[Biopython-dev] "Your XML file did not start with <?xml"

[Cymon Cox]

2009/6/14 Cymon Cox <cy at cymon.org>

> 2009/6/14 Peter <biopython at maubp.freeserve.co.uk>
>
>> On 6/14/09, Cymon Cox <cy at cymon.org> wrote:
>> > Folks,
>> >
>> >  I've been using qblast recently, and got a lot of invalid replies from
>> NCBI
>> >  of this sort:
>> >
>> >  Traceback (most recent call last):
>> >  ...
>> >  ValueError: Your XML file did not start with <?xml...
>>
>> I've seen message that from the unit test sometimes, and assumed the
>> NCBI was returning a temporary HTML error page of some kind -
>> rerunning our test would normally work. Without checking the
>> traceback, I would guess this is the same issue you have found.
>>
>> >  Which is true: NCBI is returning "\n\n". If you code around this and
>> just
>> >  keep going the results eventually arrive:
>> >  ...
>>
>> At first glance, something based on your change looks sensible. Next
>> time I spot the unit test failing I'll try and reproduce this.
>
>
> It's pretty hit or miss: I would guess once in every 10+ times I ran the
> test_NCBI_qblast I would encounter the problem.
>

I can be a little more specific; out 742 calls to qblast, 75 returned the
"Your XML" error. (This was with a different ISP.)

C.
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