[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


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #7 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-08 16:30 EST -------
(In reply to comment #6)
> > 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)."

Done in Tests/setup_BioSQL.py CVS revision 1.4, and I've also reworded
http://www.biopython.org/wiki/BioSQL slightly as a result.

Marking this bug as fixed.

Thanks Bruce,

Peter

> 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.

Sadly I don't think that would be easy.  Currently installing BioSQL is a
largely manual process, with lots and lots of options (database program, name,
username, password etc).


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