CPAN::Groonga

se namespace::autoclean;

use Data::Dumper;
use YAML;
use Storable qw(dclone);
use Try::Tiny;
use JSON;

extends 'BioX::Workflow::Command';
use BioSAILs::Utils::Traits qw(ArrayRefOfStrs);
use Capture:

    => 'rw',
    isa       => 'Str',
    required  => 0,
    predicate => 'has_path',
);

option 'json' => (
    is      => 'rw',
    isa     => 'Bool',
    default => 0,
);

option 'show_only_errors'

$self->app_log->warn('Exiting now.');
        return;
    }

    $DB::single = 2;
    if ( $self->json ) {
        capture_stderr {
            $self->inspect;
        };

    }
    else {
        $se

my ($tfh, $tfilename) = tempfile();
    my ($jfh, $jfilename) = tempfile();

    my $json = $self->serialize_to_json($jfilename);
    write_file($tfilename, $source);
    #
    my $cmd = 'biosails-bio

use File::Slurp;
use JSON;
use Try::Tiny;

has 'remove_from_json' => (
    is      => 'rw',
    isa     => 'ArrayRef',
    default => sub {
        [
            'remove_from_json', 'register_namespac

o_json {
    my $self = shift;
    my $file = shift;

    my %hacky_self = %{$self};
    foreach my $remove ( @{ $self->remove_from_json } ) {
        delete $hacky_self{$remove};
    }

    my $json 

= JSON->new->utf8->pretty->allow_blessed->encode( \%hacky_self );

    if ($file) {
        write_file( $file, $json );
    }
    return $json;
}

sub read_json_file {
    my $self = shift;
    my $fi

        {
            builder => 'create_reg_attr',
            lookup  => [
                '.*_json$',  '.*_yaml$', '.*_yml$', '.*_jsn$',
            ]
        }
    );

    $self->set_register_pro

{
            builder => 'process_directive_config',
            lookup  => [
                '.*_json$', '.*_yaml$', '.*_yml$', '.*_jsn$',
            ],
        }
    );
};

=head3 process_directive

he other functions we need to process a rule

1. Do a sanity check of the rule - it could be yaml/json friendly but not biox friendly
2. Clone the local attr
3. Check for carrying indir/outdir INPUT/O