[Bioperl-l] load_ontology/GO error

[Hilmar Lapp]

This is due to a bug in bioperl introduced shortly before the 1.4  
release series. It is fixed on both main trunk and the 1.4 branch, but  
you need to get a cvs snapshot (of the branch, if you have 1.4  
installed) because 1.4.1 has not been released yet.

	-holmar

On Monday, April 19, 2004, at 02:54  AM, Dave Howorth wrote:

> Hello again,
>
> I tried to use my shiny new bioperl_db installation to load GO but it  
> failed with the error message below.  I'm afraid it doesn't mean very  
> much to me and my searches haven't turned up anything that demystified  
> it, so I'd be grateful for any explanation or suggestions on how to  
> fix the problem.
>
> Thanks, Dave
>
> biosql$ perl load_ontology.pl --dbname biosql_1 --dbuser bioperl  
> --driver mysql --namespace "Gene Ontology" --format goflat --fmtargs  
> "-defs_file,GO.defs" function.ontology process.ontology  
> component.ontology
> Parsing input ...
> Loading ontology Gene Ontology:
> 	... terms
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were ("BBD_pathwayID:C1cyc","","","") FKs (1)
> Column 'name' cannot be null
> ---------------------------------------------------
> Could not store BBD_pathwayID:C1cyc ():
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270
> STACK (eval) load_ontology.pl:508
> STACK toplevel load_ontology.pl:490
>
> --------------------------------------
>
> -- 
> Dave Howorth
> MRC Centre for Protein Engineering
> Hills Road, Cambridge, CB2 2QH
> 01223 252960
>
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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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