Re: [Psidev-ms-dev] TraML 0.9.4 draft released

[Matthew C. <mat...@va...>]

I've updated the pwiz TraML implementation to 0.9.4 and validated the 
resulting example files against OpenMS (which revealed quite a few 
glitches in our output). I fixed almost all of them but I think there 
may be a glitch in the validator. The semantic validation seems to have 
stopped working (worked the first time then afterward just gave the 
below error) and I'm getting a non-sensical schema error.

*Validation against the schema:*
Validation error in file './files/tiny_miape.pwiz.traML' line 24 column 
18: element 'cvParam' is not allowed for content model '(cvParam,)' 
Failed: errors are listed above!

*Semantic validation:*
All reported errors are only reported once, in arbitrary order:

Error: Unexpected internal error (The value 'UO:0000269' was used but is not valid! Invalid CV identifier!)


The schema error seems to point at the first </Instrument> in:
<InstrumentList>
<Instrument id="LCQ">
<cvParam cvRef="MS" accession="MS:1000554" name="LCQ Deca" value=""/>
<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial 
number" value="23433"/>
</Instrument>
<Instrument id="QTRAP">
<cvParam cvRef="MS" accession="MS:1000139" name="4000 Q TRAP" value=""/>
</Instrument>
</InstrumentList>

And there's no UO:0000269 in the mapping file or in my document. I have 
no idea where that's coming from. I'm attaching the document.

-Matt


On 3/31/2010 6:14 PM, Eric Deutsch wrote:
>
> Hi everyone, TraML version 0.9.4 has been posted at the development 
> web page:
>
> http://www.psidev.info/index.php?q=node/405
>
> The links to HTML documentation and examples files are all updated.
>
> Please examine the materials and respond.
>
> Major changes from 0.9.3:
>
> - <RetentionTime> is now permitted for each <Transition> and <Target>
>
> Please update your implementations and example files and validators 
> and report.
>
> I think the OpenMS implementation is already at 0.9.4, and the on-line 
> validator is up-to-date. It would be great if others would update 
> their implementations and do some testing.
>
> We have three example files posted on the dev page. This is the 
> minimum number required for submission, but it would be nice to 
> collect a few more. Please implement and generate some files if you can!
>
> Thanks,
>
> Eric
>
> ----------------------------------
>
> Eric Deutsch, Ph.D.
> Institute for Systems Biology
> 1441 North 34th Street
> Seattle WA 98103
> Tel: 206-732-1397
> Fax: 206-732-1260
> Email: ede...@sy... <mailto:ede...@sy...>
> WWW: http://www.systemsbiology.org/Senior_Research_Scientists/Eric_Deutsch
>
>
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