[BioSQL-l] BioSQL bug in bugzilla

[Hilmar Lapp]

I don't think it's a good idea to just replace all varchar() types  
with type text.

First of all, having reasonable constraints is a Good Thing(tm) in my  
book as the majority of times I found them violated it revealed a  
parsing error, rather than the constraints not fitting the data.  
Second, this won't solve the problem for the other RDBMS versions for  
which there is a real performance penalty and other implications when  
having unreasonably large column widths.

That said, if the constraint is indeed not compatible with current  
data (such as Uniprot) we have a problem that needs to be fixed. So,  
what I would like to find out is

1) is this in reality a parsing error, or is there indeed a value for  
a column that in BioSQL is constrained to 40 chars, and

2) if so, which column in which table is the problem.

Erik - would you mind sending me the full error stack if you still  
have it? Usually load_seqdatabase.pl will also print an extra warning  
message saying what it couldn't store. That message would be great  
too. If you don't have either anymore, do you remember vaguely what  
those messsages said? Alternatively, do you have the offending  
uniprot entry (or its accession)?

I suspect that it's actually the constraint on dbxref.accession. Does  
that ring a bell?

	-hilmar


On Mar 1, 2008, at 3:42 PM, Chris Fields wrote:

> Hilmar,
>
> Just wanted to point out a bug which I thought was bioperl-db- 
> related but is really BioSQL.  Could you take a look to see what  
> you think?
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2389
>
> chris
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

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