mite_web

Contents

• Overview
• Documentation
• System Requirements
• Installation Guide
• Quick Start
• Attribution
• For Developers

Overview

MITE (Minimum Information about a Tailoring Enzyme) is a community-driven database for the characterization of tailoring enzymes. These enzymes play crucial roles in the biosynthesis of secondary or specialized metabolites, naturally occurring molecules with strong biological activities, such as antibiotic properties.

This repository manages the code for the MITE Webpage.

For more information, visit the MITE Data Standard Organization page or read our publication.

Documentation

This repository contains code for the MITE Webpage, allowing to visualize data and receive submissions for new and existing MITE entries.

Note that the web presence does not store MITE entries per se. The MITE ground truth dataset lives in mite_data.

System Requirements

Nota bene: this application is only tested on Linux. For an online version, see here.

OS Requirements

Local installation was tested on:

• Ubuntu Linux 20.04 and 22.04 (command line)

Python dependencies

Dependencies including exact versions are specified in the pyproject.toml file.

Installation Guide

Deploy Docker locally

• Download or clone this repository
• Add the .env file as indicated below (with at least the mandatory params)
• Build the docker image docker-compose -f docker-compose.yml build --no-cache (potentially with sudo)
• Start the docker docker-compose -f docker-compose.yml up -d (potentially with sudo)
• Open the application in any browser with the URL http://127.0.0.1:1340/
• To stop the application, run docker-compose stop (potentially with sudo)
• To take down the database, run docker-compose down -v --rmi all

Attribution

License

mite_schema is an open source tool licensed under the MIT license (see LICENSE).

Publications

See CITATION.cff or MITE online for information on citing MITE.

Acknowledgements

This work was supported by the Netherlands Organization for Scientific Research (NWO) KIC grant KICH1.LWV04.21.013.

For Developers

Nota bene: since version 1.5.0, development is only possible using the docker-container

Nota bene: regularly update uv.lock using uv lock --upgrade

Development build

• Download or clone this repository
• Add the .env file as indicated below (with at least the mandatory params)
• Populate the app by changing into mite_web and running uv run python mite_web/prepare_mite_data.py (if applicable, remove .venv, data and static/img dirs)
• Build the docker image using docker-compose build. This will mount the mite_web directory for more convenient file editing (no need to rebuild every time).
• Start the docker image with docker-compose up -d. The image will be available at http://127.0.0.1:1340/.
• Changes within the mite_web folder will be mirrored inside the docker image but require stopping and restarting the docker container with docker-compose stop && docker-compose up (gunicorn does not support reloading on change with the current build)
• Changes in the PostgreSQL DB will only be applied if old tables are dropped with docker-compose down -v

Production build

First startup

1. Clone the repository

git clone https://github.com/mite-standard/mite_web
cd mite_web

2. Create configuration file

# .env
# mandatory
POSTGRES_PASSWORD=<yoursecurepassword>
POSTGRES_DB=mite_database
# optional
GITHUB_TOKEN=<personal-access-token-classic(scopes: 'admin:public_key', 'gist', 'read:org', 'repo')>
GITHUB_NAME=<gh-acc name>
GITHUB_MAIL=<gh-acc mail>
SECRET_KEY=<your_secret_key>
ONLINE=True

3. Build Docker images

docker-compose -f docker-compose.yml build --no-cache

This builds both mite_web and nginx images. The mite_web directory is not mounted in production; all code is baked into the image.

4. Start the services

docker-compose -f docker-compose.yml up -d

(5. Remove all services)

docker-compose down -v --rmi all

Update/redeploy

Nota bene: make sure to announce the downtime in the Web App Status thread.

1. Save existing dumps (optional)

Preserves links to any open mite_data PRs on GitHub

docker cp mite_web-mite_web-1:/mite_web/mite_web/dumps .

2. Toggle maintenance mode and stop the mite_web application

docker exec mite_web-nginx-1 touch /etc/nginx/maintenance.flag
docker exec mite_web-nginx-1 nginx -s reload
docker-compose stop mite_web postgres && docker-compose rm -v postgres

This assumes that only the mite_web container needs to be updated. nginx will continue to run and automatically serve a maintenance.html page.

3. Pull the newest release

git pull

4. Build the mite_web image

docker-compose -f docker-compose.yml build --no-cache mite_web

5. Restart the mite_web image and switch off maintenance mode

docker-compose -f docker-compose.yml up -d --build --force-recreate postgres && docker-compose -f docker-compose.yml up -d --build --force-recreate mite_web
docker exec mite_web-nginx-1 rm /etc/nginx/maintenance.flag
docker exec mite_web-nginx-1 nginx -s reload

6. Transfer existing dumps

docker cp ./dumps mite_web-mite_web-1:/mite_web/mite_web && docker cp ./dumps/. mite_web-mite_web-1:/mite_web/mite_web/open_prs

7. Perform a test submission

Check if submission system works by performing a test submission. If not, there are possibly issues with the connection to GitHub.