AWS setup - RStudio container setup test

[ychae]

Distilled from #12

Test RStudio environment setup:

• [x] users can login to RStudio environment w/ default password and username
• [x] users can change their default password and username and are still able to login in RStudio environment
• [x] users see module contents in their RStudio environment (after running James' broadcast modules script)
• [x] admin user can update module content in RStudio environment across users' directories
• [x] module solution submission and evaluation works (can use module0 since it's very simple)
• [x] leaderboard on Synapse reflects module submissions

Please refer to the detailed troubleshooting in #12 for peculiarities fo the Synapse Challenge Submission Queues + Permissions.

[linglp]

@ychae I could not check the check boxes in this issue. Could you give me a higher level of permission on this repo?

[milen-sage]

@linglp I added FAIR Data's team to the repo as maintainers. You should have access now?

[milen-sage]

Thanks @linglp! I was also able to login and play around with module 0.

[linglp]

Tests summary:

1. Add users/change password
   • Admins were added by using the script: docker compose exec rstudio root/utils/add_users.sh /admin.csv. Admin.csv is kept local since that it contains password. I also tested by changing my default password for username linglp using command passwd in R studio terminal
   • I could also log in by using other people's default admin password
2. Broadcast module: I am also able to broadcast module 0 by using broadcast_module.sh script. Full command is here: docker compose exec rstudio root/utils/broadcast_module.sh /shared/modules/module0 rstudio-user
3. Module submission: I could submit to both 2021 and 2022 minidream submission synapse folder

[linglp]

Note: broadcast.sh could not delete content. I tried to add a testing folder in module 0 and re-broadcasted module 0. But I could still see my testing folder in R studio environment.

The main command in broadcast_module.sh is rsync -ur (source). Without the --delete option, rsync will not delete extraneous files from the destination. We will need to manually delete testing folder/file

[linglp]

Note: delete an empty folder for all users: docker exec rstudio find /home -name testing-folder -delete

[linglp]

Documentation can be found here: https://github.com/Sage-Bionetworks/minidream-r-env/tree/lpeng/minidream-2022

[milen-sage]

This is awesome! Thanks @linglp!

[ychae]

hi @linglp -- I see that this is marked Done on the project board, can this ticket be closed?

[linglp]

@ychae Yes. Thanks for reminding me