[Bioperl-l] DB.t failures

[Roels, Steven]

Hilmar,

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
:)

Thanks,

-Steve

*****************************************************************
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
>http://portal.open-bio.org/mailman/listinfo/bioperl-l



This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged.  This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else.  If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender.  Thank you.