Add new sub-command for bagel-CLI derivatives:

[surchs]

• Inputs:
  • imaging bagel TSV from Nipoppy or TSV with same columns
    • add check that subject ID column has no missing values
  • JSONLD from bagel pheno command, OR pheno + bids command
    • Do we need a sanity check here that the file does not already contain derivative info?
  • output file path
  • override flag
• Command should
  • Validate input columns from the bagel file against the Nipoppy bagel schema
  • Check that pipeline names and versions are part of allowed terms
  • Check that all subject IDs from the derivatives TSV are represented in the existing JSONLD, otherwise error
  • If there are imaging sessions in the JSONLD, try to match them to sessions from the derivatives TSV
  • If there are new sessions in the derivatives TSV, create new imaging sessions
  • If a session ID is missing, create a new imaging session with a custom session label
  • Extract pipeline names for a given subject-session entry in the bagel TSV, and also the completion status

[neurobagel-bot]

🚀 Issue was released in v0.3.0 🚀