[Biopython-dev] Biopython-dev Digest, Vol 77, Issue 12

[João Rodrigues]

I've been having that problem with the your XML for a while now, with
qblast. But I thought it was my connection going nuts and I used just a
retry if that happened...

Just to add to you two having that error :)

João [ .. ] Rodrigues

(Blog)   http://doeidoei.wordpress.com
(MSN)   always_asleep_ at hotmail.com
(Skype) rodrigues.jglm


On Mon, Jun 15, 2009 at 7:00 PM,
<biopython-dev-request at lists.open-bio.org>wrote:

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> Today's Topics:
>
>   1. Re: "Your XML file did not start with <?xml" (Peter)
>   2. Re: "Your XML file did not start with <?xml" (Cymon Cox)
>   3. Re: "Your XML file did not start with <?xml" (Cymon Cox)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 14 Jun 2009 19:16:08 +0100
> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython-dev] "Your XML file did not start with <?xml"
> To: Cymon Cox <cy at cymon.org>
> Cc: BioPython-Dev Mailing List <biopython-dev at lists.open-bio.org>
> Message-ID:
>        <320fb6e00906141116l4cf9a9d5u733497d3b02e1b6a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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.
>
> Peter
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 14 Jun 2009 19:26:56 +0100
> From: Cymon Cox <cy at cymon.org>
> Subject: Re: [Biopython-dev] "Your XML file did not start with <?xml"
> To: Peter <biopython at maubp.freeserve.co.uk>
> Cc: BioPython-Dev Mailing List <biopython-dev at lists.open-bio.org>
> Message-ID:
>        <7265d4f0906141126l2f00fecehaa28273af9b3681a at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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.
> --
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 15 Jun 2009 10:02:47 +0100
> From: Cymon Cox <cy at cymon.org>
> Subject: Re: [Biopython-dev] "Your XML file did not start with <?xml"
> To: Peter <biopython at maubp.freeserve.co.uk>
> Cc: BioPython-Dev Mailing List <biopython-dev at lists.open-bio.org>
> Message-ID:
>        <7265d4f0906150202j3daeefa9we304cf29c4f6cd6d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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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>
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> End of Biopython-dev Digest, Vol 77, Issue 12
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