proteobench.validation.context module#
Validation context passed to every check.
A ValidationContext bundles all inputs a check might need behind a
single, uniform object so that every check has the signature
check(ctx) -> list[ValidationIssue]. This decouples individual checks from
the orchestrator and from each other: a new check can read whatever it needs
from the context without changing any call site.
The context carries the concrete inputs available today (standardized
DataFrame, parsed parameters, reference FASTA, module config, selected tool)
plus a generic reference slot and an extras dict so future module types
can supply their own reference data (for example a de novo ground-truth table)
without changing the context shape.
- class proteobench.validation.context.ValidationContext(standard_df: DataFrame, parameters: Any = None, config: ModuleValidationConfig = <factory>, fasta: FastaReference | None = None, input_format: str | None = None, reference: Any = None, extras: Dict[str, ~typing.Any]=<factory>)[source]#
Bases:
objectInputs available to a validation check.
- standard_df#
The standardized result DataFrame produced by the module parser.
- Type:
- parameters#
Parsed parameters (a
ProteoBenchParametersor any object with the same attributes).Nonewhen no parameter file was provided.- Type:
Any, optional
- config#
Module validation configuration (column names, flags, FASTA location, resolved profile).
- Type:
- fasta#
Reference protein identifiers, for profiles that validate against a sequence database.
Nonewhen unavailable or not applicable.- Type:
FastaReference, optional
- reference#
Generic reference object for profiles whose reference is not a FASTA (for example a de novo ground-truth table).
Nonewhen unused.- Type:
Any, optional
- config: ModuleValidationConfig#
- fasta: FastaReference | None = None#