[Bioperl-l] bioperl-db and postgres8.3 - status query
cjfields at illinois.edu
Thu Aug 19 11:09:13 EDT 2010
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...
On Aug 19, 2010, at 9:58 AM, Hilmar Lapp wrote:
> Yes, unfortunately they do. The feature for obviating them (namely nested transactions) is there in Pg 8.2+, but Bioperl-db doesn't use them yet ... I have to learn more about Class::DBIx first to decide whether it's better to first implement nested transactions in the home-grown ORM that Bioperl-db in essence is, or whether it's better to reimplement everything in Class::DBIx instead.
> There are new datatypes in Bioperl, and relations in BioSQL that could hold them, and so I need to decide what's the way forward.
> On Aug 19, 2010, at 6:01 AM, Peter wrote:
>> On Thu, Aug 19, 2010 at 6:48 AM, Hilmar Lapp <hlapp at drycafe.net> wrote:
>>> Hi Dan,
>>> the casting isn't an issue anymore, I think. (And even if it were, there is
>>> actually a small script that brings back the casts that were built into
>>> 8.2.) Have you found an example where it still is?
>> Hi Hilmar,
>> Do the bioperl-db bindings for BioSQL on PostgreSQL still require those
>> extra rules in the schema?
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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