[Bioperl-l] DB.t failures

Hilmar Lapp hlapp at gnf.org
Fri Mar 5 20:05:54 EST 2004

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 Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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