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Accessing metadata through a data view using Ocarina
2020-09-07 16:00:00 +0000
2021-08-11 15:01:00 +0000
samstudio8, BioWilko
samstudio8, BioWilko

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:

  • Ocarina will give you a link to the Majora website and then wait for you to provide more information. Open the link in your browser.
  • The link will ask you to authorise the Ocarina application. Carefully check that the permissions and the owner of the application seem sensible.
  • Once authorised, the Majora website will refresh to show a "Application authorized" message. DO NOT CLOSE THE PAGE.
  • Copy the ENTIRE URL from your browser window (including https://) and paste it to your command line window.
  • Ocarina will use the link you have provided to request an access token on your behalf, and request the data view.
  • It may take a little while for your data to be ready, Ocarina will check every minute with the message: [WAIT] Giving Majora a minute to finish task.
  • When your data is ready, it will be saved to whatever output file you specify with -o.
  • If you are requesting restricted data, it is your responsibility to protect it. Save it somewhere secure. Do not save it to a location that is group or world readable.

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