Flask Backend Module for WebCAS

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+*.log
+venv/
+*.pyc

README.md

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 Web application for sepsis clinical assessment scores using batch ICU patient data
 Backend of the application will be in Flask and the project will be completely python based
 Frontend will be purely based on html, css and may be on javascript.
+
+# Dependencies
+1. Python 3.7
+
+# Installation
+1. Setup virtualenv for the project by running `virtualenv -p python3 venv`
+2. Activate the environment by `source venv/bin/activate`
+3. Install project requirements using `pip install -r requirements.txt`

requirements.txt

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+Click==7.0
+Flask==1.1.1
+Flask-Cors==3.0.8
+Flask-SQLAlchemy==2.4.0
+itsdangerous==1.1.0
+Jinja2==2.10.1
+MarkupSafe==1.1.1
+six==1.12.0
+SQLAlchemy==1.3.6
+Werkzeug==0.15.5

run.py

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+from scasBackend import app
+
+if __name__ == '__main__':
+    app.run()

scasBackend/__init__.py

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+from flask import abort, Flask, request
+
+from scasBackend.utils import get_instance_folder_path
+from scasBackend.api_routes import *
+from scasBackend.config import configure_app
+from scasBackend.models import db
+from flask_cors import CORS
+
+
+app = Flask(
+    __name__,
+    instance_path=get_instance_folder_path(),
+    instance_relative_config=True)
+
+configure_app(app) # load configurations
+db.init_app(app) # init app to db
+CORS(app) #Cross Origin Resource Sharing Plugin
+
+@app.errorhandler(404)
+def page_not_found(error):
+    app.logger.error('Page not found: %s', (request.path, error))
+    return "404"
+
+@app.errorhandler(500)
+def internal_server_error(error):
+    app.logger.error('Server Error: %s', (error))
+    return "500"
+
+@app.errorhandler(Exception)
+def unhandled_exception(error):
+    app.logger.exception(error)
+    app.logger.error('Unhandled Exception: %s', (error))
+    return "500"
+
+@app.before_first_request
+def initialize_database():
+    db.create_all()
+
+@app.after_request
+def after_request(response):
+    header = response.headers
+    header['Access-Control-Allow-Origin'] = '*'
+    return response
+
+@app.route('/')
+@app.route('/<lang_code>/')
+def home(lang_code=None):
+    return "homepage"
+    abort(404)
+
+
+# register all routes
+app.register_blueprint(api_routes, url_prefix='/api/v1')
+
+###############################################################################

scasBackend/api_routes/__init__.py

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+from flask import Blueprint
+api_routes = Blueprint('api_routes', __name__)
+
+from .index import *

scasBackend/api_routes/index.py

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+from flask import current_app
+from . import api_routes
+
+@api_routes.route('/')
+def index():
+	current_app.logger.info('/api/v1/')
+	return "this is /api/v1/"

scasBackend/config.py

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+from scasBackend.models import db
+import os
+import logging
+
+# Configs
+
+class BaseConfig(object):
+    DEBUG = False
+    TESTING = False
+    # sqlite :memory: identifier is the default if no filepath is present
+    SQLALCHEMY_DATABASE_URI = 'sqlite://'
+    SECRET_KEY = '123'
+    LOGGING_FORMAT = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+    LOGGING_LOCATION = 'scasBackend.log'
+    LOGGING_LEVEL = logging.DEBUG
+    SECURITY_CONFIRMABLE = False
+    SUPPORTED_LANGUAGES = {'en': 'English'}
+
+# Development
+class DevelopmentConfig(BaseConfig):
+    DEBUG = True
+    TESTING = False
+    SQLALCHEMY_DATABASE_URI = 'sqlite:///scasBackend.sqlite3'
+    SECRET_KEY = '456'
+
+# Testing
+class TestingConfig(BaseConfig):
+    DEBUG = False
+    TESTING = True
+    SQLALCHEMY_DATABASE_URI = 'sqlite://scasBackend.sqlite3'
+    SECRET_KEY = '789'
+
+config = {
+    "development": "scasBackend.config.DevelopmentConfig",
+    "testing": "scasBackend.config.TestingConfig",
+    "default": "scasBackend.config.DevelopmentConfig"
+}
+
+def configure_app(app):
+    # Configure above configuraton
+    config_name = os.getenv('FLASK_CONFIGURATION', 'default')
+    app.config.from_object(config[config_name])
+    app.config.from_pyfile('config.cfg', silent=True) # if it exists (for production)
+
+    # Configure logging
+    handler = logging.FileHandler(app.config['LOGGING_LOCATION'])
+    handler.setLevel(app.config['LOGGING_LEVEL'])
+    formatter = logging.Formatter(app.config['LOGGING_FORMAT'])
+    handler.setFormatter(formatter)
+    app.logger.addHandler(handler)

scasBackend/models/__init__.py

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+from flask_sqlalchemy import SQLAlchemy
+db = SQLAlchemy()

scasBackend/models/base.py

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+from . import db
+
+class Base(db.Model):
+    __abstract__ = True
+
+    created_on = db.Column(db.DateTime, default=db.func.now())
+    updated_on = db.Column(db.DateTime, default=db.func.now(), onupdate=db.func.now())
+
+    def serialize(self, return_fields=[]):
+        serialize_exclude = getattr(self, '__serialize_exclude__', set())
+        return_fields = self.__dict__.keys() if not return_fields else return_fields
+        return {
+        	key: value for key, value in self.__dict__.items()
+                # Do not serialize 'private' attributes
+                # (SQLAlchemy-internal attributes are among those, too)
+                if not key.startswith('_')
+                and key in return_fields
+                and key not in serialize_exclude}
+
+    def create(self):
+    	db.session.add(self)
+    	db.session.commit()

scasBackend/utils.py

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+import os
+
+def get_app_base_path():
+	return os.path.dirname(os.path.realpath(__file__))
+
+def get_instance_folder_path():
+	return os.path.join(get_app_base_path(), 'instance')