Design Specs: Database Connectivity

Objectives

Part of the WormBase::API. Needs to be able to connect to multiple databases (multiple instances of the same database in some cases). Should be fault tolerant if a server or database crashes.

Resources

The current connectivity code is part of the API. The API, in turn, is inside of the lib directory of the WormBase mercurial repository:

http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API/Service/

Currently, each database is a "Service". When the API is instantiated, connections are made to each required service. Database handles are cached. When a database handle is needed, the service first checks to see if it is live, if not it refreshes the connection. This would probably be the ideal location to implement failover -- check the current connection, if dead, try a different database server.

http://bitbucket.org/tharris/wormbase/src/9009075c4c5a/lib/WormBase/API/Role/Service/gff.pm

  around 'dbh' => sub {
    my $orig = shift;
    my $self = shift;
    
    my $species = $self->species;
    
    # Do we already have a dbh? HOW TO TEST THIS WITH HASH REF?
    if ($self->has_dbh) {
	$self->log->debug("     gff-dbh for $species exists and is alive!");
	return $self->$orig;
    } else {
	$self->log->debug("     gff-dbh for $species doesn't exist yet; trying to connect");
	my $dbh = $self->connect($species);
    }
 };

Note also that these Services use Moose "Roles" to define shared methods and variables like connect().

Here's the acedb service:

http://bitbucket.org/tharris/wormbase/src/tip/lib/WormBase/API/Service/acedb.pm

The acedb service "consumes" the generic Service role:

http://bitbucket.org/tharris/wormbase/src/9009075c4c5a/lib/WormBase/API/Role/Service.pm

This nomenclature and structure is a bit confusing and probably needs to be streamlined/refined!!

Plan

API/Role/Service.pm: It's a Moose Role module which contains the common attributes and behavior for different databases.

'all_host': attribute which has all the available hosts from configuration file.

connect: abstract method for the database connection, fail-over is implementation here

This Role is consumed by each Database Classes(Service module) API/Service/acedb.pm & API/Service/gff.pm

different database will use different modules for connection purpose, here we have AceDB use Ace; Ace->connect

GFF database use Bio::DB::GFF; Bio::DB::GFF->new(%$gff_args)