Test init_pipeline outside of the test process.

init_pipeline was the last script tested this way. That caused some
issues because it is not isolated from the test process, and for
instance it will register the pipeline in TheApiary. Also, the test is
more reliable if the actual script is tested.

Author: muffato

modules/Bio/EnsEMBL/Hive/Utils/Test.pm

@@ -199,20 +199,11 @@ sub init_pipeline {
         $url = (splice(@$options, $url_flag_index, 2))[1];
     }
 
-    local @ARGV = @$options;
-    unshift @ARGV, (-pipeline_url => $url, -hive_force_init => 1);
-
-    lives_ok(sub {
-        my $orig_unambig_url = Bio::EnsEMBL::Hive::Utils::URL::parse($url)->{'unambig_url'};
-        ok($orig_unambig_url, 'Given URL could be parsed');
-        my $returned_url = Bio::EnsEMBL::Hive::Scripts::InitPipeline::init_pipeline($file_or_module, $tweaks);
-        ok($returned_url, 'pipeline initialized on '.$returned_url);
-
-        my $returned_unambig_url = Bio::EnsEMBL::Hive::Utils::URL::parse($returned_url)->{'unambig_url'};
-            # Both $url and $returned_url MAY contain the password (if applicable for the driver) but can be missing the port number assuming a default
-            # Both $orig_unambig_url and $returned_unambig_url SHOULD contain the port number (if applicable for the driver) but WILL NOT contain a password
-        is($returned_unambig_url, $orig_unambig_url, 'pipeline initialized on '.$url);
-    }, sprintf('init_pipeline("%s", %s)', $file_or_module, stringify($options)));
+    my @args = ($file_or_module, -pipeline_url => $url, -hive_force_init => 1);
+    push @args, @$options;
+    push @args, map {-tweak => $_} @$tweaks if $tweaks;
+
+    return _test_ehive_script('init_pipeline', undef, \@args);
 }
 
 

t/03.scripts/generate_graph.t

@@ -39,10 +39,14 @@ GetOptions(
 
 my $server_url  = get_test_url_or_die(-tag => 'server', -no_user_prefix => 1);
 
-# Most of the test scripts test init_pipeline() from Utils::Test but we
-# also need to test the main scripts/init_pipeline.pl !
-my @init_pipeline_args = ($ENV{'EHIVE_ROOT_DIR'}.'/scripts/init_pipeline.pl', 'Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMultServer_conf', -pipeline_url => $server_url, -hive_force_init => 1, -tweak => 'pipeline.param[take_time]=0');
-test_command(\@init_pipeline_args);
+init_pipeline(
+    'Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMultServer_conf',
+    $server_url,
+    [],
+    [
+        'pipeline.param[take_time]=0',
+    ],
+);
 
 
 my $client_url  = get_test_url_or_die(-tag => 'client', -no_user_prefix => 1);
@@ -59,12 +63,6 @@ push @confs_to_test, 'GC::PipeConfig::GCPct_conf' unless $@;    # SKIP it in cas
 my ($fh, $tmp_filename) = tempfile(UNLINK => 1);
 close($fh);
 
-sub test_command {
-    my $cmd_array = shift;
-    ok(!system(@$cmd_array), 'Can run '.join(' ', @$cmd_array));
-}
-
-
 foreach my $conf (@confs_to_test) {
   subtest $conf, sub {
     my $module_name = 'Bio::EnsEMBL::Hive::Examples::'.$conf;

t/10.pipeconfig/analysis_heir.t

@@ -32,8 +32,7 @@ $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Fil
 my $pipeline_url = get_test_url_or_die();
 
 my $init_stderr = capture_stderr {
-    local @INC = @INC;
-    push @INC, $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/';
+    local $ENV{'PERL5LIB'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB};
     init_pipeline(
         'TestPipeConfig::MissingAnalysis_conf',
         $pipeline_url,

t/10.pipeconfig/gc_dataflow.t

@@ -30,8 +30,7 @@ $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Fil
 my $pipeline_url  = get_test_url_or_die();
 
 {
-    local @INC = @INC;
-    push @INC, $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/';
+    local $ENV{'PERL5LIB'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB};
     init_pipeline('TestPipeConfig::AnyFailureBranch_conf', $pipeline_url, [], ['pipeline.param[take_time]=100']);
 }
 my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $pipeline_url );

t/10.pipeconfig/pipeline_url.t

@@ -21,19 +21,18 @@ use warnings;
 
 use Test::More;
 
-use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline beekeeper get_test_url_or_die safe_drop_database);
+use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline get_test_url_or_die safe_drop_database);
 use Bio::EnsEMBL::Hive::Utils qw(destringify);
 
 # 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 $pipeline_url  = get_test_url_or_die();
 
-# Utils::Test::init_pipeline runs things internally instead of invoking init_pipeline.pl
-# Here we need to run the script to trigger the password sanitization
-my @cmd = ('env', 'PERL5LIB='.$ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB}, $ENV{'EHIVE_ROOT_DIR'}.'/scripts/init_pipeline.pl', 'TestPipeConfig::PipelineURL_conf', -pipeline_url => $pipeline_url);
-my $rc = system(@cmd);
-is($rc, 0, 'init_pipeline.pl successfully ran');
+{
+    local $ENV{'PERL5LIB'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB};
+    init_pipeline('TestPipeConfig::PipelineURL_conf', $pipeline_url);
+}
 
 my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $pipeline_url );