Is there an existing issue for this?
Expected behavior
This happened on the Donders2 (PPP) dataset. There is something wrong with the .jsonld file. I would expect init_data to catch this but to then also produce a helpful error message
Current behavior
I am getting a massive log of each validation error, and they all look like this:
2026-01-20 14:09:53 INFO (2/2) Processing file: Donders2_deriv.filtered.jsonld
2026-01-20 14:09:53 WARNING Donders2_deriv.filtered.jsonld is not a valid Neurobagel dataset JSONLD. Skipping file.
Validation errors: 8179 validation errors for Dataset
hasSamples.0.hasSession.3.PhenotypicSession.schemaKey
Input should be 'PhenotypicSession' [type=literal_error, input_value='ImagingSession', input_type=str]
For further information visit https://errors.pydantic.dev/2.12/v/literal_error
hasSamples.0.hasSession.3.ImagingSession.hasAcquisition.7.hasContrastType
Field required [type=missing, input_value={'identifier': 'nb:5d58b7...hemaKey': 'Acquisition'}, input_type=dict]
For further information visit https://errors.pydantic.dev/2.12/v/missing
hasSamples.0.hasSession.3.ImagingSession.hasAcquisition.8.hasContrastType
...
Error message
2026-01-20 14:09:53 INFO Dataset metadata successfully extracted from 1/2 JSONLD file(s); will upload the file(s) to the graph store.
2026-01-20 14:09:53 WARNING The following 1 JSONLD file(s) failed validation and will not be uploaded:
Donders2_deriv.filtered.jsonld
Environment
prod deployment with docker compose
How to reproduce
No response
Anything else?
No response
Is there an existing issue for this?
Expected behavior
This happened on the Donders2 (PPP) dataset. There is something wrong with the .jsonld file. I would expect init_data to catch this but to then also produce a helpful error message
Current behavior
I am getting a massive log of each validation error, and they all look like this:
Error message
Environment
prod deployment with docker compose
How to reproduce
No response
Anything else?
No response