Daisy Project Setup Guide¶

This guide provides concise instructions for setting up and running the Daisy project using Docker Compose. It includes commands for managing the Django application and other services within the project.

Info

For legacy deployment (<1.8.1), please refer to the Legacy deployment and administration manual.

Prerequisites¶

Docker
Docker Compose

Getting Started¶

Clone the Repository¶

git clone https://github.com/elixir-luxembourg/daisy.git
cd daisy

Environment Configuration¶

DAISY loads configuration from .env.{ENVIRONMENT} files (default: .env.development).

For production or staging, generate a secure configuration:

./scripts/create_env.sh

Then start services with:

docker compose up -d

See administration.md for all available settings.

Installation¶

Configure Nginx¶

Copy the Nginx configuration template:

cp ./docker/nginx/nginx.conf.template ./docker/nginx/nginx.conf

Customize nginx.conf as needed and then start or restart the Nginx service:

docker compose restart nginx

Build and Start Services¶

Build and start all services defined in docker-compose.yaml:

docker compose up -d --build

Initialize the Database¶

Run database migrations:

docker compose exec web python manage.py migrate

Initialize Solr Search Index¶

Solr uses a managed schema (fields are created from the Django search indexes). Ensure Solr is running, then build the index.

docker compose up -d solr
curl -s "http://localhost:8983/solr/admin/cores?action=STATUS&wt=json" | jq .
curl -s "http://localhost:8983/solr/daisy/schema/fields?wt=json" | jq .
docker compose exec web python manage.py rebuild_index --noinput

Replace host/port or drop | jq . if jq is not available.

Compile and Deploy Static Files¶

The project uses frontend assets that need to be compiled (e.g., with npm), you need to build them and collect static files.

Install npm Dependencies¶

docker compose exec web npm --prefix /static/vendor ci

Build Frontend Assets¶

docker compose exec web npm --prefix /static/vendor run build

Collect Static Files¶

From the project root:

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

Load Initial Data into the Database¶

Load initial data, such as controlled vocabularies and initial list of institutions and cohorts.

docker compose exec web bash -c "
    cd core/fixtures/ && \
    wget https://gitlab.lcsb.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/edda.json && \
    wget https://gitlab.lcsb.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hpo.json && \
    wget https://gitlab.lcsb.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hdo.json && \
    wget https://gitlab.lcsb.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hgnc.json
"
docker compose exec web python manage.py load_initial_data

Note: This step can take several minutes to complete.

Load Demo Data (Optional)¶

In case you are provisioning a demo instance, following command loads demo data, including mock datasets, projects, and a demo admin account:

docker compose exec web python manage.py load_demo_data

You can log in with the demo admin credentials provided during the demo data setup (username: admin, password:admin by default) or as one of the regular users (see the About page for more detail).

Build the Search Index¶

After loading data, build the search index for Solr:

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

Access the Application¶

The application should now be accessible on https://localhost/

Scheduled Backup with Cron¶

To ensure the backups are properly set up, please refer to the Backup manual

Restore Legacy Backup¶

To restore from a legacy backup file (e.g., daisy_prod.tar.gz):

docker compose stop nginx flower worker beat web mq solr

# Copy the legacy backup file into the backup container
docker cp ../daisy_prod.tar.gz $(docker compose ps -q backup):/code/daisy_prod.tar.gz

# Execute the legacy restore script inside the backup container
docker compose exec backup sh /code/scripts/legacy_restore.sh /code/daisy_prod.tar.gz

# Remove the backup file from the container
docker compose exec backup rm /code/daisy_prod.tar.gz

docker compose up -d solr mq web worker beat flower nginx

# Rebuild the Solr index
docker compose exec web python manage.py rebuild_index --noinput