nfdi4plants/ARCCommander

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

Brilator opened this issue · 3 comments

Brilator commented

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

  1. add some metadata info by hand
open ./assays/v1pre2-Assay/isa.assay.xlsx
  1. update
arc_osx-x64 update
  1. check
open isa.investigation.xlsx
HLWeil commented
  • 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

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

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.