Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

439 lines (332 sloc) 12.491 kB
# $Id$
#
# BioPerl module for Bio::DB::DBI::base
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::DBI::base - base class for drivers implementing Bio::DB::DBI
=head1 DESCRIPTION
Don't instantiate this module directly. Instead instantiate one of the
derived classes.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
Describe contact details here
=head1 CONTRIBUTORS
Juguang Xiao, juguang at tll.org.sg
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
#'
# Let the code begin...
package Bio::DB::DBI::base;
use vars qw(@ISA);
use strict;
use Bio::DB::DBI;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
@ISA = qw(Bio::Root::Root Bio::DB::DBI);
=head2 new
Title : new
Usage :
Function: should only be called by derived classes
Returns :
Args : named parameters with tags -dbcontext (a Bio::DB::DBContextI
implementing object) and -sequence_name (the name of the sequence
for PK generation)
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($dbc, $seqname) = $self->_rearrange([qw(DBCONTEXT SEQUENCE_NAME)],
@args);
$self->{'_dbh_pools'} = {};
$self->{'_conn_params'} = {};
$dbc && $self->dbcontext($dbc);
$self->sequence_name($seqname) if defined($seqname);
return $self;
}
=head2 sequence_name
Title : sequence_name
Usage : $obj->sequence_name($newval)
Function: Sets/Gets the name of the sequence to be used for PK generation if
that name is not passed to the respective method as an argument.
Example :
Returns : value of sequence_name (a scalar)
Args : new value (a scalar, optional)
=cut
sub sequence_name{
my ($self,$value) = @_;
if( defined $value) {
$self->{'sequence_name'} = $value;
}
return $self->{'sequence_name'};
}
=head2 build_dsn
Title : build_dsn
Usage :
Function: Constructs the DSN string from the DBContextI object. Since this
may be driver-specific, specific implementations may need to
override this method.
Example :
Returns : a string (the DSN)
Args : a Bio::DB::DBContextI implementing object
=cut
sub build_dsn{
my ($self,$dbc) = @_;
my $dsn = $dbc->dsn();
if (! defined($dsn)) {
$dsn = "DBI:" . $dbc->driver() . ":database=" . $dbc->dbname();
$dsn .= ";host=" . $dbc->host() if $dbc->host();
$dsn .= ";port=" . $dbc->port() if $dbc->port();
}
return $dsn;
}
=head2 get_connection
Title : get_connection
Usage :
Function: Obtains a connection handle to the database represented by
the the DBContextI object, passing additional args to the
DBI->connect() method if a new connection is created.
Contrary to new_connection(), this method will return
shared connections from a pool. The implementation makes
sure though that the returned handle was opened with the
given parameters.
In addition, the caller must not disconnect the obtained
handle deliberately. Instead, the implementing object will
disconnect and dispose of open handles once it is being
garbage collected, or once disconnect() is called with the
same or no parameters.
Specific drivers usually won''t need to override this
method but rather build_dsn().
This implementation will call new_connection() to actually
get a new connection if needed.
Example :
Returns : an open DBI database handle
Args : A Bio::DB::DBContextI implementing object. Additional hashref
parameter to be passed to DBI->connect().
=cut
sub get_connection{
my ($self,$dbc,$params) = @_;
# The below line is added by Juguang.
# Well, I cannot see why the dbc needs to be re-assigned here again.
$dbc ||= $self->dbcontext;
my @keyvalues = $params ? %$params : ("default");
# note that in the end the key doesn't carry meaning any more; the goal is
# rather to ensure that two invocations with the same dbcontext object and
# a hashref containing the same keys and values result in the same key
my $poolkey = "$dbc" . join(";", sort(@keyvalues));
if(! exists($self->{'_dbh_pools'}->{$poolkey})) {
$self->{'_dbh_pools'}->{$poolkey} = [];
}
my $connpool = $self->{'_dbh_pools'}->{$poolkey};
if(! @$connpool) {
push(@$connpool, $self->new_connection($dbc,$params));
}
return $connpool->[0];
}
=head2 new_connection
Title : new_connection
Usage :
Function: Obtains a new connection handle to the database represented by the
the DBContextI object, passing additional args to the DBI->connect()
method.
This method is supposed to always open a new connection. Also, the
implementing class is expected to release proper disconnection of
the handle entirely to the caller.
Specific drivers usually won''t need to override this method but
rather build_dsn().
Example :
Returns : an open DBI database handle
Args : A Bio::DB::DBContextI implementing object. Additional hashref
parameter to pass to DBI->connect().
=cut
sub new_connection{
my ($self,$dbc,$params) = @_;
$self->throw("mandatory argument dbcontext not supplied (internal error?)")
unless $dbc;
my $dsn = $self->build_dsn($dbc);
$self->debug("new_connection(): dsn=$dsn; user=" . (defined $dbc->username() ? $dbc->username() : 'undef') ."\n"); # undef: postgres 'ident sameuser' login
my $dbh;
eval {
$dbh = DBI->connect($dsn, $dbc->username(), $dbc->password(), $params);
};
if ($@ || (! $dbh)) {
$self->throw("failed to open connection: " . $DBI::errstr);
}
return $dbh;
}
=head2 disconnect
Title : disconnect
Usage :
Function: Disconnects all or a certain number of connections matching the
parameters. The connections affected are those previously obtained
through get_connection() (shared connections from a pool).
Example :
Returns : none
Args : Optionally, a Bio::DB::DBContextI implementing object.
Additional hashref parameter with settings that were passed to
get_connection().
=cut
sub disconnect{
my ($self,$dbc,$params) = @_;
my @connpools = ();
if(! $dbc) {
# disconnect all pools that we have
map { push(@connpools, $_); } (values %{$self->{'_dbh_pools'}});
} else {
my @keyvalues = $params ? %$params : ("default");
# note that in the end the key doesn't carry meaning any more; the goal
# is rather to ensure that two invocations with the same dbcontext
# object and a hashref containing the same keys and values result in
# the same key
my $poolkey = "$dbc" . join(";", sort(@keyvalues));
if(exists($self->{'_dbh_pools'}->{$poolkey})) {
push(@connpools, $self->{'_dbh_pools'}->{$poolkey});
}
}
# do they actual disconnection
foreach my $cpool (@connpools) {
while(@$cpool) {
my $dbh = shift(@$cpool);
next unless $dbh; # during DESTROY there are indeed undef values --
# I have no idea where they come from
eval {
$self->_remove_idsths($dbh);
$dbh->disconnect();
};
$self->warn("error while closing connection: ".$@) if $@;
}
}
}
=head2 conn_params
Title : conn_params
Usage : $dbi->conn_params($requestor, $newval)
Function: Gets/sets connection parameters suitable for the specific
driver and the specific requestor.
A particular implementation may choose to ignore the
requestor, but it may also use it to return different
parameters, based on, e.g., which interface the requestor
implements. Usually the caller will pass $self as the value
$requestor, but an implementation is expected to accept
a class or interface name as well.
Example :
Returns : a hashref to be passed to get_connection() or new_connection()
(which would pass it on to DBI->connect()).
Args : The requesting object, or alternatively its class name or
interface.
Optionally, on set the new value (which must be undef or a
hashref).
=cut
sub conn_params{
my ($self,$req,$params) = @_;
my $reqclass = ref($req) || $req;
if( defined $params) {
$self->{'_conn_params'}->{$reqclass} = $params;
} else {
# we try the class directly first
if(exists($self->{'_conn_params'}->{$reqclass})) {
$params = $self->{'_conn_params'}->{$reqclass};
} elsif(ref($req)) {
# for an object, try whether we have something for an interface
# it implements
foreach my $parent (keys %{$self->{'_conn_params'}}) {
if($req->isa($parent)) {
$params = $self->{'_conn_params'}->{$parent};
last;
}
}
}
$params = {} unless $params; # default is empty hash
}
return $params;
}
=head2 _idsth
Title : _idsth
Usage : $obj->_idsth($newval)
Function: Get/set the last/next id value statement handle from/to
the cache.
Consider this method 'protected' in OO-speak. I.e., call it
from derived modules, but not from outside.
Example :
Returns : a last_id_value or next_id_value prepared statement, or all
statements cached under the database handle if the key literal
is omitted
Args : the database handle for which to cache the statement,
a key literal to distinguish between statements (e.g.,
'last' and 'next'),
and optionall on set the statement handle to cache
=cut
sub _idsth{
my ($self,$dbh,$key) = @_;
$self->{'_idsth_$dbh'} = {} unless exists($self->{'_idsth_$dbh'});
return values %{$self->{'_idsth_$dbh'}} unless $key;
return $self->{'_idsth_$dbh'}->{$key} = shift if @_;
return $self->{'_idsth_$dbh'}->{$key};
}
=head2 _remove_idsths
Title : _remove_idsths
Usage :
Function: Un-caches all prepared statement handles cached under the
given handle.
Example :
Returns : the list of previously cached statement handles
Args : the database handle
=cut
sub _remove_idsths{
my ($self,$dbh) = @_;
return () unless exists($self->{'_idsth_$dbh'});
my @sths = values %{$self->{'_idsth_$dbh'}};
delete $self->{'_idsth_$dbh'};
return @sths;
}
sub DESTROY {
my ($self) = @_;
$self->disconnect();
$self->SUPER::DESTROY;
}
sub dbcontext {
my $self =shift;
$self->{_dbcontext}=shift if @_;
return $self->{_dbcontext};
}
1;
Jump to Line
Something went wrong with that request. Please try again.