Merge pull request #1966 from Clinical-Genomics/feature/fixing_test_c…

…overage

Feature/fixing test coverage

lib/MIP/Main/Qccollect.pm

@@ -38,7 +38,7 @@ BEGIN {
     our $VERSION = q{2.1.10};
 
     # Functions and variables which can be optionally exported
-    our @EXPORT_OK = qw{ mip_qccollect };
+    our @EXPORT_OK = qw{ mip_qccollect parse_limit_qc_output };
 }
 
 sub mip_qccollect {

t/analysis_variant_annotation.t

@@ -47,7 +47,7 @@ diag(   q{Test analysis_variant_annotation from Variant_annotation.pm}
       . $SPACE
       . $EXECUTABLE_NAME );
 
-my $log = test_log( { log_name => q{MIP}, no_screen => 1, } );
+test_log( { log_name => q{MIP}, no_screen => 1, } );
 
 ## Given analysis parameters
 my $recipe_name    = q{variant_annotation};
@@ -109,4 +109,24 @@ my $is_ok = analysis_variant_annotation(
 ## Then return TRUE
 ok( $is_ok, q{ Executed analysis recipe } . $recipe_name );
 
+## Given no loqusdb file in toml - alters the bcftools command
+$active_parameter{vcfanno_config} =
+  catfile( $Bin, qw{ data references grch37_vcfanno_config_bad_template-v1.0-.toml } );
+
+$is_ok = analysis_variant_annotation(
+    {
+        active_parameter_href => \%active_parameter,
+        case_id               => $case_id,
+        file_info_href        => \%file_info,
+        job_id_href           => \%job_id,
+        parameter_href        => \%parameter,
+        profile_base_command  => $slurm_mock_cmd,
+        recipe_name           => $recipe_name,
+        sample_info_href      => \%sample_info,
+    }
+);
+
+## Then still return TRUE
+ok( $is_ok, q{ Executed analysis recipe } . $recipe_name );
+
 done_testing();

t/parse_containers.t

@@ -20,7 +20,7 @@ use Modern::Perl qw{ 2018 };
 ## MIPs lib/
 use lib catdir( dirname($Bin), q{lib} );
 use MIP::Constants qw{ $COMMA $SPACE };
-use MIP::Test::Fixtures qw{ test_mip_hashes };
+use MIP::Test::Fixtures qw{ test_log test_mip_hashes };
 
 BEGIN {
 
@@ -30,7 +30,7 @@ BEGIN {
 ## Modules with import
     my %perl_module = (
         q{MIP::Environment::Container} => [qw{ parse_containers }],
-        q{MIP::Test::Fixtures}         => [qw{ test_mip_hashes }],
+        q{MIP::Test::Fixtures}         => [qw{ test_log test_mip_hashes }],
     );
 
     test_import( { perl_module_href => \%perl_module, } );
@@ -46,6 +46,8 @@ diag(   q{Test parse_containers from Container.pm}
       . $SPACE
       . $EXECUTABLE_NAME );
 
+test_log( {} );
+
 my %active_parameter = test_mip_hashes(
     {
         mip_hash_name => q{active_parameter},

t/parse_limit_qc_output.t

@@ -0,0 +1,87 @@
+#! /usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw { :all };
+use Modern::Perl qw{ 2018 };
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = ( q{MIP::Main::Qccollect} => [qw{ parse_limit_qc_output }], );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Main::Qccollect qw{ parse_limit_qc_output };
+
+diag(   q{Test parse_limit_qc_output from Qccollect.pm}
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+## Given a qc data hash
+my %qc_data = (
+    sample => {
+        sample_id => {
+            recipe_output_file => {
+                collectmultiplemetrics => {
+                    header => q{data},
+                },
+            },
+            another_file => {
+                collecthsmetrics => {
+                    header => q{data},
+                },
+            },
+        },
+    },
+);
+
+## When executing sub
+parse_limit_qc_output(
+    {
+        limit_qc_output => 1,
+        qc_href         => \%qc_data,
+    }
+);
+
+## Then remove key collectmultiplemetrics
+my %expected_qc_data = (
+    sample => {
+        sample_id => {
+            recipe_output_file => {},
+            another_file       => {
+                collecthsmetrics => {
+                    header => q{data},
+                },
+            },
+        },
+    },
+);
+
+is_deeply( \%qc_data, \%expected_qc_data, q{Delete qc data from hash} );
+
+done_testing();