Re: [Psidev-ms-dev] CV param question

[Kessner, D. E. <Dar...@cs...>]

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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