Merge branch 'develop'

lib/BioX/Workflow/Command/run/Utils/Rules.pm

@@ -696,9 +696,12 @@ sub walk_indir_outdir_sample {
     my $attr = shift;
     my $text = shift;
 
+    $DB::single = 2;
     my $use_iters    = $self->use_iterables;
     my $dummy_sample = $self->dummy_sample;
 
+    my @samples = @{$attr->samples} if $attr->has_samples;
+
     foreach my $sample ( $attr->all_samples ) {
         my $new_text = $text;
         $new_text =~ s/$dummy_sample/$sample/g;

lib/BioX/Workflow/Command/run/Utils/Samples.pm

@@ -167,11 +167,11 @@ sub get_samples {
 
     #Backwards compatibility
     #For both file_rule and sample_rule
-    if ( $self->first_index_global_keys( sub { $_ eq 'sample_rule' } ) != -1 ) {
+    if ( $self->first_index_global_keys( sub { $_ eq 'file_rule' } ) != -1 )
+    {
         $text = $self->global_attr->sample_rule;
     }
-    elsif ( $self->first_index_global_keys( sub { $_ eq 'file_rule' } ) != -1 )
-    {
+    elsif ( $self->first_index_global_keys( sub { $_ eq 'sample_rule' } ) != -1 ) {
         $text = $self->global_attr->sample_rule;
     }
     else {
@@ -234,6 +234,8 @@ sub check_sample_exist {
     if ( $self->has_samples && !$self->resample ) {
         my (@samples) = $self->sorted_samples;
         $self->samples( \@samples );
+        ## Fixes Issue #19
+        $self->global_attr->samples(\@samples);
         $self->app_log->info('Samples passed in on command line.');
         $exists = 1;
     }

t/lib/TestMethod/Base.pm

@@ -33,8 +33,14 @@ sub make_test_dir {
 sub make_test_env {
     my $self = shift;
     my $workflow = shift;
+    my $args = shift || [];
 
-    MooseX::App::ParsedArgv->new( argv => [ "run", "--workflow", $workflow ] );
+    my $init_args = [ "run", "--workflow", $workflow ];
+    if($args && ref($args) eq 'ARRAY'){
+      map { push (@{$init_args}, $_) } @{$args};
+    }
+
+    MooseX::App::ParsedArgv->new( argv => $init_args );
 
     my $test = BioX::Workflow::Command->new_with_command();
 

t/lib/TestsFor/BioX/Workflow/Command/run/Test009.pm

@@ -0,0 +1,113 @@
+package TestsFor::BioX::Workflow::Command::run::Test009;
+
+use Test::Class::Moose;
+use Cwd;
+use FindBin qw($Bin);
+use File::Path qw(make_path remove_tree);
+use Data::Dumper;
+use Capture::Tiny ':all';
+use BioX::Workflow::Command;
+use YAML::XS;
+use Data::Walk;
+use File::Slurp;
+use File::Spec;
+use DateTime;
+use DateTime::Format::Strptime;
+use Storable qw(dclone);
+
+extends 'TestMethod::Base';
+
+=head1 Purpose
+
+This tests references -
+https://github.com/biosails/BioX-Workflow-Command/issues/19 Refactoring the
+'check_sample_exists' function didn't add the samples to the global samples attr
+
+=cut
+
+sub write_test_file {
+    my $test_dir = shift;
+
+    my $fh;
+    my $href = {
+        global => [
+            { sample_rule       => "Sample_.*" },
+            { root_dir          => 'data/analysis' },
+            { root_dir          => 'data/analysis' },
+            { indir             => 'data/raw' },
+            { outdir            => 'data/processed' },
+            { jellyfish_dir     => 'data/analysis/{$sample}/jellyfish' },
+            { find_sample_bydir => 1 },
+            { by_sample_outdir  => 1 },
+            { HPC               => [ { account => 'gencore' } ] },
+        ],
+        rules => [
+            {
+                pre_assembly_jellyfish_count => {
+                    'local' => [
+                        { root_dir => 'data/raw' },
+                        { outdir   => '{$self->jellyfish_dir}' },
+                        {
+                            INPUT => '{$self->jellyfish_dir}/some_input_rule1'
+                        },
+                        { OUTPUT => '{$self->jellyfish_dir}/some_input_rule1' },
+                        { HPC    => [ { 'deps' => 'some_dep' } ] }
+                    ],
+                    process =>
+'R1: INDIR: {$self->indir} INPUT: {$self->INPUT} outdir: {$self->outdir} OUTPUT: {$self->OUTPUT}',
+                },
+            },
+        ]
+    };
+
+    #Write out the config
+    open( $fh, ">$test_dir/conf/test1.1.yml" )
+      or die print "Couldn't open file! $!";
+    my $yaml = Dump $href;
+    print $fh $yaml;
+    close($fh);
+
+    make_path( $test_dir . "/data/raw/Sample_01" );
+    write_file( $test_dir . "/data/raw/Sample_01/" . "some_input_rule1" );
+}
+
+sub construct_tests {
+    my $test_methods = TestMethod::Base->new();
+    my $test_dir     = $test_methods->make_test_dir();
+
+    write_test_file($test_dir);
+
+    my $t = "$test_dir/conf/test1.1.yml";
+    my $test = $test_methods->make_test_env( $t, [ '--samples', 'Sample_01' ] );
+    my $rules = $test->workflow_data->{rules};
+
+    return ( $test, $test_dir, $rules );
+}
+
+sub test_001 {
+    my ( $test, $test_dir, $rules ) = construct_tests;
+
+    $test->set_rule_names;
+    $test->filter_rule_keys;
+
+    foreach my $rule ( @{$rules} ) {
+        _init_rule( $test, $rule );
+    }
+
+    $test->post_process_rules;
+    is_deeply( $test->samples, ['Sample_01'] );
+
+    ok((-d 'data/analysis/Sample_01/jellyfish'));
+
+    ok(1);
+}
+
+sub _init_rule {
+    my $test = shift;
+    my $rule = shift;
+
+    $test->local_rule($rule);
+    $test->process_rule;
+    $test->p_rule_name( $test->rule_name );
+    $test->p_local_attr( dclone( $test->local_attr ) );
+}

t/test_class_tests.t

@@ -7,14 +7,15 @@ use Test::Class::Moose::Runner;
 
 Test::Class::Moose::Runner->new(
     test_classes => [
-        'TestsFor::BioX::Workflow::Command::Test001',
-        'TestsFor::BioX::Workflow::Command::run::Test001',
-        'TestsFor::BioX::Workflow::Command::run::Test002',
-        'TestsFor::BioX::Workflow::Command::run::Test003',
-        'TestsFor::BioX::Workflow::Command::run::Test004',
-        'TestsFor::BioX::Workflow::Command::run::Test005',
-        'TestsFor::BioX::Workflow::Command::run::Test006',
-        'TestsFor::BioX::Workflow::Command::run::Test007',
-        'TestsFor::BioX::Workflow::Command::run::Test008',
+        # 'TestsFor::BioX::Workflow::Command::Test001',
+        # 'TestsFor::BioX::Workflow::Command::run::Test001',
+        # 'TestsFor::BioX::Workflow::Command::run::Test002',
+        # 'TestsFor::BioX::Workflow::Command::run::Test003',
+        # 'TestsFor::BioX::Workflow::Command::run::Test004',
+        # 'TestsFor::BioX::Workflow::Command::run::Test005',
+        # 'TestsFor::BioX::Workflow::Command::run::Test006',
+        # 'TestsFor::BioX::Workflow::Command::run::Test007',
+        # 'TestsFor::BioX::Workflow::Command::run::Test008',
+        'TestsFor::BioX::Workflow::Command::run::Test009',
     ],
 )->runtests;