Re: [Psidev-ms-dev] Errors in example files

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Hi all,
> I'm afraid you're jumping the gun a bit here. The documents you mention 
> used older versions of the CV. It seems to be:
> http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo?revision=1.84&view=markup
> for PLGS and
> http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo?revision=1.75&view=markup
> for tiny.pwiz
>
> This version difference explains the validation problems you're seeing.
I see the problem, but I'm not happy with it :(
>  
> The integer value types were then obsoleted and the intensity term 
> hadn't been renamed. It's up for debate whether these examples should be 
> updated to use the newest CV, but the files are valid the way they are 
> now. 
If i remember the discussion in Turku right, we agreed on the following: 
All changes must be backward-compatible within one version number. 
Otherwise the (second/third) version number has to be incremented.
> It's good to catch this though because it's something a validator 
> will have to deal with.You can't validate a file using an old CV 
> against the newest CV and expect it to be error-free. 
Allowing all CV version will lead hundreds of dialects. In contrast to 
pwiz, OpenMS does not annotate the classes with arbitrary CV terms. We 
have modelled the functionality of mzData, mzXML and mzML with classes 
and fixed member variables. Thus, there is no way for us to support all 
CV version. The pwiz approach supports all CV version, but the problem 
arises later - programs using CV terms can never be sure which CV terms 
to expect in certain class. My conclusion is that both pwiz and OpenMS 
have really big problems to support all CV versions.
> At the same time, 
> I expect you use some compile-time magic for the CV like we do in pwiz 
> so supporting older versions of the CV could be troublesome. I'm not 
> sure how to fix the problem, but I can diagnose it. :)
>   
Right! We cannot ship all intermediate CV version with OpenMS. 
Downloading the CV version each time is not really an option either. 
There is always proxy issues or you might have no internet connection.
> On another note, it was a pain in the ass to link up the CV version to 
> the CVS version. We should definitely, definitely, definitely put RCS 
> keywords in the OBO and mapping files so that we can match up the 
> CVS/SVN revision to the OBO/mapping file itself. This will add a line like:
> remark: $Id: psi-ms.obo 1.42 2009-08-14 22:12:04Z chambm $
> to the OBO file and
> <-- $Id: ms-mapping.xml 142 2009-08-14 22:12:04Z chambm $ -->
> to the mapping file.
>
> Are there any objections to the RCS keywords?
>   
Nope.

-Marc

> Marc Sturm wrote:
>   
>> Hi all,
>>
>> I updated our semantic validator and found that two example files are 
>> not entirely valid:
>>
>> 1) plgs_example.mzML
>>
>> Error: CV term must have a unit: MS:1000042 - intensity
>> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
>> 'peak intensity'
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: CV term must have a unit: MS:1000042 - intensity
>> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
>> 'peak intensity'
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: CV term must have a unit: MS:1000042 - intensity
>> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
>> 'peak intensity'
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: CV term must have a unit: MS:1000042 - intensity
>> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
>> 'peak intensity'
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: CV term must have a unit: MS:1000042 - intensity
>> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
>> 'peak intensity'
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: CV term must have a unit: MS:1000042 - intensity
>> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
>> 'peak intensity'
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
>> the value type 'MS:1000521 ! 32-bit float'.
>>
>> 2) tiny.pwiz.1.1.mzML
>>
>> Error: CV term must have a unit: MS:1000042 - intensity
>> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
>> 'peak intensity'
>>
>> Best,
>>   Marc
>>
>>
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>>   
>>     
>
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