[Bioperl-l] 1.3.02 failed tests

[Allen Day]

> Allen, your recent change to require only 1 digit instead of 3 after 
> the colon broke the parser. The change makes the regular expressions 
> pick up EC numbers as secondary GO accessions. Did the test quoted 
> below not fail on your machine?

i tested my changes on Ontology.t and OntologyEngine.t, i didn't see
simpleGOparser.t, and so didn't run it before i checked in.  it does fail 
on my machine.

> I'm going to reverse that change. The MPATH ontology needs to be 
> accommodated in a way that doesn't break the parser, possibly by having 
> its own.

i keep loosening the regular expression to accommodate the different 
DAG-Edit IDs i enounter.  how about i write a regular expression that is 
as strict as possible but still matches everything that DAG-Edit allows?

> Also, I should urge you to add test cases for all the ontologies for 
> which you found yourself having to adapt the parser. Otherwise the 
> ability to parse those too may be abolished silently at any time by 
> anyone changing the code.
> 

sure.

-allen

> 	-hilmar
> 
> On Tuesday, October 21, 2003, at 06:57  PM, Jason Stajich wrote:
> 
> > I also get this on perl 5.8.0
> >
> > not ok 11
> > # Test 11 got: <UNDEF> (t/simpleGOparser.t at line 82)
> > #    Expected: 'EC:5.3.99.5'
> >
> >
> > and perl 5.6.0
> > not ok 11
> > # Test 11 got: <UNDEF> (t/simpleGOparser.t at line 82)
> > #    Expected: 'EC:5.3.99.5'
> >
> >
> > On Tue, 21 Oct 2003, Hilmar Lapp wrote:
> >
> >> On 10/18/03 6:34 PM, "Rob Edwards" <redwards at utmem.edu> wrote:
> >>
> >>> t/simpleGOparser.t               88    1   1.14%  11
> >>
> >> Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
> >> 5.6.0.
> >>
> >>     -hilmar
> >>
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>