[Biopython-dev] [Bug 2768] New: Bio.Entrez under a proxy

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2768

           Summary: Bio.Entrez under a proxy
           Product: Biopython
           Version: 1.49b
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Documentation
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: dalloliogm at gmail.com


I think you should add, in biopython's tutorial, a short explanation on how to
setup a proxy for modules like Bio.Entrez.

I have tried a simple query with entrez, but the first time I have received
this error:

$: ipython
>>> from Bio import Entrez
>>> handle = Entrez.einfo()
IOError  Traceback (most recent call last)
...
[Errno url error] invalid proxy for http: 'proxy.upf.es:8080'

I am using the latest biopython cvs, updated yesterday.
On my system, the proxy variables were set like this:
$http_proxy = 'proxy.upf.es:8080'
$HTTP_PROXY = 'proxy.upf.es:8080'

After a few tries, it seems that the module uses the HTTP_PROXY variable and
that it expects it to contain 'http://'

$: export HTTP_PROXY=http://proxy.upf.es:8080
$: ipython
>>> from Bio import Entrez
>>> Entrez.einfo()
<no error message>


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