changes to ensembl code to handle disconnecting databases properly -...

changes to ensembl code to handle disconnecting databases properly - disconnect_all, checking for reconnection when doing do and prepare and finishing statement handles in generic_fetch

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -309,7 +309,7 @@ sub generic_fetch {
   my $sth = $db->dbc->prepare($sql);
   $sth->execute;
   my $res = $self->_objs_from_sth($sth, $mapper, $slice);
-
+  $sth->finish();
   return $res;
 }
 

modules/Bio/EnsEMBL/DBSQL/DBConnection.pm

@@ -197,7 +197,6 @@ sub connect {
   my $self = shift;
 
   return if($self->connected);
-  $self->connected(1);
 
   if(defined($self->db_handle()) and $self->db_handle()->ping()) {
     warning("unconnected db_handle is still pingable, reseting connected boolean\n");
@@ -210,21 +209,19 @@ sub connect {
 
   my $dbh;
   eval{
-    $dbh = DBI->connect($dsn,
-                        $self->username(),
-                        $self->password(),
-                        {'RaiseError' => 1});
+    $dbh = DBI->connect($dsn, $self->username(), $self->password(), {'RaiseError' => 1});
   };
 
   if(!$dbh || $@ || !$dbh->ping()) {
     warn("Could not connect to database " . $self->dbname() .
-          " as user " . $self->username() .
-          " using [$dsn] as a locator:\n" . $DBI::errstr);
+         " 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);
   }
 
+  $self->connected(1);
   $self->db_handle($dbh);
   #print("CONNECT\n");
 }
@@ -564,6 +561,7 @@ sub prepare {
 
   # print STDERR  "SQL(".$self->dbname."):$string\n";
 
+   $self->connect() unless $self->connected();
    my $sth = $self->db_handle->prepare($string);
 
    # return an overridden statement handle that provides us with
@@ -598,6 +596,7 @@ sub do {
 
    #info("SQL(".$self->dbname."):$string");
 
+   $self->connect() unless $self->connected();
    my $result = $self->db_handle->do($string);
 
    # disconnect if the disconnect when inactive flag is set and
@@ -659,6 +658,7 @@ sub disconnect_if_idle {
   $self->connected(undef);
   $self->disconnect_count($self->disconnect_count()+1);
   #print("DISCONNECT\n");
+  $self->db_handle(undef);
   return 0;
 }
 

modules/Bio/EnsEMBL/Registry.pm

@@ -604,19 +604,21 @@ sub alias_exists{
 }
 
 sub set_disconnect_when_inactive{
-
-  foreach my $dba ( @{$registry_register{'_DBA'}}){
+  foreach my $dba ( @{get_all_DBAdaptors()}){
     my $dbc = $dba->dbc;
     #disconnect if connected
-    if($dbc->connected()){
-      $dbc->disconnect();
-      $dbc->connected(undef);
-    }
-
+    $dbc->disconnect_if_idle() if $dbc->connected();
     $dbc->disconnect_when_inactive(1);
   }
 }
 
+sub disconnect_all {
+  foreach my $dba ( get_all_DBAdaptors() ){
+    my $dbc = $dba->dbc;
+    #disconnect if connected
+    $dbc->disconnect_if_idle() if $dbc->connected();
+  }
+}
 =head2 change_access
 
   Will change the username and password for a set of databases.