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Comments (5)

andrewrobertjones avatar andrewrobertjones commented on July 28, 2024

@fghali Would you mind fixing these and try running the file past the latest mzid validator: https://github.com/HUPO-PSI/mzIdentML/releases

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fawazghali avatar fawazghali commented on July 28, 2024

I have update the example file and changed '/' to '' and removed the spaces from the file name.

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edeutsch avatar edeutsch commented on July 28, 2024

Today's validation says:
Validating for XSD conformation in file mzidLib_peaklist2a_plus_ecoli_versus_unimod_full_xtandem_fdr_threshold_groups.mzid

Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/mzidLib_peaklist2a_plus_ecoli_versus_unimod_full_xtandem_fdr_threshold_groups.mzid, line 348,
char 146
Message: Datatype error: Type:InvalidDatatypeValueException, Message:Value 'C:\Work\PSI\mzIdentML\ProteinInference\Rosetta2\tandem\peaklist2a_plus_
ecoli_versus_unimod_full.xml' is NOT a valid URI .

Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/mzidLib_peaklist2a_plus_ecoli_versus_unimod_full_xtandem_fdr_threshold_groups.mzid, line 353,
char 191
Message: Datatype error: Type:InvalidDatatypeValueException, Message:Value 'C:\Work\PSI\mzIdentML\ProteinInference\Rosetta2\FASTAs\Rosetta_uniprot_
20130402_mouse_FULL_UNIPROT_can_iso.fasta' is NOT a valid URI .

Error at file /net/db/projects/PSI/mzIdentML/1.2/genDoc/mzidLib_peaklist2a_plus_ecoli_versus_unimod_full_xtandem_fdr_threshold_groups.mzid, line 361,
char 135
Message: Datatype error: Type:InvalidDatatypeValueException, Message:Value 'C:\Work\PSI\mzIdentML\ProteinInference\Rosetta2\Peak_lists_with_ecoli\R
osetta_peak_spectra.mgf' is NOT a valid URI .

I think the issue is that you can't start a URL with C:. URIs have to start with file:/// or something like that.

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fawazghali avatar fawazghali commented on July 28, 2024

I've changed the URI to start with file:/// but I cannot tell if this fix the URI issue since I cannot reproduce it.

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edeutsch avatar edeutsch commented on July 28, 2024

This file appears fully valid now, thanks.

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