Nordic Microalgae: Backend

This repository contains source code for the backend used in Nordic Microalgae.

The backend consists of a REST API and administration interface and is written in Python and uses, as of writing, the latest LTS version (4.2) of Django as web framework. PostgreSQL is used as datbase layer and JSONB is being used heavily to store generated information in read-only tables, as well as for storing metadata in some of the user-writable tables.

Install and run locally

Required repositories and folders

Clone backend into a dedicated nordicmicroalgae directory:

mkdir nordicmicroalgae
cd nordicmicroalgae
git clone https://github.com/nordicmicroalgae/backend.git

Create a nordicmicroalgae/shared directory:

mkdir shared

Clone content into the shared directory:

cd shared
git clone https://github.com/nordicmicroalgae/content.git

Optionally, create nordicmicroalgae/shared/media directory for user-contributed images:

mkdir media

Postgres database

Option 1: Local database

Create postgres user:

createuser nordicmicroalgae -P -s

Create database:

createdb -U nordicmicroalgae -E utf8 -O nordicmicroalgae -T template0

Option 2: Database in container

Create the container (here using podman and a local registry):

podman run -d --name pg-local \
  -e POSTGRES_PASSWORD=postgres \
  -e POSTGRES_USER=postgres \
  -p 5432:5432 \
  -v pgdata:/var/lib/postgresql/data \
  r-harbor.smhi.se/public/postgres:16-alpine

Create postgres user:

podman exec -it pg-local createuser -P -s nordicmicroalgae

Create database:

podman exec -it \
  pg-local createdb \
  -e PGPASSWORD=postgres \
  -U nordicmicroalgae \
  -E utf8 \
  -O nordicmicroalgae \
  -T template0 \
  nordicmicroalgae

Create configuration

Create a nordicmicroalgae/shared/config/environment.yaml file containing:

debug: true
secret_key: <REPLACE-WITH-SOMETHING-RANDOM>
allowed_hosts: localhost 127.0.0.1
database_name: nordicmicroalgae
database_user: nordicmicroalgae
database_password: <REPLACE-WITH-DATABASE-PASSWORD>

Setup Django application

Install uv by following instructions for your platform in the official documentation.

With uv, all python dependencies (including Python itself) is handled automatically when needed. Just make sure to run the app from within its directory (nordicmicroalgae/backend).

Setup and populate database:

uv run manage.py migrate
uv run manage.py importtaxa
uv run manage.py importsynonyms
uv run manage.py importfacts

Create Django admin superuser (optional):

uv run manage.py createsuperuser

Start the development server:

uv run manage.py runserver 5000

Open http://localhost:5000/api/ or http://localhost:5000/admin/

Development extras

The is a project configuration for pre-commit in the project root. This tool runs formatting and linting checks (using ruff) every time you commit but only if you activate it for this specific repository.

Activate pre-commit by running:

uv run pre-commit install

To commit without running checks (e.g. WIP commits):

git commit --no-verify