[Psidev-ms-dev] Recursive referenceableParamGroups (was: CV param question)

[Eric D. <ede...@sy...>]

Hi everyone, it seems like there are reasonable ideas for keeping and
removing the possibility of recursive referenceableParamGroups. Let's
make this a topic for the call.  Seems like:

Pros:
- would allow inheritance structure for similar referenceableParamGroups
- Darren has already implemented it this way
- Not a problem for the validator

Cons:
- More complicated for other implementations
- More complicated to understand

We'll decide Tuesday.

Thanks,
Eric




> From: psi...@li...
[mailto:psidev-ms-dev-
> 
> Hi all,
> 
> Just an FYI -- when writing the pwiz CVParam handling, I had assumed
> that recursive references were legal.  Internally we store the
reference
> structure (i.e. we don't resolve fully) and parameter searches are
done
> recursively on demand.  So I imagine it wouldn't be too difficult to
> handle this recursion in the validator if we want to keep this
> flexibility.
> 
> On the other hand, I won't cry if recursive param groups are removed.
> 
> 
> Darren
> 
> 
> -----Original Message-----
> From: psi...@li...
> [mailto:psi...@li...] On Behalf Of
> Lennart Martens
> Sent: Monday, April 28, 2008 9:39 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] CV param question
> 
> Hi Andy,
> 
> 
> > Another query about the cvParam structure (apologies for only
looking
> at
> > this so late in the process)...
> >
> > As I understand it, the current schema draft contains several places
> > where ParamGroup is used, which is an option to have cv terms (or
> > userParams) either inline and/or by reference to a pre-defined
> > ReferenceableParamGroup.
> >
> > The ReferenceableParamGroup inherits from ParamGroup, and so can
also
> > contain cvParam, userParam or a reference to a
> ReferenceableParamGroup.
> >
> > So... I have two questions:
> >
> > 1) Is it intended that a ParamGroup could contain inline CV/user
> > parameters  _/and/_ a reference to a pre-defined set of parameters
> (i.e.
> > this is not an explicit OR)?
> 
> The current schema does allow recursive referencing. So you could make
a
> 
> ReferenceableParamGroup with one or two params, and then derive two
> other ones from this one, which would extend the original one with
some
> more params. I'm not sure whether we really want this actually, I
think
> we just missed this.
> 
> So my proposal is to revise this. I'll bring it up in the phone con
> tomorrow, and if no one feels strongly that it should stay, it'll be
> removed.
> 
> 
> > 2) Is it intended that a ReferenceableParamGroup could contain a
> > reference to another ReferenceableParamGroup and if so what is the
> > meaning of the reference?
> 
> It would be a recursive reference.
> 
> 
> > I'm just trying to envisage how the validator works with this
> structure,
> > is it possible to map explicitly to allowed CV terms if they are
used
> in
> > the referenceableParamGroup?
> 
> In the validator code, we simply hold the referenceableParamGroups in
a
> lookup table. When one of these is referenced, we simply substitute
all
> params into the ParamGroup that is referencing, while removing the
> reference (we essentially fully resolve the soft link). So there's no
> problem with this way of working from the validators point of view.
> 
> 
> Cheers,
> 
> lnnrt.
> 
>
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