[Bioperl-l] RE: tests in bioperl-db

[Hilmar Lapp]

OK. I'm through on all tests, all changes committed. All tests pass nicely on MySQL, with and without utilizing the pre-built database. (You need to have the latest CVS snapshot from Bioperl for this.)

I've added a dbname key to DBHarness.conf (see .example for explanation). If set, the tests will utilize that database as your pre-built database, instead of going through a rebuild from scratch and destroy cycle in every script. Tests should succeed irregardless whether you have something in that database already or not.

It'd be great if someone could check Postgres and let me know if there are problems.

	-hilmar

> -----Original Message-----
> From: Hilmar Lapp [mailto:lapp@gnf.org]
> Sent: Wednesday, July 10, 2002 11:16 PM
> To: Hilmar Lapp
> Cc: BioPerl (E-mail); OBDA BioSQL (E-mail)
> Subject: Re: fuzzy locations in bioperl-db
> 
> 
> This was easy to fix as I realized: I just removed type 
> checking entirely 
> from the respective store() method since _store_component() 
> handles types.
> 
> This revealed the next bug:
> 
> ------------- EXCEPTION Bio::Root::NotImplemented -------------
> MSG: Abstract method "Bio::LocationI::each_Location" is not 
> implemented by 
> package Bio::Location::Fuzzy.
> This is not your fault - author of Bio::Location::Fuzzy 
> should be blamed!
> 
> It'd be great if someone does this little fix (should just 
> return itself 
> as far as I remember) while I get some sleep ...
> 
> There are two test scripts remaining in bioperl-db before I'm 
> through 1st
> pass. I removed seqlocation.t (I rewrote and kept remove.t) 
> as locations
> are tested anyway all over the place. There were also tests 
> which tested
> nothing, and some which worked only due to chance (e.g., one worked
> consistently 3 times out of 4 when repeated, funny isn't it), 
> fixed all of
> that.
> 
> 	-hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> On Tue, 9 Jul 2002, Hilmar Lapp wrote:
> 
> > Two tests in bioperl-db fail (fuzzy2.t being one of them) 
> because Bio::Location::Fuzzy is not handled by the 
> SeqFeatureLocation adaptor (instead it throws an exception).
> > 
> > Were there any plans laid out on how to support (i.e., 
> store) fuzzy locations in biosql?
> > 
> > 	-hilmar
> > 
> 
>