CPAN::Groonga

package HPC::Runner::Command::execute_array;

use MooseX::App::Command;
use MooseX::Types::Path::Tiny qw/Path Paths AbsPath AbsFile/;
use JSON::XS;
use Try::Tiny;

extends 'HPC::Runner::Command';

with 'HPC::Runner::Command::Logger::JSON';
with 'HPC::Runner::Command::Utils::Base';
with 'HPC::Runner::Command::Utils::Log';
# with 'HPC::Runner::Command::Utils::Git';
with 'BioSAILs::Integrations::Github';

with 'HPC::Runner::Command::execute_job::Utils::MCE';

command_short_description 'Execute commands';
command_long_description
  'Take the parsed files from hpcrunner.pl submit_jobs and executes the code';

option 'batch_index_start' => (
    is       => 'rw',
    isa      => 'Num',
    required => 1,
    predicate => 'has_batch_index_start',
    documentation => 'Counter to tell execute_array where to start reading in the infile'
);

## For the scheduler we get this from the environment
has 'task_id' => (
    is      => 'rw',
    default => sub {
        return
             $ENV{'SLURM_ARRAY_TASK_ID'}
          || $ENV{'SBATCH_ARRAY_TASK_ID'}
          || $ENV{'PBS_ARRAYID'}
          || $ENV{'SGE_TASK_ID'}
          || 0;
    },
    required => 0,
);

sub BUILD { }

after 'BUILD' => sub {
    my $self = shift;

    if ( !$self->task_id && !$self->infile ) {
        $self->app_log->fatal(
'There is no infile and this does not seem to be an array job. Aborting mission!'
        );
        exit 1;
    }


    # $self->get_infile;
    ##The Task ID is the initial value for the job array that is caught by an environmental variable
    ##Once we get it we use the counter for both execute_job and execute_array
    ##Except for the read_command, which uses the task_id
    $self->counter( $self->task_id );

    $self->gen_load_plugins;
    $self->job_load_plugins;

    # my $tar = $self->set_archive;
    # $self->archive($tar);
};

sub execute {
    my $self = shift;

    $self->git_things;
    $self->run_mce;
}

1;