disallowed extra fields in models, and updated ingest and export code to handle these #127
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| def filter_model_dictionary(dictionary: dict, target_model: Type[BaseModel]): |
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I wonder whether this has utility beyond just the export code, and would be better off as a utils in the shared_models package. Thoughts?
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- Are you referring to
persistorfilter_model_dictionary - Do you mean 'import code' in comment above? It seems both
importandexportusepersist- So having it in a common place sounds good. However, I assumeexportis only reading data models so will not need the filter functionality (but will need the persisting).
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filter_model_dictionary
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i meant import. But the export could use it with slightly different data models (e.g. the study model for export is the study model + dataset model + biosample, protocols, Image Acquisitions etc.) so having a filter model dictionary method might be helpful.
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For persist - While both might want to write out to files, it feels like the directory/file structure might be very different for the export and ingest code, so i don't know how reusable the methods would be. Additionally, the functions related to filtering models makes sense to store in the model package since it's related and is going to be imported by both, but it's less obvious where we should put the persisting.
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| def filter_model_dictionary(dictionary: dict, target_model: Type[BaseModel]): |
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Nice workaround for the filter!
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| def get_test_specimen_growth_protocol() -> List[bia_data_model.ImageAcquisition]: |
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This whole method was just a duplicate, so i removed it.
See: https://app.clickup.com/t/86956q84r
Also updated website export code to use input that are at least as complex as the BIA data models (i.e. with the various api fields), since it will make using the clients easier.