APIConfig

class VmaxBuilder.config.dataclasses.APIConfig(trimming: MValueTrimmingConfig = <factory>, run_target_transcript_gene_level: str = 'gene', model: ModelConfig = <factory>, expression: ExpressionInputConfig = <factory>, transcript_processing: TranscriptProcessingConfig = <factory>, ptr: PTRInputConfig = <factory>, proteomics: ProteomicsInputConfig = <factory>, protein: ProteinConfig = <factory>, allocation: AllocationConfig = <factory>, vmax: VmaxConfig = <factory>, metadata: dict[str, ~typing.Any]=<factory>)[source]

Generated: validation needed.

Description:

Root configuration container for orchestrator, validation, loading, and stage config.

Parameters:

  • validation (ValidationPolicy) – Validation policy for config and stage inputs.

  • loading (LoadingPolicy) – File/path loading policy.

  • run_target_transcript_gene_level (str) – Target analysis granularity, transcript or gene.

  • transcript_processing (TranscriptProcessingConfig) – Transcript processing options for aggregation and transcript metadata retrieval.

  • model (ModelConfig) – Model stage configuration.

  • expression (ExpressionInputConfig) – Expression input option group.

  • ptr (PTRInputConfig) – PTR input option group.

  • proteomics (ProteomicsInputConfig) – Proteomics input option group.

  • protein (ProteinConfig) – Protein stage configuration.

  • allocation (AllocationConfig) – Allocation stage configuration.

  • vmax (VmaxConfig) – Vmax stage configuration.

  • metadata (dict[str, Any]) – Arbitrary run metadata.

Public Methods

get_stage_config(…)

Generated: validation needed.

resolve_trimming_implementation(…)

Resolve trimming implementation and expected trimming-config class.

trimming

run_target_transcript_gene_level

model

expression

transcript_processing

ptr

proteomics

protein

allocation

vmax

metadata

resolve_trimming_implementation() → tuple[type, type | None][source]

Resolve trimming implementation and expected trimming-config class.

Returns:

tuple[type, type|None] – (implementation class, trimming-config class or None)

Behavior:

  • Look up implementation FQCN from allocation.trim_assesment_method.

  • Import implementation class dynamically.

  • Read implementation attributejjjjjjjjj CONFIG_CLASS if present to indicate which trimming config class pairs with implementation.

Raises:

  • ValueError – When method unknown or allocation.trim_assesment_method empty.

  • ImportError / AttributeError – If module/class cannot be imported.

get_stage_config(stage_name: StageName) → ModelConfig | ProteinConfig | AllocationConfig | VmaxConfig[source]

Generated: validation needed.

Description:

Return stage configuration object for one top-level stage.

Parameters:

stage_name (StageName) – Stage name to resolve.

Returns:

StageConfig – Requested stage configuration object.

Raises:

ValueError – If stage name is unknown.