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config

Config for the biomarker_tabulation step (v2).

v1's fields plus rename_columns. The version exists primarily for the task signature — v2 additionally consumes the lesion_calculation cache and, optionally, criteria_matching's evaluations — and rename_columns is the one config addition those new inputs demand (the eligibility failure-reason text is baked during tabulation, so it needs the display map before csv_report runs). Re-exporting v1's class would tie the two versions' schemas together for as long as both are supported.

Classes​

BiomarkerTabulationConfig​

class BiomarkerTabulationConfig(**data: Any):

Config selecting which biomarker columns land in the CSV report.

The biomarker filter operates on the TECHNICAL (internal) column names; display renaming happens downstream in the csv_report step. The one exception is the eligibility failure-reason text, which is baked during tabulation (before csv_report renames anything) and so needs the display map here — see rename_columns.

Arguments

  • biomarker_groups: Biomarker group names to include (empty ⇒ all groups).
  • biomarker_names: Individual technical column names to include (empty ⇒ none beyond the selected groups).
  • rename_columns: Display-name map used only for the eligibility failure-reason strings, so the projected reasons match the CSV report's display columns. Has no effect on the biomarker column selection, which stays technical.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Variables​

  • static biomarker_groups : list[str]
  • static biomarker_names : list[str]
  • static model_config
  • static rename_columns : dict[str, str]