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Commoning Biomedicine

Architecture

Requirements

  • Python 3.10 (optional, development should be done in the provided Docker environment)
  • Docker Desktop (or Docker Compose)

Build and run

Note: update the environment variables in env folder before running the following commands:

cd <project-folder>
docker-compose build
docker-compose up  # or "docker-compose up -d" to run in detached mode

Go to http://localhost:8081

Installation on a DigitalOcean Droplet and nginx (Optional)

Demo Architecture

If you don't have a DigitalOcean account yet, create one using my referral link.

  1. Create a Domain and add an A record pointing to your Droplet.
  2. Inside your Droplet, create an SSL certificate:
certbot --nginx -d <domain>
  1. Edit the nginx configuration (usually /etc/nginx/sites-available/default) and update the location / block just below the domain created by certbot (look for server_name <domain>; # managed by Certbot):
	location / {
            proxy_pass http://127.0.0.1:8081$request_uri;
            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
            proxy_set_header Host $http_host;
            proxy_set_header X-Forwarded-Proto $scheme;
            proxy_redirect off;
	}
  1. Reload nginx:
service nginx reload

Scaling

To scale up, add --scale web=N parameter. For example:

docker-compose up --scale web=3

Add translations

poetry run python manage.py makemessages -l <language_code>
# edit and translate locale/<language_code>/LC_MESSAGES/django.po

Development

Go in the web container by doing

docker exec -it combio_web bash

You can then run the following commands.

CSS / Tailwind

  1. python manage.py tailwind start - starts the tailwind watcher, which recompiles the css file on every change
  2. python manage.py collectstatic --no-input - creates the static files, necessary to update the css file used by the templates

Loading Dummy Test Data

  1. python manage.py loaddummydata - loads dummy test data

Elasticsearch Index update

  1. python manage.py search_index --rebuild - rebuilds the elasticsearch index

Create Superuser

  1. python manage.py createsuperuser - creates a super user, necessary to access the admin area at /admin

Make Commands

Use the Makefile included for running different development tasks:

  1. make install - installs the packages needed for development.
  2. make build - build application.
  3. make start - start application.
  4. make format - runs autoflake, isort and black for fixing coding style.
  5. make lint - runs autoflake, isort, black, flake8 and mypy checks.
  6. make test - run unit tests.
  7. make migrations - generate migration scripts, if applicable.
  8. make migrate - run migrations, if applicable.
  9. make superuser - create superuser.
  10. make messages - update messages.
  11. make compilemessages - compile messages.
  12. make dumpdata - backup data.
  13. make loaddata - load data from backup.