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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| package TestsFor::BioX::Workflow::Command::run::Test007; | ||
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| use Test::Class::Moose; | ||
| use Cwd; | ||
| use FindBin qw($Bin); | ||
| use File::Path qw(make_path remove_tree); | ||
| use Data::Dumper; | ||
| use Capture::Tiny ':all'; | ||
| use BioX::Workflow::Command; | ||
| use YAML::XS; | ||
| use Data::Walk; | ||
| use File::Slurp; | ||
| use File::Spec; | ||
| use DateTime; | ||
| use DateTime::Format::Strptime; | ||
| use Storable qw(dclone); | ||
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| extends 'TestMethod::Base'; | ||
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| sub write_test_file { | ||
| my $test_dir = shift; | ||
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| my $fh; | ||
| my $href = { | ||
| global => [ | ||
| { sample_rule => "Sample_.*" }, | ||
| { root_dir => 'data/raw' }, | ||
| { indir => '{$self->root_dir}' }, | ||
| { outdir => 'data/processed' }, | ||
| { find_sample_bydir => 1 }, | ||
| { by_sample_outdir => 1 }, | ||
| { chroms_list => [1,2,3,4,5]}, | ||
| { samples => ['Sample_01']}, | ||
| ], | ||
| rules => [ | ||
| { | ||
| t3_rule1 => { | ||
| 'local' => [ | ||
| { root_dir => 'data/raw' }, | ||
| { | ||
| INPUT => | ||
| '{$self->root_dir}/{$sample}/some_input_rule1.{$self->chunk}' | ||
| }, | ||
| { OUTPUT => ['some_output_rule1'] }, | ||
| { use_chunks => 1 }, | ||
| ], | ||
| process => | ||
| 'R1: INDIR: {$self->indir} INPUT: {$self->INPUT} outdir: {$self->outdir} OUTPUT: {$self->OUTPUT->[0]}', | ||
| }, | ||
| }, | ||
| ] | ||
| }; | ||
|
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| #Write out the config | ||
| open( $fh, ">$test_dir/conf/test1.1.yml" ) | ||
| or die print "Couldn't open file! $!"; | ||
| my $yaml = Dump $href; | ||
| print $fh $yaml; | ||
| close($fh); | ||
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| make_path( $test_dir . "/data/raw/Sample_01" ); | ||
| make_path( $test_dir . "/data/raw/Sample_02" ); | ||
| write_file( $test_dir . "/data/raw/Sample_01/" . "some_input_rule1" ); | ||
| write_file( $test_dir . "/data/raw/Sample_02/" . "some_input_rule1" ); | ||
| } | ||
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| sub construct_tests { | ||
| my $test_methods = TestMethod::Base->new(); | ||
| my $test_dir = $test_methods->make_test_dir(); | ||
| write_test_file($test_dir); | ||
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| my $t = "$test_dir/conf/test1.1.yml"; | ||
| my $test = $test_methods->make_test_env($t); | ||
| my $rules = $test->workflow_data->{rules}; | ||
|
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| return ( $test, $test_dir, $rules ); | ||
| } | ||
|
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| sub test_001 { | ||
| my ( $test, $test_dir, $rules ) = construct_tests; | ||
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| $test->check_sample_exist; | ||
| is_deeply($test->samples, ['Sample_01']); | ||
| is_deeply($test->global_attr->chroms_list, [1,2,3,4,5]); | ||
|
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| # $test->stdout(1); | ||
| $test->set_rule_names; | ||
| $test->filter_rule_keys; | ||
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| foreach my $rule ( @{$rules} ) { | ||
| _init_rule( $test, $rule ); | ||
| } | ||
|
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| $test->post_process_rules; | ||
| is_deeply($test->samples, ['Sample_01']); | ||
|
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| diag Dumper ($test->global_attr->chroms_list); | ||
| diag Dumper ($test->global_attr->samples); | ||
| diag Dumper($test->global_attr->has_samples); | ||
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|
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| ok(1); | ||
| } | ||
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| sub _init_rule { | ||
| my $test = shift; | ||
| my $rule = shift; | ||
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| $test->local_rule($rule); | ||
| $test->process_rule; | ||
| $test->p_rule_name( $test->rule_name ); | ||
| $test->p_local_attr( dclone( $test->local_attr ) ); | ||
| } |
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