Reverted Production DB dependency in order to allow Xref pipeline to run....

Reverted Production DB dependency in order to allow Xref pipeline to run. Changes can be reinstated once slightly more mature.

modules/Bio/EnsEMBL/Registry.pm

@@ -150,7 +150,6 @@ my %group2adaptor = (
       'ontology'  => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor',
       'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
       'pipeline'      => 'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
-      'production' => 'Bio::EnsEMBL::Production::DBSQL::DBAdaptor',
       'snp'       => 'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
       'stable_ids' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
       'variation' => 'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
@@ -1588,9 +1587,6 @@ sub load_registry_from_db {
   my $ontology_db;
   my $ontology_version;
 
-  my $production_db;
-  my $production_version;
-
   my $stable_ids_db;
   my $stable_ids_version;
 
@@ -1656,19 +1652,6 @@ sub load_registry_from_db {
         $ontology_db      = $db;
         $ontology_version = $1;
       }
-    } elsif ( $db =~ /^ensembl(?:genomes)?_production(_\d+)?/x ) {
-      # production db can come with no version (i.e. that on ens-staging1),
-      # but it's backed up with a release number
-      my $version = $1;
-      if ($version) {
-	$version =~ s/_//;
-	if ($software_version and $version eq $software_version) {
-	  $production_db      = $db;
-	  $production_version = $version;
-	} 
-      } else { # this is the default choice
-	$production_db = $db if $db =~ /^ensembl(?:genomes)?_production$/;
-      }
     } elsif ( $db =~ /^ensembl(?:genomes)?_stable_ids_(?:\d+_)?(\d+)/x ) {
       if ( $1 eq $software_version ) {
         $stable_ids_db      = $db;
@@ -2144,30 +2127,6 @@ sub load_registry_from_db {
     print("No ontology database found\n");
   }
 
-  # Production
-
-  if ( defined($production_db) ) {
-    require Bio::EnsEMBL::Production::DBSQL::DBAdaptor;
-
-    my $dba =
-      Bio::EnsEMBL::Production::DBSQL::DBAdaptor->new(
-                                '-species' => 'multi' . $species_suffix,
-                                '-group'   => 'production',
-                                '-host'    => $host,
-                                '-port'    => $port,
-                                '-user'    => $user,
-                                '-pass'    => $pass,
-                                '-dbname'  => $production_db, );
-
-    if ($verbose) {
-      printf( "%s loaded\n", $production_db );
-    }
-  }
-  elsif ($verbose) {
-    print("No production database found\n");
-  }
-
-  # Stable IDs
 
   if ( defined($stable_ids_db) && $stable_ids_version != 0 ) {
 
@@ -2196,9 +2155,6 @@ sub load_registry_from_db {
     -species => 'multi'.$species_suffix,
     -alias   => ['ontology'.$species_suffix] );
 
-  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-    -species => 'multi'.$species_suffix,
-    -alias   => ['production'.$species_suffix] );
 
   Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
     -species => 'multi'.$species_suffix,