Merge c41b625 into b29329f

Clinical-Genomics · Jan 7, 2021 · 1478804 · 1478804
2 parents b29329f + c41b625
commit 1478804
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Showing 11 changed files with 197 additions and 80 deletions.
diff --git a/lib/MIP/Active_parameter.pm b/lib/MIP/Active_parameter.pm
@@ -5,7 +5,7 @@ use Carp;
 use charnames qw{ :full :short };
 use Cwd;
 use English qw{ -no_match_vars };
-use File::Spec::Functions qw{ catfile splitpath };
+use File::Spec::Functions qw{ catdir catfile splitpath };
 use FindBin qw{ $Bin };
 use open qw{ :encoding(UTF-8) :std };
 use Params::Check qw{ allow check last_error };
@@ -46,6 +46,7 @@ BEGIN {
       parse_recipe_resources
       parse_vep_plugin
       remove_sample_id_from_gender
+      set_conda_path
       set_default_analysis_type
       set_default_human_genome
       set_default_infile_dirs
@@ -1300,6 +1301,50 @@ sub remove_sample_id_from_gender {
     return;
 }
 
+sub set_conda_path {
+
+## Function : Set path to root conda dir and the conda_environment_path based on the root path
+## Returns  :
+## Arguments: $active_parameter_href => Active parameters for this analysis hash {REF}
+##          : $environment_name      => MIP conda environment name
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $active_parameter_href;
+    my $environment_name;
+
+    my $tmpl = {
+        active_parameter_href => {
+            default     => {},
+            defined     => 1,
+            required    => 1,
+            store       => \$active_parameter_href,
+            strict_type => 1,
+        },
+        environment_name => {
+            defined     => 1,
+            required    => 1,
+            store       => \$environment_name,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    use MIP::Environment::Path qw{ get_conda_path };
+
+    ## Get path to conda
+    $active_parameter_href->{conda_path} = $active_parameter_href->{conda_path}
+      // get_conda_path( {} );
+
+    ## Set path to conda env
+    $active_parameter_href->{conda_environment_path} =
+      catdir( $active_parameter_href->{conda_path}, q{envs}, $environment_name );
+
+    return;
+}
+
 sub set_default_analysis_type {
 
 ## Function : Set default analysis type to active parameters

diff --git a/lib/MIP/Install.pm b/lib/MIP/Install.pm
@@ -29,31 +29,36 @@ sub check_mip_executable {
 
 ## Function : Check if mip installation exists and is executable
 ## Returns  :
-##          : $conda_prefix_path => Conda prefix path
+##          : $conda_environment_path => Conda environment name path
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
-    my $conda_prefix_path;
+    my $conda_environment_path;
 
     my $tmpl = {
-        conda_prefix_path => {
+        conda_environment_path => {
             defined     => 1,
             required    => 1,
-            store       => \$conda_prefix_path,
+            store       => \$conda_environment_path,
             strict_type => 1,
         },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
+    use MIP::Validate::Data qw{ %constraint };
+
     my $log = Log::Log4perl->get_logger($LOG_NAME);
 
-    return 1 if ( not -x catfile( $conda_prefix_path, qw{ bin mip } ) );
+    my $mip_executable = catfile( $conda_environment_path, qw{ bin mip } );
+
+    return 1 if ( not $constraint{file_is_executable}->($mip_executable) );
 
     $log->info(q{MIP is already installed in the specified conda environment.});
 
     $log->warn(q{This will overwrite the current installation of MIP});
+
     return;
 }
 

diff --git a/lib/MIP/Main/Install.pm b/lib/MIP/Main/Install.pm
@@ -12,15 +12,14 @@ use warnings qw{ FATAL utf8 };
 use warnings;
 
 ## MIPs lib/
-use MIP::Active_parameter qw{ update_to_absolute_path };
+use MIP::Active_parameter qw{ set_conda_path update_to_absolute_path };
 use MIP::Config qw{ check_cmd_config_vs_definition_file set_config_to_active_parameters };
 use MIP::Constants qw{ $COLON $MIP_VERSION $SPACE };
 use MIP::Environment::Container qw{ parse_containers };
 use MIP::Io::Read qw{ read_from_file };
 use MIP::Log::MIP_log4perl qw{ get_log };
 use MIP::Parameter qw{ set_default };
 use MIP::Pipeline qw{ run_install_pipeline };
-use MIP::Set::Parameter qw{ set_conda_path };
 
 BEGIN {
     use base qw{ Exporter };
@@ -112,25 +111,22 @@ sub mip_install {
         }
     );
     $log->info( q{MIP Version: } . $MIP_VERSION );
-    $log->info( q{Writing log messages to}
-          . $COLON
-          . $SPACE
-          . $active_parameter_href->{log_file} );
+    $log->info( q{Writing log messages to} . $COLON . $SPACE . $active_parameter_href->{log_file} );
 
     ## Set default from parameter hash to active_parameter for uninitilized parameters
     set_default(
         {
-            active_parameter_href => $active_parameter_href,
-            custom_default_parameters_ref =>
-              $parameter_href->{custom_default_parameters}{default},
-            parameter_href => $parameter_href,
+            active_parameter_href         => $active_parameter_href,
+            custom_default_parameters_ref => $parameter_href->{custom_default_parameters}{default},
+            parameter_href                => $parameter_href,
         }
     );
 
-    ## Set path to conda
+    ## Set path to conda and conda env path
     set_conda_path(
         {
             active_parameter_href => $active_parameter_href,
+            environment_name      => $active_parameter_href->{environment_name},
         }
     );
 

diff --git a/lib/MIP/Recipes/Install/Mip_scripts.pm b/lib/MIP/Recipes/Install/Mip_scripts.pm
@@ -58,8 +58,8 @@ sub install_mip_scripts {
 
     Readonly my $MOVE_DIRS_UP => 5;
 
-    my $conda_prefix_path = $active_parameter_href->{conda_prefix_path};
-    my @select_programs   = @{ $active_parameter_href->{select_programs} };
+    my $conda_environment_path = $active_parameter_href->{conda_environment_path};
+    my @select_programs        = @{ $active_parameter_href->{select_programs} };
 
     return if ( none { $_ eq q{mip_scripts} } @select_programs );
 
@@ -104,15 +104,15 @@ sub install_mip_scripts {
     # mip is proxy for all mip scripts
     check_mip_executable(
         {
-            conda_prefix_path => $conda_prefix_path,
+            conda_environment_path => $conda_environment_path,
         }
     );
 
     ## Create directories
   DIRECTORY:
     foreach my $directory ( keys %mip_sub_script ) {
 
-        path( catdir( $conda_prefix_path, q{bin}, $directory ) )->mkpath();
+        path( catdir( $conda_environment_path, q{bin}, $directory ) )->mkpath();
     }
 
   DIRECTORY:
@@ -121,8 +121,8 @@ sub install_mip_scripts {
         my @cp_cmds = gnu_cp(
             {
                 force        => 1,
-                infile_path  => catdir( $mip_dir_path,      $directory ),
-                outfile_path => catdir( $conda_prefix_path, q{bin} ),
+                infile_path  => catdir( $mip_dir_path,           $directory ),
+                outfile_path => catdir( $conda_environment_path, q{bin} ),
                 recursive    => 1,
             }
         );
@@ -146,7 +146,7 @@ sub install_mip_scripts {
     foreach my $script (@mip_scripts) {
 
         my $src_path = catfile( $mip_dir_path, $script );
-        my $dst_path = catfile( $conda_prefix_path, q{bin}, $script );
+        my $dst_path = catfile( $conda_environment_path, q{bin}, $script );
         path($src_path)->copy($dst_path);
         path($dst_path)->chmod(q{a+x});
     }
@@ -158,7 +158,7 @@ sub install_mip_scripts {
         foreach my $script ( @{ $mip_sub_script{$directory} } ) {
 
             my $src_path = catfile( $mip_dir_path, $directory, $script );
-            my $dst_path = catfile( $conda_prefix_path, q{bin}, $directory, $script );
+            my $dst_path = catfile( $conda_environment_path, q{bin}, $directory, $script );
 
             path($src_path)->copy($dst_path);
             path($dst_path)->chmod(q{a+x});

diff --git a/lib/MIP/Set/Parameter.pm b/lib/MIP/Set/Parameter.pm
@@ -20,49 +20,11 @@ BEGIN {
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{
-      set_conda_path
       set_container_bind_paths
       set_programs_for_installation
     };
 }
 
-sub set_conda_path {
-
-## Function : Set path to conda
-## Returns  :
-## Arguments: $active_parameter_href => Active parameters for this analysis hash {REF}
-
-    my ($arg_href) = @_;
-
-    ## Flatten argument(s)
-    my $active_parameter_href;
-
-    my $tmpl = {
-        active_parameter_href => {
-            default     => {},
-            defined     => 1,
-            required    => 1,
-            store       => \$active_parameter_href,
-            strict_type => 1,
-        },
-    };
-
-    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
-
-    use MIP::Environment::Path qw{ get_conda_path };
-
-    ## Get path to conda
-    $active_parameter_href->{conda_path} = $active_parameter_href->{conda_path}
-      // get_conda_path( {} );
-
-    ## Set path to conda env
-    my $environment_name = $active_parameter_href->{environment_name};
-    $active_parameter_href->{conda_prefix_path} =
-      catdir( $active_parameter_href->{conda_path}, q{envs}, $environment_name );
-
-    return;
-}
-
 sub set_programs_for_installation {
 
 ## Function : Process the lists of programs that has been selected for installation

diff --git a/lib/MIP/Validate/Data.pm b/lib/MIP/Validate/Data.pm
@@ -23,11 +23,12 @@ BEGIN {
 }
 
 our %constraint = (
-    file_exists       => sub { return 1 if ( -e $_[0] );                  return; },
-    dir_exists        => sub { return 1 if ( -d $_[0] );                  return; },
-    is_digit          => sub { return 1 if ( $_[0] =~ / \A \d+ \z /sxm ); return; },
-    is_gzipped        => sub { return 1 if ( $_[0] =~ / [.]gz$ /xms );    return 0; },
-    plain_file_exists => sub { return 1 if ( -f $_[0] );                  return; },
+    file_exists        => sub { return 1 if ( -e $_[0] );                  return; },
+    file_is_executable => sub { return 1 if ( -x $_[0] );                  return; },
+    dir_exists         => sub { return 1 if ( -d $_[0] );                  return; },
+    is_digit           => sub { return 1 if ( $_[0] =~ / \A \d+ \z /sxm ); return; },
+    is_gzipped         => sub { return 1 if ( $_[0] =~ / [.]gz$ /xms );    return 0; },
+    plain_file_exists  => sub { return 1 if ( -f $_[0] );                  return; },
 );
 
 1;

diff --git a/t/check_mip_executable.t b/t/check_mip_executable.t
@@ -50,26 +50,26 @@ diag(   q{Test check_mip_executable from Install.pm}
 test_log( {} );
 
 ## Given no existing mip binary
-my $conda_prefix_path = q{does_not_exists};
+my $conda_environment_path = q{does_not_exists};
 
 ## When checking for executable
 my $is_not_found = check_mip_executable(
     {
-        conda_prefix_path => $conda_prefix_path,
+        conda_environment_path => $conda_environment_path,
     }
 );
 
 ## Then return true
 ok( $is_not_found, q{Found no existing executable} );
 
 ## Given an existing mip binary
-$conda_prefix_path = catfile( $Bin, qw{ data modules miniconda envs mip_ci } );
+$conda_environment_path = catfile( $Bin, qw{ data modules miniconda envs mip_ci } );
 
 ## When checking for executable
 trap {
     check_mip_executable(
         {
-            conda_prefix_path => $conda_prefix_path,
+            conda_environment_path => $conda_environment_path,
         }
     )
 };

diff --git a/t/constraint.t b/t/constraint.t
@@ -66,6 +66,20 @@ my $file_exist = catfile( $Bin, qw{ constraint.t } );
 ## Then return true
 is( $constraint{file_exists}->($file_exist), 1, q{File exists - file exist} );
 
+## Given a not executable file
+my $file_is_not_executable = catfile( $Bin, qw{ constraint.t } );
+
+## Then return false
+is( $constraint{file_is_executable}->($file_is_not_executable),
+    undef, q{File is executable - file is not executable} );
+
+## Given an executable file
+my $file_is_executable = catfile( $Bin, qw{ data modules miniconda envs mip_ci bin mip} );
+
+## Then return true
+is( $constraint{file_is_executable}->($file_is_executable),
+    1, q{File is executable - file is executable} );
+
 ## Given a not gzipped file
 my $filename = catfile(q{text.txt});
 

diff --git a/t/data/test_data/install_active_parameters.yaml b/t/data/test_data/install_active_parameters.yaml
@@ -3,7 +3,7 @@ bash_set_errexit: '1'
 bash_set_nounset: '0'
 bash_set_pipefail: '1'
 conda_path: <user_path>/miniconda3
-conda_prefix_path: <user_path>/miniconda3/envs/mip_ci
+conda_environment_path: <user_path>/miniconda3/envs/mip_ci
 config_file: <user_path>/MIP/templates/mip_install_config.yaml
 container:
   arriba:

diff --git a/t/install_mip_scripts.t b/t/install_mip_scripts.t
@@ -33,8 +33,7 @@ BEGIN {
 ## Modules with import
     my %perl_module = (
         q{MIP::Recipes::Install::Mip_scripts} => [qw{ install_mip_scripts }],
-        q{MIP::Test::Fixtures} =>
-          [qw{ test_constants test_log test_mip_hashes }],
+        q{MIP::Test::Fixtures}                => [qw{ test_constants test_log test_mip_hashes }],
     );
 
     test_import( { perl_module_href => \%perl_module, } );
@@ -54,11 +53,10 @@ test_log( { no_screen => 1, } );
 test_constants( {} );
 
 ## Given install parameters
-my %active_parameter =
-  test_mip_hashes( { mip_hash_name => q{install_active_parameter}, } );
-my $conda_prefix_path = catdir( $Bin, qw{data modules miniconda envs install_test} );
+my %active_parameter       = test_mip_hashes( { mip_hash_name => q{install_active_parameter}, } );
+my $conda_environment_path = catdir( $Bin, qw{data modules miniconda envs install_test} );
 
-$active_parameter{conda_prefix_path} = $conda_prefix_path;
+$active_parameter{conda_environment_path} = $conda_environment_path;
 
 my $is_ok = install_mip_scripts(
     {
@@ -90,6 +88,6 @@ trap {
 is( $trap->leaveby, q{die}, q{Error in case of install failure} );
 like( $trap->die, qr/Error \s+ message /xms, q{Print error} );
 
-path($conda_prefix_path)->remove_tree;
+path($conda_environment_path)->remove_tree;
 
 done_testing();