Update API entrypoint and add logger configuration

[critch646]

Problem

The API has no logging for developers to use.

Solution

• Added logger to FastAPI main entry point.
• Created api/logger_config.yaml with configurations for formatters and loggers
• Updated docker-compose.yaml services api and apitarget commands to use api/logger_config.yaml
• Added logger to api/models/patient_encounter.py and completed TODO

Ticket URL

https://mediform.atlassian.net/browse/MEDI-15

Documentation

N/A

Tests Run

• Tested locally. Rebuilt api image and spun up container.
• Checked logs and logger uses new format.
• For testing purposes, had line that logged on loading patient_encounter.py and line was represented in logs. Line removed for production.

[MadelaineJ]

Look good. Just a couple questions from me.

[MadelaineJ]

Is there a reason we need these lines in app.py if we're not logging anything from the file?

[MadelaineJ]

maybe it is needed because this is the entry point of the app? Did you test without it and it failed?

[critch646]

I removed the entry point logger, which works with the customer format elsewhere. Since this log config is passed to uvicorn at the start the logger inherits the config in different modules in the API.

[MadelaineJ]

do we want to add exc_info=True? I am not sure if we do but something to consider.
reference: https://www.loggly.com/blog/exceptional-logging-of-exceptions-in-python/#:~:text=Setting%20exc_info%20to%20True%20will,than%20error%3A%20Just%20replace%20logger.

[critch646]

I looked into that flag and I think it is worth putting in. I added it in the latest commit.