From 549e6b9a00babe1ac019ab460a185b2cff9a285f Mon Sep 17 00:00:00 2001
From: Jessica Severin <jessica@sanger.ac.uk>
Date: Wed, 10 Mar 2004 13:12:40 +0000
Subject: [PATCH] added disconnect method. smart enough to deal with shared
db_handles 'reconnect' is automatic when any access to the handle (db_handle,
prepare) is requested. Also added explicit connect method which returns if
the handle is already connected (shouldn't need to be called)
---
modules/Bio/EnsEMBL/DBSQL/DBConnection.pm | 110 +++++++++++++++++-----
modules/t/dbConnection.t | 27 +++++-
2 files changed, 115 insertions(+), 22 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
index 923e01ed74..f0ccb4d881 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
@@ -100,16 +100,18 @@ sub new {
throw("Bio::EnsEMBL::DBSQL::DBConnection argument expected.");
}
+ #share a common db_handle, use a shared scalar ref_count to track # connections
my $rcount = $dbconn->ref_count();
$$rcount++; # dereference and increment shared var
$self->ref_count($rcount);
+ $self->db_handle($dbconn->db_handle());
$self->driver($dbconn->driver());
$self->host($dbconn->host());
+ $self->port($dbconn->port());
+ $self->dbname($dbconn->dbname());
$self->username($dbconn->username());
$self->password($dbconn->password());
- $self->port($dbconn->port());
- $self->db_handle($dbconn->db_handle());
return Bio::EnsEMBL::Container->new($self);
}
@@ -127,6 +129,7 @@ sub new {
$port = 3306;
}
+=head1
my $dsn = "DBI:$driver:database=$db;host=$host;port=$port";
my $dbh;
@@ -140,6 +143,7 @@ sub new {
my $ref_count = 1;
$self->ref_count(\$ref_count);
$self->db_handle($dbh);
+=cut
$self->username( $user );
$self->host( $host );
@@ -148,6 +152,8 @@ sub new {
$self->port($port);
$self->driver($driver);
+ $self->connect();
+
# 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.
@@ -155,6 +161,45 @@ sub new {
}
+=head2 connect
+
+ Example : $db_connection->connect()
+ Description: Explicitely connect to database if not connected
+ Returntype : none
+ Exceptions : none
+ Caller : new, db_handle
+
+=cut
+
+sub connect {
+ my $self = shift;
+
+ if($self->{'_db_handle'}) { return; }
+
+ my $host = $self->host();
+ my $driver = $self->driver();
+ my $user = $self->username();
+ my $password = $self->password();
+ my $port = $self->port();
+ my $db = $self->dbname();
+
+ my $dsn = "DBI:$driver:database=$db;host=$host;port=$port";
+
+ my $dbh;
+ eval{
+ $dbh = DBI->connect("$dsn","$user",$password, {RaiseError => 1});
+ };
+
+ $dbh || throw("Could not connect to database $db user " .
+ "$user using [$dsn] as a locator\n" . $DBI::errstr);
+
+ #print STDERR "DBConnection : CONNECT\n";
+ my $ref_count = 1;
+ $self->ref_count(\$ref_count);
+ $self->{'_db_handle'} = $dbh;
+}
+
+
=head2 driver
Arg [1] : (optional) string $arg
@@ -420,12 +465,12 @@ sub db_handle {
if( defined $value) {
$self->{'_db_handle'} = $value;
- }
- return $self->{'_db_handle'};
+ }
+ else { $self->connect(); }
+ return $self->{'_db_handle'};
}
-
=head2 prepare
Arg [1] : string $string
@@ -446,13 +491,13 @@ sub prepare {
if( ! $string ) {
throw("Attempting to prepare an empty SQL query.");
}
- if( !defined $self->{_db_handle} ) {
+ if( !defined $self->db_handle ) {
throw("Database object has lost its database handle.");
}
#info("SQL(".$self->dbname."):$string");
- return $self->{_db_handle}->prepare($string);
+ return $self->db_handle->prepare($string);
}
@@ -612,23 +657,46 @@ sub DESTROY {
#print STDERR "DESTROYING DBConnection\n";
- my $dbh = $obj->{'_db_handle'};
+ $obj->disconnect();
+}
- if( $dbh ) {
- my $refcount = $obj->ref_count();
- $$refcount--;
- # Do not disconnect if the InactiveDestroy flag has been set
- # this can really screw up forked processes.
- # Also: do not disconnect if this database handle is shared by
- # other DBConnections (as indicated by the refcount)
- if(!$dbh->{'InactiveDestroy'} && $$refcount == 0) {
- $dbh->disconnect;
- }
+=head2 disconnect
- $obj->{'_db_handle'} = undef;
- }
-}
+ Example : $db_connection->disconnect()
+ Description: Explicitely disconnect from database if connected
+ Returntype : none
+ Exceptions : none
+ Caller : ?, DESTROY
+
+=cut
+
+sub disconnect {
+ my $self = shift;
+
+ my $dbh = $self->{'_db_handle'};
+ if( $dbh ) {
+ my $refcount = $self->ref_count();
+ $$refcount--;
+ #print STDERR "DBConnection : ref_count-- ";
+
+ # Do not disconnect if the InactiveDestroy flag has been set
+ # this can really screw up forked processes.
+ # Also: do not disconnect if this database handle is shared by
+ # other DBConnections (as indicated by the refcount)
+ if(!$dbh->{'InactiveDestroy'} && $$refcount == 0) {
+ $dbh->disconnect;
+ #print STDERR ": DISCONNECT ";
+ }
+ #print STDERR "\n";
+
+ $self->{'_db_handle'} = undef;
+ #unlink shared ref_count variable since no longer sharing db_handle
+ my $unlinked_refcount = 0;
+ $self->ref_count(\$unlinked_refcount);
+ }
+
+}
1;
diff --git a/modules/t/dbConnection.t b/modules/t/dbConnection.t
index 453684b6fc..b96cbac0de 100644
--- a/modules/t/dbConnection.t
+++ b/modules/t/dbConnection.t
@@ -5,7 +5,7 @@ use warnings;
BEGIN { $| = 1;
use Test;
- plan tests => 15;
+ plan tests => 19;
}
use MultiTestDB;
@@ -91,6 +91,7 @@ ok(test_getter_setter($dbc, 'db_handle', $db->db_handle));
my $sth = $dbc->prepare('SELECT * from gene limit 1');
$sth->execute;
ok($sth->rows);
+$sth->finish;
#
# 12 add_db_adaptor
@@ -114,7 +115,31 @@ $dbc->remove_db_adaptor('core');
ok(!defined $dbc->get_db_adaptor('core'));
ok(!defined $dbc->get_all_db_adaptors->{'core'});
+#
+# 16-17 disconnect and auto-reconnect via a prepare
+#
+ok($dbc->disconnect);
+$sth = $dbc->prepare('SELECT * from gene limit 1');
+$sth->execute;
+ok($sth->rows);
+$sth->finish;
+#
+# 18-19 make new connection with shared dbhandle,
+# test copied/shared connection
+# disconnect original,
+# use copy with shared handle (that shouldn't have been disconnected)
+#
+my $dbc2 = Bio::EnsEMBL::DBSQL::DBConnection->new(-dbconn => $dbc);
+$sth = $dbc2->prepare('SELECT * from gene limit 1');
+$sth->execute;
+ok($sth->rows);
+$sth->finish;
+$dbc->disconnect;
+$sth = $dbc2->prepare('SELECT * from gene limit 1');
+$sth->execute;
+ok($sth->rows);
+$sth->finish;
--
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