Create separate nodes for the PPMI and QPN

[alyssadai]

Ideally, these datasets would live on two different different databases (with different APIs) in the same graph server.

In order to allow two different APIs to talk to the same graph container, we may need to create a new docker-compose.yml or otherwise connect one of the API container to an existing docker network (see https://docs.docker.com/engine/reference/commandline/network_connect/).

Steps to implement

• Launch GraphDB container on st-viateur and add two new PD databases (mni_ppmi and mni_qpn)
• Launch api_qpn along with graph stack in non-aggregated aggregate mode
• Launch api_ppmi in aggregate mode
• Add api_ppmi to api_qpn Docker network (arbitrary) and rename network
  • verify via interactive docs that api_ppmi can reach a db in the graph container
• for easier relaunching, create a custom docker-compose.yml for the PD databases
  • under ~/projects/pd_compose
  • values for non-API variables hardcoded in the yml
• Ensure both are accessible without vpn
  • Update security rules for st-viateur to allow ingress on each new API's port

[alyssadai]

For reviewer, see on st-viateur:

• database-specific .env files and docker-compose.yml at ~/projects/pd_compose
• contents of docker network pd_compose_default (default name based on compose config location) using:
  docker network inspect pd_compose_default
• newly created PD GraphDB databases, with curl -u "admin:<PASSWORD>" http://localhost:7200/repositories

[surchs]

Thanks @alyssadai! All config files look great, excellent choice of credentials. However I am getting error 403 from the QPN API:

{"detail":": Forbidden (HTTP status 403)\n"}

I'm assuming that's not what we want?

[alyssadai]

Thanks for catching that @surchs.

I've re-granted RW permissions to both the mni_qpn and mni_ppmi databases for the database user I set up. If you try to access the QPN API again it should now work.

I've also opened an issue to document the (problem of) non-additive GraphDB permissions here neurobagel/documentation#116.

[alyssadai]

Hey @surchs, following recent discussions about the privacy of QPN I've updated the API config for the mni_qpn database to run in aggregate mode as well.

Let me know if this issue looks good to close now 🙂

[surchs]

@alyssadai I checked the requests and it now works for me with no auth error! Thanks a lot. I think we can close