Merge branch 'develop'

Author: jerowe

lib/BioX/Workflow/Command/Utils/Files/TrackChanges.pm

@@ -6,19 +6,18 @@ use File::Spec;
 
 #TODO most of these should be in run
 
-has 'track_files' => (
-    is      => 'rw',
-    isa     => 'DBM::Deep',
-    lazy    => 1,
-    default => sub {
-        my $self = shift;
-        my $file = File::Spec->catfile( $self->cache_dir, 'track_files.db' );
-        my $db   = DBM::Deep->new($file);
-        return $db;
-    },
-);
-
-
-
+# DBM::Deep and sqlite do not play nicely with Lustre file systems
+# Tabling this functionality for now
+# has 'track_files' => (
+#     is      => 'rw',
+#     isa     => 'DBM::Deep',
+#     lazy    => 1,
+#     default => sub {
+#         my $self = shift;
+#         my $file = File::Spec->catfile( $self->cache_dir, 'track_files.db' );
+#         my $db   = DBM::Deep->new($file);
+#         return $db;
+#     },
+# );
 
 1;

lib/BioX/Workflow/Command/file_log.pm

@@ -59,7 +59,7 @@ sub execute {
 
         my $details = File::Details->new($file);
         my $mtime   = ctime( stat($file)->mtime );
-        $self->track_files->{$file}->{mtime} = $mtime;
+        # $self->track_files->{$file}->{mtime} = $mtime;
     }
 
     #Preserve the exit code of the previous process

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

@@ -23,10 +23,11 @@ class_type 'Path';
 class_type 'Paths';
 
 use Memoize;
-memoize('my_broken');
 
 use namespace::autoclean;
 
+our $c = new Safe;
+
 =head2 File Options
 
 =head3 indir outdir
@@ -580,33 +581,47 @@ sub create_ITERABLE_attr {
     $self->create_BOOL_attr( $meta, $t );
 }
 
+has 'interpol_directive_cache' => (
+    is      => 'rw',
+    isa     => 'HashRef',
+    default => sub { {} },
+);
+
 sub interpol_directive {
     my $self   = shift;
     my $source = shift;
     my $text   = '';
 
-    if ( !$source ) {
-        return '';
+    if ( exists $self->interpol_directive_cache->{$source} ) {
+        return $self->interpol_directive_cache->{$source};
+    }
+
+    if ( $source !~ m/{\$/ ) {
+        $self->interpol_directive_cache->{$source} = $source;
+        return $source;
     }
 
-    my $c        = new Safe;
     my $template = Text::Template->new(
         TYPE   => 'STRING',
         SOURCE => $source,
         SAFE   => $c,
     );
 
     my $fill_in = { self => \$self };
+
     #TODO reference keys by value instead of $self->
     # my @keys = keys %{$self};
-    $fill_in->{INPUT} = $self->INPUT;
+    # $fill_in->{INPUT} = $self->INPUT;
     $fill_in->{sample} = $self->sample if $self->has_sample;
 
     $text = $template->fill_in( HASH => $fill_in, BROKEN => \&my_broken );
 
+    $self->interpol_directive_cache->{$source} = $text;
     return $text;
 }
 
+memoize('my_broken');
+
 sub my_broken {
     my %args    = @_;
     my $err_ref = $args{arg};
@@ -667,13 +682,13 @@ sub process_directive {
           $self->$k;
     }
     else {
-        my $text = $self->interpol_directive($v);
+        my $text = '';
+        $text = $self->interpol_directive($v) if $v;
         if ( $path && $text ne '' ) {
             $text = path($text)->absolute if $self->coerce_abs_dir;
             $self->$k("$text");
             return;
         }
-
         $self->$k($text);
     }
 }
@@ -697,7 +712,8 @@ sub walk_directives {
     return if ref($ref);
     return unless $ref;
 
-    my $text = $self->interpol_directive($ref);
+    my $text = '';
+    $text = $self->interpol_directive($ref) if $ref;
     if ($path) {
         $text = path($text)->absolute if $self->coerce_abs_dir;
         $text = "$text";
@@ -732,9 +748,15 @@ sub update_directive {
         #We are getting the whole hash, just return
         return;
     }
-
 }
 
+sub BUILD { }
+
+after 'BUILD' => sub {
+    my $self = shift;
+    $self->interpol_directive_cache( {} );
+};
+
 no Moose;
 __PACKAGE__->meta->make_immutable;
 

lib/BioX/Workflow/Command/run/Utils/Files/ResolveDeps.pm

@@ -58,10 +58,10 @@ sub post_process_rules {
 
     #Create flags for outputs that have a similar input
     $self->app_log->info();
-    $self->app_log->info( 'Selected rules:' . "\t"
-          . join( ', ', @{ $self->select_rule_keys } )
-          . "\n" )
-      if $self->use_timestamps;
+    # $self->app_log->info( 'Selected rules:' . "\t"
+    #       . join( ', ', @{ $self->select_rule_keys } )
+    #       . "\n" )
+    #   if $self->use_timestamps;
     # $self->app_log->info( 'Looking for orphan INPUTs '
     #       . '(INPUTs with no corresponding OUTPUTs)' );