Re: No defaults in SBML L3
21 Sep '09 12:19
On Mon, 21 Sep 2009 11:39:46 -0600
"Chris J. Myers" <email@example.com> wrote:
> > If a developer wants as minimal impact on his code as possible
> > they are
> > free to keep coding towards L2 for which libsml provides well
> > defined default values. For L3 support one can use the excellent
> > libsbml conversion facilities to read and write.
> I'd really like to stop hearing this argument being made. I don't
> think we should be advocating continued use of L2 but rather
> developing an L3 that people are happy with. If the answer to all
> suggestions is if you don't like it, use L2, then L3 will never gain
> acceptance. In which case, why is L3 being developed? What good is
> a clean language if no one uses it?
I agree with that completely. However I do not understand why you want
to water down the achievements by reintroducing the defaults in the
libsbml API for convenience.
> A better approach, in my opinion, is to come up with ways that
> people can use L3 for their needs. Case in point is my suggestion of
> adding a readSBML that provides defaults to required entries. Or, a
> readAndConvert function which would also need to provide defaults
> since L2 had defaults. I really think it is problematic to allow
> SBML files to be read that have missing, unspecified, required
I agree again. However, I do not advocate to introduce the fix
functions you suggest. An L3 file which does not contain mandatory
elements is not valid and can not be fixed.
A convenient method for writing L2 or even L1V2 files which
explicitly spells out all defaults would help even the older
Levels to gain clarity.
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Bioinformatics Facility II
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606
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