Merge branch 'develop'

biosails · Jul 6, 2017 · c7c1e8e · c7c1e8e
2 parents 8fa302a + 2d7f344
commit c7c1e8e
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Showing 4 changed files with 48 additions and 201 deletions.
diff --git a/lib/BioX/Workflow/Command/run/Rules/Directives/Types/Path.pm b/lib/BioX/Workflow/Command/run/Rules/Directives/Types/Path.pm
@@ -38,6 +38,17 @@ has 'outdir' => (
     documentation => q(Output directories for rules and processes),
 );
 
+has 'cwd' => (
+    is            => 'rw',
+    isa           => Path,
+    coerce        => 1,
+    required      => 0,
+    default       => sub { cwd(); },
+    predicate     => 'has_cwd',
+    clearer       => 'clear_cwd',
+    documentation => q(Placeholder for the cwd.),
+);
+
 =head3 INPUT OUTPUT
 
 Special variables that can have input/output

diff --git a/lib/BioX/Workflow/Command/run/Utils/Files/ResolveDeps.pm b/lib/BioX/Workflow/Command/run/Utils/Files/ResolveDeps.pm
@@ -44,8 +44,7 @@ sub add_graph {
     my $self = shift;
     my $cond = shift;
 
-    for my $pair ( $self->files_pairs ) {
-        my $file = $pair->[0];
+    for my $file ( $self->all_files ) {
         if ( !exists $self->rule_deps->{ $self->rule_name }->{$cond}->{$file} )
         {
             $self->rule_deps->{ $self->rule_name }->{$cond}->{$file} = 1;

diff --git a/lib/BioX/Workflow/Command/run/Utils/Files/TrackChanges.pm b/lib/BioX/Workflow/Command/run/Utils/Files/TrackChanges.pm
@@ -7,249 +7,85 @@ use File::stat;
 use Time::localtime;
 use File::Basename;
 use DateTime::Format::Strptime;
-# use Memoize;
 
 with 'BioX::Workflow::Command::Utils::Files::TrackChanges';
 
 =head3 files
 
 Files just for this rule
 
+##TODO Make this a hash?
 =cut
 
-has 'files' => (
-    traits  => ['Hash'],
-    is      => 'rw',
-    isa     => 'HashRef',
-    default => sub { {} },
-    handles => {
-        files_pairs => 'kv',
-        clear_files => 'clear',
-    },
-);
+# has 'files' => (
+#     traits  => ['Hash'],
+#     is      => 'rw',
+#     isa     => 'HashRef',
+#     default => sub { {} },
+#     handles => {
+#         files_pairs => 'kv',
+#         clear_files => 'clear',
+#     },
+# );
 
-
-#TODO Update this
-#No longer seen_modify - since we are not checking for timestamps anymore
-has 'seen_modify' => (
-    traits  => ['Hash'],
+has 'files' => (
+    traits  => ['Array'],
     is      => 'rw',
-    isa     => 'HashRef',
-    default => sub { {} },
+    isa     => 'ArrayRef',
+    default => sub { [] },
     handles => {
-        seen_modify_pairs => 'kv',
-        clear_seen_modify => 'clear',
+        has_files  => 'count',
+        all_files  => 'elements',
+        push_files => 'push',
+        sort_files => 'sort_in_place',
+        uniq_files => 'uniq',
     },
+    clearer => 'clear_files',
 );
 
 sub walk_FILES {
     my $self = shift;
     my $attr = shift;
 
-    $self->seen_modify->{local} = {};
-
-    # my $mod_input = $self->pre_FILES( $attr, 'INPUT' );
     $self->pre_FILES( $attr, 'INPUT' );
     $self->add_graph('INPUT');
     $self->clear_files;
 
-    # $self->app_log->info('Between checks...');
-    # my $mod_output = $self->pre_FILES( $attr, 'OUTPUT' );
-    $self->pre_FILES($attr, 'OUTPUT');
+    $self->pre_FILES( $attr, 'OUTPUT' );
     $self->add_graph('OUTPUT');
     $self->clear_files;
-    # $self->local_attr->{_modified} = 1 if $mod_input;
-
-    # TODO add check for when we have actually modified the output
 }
 
 sub pre_FILES {
     my $self = shift;
     my $attr = shift;
     my $cond = shift;
 
-    # $self->app_log->info( 'Beginning modification checks for ' . $cond );
-    # REF check?
     walk {
         wanted => sub { $self->walk_INPUT(@_) }
       },
       $attr->$cond;
-
-    # Once we get to the input we want to see if we are processing a new file or no
-    # my $modify = $self->iterate_FILES;
-    $self->iterate_FILES;
-
-    # return $modify;
+    $self->uniq_files;
+    $self->sort_files;
 }
 
-sub iterate_FILES {
-    my $self = shift;
+=head3 walk_INPUT
 
-    # my $modify = 0;
-    for my $pair ( $self->files_pairs ) {
-        my $file = $pair->[0];
-        $self->seen_modify->{local}->{$file} = 1;
-        # if ( $self->seen_modify->{all}->{$file} ) {
-        #     my $tmodify = $self->seen_modify->{all}->{$file};
-        #     $modify = 1 if $tmodify;
-        #     $self->update_seen( $file, $modify );
-        #     next;
-        # }
-        # elsif ( !-e $file ) {
-        #     $self->update_seen( $file, 1 );
-        #     $modify = 1;
-        #     next;
-        # }
-        #
-        # if ( $self->process_file($file) ) {
-        #     $modify = 1;
-        # }
-    }
-
-    # return $modify;
-}
-
-=head3 process_file
+walk the INPUT/OUTPUT and catch all Path::Tiny references
 
 =cut
 
-# sub process_file {
-#     my $self = shift;
-#     my $file = shift;
-#
-#     $self->seen_modify->{local}->{$file} = 1;
-#     # my $details = File::Details->new($file);
-#     # my $mtime   = ctime( stat($file)->mtime );
-#     #
-#     # if ( exists $self->track_files->{$file}->{mtime} ) {
-#     #
-#     #     # Check to see if we have a difference
-#     #     my $p_mtime = $self->track_files->{$file}->{mtime};
-#     #     if ( compare_mtimes( $p_mtime, $mtime ) ) {
-#     #         # $self->flag_for_process( $file, $p_mtime, $mtime );
-#     #         $self->update_seen( $file, 1 );
-#     #
-#     #         return 1;
-#     #     }
-#     #     else {
-#     #         # This is the only time we should return 0
-#     #         $self->update_seen( $file, 0 );
-#     #         return 0;
-#     #     }
-#     # }
-#     # else {
-#     #     $self->update_seen( $file, 1 );
-#     #     return 1;
-#     # }
-# }
-
-# This is really more of a sanity check
-sub flag_for_process {
-    my $self    = shift;
-    my $file    = shift;
-    my $p_mtime = shift;
-    my $mtime   = shift;
-
-    my $basename = basename($file);
-
-    # #TO LOG OR NOT TO LOG
-    # $self->app_log->warn(
-    #     'File ' . $file . ' has been modified since your last analysis.' );
-    # $self->app_log->warn( $basename
-    #       . ":\n\tLast Recorded Modification:\t"
-    #       . $p_mtime
-    #       . "\n\tMost Recent Modification:\t"
-    #       . $mtime );
-
-    # TODO We only want this in run...
-    # TODO Add an override here
-    # if ( !$self->check_select && !$self->use_timestamps ) {
-    #     $self->app_log->warn( 'You have selected to skip rule '
-    #           . $self->rule_name
-    #           . ', but this file has changed since last your last analysis.' );
-    #
-    # }
-}
-
 sub walk_INPUT {
     my $self = shift;
     my $ref  = shift;
 
-    return if ref($ref);
     return unless $ref;
 
-    if ( !exists $self->files->{$ref} ) {
-        $self->files->{$ref} = 1;
-    }
-}
-
-# memoize('compare_mtimes');
-# sub compare_mtimes {
-#     my $pmtime = shift;
-#     my $mtime  = shift;
-#
-#     my $strp = DateTime::Format::Strptime->new(
-#         pattern   => '%a %b %e %T %Y',
-#         time_zone => 'local',
-#     );
-#
-#     my $dt1 = $strp->parse_datetime($pmtime);
-#     my $dt2 = $strp->parse_datetime($mtime);
-#
-#     #For reasons unknown there is something off by 1 second either way
-#     #my $cmp = DateTime->compare( $dt1, $dt2 );
-#     my $dur = $dt2->subtract_datetime($dt1);
-#
-#     # TODO Add this formatting to HPC::Runner
-#     my ( $days, $hours, $minutes, $seconds ) =
-#       $dur->in_units( 'days', 'hours', 'minutes', 'seconds' );
-#
-#     if ( $days >= 1 || $hours >= 1 || $minutes >= 1 ) {
-#         return 1;
-#     }
-#     elsif ( $seconds >= 2 ) {
-#         return 1;
-#     }
-#     else {
-#         return 0;
-#     }
-# }
-#
-# sub update_seen {
-#     my $self   = shift;
-#     my $file   = shift;
-#     my $update = shift;
-#
-#     # $self->seen_modify->{all}->{$file}   = $update;
-#     $self->seen_modify->{local}->{$file} = $update;
-# }
-
-sub write_file_log {
-    my $self = shift;
+    my $ref_name = ref($ref);
+    return unless $ref_name;
+    return unless $ref_name eq 'Path::Tiny';
 
-    my $text  = "";
-    my @files = keys %{ $self->seen_modify->{local} };
-    @files = sort @files;
-
-    $self->seen_modify->{local} = {};
-
-    if (@files) {
-        $text = <<EOF;
-; \\
-biox file_log \\
-\t--exit_code `echo \$\?`  \\
-EOF
-    }
-
-    my $last = pop(@files);
-    foreach my $file (@files) {
-        $text .= <<EOF;
-\t--file $file \\
-EOF
-    }
-    $text .= "\t--file $last\n\n" if $last;
-
-    return $text;
+    $self->push_files( $ref->absolute );
 }
 
 1;
diff --git a/lib/BioX/Workflow/Command/stats.pm b/lib/BioX/Workflow/Command/stats.pm
@@ -10,6 +10,7 @@ use File::Details;
 use File::Basename;
 use List::MoreUtils qw(uniq);
 use Try::Tiny;
+use Path::Tiny;
 
 extends qw(  BioX::Workflow::Command );
 
@@ -78,11 +79,11 @@ has 'table_log' => (
     }
 );
 
-option 'use_full' => (
+option 'use_abs' => (
     is            => 'rw',
     isa           => 'Bool',
     default       => 0,
-    documentation => 'Use the full path name instead of the basename'
+    documentation => 'Use the absolute path name instead of the basename'
 );
 
 our $human = Number::Bytes::Human->new(
@@ -119,8 +120,8 @@ around 'pre_FILES' => sub {
 
     $self->$orig( $attr, $cond );
 
-    for my $pair ( $self->files_pairs ) {
-        $self->preprocess_row( $pair->[0], $cond );
+    for my $file ( $self->all_files ) {
+        $self->preprocess_row( $file, $cond );
     }
 };
 
@@ -149,7 +150,7 @@ sub gen_row {
 
         my $rel = '';
         $rel = $file;
-        $rel = File::Spec->abs2rel($file) if $self->use_full;
+        $rel = path($file)->absolute if $self->use_full;
 
         my $basename = basename($file) unless $self->use_full;