Automate mzTab validation

[wsnoble]

To be sure our mzTab stays compliant, we should incorporate the validator into our github actions. This should be done after resolving issues 322 and 201.

[wsnoble]

Is this already done?

[bittremieux]

No.

[Lilferrit]

Unfortunately I couldn't for the life of me find a binary for the jmzTab cli. I also tried cloning the jmzTab repo and building the binary from source, but unfortunately jmzTab has dependencies that seem to be no longer publicly available.

[wsnoble]

Who wrote it? Can we reach out to the authors to ask about its status?

[Lilferrit]

The jmzTab repo (https://github.com/PRIDE-Utilities/jmzTab) is archived and has been read only for about 2 years now which tells me they don't intend on maintaining jmzTab anymore. I can try to reach out to the original authors and see if they have access to a binary still.

[bittremieux]

jmzTab indeed doesn't seem supported anymore. I've sent the authors an email to verify this.

Alternatively, the validator Bill pointed to is for jmzTab-M (M = metabolomics), which is a related but different standard format. However, the online validator does have a drop-down to switch between mzTab 2.0 (which is for metabolomics) and mzTab 1.0 (which is what we want).

@Lilferrit could you look into whether the jmzTab-M repository has a built binary that can be used to validate our mzTab files?

[Lilferrit]

Unfortunately the link they have to the binaries is also broken on the jmzTab-M repository. I also wasn't able to successfully build the binary on windows but I have access to an ubuntu machine so I'll try it on there as well.

[bittremieux]

The jar from here seems to work. It isn't advertised anywhere, I just found it through Google, and compiling it myself also didn't work, so the provenance is maybe a bit questionable. But it did correctly complain about the floating point charges in older mzTab outputs and was happy after I fixed that.

java -jar jmzTabValidator-3.0.10-SNAPSHOT.jar -check inFile=sample.mztab

Maybe you can try to set up an mzTab validation workflow with this?