refactoring begun

Author: jerowe

lib/BioX/Workflow/Command/run.pm

@@ -7,7 +7,7 @@ use File::Copy;
 
 extends 'BioX::Workflow::Command';
 use BioX::Workflow::Command::Utils::Traits qw(ArrayRefOfStrs);
-use BioX::Workflow::Command::run::Utils::Directives;
+use BioX::Workflow::Command::run::Rules::Directives;
 
 with 'BioX::Workflow::Command::run::Utils::Samples';
 with 'BioX::Workflow::Command::run::Utils::Attributes';

…Workflow/Command/run/Utils/Directives.pm …Workflow/Command/run/Rules/Directives.pmlib/BioX/Workflow/Command/run/Utils/Directives.pm renamed to lib/BioX/Workflow/Command/run/Rules/Directives.pm lib/BioX/Workflow/Command/run/Utils/Directives.pm renamed to lib/BioX/Workflow/Command/run/Rules/Directives.pm

@@ -1,6 +1,9 @@
-package BioX::Workflow::Command::run::Utils::Directives;
+package BioX::Workflow::Command::run::Rules::Directives;
 
 use Moose;
+use namespace::autoclean;
+
+with 'BioX::Workflow::Command::run::Rules::Directives::Types::HPC';
 
 use BioX::Workflow::Command::Utils::Traits qw(ArrayRefOfStrs);
 use MooseX::Types::Path::Tiny qw/Path Paths AbsPath AbsFile/;
@@ -14,18 +17,10 @@ use Scalar::Util 'blessed';
 use Try::Tiny;
 use Safe;
 use Storable qw(dclone);
-
 # use File::Basename;
 use File::Spec;
-
-use Moose::Util::TypeConstraints;
-class_type 'Path';
-class_type 'Paths';
-
 use Memoize;
 
-use namespace::autoclean;
-
 our $c = new Safe;
 
 =head2 File Options
@@ -443,6 +438,7 @@ sub create_attr {
                 elsif($self->can($k)){
                   next;
                 }
+                ##TODO Clean this up for Types
                 elsif ( $k =~ m/_list/ ) {
                     $self->create_ITERABLE_attr( $meta, $k );
                 }
@@ -661,6 +657,7 @@ sub my_broken {
 EOF
 }
 
+##TODO Register Types
 sub walk_process_data {
     my $self = shift;
     my $keys = shift;
@@ -778,4 +775,5 @@ after 'BUILD' => sub {
 no Moose;
 __PACKAGE__->meta->make_immutable;
 
+
 1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types.pm

@@ -0,0 +1,5 @@
+use strict;
+use warnings;
+package BioX::Workflow::Command::run::Rules::Directives::Types;
+
+1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types/Array.pm

@@ -0,0 +1,5 @@
+use strict;
+use warnings;
+package BioX::Workflow::Command::run::Rules::Directives::Types::Array;
+
+1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types/CSV.pm

@@ -0,0 +1,5 @@
+use strict;
+use warnings;
+package BioX::Workflow::Command::run::Rules::Directives::Types::CSV;
+
+1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types/Config.pm

@@ -0,0 +1,5 @@
+use strict;
+use warnings;
+package BioX::Workflow::Command::run::Rules::Directives::Types::Config;
+
+1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types/HPC.pm

@@ -0,0 +1,11 @@
+package BioX::Workflow::Command::run::Rules::Directives::Types::HPC;
+
+use Moose::Role;
+
+has 'HPC' => (
+    is      => 'rw',
+    isa     => 'HashRef|ArrayRef',
+    default => sub { {} }
+);
+
+1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types/Hash.pm

@@ -0,0 +1,5 @@
+use strict;
+use warnings;
+package BioX::Workflow::Command::run::Rules::Directives::Types::Hash;
+
+1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types/List.pm

@@ -0,0 +1,5 @@
+use strict;
+use warnings;
+package BioX::Workflow::Command::run::Rules::Directives::Types::List;
+
+1;

lib/BioX/Workflow/Command/run/Rules/Directives/Types/Path.pm

@@ -0,0 +1,5 @@
+use strict;
+use warnings;
+package BioX::Workflow::Command::run::Rules::Directives::Types::Path;
+
+1;