/MatD3

Database for experimental and theoretical data on solid materials.

Primary LanguageJavaScriptOtherNOASSERTION

MatD3 database software

MatD3 is a database and a web application for experimental and theoretical data on solid materials. The objective is to ensure better access and reproducibility of research data and it is intended to be used by any research group wishing to make their scientific results publicly available.

Installation

From source code

These instructions are for quickly setting up a local server on your personal computer. For setting up a real server, see the full documentation at https://hybrid3-database.readthedocs.io/en/latest/.

  • Clone the project

    git clone https://github.com/HybriD3-database/MatD3.git
    cd MatD3
    
  • In the root directory of the project, create a virtual Python environment

    python3 -m venv venv
    source venv/bin/activate
    
  • Upgrade pip and install all the requirements

    pip install --upgrade pip
    pip install -vr requirements.txt
    

    If you run into any issues, install the prerequisites as requested by the error messages. On Ubuntu, it might be necessary to install the following packages first:

    sudo apt install libmysqlclient-dev
    sudo apt install python3-dev
    sudo apt install firefox-geckodriver
    

    On a Mac, it might be necessary to run

    brew install mariadb
    

    If there are issues with installing MySQL/MariaDB and you only plan to use SQLite, remove the line mysqlclient==1.4.2 from requirements.txt and proceed with the installation.

  • Define your environment in .env in the root directory of the project

    cp env.example .env
    # edit .env
    

    If you wish to use anything other than the SQLite database, you first need to set up that database (e.g., MariaDB). See https://hybrid3-database.readthedocs.io/en/latest/setup.html for more details.

  • Initialize static files and perform database migrations

    ./manage.py collectstatic
    ./manage.py migrate
    
  • Run tests

    ./manage.py test
    

    Make sure the line

    127.0.0.1 localhost
    

    is in your /etc/hosts.

  • Create a superuser

    ./manage.py createsuperuser
    
  • Start the server

    ./manage.py runserver
    
  • Open a web browser and go to http://127.0.0.1:8000/.

Using Docker

  • Run the MatD3 Docker container in detached mode:

    docker run -d --rm --name matd3 --env-file=env_file -p 80:80 matd3/matd3:1.0.0 python manage.py runserver 0.0.0.0:80
    

    where env_file (rename if you like) contains the necessary enrironment variables. See here for example contents. You can view the website by opening 0.0.0.0 in a web browser. If you wish to run the container on a different port, replace 80 in the command with the number of that port.

  • Initialize static files and perform database migrations

    docker exec matd3 python manage.py collectstatic --noinput
    docker exec matd3 python manage.py migrate
    
  • Create super user

    docker exec -it matd3 python manage.py createsuperuser
    
  • You can stop the container with

    docker container stop matd3
    

Usage

In order to enter data into the database, start by creating a new user (click on Register and follow instructions) or login as the superuser. Next, click on Add Data on the navigation bar in order to submit a data set into the database. Existing data can be viewed by using the Search function on the navigation bar.