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

Fri Apr 18 16:57:41 EDT 2014

Maybe they did a slight change to the output and thought was so minor that
no one get disturbed by it. However if remain in this form I think it's not
too difficult extract it with a regex.

I haven't time to look to the other issues in the Win 64 build raised, they
are different from python 2.7 to 3.4.

I'll build manually more or less once a day until we get the buildbot in
order. If something else get raised up, I'll post here.

Manlio

On Fri, Apr 18, 2014 at 10:24 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Thanks Lenna,
>
> Strange - although I was sure it was working perfectly on Linux
> at work this afternoon, I can reproduce this as well now.
>
> This commit adds a more informative error message:
>
> https://github.com/biopython/biopython/commit/e5c656e7ce7496db0291f0055da61c492c5054aa
>
> e.g.
>
> ValueError: Expected an integer from URL
> http://togows.dbcls.jp/search/pubmed/TogoWS/count, got: '<!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" content="text/html; charset=UTF-8"
> />\n</head>\n<body>\n<div>1</div>\n\n</body>\n</html>\n'
>
> i.e. Rather than plain text, it is HTML with the value
> inside a <div> tag. This may be a content negotiation
> problem, but I will raise this with the TogoWS team.
>
> Manlio - we can ignore this for now for 64 bit Windows
> testing,
>
> Thanks,
>
> Peter
>
> On Fri, Apr 18, 2014 at 7:53 PM, Lenna Peterson <arklenna at gmail.com>
> wrote:
> > 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
> >>
> >> ----------------------------------------------------------------------
> >> _______________________________________________
> >> Biopython-dev mailing list
> >> Biopython-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biopython-dev
> >
> >
>