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Backend architecture

The backend services (DDS and AMS) are built with Quarkus, a Kubernetes-native Java framework optimised for fast startup and low memory usage.

Project structure​

Key directories of the backend codebase include:

gdi-userportal-{service}/
├── src/main/java/
│   └── io/github/genomicdatainfrastructure/
│       ├── {service}/
│       │   ├── api/          # REST endpoint implementations
│       │   ├── model/        # Domain models and DTOs
│       │   ├── services/     # Business logic
│       │   ├── ports/        # Hexagonal architecture ports
│       │   └── adapters/     # External service adapters
│       └── Application.java  # Main application class
├── src/main/resources/
│   ├── application.properties
│   └── db/migration/         # Flyway database migrations
└── src/test/                 # Unit and integration tests

Key patterns​

The backend architecture follows established patterns for building maintainable and scalable Java applications:

Hexagonal architecture​

  • Ports: Interfaces defining business capabilities
  • Adapters: Implementations for external systems (CKAN, REMS, database)
  • Domain: Business logic independent of infrastructure

REST API design​

  • JAX-RS annotations for endpoints
  • DTOs for request/response mapping
  • OpenAPI/Swagger documentation

Dependency injection​

  • CDI (@Inject) for dependency management
  • @ApplicationScoped for singletons
  • @RequestScoped for per-request instances

Database access​

  • Hibernate Panache for ORM
  • Flyway for database migrations
  • Transactional boundaries with @Transactional