Neurobagel can search IDPs

[surchs]

Context

Rolling out nipoppy to collaborators

Why

• So we can find IDPs

Outcomes

• The Neurobagel data model understands IDPs
• A user who has used Nipoppy to generate IDPs can tell Neurobagel about them with no additional manual tasks (other than running tools)
• A user can search for subjects processed with a given pipeline and version
• There exists a list (vocabulary) of standardized pipeline names that nipoppy knows about (each with their known version names)

What

Nipoppy:

• Create or get examples of the nipoppy imaging bagel format for testing
• Get a copy of the imaging bagel validation schema from Nipoppy
• Create vocabulary repo with one file per pipeline

Neurobagel:

• Update examples with pipeline metadata neurobagel_examples#33
• Make CLI understand pipeline metadata bagel-cli#342
• Rename custom session created when no session level exists bagel-cli#262
• Allow querying for pipeline name and version api#341
• nb_vocab.ttl file is missing classes in current data model recipes#88
• Create new endpoint to return pipeline vers. for specific pipeline name for query tool api#344
• Allow querying for pipeline name and version federation-api#113
• Create new endpoint to return pipeline vers. for specific pipeline name for query tool federation-api#117
• Allow querying for pipeline name and version query-tool#282
• Document derivatives command for bagel-cli documentation#230
• Re-release:
  • f-API
  • n-API
  • query tool
  • CLI
• Use Nipoppy schema to validate proc status TSV for bagel derivatives command bagel-cli#352

[alyssadai]

Closing as all key issues have been addressed; we will address neurobagel/bagel-cli#352 separately as it is currently blocked by neurobagel/bagel-cli#180.