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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2589





------- Comment #6 from bsouthey at gmail.com  2008-10-08 15:44 EST -------
(In reply to comment #5)
> 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).
> 

I think that a user must be forced to change Tests/setup_BioSQL.py or similar
because these settings may not be correct. Especially if dbuser is not root,
dbuser lacks permissions and necessary privileges or dbuser has a password
(security). So the current message you get if DBDRIVER is not defined is okay:

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

A stray thought is to create a BioSQL configuration file (which is what
Tests/setup_BioSQL.py is) when a user installs BioSQL. This would permit
removing the need to enter that information when using BioSQL.


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