Re: [Psidev-ms-dev] TraML Validator available (alpha version)

[Marc S. <st...@in...>]

sorry, for the last post. It was meant for Andreas only. The correct URL is

http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/TraML/

-Marc




> Hi psi-ms enthusiasts,
>
> as promised, I created a alpha version of the TraML validator. The URL  
> is
>
> http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/TraML
>
> At the bottom is the output of the validation of the toy example.
>
>
> Cheers,
> A.
>
>
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> There are not many files to validate at the moment ;) the toy example  
> gives the fallowing errors/warnings:
>
> Upload: Successfully uploaded the file ToyExample1.TraML.
>
> Validation against the schema:
> Success: the file is valid!
>
> Semantic validation:
> All reported errors are only reported once, in arbitrary order:
>
> CV term must have a unit: MS:1000045 - collision energy
> CV term must have a unit: MS:1000502 - dwell time
> CV term must have a unit: MS:1000869 - collision gas pressure
> CV term must have a unit: MS:1000875 - declustering potential
> CV term must have a unit: MS:1000876 - cone voltage
> CV term must have a unit: MS:1000877 - tube lens
> CV term must have a unit: MS:1001117 - theoretical mass
> CV term used in invalid element: 'MS:1000857 - interchannel delay' at  
> element '/TraML/transitionList/transition/configurationList/ 
> configuration'
> Name of CV term not correct: 'MS:1000587 - contact organization'  
> should be 'contact address'
> Name of CV term not correct: 'MS:1000857 - interchannel delay' should  
> be 'run attribute'
> Name of CV term not correct: 'MS:1000863 - predicted pI' should be  
> 'predicted isoelectric point'
> Value of CV term not allowed: 'MS:1000857 - interchannel delay'  
> value='0.01' at element '/TraML/transitionList/transition/ 
> configurationList/configuration'
> Value of CV term not allowed: 'MS:1000863 - predicted pI' value='5.22'  
> at element '/TraML/compoundList/peptide'
> Value of CV term not allowed: 'MS:1000866 - molecular formula'  
> value='C2HO3' at element '/TraML/compoundList/compound'
> Value of CV term not allowed: 'MS:1000868 - SMILES string' value='[CH] 
> (=[O])[C](=[O])[O-]' at element '/TraML/compoundList/compound'
> Violated mapping rule 'configuration_may' number of term repeats at  
> element '/TraML/transitionList/transition/configurationList/ 
> configuration'
> Violated mapping rule 'contact_must' at element '/TraML/contactList/ 
> contact', 2 should be present, 1 found!
>
>
> --
> Div. for Simulation of Biological Systems, WSI, University of Tuebingen
> Room C322, Sand 14, 72076 Tuebingen, Germany
> phone: +49-7071-29-70461 fax: +49-7071-29-5152
> http://www-bs.informatik.uni-tuebingen.de
>
>
>
>
>
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