openBISmantic

Demonstrator of an Export Mechanism for openBIS Data to Semantic Data.

This Repository

This repository contains the openBISmantic API as well as a demonstrator openBIS istance filled with data from the LebeDigital project.

openBISmantic API

The openBISmantic API provices access to most entities in your openBIS instance as linked RDF. To do that, it defines persistent, resolvable IRIs using their Openbis permIds.

Setting Up the Demo Installation

pull repository

git clone https://github.com/Mat-O-Lab/OpenBISmantic.git
cd OpenBISmantic

create a .env file with

ADMIN_PASS=<adminpassw>
OBSERVER_PASS=<observerpassw>
HOST_NAME=<fqurlofhost> (e.g., openbis.matolab.org)
OPENBIS_PORT=<port> (e.g., 80)
OPENBIS_SSL_PORT=<port> (e.g., 443)
POSTGRES_PASSWORD=<postgrespassw>
GROUP_NAME=<groupname> (e.g., matolab)
GROUP_ID=<gid> (e.g., 12940)
OPENBISMANTIC_URL=<url> (e.g., https://openbis.matolab.org)

run server

docker compose up -d

This should set up the demo instance with example data. The openbismantic API is accessible on /openbismantic.

stop server and clean up

docker compose down
docker system prune --all

Running the openBISmantic API With an Existing Instance of Openbis

The openBISmantic API can be started on its own and connect to an existing Openbis instance. It is controlled with environmental variables.

Example:

OPENBIS_URL=https://openbis.iwm.fraunhofer.de \
BASE_URL=https://openbis.iwm.fraunhofer.de \
uvicorn app:app

Notes

data retention

The current configuration is intended to not support data retention. If required, please add to docker-compose.yml the following lines:

    openbis:
        ...
        volumes:
        - openbis_vol:/home/openbis/openbis_state
    
volumes:
    openbis_vol:
        name: openbis_vol