Validation issues with OpenxQuest_example.mzid

[edeutsch]

WARNING: XL:00002 should be 'DSS' instead of 'Xlink:DSS'

ERROR: cvParam retention time has an illegal unit accession number "second"!

The latter is complaining about this:
cvParam accession="MS:1000894" cvRef="PSI-MS" name="retention time" value="5458.13539999998" unitAccession="second" unitName="" unitCvRef="se"/>

The name is written in the accession. There is no name. Also in error the unitCvRef is "se", but in the cvlist, the ID is "UO":

[edeutsch]

These same problems apply to OpenxQuest_example_added_annotations.mzid

[germa]

It seems that these examples also violate the .mzid XML schema definition

[germa]

I think for the moment it would suffice to replace

xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.2.0 https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd"
xmlns="http://psidev.info/psi/pi/mzIdentML/1.2.0"

by
xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.2 https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd"
xmlns="http://psidev.info/psi/pi/mzIdentML/1.2"

[edeutsch]

and:
Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/OpenxQuest_example.mzid, line 173, char 114
Message: Datatype error: Type:InvalidDatatypeValueException, Message:Value 'file:///C:\MSData\S26_Yeast_RAW/aleitner_M1012_004.mzML' is NOT a valid URI .

Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/OpenxQuest_example.mzid, line 312, char 13
Message: The key for identity constraint of element 'MzIdentML' is not found.

[mwalzer]

Yes, unit is a problem in the way we generate that cv element that slipped my attention.

[mwalzer]

so, the version scheme of 1.2.0 to change to 1.2 is done readily, but @germa are there other schema violations my checker isnt telling me or was it that schema validation didnt find anything under 1.2.0?

[mwalzer]

one warning remains though:

Message 2:
    Level: WARN
    --> unanticipated terms for XPath '/MzIdentML/DataCollection/AnalysisData/SpectrumIdentificationList/spectrumIdentificationResult/spectrumIdentificationItem/cvParam/@accession' : [MS:1000894]

which comes from the rt cv at SII instead of at SIR, which is needed, because of referencing several spectra ...

[mwalzer]

@andrewrobertjones @germa should this be reflected in the rules?

[edeutsch]

CV validation issues today:

ERROR: cvParam retention time has an illegal unit second!
(word "second" in place of accession number)

WARNING: XL:00002 should be 'cross-linker related PTM' instead of 'Xlink:DSS'
(XL accessions changed!)

[edeutsch]

also, in addition to the CV issues above, the XML name space is incorrect:

Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/OpenxQuest_example.mzid, line 7, char 37
Message: Schema in mzIdentML1.2.0.xsd has a different target namespace from the one specified in the instance document http://psidev.info/psi/pi/mzIdentML/1.2.0.

[mwalzer]

@edeutsch I have not merged the pull request yet, to leave the option to comment and my guess is you checked the master branch. In the PR, the issues should be resolved; for example the seconds issue like this

@edeutsch but thank you for checking, could you check the two from the branch? Here are the direct links to the files: OpenxQuest_example.mzid OpenxQuest_example_added_annotations.mzid
They checked out with the validator from the repository, now I'd be curious to what your validator reads before merging.

[germa]

@mwalzer: Use of XLMOD:nnnnn instead of XL:nnnnn, see also GitHub issue #60

[andrewrobertjones]

@mwalzer Can you fix all the issues and then close the issue. I would like to assemble all material for submission to PSI process next week.

[edeutsch]

The only remaining issue I see still is the one mentioned above. XL: needs to be XLMOD:

[mwalzer]

fixed in #77