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

[Cymon Cox]

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.

Cheers, C.
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