[Bioperl-l] Re: bioperl-db and postgres8.3 - status query
sidd.basu at gmail.com
Fri Aug 20 11:59:59 EDT 2010
On Thu, 19 Aug 2010, Robert Buels wrote:
> 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.
I would vouch for that at least as far as chado in oracle is concerned.
So, far BCS works out flawlessly with our oracle chado instance at
dictybase. Quite a chunk of BCS based code is also active in couple of
our Mojo based webapps. The part which i still couldn't use directly is
the 'synonym' table as it clashes with oracle specific reserved keywords.
However, overall it seems to quite cross-RDMS compatible and highly
>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
> 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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