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We should have some utilities to validate and re-cast to the target schema given they exist in functional forms. #37
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Here is a similar function for the data schema: https://github.com/mmcdermott/MEDS_transforms/blob/fd8ffccf7823bd957165d99a1a2aa5e97943fd0c/src/MEDS_transforms/extract/finalize_MEDS_data.py#L16 |
@EthanSteinberg, thoughts on this? If you think this would be useful, I'd be a proponent of bringing it over now rather than later. |
I agree, it would be useful to put these validation checks here. |
I think we want this validation code to use pyarrow though. I don't want to add another dependency (polars) to this repository |
I agree that we don't want to add a dependency and think the main validation code or re-typing code should be in pyarrow. I think we could consider having code that is only runnable if try:
import polars as pl
# validation code here...
except:
pass but I think starting with pyarrow would still be very helpful. |
Sample code for the label schema as well, in case it is helpful once we decide to implement this: https://github.com/justin13601/ACES/blob/e9655390f25bf79167370a802176bcf671cefa44/src/aces/__main__.py#L35 |
Some possibly related libraries: |
E.g., see this function: https://github.com/mmcdermott/MEDS_transforms/blob/573816cbf3f6005a8fc25eb25424706ca0c97b6e/src/MEDS_transforms/extract/finalize_MEDS_metadata.py#L28
This is polars specific, obviously, which we don't want to be, but having the ability to identify if a
codes.parquet
or adata/*.parquet
file meets a valid extended schema and converting to the right pyarrow schema is very useful (especially because there exist minor differences we should be cognizant of likelarge_string
vsstring
, etc.).Tagging @EthanSteinberg for your input.
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