refactoring to use flasks app factory

routes are now a blueprint and registered separately in create_app
this will allow pytest to run properly

Author: Moritz Wolf

app/__init__.py

@@ -1,21 +1,57 @@
 from flask import Flask
+from setuptools import setup
 from app.db import get_db, init_app
 from flask_login import LoginManager
 import os
 import logging
+from flask.logging import create_logger
 from flask_cors import CORS
+from app.user_handler import User, load_user
+from app.error_handler import handle_database_error,  handle_unknown_error, UnknownError, DatabaseError, page_not_found
 
-app = Flask(__name__)
-CORS(app)
-logging.basicConfig(level=logging.DEBUG)
-app.config.from_mapping(
-    SECRET_KEY='dev',
-    DATABASE=os.path.join(app.instance_path, 'database.sqlite'),
-)
-init_app(app)
 
-login_manager = LoginManager(app)
-login_manager.init_app(app)
-login_manager.login_view = 'login'
+def create_app(test_config=None, debug=True):
+    print('went into __init__')
+    app = Flask(__name__)
+    CORS(app)
+    app.config.from_mapping(
+        SECRET_KEY='dev',
+        DATABASE=os.path.join(app.instance_path, 'database.sqlite'),
+        DEBUG=debug,
+        TESTING=debug
+    )
+    if test_config is None:
+        # load the instance config, if it exists, when not testing
+        app.config.from_pyfile("config.py", silent=True)
+    else:
+        # load the test config if passed in
+        app.config.update(test_config)
 
-from app import routes
+    print(app.debug)
+    init_app(app)
+
+    login_manager = LoginManager(app)
+    login_manager.init_app(app)
+    login_manager.login_view = 'routes.login'
+
+    login_manager.user_loader(load_user)
+    # logger
+    # when running via flask run:
+    # logging.basicConfig(level=logging.DEBUG)
+
+    # app.logger = create_logger(app)
+    # when running gunicorn
+    gunicorn_logger = logging.getLogger('gunicorn.error')
+    app.logger.handlers.extend(gunicorn_logger.handlers)
+    app.logger = gunicorn_logger
+    # transitions logger
+    logging.getLogger('transitions').setLevel(logging.ERROR)
+
+    from app import routes
+    app.register_blueprint(routes.app)
+
+    app.register_error_handler(DatabaseError, handle_database_error)
+    app.register_error_handler(UnknownError, handle_unknown_error)
+    app.register_error_handler(404, page_not_found)
+
+    return app

app/automaton.py

@@ -159,15 +159,15 @@ def print_debug(self, **kwargs): print(self.current_state)
 
 
     @staticmethod
-    def setup():
+    def setup(protocol:str='protocol.yml'):
         # TODO: Check Correctness
         # needs: Transition to end, no unreachable nodes, no unknown task types
         # Build database
         # Handle api calls and predictions
 
         automaton = AnnotationAutomaton()
 
-        with open('protocol.yml') as f:
+        with open(protocol) as f:
             yaml = YAML(typ='safe')
             protocol: dict = next(yaml.load_all(f))
 

app/db.py

@@ -43,7 +43,6 @@ def init_db():
 
     with current_app.open_resource('schema.sql') as f:
         db.executescript(f.read().decode('utf8'))
-    columns_from_automaton()
 
 def columns_from_automaton():
     from app.automaton import AnnotationAutomaton
@@ -89,6 +88,8 @@ def init_db_command():
                 break
         save_db('all')
         init_db()
+        columns_from_automaton()
+
     click.echo('Initialized the database.')
 
 @click.command('db-from-csv')

app/error_handler.py

@@ -1,5 +1,7 @@
 from flask import render_template
-from app import app
+# from app import app
+# from flask import current_app as app
+
 from flask_login import current_user
 
 class DatabaseError(Exception):
@@ -20,8 +22,8 @@ def __init__(self, message, status_code=None, payload=None):
             self.status_code = status_code
             self.payload = payload
 
-@app.errorhandler(UnknownError)
-def unknown_error(self):
+# @app.errorhandler(UnknownError)
+def handle_unknown_error(self):
     error_tile = "Unknown Error Occurred."
     error_message = self.message
     error_info = None
@@ -31,8 +33,8 @@ def unknown_error(self):
         return render_template('error.html', error_tile = error_tile, error_message = error_message, error_info = error_info)
 
 
-@app.errorhandler(DatabaseError)
-def handle_database_error(error):
+# @app.errorhandler(DatabaseError)
+def handle_database_error(self):
     error_tile = "Database error occurred."
     error_message = self.message
     error_info = None
@@ -42,7 +44,7 @@ def handle_database_error(error):
         return render_template('error.html', error_tile = error_tile, error_message = error_message, error_info = error_info)
 
 ## Error 404 page not found
-@app.errorhandler(404)
+# @app.errorhandler(404)
 def page_not_found(internal_error):
     error_tile = "Page not found Error."
     error_message = "The page you are trying to access cannot not be found or does not exist."