Re: [Psidev-ms-dev] referenceableParamGroup

[Fredrik L. <Fre...@im...>]

Hi Wilfred,

The on-line validator has now been updated to use the latest code from 
Lennart, so please try it with your file and report back if there are 
problems.

There is also an example file in which referencableParamGroups are used 
in the binary data array blocks at:
http://trac.thep.lu.se/trac/fp6-prodac/browser/trunk/mzML/plgs_ref_params.mzML?format=raw
It may be useful for testing mzML parsers.

Cheers

Fredrik

Lennart Martens wrote:
> Hi Wilfred,
>
>
>   
>>  > The validator, however, currently is NOT properly handling the
>>  > referenceable param groups. I did a controlled experiment where
>>  > information was written out (1) using referenceable param group
>>  > references, or (2) writing out the actual data elements represented
>>  > by the referenceable param group references. The validator does
>>  > parse things properly for case (2) but not for case (1).
>>     
>
> You are absolutely right! The validator doesn't function correctly in 
> these cases!
>
> The reason for this was simple: while jmzML nicely resolved the 
> ReferenceableParamGroupRefs into ReferenceableParamGroup instances, it 
> didn't connect the last few dots, as it forgot to then initialize the CV 
> and user params in the ReferenceableParamGroup on the object's CV and 
> user param lists.
>
> Thus: essentially, a silly oversight on our behalf.
>
> Well spotted! Thanks for highlighting this serious bug.
>
> The problem has now been fixed in the latest jmzML version 
> (0.2-SNAPSHOT), and by plugging this version (rather than the original 
> 0.1-SNAPSHOT) into the validator, things will be OK again.
> Unfortunately, while Google Code allowed me to commit the jmzML changes, 
> its SVN currently seems down for developer access, and I haven't managed 
> to commit the latest Maven POM file for the validator yet. I'll do that 
> as soon as Google get their act back together again. Meanwhile, I'm 
> notifying Fredrik directly on how to fix the online validator already.
>
> Thanks once again for helping to spot the nasty bug, and hope you'll 
> have some more fun with the validator!
>
>
> Cheers,
>
> lnnrt.
>
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