bug fix for outdirs

Author: jerowe

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

@@ -592,14 +592,14 @@ sub interpol_directive {
     my $source = shift;
     my $text   = '';
 
-    # if ( exists $self->interpol_directive_cache->{$source} && $source !~ m/{\$/ ) {
-    #     return $self->interpol_directive_cache->{$source};
-    # }
-
-    # if ( $source !~ m/{\$/ ) {
-    #     $self->interpol_directive_cache->{$source} = $source;
-    #     return $source;
-    # }
+    if ( exists $self->interpol_directive_cache->{$source} && $source !~ m/{\$/ ) {
+        return $self->interpol_directive_cache->{$source};
+    }
+
+    if ( $source !~ m/{\$/ ) {
+        $self->interpol_directive_cache->{$source} = $source;
+        return $source;
+    }
 
     my $template = Text::Template->new(
         TYPE   => 'STRING',

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

@@ -520,7 +520,6 @@ EOF
     $self->app_log->fatal($rule_example);
 }
 
-
 =head3 template_process
 
 Do the actual processing of the rule->process
@@ -594,7 +593,7 @@ sub check_iterables {
     #First check the global for any lists
     my $use_iters = $self->use_iterables;
 
-    $self->walk_indir_outdir($use_iters);
+    # $self->walk_indir_outdir($use_iters);
 
     if ( !$use_iters ) {
         $texts = $self->in_template_process( $sample, $texts );
@@ -642,8 +641,6 @@ sub walk_attr {
     my $attr = dclone( $self->local_attr );
     $self->check_indir_outdir($attr);
 
-    $DB::single = 2;
-
     $attr->walk_process_data( $self->rule_keys );
 
     return $attr;
@@ -655,6 +652,8 @@ sub eval_process {
     my $attr = $self->walk_attr;
     $attr->sample( $self->sample ) if $self->has_sample;
 
+    $self->walk_indir_outdir($attr);
+
     my $process = $self->local_rule->{ $self->rule_name }->{process};
     my $text    = $attr->interpol_directive($process);
     $text = clean_text($text);
@@ -701,43 +700,56 @@ sub get_keys {
     $self->rule_keys( \@global_keys );
 }
 
-##TODO Clean this up and merge with the other walk_iterables
 ##TODO Write more tests
 sub walk_indir_outdir {
-    my $self      = shift;
-    my $use_iters = shift;
+    my $self = shift;
+    my $attr = shift;
 
-    ##TODO This is redundant...
-    my $attr = dclone( $self->local_attr );
-    my $dummy_sample = $self->dummy_sample;
-    $attr->sample($dummy_sample);
+    my $text = $attr->interpol_directive( $attr->outdir );
 
-    if ( $attr->outdir =~ m/\{\$/ ) {
-        $attr->walk_process_data( $self->rule_keys );
-    }
+    $DB::single = 2;
+    $self->walk_indir_outdir_sample( $attr, $text );
+}
 
-    my $text = $attr->interpol_directive( $self->local_attr->outdir );
+sub walk_indir_outdir_sample {
+    my $self = shift;
+    my $attr = shift;
+    my $text = shift;
 
-    if ( !$use_iters ) {
-        foreach my $sample ( $attr->all_samples ) {
-            my $new_text = $text;
-            $new_text =~ s/$dummy_sample/$sample/g;
+    my $use_iters    = $self->use_iterables;
+    my $dummy_sample = $self->dummy_sample;
+
+    foreach my $sample ( $attr->all_samples ) {
+        my $new_text = $text;
+        $new_text =~ s/$dummy_sample/$sample/g;
+        $DB::single = 2;
+
+        if ($use_iters) {
+            $self->walk_indir_outdir_iters(  $use_iters, $attr,
+                $new_text );
+        }
+        else {
             $new_text = path($new_text)->absolute if $attr->coerce_abs_dir;
             $new_text = path($new_text)           if !$attr->coerce_abs_dir;
             $self->decide_create_outdir( $attr, $new_text );
         }
-        return;
     }
+}
+
+sub walk_indir_outdir_iters {
+    my $self      = shift;
+    my $use_iters = shift;
+    my $attr      = shift;
+    my $text      = shift;
+
+    return unless $use_iters;
 
     my $all  = $use_iters->[0];
     my $elem = $use_iters->[1];
 
-    ##TODO This should be a separate function
     my $dummy_iter = $self->dummy_iterable;
     $attr->$elem($dummy_iter);
 
-    ##BUG FIX - If outdirs have iterables this will be bad
-
     foreach my $chunk ( $self->local_attr->$all ) {
         my $new_text = $text;
         $new_text =~ s/$dummy_iter/$chunk/g;

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

@@ -89,6 +89,13 @@ sub write_workflow_meta_start {
     $self->fh->say("$self->{comment_char} Starting Workflow\n");
     $self->fh->say("$self->{comment_char}");
     $self->fh->say("$self->{comment_char}");
+
+
+    $self->fh->say("$self->{comment_char} Samples:");
+    $self->fh->say("$self->{comment_char} \t".join(', ', @{$self->samples}));
+    $self->fh->say("$self->{comment_char}");
+    $self->fh->say("$self->{comment_char}");
+
     $self->fh->say("$self->{comment_char} Global Variables:");
 
     foreach my $k ( $self->all_global_keys ) {

t/lib/TestsFor/BioX/Workflow/Command/run/Test006.pm

@@ -134,6 +134,7 @@ sub test_002 {
     my ( $test, $test_dir, $rules ) = construct_tests;
 
     $test->samples( [ 'Sample_01', 'Sample_02' ] );
+    $test->global_attr->samples( [ 'Sample_01', 'Sample_02' ] );
 
     # $test->stdout(1);
     $test->set_rule_names;
@@ -143,6 +144,9 @@ sub test_002 {
         _init_rule( $test, $rule );
     }
 
+    ok(-d 'data/processed/Sample_01', 'Sample Dir exists');
+    ok(-d 'data/processed/Sample_02', 'Sample Dir exists');
+
     # diag Dumper( $test->global_attr->some_list );
     # diag Dumper( $test->global_attr->use_somes );
     # diag Dumper( $test->global_attr->some );