[Bioperl-l] DB.t failures

Roels, Steven Steven.Roels at mpi.com
Sat Mar 6 17:00:33 EST 2004


See bugs #1594 (which describes the problem below) and #1595, which
mentions a $NUMTESTS problem with the penultimate tests in DB.t.

You may have seen them already, but if not - you just fixed at least one



Steve Roels, Ph.D.                       
Senior Scientist I - Computational Biology     Phone: (617) 761-6820
Millennium Pharmaceuticals, Inc.         FAX:   (617) 577-3555
640 Memorial Drive                       Email: roels at mpi.com
Cambridge, MA 02139-4853

>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf
>Of Hilmar Lapp
>Sent: Friday, March 05, 2004 8:06 PM
>To: Bioperl
>Subject: [Bioperl-l] DB.t failures
>The date range query on Onchocerca volvulus[Organism] is failing on
>both main trunk and stable branch for two reasons.
>First, NCBI either changed, or now enforces, the date syntax as
>YYYY/MM/DD. The MM/DD/YYYY format documented in Bio::DB::Query::GenBank
>(and possibly elsewhere) will not raise an exception; instead it just
>produces zero results. I changed the POD and the test to use the
>correct format.
>Second, after this correction some tests still fail because not really
>expectedly the query produces different results meanwhile as the
>default is to query by modification date, which at some point will get
>updated, thereby yielding a different query result. There are tests
>which test the first three sequences returned for an expected length.
>I changed those tests to use the new results, but this won't last long.
>Either, those tests need to be dropped, or maybe a safer query is to
>constrain by publication date if that's possible.
>Any opinions? Any takers?
>BTW I also fixed a couple of other errors and poor dealing with
>undefined values as the tests on the main trunk got way too noisy for
>my taste.
>	-hilmar
>Hilmar Lapp                            email: lapp at gnf.org
>GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

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