Opps reverting back to previous version as i mean't to commit on the branch not here

modules/Bio/EnsEMBL/DBSQL/DBConnection.pm

@@ -3,12 +3,10 @@
 =head1 SYNOPSIS
 
     $db = Bio::EnsEMBL::DBSQL::DBConnection->new(
-        -user    => 'anonymous',
-        -dbname  => 'homo_sapiens_core_20_34c',
-        -host    => 'ensembldb.ensembl.org',
-        -driver  => 'mysql',
-        -species => 'Homo Sapiens',
-        -group   => 'core'
+        -user   => 'anonymous',
+        -dbname => 'homo_sapiens_core_20_34c',
+        -host   => 'ensembldb.ensembl.org',
+        -driver => 'mysql',
         );
 
 
@@ -42,9 +40,7 @@ package Bio::EnsEMBL::DBSQL::DBConnection;
 use vars qw(@ISA);
 use strict;
 
-#use Bio::EnsEMBL::Container; ## Container no longer needed here
-use Bio::EnsEMBL::Registry;
-my $reg = "Bio::EnsEMBL::Registry";
+use Bio::EnsEMBL::Container;
 use Bio::EnsEMBL::Root;
 use DBI;
 
@@ -84,65 +80,33 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
                  which would otherwise keep open a lot of connections to the
                  database.  Database connections are automatically reopened
                  when required.
-  Arg [DNADB] :  (optional)  Bio::EnsEMBL::DBSQL::DBConnection
-                 The dbconnection to get the dna from.
-  Arg [SPECIES]: (optional) string
-                 Name of the species to be labelled as.
-  Arg [GROUP]: (optional) string
-                 Name of the group to be labelled as. (e.g. core, estgene, vega etc)
   Example    : $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new
                   (-user   => 'anonymous',
                    -dbname => 'homo_sapiens_core_20_34c',
                    -host   => 'ensembldb.ensembl.org',
-                   -driver => 'mysql'
-                   -species => 'Homo Sapiens',
-                   -group   => 'core');
+                   -driver => 'mysql');
 
   Description: Constructor for a DatabaseConenction. Any adaptors that require
                database connectivity should inherit from this class.
   Returntype : Bio::EnsEMBL::DBSQL::DBConnection
   Exceptions : thrown if USER or DBNAME are not specified, or if the database
                cannot be connected to.
-  Caller     : Bio::EnsEMBL::::Utils::ConfigRegistry ( for newer code using the registry)
-               Bio::EnsEMBL::DBSQL::DBAdaptor        ( for old style code)
+  Caller     : Bio::EnsEMBL::DBSQL::DBAdaptor
 
 =cut
 
 sub new {
   my $class = shift;
 
-  my ($db,$host,$driver,$user,$password,$port, $inactive_disconnect, $dbconn, $species, $group, $dnadb) =
+  my ($db,$host,$driver,$user,$password,$port, $inactive_disconnect, $dbconn) =
     rearrange([qw(DBNAME HOST DRIVER USER PASS PORT
-                  DISCONNECT_WHEN_INACTIVE DBCONN SPECIES GROUP DNADB)], @_);
+                  DISCONNECT_WHEN_INACTIVE DBCONN)], @_);
 
   my $self = {};
   bless $self, $class;
 
- # make sure the register can find the species name in the alias list as itself.
-
-  if(!defined($species)){
-    $species= "DEFAULT";
-    $group = "core";
-
-    Bio::EnsEMBL::Registry->add_alias($species,$species); #set needed self alias
-
-    my $free=0;
-    my $i = 1;
-    while(!$free){
-      Bio::EnsEMBL::Registry->add_alias($species.$i,$species.$i); #set needed self alias
-      if(!defined(Bio::EnsEMBL::Registry->get_DBAdaptor($species.$i, $group))){
-	$free =1;
-      }
-      else{
-	$i++;
-      }
-    }
-    $species .= $i;
-  }
-
   if($dbconn) {
-    if($db || $host || $driver || $password || $port || $inactive_disconnect
-      || $dnadb) {
+    if($db || $host || $driver || $password || $port || $inactive_disconnect) {
       throw("Cannot specify other arguments when -DBCONN argument used.");
     }
 
@@ -152,8 +116,6 @@ sub new {
     $self->password($dbconn->password());
     $self->port($dbconn->port());
     $self->driver($dbconn->driver());
-    $self->species($dbconn->species());
-    $self->group($dbconn->group());
 
     $self->connect();
 
@@ -162,7 +124,6 @@ sub new {
     }
   } else {
 
-
     $db   || throw("-DBNAME argument is required.");
     $user || throw("-USER argument is required.");
 
@@ -179,34 +140,18 @@ sub new {
     $self->port($port);
     $self->driver($driver);
 
-
     $self->connect();
 
-    
-    if($species){
-#      print "setting species to $species\n";
-      Bio::EnsEMBL::Registry->add_alias($species,$species);
-      $self->species($species);
-#      print "setting species to $species\n";
-    }
-    else{
-      throw("No species specified\n");
-    }
-    if($group){
-      $self->group($group);
-    }
-
-
     if($inactive_disconnect) {
       $self->disconnect_when_inactive($inactive_disconnect);
     }
 
+    # be very sneaky and actually return a container object which is outside
+    # of the circular reference loops and will perform cleanup when all 
+    # references to the container are gone.
   }
 
-  if(defined $dnadb) {
-    $self->dnadb($dnadb);
-  }
-  return $self;
+  return new Bio::EnsEMBL::Container($self);
 }
 
 
@@ -238,9 +183,6 @@ sub connect {
   };
 
   if(!$dbh || $@) {
-    warn("Could not connect to database " . $self->dbname() .
-          " as user " . $self->username() .
-          " using [$dsn] as a locator:\n" . $DBI::errstr);
     throw("Could not connect to database " . $self->dbname() .
           " as user " . $self->username() .
           " using [$dsn] as a locator:\n" . $DBI::errstr);
@@ -390,53 +332,6 @@ sub password {
   $self->{_password};
 }
 
-=head2 species
-
-  Arg [1]    : (optional) string $arg
-               The new value of the species used by this connection. 
-  Example    : $host = $db_connection->species()
-  Description: Getter/Setter for the species of to use for 
-               this connection.  There is currently no point in setting 
-               this value after the connection has already been established 
-               by the constructor.
-  Returntype : string
-  Exceptions : none
-  Caller     : new
-
-=cut
-
-sub species {
-  my ($self, $arg ) = @_;
-  ( defined $arg ) &&
-    ( $self->{_species} = $arg );
-  return $self->{_species};
-}
-
-
-=head2 group
-
-  Arg [1]    : (optional) string $arg
-               The new value of the group used by this connection. 
-  Example    : $host = $db_connection->group()
-  Description: Getter/Setter for the group of to use for 
-               this connection.  There is currently no point in setting 
-               this value after the connection has already been established 
-               by the constructor.
-  Returntype : string
-  Exceptions : none
-  Caller     : new
-
-=cut
-
-sub group {
-  my ($self, $arg ) = @_;
-  ( defined $arg ) &&
-    ( $self->{_group} = $arg );
-  return $self->{_group};
-}
-
-
-
 
 =head2 disconnect_when_inactive
 
@@ -631,4 +526,226 @@ sub disconnect_if_idle {
 }
 
 
+=head2 _get_adaptor
+
+  Arg [1]    : string $module
+               the fully qualified of the adaptor module to be retrieved
+  Arg [2..n] : (optional) arbitrary list @args
+               list of arguments to be passed to adaptors constructor
+  Example    : $adaptor = $self->_get_adaptor("full::adaptor::name");
+  Description: PROTECTED Used by subclasses to obtain adaptor objects
+               for this database connection using the fully qualified
+               module name of the adaptor. If the adaptor has not been 
+               retrieved before it is created, otherwise it is retreived
+               from the adaptor cache.
+  Returntype : Adaptor Object of arbitrary type
+  Exceptions : thrown if $module can not be instantiated
+  Caller     : Bio::EnsEMBL::DBAdaptor
+
+=cut
+
+sub _get_adaptor {
+  my( $self, $module, @args) = @_;
+
+  my( $adaptor, $internal_name );
+
+  #Create a private member variable name for the adaptor by replacing
+  #:: with _
+
+  $internal_name = $module;
+
+  $internal_name =~ s/::/_/g;
+
+  unless (defined $self->{'_adaptors'}->{$internal_name}) {
+    eval "require $module";
+
+    if($@) {
+      warning("$module cannot be found.\nException $@\n");
+      return undef;
+    }
+
+    $adaptor = "$module"->new($self, @args);
+
+    $self->{'_adaptors'}->{$internal_name} = $adaptor;
+  }
+
+  return $self->{'_adaptors'}->{$internal_name};
+}
+
+
+
+=head2 add_db_adaptor
+
+  Arg [1]    : string $name
+               the name of the database to attach to this database
+  Arg [2]    : Bio::EnsEMBL::DBSQL::DBConnection
+               the db adaptor to attach to this database
+  Example    : $db->add_db_adaptor('lite', $lite_db_adaptor);
+  Description: Attaches another database instance to this database so 
+               that it can be used in instances where it is required.
+  Returntype : none
+  Exceptions : none
+  Caller     : EnsWeb
+
+=cut
+
+sub add_db_adaptor {
+  my ($self, $name, $adaptor) = @_;
+
+  unless($name && $adaptor && ref $adaptor) {
+    throw('adaptor and name arguments are required');
+  }
+
+  #avoid circular references and memory leaks
+  if($adaptor->isa('Bio::EnsEMBL::Container')) {
+      $adaptor = $adaptor->_obj;
+  }
+
+  $self->{'_db_adaptors'}->{$name} = $adaptor;
+}
+
+
+=head2 remove_db_adaptor
+
+  Arg [1]    : string $name
+               the name of the database to detach from this database.
+  Example    : $lite_db = $db->remove_db_adaptor('lite');
+  Description: Detaches a database instance from this database and returns
+               it.
+  Returntype : none
+  Exceptions : none
+  Caller     : ?
+
+=cut
+
+sub remove_db_adaptor {
+  my ($self, $name) = @_;
+
+  my $adaptor = $self->{'_db_adaptors'}->{$name};
+  delete $self->{'_db_adaptors'}->{$name};
+
+  unless($adaptor) {
+      return undef;
+  }
+
+  return $adaptor;
+}
+
+
+=head2 get_all_db_adaptors
+
+  Arg [1]    : none
+  Example    : @attached_dbs = values %{$db->get_all_db_adaptors()};
+  Description: returns all of the attached databases as 
+               a hash reference of key/value pairs where the keys are
+               database names and the values are the attached databases  
+  Returntype : hash reference with Bio::EnsEMBL::DBSQL::DBConnection values
+  Exceptions : none
+  Caller     : Bio::EnsEMBL::DBSQL::ProxyAdaptor
+
+=cut
+
+sub get_all_db_adaptors {
+  my ($self) = @_;
+
+  unless(defined $self->{'_db_adaptors'}) {
+    return {};
+  }
+
+  return $self->{'_db_adaptors'};
+}
+
+
+
+=head2 get_db_adaptor
+
+  Arg [1]    : string $name
+               the name of the attached database to retrieve
+  Example    : $lite_db = $db->get_db_adaptor('lite');
+  Description: returns an attached db adaptor of name $name or undef if
+               no such attached database exists
+  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
+  Exceptions : none
+  Caller     : ?
+
+=cut
+
+sub get_db_adaptor {
+  my ($self, $name) = @_;
+
+  unless($self->{'_db_adaptors'}->{$name}) {
+      return undef;
+  }
+
+  return $self->{'_db_adaptors'}->{$name};
+}
+
+
+#
+# This method is automatically called by the Container DESTROY method to
+# break circular references. Do not call it directly.
+#
+sub deleteObj {
+  my $self = shift;
+
+  #print STDERR "DBConnection::deleteObj : Breaking circular references:\n";
+
+  if(exists($self->{'_adaptors'})) {
+    foreach my $adaptor_name (keys %{$self->{'_adaptors'}}) {
+      my $adaptor = $self->{'_adaptors'}->{$adaptor_name};
+
+      #call each of the adaptor deleteObj methods
+      if($adaptor && $adaptor->can('deleteObj')) {
+        #print STDERR "\t\tdeleting adaptor\n";
+        $adaptor->deleteObj();
+      }
+
+      #break dbadaptor -> object adaptor references
+      delete $self->{'_adaptors'}->{$adaptor_name};
+    }
+  }
+
+  #print STDERR "Cleaning up attached databases\n";
+
+  #break dbadaptor -> dbadaptor references
+  foreach my $db_name (keys %{$self->get_all_db_adaptors()}) {
+    #print STDERR "\tbreaking reference to $db_name database\n";
+    $self->remove_db_adaptor($db_name);
+  }
+}
+
+
+=head2 DESTROY
+
+  Arg [1]    : none
+  Example    : none
+  Description: Called automatically by garbage collector.  Should
+               never be explicitly called.  The purpose of this destructor
+               is to disconnect any active database connections.
+  Returntype : none 
+  Exceptions : none
+  Caller     : Garbage Collector
+
+=cut
+
+sub DESTROY {
+   my ($obj) = @_;
+
+   #print STDERR "DESTROYING DBConnection\n";
+
+   my $dbh = $obj->db_handle();
+
+   if($dbh) {
+     # don't disconnect if InactiveDestroy flag is set, this can really
+     # screw up forked processes
+     if(!$dbh->{'InactiveDestroy'}) {
+       $dbh->disconnect();
+     }
+   }
+
+   $obj->db_handle(undef);
+}
+
+
+
 1;

modules/Bio/EnsEMBL/DBSQL/ProxySNPAdaptor.pm

@@ -40,29 +40,6 @@ use vars '@ISA';
 @ISA = qw(Bio::EnsEMBL::DBSQL::ProxyAdaptor);
 
 
-
-sub set_primary{
-  my ($self, $primary_adaptor) = @_;
-
-#
-# For old style code i will have to add primary db later when get is called
-#
-  unless($primary_adaptor) {
-    throw("The primary_adaptor argument is required\n");
-    return undef;
-  }
-#  
-#  #determine the type of adaptor the proxy is filling in for
-  $self->{'_proxy_type'} = ref($primary_adaptor);
-#  
-  #strip out fully qualified package name
-  $self->{'_proxy_type'} =~ s/.*:://;
-
-  $self->{'_primary_adaptor'} = $primary_adaptor;
-#
-}
- 
-
 =head2 fetch_by_Slice
 
   Arg [1]    : list of arbitrary args @args
@@ -79,19 +56,15 @@ sub set_primary{
 sub fetch_all_by_Slice {
   my ($self, @args) = @_;
 
-  my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');#$self->db()->get_db_adaptor('lite');
-  my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP'); #$self->db()->get_db_adaptor('SNP');
+  my $lite_db = $self->db()->get_db_adaptor('lite');
+  my $snp_db = $self->db()->get_db_adaptor('SNP');
 
   if(defined $lite_db) {
     #use the Lite database if it is available
-    my $lite_adaptor =  Bio::EnsEMBL::Registry->get_adaptor( 
-                          $lite_db->species, $lite_db->group ,"lite");
-    return $lite_adaptor->fetch_all_by_Slice(@args);
+    return $lite_db->get_SNPAdaptor()->fetch_all_by_Slice(@args);
   } elsif(defined $snp_db) {
     #use the snp database if it is available
-    my $snp_adaptor =  Bio::EnsEMBL::Registry->get_adaptor( 
-			  $snp_db->species, $snp_db->group ,"SNP");   
-    return $snp_adaptor->fetch_all_by_Slice(@args);
+    return $snp_db->get_SNPAdaptor()->fetch_all_by_Slice(@args);
   }
 
   #There is no core SNPAdaptor so throw an exception if lite and SNP