[Bioperl-l] bioperl-db and postgres8.3 - status query

Robert Buels rmb32 at cornell.edu
Thu Aug 19 18:19:11 EDT 2010

Chris Fields wrote:
> I think it's worth exploring having a DBIx::Class-based middle-ware approach similar to what Rob Buels has done for Chado.  That would be fairly easy to get started using DBIx::Class::Schema::Loader.
> After that it would require optimization and tweaking, which is potentially more complex than Rob's setup as Chado is very Pg-specific, but maybe Rob can elaborate...

Elaborating on how Bio::Chado::Schema is developed:

The vast majority of the code and POD in BCS is autogenerated by 
DBIx::Class::Schema::Loader.  DBICSL gives you a baseline set of 
DBIx::Class classes that covers all the tables, views, columns, unique 
constraints, and foreign key relationships.

Beyond that, you have to add on yourself.  In BCS, we have mostly done 
things like:

   * make better-named aliases for some of the autogenerated
     relationships (though DBICSL does a surprisingly good job of naming
     relationships automatically most of the time)
   * add a tiny bit of bioperl compatibility (this needs a lot more work
     by somebody, volunteers needed!)
   * add convenience methods for using some of the Chado property tables
   * use DBIx::Class::Tree::NestedSet to add some powerful ways of
     traversing phylogenetic tree relationships

Regarding DB backend specificity, BCS isn't Pg-specific at all, because 
DBIx::Class itself goes to great lengths to be compatible (and 
performant!) with just about every relational database out there.  In 
fact, the BCS test suite deploys a Chado schema into a temporary SQLite 
database using DBIC::Schema's deploy() method, and runs all of its tests 
on that.  Very handy.

Chado's Pg-specific server-side functions can of course be called 
through BCS if they are present, but it's perfectly possible to use 
Chado without any of the server-side functions, and mostly the way I use it.


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