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

Hilmar Lapp hlapp at drycafe.net
Thu Aug 19 01:48:19 EDT 2010

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?


On Aug 18, 2010, at 10:15 PM, Dan Kortschak wrote:

> Hi Everyone,
> I'm wanting to set up a persistent data store for some of my work  
> and am
> in the process of choosing parts for my system. From my brief look
> around I think I'd like to use BioSQL (next best choice being Chado -
> but BioPerl bindings in bioperl-db for BioSQL being the decider here),
> but have noticed comments some time back that bioperl-db and  
> PostgreSQL
> 8.3 (my prefered engine - though MySQL is possible, but makes the  
> whole
> system messier) don't play well together.
> What is the status of the casting expectation conflict between
> bioperl-db and Pg8.3? The scripts are run with safe data, so
> placeholders aren't strictly crucial (though speed may be an issue?)  
> and
> `$dbh->{pg_server_prepare} = 0;' seems like it could be an option.
> Can anybody provide any advice on this issue?
> thanks
> Dan Kortschak
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: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :

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