[BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb

[Hilmar Lapp]

On Sep 3, 2008, at 9:11 PM, Nick Matzke wrote:

> Those weren't fatal, but eventually I hit this and it crashed:
>
> ==========================================
> note: node (4484;312017;4483;species;;) is retired; failed to  
> delete: Cannot delete or update a parent row: a foreign key  
> constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry`  
> FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`))
> note: node (4490;324602;4489;species;;) is retired; failed to  
> delete: Cannot delete or update a parent row: a foreign key  
> constraint fails (`bioseqdb/bioentry`, CONSTRAINT `FKtaxon_bioentry`  
> FOREIGN KEY (`taxon_id`) REFERENCES `taxon` (`taxon_id`))
> failed to insert node (4577;4577;4575;species;1;1): Duplicate entry  
> '4577' for key 2 at /bioinformatics/pythonstuff/biosql-1.0.0/scripts/ 
> load_ncbi_taxonomy.pl line 581.
> ==========================================
>
> ...but like I said it worked fine on an empty database which was  
> fine for my purposes.

I think this might be fixed in BioSQL v1.0.1. (v1.0.1 fixes the  
load_ncbi_taxonomy.pl script to no longer assume or require the  
primary key and the NCBI taxonID be identical, which I think is the  
reason the failing insert above was an insert rather than the update  
it should have been).

	-hilmar

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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