Use Flask custom CLI commands for custom scripts

[lorenyu]

Ticket

Resolves #90

Changes

• Use Flask custom CLI commands for custom scripts
• Remove main() entry point from create_user_csv service
• Remove script_utils
• Rename api.route package to api.api, and organize all things related to blueprints together:
  • X_blueprint.py
  • X_commands.py
  • X_routes.py
  • X_schemas.py
• Rewrite test_create_user_csv to use test_cli_runner rather than only test the service
• Add migration to cascade on delete
• Rewrite test_create_user_csv to truncate the user table rather than requiring an isolated db schema
• Remove now unused isolated_db fixture
• Remove unused transaction rollback functionality in db_session test fixture
• Rename /user REST resource to /users

Other changes

• Organize Makefile commands:
  • move setup-local to top
  • group openapi-spec with other CLI commands)
• Install pytest-lazy-fixture dev dependency
• Move empty_schema fixture to test_migrations, the only place it's used

Context for reviewers

This PR consolidates the way we run the API server and the way we run background scripts to both use Flask's create_app factory. This removes the need to have two separate main() entrypoints, two separate ways to initialize the database, logger, etc. To do this, we leverage Flask's built-in method of creating custom CLI commands which itself is based on the click library, a popular library for building Python command line applications that's more powerful than argparse. This allows us to remove the script_utils file.

This PR also renames the api.route package to api.api since we want to add "commands" to the user blueprint, so "route" is no longer an appropriate name that applies to everything in the blueprint. We could also consider other names like api.components or api.blueprints, and/or we could consider renaming the top level source code folder to something like src rather than api.

Finally, we made test_create_user_csv test things at using the test_cli_runner to be closer to the way we test routes using the test_client. This approach has more end-to-end test coverage.

Other tangential changes include making REST resources use plural names to follow REST resource naming conventions.

Testing

Running `make cmd args='--help' prints out

... a bunch of general help stuff ...
Commands:
  routes  Show the routes for the app.
  run     Run a development server.
  shell   Run a shell in the app context.
  spec    Show the OpenAPI spec.
  user    User commands

Running make cmd-user-create-csv args='--help' prints out

Usage: flask user create-csv [OPTIONS]

  Create a CSV of all users and their roles

Options:
  --dir TEXT       Directory to save output file in. Can be an S3 path (e.g.
                   's3://bucketname/folder/') Defaults to current directory
                   ('.').
  --filename TEXT  Filename to save output file as. Defaults to
                   '[timestamp]-user-roles.csv.
  --help           Show this message and exit.

Actually running it produces a file like

"User Name","Roles","Is User Active?"
"Jon Doe","","True"
"Jane Doe","","True"
"Jack Dougherty","","True"
"User One","USER","True"
"Player One","USER","True"
"Player Two","USER","True"
"Admin One","ADMIN","True"
"Admin Two","ADMIN","True"
"Godzilla Dinosaur","ADMIN USER","True"

(these were the users i had in my db)

[lorenyu]

@chouinar ok, I made the changes we discussed and created follow-on tickets for:

• Rename api to src #144 rename source code directory from api to src
• Document testing best practices for tests that touch the database #145 create a document for testing best practices
• Add service level tests #143 add service level tests

[chouinar]

LGTM!

[chouinar]

Something in the setup-local command?

[chouinar]

Maybe call out that they're from other tests?

[lorenyu]

done!