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modified records #62

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@zzjl20 @meier-rene @schymane
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commented Apr 17, 2019

I found that current validator maybe malfunction on 2.5.1 Subtag: PRECURSOR_TYPE:
MS$FOCUSED_ION: PRECURSOR_TYPE [(M+CH3COOH)-H]-
But other type (like [M+H]+ or [M-H]- ...) can pass the validator.
Can somebody tell me what's wrong with my record?

zzjl20 added some commits Apr 17, 2019

@zzjl20
MS2 record from Riken IMS
50cb1d1
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add positive in LQB
6edfb63
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Delete .DS_Store
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Delete .DS_Store
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commented Apr 17, 2019

Please try without parentheses. [M+CH3COOH-H]- will pass the validator. We have not implemented parentheses in PRECURSOR_TYPE.
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commented Apr 18, 2019

Thank you so much!
Would you mind to modify 2.5.1 Sutag
@zzjl20
format adjust 
correct wrong spelling.
PRECURSOR_TYPE [(M+CH3COOH)-H]-
->
PRECURSOR_TYPE [M+CH3COOH-H]-
remove intensity
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@zzjl20 zzjl20 changed the title Not pass the validator modified records Apr 18, 2019

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add 63 records 
MSJ00083 can not pass validator for Instrument_type is SIMS-BE.
Other 62 record pass the validator
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commented Apr 25, 2019

Thank you so much!
Would you mind to modify 2.5.1 Sutag

Thank you. I fixed this.

@meier-rene meier-rene changed the base branch from master to dev Apr 25, 2019

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commented Apr 29, 2019 •
edited

Thank you for contribution. I would like to integrate your pull request. But because there were some issues i have forked your repo and fixed things there. I will give you a list with issues, so that you can adjust your release procedure for future contribution.
-Please make sure that there are no tabs or aditional whitespaces in the peak list. We found that this breaks our RecordDisplay. Thats why we made the validator more strict.
-Please check your InChI to have 'InChI=1S/' in the biginning, not just 'InChI=1/'
-We do not support directory sturtures deeper than contributor/recordfile.txt. Thats why I merged the LQA and LQB subdirs

We also try to make our release procedure more robust at the moment and we constantly improve the validator to identify all known issues. Part of the new release procedure is to commit pull requests to a development branch only and to use the development branch of the validator for validation. I will adjust instructions on the README soon.
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commented Apr 29, 2019

Re the InChIs, depending how they are generated, you will need to select the "standard InChI" option to generate with IS/ at the beginning, not 1/ ...
Please also check that the InChIKeys are also the standard ones (SA-N at the end ...)

image
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commented Apr 29, 2019

@meier-rene did you just substitute letters, or regenerate the entire InChIs and InChIKeys?
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commented Apr 29, 2019

I fixed the InChI by substituting '1' with '1S' and regenerated the InChI-Key from the InChI.

After the modification of the InChIs the InChI-Keys didnt fit to the InChIs any more and the validator was marking them invalid. '1'->'1S' change did only change the last 2 letters of the InChI-Key.
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commented Apr 29, 2019

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