Added development db for Sanctuary

[MadelaineJ]

Problem
We need to create a database for Sanctuary

Solution

• added script to db container to create sanctuary db
• modified alembic to have one central alembic folder that contains folders for each db we want migrations for
• modified docker-compose.yaml and Makefile to run migrations for both databases
• modified Intakes.py to be added to sanctuary db with BaseSanctuary
• added UserMedical and UserSantuary class that inherit from user class.

TODOs:

• Create separate user and pass for accessing sanctuary db
• Write intstructions for adding a new database in README
• Rename all instances of "example" db to "medical"
• Tested that users and encounters can still be added to Medical db through api

Ticket URL
https://mediform.atlassian.net/browse/MEDI-30

Documentation
https://docs.google.com/document/d/10Pz324rr6zxEArmOlQne0Kwj9Ow61iKnUfkfU9OH8tY/edit

Tests Run
make clean && make all && make env -> creates the database make automig -> generates appropriate revisions
make mig -> applies appropriate revisions to appropriate database

[critch646]

Code quality is excellent!

I tested your branch locally and there is an issue. I followed your test instructions and I noticed some odd behaviour: If I do make all the migrations wouldn't happen. I would have to use make mig first the do make all for the db migration to be performed, and I figured out why.

In the Makefile, the all target executes docker compose up -d web which then docker compose the dependencies for web in the yaml file and starts services accordingly while the yaml for migs has - DB_NAME=${DB_NAME} and command: bash -c "cd /app/api && alembic --name=${DB_NAME} upgrade head" In the terminal I keep getting

WARN[0000] The "DB_NAME" variable is not set. Defaulting to a blank string.
WARN[0000] The "DB_NAME" variable is not set. Defaulting to a blank string.

Whenever I run anything but make mig. I added the DB_NAME to my .env and gave it some value, but the error keeps happening

Also if I run make all before make mig and I check the logs for migs I get this:

critch646@HYRDA-WIN:~/source/repos/project-ct$ docker compose logs migs
WARN[0000] The "DB_NAME" variable is not set. Defaulting to a blank string.
WARN[0000] The "DB_NAME" variable is not set. Defaulting to a blank string.
migs  | FAILED: No config file 'alembic.ini' found, or file has no '[]' section

[MadelaineJ]

It should be fixed. Issue was that some services rely on migs. Those services weren't passing DB_NAME.

I changed it to make another service for migssanctuary. I didn't make the other services rely on it. I think we can worry about including sanctuary migrations for production environment later.

[critch646]

I pulled your changes and when I do make all it works for medical db but not sanctuary. In the docker-compose.yaml file for the api service if you add - migssanctuary under depends_on: it will start the that service as well.

[MadelaineJ]

Done

[critch646]

you did it!