Comments (15)
These same problems apply to OpenxQuest_example_added_annotations.mzid
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It seems that these examples also violate the .mzid XML schema definition
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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"
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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.
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Yes, unit is a problem in the way we generate that cv element that slipped my attention.
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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?
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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 ...
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@andrewrobertjones @germa should this be reflected in the rules?
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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!)
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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.
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@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.
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@mwalzer: Use of XLMOD:nnnnn instead of XL:nnnnn, see also GitHub issue #60
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@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.
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The only remaining issue I see still is the one mentioned above. XL: needs to be XLMOD:
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fixed in #77
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Related Issues (20)
- can't launch the validator HOT 12
- Mod scores - problem reporting a combined score for multiple sites HOT 1
- XLMOD:02258 has malformed spaceLength value
- Provide an OWL version xlmod? HOT 14
- Add obofoundry topic to repo metadata HOT 2
- SearchModification MAY supply a *child* term of MS:1001471 (peptide modification details) only once? HOT 2
- current correct way to encode the ion series searched for HOT 5
- file format for extension documents? HOT 4
- 1.2.0 spec doc refers to nonexistent sections of itself? HOT 2
- cv mapping rules for Threshold? HOT 4
- example CV params for SpecificityRules
- question/comment about mzIdentML1.2.1-draft.docx
- incorrect example cvParams given for DatabaseName (6.20)
- example CV terms in ProteinDetectionHypothesis HOT 2
- XML fragment in 7.5 (p.91) shows PeptideEvidence in wrong place?
- Section 5.2.7 example (names and values reversed in CV terms) HOT 2
- mistake in SpectraDataType definition in .xsd? (missing FileFormat?) HOT 3
- V1.2.0 de novo sequence representation HOT 10
- Examples using non-exported Unimod crosslink mods HOT 3
- section 7.4 mistakenly refers to <SpectrumDetectionProtocol> instead of <SpectrumIdentificationProtocol>
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