Simplify Config setup and move some functions to dedicated files

app/__init__.py

@@ -1,7 +1,8 @@
-from config import config
+from config import Config
 from flask import Flask
 from flask_login import LoginManager
 from flask_mail import Mail
+from flask_migrate import Migrate
 from flask_paranoid import Paranoid
 from flask_socketio import SocketIO
 from flask_sqlalchemy import SQLAlchemy
@@ -10,23 +11,26 @@ import flask_assets
 
 assets = flask_assets.Environment()
 db = SQLAlchemy()
-login_manager = LoginManager()
-login_manager.login_view = 'auth.login'
+login = LoginManager()
+login.login_view = 'auth.login'
+login.login_message = 'Please log in to access this page.'
 mail = Mail()
+migrate = Migrate()
 paranoid = Paranoid()
 paranoid.redirect_view = '/'
 socketio = SocketIO()
 
 
-def create_app(config_name):
+def create_app(config_class=Config):
     app = Flask(__name__)
-    app.config.from_object(config[config_name])
+    app.config.from_object(config_class)
 
     assets.init_app(app)
-    config[config_name].init_app(app)
+    config_class.init_app(app)
     db.init_app(app)
-    login_manager.init_app(app)
+    login.init_app(app)
     mail.init_app(app)
+    migrate.init_app(app, db)
     paranoid.init_app(app)
     socketio.init_app(
         app, message_queue=app.config['NOPAQUE_SOCKETIO_MESSAGE_QUEUE_URI'])

app/cli.py

@@ -0,0 +1,25 @@
+from .models import Role
+from flask_migrate import upgrade
+
+
+def register(app):
+    @app.cli.command()
+    def deploy():
+        """Run deployment tasks."""
+        # migrate database to latest revision
+        upgrade()
+        # create or update user roles
+        Role.insert_roles()
+
+    @app.cli.command()
+    def tasks():
+        from app.tasks import TaskRunner
+        task_runner = TaskRunner()
+        task_runner.run()
+
+    @app.cli.command()
+    def test():
+        """Run the unit tests."""
+        import unittest
+        tests = unittest.TestLoader().discover('tests')
+        unittest.TextTestRunner(verbosity=2).run(tests)

app/models.py

@@ -1,11 +1,11 @@
 from datetime import datetime, timedelta
 from flask import current_app, url_for
-from flask_login import UserMixin, AnonymousUserMixin
+from flask_login import UserMixin
 from itsdangerous import BadSignature, TimedJSONWebSignatureSerializer
 from time import sleep
 from werkzeug.security import generate_password_hash, check_password_hash
 import xml.etree.ElementTree as ET
-from . import db, login_manager
+from . import db, login
 import base64
 import logging
 import os
@@ -285,18 +285,6 @@ class User(UserMixin, db.Model):
         return user
 
 
-class AnonymousUser(AnonymousUserMixin):
-    '''
-    Model replaces the default AnonymousUser.
-    '''
-
-    def can(self, permissions):
-        return False
-
-    def is_administrator(self):
-        return False
-
-
 class JobInput(db.Model):
     '''
     Class to define JobInputs.
@@ -722,13 +710,6 @@ class QueryResult(db.Model):
         return '<QueryResult {}>'.format(self.title)
 
 
-'''
-' Flask-Login is told to use the application’s custom anonymous user by setting
-' its class in the login_manager.anonymous_user attribute.
-'''
-login_manager.anonymous_user = AnonymousUser
-
-
-@login_manager.user_loader
+@login.user_loader
 def load_user(user_id):
     return User.query.get(int(user_id))