[Bioperl-l] Re: Bio::Species validation broken

[Steve Chervitz]

RestrictionEnzyme.t passes now (branch and trunk).

Steve 

--- Hilmar Lapp <hlapp@gnf.org> wrote:
> Fixed and committed. Along the way I replaced t/data/revcomp_mrna.gb 
> with a current ensembl download (and truncated after 50 kb). The 
> previous version raised an error with the functional validation in 
> place due one trailing whitespace at the end of line. Now all tests 
> pass except RestrictionEnzyme.t.
> 
> 	-hilmar
> 
> On Friday, August 30, 2002, at 12:42  PM, Hilmar Lapp wrote:
> 
> > I just came across this by chance as the test case in bioperl-db 
> > gave wrong results for binomial, the reason being that the order of 
> > @classification on instantiation was reversed, which should have 
> > been caught by $species->validate_[species_]name() but wasn't. It 
> > turns out these validations are completely broken.
> >
> > First off,
> >
> > 	return $string =~ /yourregexp here/ or $self->throw("oops");
> >
> > will always return and never throw the exception. (Why? Doesn't 
> > look intuitively so, but it is true at least on Perl 5.6.0, Mac OS 
> > X). Safe, and more readable is
> >
> > 	return 1 if $string =~ /yourregexp here/;
> > 	$self->throw("oops");
> >
> > Second, can anyone explain why the validating regexp for species 
> > name was set to be
> >
> > 	/^[\S\d\.]+$||""/
> >
> > This regexp is not only redundant in itself, it also matches every 
> > possible string.
> >
> > I'm going to fix this now, expect exceptions to be thrown finally ...
> >
> > 	-hilmar
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
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=====
Steve Chervitz
sac@bioperl.org

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