[Biojava-l] Re: BioSQL implementation bugs

[Thomas Down]

On Fri, Mar 08, 2002 at 01:40:18PM -0500, Simon Foote wrote:
> I've been messing with the BioSQL implementation and have found a couple 
> of bugs.  Both are the result of the term_name in the ontology_term 
> table being a fixed length char (255).
> 
> 1)  The feature.byType() method gives the 255 char string, thus if you 
> want to filter by, for example "cds", it fails unless you put a trim() 
> on the string, but no sure where this needs to go for the filter.
> 
> 2) Same thing happens with keys for the getAnnotation().getProperty() 
> method.


Hi...

This fell out of a recent schema change -- these columns
got changed from varchar to char.  This didn't break
the hackathon testing (mostly using MySQL) because MySQL
strips trailing spaces when retrieving char(n) attributes.
But it's broken a lot of other databases.

Thanks for suggesting the trim()'s.  Do you have a CVS
account to check that fix in?  Otherwise, I'll put them
in tommorow.

I'd quite like to see the schema changed back, though.

Thanks,

    Thomas.