Question

Biopython - E-Utilities Problem

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12.6 years ago

Olivier ▴ 440

Hello I have installed python 2.73 and Biopython 1.57 on Ubuntu 11.10. All of the Bio modules I have tried are working fine, except for the Entrez. None of the e-utils are working - the online tests failed after the installation of biopython. Do I have to register to use the E-utils? Even when I try try "urllib.urlopen('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi')", idle-python hangs..(But the url works on Firefox.) Changing socket defaulttimeout doesn't help either. Here's what I get when I try einfo()

>>> from Bio import Entrez
>>> Entrez.email = 'my_email_address'
>>> handle = Entrez.einfo()
Traceback (most recent call last):
  File "<pyshell#2>", line 1, in <module>
    handle = Entrez.einfo()
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/__init__.py", line 186, in einfo
    return _open(cgi, variables)
  File "/usr/lib/pymodules/python2.7/Bio/Entrez/__init__.py", line 358, in _open
    handle = urllib2.urlopen(cgi)
  File "/usr/lib/python2.7/urllib2.py", line 126, in urlopen
    return _opener.open(url, data, timeout)
  File "/usr/lib/python2.7/urllib2.py", line 394, in open
    response = self._open(req, data)
  File "/usr/lib/python2.7/urllib2.py", line 412, in _open
    '_open', req)
  File "/usr/lib/python2.7/urllib2.py", line 372, in _call_chain
    result = func(*args)
  File "/usr/lib/python2.7/urllib2.py", line 1201, in http_open
    return self.do_open(httplib.HTTPConnection, req)
  File "/usr/lib/python2.7/urllib2.py", line 1171, in do_open
    raise URLError(err)
URLError: <urlopen error [Errno 110] Connection timed out>

Grateful if you could help.

biopython • 7.1k views

ADD COMMENT • link updated 10.7 years ago by Biostar 20 • written 12.6 years ago by Olivier ▴ 440

score 2 · Answer 1 · 2012-05-09

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12.6 years ago

Olivier ▴ 440

The code below was included at the top of the scripts that I tried.

import os os.environ['http_proxy'] = '130.14.29.110:80'

ADD COMMENT • link 12.6 years ago by Olivier ▴ 440

Istvan Albert · Answer 2 · 2012-05-05

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12.6 years ago

Istvan Albert 101k

As the error says it is unable to connect to the internet.

It is either that the website does not allow your IP for some reason or perhaps there is a firewall blocking the outgoing connection.

ADD COMMENT • link 12.6 years ago by Istvan Albert 101k

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Thanks for the help. I've tried disabling my firewall, but the problem is still unchanged. I wonder why the link works in firefox but not through biopython. I've read it could be a proxy problem. I have the proxy address of my ISP but I not sure how to set it up. I'm not very familiar with these. I tried to set up the default http port with the ISP's ip 'xxx.xxx.xxx.xxx:80' but it does not work. (When I ping the proxy it doesn't reply back.) Here's how I tried it on python:

import os os.environ["http_proxy"] = ["http://xxx.xxx.xxx.xxx:80"]

Grateful if you could help. I'm stuck at this part of the biopython tutorial.

ADD REPLY • link 12.6 years ago by Olivier ▴ 440

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Have you checked if you can use Python's urllib to connect to ANY website? That will tell you if this is an NCBI specific problem, or more general.

ADD REPLY • link 12.6 years ago by Peter 6.0k

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as Peter says try:

import urllib
urllib.urlopen('http://www.ncbi.nlm.nih.gov/')

ADD REPLY • link 12.6 years ago by Istvan Albert 101k

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It hangs for ncbi, but when i tried an article on wikipedia, it works. 'yahoo.com' also works

>>> urllib.urlopen('http://en.wikipedia.org/wiki/K-mer')
<addinfourl at="" 161140204="" whose="" fp="&lt;socket._fileobject" object="" at="" 0x99b42ec="">>
>>> wiki = urllib.urlopen('http://en.wikipedia.org/wiki/K-mer')
>>> wiki.read()
'\n<html xmlns="&lt;a href=" http:="" www.w3.org="" 1999="" xhtml"="" rel="nofollow">http://www.w3.org/1999/xhtml" xml:lang="en"

...etc

What can I do?

ADD REPLY • link updated 12.6 years ago by Istvan Albert 101k • written 12.6 years ago by Olivier ▴ 440

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Hello Can somebody help? I'm still stuck, not being able to access anything on NCBI using Biopython. Tried to contact NCBI helpdesk to know if I'm blocked, but I have got no reply.

ADD REPLY • link 12.6 years ago by Olivier ▴ 440

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this is a problem on your system - for some reason you are not allowed to connect. Move to a different computer on a different network.

ADD REPLY • link 12.6 years ago by Istvan Albert 101k

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Thanks. I'll try a different network tomorrow. Could it it be because I'm behind a router that it's not working?

ADD REPLY • link 12.6 years ago by Olivier ▴ 440

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Finally found the answer :-) I only had to add the e-utils IP as proxy. And it works. I hope it's the right procedure.

os.environ['http_proxy'] = '130.14.29.110:80'

Thanks a lot for your help Istvan and Peter.

ADD REPLY • link 12.6 years ago by Olivier ▴ 440