bioimage-io / collection-bioimage-io

(deprecated in favor of bioimage-io/collection) RDF collection for BioImage.IO
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Current models in collection seem to fail valitation using spec validator 0.4.9post5 #701

Closed jmetz closed 8 months ago

jmetz commented 8 months ago

Suggest cleaning empty fields on the spec validator side, so that eg empty email strings are deleted and returned to the client after calling validation.

Will close this issue here and raise on spec repo.

Original Issue

Am adding what are hopefully the finishing touches to the uploader, but still get validation failure, even on a model I just downloaded from the zoo.

The failure on this model is related to maintainer-email being missing:

Plugin BIO-RDF-Validator_gxhiy1706013343072: Validation results: {'bioimageio_spec_version': '0.4.9post5', 'error': {'maintainers': {0: {'email': ['Not a valid email address.']}}}, 'name': 'bioimageio.spec static validation of  RDF ', 'nested_errors': {}, 'source_name': '{name: NucleiSegmentationBoundaryModel, ...}', 'status': 'failed', 'traceback': None, 'warnings': {'tags': "could not check tag categories (No module named 'requests')"}}

The spec version used in the validation plugin is 0.4.9post5, and the model used for testing is the nucleisegmentationboundarymodel, ie https://bioimage.io/#/?id=10.5281%2Fzenodo.5764892

Are there plans to update the zenodo models to make them compliant?

jmetz commented 8 months ago

Opps, never mind, this is the same issue I've been facing with other fields - my front-end code currently sets fields to empty strings... so I'm having to delete empty-string fields as a cleaning step.

Ideally I'd suggest this could perhaps just be automated on the spec side... otherwise all clients would have to do this cleaning (where necessary) .