added wait_timeout optional parameter

modules/Bio/EnsEMBL/DBSQL/DBConnection.pm

@@ -88,6 +88,12 @@ 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 [WAIT_TIMEOUT]: (optional) integer
+                 Time in seconds for the wait timeout to happen. Time after which
+                 the connection is deleted if not used. By default this is 28800 (8 hours)
+                 on most systems. 
+                 So set this to greater than this if your connection are getting deleted.
+                 Only set this if you are having problems and know what you are doing.
 
   Example    : $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new
                   (-user   => 'anonymous',
@@ -109,9 +115,9 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
 sub new {
   my $class = shift;
 
-  my ($db,$host,$driver,$user,$password,$port, $inactive_disconnect, $dbconn) =
+  my ($db,$host,$driver,$user,$password,$port, $inactive_disconnect, $dbconn, $wait_timeout) =
     rearrange([qw(DBNAME HOST DRIVER USER PASS PORT 
-                  DISCONNECT_WHEN_INACTIVE DBCONN )], @_);
+                  DISCONNECT_WHEN_INACTIVE DBCONN WAIT_TIMEOUT)], @_);
 
   my $self = {};
   bless $self, $class;
@@ -138,6 +144,7 @@ sub new {
     $driver ||= 'mysql';
     $host   ||= 'mysql';
     $port   ||= 3306;
+    $wait_timeout   ||= 0;
 
     $self->username( $user );
     $self->host( $host );
@@ -145,6 +152,7 @@ sub new {
     $self->password( $password );
     $self->port($port);
     $self->driver($driver);
+    $self->timeout($wait_timeout);
 
     if($inactive_disconnect) {
       $self->disconnect_when_inactive($inactive_disconnect);
@@ -221,8 +229,10 @@ sub connect {
           " as user " . $self->username() .
           " using [$dsn] as a locator:\n" . $DBI::errstr);
   }
-
   $self->db_handle($dbh);
+  if($self->timeout()){
+    $dbh->do("SET SESSION wait_timeout=".$self->timeout());
+  }
   #print("CONNECT\n");
 }
 
@@ -255,6 +265,16 @@ sub disconnect_count {
   return $self->{'disconnect_count'};
 }
 
+sub timeout{
+  my($self, $arg ) = @_;
+
+  (defined $arg) &&
+    ($self->{_timeout} = $arg );
+
+  return $self->{_timeout};
+
+}
+
 sub query_count {
   my $self = shift;
   return $self->{'_query_count'} = shift if(@_);

modules/Bio/EnsEMBL/Registry.pm

@@ -1035,6 +1035,11 @@ sub load_registry_from_url {
                work properly. This option should only be used for
                production or testing purposes and if you really know what
                you are doing.
+  Arg [WAIT_TIMEOUT]: (optional) integer
+                 Time in seconds for the wait timeout to happen. Time after which
+                 the connection is deleted if not used. By default this is 28800 (8 hours)
+                 So set this to greater than this if your connection are getting deleted.
+                 Only set this if you are having problems and know what you are doing.
 
   Example : load_registry_from_db( -host => 'ensembldb.ensembl.org',
 				   -user => 'anonymous',
@@ -1051,8 +1056,8 @@ sub load_registry_from_url {
 
 sub load_registry_from_db {
   my($self, @args) = @_;
-  my ($host, $port, $user, $pass, $verbose, $db_version) =
-    rearrange([qw(HOST PORT USER PASS VERBOSE DB_VERSION)], @args);
+  my ($host, $port, $user, $pass, $verbose, $db_version, $wait_timeout) =
+    rearrange([qw(HOST PORT USER PASS VERBOSE DB_VERSION WAIT_TIMEOUT )], @args);
 
 
 
@@ -1061,6 +1066,7 @@ sub load_registry_from_db {
 
   $user ||= "ensro";
   $port ||= 3306;
+  $wait_timeout ||= 0;
   my $db = DBI->connect( "DBI:mysql:host=$host;port=$port" , $user, $pass );
 
   my $res = $db->selectall_arrayref( "show databases" );
@@ -1108,7 +1114,8 @@ sub load_registry_from_db {
 	-user => $user,
 	-pass => $pass,
 	-port => $port,
-	-dbname => $coredb
+	-dbname => $coredb,
+        -wait_timeout => $wait_timeout
       );
     (my $sp = $species ) =~ s/_/ /g;
     $self->add_alias( $species, $sp );
@@ -1128,7 +1135,8 @@ sub load_registry_from_db {
 	-user => $user,
 	-pass => $pass,
 	-port => $port,
-	-dbname => $cdnadb
+	-dbname => $cdnadb,
+        -wait_timeout => $wait_timeout
       );
     (my $sp = $species ) =~ s/_/ /g;
     $self->add_alias( $species, $sp );
@@ -1146,6 +1154,7 @@ sub load_registry_from_db {
 	-user => $user,
 	-pass => $pass,
 	-port => $port,
+        -wait_timeout => $wait_timeout,
 	-dbname => $vegadb
       );
     (my $sp = $species ) =~ s/_/ /g;
@@ -1164,6 +1173,7 @@ sub load_registry_from_db {
 	-user => $user,
 	-pass => $pass,
 	-port => $port,
+        -wait_timeout => $wait_timeout,
 	-dbname => $other_db
       );
       (my $sp = $species ) =~ s/_/ /g;
@@ -1189,6 +1199,7 @@ sub load_registry_from_db {
 	  -user => $user,
 	  -pass => $pass,
 	  -port => $port,
+          -wait_timeout => $wait_timeout,
 	  -dbname => $variation_db
 	);
       print $variation_db." loaded\n" if ($verbose);
@@ -1212,6 +1223,7 @@ sub load_registry_from_db {
 			-user => $user,
 			-pass => $pass,
 			-port => $port,
+		        -wait_timeout => $wait_timeout,
 			-dbname => $funcgen_db
 		  );
 		print $funcgen_db." loaded\n" if ($verbose);
@@ -1236,6 +1248,7 @@ sub load_registry_from_db {
 	  -user => $user,
 	  -pass => $pass,
 	  -port => $port,
+          -wait_timeout => $wait_timeout,
 	  -dbname => $compara_db
 	);
       print $compara_db." loaded\n" if ($verbose);