[Biopython-dev] TogoWS test failure, was: Compiling Biopython on 64 bit Windows

Fri Apr 18 14:53:56 EDT 2014

I see similar errors (Ubuntu 12.04, Python 2.7.3, university network).

I can test whether the same thing happens while I'm off-campus.

Lenna

On Fri, Apr 18, 2014 at 2:26 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Apr 17, 2014 at 7:57 AM, Manlio Calvi <manlio.calvi at gmail.com>
> wrote:
> > Update from the first round of fights :)
> >
>
> Following a successful build (the emails didn't get CC'd to
> the list - can we forward them?), Manlio reported some test
> failures including with TogoWS (both Python 2.7 and 3.4),
> pasted at the end of this email.
>
> Something is amiss in the call to Bio.TogoWS.search_count(...)
> where we expect TogoWS to return a plain text file with an
> integer count in it.
>
> Somehow some XHTML is being returned instead.
>
> Has anyone else seen this before? I wonder if it is a proxy
> problem or something like that?
>
> Thanks,
>
> Peter
>
> --
>
>
> ======================================================================
> ERROR: test_pubmed_search_bioruby (test_TogoWS.TogoSearch)
> Bio.TogoWS.search_iter("pubmed", "BioRuby") etc
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_TogoWS.py",
> line 425, in test_pubmed_search_bioruby
>     "20739307", "20015970", "14693808"])
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_TogoWS.py",
> line 463, in check
>     search_count = TogoWS.search_count(database, search_term)
>   File
> "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\TogoWS\__init__.py",
> line 167, in search_count
>     count = int(handle.read().strip())
> ValueError: invalid literal for int() with base 10: '<!DOCTYPE html
> PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n<html
> xmlns="http://www.w3.org/1999/xhtml">\n<head>\n  <meta
> http-equiv="Content-Type" c
>
> ======================================================================
> ERROR: test_pubmed_search_porin (test_TogoWS.TogoSearch)
> Bio.TogoWS.search_iter("pubmed", "human porin") etc
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_TogoWS.py",
> line 434, in test_pubmed_search_porin
>     self.check("pubmed", "human porin", ["21189321", "21835183"])
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_TogoWS.py",
> line 463, in check
>     search_count = TogoWS.search_count(database, search_term)
>   File
> "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\TogoWS\__init__.py",
> line 167, in search_count
>     count = int(handle.read().strip())
> ValueError: invalid literal for int() with base 10: '<!DOCTYPE html
> PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n<html
> xmlns="http://www.w3.org/1999/xhtml">\n<head>\n  <meta
> http-equiv="Content-Type" c
>
> ======================================================================
> ERROR: test_pubmed_search_togows (test_TogoWS.TogoSearch)
> Bio.TogoWS.search_iter("pubmed", "TogoWS") etc
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_TogoWS.py",
> line 420, in test_pubmed_search_togows
>     self.check("pubmed", "TogoWS", ["20472643"])
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_TogoWS.py",
> line 463, in check
>     search_count = TogoWS.search_count(database, search_term)
>   File
> "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\TogoWS\__init__.py",
> line 167, in search_count
>     count = int(handle.read().strip())
> ValueError: invalid literal for int() with base 10: '<!DOCTYPE html
> PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n<html
> xmlns="http://www.w3.org/1999/xhtml">\n<head>\n  <meta
> http-equiv="Content-Type" c
>
> ----------------------------------------------------------------------
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