Ln/fhir2dataset postproc - Githubissues

arkhn / jpyltime

Wrapper of FHIR2Dataset with an API for Demoët

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Ln/fhir2dataset postproc #3

Closed naudinlo closed 3 years ago

naudinlo commented 3 years ago

Description

Full wrapper pipeline for FHIR2Dataset:

Check given attributes are valid
Filter on patient from a group id
Update given attributes with constraints on birthdate condition
Generate sql query based on attributes and constraints
// run api on generated sql query //
Apply transformation to the dataFrame

Preprocessing:

Adapt a list of attributes to generate a correct sql query to request the fhir api

Postprocessing:

Improve readibility and display of a given dataFrame, by:

Concatenated some columns, ex Value with Unit (| 30 | mg | => | 30 mg | )
Groupby one column to reduce redundancy
Anonymize sensitive data

clementjumel commented 3 years ago

Could you deal with the conflicts, @naudinlo ? 🙂 Just keep in mind that we don't want to output the table using pandas.to_json() anymore, we want to output an actual file, now (which is done on main but not on your branch) 😇