bugfix: back to supporting -pipeline_name , making sure it gets post-…

…processed
Ensembl · Dec 15, 2016 · 8dd0f4c · 8dd0f4c
1 parent 09acf0e
commit 8dd0f4c
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Showing 2 changed files with 18 additions and 18 deletions.
diff --git a/modules/Bio/EnsEMBL/Hive/PipeConfig/EnsemblGeneric_conf.pm b/modules/Bio/EnsEMBL/Hive/PipeConfig/EnsemblGeneric_conf.pm
@@ -67,7 +67,7 @@ sub default_options {
         'rel_suffix'            => '',                                                                  # an empty string by default, a letter otherwise
         'rel_with_suffix'       => $self->o('ensembl_release').$self->o('rel_suffix'),
 
-        'pipeline_name'         => $self->processed_pipeline_name().'_'.$self->o('rel_with_suffix'),
+        'pipeline_name'         => $self->default_pipeline_name().'_'.$self->o('rel_with_suffix'),
 
         'user'                  => $ENV{'EHIVE_USER'} || 'ensadmin',
         'password'              => $ENV{'EHIVE_PASS'} // $ENV{'ENSADMIN_PSW'} // $self->o('password'),  # people will have to make an effort NOT to insert it into config files like .bashrc etc

diff --git a/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm b/modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
@@ -113,13 +113,15 @@ sub default_options {
         'hive_force_init'                   => 0,       # setting it to 1 will drop the database prior to creation (use with care!)
         'hive_no_init'                      => 0,       # setting it to 1 will skip pipeline_create_commands (useful for topping up)
 
+        'pipeline_name'                     => $self->default_pipeline_name(),
+
         'pipeline_db'   => {
             -driver => $self->o('hive_driver'),
             -host   => $self->o('host'),
             -port   => $self->o('port'),
             -user   => $self->o('user'),
             -pass   => $self->o('password'),
-            -dbname => $self->o('dbowner').'_'.$self->processed_pipeline_name(),
+            -dbname => $self->o('dbowner').'_'.$self->o('pipeline_name'),
         },
     };
 }
@@ -138,7 +140,7 @@ sub pipeline_create_commands {
     my $pipeline_url    = $self->pipeline_url();
     my $second_pass     = $pipeline_url!~ /^#:subst/;
 
-    my $parsed_url      = $second_pass && Bio::EnsEMBL::Hive::Utils::URL::parse( $pipeline_url );
+    my $parsed_url      = $second_pass && (Bio::EnsEMBL::Hive::Utils::URL::parse( $pipeline_url ) || die "Could not parse the '$pipeline_url' as the database URL");
     my $driver          = $second_pass ? $parsed_url->{'driver'} : '';
     my $hive_force_init = $self->o('hive_force_init');
 
@@ -238,7 +240,7 @@ sub hive_meta_table {
 
     return {
         'hive_sql_schema_version'           => Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_code_sql_schema_version(),
-        'hive_pipeline_name'                => $self->processed_pipeline_name(),
+        'hive_pipeline_name'                => $self->o('pipeline_name'),
         'hive_use_param_stack'              => $self->o('hive_use_param_stack'),
         'hive_auto_rebalance_semaphores'    => $self->o('hive_auto_rebalance_semaphores'),
     };
@@ -299,19 +301,14 @@ sub db_cmd {
 }
 
 
-sub processed_pipeline_name {
-    my $self            = shift @_;
+sub process_pipeline_name {
+    my ($self, $ppn) = @_;
 
-    unless($self->{'_processed_pipeline_name'}) {   # due to the way substitution works in DependentOptions, caching is essential here
-        my $ppn   = $self->root()->{'pipeline_name'} || $self->default_pipeline_name();
-           $ppn=~s/([[:lower:]])([[:upper:]])/${1}_${2}/g;   # CamelCase into Camel_Case
-           $ppn=~s/\s/_/g;                                   # remove all spaces
-           $ppn = lc($ppn);
+    $ppn=~s/([[:lower:]])([[:upper:]])/${1}_${2}/g;   # CamelCase into Camel_Case
+    $ppn=~s/\s/_/g;                                   # remove all spaces
+    $ppn = lc($ppn);
 
-        $self->{'_processed_pipeline_name'} = $ppn;
-    }
-
-    return $self->{'_processed_pipeline_name'};
+    return $ppn;
 }
 
 
@@ -345,7 +342,6 @@ sub process_options {
         # pre-patch definitely_used_options:
     $self->{'_extra_options'} = $self->load_cmdline_options( $self->pre_options() );
     $self->root()->{'pipeline_url'}     = $self->{'_extra_options'}{'pipeline_url'};
-    $self->root()->{'pipeline_name'}    = $self->{'_extra_options'}{'pipeline_name'};
 
     my @use_cases = ( 'pipeline_wide_parameters', 'resource_classes', 'pipeline_analyses', 'beekeeper_extra_cmdline_options', 'hive_meta_table' );
     if($include_pcc_use_case) {
@@ -354,7 +350,11 @@ sub process_options {
     }
     $self->use_cases( \@use_cases );
 
-    return $self->SUPER::process_options();
+    $self->SUPER::process_options();
+
+        # post-processing:
+    $self->root()->{'pipeline_name'}            = $self->process_pipeline_name( $self->root()->{'pipeline_name'} );
+    $self->root()->{'pipeline_db'}{'-dbname'} &&= $self->process_pipeline_name( $self->root()->{'pipeline_db'}{'-dbname'} );    # may be used to construct $self->pipeline_url()
 }
 
 
@@ -589,7 +589,7 @@ sub useful_commands_legend {
     my $self  = shift @_;
 
     my $pipeline_url    = '"' . $self->pipeline_url() . '"';
-    my $pipeline_name   = $self->processed_pipeline_name();
+    my $pipeline_name   = $self->o('pipeline_name');
     my $extra_cmdline   = $self->beekeeper_extra_cmdline_options();
 
     my @output_lines = (