[Open-bio-l] BioSQL schema: some questions

[Chris Mungall]

On Tue, 30 Apr 2002, Thomas Down wrote:

> On Tue, Apr 30, 2002 at 11:26:22AM -0700, Chris Mungall wrote:
> >
> > > Shouldn't there be a UK constraint on biodatabase.name?
> > >
> > > I've found couple of other little things that probably need to be
> > > cleaned up, and as I'm going over every entity I may find more. I can
> > > try to list them all, or if you prefer (would probably be easier for me,
> > > too) I can fix them directly in the repository.
> >
> > fixing in the repository is best, so long as the bioperl-db test suite
> > still passes.
>
> Ahem.

Sorry, deliberate provocation - I really think every adapter should have a
test suite so that we can make minor schema changes without guessing if it
will break code.

> bioperl-db isn't the only codebase to hang off these schemas.
> There are certainly equivalents in BioJava and Biopython, and
> (I think) some others as well (Ruby?).  Everyone will be using
> rather different adaptor designs, and different `styles' of
> SQL query to access to database.
>
> Could I reiterate my request that any changes, however minor,
> get notified to open-bio-l?  Actually, this repository might
> be one case where it's really worth having one of those automatic
> CVS-logging mailing lists.  Checkins should (hopefully) be
> sufficiently rare than it won't be a full-time job reading
> the commit logs, but it would avoid the ``hey, this is such
> a minor fix that nobody else will notice'' syndrome.

I think both cvs logging and explicit notification is good

> Sorry to be a nag about this -- I'm just a little paranoid about
> our hard-won interoperability :-).
>
>     Thomas.
>