View the Project on GitHub COG-UK/docs

Updated 2021-08-11 by @samstudio8, BioWilko

Accessing metadata through a data view using Ocarina

0. Set up Ocarina

Follow these instructions to set up Ocarina for the first time

1. Acquire permission to access a data view

A data view is basically a list of metadata fields. If you are granted access to a data view, you can see all of the fields covered by that data view. Every data view is associated with a short name, which we sometimes call a code or Majora data view code (mdv code).

Guidance on how to obtain access to a view is in progress, check back after the consortium agreement has been distributed. This document has been written ahead of time and we are not currently granting permissions to any restricted views. Do not attempt to contact anyone to arrange access at this time.

Once this has been set up, you are ready to retrieve data.

2. Use Ocarina to request the data from the view

ocarina --oauth get dataview --mdv CODE --task-wait --output-table -o my_data.tsv

Replace CODE with the appropriate data view name. Ocarina will reject your request if you attempt to access a data view you do not have permission to view. Use the command exactly as stated (do not skip providing --task-wait) for ease of use.

When you submit this command, you will need to authenticate yourself through the following process:

This is an experimental feature and can change at any time. Please visit #metadata-apis if you have questions or trouble.

Published 2020-09-07. Updated 2021-08-11. Page maintainer @samstudio8, BioWilko.