[ENH] replace bind-mount for graphDB home with docker volume

[surchs]

Is there an existing issue for this?

• I have searched the existing issues

New feature

Right now, we store the graphDB home for each docker compose stack on the host FS directly via bind-mounts:

recipes/docker-compose.yml

Lines 34 to 35 in f7715a2

	volumes:
	- "${NB_GRAPH_ROOT_HOST:-~/graphdb-home}:${NB_GRAPH_ROOT_CONT:-/opt/graphdb/home}"

This causes at least these issues

• user has to define a path for the graphDB home on the host
• if the user leaves the default path and starts multiple compose stacks, they may end up sharing the same graphDB home, leading to conflicts
• removing or cleaning up the graphDB home is something the user has to do outside of docker/docker-compose via regular FS operations (i.e. rm -rf ...)

There will never be a use case for us to write to the graphDB home from the host computer because only the container will write to it and read from it. I.e.: as long as the container has access to the graphDB home, we don't care if the host can see this directory as well. That's exactly what docker volumes are meant to handle: https://docs.docker.com/storage/volumes/

So we should switch from bind-mounts to volumes for graphDB

Unclear documentation

No response

[neurobagel-bot]

🚀 Issue was released in v0.0.1 🚀