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Management and administration

Access the Web Service

Shell into the web container:

docker compose exec web /bin/bash

Run Django Commands

Run Django management commands, e.g. makemigrations, migrate, createsuperuser, etc., using the web service:

docker compose exec web python manage.py <django-command>

See docker compose exec web python manage.py --help for all available commands.

Collect Static Files

docker compose exec web python manage.py collectstatic --noinput

Rebuild Solr Index

docker compose exec web python manage.py rebuild_index --noinput

Managing Other Services

PostgreSQL Database (db Service)

Access the Database Shell

docker compose exec db psql -U daisy -d

Execute SQL Commands

Run SQL commands directly:

docker compose exec db psql -U daisy -d daisy -c "SELECT * FROM user;"

Solr (solr Service)

Access Solr Admin Interface

Solr runs on port 8983. Access it via:

http://localhost:8983/solr/

RabbitMQ (mq Service)

Access RabbitMQ Management Interface

RabbitMQ management runs on port 15672. Access it via:

http://localhost:15672/
  • Username: guest
  • Password: guest

Celery Worker (worker Service)

Logs for the Celery worker can be viewed with:

docker compose logs -f worker

Celery Beat (beat Service)

Logs for Celery Beat can be viewed with:

docker compose logs -f beat

Flower Monitoring Tool (flower Service)

Access Flower for task monitoring on port 5555:

http://localhost:5555/

Administration

To access the admin interface:

  1. Create a Superuser Account:

    docker compose exec web python manage.py createsuperuser

  2. Access the Admin Site:

    http://localhost/admin/

    Log in with your superuser credentials.

Settings Reference

To get access to the admin page, you must log in with a superuser account.
On the Users section, you can give any user a staff status and he will be able to access any project/datasets.

local_settings.py reference

Display

Key Description Expected values Example value
COMPANY A name that is used to generate verbose names of some models str 'LCSB'
DEMO_MODE A flag which makes a simple banneer about demo mode appear in About page bool False
INSTANCE_LABEL A name that is used in navbar header to help differentiate different deployments str 'Staging test VM'
INSTANCE_PRIMARY_COLOR A color that will be navbar header's background str of a color '#076505'
LOGIN_USERNAME_PLACEHOLDER A helpful placeholder in login form for logins str '@uni.lu'
LOGIN_PASSWORD_PLACEHOLDER A helpful placeholder in login form for passwords str 'Hint: use your AD password'

Integration with other tools

ID Service
Key Description Expected values Example value
IDSERVICE_FUNCTION Path to a function (lambda: str) that generates IDs for entities which are published str 'web.views.utils.generate_elu_accession'
IDSERVICE_ENDPOINT In case LCSB's idservice function is being used, the setting contains the IDservice's URI str 'https://192.168.1.101/v1/api/
REMS
Key Description Expected values Example value
REMS_INTEGRATION_ENABLED A feature flag for REMS integration. In practice, there's a dedicated endpoint which processes the information from REMS about dataset entitlements str True
REMS_SKIP_IP_CHECK If set to True, there will be no IP checking if the request comes from trusted REMS instance. bool False
REMS_ALLOWED_IP_ADDRESSES A list of IP addresses that should be considered trusted REMS instances. Beware of configuration difficulties when using reverse proxies. The check can be skipped with REMS_SKIP_IP_CHECK dict[str] ['127.0.0.1', '192.168.1.101']
Keycloak
Key Description Expected values Example value
KEYCLOAK_INTEGRATION A feature flag for importing user information from Keycloak (OIDC IDs) bool True
KEYCLOAK_URL URL to the Keycloak instance str 'https://keycloak.lcsb.uni.lu/auth/'
KEYCLOAK_REALM_LOGIN Realm's login name in your Keycloak instance str 'master'
KEYCLOAK_REALM_ADMIN Realm's admin name in your Keycloak instance str 'master'
KEYCLOAK_USER Username to access Keycloak str 'username'
KEYCLOAK_PASS Password to access Keycloak str 'secure123'

Others

Key Description Expected values Example value
SERVER_SCHEME A URL's scheme to access your DAISY instance (http or https) str 'https'
SERVER_URL A URL to access your DAISY instance (without the scheme) str 'example.com'
GLOBAL_API_KEY An API key that is not connected with any user. Disabled if set to None optional[str] 'in-practice-you-dont-want-to-use-it-unless-debugging'

Additional Tips

  • Running Custom Commands: Use docker compose run for one-off commands without starting the entire service.

    Example:

    docker compose run --rm web python manage.py shell

  • Accessing Other Services: You can shell into other services similarly:

    docker compose exec db /bin/bash
docker compose exec solr /bin/bash

  • Environment Variables: Override environment variables when running commands:

    DB_NAME=custom_db docker compose up -d

Docker Compose Services Overview

  • web: Django application server using Gunicorn.
  • db: PostgreSQL database.
  • nginx: Reverse proxy and static file server.
  • solr: Apache Solr for full-text search.
  • mq: RabbitMQ message broker.
  • flower: Monitoring tool for Celery tasks.
  • worker: Celery worker for asynchronous tasks.
  • beat: Celery Beat scheduler.
  • backup: Manages database backups and restoration.

Logs and Monitoring

View Service Logs

View logs for a specific service:

docker compose logs -f <service_name>

Replace <service_name> with web, db, worker, etc.

Check Container Status

docker compose ps

Clean Up

Remove All Containers and Volumes

Stop containers and remove containers, networks, volumes, and images:

docker system prune -a
docker compose down -v --rmi all

Importing and Exporting Data

In addition to loading of initial data, DAISY database can be populated by importing Project, Dataset and Partners records from JSON files using commands import_projects, import_datasets and import_partners respectively. JSON files are validated using the Elixir-LU JSON schemas.

Import Data

You can import data from JSON files using Django management commands.

Import Projects

docker compose exec web python manage.py import_projects -f /path/to/projects.json

Import Datasets

docker compose exec web python manage.py import_datasets -f /path/to/datasets.json

Import Partners

docker compose exec web python manage.py import_partners -f /path/to/partners.json

To import multiple JSON files from a directory:

docker compose exec web python manage.py import_projects -d /path/to/directory/

Export Data

Information in the DAISY database can be exported to JSON files. The command for export are given below:

Export Projects

docker compose exec web python manage.py export_projects -f /path/to/output/projects.json

Export Datasets

docker compose exec web python manage.py export_datasets -f /path/to/output/datasets.json

Export Partners

docker compose exec web python manage.py export_partners -f /path/to/output/partners.json