Unset minimum cell size in .env file leads to undeployable stack

[surchs]

Is there an existing issue for this?

• I have searched the existing issues

Expected Behavior

I can launch my local node stack without uncommenting the minimum cell size value in the .env file

Current Behavior

If I launch a local_node without first uncommenting the minimum cell size value in the .env file, the api service quits with an error.

Error message

...
  File "/usr/local/lib/python3.10/site-packages/uvicorn/server.py", line 67, in serve
    config.load()
  File "/usr/local/lib/python3.10/site-packages/uvicorn/config.py", line 477, in load
    self.loaded_app = import_from_string(self.app)
  File "/usr/local/lib/python3.10/site-packages/uvicorn/importer.py", line 21, in import_from_string
    module = importlib.import_module(module_str)
  File "/usr/local/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/src/./app/main.py", line 14, in <module>
    from .api import utility as util
  File "/usr/src/./app/api/utility.py", line 41, in <module>
    "NB_MIN_CELL_SIZE", int(os.environ.get("NB_MIN_CELL_SIZE", 0))
ValueError: invalid literal for int() with base 10: ''

Environment

We were using a special docker-compose recipe for deploying several local nodes behind a reverse proxy: https://gist.github.com/alyssadai/0f3d6b77c41cf77992d37e7d98bcbef9

How to reproduce

Use the linked gist and deploy a local_node profile, leave the NB_MIN_CELL_SIZE value commented out in the .env file

Anything else?

This could be linked to the fact that there is no default value defined in the docker-compose file for NB_MIN_CELL_SIZE.

• This issue could be prevented using a compatibility test of our deployment recipe, Fix flaky compatibility tests #101

[alyssadai]

This bug is fixed by #106, but the underlying cause is described in and will be fixed by the PR for neurobagel/api#411.