Backend/feature/db models (#19)

* Basic db definition in flask

* main.py

* Defined official db model in SQLalchemy

* db model definitions in sqlalchemy

* flask_sqlalchemy in requirements

* foutje

* fixed db_uri

* db initialization inside create_app

* db_uri and code clean

* import order fix

* database uri added

* .env added to ignore

* Updated docs and .gitignore

* A first succesfull test for user model

* Doc cleanup and test function for courses and course_relations models added

* Project and submission test added

* added psycopg to dependencies

* dockerized tests to host postgres server

* created test script

* created test directory to test models

* waiting for postgres service to start before running test scripts and moved env variables

* changed github action to run test script instead

* constructing pytests for models

* running test script with sudo

* adding bash to run script

* fixing pytest

* pytests fixed, 1 warning left

* warning fix

* fixed: run github action job on self-hosted runner

* fixed: no longer running test script with privileges

* added: installing docker-compose to run our backend tests

* fixed: no longer running compose install with permissions

* using ubuntu-latest runner until docker-compose is installed on our self-hosted runner

---------

Co-authored-by: warre <warre.provoost@ugent.be>
Co-authored-by: Aron Buzogany <aronsaps@gmail.com>
Co-authored-by: abuzogan <aron.buzogany@ugent.be>

.github/workflows/ci-tests.yml

@@ -37,7 +37,7 @@ jobs:
         working-directory: ./frontend
         run: npm run lint
   Backend-tests:
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
@@ -50,10 +50,10 @@ jobs:
       - name: Install dependencies
         working-directory: ./backend
         run: pip3 install -r requirements.txt && pip3 install -r dev-requirements.txt
-
+      
       - name: Running tests
         working-directory: ./backend
-        run: pytest
+        run: bash ./run_tests.sh
 
       - name: Run linting
         working-directory: ./backend

backend/.gitignore

@@ -7,4 +7,5 @@ __pycache__/
 htmlcov/
 docs/_build/
 dist/
-venv/
+venv/
+.env

backend/Dockerfile.test

@@ -0,0 +1,15 @@
+FROM python:3.9-slim
+
+# Set the working directory
+WORKDIR /app
+
+# Copy the application code into the container
+COPY . /app
+
+# Install dependencies
+RUN apt-get update 
+RUN apt-get install -y --no-install-recommends python3-pip
+RUN pip3 install --no-cache-dir -r requirements.txt -r dev-requirements.txt
+
+# Command to run the tests
+CMD ["pytest"]

backend/project/__init__.py

@@ -2,17 +2,34 @@
 This file is the base of the Flask API. It contains the basic structure of the API.    
 """
 
-from flask import Flask, jsonify
+from flask import Flask
+from flask_sqlalchemy import SQLAlchemy
 from .endpoints.index import index_bp
 
+db = SQLAlchemy()
+
 def create_app():
     """
     Create a Flask application instance.
     Returns:
         Flask -- A Flask application instance
     """
-    app = Flask(__name__)
 
+    app = Flask(__name__)
     app.register_blueprint(index_bp)
 
     return app
+
+def create_app_with_db(db_uri:str):
+    """
+    Initialize the database with the given uri 
+    and connect it to the app made with create_app.
+    Parameters:
+    db_uri (str): The URI of the database to initialize.
+    Returns:
+        Flask -- A Flask application instance
+    """
+    app = create_app()
+    app.config["SQLALCHEMY_DATABASE_URI"] = db_uri
+    db.init_app(app)
+    return app

backend/project/__main__.py

@@ -1,9 +1,12 @@
 """Main entry point for the application."""
 from sys import path
+from os import getenv
+from dotenv import load_dotenv
+from project import create_app_with_db
 
 path.append(".")
 
 if __name__ == "__main__":
-    from project import create_app
-    app = create_app()
+    load_dotenv()
+    app = create_app_with_db(getenv("DB_HOST"))
     app.run(debug=True)

backend/project/endpoints/index.py

@@ -1,10 +1,17 @@
+"""Index api point"""
 from flask import Blueprint
 from flask_restful import Resource
 
 index_bp = Blueprint("index", __name__)
 
+
 class Index(Resource):
+    """Api endpoint for the / route"""
+
     def get(self):
+        """Example of an api endpoint function that will respond to get requests made to /
+        return a json data structure with key Message and value Hello World!"""
         return {"Message": "Hello World!"}
-
-index_bp.add_url_rule("/", view_func=Index.as_view("index"))
+
+
+index_bp.add_url_rule("/", view_func=Index.as_view("index"))

backend/project/models/course_relations.py

@@ -0,0 +1,31 @@
+"""Models for relation between users and courses"""
+# pylint: disable=too-few-public-methods
+
+from sqlalchemy import Integer, Column, ForeignKey, PrimaryKeyConstraint, String
+from project import db
+from project.models.users import Users
+from project.models.courses import Courses
+
+class BaseCourseRelation(db.Model):
+    """Base class for course relation models,
+    both course relation tables have a 
+    course_id of the course to wich someone is related and
+    an uid of the related person"""
+
+    __abstract__ = True
+
+    course_id = Column(Integer, ForeignKey('courses.course_id'), nullable=False)
+    uid = Column(String(255), ForeignKey("users.uid"), nullable=False)
+    __table_args__ = (
+        PrimaryKeyConstraint("course_id", "uid"),
+    )
+
+class CourseAdmins(BaseCourseRelation):
+    """Admin to course relation model"""
+
+    __tablename__ = "course_admins"
+
+class CourseStudents(BaseCourseRelation):
+    """Student to course relation model"""
+
+    __tablename__ = "course_students"

backend/project/models/courses.py

@@ -0,0 +1,15 @@
+"""The Courses model"""
+# pylint: disable=too-few-public-methods
+from sqlalchemy import Integer, Column, ForeignKey, String
+from project import db
+from project.models.users import Users
+
+class Courses(db.Model):
+    """This class described the courses table, 
+    a course has an id, name, optional ufora id and the teacher that created it"""
+
+    __tablename__ = "courses"
+    course_id = Column(Integer, primary_key=True)
+    name = Column(String(50), nullable=False)
+    ufora_id = Column(String(50), nullable=True)
+    teacher = Column(String(255), ForeignKey("users.uid"), nullable=False)

backend/project/models/projects.py

@@ -0,0 +1,28 @@
+"""Model for projects"""
+# pylint: disable=too-few-public-methods
+from sqlalchemy import ARRAY, Boolean, Column, DateTime, ForeignKey, Integer, String, Text
+from project import db
+from project.models.courses import Courses
+
+class Projects(db.Model):
+    """This class describes the projects table,
+    a projects has an id, a title, a description, 
+    an optional assignment file that can contain more explanation of the projects,
+    an optional deadline,
+    the course id of the course to which the project belongs,
+    visible for students variable so a teacher can decide if the students can see it yet,
+    archieved var so we can implement the archiving functionality,
+    a test path,script name and regex experssions for automated testing"""
+
+    __tablename__ = "projects"
+    project_id = Column(Integer, primary_key=True)
+    title = Column(String(50), nullable=False, unique=False)
+    descriptions = Column(Text, nullable=False)
+    assignment_file = Column(String(50))
+    deadline = Column(DateTime(timezone=True))
+    course_id = Column(Integer, ForeignKey("courses.course_id"), nullable=False)
+    visible_for_students = Column(Boolean, nullable=False)
+    archieved = Column(Boolean, nullable=False)
+    test_path = Column(String(50))
+    script_name = Column(String(50))
+    regex_expressions = Column(ARRAY(String(50)))

backend/project/models/submissions.py

@@ -0,0 +1,25 @@
+"""Model for submissions"""
+# pylint: disable=too-few-public-methods
+from sqlalchemy import Column,String,ForeignKey,Integer,CheckConstraint,DateTime,Boolean
+from project import db
+from project.models.users import Users
+
+class Submissions(db.Model):
+    """This class describes the submissions table,
+    submissions can be made to a project, a submission has
+    and id, a uid from the user that uploaded it, 
+    the project id of the related project,
+    an optional grading,
+    the submission time,
+    submission path,
+    and finally the submission status
+    so we can easily present in a list which submission succeeded the automated checks"""
+
+    __tablename__ = "submissions"
+    submission_id = Column(Integer, nullable=False, primary_key=True)
+    uid = Column(String(255), ForeignKey("users.uid"), nullable=False)
+    project_id = Column(Integer, ForeignKey("projects.project_id"), nullable=False)
+    grading = Column(Integer, CheckConstraint("grading >= 0 AND grading <= 20"))
+    submission_time = Column(DateTime(timezone=True), nullable=False)
+    submission_path = Column(String(50), nullable=False)
+    submission_status = Column(Boolean, nullable=False)

backend/project/models/users.py

@@ -0,0 +1,16 @@
+"""Model for users"""
+# pylint: disable=too-few-public-methods
+from sqlalchemy import Boolean, Column, String
+from project import db
+
+
+class Users(db.Model):
+    """This class defines the users table,
+    a user has an uid,
+    is_teacher and is_admin booleans because a user 
+    can be either a student,admin or teacher"""
+
+    __tablename__ = "users"
+    uid = Column(String(255), primary_key=True)
+    is_teacher = Column(Boolean)
+    is_admin = Column(Boolean)

backend/requirements.txt

@@ -1,2 +1,5 @@
 flask
 flask-restful
+flask-sqlalchemy
+python-dotenv
+psycopg2-binary

backend/run_tests.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+# Run Docker Compose to build and start the services, and capture the exit code from the test runner service
+docker-compose -f tests.yaml up --build --exit-code-from test-runner
+
+# Store the exit code in a variable
+exit_code=$?
+
+# After the tests are finished, stop and remove the containers
+docker-compose -f tests.yaml down
+
+# Check the exit code to determine whether the tests passed or failed
+if [ $exit_code -eq 0 ]; then
+    echo "Tests passed!"
+else
+    echo "Tests failed!"
+fi
+
+# Exit with the same exit code as the test runner service
+exit $exit_code

backend/tests.yaml

@@ -0,0 +1,31 @@
+version: '3.8'
+
+services:
+  postgres:
+    image: postgres:latest
+    environment:
+      POSTGRES_USER: test_user
+      POSTGRES_PASSWORD: test_password
+      POSTGRES_DB: test_database
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -U test_user -d test_database"]
+      interval: 5s
+      timeout: 3s
+      retries: 3
+      start_period: 5s
+
+  test-runner:
+    build:
+      context: .
+      dockerfile: Dockerfile.test
+    depends_on:
+      postgres:
+        condition: service_healthy
+    environment:
+      POSTGRES_HOST: postgres  # Use the service name defined in Docker Compose
+      POSTGRES_USER: test_user
+      POSTGRES_PASSWORD: test_password
+      POSTGRES_DB: test_database
+    volumes:
+      - .:/app
+    command: ["pytest"]