Support configurable paths for pre-loaded digest files

[alyssadai]

At the moment, we support pre-loaded imaging and phenotypic digest files for QPN. However, currently the app hardcodes the path to the QPN data, meaning if the name, URL, structure, etc. of the parent data repo changes, we need to modify the code so the app can find the digest files again.

digest/digest/utility.py

Lines 28 to 46 in 3654b77

	# TODO:
	# Could also use URLs for "imaging" or "phenotypic" locations if fetching from a remote repo doesn't slow things down too much.
	# Note that this would only work for public repos or private repos with a token.
	# TODO: move this to a config file?
	PUBLIC_DIGEST_FILE_PATHS = {
	"qpn": {
	"name": "Quebec Parkinson Network",
	"imaging": Path(__file__).absolute().parents[2]
	/ "nipoppy-qpn"
	/ "nipoppy"
	/ "digest"
	/ "qpn_imaging_availability_digest.csv",
	"phenotypic": Path(__file__).absolute().parents[2]
	/ "nipoppy-qpn"
	/ "nipoppy"
	/ "digest"
	/ "qpn_tabular_availability_digest.csv",
	}
	}

To make this more maintainable and extendable (e.g., a user running their own digest instance wants to supply their own pre-loaded digest files), we could factor out the above section into a JSON file that a user can modify. With this change, we would then only need to require the user to provide a single directory path in which all their digest files live. This user-specified directory would be mounted into a consistent path inside the container. Then, in the JSON file, the user need only to specify the relative path to each digest of interest.

For the mounting portion, one option could be to create a named volume ahead of time, and then either manually mount it every time the container starts - or to just add a docker-compose file for this one container and define the volume in there.

Originally posted by @surchs in #150 (comment)

Example:

# get QPN data
git clone https://github.com/neurodatascience/nipoppy-qpn.git
# Make (initially empty QPN volume)
docker volume create qpn_data
# use silly-container just to copy data into the volume
docker run --rm -v qpn_data:/target -v $(PWD)/nipoppy-qpn:/source alpine cp -a /source/. /target/
# Use the volume as read-only access
docker run -d -p 8050:8050 -v qpn_data:/app/nipoppy-qpn neurobagel/digest:nightly

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