6
condition			n/a
subroutine	6	6	100.0
pod			n/a
total	38	41	92.6

package Bio::Roary::JobRunner::Role;
$Bio::Roary::JobRunner::Role::VERSION = '3.11.0';
# ABSTRACT: A role to add job runner functionality


use Moose::Role;
use Log::Log4perl qw(:easy);
use File::Spec;

has 'job_runner'        => ( is => 'rw', isa => 'Str',  default  => 'Local' );
has '_job_runner_class' => ( is => 'ro', isa => 'Str',  lazy => 1, builder => '_build__job_runner_class' );
has 'memory_in_mb'      => ( is => 'rw', isa => 'Int',  default => '200' );
has '_queue'            => ( is => 'rw', isa => 'Str',  default => 'normal' );
has 'dont_wait'         => ( is => 'rw', isa => 'Bool', default => 0 );
has 'cpus'              => ( is => 'ro', isa => 'Int',      default => 1 );
has 'logger'            => ( is => 'ro', lazy => 1, builder => '_build_logger');
has 'verbose'           => ( is => 'rw', isa => 'Bool', default => 0 );

sub _build_logger
{
    my ($self) = @_;
    my $level = $ERROR;
    if($self->verbose)
    {
       $level = $DEBUG;
    }
    Log::Log4perl->easy_init($level);
    my $logger = get_logger();
    return $logger;
}

sub _build__job_runner_class {
    my ($self) = @_;
    my $job_runner_class = "Bio::Roary::JobRunner::" . $self->job_runner;
    eval "require $job_runner_class";
    return $job_runner_class;
}

sub _find_exe {
  my($self,$executables) = @_;

  # If there is an explicit full path passed in, just return.
  if($executables->[0] =~ m!/!)
  {
	  return $executables->[0];
  }

  for my $dir (File::Spec->path) {
	  for my $exec (@{$executables})
	  {
        my $exe = File::Spec->catfile($dir, $exec);
        return $exe if -x $exe;
      }
  }
  return $executables->[0];
}


1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Roary::JobRunner::Role - A role to add job runner functionality

=head1 VERSION

version 3.11.0

=head1 SYNOPSIS

A role to add job runner functionality
   with 'Bio::Roary::JobRunner::Role';

=head1 AUTHOR

Andrew J. Page <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut