Visualization of metabolomics data does not work correctly

[keesvanbochove]

On studies.nmcdsp.org, visualization of metabolomics data only gives the 'table' option, for example for the TIFN study. I'm not sure if this problems resides in GSCF or in the metabolomics module, or in the data. I cannot reproduce it locally in my current setup, but will try to pinpoint the problem.

[4np]

Could it possibly be related to the same issue I was having with fetching data from the metabolomics module through the API I was developing? See trac ticket 65 and Michael's fix (1 & 2) for that issue.

You could try to retrieve the same data through the api, and see what that returns?

[keesvanbochove]

I don't think that is related, I do get data, it's just textual instead of numerical, causing the visualization module to classify it as categorical rather than numerical, and thus correctly showing only a tabulation table as a viable visualization option. I have some changes locally that might fix it, which I will merge hopefully later today.

Thanks for pointing that fix out though, it looks suspicious - it's at least very inefficient (fetching all assay sample tokens into memory even if only a few might have been requested?). That is closely related to https://github.com/NetherlandsMetabolomicsCentre/metabolomicsModule/issues/3.

[keesvanbochove]

I still cannot reproduce this locally. Maybe it should be solved by re-importing this particular study in nmcdsp.org.

Concerning the fix for fetching the assay sample tokens, this was refactored/changed in 0e9ee349986264abd23640c03049982161bd5a56.