[BioSQL-l] Proposal on Bio::DB::BioSQL::MultiDB

[Juguang Xiao]

Hi guys,

I wrote the module to solve the actual problem happened in our project. 
I hope that is general enough to put here.

Comments are most welcomed. Thanks

Juguang
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# Adaptor for Multiple BioSQL databases.
# By Juguang Xiao <juguang at tll.org.sg>

=head1 NAME

     Bio::DB::BioSQL::MultiDB

=head1 DESCRIPTION

The scalability issue will arise, when multiple huge bio databases are 
loaded
in a single database in RDBMS, due to the scalability of the RDBMS. So 
one
solution to solve it is simply to distribute them into multiple physical
database, while a user expects to manage them by one logic adaptor.

So here you go, MultiDB aims at such issue to solve. The way to apply 
that is
pretty simple. You, first, load data from different biodatabase, such as
swissprot or embl, into physical RDBMS databases; then create a db 
adaptor
for each simple physical biosql db; finally register these adaptors into
MultiDB and use it as that was a normal dbadaptor.

=head1 USAGE

use Bio::DB::BioSQL::MultiDB;

# create the common biosql db adaptors
my $swissprot_db;  # Physical databases may be located on different 
servers
my $embl_db;       # or accessible by different users.

# register them by bio-database
my $multiDB = Bio::DB::BioSQL::MultiDB->new(
     'swissprot' => $swissprot_db,
     'embl' => $embl_db
);

# Each time before you want to create a persistent object for Bio::Seq,
# assign the 'namescape' sub of seq object first, as the biodatabase 
name.
my $seq;    # for either store or fetch.
$seq->namespace('swissprot');

# OR you need to assign the default namespace for multiDB
$multiDB->namespace('swissport');

my $pseq = $multiDB->create_persistent($seq);
$pseq->store;


# If you want to fetch a seq, then you have to specify namespace for 
multiDB first
$multiDB->namespace('swissport');
$pseq = $multiDB->get_object_adaptor->find_by_unique_key($seq);

=cut

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Juguang Xiao
Temasek Life Sciences Laboratory, National University of Singapore
1 Research Link,  Singapore 117604
juguang at tll.org.sg