[Bioperl-l] Re: [BioSQL-l] tigr.pm

[Hilmar Lapp]

Strand is NOT NULLable in all three (MySQL, Pg, Oracle) versions of the 
schema.

This constraint could be relaxed, as Strand is not part of any unique 
key constraint.

OTOH the designated value for an unknown strand is 0 in bioperl, not 
NULL or undef.

Furthermore, the schema defines 0 as the default value for the Strand 
column. Unfortunately, this doesn't help if the column is explicitly 
inserted as NULL.

I could add a fix to the LocationAdapter to default a null strand to 0.

Any opinions? I'm leaning towards adding a fix to LocationAdapter to 
fix this problem immediately and forever.

	-hilmar

On Dec 10, 2004, at 2:49 AM, matthieu CONTE wrote:

> I am trying to load tigr rice data in my biosql db with the 
> load_seqdatabase.pl using the lastest tigr parser on the CVS.
> I still have the same problem with null field
>
> Thanks
>
> perl load_seqdatabase.pl --dbuser biosql --dbpass biosql --namespace 
> tigr_arath --format tigr 
> /home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml
> Loading 
> /home/conte/pipeline_orthologues/data/arath_tigr/CHR1.R5v01212004.xml 
> ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed, 
> values were ("130","2000","","1") FKs (16962,<NULL>)
> Column 'strand' cannot be null
> ---------------------------------------------------
>
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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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