Merge 012612b into ec1d691

Clinical-Genomics · Jan 10, 2021 · 643a8b1 · 643a8b1
2 parents ec1d691 + 012612b
commit 643a8b1
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Showing 135 changed files with 2,798 additions and 3,748 deletions.
diff --git a/lib/MIP/Active_parameter.pm b/lib/MIP/Active_parameter.pm
@@ -42,6 +42,7 @@ BEGIN {
       get_not_allowed_temp_dirs
       get_package_env_attributes
       get_package_env_cmds
+      get_recipe_resources
       get_user_supplied_pedigree_parameter
       parse_infiles
       parse_recipe_resources
@@ -1055,6 +1056,87 @@ sub get_package_env_cmds {
     return @env_method_cmds;
 }
 
+sub get_recipe_resources {
+
+## Function : Return recipe resources
+## Returns  : $recipe_resource | %recipe_resource
+## Arguments: $active_parameter_href => The active parameters for this analysis hash {REF}
+##          : $recipe_name           => Recipe name
+##          : $recipe_resource       => Recipe parameter key
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $active_parameter_href;
+    my $recipe_name;
+    my $resource;
+
+    my $tmpl = {
+        active_parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$active_parameter_href,
+            strict_type => 1,
+        },
+        recipe_name => {
+            defined     => 1,
+            required    => 1,
+            store       => \$recipe_name,
+            strict_type => 1,
+        },
+        resource => {
+            allow       => [qw{ core_number gpu_number load_env_ref memory mode time }],
+            store       => \$resource,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    use MIP::Active_parameter qw{ get_package_env_cmds };
+    use MIP::Environment::Cluster qw{ check_recipe_memory_allocation };
+
+    ## Initilize variable
+    my @environment_cmds = get_package_env_cmds(
+        {
+            active_parameter_href => $active_parameter_href,
+            package_name          => $recipe_name,
+        }
+    );
+
+    my $core_number     = $active_parameter_href->{recipe_core_number}{$recipe_name};
+    my $process_memory  = $active_parameter_href->{recipe_memory}{$recipe_name};
+    my $core_ram_memory = $active_parameter_href->{core_ram_memory};
+
+    my $memory =
+        ( $process_memory     and $core_number )     ? $process_memory * $core_number
+      : ( not $process_memory and $core_number )     ? $core_number * $core_ram_memory
+      : ( not $process_memory and not $core_number ) ? $core_ram_memory
+      :                                                $process_memory;
+
+    check_recipe_memory_allocation(
+        {
+            node_ram_memory          => $core_ram_memory,
+            recipe_memory_allocation => $memory,
+        }
+    );
+
+    my %recipe_resource = (
+        core_number  => $core_number,
+        gpu_number   => $active_parameter_href->{recipe_gpu_number}{$recipe_name},
+        load_env_ref => \@environment_cmds,
+        memory       => $memory,
+        mode         => $active_parameter_href->{$recipe_name},
+        time         => $active_parameter_href->{recipe_time}{$recipe_name},
+    );
+
+    return $recipe_resource{$resource} if ( defined $resource && $resource );
+
+    return %recipe_resource;
+
+}
+
 sub get_user_supplied_pedigree_parameter {
 
 ## Function : Detect if user supplied info on parameters otherwise collected from pedigree

diff --git a/lib/MIP/Get/Parameter.pm b/lib/MIP/Get/Parameter.pm
diff --git a/lib/MIP/Parameter.pm b/lib/MIP/Parameter.pm
@@ -32,6 +32,7 @@ BEGIN {
       get_order_of_parameters
       get_parameter_attribute
       get_program_executables
+      get_recipe_attributes
       parse_reference_path
       parse_parameter_files
       parse_parameter_recipe_names
@@ -422,6 +423,54 @@ sub get_program_executables {
     return uniq(@program_executables);
 }
 
+sub get_recipe_attributes {
+
+## Function : Return recipe attributes
+## Returns  : $attribute | %attribute
+## Arguments: $attribute      => Attribute key
+##          : $parameter_href => Holds all parameters
+##          : $recipe_name    => Recipe name
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $attribute;
+    my $parameter_href;
+    my $recipe_name;
+
+    my $tmpl = {
+        attribute => {
+            store       => \$attribute,
+            strict_type => 1,
+        },
+        parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$parameter_href,
+            strict_type => 1,
+        },
+        recipe_name => {
+            defined     => 1,
+            required    => 1,
+            strict_type => 1,
+            store       => \$recipe_name,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    if ( not exists $parameter_href->{$recipe_name} ) {
+        croak(qq{Recipe name: $recipe_name. Does not exists in parameter hash});
+    }
+
+    ## Get attribute value
+    return $parameter_href->{$recipe_name}{$attribute} if ( defined $attribute and $attribute );
+
+    ## Get recipe attribute hash
+    return %{ $parameter_href->{$recipe_name} };
+}
+
 sub parse_parameter_files {
 
 ## Function : Parse parameter file objects and checks that their paths exist

diff --git a/lib/MIP/Parse/File.pm b/lib/MIP/Parse/File.pm
@@ -134,7 +134,7 @@ sub parse_io_outfiles {
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
     use MIP::Get::File qw{ get_io_files };
-    use MIP::Get::Parameter qw{ get_recipe_attributes };
+    use MIP::Parameter qw{ get_recipe_attributes };
     use MIP::Set::File qw{ set_io_files };
 
     my @file_paths = @{$file_paths_ref};