mite_web

Repository for the MITE web presence

https://github.com/mite-standard/mite_web

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.8%) to scientific vocabulary

Scientific Fields

Biology Life Sciences - 84% confidence

Chemistry Physical Sciences - 83% confidence

Last synced: 4 months ago · JSON representation ·

Repository

Repository for the MITE web presence

Basic Info

Host: GitHub
Owner: mite-standard
License: mit
Language: HTML
Default Branch: main
Size: 16.8 MB

Statistics

Stars: 1
Watchers: 1
Forks: 0
Open Issues: 2
Releases: 27

Created about 1 year ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

mite_web

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 locally

Download or clone this repository
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

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

Development build

Download or clone this repository
Create a file mite_web/instance/config.py with the content indicated below. Set Online to False
Add the .env file with content indicated below
Run the data preparation script from inside the mite_web folder using hatch run python mite_web/prepare_mite_data.py.
Remove the hatch environment again with hatch env remove
Build the docker image docker-compose build. This will mount the mite_web dir for more convenient file editing (no need to rebuild every time).
Start the docker image with docker-compose up
Changes within the mite_web folder will be mirrored inside the docker image but require stopping and restarting the docker container (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

Download or clone this repository
Create a file mite_web/instance/config.py with the content indicated below
Add the .env file with content indicated below
Build the docker image docker-compose -f docker-compose.yml build --no-cache (potentially with sudo). Will not mount the mite_web dir.
Start the docker docker-compose -f docker-compose.yml up -d (potentially with sudo)

Update

Save dumps dir (preserves open mite_data PR previews) docker cp mite_web-mite_web-1:/mite_web/mite_web/dumps .
To stop the application, run docker-compose stop (potentially with sudo)
Take the database down with docker-compose down -v
Pull the newest release
Build the docker image docker-compose -f docker-compose.yml build --no-cache (potentially with sudo). Will not mount the mite_web dir.
Start the docker docker-compose -f docker-compose.yml up -d (potentially with sudo)
Transfer the dumps folder: docker cp ./dumps mite_web-mite_web-1:/mite_web/mite_web

Config files

config.py python SECRET_KEY: str = "your_secret_key" ONLINE: bool = True

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

Owner

Name: MITE Data Standard
Login: mite-standard
Kind: organization

Repositories: 1
Profile: https://github.com/mite-standard

Governing body for MITE data standard and affiliated repositories

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: mite_web
message: >-
  If you use this software, please cite the referenced
  paper.
type: software
authors:
  - affiliation: 'Wageningen University and Research'
    family-names: Zdouc
    given-names: Mitja M.
    orcid: 'https://orcid.org/0000-0001-6534-6609'
repository-code: 'https://github.com/mite-standard/mite_web'
abstract: >-
    A repository containing the MITE Wep portal code.
keywords:
  - python
  - tailoring enzymes
  - data standard
license: MIT
preferred-citation:
  type: preprint
  authors:
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Zdouc
      given-names: Mitja M.
      orcid: 'https://orcid.org/0000-0001-6534-6609'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Meijer
      given-names: David
      orcid: 'https://orcid.org/0000-0001-6406-4394'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Biermann
      given-names: Friederike
    - address: 'SINTEF Industry, P.O. Box 4760 Torgard, N-7465, Trondheim, Norway'
      affiliation: 'Department of Biotechnology and Nanomedicine'
      family-names: Holme
      given-names: Jonathan
      orcid: 'https://orcid.org/0009-0007-1652-9477'
    - address: 'University of Tübingen, Germany'
      affiliation: 'Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT)'
      family-names: Korenskaia
      given-names: Aleksandra
      orcid: 'https://orcid.org/0000-0003-3002-6458'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Lien
      given-names: Annette
      orcid: 'https://orcid.org/0009-0006-0578-9225'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Louwen
      given-names: Nico L. L.
      orcid: 'https://orcid.org/0000-0002-4431-5499'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Navarro-Muñoz
      given-names: Jorge C.
      orcid: 'https://orcid.org/0000-0003-2992-1607'
    - address: 'SINTEF Industry, P.O. Box 4760 Torgard, N-7465, Trondheim, Norway'
      affiliation: 'Department of Biotechnology and Nanomedicinev'
      family-names: Nguyen
      given-names: Giang-Son
      orcid: 'https://orcid.org/0000-0001-5730-3326'
    - address: 'ETH Zurich, Zurich, Switzerland'
      affiliation: 'Institute of Molecular Systems Biology'
      family-names: Rutz
      given-names: Adriano
      orcid: 'https://orcid.org/0000-0003-0443-9902'
    - address: 'Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Sveshnikova
      given-names: Anastasia
      orcid: 'https://orcid.org/0000-0001-9291-0965'
    - address: 'University of Denmark, Kgs. Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical'
      family-names: Szenei
      given-names: Judith
    - address: 'Sylviusweg 72, 2333 BE Leiden, The Netherlands'
      affiliation: 'Institute of Biology, Leiden University'
      family-names: Terlouw
      given-names: Barbara
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Torres Ortega
      given-names: Rosina
    - address: 'Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Feuermann
      given-names: Marc
    - address: 'Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Bridge
      given-names: Alan J.
      orcid: 'https://orcid.org/0000-0003-2148-9135'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Hooft
      name-particle: van der
      given-names: Justin J. J.
      orcid: 'https://orcid.org/0000-0002-9340-5511'
    - address: 'University of Denmark, Kgs. Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical'
      family-names: Weber
      given-names: Tilmann
    - address: 'University of Tübingen, Germany'
      affiliation: 'Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT)'
      family-names: Ziemert
      given-names: Nadine
    - address: 'University of Denmark, Kgs. Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical'
      family-names: Blin
      given-names: Kai
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Wageningen University and Research'
      family-names: Medema
      given-names: Marnix H.
  title: The Minimum Information about a Tailoring Enzyme/Maturase data standard for capturing natural product biosynthesis.
  journal: ChemRxiv
  year: 2024
  doi: 10.26434/chemrxiv-2024-78mtl

GitHub Events

Total

Create event: 46
Release event: 24
Issues event: 17
Watch event: 1
Delete event: 23
Issue comment event: 1
Push event: 248
Pull request event: 49

Last Year

Create event: 46
Release event: 24
Issues event: 17
Watch event: 1
Delete event: 23
Issue comment event: 1
Push event: 248
Pull request event: 49

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 2
Total pull requests: 13
Average time to close issues: about 2 months
Average time to close pull requests: 4 days
Total issue authors: 1
Total pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 13
Average time to close issues: about 2 months
Average time to close pull requests: 4 days
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.0
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

mmzdouc (10)

Pull Request Authors

mmzdouc (25)

Top Labels

Issue Labels

enhancement (4)

Pull Request Labels

enhancement (1)

Dependencies

compose/mite_web/Dockerfile docker

ubuntu 22.04 build

compose/nginx/Dockerfile docker

nginx 1.19-alpine build

docker-compose.yml docker

mite_web/pyproject.toml pypi

AlphaFetcher ~=0.2
Flask ~=3.0
Flask-Mail ~=0.9
Flask-WTF ~=1.2
biopython ~=1.84
coloredlogs ~=15.0
flask-restx ~=1.3
gevent ~=24.2
gunicorn ~=23.0
jsondiff ~=2.2
mite_extras ==1.4.1
pandas ~=2.2
rdkit ==2024.3.6
requests ~=2.32

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

mite_web

Science Score: 67.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

mite_web

Deploy Docker locally

For developers

Development build

Production build

First startup

Update

Config files

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies