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mite_web

DOI

This repository contains code for web presence of the Minimum Information about a Tailoring Enzyme (MITE) data standard and repository.

The MITE web presence contains functionality to visualize data and receive submissions for new and existing MITE entries. However, the web presence does not store MITE entries per se. The MITE ground truth dataset lives in mite_data.

For more information, see the README of the MITE-Standard organisation page.

Nota bene: this application is only tested on Linux and not intended to be run locally. For an online version, see here.

Deploy Docker

Quick start

  • Download or clone this repository
  • Create a file mite_web/instance/config.py with the content indicated below
  • Build the docker image docker-compose build --no-cache (potentially with sudo)
  • Start the docker docker-compose up -d (potentially with sudo)
  • Open the application in any browser with the URL http://0.0.0.0:8004/
  • To stop the application, run docker-compose stop (potentially with sudo)

For developers

Install and quick start

Nota bene: This installation will only work on (Ubuntu) Linux.

  • Install python3
  • Install hatch using one of the methods described here
  • Download or clone this repository and change into mite_dev (where the pyproject.toml file resides)
  • Run hatch -v env create dev
  • Run hatch run dev:pre-commit install. This will set up pre-commit
  • Install BLAST+ by running sudo apt-get install ncbi-blast+
  • Install Pymol by running sudo apt-get install pymol
  • Run the script hatch run dev:python mite_web/prepare_mite_data.py to populate the application with data
  • Run the script ./run_pymol.sh to populate the application with data
  • Move into the mite_web directory and run hatch run dev:flask --app mite_web run --debug

Config-file

SECRET_KEY: str = "your_secret_key"
ONLINE: bool = False
MAIL_TARGET: str = "email_target"
MAIL_DEFAULT_SENDER: str = "sender"
MAIL_SERVER: str = "server"
MAIL_PORT: int = "port"
MAIL_USE_TLS: bool = False
MAIL_USE_SSL: bool = False