[Bioperl-l] Biosql schema for use w/ bioperl-1.2.1

[Steve Mathias]

Hello All,

I cannot seem to find a version of the BioSQL schema that will work with
load_sequence_database.pl and bioperl-1.2.1.  I've tried both the
current cvs version of the schema as well as the before-singapore-change
version (the respective stack traces are pasted below).  Can anyone
point me at a BioSQL schema (MySQL or Postgres) that will work
with bioperl-1.2.1?

Thanks.

Steve

Message w/ latest CVS schema:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not store NP_000358: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: error while executing statement in Bio::DB::BioSQL::SpeciesAdaptor::find_by_unique_key: Unknown column 'taxon_name.ncbi_taxon_id' in 'field list'
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:342
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:898
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:809
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:180
STACK: Bio::DB::Persistent::PersistentObject::create /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:242
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:167
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:238
STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:266
STACK: ./load_seqdatabase.pl:433
-----------------------------------------------------------

Message w/ before-singapore-change schema:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not store NP_000358: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: error while executing statement in Bio::DB::BioSQL::SpeciesAdaptor::find_by_unique_key: Table 'biosql.taxon_name' doesn't exist
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:342
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:898
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:809
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:180
STACK: Bio::DB::Persistent::PersistentObject::create /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:242
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:167
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:238
STACK: Bio::DB::Persistent::PersistentObject::store /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:266
STACK: ./load_seqdatabase.pl:433
-----------------------------------------------------------

-- 
-------------------------------------------------------------
Steve Mathias                         email: smathias at unm.edu
UNM Office of Biocomputing              phone: (505) 272-8111
-------------------------------------------------------------