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 brew install geckodriver

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

Importantly, the the access permissions for the .env file on the server MUST be set to

-r--r-----

i.e., owner- and group readable but NOT world readable (otherwise, the .env file will be downloadable by anyone along with the remainder of the database). Use the chmod command to set the permissions correctly.

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/development.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

• If you want to customize the index page, make a copy of home_default.html,

cp -v mainproject/templates/mainproject/home{_default,}.html

and edit accordingly. Any images that home.html refers to should be placed in mainproject/static/mainproject/images.

• 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.