[Biopython-dev] test_Entrez.py fails on Linux?

[Peter]

Hi Michiel,

I've just tried the unit tests on a clean checkout on Linux, and there
is a problem with test_Entrez.py (shown below).  I'm pretty sure it
was working for me on Mac OS X this afternoon, so this may be platform
specific.  I haven't using Biopython on Windows recently so I don't
know if that is working or not.

If you can't reproduce this, let me know and I do some investigation
here.  The good news is all the other tests seem fine on Linux (bar
the GFF, dnal and the population genetics tests for which I don't have
the external dependencies installed).

Peter

This is the output I get on python 2.4.3, using 64bit Ubuntu Dapper
Drake (a little old now).

maubp at shuttle2:~/repository/biopython/Tests$ python test_Entrez.py
Test parsing database list returned by EInfo ... ok
Test parsing database info returned by EInfo ... ok
Test parsing XML returned by ESearch from the Journals database ... ok
Test parsing XML returned by ESearch when no items were found ... ok
Test parsing XML returned by ESearch from the Nucleotide database ... ok
Test parsing XML returned by ESearch from PubMed Central ... ok
Test parsing XML returned by ESearch from the Protein database ... ok
Test parsing XML returned by ESearch from PubMed (first test) ... ok
Test parsing XML returned by ESearch from PubMed (second test) ... ok
Test parsing XML returned by ESearch from PubMed (third test) ... ok
Test parsing XML returned by EPost ... ok
Test parsing XML returned by EPost with an invalid id (overflow tag) ... ok
Test parsing XML returned by EPost with incorrect arguments ... ERROR
Test parsing XML returned by ESummary from the Journals database ... ok
Test parsing XML returned by ESummary from the Nucleotide database ... ok
Test parsing XML returned by ESummary from the Protein database ... ok
Test parsing XML returned by ESummary from PubMed ... ok
Test parsing XML returned by ESummary from the Structure database ... ok
Test parsing XML returned by ESummary from the Taxonomy database ... ok
Test parsing XML returned by ESummary from the UniSTS database ... ok
Test parsing XML returned by ESummary with incorrect arguments ... ERROR
Test parsing cancerchromosomes links returned by ELink ... ok
Test parsing medline indexed articles returned by ELink ... ok
Test parsing Nucleotide to Protein links returned by ELink ... ok
Test parsing pubmed links returned by ELink (first test) ... ok
Test parsing pubmed links returned by ELink (second test) ... ok
Test parsing pubmed link returned by ELink (third test) ... ok
Test parsing pubmed links returned by ELink (fourth test) ... ok
Test parsing pubmed links returned by ELink (fifth test) ... ok
Test parsing pubmed links returned by ELink (sixth test) ... ok
Test parsing XML returned by EFetch, Journals database ... ok
Test parsing XML returned by EFetch, Nucleotide database (first test) ... ok
Test parsing XML returned by EFetch, Protein database ... ok
Test parsing XML returned by EFetch, OMIM database ... ok
Test parsing XML returned by EFetch, PubMed database (first test) ... ok
Test parsing XML returned by EFetch, PubMed database (second test) ... ok
Test parsing XML returned by EFetch, Taxonomy database ... ok
Test parsing XML output returned by EGQuery (first test) ... ok
Test parsing XML output returned by EGQuery (second test) ... ok
Test parsing XML output returned by ESpell ... ok

======================================================================
ERROR: Test parsing XML returned by EPost with incorrect arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 560, in t_wrong
    assert exception.message=="Wrong DB name"
AttributeError: RuntimeError instance has no attribute 'message'

======================================================================
ERROR: Test parsing XML returned by ESummary with incorrect arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 943, in t_wrong
    assert exception.message=="Neither query_key nor id specified"
AttributeError: RuntimeError instance has no attribute 'message'

----------------------------------------------------------------------
Ran 40 tests in 0.471s

FAILED (errors=2)