access app config variables in Flask app

you need to import the file, from where you are calling the create_app method. My guess is that it is the application.py.

--- D_file.py

app = create_app(your_config)

--- queries.py

from D_file import appDB_URI = app.config['DATABASE_URI']

Why are you involving the Flask application at all in the SQLAlchemy setup? You have a configuration object available to you, use that directly. Then you can attach a session to the flask global object, or create a session dynamically.

In queries.py

import get_config from configconfig_object = get_config()engine = create_engine(config_object['DATABASE_URI'])session_factory = sessionmaker(bind=engine)Session = scoped_session(session_factory)def get_all_users():    session = Session()    users = session.query(User).all()    session.close()    return users

And in your app factory:

from flask import Flask, gfrom myapp import routesfrom myapp.queries import Sessiondef create_app(config_object):    app = Flask(__name__)    app.config.from_object(config_object)    app.register_blueprint(routes.main)    # automatically set up and close a session for each request    @app.before_request    def before_request(response):        g.session = Session()    @app.after_request    def after_request(response):        g.session.close()    return app