psidev-ms-dev

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

[Andreas B. <be...@in...>]

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.










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

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

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

Hi Andreas,

da fehlt ein / am Ende:

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

So geht es nicht von außen...

Viele Grüße,
  Marc


> 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.
>
>
>
>
>
>
>
>
>
>
> 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
>
>
>
>
>
> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT 
> is a gathering of tech-side developers & brand creativity professionals. Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, & 
> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian 
> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
> _______________________________________________
> Psidev-ms-dev mailing list
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> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>   

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

[Andreas B. <be...@in...>]

Ok as Marc said, the correct URL is with a '/' at the end:


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

> da fehlt ein / am Ende:
> So geht es nicht von außen...

--
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

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.
>
>
>
>
>
>
>
>
>
>
> 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
>
>
>
>
>
> ------------------------------------------------------------------------------
> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT 
> is a gathering of tech-side developers & brand creativity professionals. Meet
> the minds behind Google Creative Lab, Visual Complexity, Processing, & 
> iPhoneDevCamp as they present alongside digital heavyweights like Barbarian 
> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com 
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>