Endpoint to Download Clinical Data for Files

joneubank commented 9 months ago

Description of Changes

New endpoint added at POST /clinical/api/donors/data-for-files which accepts a list of File IDs and will return the clinical data for the Donor(s) associated with those files. The Gateway will perform several permission checks before requesting the required data from the Clinical API:

Requested files need to be listed as has_clinical_data in the file centric index.
User must have permission to download each of the requested files, Embargo rules are enforced.
User must have DACO access permission

The endpoint will return the download of a zip file containing all clinical entity TSVs relating to the donors for the requested files. This is the same TSV bundle that we generate for program data download for program submitters.

Type of Change

[ ] Bug
[x] New Feature

Breaking Changes

The existing clinical proxy endpoint URLs have been modified and will need to be updated where used in the platform UI. The paths used to be /clinical/{{path}} and need to be updated to be /clinical/proxy/{{path}}

joneubank commented 9 months ago

Converted to draft so that this doesn't get merged before the UI has changes made to acommodate breaking changes.

joneubank commented 9 months ago

Ready for review. Platform-UI relevant changes here: https://github.com/icgc-argo/platform-ui/pull/2715

icgc-argo / platform-api