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

[Hilmar Lapp]

You need the latest CVS HEAD revision from both biosql-schema and  
bioperl-db. Earlier versions of biosql-schema will not work with the  
latest bioperl-db. It sounds like you're not running the latest  
bioperl-db? Is NP_000358 the first entry in your input file? There  
should have been some DBI-generated noise preceding that stack trace.

did bioperl-db pass all tests? Specifically, what's the output for

	$ make test_species TEST_VERBOSE=1

If any one of those tests fails, please do

	$ setenv HARNESS_VERBOSE 1 # csh, tcsh
or
	$ export HARNESS_VERBOSE=1 # ksh, bash

then run the above command again and send me the output.

	-hilmar

On Tuesday, April 22, 2003, at 10:16  AM, Steve Mathias wrote:

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