OSTREA

Oyster Spatio-Temporal Dispersal Atlas - Visualization of simulated oyster larval dispersal connectivity in the North Sea.

Quick Start

Docker Compose (Recommended for Local Development)

Clone and enter the repository:

git clone https://github.com/geomar-od-lagrange/2024_hex_dashboard.git
cd 2024_hex_dashboard

Create environment file from example:

cp .env.example .env

Build and run (database auto-initializes):

docker compose build
docker compose up

Open http://localhost:5173/ in your browser.

Kubernetes (kind)

The Helm chart supports vanilla Kubernetes using kind. An nginx proxy handles /api routing.

kind create cluster --name ostrea
docker compose build
kind load docker-image ostrea-api:latest ostrea-frontend:latest ostrea-db-init:latest --name ostrea
kubectl create namespace ostrea
kubectl create secret generic db-secret \
  --from-literal=POSTGRES_USER=user \
  --from-literal=POSTGRES_PASSWORD=$(openssl rand -base64 24) \
  --from-literal=POSTGRES_DB=db \
  -n ostrea
helm template ostrea ./helm/ostrea --namespace ostrea | kubectl apply --namespace ostrea -f -
kubectl port-forward -n ostrea svc/nginx 5173:8080

Open http://localhost:5173/

For detailed instructions, see docs/kind-deployment-test.md.

Kubernetes (OpenShift)

The Helm chart also supports OpenShift clusters using Routes for ingress (--set openshift=true).

kubectl create namespace ostrea
kubectl create secret generic db-secret \
  --from-literal=POSTGRES_USER=user \
  --from-literal=POSTGRES_PASSWORD=$(openssl rand -base64 24) \
  --from-literal=POSTGRES_DB=db \
  -n ostrea
helm template ostrea ./helm/ostrea --namespace ostrea \
  --set openshift=true \
  --set registry=<registry>/ \
  | kubectl apply --namespace ostrea -f -

For local OpenShift testing with MicroShift, see docs/microshift-deployment-test.md.

Project Structure

.
├── api/                    # Node.js/Express API server
├── database/
│   ├── data/               # Processed data (parquet, geojson, json)
│   │   └── source/         # Original data + processing notebook
│   ├── init/               # Database init container
│   └── src/hex_db_loader/  # Python data loading package
├── frontend/               # React + deck.gl + MapLibre frontend
├── helm/ostrea/            # Helm chart for Kubernetes/OpenShift
├── images/                 # Screenshots
├── security/               # CVE scan results
├── volumes/                # Docker volumes (gitignored)
├── .env                    # Environment variables (gitignored)
├── .env.example            # Environment template
└── docker-compose.yml

Development

Prerequisites

• Docker (via Docker Desktop or CLI)
• pixi (for Python development in database/)

Running Locally

Foreground mode with live logs (Ctrl+C to stop):

docker compose up

Background mode:

docker compose up -d
docker compose logs -f
docker compose down
docker compose down -v  # also removes volumes

Database Loaders

The database initializes automatically. For manual data loading:

cd database
pixi run python -m hex_db_loader.connectivity
pixi run python -m hex_db_loader.geojson
pixi run python -m hex_db_loader.metadata

License

MIT License. See LICENSE.

Contributors

• Willi Rath (@willirath)
• Ingmar Eissfeldt (@IngmarEissfeldt)
• Felix Kirch (@felixkirch)
• Lara Schmittmann (@laraschmittmann)