feat(remove): parse_program_executables

Clinical-Genomics · Nov 9, 2020 · 0988017 · 0988017
1 parent 158fdb9
commit 0988017
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diff --git a/lib/MIP/Active_parameter.pm b/lib/MIP/Active_parameter.pm
@@ -46,7 +46,6 @@ BEGIN {
       get_package_env_attributes
       get_user_supplied_pedigree_parameter
       parse_infiles
-      parse_program_executables
       parse_recipe_resources
       parse_vep_plugin
       remove_sample_id_from_gender
@@ -1097,64 +1096,6 @@ sub parse_infiles {
     return 1;
 }
 
-sub parse_program_executables {
-
-## Function : Checking commands in your path and executable
-## Returns  :
-## Arguments: $active_parameter_href => Active parameters for this analysis hash {REF}
-##          : $parameter_href        => Parameter hash {REF}
-
-    my ($arg_href) = @_;
-
-    ## Flatten argument(s)
-    my $active_parameter_href;
-    my $parameter_href;
-
-    my $tmpl = {
-        active_parameter_href => {
-            default     => {},
-            defined     => 1,
-            required    => 1,
-            store       => \$active_parameter_href,
-            strict_type => 1,
-        },
-        parameter_href => {
-            default     => {},
-            defined     => 1,
-            required    => 1,
-            store       => \$parameter_href,
-            strict_type => 1,
-        },
-    };
-
-    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
-
-  PARAMETER:
-    foreach my $parameter_name ( keys %{$active_parameter_href} ) {
-
-        ## Only check path(s) for parameters with "type" key
-        next PARAMETER
-          if ( not exists $parameter_href->{$parameter_name}{type} );
-
-        ## Only check path(s) for parameters with type value eq "recipe"
-        next PARAMETER
-          if ( not $parameter_href->{$parameter_name}{type} eq q{recipe} );
-
-        ## Only check path(s) for active recipes
-        next PARAMETER if ( not $active_parameter_href->{$parameter_name} );
-
-        ## Alias
-        my $program_executables_ref =
-          \@{ $parameter_href->{$parameter_name}{program_executables} };
-
-      PROGRAM:
-        foreach my $program ( @{$program_executables_ref} ) {
-
-        }
-    }
-    return;
-}
-
 sub parse_recipe_resources {
 
 ## Function : Check core number and memory requested against environment provisioned

diff --git a/lib/MIP/Main/Analyse.pm b/lib/MIP/Main/Analyse.pm
@@ -32,7 +32,6 @@ use MIP::Active_parameter qw{
   check_load_env_packages
   check_recipe_mode
   get_not_allowed_temp_dirs
-  parse_program_executables
   parse_recipe_resources
   set_gender_sample_ids
   set_parameter_reference_dir_path
@@ -343,14 +342,6 @@ sub mip_analyse {
     ## Check core number requested against environment provisioned
     parse_recipe_resources( { active_parameter_href => $active_parameter_href, } );
 
-    ## Check programs in path, is executable, and set binary_path
-    parse_program_executables(
-        {
-            active_parameter_href => $active_parameter_href,
-            parameter_href        => $parameter_href,
-        }
-    );
-
     ## Check that the case_id and the sample_id(s) exists and are unique. Check if id sample_id contains "_".
     check_sample_ids(
         {

diff --git a/t/parse_program_executables.t b/t/parse_program_executables.t