adding new test db for unit tests (#63)

Problem
Unit tests currently use the development database

Solution
- updated database.py to create new database
- updated dockerfile to pass new db name to unit Tests
- updated README for running tests locally
- also updated seeder reqs to work on macos

Ticket URL
https://mediform.atlassian.net/browse/MEDI-16

Documentation
NA

Tests Run
Tested that unit tests now use the test db

app/api/README.md

@@ -50,7 +50,8 @@ This should be done inside your dev container
 To run API tests locally, run the following commands:
 
 ```bash
-docker-compose up --detach db
+docker-compose up --detach db 
+export POSTGRES_DB=example_test
 pytest
 ```
 

app/api/main/database.py

@@ -4,6 +4,7 @@
 from sqlalchemy import create_engine
 from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.orm import sessionmaker
+from sqlalchemy_utils import database_exists, create_database
 
 from api.config import load_env
 
@@ -20,19 +21,20 @@
 )
 
 engine = create_engine(SQLALCHEMY_DATABASE_URL, pool_pre_ping=True)
+if not database_exists(engine.url): # Check if the db exists
+        create_database(engine.url)     # Create new DB    
+
 SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
 
 Base = declarative_base()
 
-
 def get_db() -> Generator:
     db = SessionLocal()
     try:
         yield db
     finally:
         db.close()
 
-
 def create_all_tables() -> None:
     Base.metadata.create_all(engine, checkfirst=True)
 

app/api/requirements.txt

@@ -42,4 +42,5 @@ toml==0.10.2
 typing_extensions==4.2.0
 urllib3==1.26.9
 uvicorn==0.13.4
-gunicorn==20.1.0
+gunicorn==20.1.0
+SQLAlchemy-Utils==0.41.1

app/api/seeder/seeder_reqs.txt

@@ -4,7 +4,7 @@ cffi==1.15.0
 email-validator==1.2.1
 fastapi==0.65.1
 passlib==1.7.4
-psycopg2-binary==2.8.6
+psycopg2-binary
 py==1.11.0
 pyasn1==0.4.8
 python-dateutil==2.8.2

app/api/tests/conftest.py

@@ -1,5 +1,4 @@
 import os
-
 from functools import lru_cache
 from typing import Generator
 
@@ -31,7 +30,6 @@ def pytest_configure(config):
         "needs(*): mark test to run only when dependencies are available.",
     )
 
-
 @lru_cache
 def postgres_is_running() -> bool:
     """
@@ -72,16 +70,15 @@ def setup_and_teardown_db(request) -> None:
     Set up the database at the start of the pytest session, and then
     tear down all created tables once tests have completed
     """
-    # TODO: Create a separate database only for testing. Otherwise
-    # uncommenting the following will delete all migrations in the database.
-    # database.drop_all_tables(check_first=True)
+
+    database.drop_all_tables(check_first=True)
 
     database.create_all_tables()
 
-    # def teardown():
-    #     database.drop_all_tables()
+    def teardown():
+        database.drop_all_tables()
 
-    # request.addfinalizer(teardown)
+    request.addfinalizer(teardown)
 
 
 @pytest.fixture(scope="session")

docker-compose.yaml

@@ -69,6 +69,7 @@ services:
     env_file: app/api/.env
     environment:
       - POSTGRES_HOST=db
+      - POSTGRES_DB=example_test
     # run as module so basedir (root) is added to python path
     command: python -m pytest api/tests/
     volumes: