allow nirs upload with plot ids

[lukasmueller]

Expected Behavior

For Bugs:

Environment

Steps to Reproduce

[bellerbrock]

@nickmorales, @jmh579 it looks like this functionality used to exist, but was removed. Was there a reason to restrict uploads to samples only that we are missing?

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[jmh579]

@bellerbrock I think that it was changed because you can have scans from multiple different tissues per plot, each tissue will give a different spectral pattern. With plot-level data, it isn't clear which tissue was scanned. This could lead to the averaging of scans from different tissues, which we don't want.

There might be a better way to specify tissue type within the high dimensional phenotype storage itself to avoid having to create a bunch of different tissue samples within the database. I can bring it up with the BrAPI High Dimensional Phenotypes group on Friday. I'll send you a slack message with the meeting info in case you want to join.

[bellerbrock]

Thanks @jmh579 . Per the discussion today in the high-dimensional phenotypes weekly meeting:

• It's crucial to have high-dimensional phenos linked to the specific tissues on which they were made. Plot and plant ids are not specific enough, tissue samples are necessary.
• Stopping and manually creating a sampling trial and tissue sample ids before upload is a lot to ask, especially of programs that only work with one tissue.

Proposed solution: Let users use plot/plant ids in their upload file. But have them select the relevant tissue in a dropdown, and create a sampling trial and tissue sample ids in the background during the upload.

[lukasmueller]

@bellerbrock I like that idea, can you implement it?

[bellerbrock]

Working on this now. Another scenario to make sure to address - cases where technical replicates (many spectra collected on the same processed sample) are included in the nirs upload

[lukasmueller]

Has this been implemented? If so, we should close the ticket.