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Fix/use #51

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Fix/use #51

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@teslajoy teslajoy commented Nov 7, 2024

Added minor changes needed to pass HAPI FHIR testing for GDC data.
Added cli g3t validation.
Updated Cellosaurus based on current learning context on mintids, and age extension for Patient.

@teslajoy teslajoy requested a review from bwalsh December 4, 2024 16:19
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teslajoy commented Dec 5, 2024

@bwalsh re-writing GDC. hold on to the review.

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teslajoy commented Dec 5, 2024

noted this new criterion

1 validation error for DocumentReference
content.0.attachment.size
Input should be less than or equal to 2147483647 [type=less_than_equal, input_value=107991595707, input_type=int]
For further information visit https://errors.pydantic.dev/2.10/v/less_than_equal

for bioinformatics files like this bems file the size is ~107GB where the new content.0.attachment.size limit is now 2GB

converting size from bytes to MB to surpass 2GB min file-size in (Pydantic 2.10 - FHIR 8.0.0 requirement)
alternatively it could be placed the file size in Observation focus -> DocumentReference

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teslajoy commented Dec 6, 2024

@bwalsh it's ready for another review. what worries me about this new version:

  1. serialization issues. Noted the types are converted to str. tried to cast to int for example, but the model_dum() function seems to have some new serialization features.
fhirizer/venv/lib/python3.13/site-packages/fhir_core/fhirabstractmodel.py:427: UserWarning: Pydantic serializer warnings:
    Expected `Observation` but got `dict` with value `{'reference': 'Observatio...5b1d-a199-a07cc2adaa7c'}` - serialized value may not be as expected
    return serialize(value)

Passes g3t validation.

  1. The DocumentReference.content.[0].attachment.size now has a 2GB limit. I converted all the file sizes to MB for now.

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