Muler

Muler is a Flask app that allows users to search for pharmacological information by generic or proprietary drug names. The information is sourced from a DrugBank dataset under a CC BY-NC 4.0 license. The original dataset is a fairly large XML file, which has been processed into an SQLite database a MySQL database using a Python script.

Running Muler locally

1. Enter the 'muler' directory

cd <basedir>/muler

2. Start the Flask server

flask run 

Add --host 0.0.0.0:<port> to access the app from other devices on the local network. Note that use of the Flask server in production is strongly discouraged.

Instead of using Flask, you can also run Muler as on the command line from the base directory.

python3 -m muler.query

Deploying to PythonAnywhere

General method to deploy Flask app on PythonAnywhere.

1. Pull from origin/master.

git stash
git stash drop
git pull

WARNING: This will destroy local changes.

2. Update sys.path and imports in WSGI config if needed. Current config with muler set up as a package:

path = '/home/muler/muler'  # /home/<username>/<basedir>
if path not in sys.path:
    sys.path.append(path)
# Import applciation factory
from muler.app import create_app
application = create_app()

3. Make sure config.py (contains database paths) is uploaded, which is untracked by Git. Make sure it's located in /home/muler/muler/muler/ (I know, sigh).

4. Edit db_config key in db_session function in query.py to make sure the app is pointed to the right database URL.

TODO

• Search db

  • Levenshtein distance (spellfix/editdist3) [DONE]
  • Autocomplete.js

• Flask app

  • HTML form validation
    • Remove trailing whitespace [DONE]
  • CSS
    • Remove borders on searchbar focus on mobile
  • SQLalchemy
    • Switch to scoped_session

• CLI app

  • Implement CLI version using Click instead of gazillions of print statements

• Update rofecoxib and mephenytoin mechanism of action [DONE]

• Approved/withdrawn/investigational (Groups)

Changelog

2021-01-12

• Migrated from SQLite to MySQL using sqlite3-to-mysql.py

2021-07-16

• Input sanitisation and minor optimisations for faster response time (not formally measured)
• Rewrote functions to search database using user input with class methods

2021-07-18

• Added exception handling to roll back invalid database transactions

2021-07-25

• Added dark mode 😎 (many thanks to calvinmorett)