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FAIR Data Station

FAIR Data Station API

Usage

The recommended use is with Docker and Docker Compose and configuration via environment variables:

  fds:
    image: fairdata/fairdatastation:latest
    restart: unless-stopped
    # ports:
    #   - 127.0.0.1:8080:8080
    depends_on:
      - postgres
    # volumes:
    #   - ${PROJECT_ROOT}/application.fds.yml:/app/application.yml:ro
    environment:
      FDS_FDP_URL: http://fdp-client
      FDS_POSTGRES_DB: ${POSTGRES_DB}
      FDS_POSTGRES_USER: ${POSTGRES_USER}
      FDS_POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
      # FHIR endpoint (for FHIR Trains)
      FDS_FHIR_BASE_URL: ${FHIR_API_BASE}
      # Triple Store (for SPARQL Trains)
      FDS_TRIPLE_STORE_TYPE: 4
      FDS_TRIPLE_STORE_URL: ${GRAPHDB_URL}
      FDS_TRIPLE_STORE_REPOSITORY: ${GRAPHDB_DATA_REPO}
      FDS_TRIPLE_STORE_USERNAME: ${GRAPHDB_USERNAME}
      FDS_TRIPLE_STORE_PASSWORD: ${GRAPHDB_PASSWORD}

Development

For development, we highly recommend using IDE and run Maven commands or the Spring Boot application from it.

Technology Stack

  • Java (JDK 17)
  • PostgreSQL DB (13 or higher)
  • Maven (3.6 or higher)
  • Docker (20.10 or higher) - for building Docker image only

Build & Run

To run the application, a PostgreSQL DB is required to be running. To configure the standard connection suitable for development (postgresql://localhost/fds), simply instruct Spring Boot to use the dev profile:

$ mvn spring-boot:run -Dspring-boot.run.profiles=dev

Alternatively, create an application.yml file (or edit appropriate one) in the project root, and then run:

$ mvn spring-boot:run

Run tests

Run from the root of the project:

$ mvn test

Package the application

Run from the root of the project:

$ mvn package

Create a Docker image

Run from the root of the project (requires building jar file using mvn package as shown above):

$ docker build -t fairdatastation:local .

Note: Supplied Dockerfile is multistage and as such does not require Java nor Maven to be installed directly.

Contributing

We maintain a CHANGELOG, you should also take a look at our Contributing Guidelines and Security Policy.

License

This project is licensed under the MIT License - see the LICENSE file for more details.

Acknowledgments

This code is based on work contucted across a number of projects, in particular C4yourself (funder: Health Holland—Top Sector Life Sciences and Health, grant number: LSHM 21044_C4YOUR- SELF) and Personal Genetic Locker (funder: Nederlandse Organisa- tie voor Wetenschappelijk Onderzoek, grant number: 628.011.022).