ejp-rd-vp/fdp-populator

Populate FDP with content via github actions

FAIR Data Point Populator

Introduction

The FAIR Data Point Populator was created to help people not very familiar with FAIR, to create metadata in Excel sheets, and have these published in a FAIR Data Point (https://www.fairdatapoint.org/). The FAIR Data Point Populator is a GitHub workflow, that reads the metadata from the repository, transforms this into RDF, and then publishes this on a FAIR Data Point.

Set up

• If there is no FAIR Data Point yet, set one up locally (https://fairdatapoint.readthedocs.io/en/latest/deployment/local-deployment.html) or online (https://fairdatapoint.readthedocs.io/en/latest/deployment/production-deployment.html).
• Make a metadata repository like https://github.com/LUMC-BioSemantics/ejprd-wp13-metadata, for example, by cloning it. This repository is connected to the FAIR Data Point Populator GitHub repository.
• Connect the metadata repository to a FAIR Data Point by setting the following GitHub secrets in the metadata repository.
  • FDP URL (URL of the FAIR Data Point)
  • FDP Persistant URL (Persistant URL of the FAIR Data Point if available (e.g. w3id), URL of the FAIR Data Point otherwise.)
  • Username (username in the FAIR Data Point)
  • password (password in the FAIR Data Point)

Set up alternative

Alternatively, this Jupyter notebook can be used. This still requires a FAIR Data Point to be available.

Use

• The user fills in the FPD or EJP RD template.
• The user uploads the template to the metadata repository (or hands it over to the administrator for the administrator to upload).
• The administrator checks the metadata, and in the case of the FDP template, extracts a datasets.csv and distributions.csv file.
• The administrator sets the target metadata and target catalog in the config.yml file (see the config file for an example), and starts the workflow using the start workflow button.
• The FDPP converts the metadata from the Excel sheet into RDF documents.
• The FDPP publishes the RDF into the connected FAIR Data Point.

EJP RD

The EJP RD version of this tool requires special configuration of the FAIR Data Point, following the EJP RD metadata schema.