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TheAxonLab / hcph-sops

SOPs of the HCPh project
https://www.axonlab.org/hcph-sops/
Creative Commons Attribution 4.0 International
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ENH: Data management improvements in wave 2 collection #502

Open oesteban opened 3 months ago

oesteban commented 3 months ago

Just FYI @celprov, so that you can check how to automatically generate PRs out of data. The new script add_session.sh does the following:

  1. Takes the path of the DICOM folder downloaded from PACs, and extracts the session code (this is why it is important that the correct 'participant id' is encoded when registering a new patient).
  2. Updates the git/git-annex with datalad update and branches into a clean branch called `add/
  3. Runs HeuDiConv, based off of the script/parameters we had for wave 1
  4. Clean up spurious files added by HeuDiConv and adds the new files to the annex.
  5. Pushes to github and to ria-storage. The push to ria-storage is critical: this is when data are uploaded into curnagl
  6. Creates a PR with the GitHub CLI tool <-- DON'T MISS THIS, this will be useful in the future to automate stuff and look like a real geek where you work.
  7. Compact the DICOMS into a tarball and clean up the uncompressed data (critical to save space on curnagl).

I'm opening it as a draft for now, as I want to improve the documentation.