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

Hilmar Lapp hlapp at drycafe.net
Thu Aug 19 10:58:46 EDT 2010

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?
>>        -hilmar
> Hi Hilmar,
> Do the bioperl-db bindings for BioSQL on PostgreSQL still require  
> those
> extra rules in the schema?
> http://bugzilla.open-bio.org/show_bug.cgi?id=2839
> Peter

: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :

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