[BioSQL-l] bioSQL schema loading probs

[Hilmar Lapp]

What you see is due to a bug (2 bugs in fact) in the SpeciesAdaptor. I 
fixed it. You will need to update from the anonymous CVS repository.

	-hilmar

On Wednesday, May 21, 2003, at 06:16  AM, Ulrik Plate wrote:

> When I try to load the schemas with the flatfile I receive a long list 
> of
> error messages like this one. Has anybody got a clue about what to do?
>
>
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: Could not store AJ131315:
> ------------- EXCEPTION  -------------
> MSG: Invalid species name 'subsp. VAL81'
> STACK Bio::Species::validate_species_name
> /home/ulrik/bioperl-live/Bio/Species.pm:322
> STACK Bio::Species::classification 
> /home/ulrik/bioperl-live/Bio/Species.pm:153
> STACK Bio::DB::Persistent::PersistentObject::AUTOLOAD
> /home/ulrik/bioperl-db/Bio/DB/Persistent/PersistentObject.pm:488
> STACK Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
> /home/ulrik/bioperl-db/Bio/DB/BioSQL/SpeciesAdaptor.pm:268
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
> /home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1238
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
> /home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:923
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
> /home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:809
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:180
> STACK Bio::DB::Persistent::PersistentObject::create
> /home/ulrik/bioperl-db/Bio/DB/Persistent/PersistentObject.pm:242
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> /home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:167
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> /home/ulrik/bioperl-db/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:238
> STACK Bio::DB::Persistent::PersistentObject::store
> /home/ulrik/bioperl-db/Bio/DB/Persistent/PersistentObject.pm:266
> STACK (eval) load_seqdatabase.pl:424
> STACK toplevel load_seqdatabase.pl:423
>
> --------------------------------------
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------