Avoid chdir+tempdir to enable Devel::Cover on these pipelines

Wonder how ? It looks like Devel::Cover is completely lost when run in a sub-script from a different working directory. The issue appeared since I made Utils::Test::runWorker() call runWorker.pl instead of running Scripts::RunWorker. Fortunately, in these pipelines we can have a runnable parameter to control the location of the output files.
Ensembl · Dec 10, 2016 · 35841ab · 35841ab
1 parent 1cff8bb
commit 35841ab
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Showing 8 changed files with 13 additions and 13 deletions.
diff --git a/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineAoHIP_conf.pm b/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineAoHIP_conf.pm
@@ -117,6 +117,7 @@ sub default_options {
           # it in EHIVE_ROOT_DIR, if it is not already set in the shell
 	  'inputfile' => $ENV{'EHIVE_ROOT_DIR'} . '/t/input_fasta.fa',
 	  'chunk_size' => 40,
+	  'output_dir' => '.',
 	  'output_prefix' => 'k_split_',
 	  'output_suffix' => '.fa',
 	 };
@@ -208,6 +209,7 @@ sub pipeline_analyses {
 	  		    'input_format' => $self->o('input_format'),
 	  		    'inputfile' => $self->o('inputfile'),
 	  		    'chunk_size' => $self->o('chunk_size'),
+                            'output_dir' => $self->o('output_dir'),
 	  		    'output_prefix' => $self->o('output_prefix'),
 	  		    'output_suffix' => $self->o('output_suffix'),
 			    'k' => $self->o('k'),

diff --git a/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineAoH_conf.pm b/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineAoH_conf.pm
@@ -116,6 +116,7 @@ sub default_options {
           # it in EHIVE_ROOT_DIR, if it is not already set in the shell
 	  'inputfile' => $ENV{'EHIVE_ROOT_DIR'} . '/t/input_fasta.fa',
 	  'chunk_size' => 40,
+	  'output_dir' => '.',
 	  'output_prefix' => 'k_split_',
 	  'output_suffix' => '.fa',
 	 };
@@ -209,6 +210,7 @@ sub pipeline_analyses {
 	  		    'input_format' => $self->o('input_format'),
 	  		    'inputfile' => $self->o('inputfile'),
 	  		    'chunk_size' => $self->o('chunk_size'),
+                            'output_dir' => $self->o('output_dir'),
 	  		    'output_prefix' => $self->o('output_prefix'),
 	  		    'output_suffix' => $self->o('output_suffix'),
 			    'k' => $self->o('k'),

diff --git a/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineHoA_conf.pm b/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineHoA_conf.pm
@@ -116,6 +116,7 @@ sub default_options {
           # it in EHIVE_ROOT_DIR, if it is not already set in the shell
 	  'inputfile' => $ENV{'EHIVE_ROOT_DIR'} . '/t/input_fasta.fa',
 	  'chunk_size' => 40,
+	  'output_dir' => '.',
 	  'output_prefix' => 'k_split_',
 	  'output_suffix' => '.fa',
 	 };
@@ -209,6 +210,7 @@ sub pipeline_analyses {
 	  		    'input_format' => $self->o('input_format'),
 	  		    'inputfile' => $self->o('inputfile'),
 	  		    'chunk_size' => $self->o('chunk_size'),
+                            'output_dir' => $self->o('output_dir'),
 	  		    'output_prefix' => $self->o('output_prefix'),
 	  		    'output_suffix' => $self->o('output_suffix'),
 			    'k' => $self->o('k'),

diff --git a/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineHoH_conf.pm b/modules/Bio/EnsEMBL/Hive/Examples/Kmer/PipeConfig/KmerPipelineHoH_conf.pm
@@ -116,6 +116,7 @@ sub default_options {
           # it in EHIVE_ROOT_DIR, if it is not already set in the shell
 	  'inputfile' => $ENV{'EHIVE_ROOT_DIR'} . '/t/input_fasta.fa',
 	  'chunk_size' => 40,
+	  'output_dir' => '.',
 	  'output_prefix' => 'k_split_',
 	  'output_suffix' => '.fa',
 	 };
@@ -209,6 +210,7 @@ sub pipeline_analyses {
 	  		    'input_format' => $self->o('input_format'),
 	  		    'inputfile' => $self->o('inputfile'),
 	  		    'chunk_size' => $self->o('chunk_size'),
+                            'output_dir' => $self->o('output_dir'),
 	  		    'output_prefix' => $self->o('output_prefix'),
 	  		    'output_suffix' => $self->o('output_suffix'),
 			    'k' => $self->o('k'),

diff --git a/modules/Bio/EnsEMBL/Hive/Examples/Kmer/RunnableDB/SplitSequence.pm b/modules/Bio/EnsEMBL/Hive/Examples/Kmer/RunnableDB/SplitSequence.pm
@@ -72,6 +72,7 @@ use base ('Bio::EnsEMBL::Hive::Process');
 sub param_defaults {
 
   return {
+	  'output_dir'        => '.',
 	  'output_prefix'     => 'my_chunk_',
 	  'output_suffix'     => '.fasta',
 	  'input_format'      => 'FASTA',
@@ -159,7 +160,7 @@ sub write_output {
     my $seq_object = Bio::Seq->new(-seq => $split_sequences[$i],
 				   -id => "split_" . $i);
 
-    my $chunk_filename = $self->param('output_prefix') . $i . $self->param('output_suffix');
+    my $chunk_filename = ($self->param('output_dir') ? $self->param('output_dir') . '/' : '' ) . $self->param('output_prefix') . $i . $self->param('output_suffix');
     my $chunk_seqio = Bio::SeqIO->new(-file => '>' . $chunk_filename,
 				      -format => 'fasta');
 

diff --git a/t/10.pipeconfig/analysis_heir.t b/t/10.pipeconfig/analysis_heir.t
@@ -20,7 +20,6 @@ use warnings;
 
 use Test::More;
 use Data::Dumper;
-use File::Temp qw{tempdir};
 use Capture::Tiny 'capture_stderr';
 
 use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline runWorker get_test_url_or_die);
@@ -30,9 +29,6 @@ my $expected_error_pattern = qq{WARNING: Could not find a local analysis named '
 # eHive needs this to initialize the pipeline (and run db_cmd.pl)
 $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) ) );
 
-my $dir = tempdir CLEANUP => 1;
-my $original = chdir $dir;
-
 my $pipeline_url = get_test_url_or_die();
 
 my $init_stderr = capture_stderr {
@@ -57,4 +53,3 @@ unlike($gc_init_stderr, qr/WARNING/, 'no warning from pipeline without missing a
 
 done_testing();
 
-chdir $original;
diff --git a/t/10.pipeconfig/gcpct.t b/t/10.pipeconfig/gcpct.t
@@ -32,7 +32,6 @@ $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Fil
 my $inputfile = File::Basename::dirname( File::Basename::dirname( Cwd::realpath($0) ) ).'/input_fasta.fa';
 
 my $dir = tempdir CLEANUP => 1;
-my $original = chdir $dir;
 
 my $ehive_test_pipeconfigs   = $ENV{'EHIVE_TEST_PIPECONFIGS'} || 'GCPct_conf';
 
@@ -47,7 +46,7 @@ warn "\nInitializing the $gcpct_version pipeline ...\n\n";
             # override the 'take_time' PipelineWideParameter in the loaded HivePipeline object to make the internal test Worker run quicker:
         my $url         = init_pipeline(
                             'Bio::EnsEMBL::Hive::Examples::GC::PipeConfig::'.$gcpct_version,
-                            [-pipeline_url => $pipeline_url, -hive_force_init => 1, -inputfile => "$inputfile"],
+                            [-pipeline_url => $pipeline_url, -hive_force_init => 1, -inputfile => "$inputfile", -output_dir => $dir],
                             ['pipeline.param[take_time]=0'],
                         );
 
@@ -104,5 +103,3 @@ warn "\nInitializing the $gcpct_version pipeline ...\n\n";
 
 done_testing();
 
-chdir $original;
-
diff --git a/t/10.pipeconfig/kmer.t b/t/10.pipeconfig/kmer.t
@@ -36,7 +36,6 @@ my $inputfastq = $ENV{'EHIVE_ROOT_DIR'}.'/t/input_fastq.fastq';
 
 
 my $dir = tempdir CLEANUP => 1;
-my $original = chdir $dir;
 
 
 my $all_longmult_configs = find_submodules 'Bio::EnsEMBL::Hive::Examples::Kmer::PipeConfig';
@@ -46,13 +45,15 @@ my $kmer_pipeline_modes      = 'short long';
 my $kmer_param_configs       = {'short' => [-seqtype => "short",
 					    -inputfile => "$inputfastq",
 					    -chunk_size => 40,
+					    -output_dir => $dir,
 					    -output_prefix => "k_split_",
 					    -output_suffix => ".fastq",
 					    -input_format => "FASTQ",
 					    -k => 5],
 				'long' => [-seqtype => "long",
 					   -inputfile => "$inputfasta",
 					   -chunk_size => 40,
+					   -output_dir => $dir,
 					   -output_prefix => "k_split_",
 					   -output_suffix => ".fa",
 					   -input_format => "FASTA",
@@ -146,5 +147,3 @@ my $pipeline_url = get_test_url_or_die();
 
 done_testing();
 
-chdir $original;
-