[Biopython] ERROR: Bio.Entrez.efetch(genome, X52960, ...) and ERROR: Bio.ExPASy.get_sprot_raw("O23729")

[ming.xue at boehringer-ingelheim.com]

Hi,

I installed python-ntlm from http://code.google.com/p/python-ntlm/ and tried
their example using urllib2 to retrieve Google home page but still get "407:
Proxy Authentication Required" error. I tried ntlmaps-0.9.9.0.1 and it didn't
solve the problem either. I am not going to try to fix the issue as I only
need to parse behind the firewall. Thanks a lot.

Cheers,
MX

-----Original Message-----
From: p.j.a.cock at googlemail.com [mailto:p.j.a.cock at googlemail.com] On Behalf
Of Peter
Sent: Monday, November 22, 2010 10:18 AM
To: Xue,Ming IT BIP-US-R
Cc: biopython at lists.open-bio.org
Subject: Re: [Biopython] ERROR: Bio.Entrez.efetch(genome, X52960, ...) and
ERROR: Bio.ExPASy.get_sprot_raw("O23729")

On Mon, Nov 22, 2010 at 2:58 PM,  <ming.xue at boehringer-ingelheim.com> wrote:
> Hi All,
>
> I was installing biopython 1.55 over python 2.6 and testing generated the
> error:
> ======================================================================
> ERROR: Bio.Entrez.efetch(genome, X52960, ...)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> ...
> ValueError: No records found in handle
>
> ======================================================================
> ERROR: Bio.ExPASy.get_sprot_raw("O23729")
> ----------------------------------------------------------------------
> ...
> MissingExternalDependencyError: internet (or maybe just ExPASy) not
available
>
> ----------------------------------------------------------------------
> Ran 144 tests in 93.664 seconds
>
> FAILED (failures = 1)
>
> Since I am behind proxy with ntlm authentication, my guess the issue is
> related to firewall. I tried some solution from internet such as ntlm-map
and
> python-ntlm but no luck. Any suggestions?
>
> Best and thanks,
>
> MX

Hi,

I see similar errors on my Windows machine, and I think this is down
to needing to use the institute proxy.

Currently Bio.Entrez uses urllib (version 1), and I don't know if this
can be modified to work with python-ntlm or not. What have you
tried? If you are happy to try experimenting, you could modify
the Bio.Entrez _open function to use urllib2 with python-ntlm.

If you had a simple proxy (without authentication) you'd do something
like this:

import os
os.environ["http_proxy"] = "http://proxyhost.example.com:8080"

See the "Using a proxy" section in the Entrez chapter of the tutorial
for more details.

Regards,

Peter