[Biopython-dev] [Bug 2589] Errors in running tests in 1.48

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Oct 8 15:48:18 UTC 2008


------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-08 11:48 EST -------
I believe the only remaining issue on this bug is improving the failure/skip
message from the BioSQL tests.  On a CVS checkout, this can vary depending on
if MySQLdb is installed or not.

If MySQLdb is not installed, the message is:

> Install MySQLdb or correct Tests/setup_BioSQL.py (not important if
> you do not plan to use BioSQL).

If MySQLdb is installed, currently setup_BioSQL.py includes the default
settings used on http://www.biopython.org/wiki/BioSQL which if not setup gives:

> Connection failed, check settings in Tests/setup_BioSQL.py
> if you plan to use BioSQL: ...

(The actual database driver error is included as I found this very helpful in
actually getting BioSQL setup and working.)

Alternatively, we can leave setup_BioSQL.py with missing settings, which would
currently show the following message:

> Enter your settings in Tests/setup_BioSQL.py
> (not important if you do not plan to use BioSQL).

My intention with setup_BioSQL.py was that it would all be "ready to go" for
people trying out BioSQL following the wiki.  People without mySQLdb installed
wouldn't see a nasty message.  The only downside (the message you saw) is for
people who have mySQLdb installed, but have not setup BioSQL yet.

I suggest we either leave this as it is, or change Tests/setup_BioSQL.py to
have no default settings (making setting up and testing BioSQL just a little
bit harder).

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