From cfd74798db0b891316646cef998a1b6dd04e0c2a Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 5 Mar 2004 18:02:58 +0000
Subject: [PATCH] Made it possible to share the same database handle between
multiple DBConnections This is useful if you want to conserve db connections
and use the same db for compara/pipeline etc.
---
modules/Bio/EnsEMBL/DBSQL/DBConnection.pm | 125 +++++++++++++++-------
1 file changed, 86 insertions(+), 39 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
index a5c57dbdb8..923e01ed74 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm
@@ -17,6 +17,11 @@
If you go through prepare you could log all your select statements.
+ If you want to share a database handle with other database connections
+ you can do the following:
+
+ $db2 = Bio::EnsEMBL::DBSQL::DBConnection->new(-dbconn => $db);
+
=head1 DESCRIPTION
This only wraps around the perl DBI->connect call,
@@ -24,17 +29,15 @@
=head1 CONTACT
-Describe contact details here
+ This module is part of the Ensembl project: www.ensembl.org
-=head1 APPENDIX
+ Ensembl development mailing list: <ensembl-dev@ebi.ac.uk>
-The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+=head1 METHODS
=cut
-# Let the code begin...
-
package Bio::EnsEMBL::DBSQL::DBConnection;
use vars qw(@ISA);
@@ -45,6 +48,7 @@ use Bio::EnsEMBL::Root;
use DBI;
use Bio::EnsEMBL::Utils::Exception qw(throw info warning);
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
@ISA = qw(Bio::EnsEMBL::Root);
@@ -66,10 +70,13 @@ use Bio::EnsEMBL::Utils::Exception qw(throw info warning);
Arg [DRIVER] : (optional) string
The type of database driver to use to connect to the DB
mysql by default.
- Example :$dbc = new Bio::EnsEMBL::DBSQL::DBConnection(-user=> 'anonymous',
- -dbname => 'pog',
- -host => 'caldy',
- -driver => 'mysql');
+ Example : $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new
+ (-user=> 'anonymous',
+ -dbname => 'pog',
+ -host => 'caldy',
+ -driver => 'mysql');
+
+ $dbc2 = Bio::EnsEMBL::DBSQL::DBConnection->new(-DBCONN => $dbc);
Description: Constructor for a DatabaseConenction. Any adaptors that require
database connectivity should inherit from this class.
Returntype : Bio::EnsEMBL::DBSQL::DBConnection
@@ -82,25 +89,30 @@ use Bio::EnsEMBL::Utils::Exception qw(throw info warning);
sub new {
my $class = shift;
+ my ($db, $dbconn,$host,$driver,$user,$password,$port) =
+ rearrange([qw(DBNAME DBCONN HOST DRIVER USER PASS PORT)],@_);
+
my $self = {};
bless $self, $class;
- my (
- $db,
- $host,
- $driver,
- $user,
- $password,
- $port,
- ) = $self->_rearrange([qw(
- DBNAME
- HOST
- DRIVER
- USER
- PASS
- PORT
- )],@_);
-
+ if($dbconn) {
+ if(!ref($dbconn) || !$dbconn->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
+ throw("Bio::EnsEMBL::DBSQL::DBConnection argument expected.");
+ }
+
+ my $rcount = $dbconn->ref_count();
+ $$rcount++; # dereference and increment shared var
+ $self->ref_count($rcount);
+
+ $self->driver($dbconn->driver());
+ $self->host($dbconn->host());
+ $self->username($dbconn->username());
+ $self->password($dbconn->password());
+ $self->port($dbconn->port());
+ $self->db_handle($dbconn->db_handle());
+
+ return Bio::EnsEMBL::Container->new($self);
+ }
$db || throw("Database object must have a database name");
$user || throw("Database object must have a user");
@@ -121,10 +133,12 @@ sub new {
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);
+ my $ref_count = 1;
+ $self->ref_count(\$ref_count);
$self->db_handle($dbh);
$self->username( $user );
@@ -134,9 +148,9 @@ sub new {
$self->port($port);
$self->driver($driver);
- #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.
+ # 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.
return new Bio::EnsEMBL::Container($self);
}
@@ -280,6 +294,34 @@ sub password {
}
+=head2 ref_count
+
+ Arg [1] : (optional) ref to int $ref_count
+ Example : $count = 1; $self->ref_count(\$count);
+ Description: Getter/setter for the number of existing references to
+ this DBConnections database handle. This is a reference to
+ a scalar because it is shared by all database connections which
+ share the same database handle. This is used by the DESTROY
+ method to decide whether it should disconnect from the database.
+ Returntype : reference to int
+ Exceptions : throw on bad argument
+ Caller : new
+
+=cut
+
+sub ref_count {
+ my $self = shift;
+
+ if(@_) {
+ my $ref_count = shift;
+ if(ref($ref_count) ne 'SCALAR') {
+ throw("Reference to scalar argument expected.");
+ }
+ $self->{'ref_count'} = $ref_count;
+ }
+ return $self->{'ref_count'};
+}
+
=head2 locator
@@ -296,7 +338,7 @@ sub password {
sub locator {
my $self = shift;
-
+
my $ref;
if($self->isa('Bio::EnsEMBL::Container')) {
@@ -336,22 +378,22 @@ sub _get_adaptor {
}
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;
@@ -408,7 +450,7 @@ sub prepare {
throw("Database object has lost its database handle.");
}
- info("SQL(".$self->dbname."):$string");
+ #info("SQL(".$self->dbname."):$string");
return $self->{_db_handle}->prepare($string);
}
@@ -573,11 +615,16 @@ sub DESTROY {
my $dbh = $obj->{'_db_handle'};
if( $dbh ) {
- #don't disconnect if the InactiveDestroy flag has been set
- #this can really screw up forked processes
- if(!$dbh->{'InactiveDestroy'}) {
+ 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;
- }
+ }
$obj->{'_db_handle'} = undef;
}
--
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