Merge b64fc9c into ba1746e

genome · Aug 20, 2018 · e99cedc · e99cedc
2 parents ba1746e + b64fc9c
commit e99cedc
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Showing 2 changed files with 22 additions and 6 deletions.
diff --git a/lib/Pacbio/Command/Assembly/BaxToBam/GenerateCommands.pm b/lib/Pacbio/Command/Assembly/BaxToBam/GenerateCommands.pm
@@ -42,7 +42,7 @@ class Pacbio::Command::Assembly::BaxToBam::GenerateCommands {
     },
     has_optional_transient => {
         _analyses => { is => 'ARRAY', },
-        _commands_fh => { is => 'IO::Handle', },
+        _commands_fh => { },
         _bam_output_directory => { is => 'Text', },
     },
     doc => 'insert missing primary contigs from haplotigs',
@@ -71,8 +71,9 @@ sub __init__ {
     $self->_commands_fh(
         ( $commands_file eq '-' )
         ? 'STDOUT'
-        : IO::File->new($commands_file, 'r')
+        : IO::File->new($commands_file, 'w')
     );
+    $self->fatal_message('Failed to open commands file! %s', $commands_file) if not $self->_commands_fh;
 
     my $bam_output_directory = $self->bam_output_directory;
     if ( $bam_output_directory ) {
@@ -127,6 +128,7 @@ sub execute {
         $self->_commands_fh->print("$cmd\n");
     }
 
+    $self->_commands_fh->close if $self->commands_file ne '-';
     1;
 }
 

diff --git a/t/Pacbio-Command-Assembly-BaxToBam-GenerateCommands.t b/t/Pacbio-Command-Assembly-BaxToBam-GenerateCommands.t
@@ -8,7 +8,7 @@ use TenxTestEnv;
 use File::Temp;
 use File::Slurp;
 use Test::Exception;
-use Test::More tests => 5;
+use Test::More tests => 6;
 
 my %test = ( class => 'Pacbio::Command::Assembly::BaxToBam::GenerateCommands', );
 subtest 'setup' => sub{
@@ -18,7 +18,7 @@ subtest 'setup' => sub{
 
     $test{data_dir} = TenxTestEnv::test_data_directory_for_class($test{class});
     ok(-d $test{data_dir}->stringify, 'data dir exists');
-    $test{tempdir} = File::Temp::tempdir(CLEANUP => 1);
+    $test{tempdir} = Path::Class::dir( File::Temp::tempdir(CLEANUP => 1) );
 
     $test{run_directories} = TenxTestEnv::test_data_directory_for_class('Pacbio::Run');
     ok(-d $test{run_directories}->stringify, 'run dirs exists');
@@ -49,19 +49,20 @@ subtest 'execute with runs' => sub{
 subtest 'execute with runs and library name' => sub{
     plan tests => 4;
 
+    my $output_file = $test{tempdir}->file('runs-and-library-name.txt');
     my $library_name = 'EEAI';
     my $cmd = $test{class}->create(
         bax_sources => [ $test{data_dir}->file('6U00E3')->stringify, ],
         bam_to_bax_command => 'bsub -q long -o %LOG bam2bax',
         library_name => $library_name,
+        commands_file => "$output_file",
     );
     ok($cmd, 'create command');
 
-    my $output;
-    open local(*STDOUT), '>', \$output or die $!;
     lives_ok(sub{ $cmd->execute }, 'execute');
     ok($cmd->result, 'command result');
 
+    my $output = File::Slurp::slurp("$output_file");
     my $expected_output = File::Slurp::slurp( $test{data_dir}->file( join('.', 'expected', $library_name, 'out') )->stringify );
     my $base_test_data_dir = TenxTestEnv::test_data_directory();
     $expected_output =~ s/\%TDD/$base_test_data_dir/g;
@@ -120,4 +121,17 @@ subtest 'execute with some bams completed' => sub{
 
 };
 
+subtest 'failures' => sub{
+    plan tests => 2;
+
+    my $cmd = $test{class}->create(
+        bax_sources => [ $test{data_dir}->file('6U00E3')->stringify, ],
+        bam_to_bax_command => 'bsub -q long -o %LOG bam2bax',
+        commands_file => '/blah',
+    );
+    ok($cmd, 'create command');
+    throws_ok(sub{ $cmd->execute; }, qr/Failed to open commands file/, 'fails when cannot open commands file');
+
+};
+
 done_testing();