Stop dropping root in segmenter container #22
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This was referenced Feb 26, 2024
|
I don't encounter any errors in basic and full testing (i.e. with a real dataset) of the modified segmenter, so I'll merge in this PR now. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR reverts a change introduced in #17, which had dropped the user from
roottopifor security reasons. However, that caused problems because bind mounts of nonexistent directories on the host are created by the Docker daemon (which we're running with root privileges) with root ownership, so that the segmenter container itself is unable to access such directories; and because subdirectories of/home/pi/data/imgare created on the host by the Python hardware controller with root ownership, so that the segmenter container is unable to createdone.txtfiles under those subdirectories (as reported by @tpollina in https://planktoscope.slack.com/archives/C015K99AJAE/p1708530438903539).A longer-term solution would be to switch from Docker to Podman (so that we can run all these containers as a non-
rootuser) and/or to make the Python hardware controller run without root. For now, this PR just reverts the segmenter to run as root so that it won't break in unexpected ways on files/directories created withrootownership.