[Bioperl-l] Error in loading into biosql database

[Hilmar Lapp]

You picked up the main trunk of biosql-schema and bioperl-db at a time  
where you shouldn't without making sure on the list ... We're heading  
towards releases in both modules, hopefully (still on target) by the  
end of the month, but until then things can change in biosql-schema and  
bioperl-db won't have caught up yet.

The problem you saw will be fixed by tomorrow night at the latest, but  
I don't recommend you try the main trunk right now unless you want to  
live on the edge.

If you want a combination that works, and you want it right now, then  
go for before-singapore-change tags on both biosql-schema and  
bioperl-db, in combination with bioperl 1.2.0. (*not* the bioperl main  
trunk, nor the upcoming 1.2.1.).

Otherwise, you need to be patient for 1 or more 2 weeks as things are  
shaping up towards a schema freeze.

	-hilmar

On Sunday, March 16, 2003, at 01:22  PM, Siddhartha Basu wrote:

> Hi,
>
> I am using the script 'load_seqdatabase.pl' to upload the swissprot  
> entries in the biosql database. But i am getting the following error
>
> ======================================================================
>
>
> DBD::mysql::st execute failed: Table 'biosql.ontology_term' doesn't  
> exist at  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm  
> line 791, <GEN0> line 111.
>
> ------------- EXCEPTION  -------------
> MSG: Could not store #1946:
> ------------- EXCEPTION  -------------
> MSG: error while executing statement in  
> Bio::DB::BioSQL::SimpleValueAdaptor::find_by_unique_key: Table  
> 'biosql.ontology_term' doesn't exist
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:797
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:182
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:240
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:266
> STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:218
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:205
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:240
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:266
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/SeqAdaptor.pm:225
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:205
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:240
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:266
> STACK (eval) /home/basu/bin/load_seqdatabase.pl:424
> STACK toplevel /home/basu/bin/load_seqdatabase.pl:423
>
> --------------------------------------
>
>
> STACK toplevel /home/basu/bin/load_seqdatabase.pl:433
>
> ======================================================================= 
> ====
>
> As far as i understand that the error points to the table  
> ontologly_term which does not exist in latest biosql schema and it has  
> been changed to the table term in its latest version.  So the question  
> is why the script is trying to find a table which does not exist the  
> sql schema.
>
> Any ideas/suggestions how to get around this problem.
>
>
>
> -Siddhartha
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------