Skip to content

Commit

Permalink
Extended test
Browse files Browse the repository at this point in the history
  • Loading branch information
@henrikstranneheim
henrikstranneheim committed Dec 10, 2018
1 parent daaf571 commit dfff712
Show file tree
Hide file tree
Showing 2 changed files with 65 additions and 124 deletions.
23 changes: 11 additions & 12 deletions lib/MIP/Get/File.pm
View file
Expand Up @@ -23,7 +23,7 @@ BEGIN {
use base qw{ Exporter };

# Set the version for version checking
our $VERSION = 1.03;
our $VERSION = 1.04;

# Functions and variables which can be optionally exported
our @EXPORT_OK = qw{
Expand Down Expand Up @@ -114,17 +114,16 @@ sub get_exom_target_bed_file {
return $exome_target_bed_file;
}
}
if ( not defined $seen{$sample_id} ) {

$log->fatal(
q{Could not detect }
. $sample_id
. q{ in '-exome_target_bed' associated files in sub routine get_exom_target_bed_file},
$NEWLINE
);
exit 1;
}
return;
## Found exome target bed file for sample
return if ( $seen{$sample_id} );

$log->fatal(
q{Could not detect }
. $sample_id
. q{ in '-exome_target_bed' associated files in sub routine get_exom_target_bed_file},
$NEWLINE
);
exit 1;
}

sub get_fastq_file_header_info {
Expand Down
166 changes: 54 additions & 112 deletions t/get_exom_target_bed_file.t
View file
@@ -1,93 +1,54 @@
#!/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 basename };
use File::Spec::Functions qw{ catdir catfile };
use File::Temp;
use File::Basename qw{ dirname };
use File::Spec::Functions qw{ catdir };
use FindBin qw{ $Bin };
use Getopt::Long;
use open qw{ :encoding(UTF-8) :std };
use Params::Check qw{ check allow last_error };
use Params::Check qw{ allow check last_error };
use Test::More;
use utf8;
use warnings qw{ FATAL utf8 };
use 5.026;

## CPANM
use autodie;
use autodie qw { :all };
use Modern::Perl qw{ 2014 };
use Readonly;
use Test::Trap;

## MIPs lib/
use lib catdir( dirname($Bin), q{lib} );
use MIP::Script::Utils qw{ help };
use MIP::Log::MIP_log4perl qw{ initiate_logger };

our $USAGE = build_usage( {} );

##Constants
Readonly my $COMMA => q{,};
Readonly my $NEWLINE => qq{\n};
Readonly my $SPACE => q{ };
Readonly my $UNDERSCORE => q{_};
use MIP::Test::Fixtures qw{ test_log test_standard_cli };

my $VERBOSE = 1;
our $VERSION = q{1.0.0};

###User Options
GetOptions(

# Display help text
'h|help' => sub {
done_testing();
say {*STDOUT} $USAGE;
exit;
},

# Display version number
'v|version' => sub {
done_testing();
say {*STDOUT} $NEWLINE . basename($PROGRAM_NAME) . $SPACE . $VERSION,
$NEWLINE;
exit;
},
'vb|verbose' => $VERBOSE,
)
or (
done_testing(),
help(
{
USAGE => $USAGE,
exit_code => 1,
}
)
);

BEGIN {
our $VERSION = 1.00;

### Check all internal dependency modules and imports
$VERBOSE = test_standard_cli(
{
verbose => $VERBOSE,
version => $VERSION,
}
);

## Modules with import
my %perl_module;
## Constants
Readonly my $COMMA => q{,};
Readonly my $SPACE => q{ };

$perl_module{q{MIP::Script::Utils}} = [qw{ help }];
$perl_module{q{MIP::Log::MIP_log4perl}} = [qw{ initiate_logger }];
BEGIN {

PERL_MODULE:
while ( my ( $module, $module_import ) = each %perl_module ) {
use_ok( $module, @{$module_import} )
or BAIL_OUT q{Cannot load } . $module;
}
use MIP::Test::Fixtures qw{ test_import };

## Modules
my @modules = (q{MIP::Get::File});
### Check all internal dependency modules and imports
## Modules with import
my %perl_module = (
q{MIP::Get::File} => [qw{ get_exom_target_bed_file }],
q{MIP::Test::Fixtures} => [qw{ test_log test_standard_cli }],
);

MODULE:
for my $module (@modules) {
require_ok($module) or BAIL_OUT q{Cannot load } . $module;
}
test_import( { perl_module_href => \%perl_module, } );
}

use MIP::Get::File qw{ get_exom_target_bed_file };
Expand All @@ -101,15 +62,8 @@ diag( q{Test get_exom_target_bed_file from File.pm v}
. $SPACE
. $EXECUTABLE_NAME );

## Create temp logger
my $test_dir = File::Temp->newdir();
my $test_log_path = catfile( $test_dir, q{test.log} );
my $log = initiate_logger(
{
file_path => $test_log_path,
log_name => q{MIP},
}
);
## Create log
my $log = test_log();

## Base arguments
my $sample_1 = q{sample_1};
Expand All @@ -120,6 +74,7 @@ my %exome_target_bed = (
q{exome_target_file_2.bed} => $sample_3,
);

## Given a sample_id
my $exome_target_bed_file = get_exom_target_bed_file(
{
exome_target_bed_href => \%exome_target_bed,
Expand All @@ -128,9 +83,11 @@ my $exome_target_bed_file = get_exom_target_bed_file(
}
);

## Then return exome target bed file for sample
is( q{exome_target_file.bed}, $exome_target_bed_file,
q{Get exom target bed file for sample_1} );

## Given a sample id and a file ending
$exome_target_bed_file = get_exom_target_bed_file(
{
exome_target_bed_href => \%exome_target_bed,
Expand All @@ -140,10 +97,11 @@ $exome_target_bed_file = get_exom_target_bed_file(
}
);

## Then return exome target file with interval list file ending
is( q{exome_target_file.bed.interval_list},
$exome_target_bed_file,
q{Get exom target bed.interval_list file for sample_1} );
$exome_target_bed_file, q{Get exom target bed.interval_list file for sample_1} );

## Given another sample id
$exome_target_bed_file = get_exom_target_bed_file(
{
exome_target_bed_href => \%exome_target_bed,
Expand All @@ -152,43 +110,27 @@ $exome_target_bed_file = get_exom_target_bed_file(
}
);

## Then return exome target bed file for sample id
is( q{exome_target_file_2.bed}, $exome_target_bed_file,
q{Get exom target bed file for sample_3} );

done_testing();

######################
####SubRoutines#######
######################

sub build_usage {

##build_usage

##Function : Build the USAGE instructions
##Returns : ""
##Arguments: $program_name
## : $program_name => Name of the script

my ($arg_href) = @_;

## Default(s)
my $program_name;

my $tmpl = {
program_name => {
default => basename($PROGRAM_NAME),
strict_type => 1,
store => \$program_name,
},
};

check( $tmpl, $arg_href, 1 ) or croak qw{Could not parse arguments!};
## Given a not exisitng sample id
trap {
get_exom_target_bed_file(
{
exome_target_bed_href => \%exome_target_bed,
sample_id => q{not_a_sample_id},
log => $log,
}
)
};

## Then exit and throw FATAL log message
ok( $trap->exit, q{Exit if sample id cannot be found} );
like(
$trap->stderr,
qr/Could \s+ not \s+ detect/xms,
q{Throw fatal log message if sample id cannot be found}
);

return <<"END_USAGE";
$program_name [options]
-vb/--verbose Verbose
-h/--help Display this help message
-v/--version Display version
END_USAGE
}
done_testing();

0 comments on commit dfff712

Please sign in to comment.