[BUG] `arc update` does not transfer all info from isa.assay (v1-pre2)

nfdi4plants / ARCCommander

Tool to manage your ARCs

MIT License

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[BUG] `arc update` does not transfer all info from isa.assay (v1-pre2) #229

Open Brilator opened 8 months ago

Brilator commented 8 months ago

Describe the bug

arc update does not transfer all info from isa.assay. Sections STUDY PROTOCOLS and STUDY CONTACTS are not updated.

Version: https://github.com/nfdi4plants/ARCCommander/releases/download/v1.0.0-preview.2/arc_osx-x64

To Reproduce

add some metadata info by hand

open ./assays/v1pre2-Assay/isa.assay.xlsx

update

arc_osx-x64 update

check

open isa.investigation.xlsx

HLWeil commented 8 months ago

Keeping the persons in the assay and not copy them to the study is by design, see #216
The protocols is more of a technical thing, as it's kind of a mess to keep all these places in the specification with similar information updated against each other but still separated. If the information from the assay is migrated into the study, you can't really distinguish where it came from (similar to persons)

HLWeil commented 8 months ago

What the arc update mostly does now is updating the Input and Outputs, so that all these Source Name inputs that actually are samples or data files are now correctly saved as Input [Sample Name] and so on..

andreaschrader commented 7 months ago

We experienced something similar when providing ASSAY INFORMATION and ASSAY PERFORMERS in the isa.assay file, nothing was updated in the isa.investigation file upon 'arc update'.

I would expect the isa.investigation file to capture all information. I would expect information from ASSAY INFORMATION to be updated in the isa.investigation file and ASSAY PERFORMERS to be listed there as ASSAY PERFORMERS for the respective assay.