[Bioperl-l] BioFetch_DB.t fails 4 tests

[Hilmar Lapp]

Cool. Aaron if you want help migrating the fix to the branch let me  
know.

	-hilmar

On Monday, March 10, 2003, at 06:38  AM, Heikki Lehvaslaiho wrote:

>
> This is great. Cleaner than Elia's hack. Could you make sure it gets
> into 1.2 branch as well.
>
> 	-heikki
>
>
> On Mon, 2003-03-10 at 12:39, Aaron J Mackey wrote:
>> I've got a fix for the fasta.pm parser to ignore leading whitespace  
>> before
>> the first entry ... just running all the tests now to make sure it's  
>> good.
>>
>> -Aaron
>>
>> On 10 Mar 2003, Heikki Lehvaslaiho wrote:
>>
>>> Only one test fails now for me:
>>>
>>> not ok 18
>>> # Test 18 got: '0' (t/BioFetch_DB.t at line 92)
>>> #    Expected: '103'
>>>
>>> This is caused by asking sequence in fasta format from swall  
>>> database.
>>> Setting verbose to 2 gives:
>>>
>>> request is POST http://www.ebi.ac.uk/cgi-bin/dbfetch
>>> Content-Length: 43
>>> Content-Type: application/x-www-form-urlencoded
>>>
>>> db=swall&id=P43780&format=fasta&style=raw
>>>
>>> Which pasted into browser as:
>>>
>>> http://www.ebi.ac.uk/cgi-bin/ 
>>> dbfetch?db=swall&id=P43780&format=fasta&style=raw
>>>
>>> retieves the enry ok.
>>>
>>>
>>> Retrieving anything in fasta format using BioFetch is now broken,  
>>> but I
>>> can not figure out where the error comes from. Anyone?
>>>
>>> 	-Heikki
>>>
>>>
>>> On Fri, 2003-03-07 at 02:11, Hilmar Lapp wrote:
>>>> not ok 18
>>>> # Test 18 got: '0' (t/BioFetch_DB.t at line 92)
>>>> #    Expected: '103'
>>>> ok 19
>>>> not ok 20
>>>> # Test 20 got: '0' (t/BioFetch_DB.t at line 115)
>>>> #    Expected: '408'
>>>> not ok 21
>>>> # Test 21 got: '408' (t/BioFetch_DB.t at line 116)
>>>> #    Expected: '1611'
>>>> not ok 22
>>>> # Test 22 got: '1611' (t/BioFetch_DB.t at line 117)
>>>> #    Expected: '200'
>>>>
>>>> All others are ok.
>>>
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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