ifb-openlink 1.0.0

A dashboard that establish links between the structure of a research project and multiple data sources

OpenLink - A gateway for research data management plateform

OpenLink is a web application designed to provide the researcher with a clear view of the data associated with each research project. It reduces the barriers to adopting the FAIR principles and assists researchers in publishing data

OpenLink let's you create links between the structure of a research project described using the ISA model (Investigatio, Study, Assay) and multiple data sources. It supports an evolving collection of data sources including LabGuru, Omero, Seafile, SSH endpoints and Zenodo. It also embed features that facilitate data manipulation and assist researchers in publishing their data.

OpenLink has been developped within Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) at Strasbourg, France. The proof of concept has been funded by ANR in 2019 and since 2021, The French Institut of Bioinformatic (IFB) is funding OpenLink in order to make it a more mature product.

Openlink installation

This section describes the best way to install Openlink.

Openlink releases can be downloaded from Pypi or on GitLab

Requirements

Openlink requires Python 3.6 or later

Install openlink package

The recommended way of installing Openlink is via pip inside a virtual environment

python3 -m venv venv
source venv/bin/activate
pip install ifb-openlink

Initializing the Openlink database

OpenLink supports MariaDB/MySQL, PostgreSQL, and SQLite. See the complete guide on configuring Openlink for more details. By default, Openlink will use SQLite and create a database file in your current working directory.

After configuring your database of choice you must first initialize the Openlink database. This should only be done once:

openlink migrate

Add a superuser and start openlink server

Add a superuser account in your database by running the following command:

openlink createsuperuser

Start Redis Queue worker

Openlink is able to handle asynchronous tasks in the background using RQ workers. You can find documentation on installing a Redis server on the Redis website

Once Redis is installed and runnning, start OpenLink RQ worker with the following command:

python openlink rqworker default

Start Openlink server

Use runserver command to quickly start a developpement web server:

openlink runserver

OpenLink is now running.

Point your browser to http://localhost:8000 and login with the super user account you created.

License

OpenLink is released under the GPLv3 license. See the LICENSE file.