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

[Siddhartha Basu]

On Fri, 20 Aug 2010, Chris Fields wrote:

> On Fri, 2010-08-20 at 10:59 -0500, Siddhartha Basu wrote:
> > Hi, 
> > 
> > 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
> > recommended.
> > 
> > -siddhartha
> 
> Just to point out, I didn't say BCS is Pg-specific, but that Chado is
> (that was the DBMS it was designed for).  Maybe that should be amended
> to 'was' now :)
> 
> I recall seeing a page on this somewhere on the GMOD website along the
> lines of "MySQL has problems so we chose Pg", and that Chado support
> would focus on Pg.  
As far as i understand GMOD stongly recommends and the popular backend
for chado is Pg. However, my point was if anybody wants to use or tryout chado
schema on a different backend or have an existing setup,  
tools like DBIx::Class or particularly BCS makes it quite easier to do
so. The code developed on top also become quite robust and portable.

-siddhartha 

>I'm guessing that's no longer the case?  Or is only
> the server-side stuff Pg-specific.
> 
> > >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.
> > >
> > > Rob
> 
> I think this opens up the possibility of starting a DBIx::Class-based
> middleware solution.  Hilmar, did you want to take that on?
> 
> chris
> 
>