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LInk to the project: https://github.com/virtual-imaging-platform/Complementary-tools

The Complementary Tools project provides the link between VIP and Zenodo.

What is Zenodo?

Zenodo is an open-access research data repository. It allows researchers from around the world to deposit, preserve, and share their research outputs.

Zenodo documentation: https://help.zenodo.org/

VIP + Zenodo

Zenodo serves as the final destination. Once your computations are completed on the VIP server, the uploader takes over to:

• Transform raw results into a scientific publication
• Attach metadata (title, author, etc.) to the files
• Make results reproducible and accessible to the community

Project Structure

The project is divided into two main parts:

• Replayer: Used to rerun computations on VIP from existing configuration files
• Uploader: Used to archive the results of these computations on Zenodo.

Command to run:

python uploader.py config.ini summary.json --v

Prerequisites + Two usage scenarios: https://github.com/virtual-imaging-platform/VIP-portal/blob/master/vip-application/src/main/resources/repro_vip.md

Using the uploader script:

• You need to create a configuration file (see example in the repository). This requires a Zenodo account with an API key.
• You need to retrieve the “summary” file generated by the portal (it should be located in /vip/reproVip/ with the corresponding execution ID).
• Run the Python script uploader.py.

Using the replayer script:

• A VIP API key is required, as well as a Girder API key if the data is stored on Girder (and not locally).
• You need to retrieve the descriptor and inputs files contained in the Zenodo archive.
• If the data was stored locally (and not on Girder), the script execution will prompt you to download the data and place it in the specified location.