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Publishing metadata in FDP using SeMPyRO

Publishing metadata in FDP using SeMPyRO

Owned by Kees Burger
Last updated: Dec 09, 2024
4 min read

Intro

This guide will describe the process of publishing an example metadata set using SeMPyRO to a FAIR Data Point. The Publishing metadata in FDP using SeMPyRO | Video guide will show the process from beginning to end, while the Publishing metadata in FDP using SeMPyRO | Step by step guide will highlight key steps in the process.

Video guide

The video below will run through the process of creating and publising metadata using SeMPyRO. The prerequisites for the environment demonstrated in the video are described in the Publishing metadata in FDP using SeMPyRO | Setup below.

sempyro-step-by-step.mov
Screen recording of executing the SeMPyRO notebook.

Step-by-step guide

Stepping through the prerequisites and running the notebook to publish metadata.

Setup

This guide assumes a (local) FDP is installed, configured with the v1.0.0 shapes (available at https://github.com/Health-RI/health-ri-metadata/tree/v1.0.0/Formalisation(shacl)/Core/PiecesShape).

The jupyter notebook from the SeMPyRO repository runs the steps to create and publish core metadata, specifically using the https://github.com/Health-RI/SeMPyRO/blob/main/docs/Usage_example_FDP_HealthRI_core.ipynb notebook.

You can run the notebook in your preferred way. As an example, you can run the notebook using Hatch - Hatch:

  • Clone the SeMPyRO repository

  • Navigate to the docs folder

  • Use hatch to run the notebook: hatch run docs:jupyter lab

  • Navigate to localhost:8888

Executing the notebook

Stepping through the cells in the notebook, some cells will print output (like urls/identifiers of metadata published) or require user input. The cells of note are addressed below.

Cell [2] asks for input on the FDP address. In the example steps, the local FDP on the default port is used, so the value entered is http://localhost/.

image-20241209-104416.png

Cell [3] asks for input on the FDP username. The default admin user on the local FDP is used, so the value entered is albert.einstein@example.com.

Cell [4] asks for input on the FDP password. The default admin user credentials are used.

Cell [5] publishes the catalog defined in cell [2] to the local FDP. When successful, the notebook prints the address of the newly created catalog.

The notebook prints an underlying urllib3 warning about the SSL libraries being used. Usually this warning can be ignored.

When the FDP landing page is refreshed, the catalog should now be visible.

Navigating to the catalog, it should display the catalog’s metadata. Note the dataset is still empty.

Cell [7] publishes the dataset defined in cell [6]. When succesul, the notebook prints the address of the newly created dataset.

When the catalog is refreshed, the dataset should now be visible.

Navigating to the dataset, it should display the dataset’s metadata. Note the distribution is still empty.

cell [9] publishes the distribution defined in cell [8]. When successful, the notebook prints the address of the newly created distribution.

When the dataset is refreshed, the distribution should now be visible.

Navigating to the distribution, it should display the distribution’s metadata.