Environment variable for mounted GraphDB home directory not used

[alyssadai]

The setup script includes a line to set the graphDB home inside the container to a directory /opt/graphdb,

https://github.com/neurobagel/recipes/blob/b5cf9d86529c43091e7df0c4810d41f3698a2adc/dev/setup.sh#L3

but this hardcoded path is both different from the default path for the home directory inside the container (/opt/graphdb/home) which is mounted, and also does not use the configurable variable for the container home directory, $NB_GRAPH_ROOT_CONT

https://github.com/neurobagel/recipes/blob/b5cf9d86529c43091e7df0c4810d41f3698a2adc/dev/docker-compose.yml#L30

as a result, the actual mounted host path ${NB_GRAPHROOTHOST} never gets any contents, because the container path it is pointing to (/opt/graphdb/home by default) is not the home directory inside the container that is actually being used. This currently means that when the containers are spun down, all the data/configuration for the GraphDB server is erased.

To resolve this, we should for now

• [x] replace /opt/graphdb/ in the setup.sh with a reference to the variable ${NB_GRAPH_ROOT_CONT}

(in future, we may want to remove this variable altogether - but we should still ensure that the actual mounted path is correct with what's used in the setup.sh script.

[surchs]

@alyssadai are you referring to NB_GRAPH_ROOT_HOST here? i.e. setting NB_GRAPH_ROOT_HOST in the .env file to something other than ~/graphdb-home has no effect and the graph service still starts with ~/graphdb-home?

[alyssadai]

Forgot to reply - I updated the description with more details yesterday :) hope that helps!

[neurobagel-bot[bot]]

:rocket: Issue was released in v0.0.1 :rocket: