[Bioperl-l] bioperl-db: posqgresql adaptor

[Yves Bastide]

Hilmar Lapp wrote:
> Cool - you must have dug yourself into the code layout - I'm impressed.

Nope--I just copied your code. :)

> 
> The exception you mention - can you provide a stack trace for this? It 
> sounds more like a general bug to me. Under which circumstances does it 
> happen?

This is in BasePersistenceAdaptor::find_by_query, when columns are 
bound.  In writing the SQL query, some attributes are removed according 
to the adaptor's %slot_attribute_map, e.g. in the case of comment: 
"Bio::DB::BioSQL::SeqFeatureAdaptor" => undef.
Such removals are written in SQL as the condition "1 = 1".  So when it's 
time to bind the column, the DBD, expecting "attribute = ?", is confused.
Your code tests if bind_param was successful, with a comment explaining 
these cases; but DBD::Pg chooses to raise an exception.

So, in short:  Is this a more general bug? Perhaps, conceptually.  Does 
it deserve a better fix? Nope, don't think so.

> 
> I'll incorporate this.

Thanks!

> 
>     -hilmar

yves

> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
>