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

Fri Apr 18 14:26:00 EDT 2014

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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