1. Bash: start with or without access token
   1. If file, read from file
   2. If string, use string and message "you can also store the token and specify the path here"
   3. if empty, print message "only public ARCs will be searched"
2. Bash: Store a list of all available projects (e.g. tab)
3. Bash: for loop over project trees
   1. check for isa.investigation file
      1. present: download raw and dump to temp
      2. absent: leave loop
4. (Bash: unzip xlsx)
5. (R: read xml of first sheet)

general

• move data wrangling out of app (only load ready data) to make it CLI executable
• execute from terminal

design

• render results in tabs (one per ARC)
• add link to ARC

errors

• "Must subset rows with a valid subscript vector."

Downloading these two xlsx works like this, ...

curl --request GET --header "PRIVATE-TOKEN: <my token>" "https://git.nfdi4plants.org/api/v4/projects/50/repository/files/isa.investigation.xlsx/raw?ref=main" > test.xlsx
curl --request GET --header "PRIVATE-TOKEN: <my token>" "https://git.nfdi4plants.org/api/v4/projects/52/repository/files/isa%2Einvestigation%2Exlsx/raw?ref=main" -o test2.xlsx

...but not in the loop.

05_final_pipeline/02_read_from_gitlab.sh