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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.

Prerequisites

  • Docker
  • Docker Compose

Getting Started

Clone the Repository

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

Environment Variables

Create a .env file in the project root to override default environment variables if necessary. See .env.template file for more detail. Additionally, create elixir_daisy/settings_local.py file from elixir_daisy/settings_local.template.py.

Installation

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

Build the Solr Schema

Build the Solr schema required for full-text search:

docker compose exec web python manage.py build_solr_schema -c /solr/daisy/conf -r daisy -u default

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 web/static/vendor ci

Build Frontend Assets

docker compose exec web npm --prefix web/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://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/edda.json && \
    wget https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hpo.json && \
    wget https://git-r3lab.uni.lu/pinar.alper/metadata-tools/raw/master/metadata_tools/resources/hdo.json && \
    wget https://git-r3lab.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