pizzamyheart / muler Goto Github PK

View Code? Open in Web Editor NEW

55.0 3.0 6.0 15.07 MB

A search engine for drug information built with Flask.

Home Page: https://muler.pythonanywhere.com

License: MIT License

Python 58.96% HTML 18.55% CSS 18.16% JavaScript 4.33%

flask drug

muler's Introduction

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

Enter the 'muler' directory

cd <basedir>/muler

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.

Pull from origin/master.

git stash
git stash drop
git pull

WARNING: This will destroy local changes.

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()

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).
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Approved/withdrawn/investigational (Groups)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)

muler's People

Contributors

Stargazers

Watchers

Forkers

0xack13 hirajanwin mukeshtiwari1987 eshack94 sc0h0 calvinmorett

muler's Issues

Feature Request: Multi - Find for Drug Search Results

Feature Request:

Multi-find that will display different highlighted colors for found text. The found text will maintain it's highlighted color unless it's removed.

Concept Redesign

Concept:
https://codepen.io/CalvinMorett/pen/xxdrXdp?editors=1100

Top bar, consists of branding, then the search field input, followed by navigation.

The the features of the product displays where the content will be on drug pages.

Then we could allow room for the changelog as a sidebar, and then reuse the some space for "symptoms/products" for single page drug search results.

Alternative styling for Dark/Light Mode

.theme-switch input:checked + .slider { background-color: #ffffff; } .theme-switch .slider { background-color: #fff; bottom: 0; cursor: pointer; left: 0; position: absolute; right: 0; top: 0; transition: 0.34s ease; } .theme-switch-wrapper .theme-switch { display: inline-block; height: 20px; position: relative; width: 20px; } .theme-switch .slider::before { background-color: #ffb12f; box-shadow: 0 0 0 2px white; bottom: 0px; content: ""; height: 20px; left: 0px; position: absolute; transition: 0.4s; width: 20px; } [data-theme="dark"] .theme-switch .slider:before { background-color: var(--bg-color); bottom: 5px; content: ""; height: 18px; left: -7px; position: absolute; transition: 0.4s; width: 18px; opacity: 1; box-shadow:0 0 0 2px transparent; } [data-theme="light"] .theme-switch .slider { background-color: #fff; box-shadow: inset 0 0 0 2px; bottom: 0; cursor: pointer; left: 0; position: absolute; right: 0; top: 0; transition: left 0.4s ease, right .4s ease; opacity: 1; }

Suggest to loosen the dependency on fuzzywuzzy

Hi, your project muler requires "fuzzywuzzy==0.18.0" in its dependency. After analyzing the source code, we found that some other versions of fuzzywuzzy can also be suitable without affecting your project, i.e., fuzzywuzzy 0.17.0. Therefore, we suggest to loosen the dependency on fuzzywuzzy from "fuzzywuzzy==0.18.0" to "fuzzywuzzy>=0.17.0,<=0.18.0" to avoid any possible conflict for importing more packages or for downstream projects that may use muler.

May I pull a request to loosen the dependency on fuzzywuzzy?

By the way, could you please tell us whether such dependency analysis may be potentially helpful for maintaining dependencies easier during your development?

For your reference, here are details in our analysis.

Your project muler(commit id: cd02c46) directly uses 1 APIs from package fuzzywuzzy.

fuzzywuzzy.fuzz.token_sort_ratio

From which, 19 functions are then indirectly called, including 15 fuzzywuzzy's internal APIs and 4 outsider APIs, as follows (neglecting some repeated function occurrences).

[/PizzaMyHeart/muler]
+--fuzzywuzzy.fuzz.token_sort_ratio
|      +--fuzzywuzzy.fuzz._token_sort
|      |      +--fuzzywuzzy.fuzz._process_and_sort
|      |      |      +--fuzzywuzzy.utils.full_process
|      |      |      |      +--fuzzywuzzy.utils.asciidammit
|      |      |      |      |      +--fuzzywuzzy.utils.asciionly
|      |      |      |      |      +--fuzzywuzzy.utils.asciidammit
|      |      |      |      +--fuzzywuzzy.string_processing.StringProcessor.replace_non_letters_non_numbers_with_whitespace
|      |      +--fuzzywuzzy.fuzz.partial_ratio
|      |      |      +--fuzzywuzzy.utils.make_type_consistent
|      |      |      +--difflib.SequenceMatcher
|      |      |      +--fuzzywuzzy.StringMatcher.StringMatcher.__init__
|      |      |      |      +--warnings.warn
|      |      |      |      +--fuzzywuzzy.StringMatcher.StringMatcher._reset_cache
|      |      |      +--difflib.SequenceMatcher.get_matching_blocks
|      |      |      +--fuzzywuzzy.StringMatcher.StringMatcher.get_matching_blocks
|      |      |      |      +--fuzzywuzzy.StringMatcher.StringMatcher.get_opcodes
|      |      |      +--difflib.SequenceMatcher.ratio
|      |      |      +--fuzzywuzzy.StringMatcher.StringMatcher.ratio
|      |      |      +--fuzzywuzzy.utils.intr
|      |      +--fuzzywuzzy.fuzz.ratio
|      |      |      +--fuzzywuzzy.utils.make_type_consistent
|      |      |      +--difflib.SequenceMatcher
|      |      |      +--fuzzywuzzy.StringMatcher.StringMatcher.__init__
|      |      |      +--fuzzywuzzy.utils.intr
|      |      |      +--difflib.SequenceMatcher.ratio
|      |      |      +--fuzzywuzzy.StringMatcher.StringMatcher.ratio

We scan fuzzywuzzy's versions among [0.17.0] and 0.18.0, the changing functions (diffs being listed below) have none intersection with any function or API we mentioned above (either directly or indirectly called by this project).

diff: 0.18.0(original) 0.17.0
['fuzzywuzzy.process.extractWithoutOrder']

As for other packages, the APIs of @outside_package_name are called by fuzzywuzzy in the call graph and the dependencies on these packages also stay the same in our suggested versions, thus avoiding any outside conflict.

Therefore, we believe that it is quite safe to loose your dependency on fuzzywuzzy from "fuzzywuzzy==0.18.0" to "fuzzywuzzy>=0.17.0,<=0.18.0". This will improve the applicability of muler and reduce the possibility of any further dependency conflict with other projects/packages.

When you search for a drug, and see suggestions as "Did you mean: Example Drug Link, Example 2 Link, Example 3 Link"
If you click any of these suggested links, you will get a page that display a "404 Not Found" error - referencing issues with the URL.
This is due to the URL redirection being ...muler.com/example and not prefixed with /search/.. in the path, such as ...muler.com/search/example

2. Steps to reproduce

Drug search pond or go to URL, https://muler.pythonanywhere.com/search/pond
You will arrive to the page with the top suggesting, Showing results for 'Ponds'
Click any suggestion, such as Siponimod
Which will redirect you

3. Expected Result
Expected the link to direct me to the drug page for Siponimod.

4. Actual Result
Redirects me to a "404 Not Found" page, with the URL path, https://muler.pythonanywhere.com/Siponimod