dnadb now holds name core and not the adaptor so that forking and order are not important

modules/Bio/EnsEMBL/Registry.pm

@@ -382,12 +382,17 @@ sub get_all_DBAdaptors{
 =cut
 
 sub add_DNAAdaptor{
-  my ($class, $species, $group, $adap) = @_;
+  my ($class, $species, $group, $dnadb_group) = @_;
 
   $species = $class->get_alias($species);
-
-  $registry_register{$species}{$group}{'_DNA'} = $adap;
-
+  if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
+#    print STDERR "AHHH ".caller()."\n";
+    $registry_register{$species}{$group}{'_DNA'} = $dnadb_group->group();
+  }
+  else{
+#    print STDERR "AHHH MEN ".caller()."\n";
+    $registry_register{$species}{$group}{'_DNA'} = $dnadb_group;
+  }
 }
 
 =head2 get_DNAAdaptor
@@ -404,7 +409,12 @@ sub get_DNAAdaptor{
   my ($class, $species, $group) = @_;
 
   $species = $class->get_alias($species);
-  return  $registry_register{$species}{$group}{'_DNA'};
+  my $new_group = $registry_register{$species}{$group}{'_DNA'};
+  if( defined $new_group ) {
+    return  $class->get_DBAdaptor($species,$new_group);
+  } else {
+    return undef;
+  }
 }
 
 #
@@ -489,11 +499,11 @@ sub add_adaptor{
 
 =cut
 
-sub set_get_via_dnadb_if_set{
-  my ($class,$species,$type) = @_;
-
-  $registry_register{$class->get_alias($species)}{$type}{'DNADB'} = 1;
-}
+#sub set_get_via_dnadb_if_set{
+#  my ($class,$species,$type) = @_;
+#
+#  $registry_register{$class->get_alias($species)}{$type}{'DNADB'} = 1;
+#}
 
 =head2 get_adaptor
 
@@ -508,15 +518,27 @@ sub set_get_via_dnadb_if_set{
 
 sub get_adaptor{
   my ($class,$species,$group,$type)= @_;
-
-  $species = $class->get_alias($species);
  
-  #throw in a check to see if we should get the dnadb one and not the normal
-  if(defined($registry_register{$species}{$type}{'DNADB'}) && $class->get_DNAAdaptor($species,$group)){
-    my $dna = $class->get_DNAAdaptor($species,$group);
-    $species = $dna->species();
-    $group = $dna->group();
+  $species = $class->get_alias($species);
+  my %dnadb_adaptors = qw(Sequence  1 AssemblyMapper 1  KaryotypeBand 1 RepeatFeature 1 CoordSystem 1  AssemblyExceptionFeature 1 );
+
+  my $dnadb_group =  $registry_register{$species}{$group}{_DNA};
+
+  if( defined($dnadb_group) && defined($dnadb_adaptors{$type}) ) {
+#      print STDERR "new### $group  $dnadb_group \n";
+      $group = $dnadb_group;
   }
+#  else{
+#    if (defined($dnadb_adaptors{$type}) ) {
+#      print STDERR "old### $species $group $type no dnadb \n";    
+#    }
+#  }
+#throw in a check to see if we should get the dnadb one and not the normal
+#  if(defined($registry_register{$species}{$type}{'DNADB'}) && $class->get_DNAAdaptor($species,$group)){
+#    my $dna = $class->get_DNAAdaptor($species,$group);
+#    $species = $dna->species();
+#    $group = $dna->group();
+#  }
 
   my $ret = $registry_register{$species}{$group}{$type};
   if(!defined($ret)){

modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm

@@ -110,16 +110,19 @@ sub gen_load{
   }
   elsif($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
     #vega uses the core DBAdaptor so test if vega is in the dbname
-    if($dba->dbc->dbname() =~ /vega/){
-      if(!defined($dba->group())){
-	$dba->group('vega');
-      }
+    if(!defined($dba->group())){
+      $dba->group('core');
+    }
+    if($dba->group eq "estgene"){
+      $config_sub =  \&Bio::EnsEMBL::Utils::ConfigRegistry::load_estgene;
+     }
+    elsif($dba->group eq "est"){
+      $config_sub =  \&Bio::EnsEMBL::Utils::ConfigRegistry::load_est;
+     }
+    elsif($dba->group eq "vega"){
       $config_sub =  \&Bio::EnsEMBL::Utils::ConfigRegistry::load_vega;
      }
     else{
-      if(!defined($dba->group())){
-	$dba->group('core');
-      }
       $config_sub =  \&Bio::EnsEMBL::Utils::ConfigRegistry::load_core;
     }
   }
@@ -195,10 +198,6 @@ sub load_core{
   }
 
 
-  foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
-    Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
-  }
-
 }
 
 
@@ -221,7 +220,6 @@ sub load_SNP{
 sub attach_database{
   my ($class, $species, $core, $name1) = @_;
 
-  print STDERR "attach_databse called ".caller(). "\n";
 
   my $first =  Bio::EnsEMBL::Registry->get_DBAdaptor($species,$name1);
   my $coredb = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$core);
@@ -232,7 +230,6 @@ sub attach_database{
 
 sub attach_dna{
   my ($class, $species, $main, $attach) = @_; 
-  print STDERR "attach_dna called ".caller(). "\n";
 
   my $no_seq =  Bio::EnsEMBL::Registry->get_DBAdaptor($species,$main);
   my $seq = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$attach);
@@ -282,16 +279,14 @@ sub load_estgene{
     Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key});
   }
 
-  #if dnadb has been set then for the follwing use it.
-  foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
-    Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
-  }
+  
 
-  ## if the core exists then set this for the dna getting
-  my $core = $reg->get_DBAdaptor($dba->species,"core");
-  if(defined($core)){
-    $reg->add_DNAAdaptor($dba->species,$dba->group,$core); 
-  }
+#  #if dnadb has been set then for the follwing use it.
+#  foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
+#    Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
+#  }
+
+  $reg->add_DNAAdaptor($dba->species,$dba->group,"core"); 
 }
 
 
@@ -305,13 +300,13 @@ sub load_est{
   }
 
   #if dnadb has been set then for the follwing use it.
-  foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
-    Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
-  }
-  my $core = $reg->get_DBAdaptor($dba->species,"core");
-  if(defined($core)){
-    $reg->add_DNAAdaptor($dba->species,$dba->group,$core); 
-  }
+#  foreach my $type (qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)){
+#    Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set($dba->species,$type);
+#  }
+#  my $core = $reg->get_DBAdaptor($dba->species,"core");
+#  if(defined($core)){
+    $reg->add_DNAAdaptor($dba->species,$dba->group,"core"); 
+#  }
 }
 
 
@@ -323,10 +318,10 @@ sub load_vega{
   foreach my $key (keys %pairs){
     Bio::EnsEMBL::Registry->add_adaptor($dba->species, $dba->group, $key, $pairs{$key});
   }
-  my $core = $reg->get_DBAdaptor($dba->species,"core");
-  if(defined($core)){
-    $reg->add_DNAAdaptor($dba->species,$dba->group,$core); 
-  }
+#  my $core = $reg->get_DBAdaptor($dba->species,"core");
+#  if(defined($core)){
+    $reg->add_DNAAdaptor($dba->species,$dba->group,"core"); 
+#  }
 }
 
 
@@ -397,7 +392,6 @@ sub load_pipeline{
 sub dnadb_add{
   my $class = shift;
   my ($dnaspecies, $dnagroup, $species, $group) = @_;
-  print STDERR "dnadb_add called ".caller(). "\n";
 
   my $dnadb =  Bio::EnsEMBL::Registry->get_DBAdaptor($dnaspecies, $dnagroup);
   my $featdb = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);