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