graphDB refuses upload when disk space is under 5% free

[surchs]

Eric just ran into this issue while following step https://neurobagel.org/infrastructure/#uploading-example-neurobagel-data.

Insufficient disk space to start a transaction for repository 'my_db' due to:
The repository 'my_db' is critically low on free disk space with 4.0% (141.82 GB) free left

graphDB by default has low disk space protections (reasonable) based on percentages (reasonable?): https://graphdb.ontotext.com/documentation/10.4/low-disk-space-health-checks.html

their absolute minimal requirement is 5% free disk.

I am not completely clear if docker volumes allow us to

1. Set the size of the volume
2. Hide from the container the percentage of free disk space on the host

Would be worth investigating: https://docs.docker.com/storage/ (maybe) and then update the docs / default config. If we cannot find a solution, then we should update the docs to say: this can happen if you have a single super big disk that is almost full :shrug:

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