created seeder container for populating db with mock data (#61)

## Problem
The development database does not have mock data to aid development.

## Solution
* Created `app/api/seeder/Dockerfile.seed` for development database seeder.
* Added `seeder` service in`docker-compose.yaml` 
    - Service `api` now also depends on `seeder` service to ensure seeder is run
* Seeder container uses SQLAlchemy ORM models and `get_db` generator from API
* Added `seed` target in the project Makefile
* Some users created for seeding db.

## Ticket URL
https://mediform.atlassian.net/browse/MEDI-3

## Documentation
N/A

## Tests Run
Executed `make all` and `make seeder` to test seeder. Could sign in using mock users.

Makefile

@@ -15,6 +15,10 @@ testapi:
 	@echo "Running api unit tests..."
 	@docker compose up testapi --exit-code-from testapi
 
+seed:
+	@echo "Seeding database..."
+	@docker compose up seeder  --exit-code-from seeder
+
 db:
 	@echo "Starting db..."
 	@docker compose up -d db

app/api/seeder/Dockerfile.seed

@@ -0,0 +1,21 @@
+# Dockerfile.seed for seeding development database
+FROM python:3.9.1-slim
+
+RUN mkdir -p /app/api
+WORKDIR /app/api
+
+COPY seeder/seeder_reqs.txt /app/api
+RUN pip install --no-cache-dir -r seeder_reqs.txt
+COPY main /app/api/
+COPY models /app/api/
+COPY seeder /app/api/
+WORKDIR /app
+
+# Setup user to represent developer permissions in container
+ARG USERNAME=python
+ARG USER_UID=1000
+ARG USER_GID=1000
+RUN useradd -rm -d /home/$USERNAME -s /bin/bash -g root -G sudo -u $USER_UID $USERNAME
+USER $USERNAME
+
+EXPOSE 5000

app/api/seeder/seed_database.py

@@ -0,0 +1,110 @@
+from json import JSONDecodeError
+from passlib.hash import argon2
+from typing import List, Dict
+
+from sqlalchemy.orm import Session
+from fastapi.testclient import TestClient
+
+from api.main.app import api
+from api.models import User
+from api.main.database import get_db
+
+from api.seeder.seeds.users import USERS
+
+def create_authed_client(email: str, password: str, client: TestClient):
+    """ Create an authenticated client for testing
+
+    Args:
+        email (str): User email
+        password (str): Plain text password
+        client (FastAPI.TestClient): Test client to be authenticated
+
+    Returns:
+        FastAPI.TestClient: Authenticated test client
+    """
+
+    # Get token
+    print(f"Creating authed client for {email}")
+    login_data = {"email": email, "password": password}
+    r = client.post("/api/login", json=login_data)
+
+    # Check if login was successful
+    if r.status_code != 200:
+        print("create_authed_client response: ", r.json())
+        raise Exception("Login failed")
+
+    print("create_authed_client response: ", r.json())
+    token = r.json()["access_token"]
+
+    # Add authorization token header
+    client.headers = {"Authorization": f"Bearer {token}"}
+
+
+    return client
+
+
+def create_users(users: List[Dict], db: Session) -> List[User]:
+    """ Create users in database
+
+    Args:
+        users (List[Dict]): List of users to create
+        db (Session): Database session
+
+    Returns:
+        List[User]: List of created users
+    """
+
+    created_users = []
+
+    # Create users
+    for user in users:
+
+        # Check if user already exists
+        user_obj = db.query(User).filter(User.email == user["email"]).first()
+        if user_obj:
+            print(f"User {user_obj.email} already exists")
+            created_users.append(user_obj)
+            continue
+
+        # Hash password
+        hashed_password = argon2.hash(user["password"])
+        # Create user
+        user_obj = User(
+            email=user["email"],
+            hashed_password=hashed_password,
+        )
+        try:
+            ## Add user to database
+            db.add(user_obj)
+            db.commit()
+            db.refresh(user_obj)
+            print(
+                f"User {user_obj.email} created with uuid: {user_obj.user_uuid}"
+            )
+            created_users.append(user_obj)
+        except Exception as e:
+            print(e)
+            db.rollback()
+            db.flush()
+            print(f"User {user_obj.email} already exists")
+
+    return created_users
+
+def seed_database():
+    """ Seed database with mock data.
+    """
+
+    db = next(get_db())
+
+    # Create test client and check if healthy
+    client = TestClient(api)
+    r = client.get("/api/")
+    if r.json()["status"] == "healthy":
+        print("API is healthy")
+
+    # Create users
+    created_users = create_users(USERS, db)
+
+
+if __name__ == "__main__":
+    seed_database()

app/api/seeder/seeder_reqs.txt

@@ -0,0 +1,16 @@
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+cffi==1.15.0
+email-validator==1.2.1
+fastapi==0.65.1
+passlib==1.7.4
+psycopg2-binary==2.8.6
+py==1.11.0
+pyasn1==0.4.8
+python-dateutil==2.8.2
+python-dotenv==0.20.0
+python-editor==1.0.4
+python-jose==3.3.0
+requests==2.25.1
+SQLAlchemy==1.4.15
+typing_extensions==4.2.0

app/api/seeder/seeds/users.py

@@ -0,0 +1,21 @@
+"""
+Mock data for user model
+"""
+
+
+DEFAULT_USER = {
+    "email": "default_user@default.com",
+    "password": "Password123!"
+}
+
+TEST_USER_1 = {
+    "email": "not_bruce_wayne@gothamcity.com",
+    "password": "B@tCaveSecret1"
+}
+
+TEST_USER_2 = {
+    "email": "lethal@company.com",
+    "password": "WeMetQu0ta!"
+}
+
+USERS = [DEFAULT_USER, TEST_USER_1, TEST_USER_2]

docker-compose.yaml

@@ -1,4 +1,4 @@
-version: '3.9'
+version: "3.9"
 
 # LOCAL DEV
 
@@ -19,13 +19,14 @@ services:
       # Mount local codebase to reflect changes for local dev
       - ./app/api:/app/api
     healthcheck:
-      test: [ "CMD", "curl", "localhost:5000/api/health" ]
+      test: ["CMD", "curl", "localhost:5000/api/health"]
       interval: 5s
       timeout: 5s
       retries: 5
     depends_on:
       - migs
       - testapi
+      - seeder
 
   migs:
     container_name: migs
@@ -54,7 +55,7 @@ services:
     ports:
       - 5432:5432
     healthcheck:
-      test: [ "CMD", "pg_isready" ]
+      test: ["CMD", "pg_isready"]
       interval: 5s
       timeout: 5s
       retries: 5
@@ -75,6 +76,22 @@ services:
     depends_on:
       - migs
 
+  seeder:
+    container_name: seeder
+    user: 1000:1000
+    build:
+      context: app/api/
+      dockerfile: seeder/Dockerfile.seed
+    env_file: app/api/.env
+    tty: true
+    environment:
+      - POSTGRES_HOST=db
+    volumes:
+      - ./app/api/:/app/api
+    command: python -m api.seeder.seed_database
+    depends_on:
+      - testapi
+
   web:
     container_name: web
     user: node
@@ -114,8 +131,7 @@ services:
       - ./app/api:/app/api
     command: bash -c "cd /app/api && alembic upgrade head"
 
-
-#PRODUCTION IMAGE VERIFICATION 
+  #PRODUCTION IMAGE VERIFICATION
 
   apitarget:
     container_name: apitarget
@@ -130,17 +146,17 @@ services:
       - 5000:5000
     command: uvicorn api.main.app:api --reload --host=0.0.0.0 --port=5000
     healthcheck:
-      test: [ "CMD", "curl", "localhost:5000/api/health" ]
+      test: ["CMD", "curl", "localhost:5000/api/health"]
       interval: 5s
       timeout: 5s
       retries: 5
     depends_on:
       - migstarget
       - testapitarget
 
-  migstarget: 
+  migstarget:
     container_name: migstarget
-    build: 
+    build:
       context: app/api
       dockerfile: Dockerfile.prod
     env_file: app/api/.env
@@ -150,7 +166,7 @@ services:
     depends_on:
       db:
         condition: service_healthy
-  
+
   testapitarget:
     container_name: testapitarget
     user: 1000:1000
@@ -162,22 +178,20 @@ services:
       - POSTGRES_HOST=db
     #run as module so basedir (root) is added to python path
     command: python -m pytest api/tests/
-    depends_on: 
+    depends_on:
       - migstarget
-  
+
   webtarget:
     container_name: webtarget
     user: node
-    build: 
+    build:
       context: app/web/
       dockerfile: Dockerfile.prod
     ports:
       - 3000:3000
-    depends_on: 
+    depends_on:
       - apitarget
 
-
-
 networks:
   default:
     driver: "bridge"