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:

Create a Superuser Account:

docker compose exec web python manage.py createsuperuser

Access the Admin Site:
```
http://localhost/admin/
```
Log in with your superuser credentials.

Settings Reference¶

DAISY loads configuration from .env.{ENVIRONMENT} files. Use the interactive script to generate a production or staging config:

./scripts/create_env.sh

Environment Variables Reference¶

Core Settings¶

Defaults work for development; production requires explicit configuration.

Key	Description	Required for Production	Default value
`ENVIRONMENT`	Environment name (development, production, test)	No	`'development'`
`SECRET_KEY`	Django secret key for cryptographic signing	Yes	None
`GLOBAL_API_KEY`	API authentication key	Yes	None
`DATABASE_URL`	PostgreSQL connection string	Yes	`'postgresql://daisy:daisy@db:5432/daisy'`
`CELERY_BROKER_URL`	RabbitMQ message broker URL	Yes	`'amqp://guest:guest@mq:5672//'`
`SOLR_URL`	Solr search engine URL	Yes	`'http://solr:8983/solr/daisy'`
`SOLR_URL_TEST`	Solr test core URL	No	`'http://solr:8983/solr/daisy_test'`
`SOLR_ADMIN_URL`	Solr admin interface URL	Yes	`'http://solr:8983/solr/admin/cores'`
`ALLOWED_HOSTS`	Comma-separated list of allowed hostnames	Yes	`'*'`
`CSRF_TRUSTED_ORIGINS`	Comma-separated list of trusted origins (with scheme)	Yes	`[]`

Display Settings¶

Key	Description	Expected values	Default value
`COMPANY`	Company/organization name used in verbose model names	str	`'LCSB'`
`DEMO_MODE`	Show demo mode banner on About page	bool	`False`
`INSTANCE_LABEL`	Label shown in navbar to differentiate deployments	str	`None`
`INSTANCE_PRIMARY_COLOR`	Navbar background color	str (color)	`None`
`LOGIN_USERNAME_PLACEHOLDER`	Placeholder text in login form username field	str	`''`
`LOGIN_PASSWORD_PLACEHOLDER`	Placeholder text in login form password field	str	`''`

Integration with other tools¶

ID Service¶

Key	Description	Expected values	Default value
`IDSERVICE_FUNCTION`	Path to function that generates IDs for published entities	str	`'web.views.utils.generate_elu_accession'`
`IDSERVICE_ENDPOINT`	ID service endpoint URL (if using LCSB's idservice)	str	`None`

REMS (Resource Entitlement Management System)¶

Key	Description	Expected values	Default value
`REMS_INTEGRATION_ENABLED`	Enable REMS integration for dataset entitlements	bool	`False`
`REMS_URL`	REMS instance URL (required if enabled)	str	Required when enabled
`REMS_API_USER`	REMS API username (required if enabled)	str	Required when enabled
`REMS_API_KEY`	REMS API key (required if enabled)	str	Required when enabled
`REMS_VERIFY_SSL`	Verify SSL certificates for REMS connections	bool	`True`
`REMS_SKIP_IP_CHECK`	Skip IP address validation for REMS requests	bool	`False`
`REMS_ALLOWED_IP_ADDRESSES`	Comma-separated list of trusted REMS IP addresses	str	`''`

Keycloak¶

Key	Description	Expected values	Default value
`KEYCLOAK_INTEGRATION`	Enable Keycloak user synchronization	bool	`False`
`KEYCLOAK_URL`	Keycloak instance URL (required if enabled)	str	Required when enabled
`KEYCLOAK_REALM_LOGIN`	Keycloak login realm name	str	`'testing'`
`KEYCLOAK_REALM_ADMIN`	Keycloak admin realm name	str	`'testing'`
`KEYCLOAK_USER`	Keycloak admin username (required if enabled)	str	Required when enabled
`KEYCLOAK_PASS`	Keycloak admin password (required if enabled)	str	Required when enabled

OIDC (OpenID Connect)¶

Key	Description	Expected values	Default value
`OIDC_ENABLED`	Enable OIDC authentication	bool	`False`
`OIDC_CLIENT_ID`	OIDC client ID (required if enabled)	str	Required when enabled
`OIDC_CLIENT_SECRET`	OIDC client secret (required if enabled)	str	Required when enabled
`OIDC_METADATA_URL`	OIDC metadata URL (required if enabled)	str	Required when enabled

LDAP¶

Key	Description	Expected values	Default value
`LDAP_ENABLED`	Enable LDAP authentication	bool	`False`
`AUTH_LDAP_SERVER_URI`	LDAP server URI (required if enabled)	str	Required when enabled
`AUTH_LDAP_BIND_DN`	LDAP bind DN	str	`None`
`AUTH_LDAP_BIND_PASSWORD`	LDAP bind password (required if enabled)	str	Required when enabled

See .env.example for a complete list of all available configuration options.

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