[Biopython-dev] BioSQL

Peter biopython-dev at maubp.freeserve.co.uk
Tue Nov 20 10:13:35 UTC 2007

Michiel De Hoon wrote:
> With the Biopython currently in CVS, I get an error from test_BioSQL:

Good point, I didn't try out the situation when the database wasn't
setup correctly.

> FAIL: test_BioSQL
 > ...
> If I run test_BioSQL.py directly, I expect to get a
> Bio.MissingExternalDependencyError (as with Biopython 1.44):
> ...
>   File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 7, in <module>
>   File "build/bdist.cygwin-1.5.24-i686/egg/_mysql.py", line 6, in
> __bootstrap__
> ImportError: Permission denied

I moved the password setup etc out of test_BioSQL.py into
setup_BioSQL.py (two reasons, one I didn't want to have to check
test_BioSQL.py was up to date by hand, and two, I plan to add more tests).

I guess the problem is the default settings I put in setup_BioSQL.py,
which previously were undefined.  These settings work for me, as
described on http://www.bioperl.org/wiki/BioSQL (new).

On your system, I guess that MySQL is available but the
username/password are wrong.  If we revert these to being undefined,
then the test should fail as before with MissingExternalDependencyError.

Can you check that easily?  I should probably add an error handler to
look for permission denied too...


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