DefaultModelStageImplementation

class VmaxBuilder.model.implementation.DefaultModelStageImplementation(translation_service: TranscriptMetadataServiceProtocol | None = None)

Generated: validation needed.

Description:

Validate model/loading configuration and resolve model input reference.

Raises:

ConfigurationError – When model resolution input is missing.

Modifies:

scaffold payload for model stage artifacts and metadata.

Public Methods

run(…)

Generated: validation needed.

run(scaffold: Scaffold, config: APIConfig) → Scaffold

Generated: validation needed.

Description:

Execute model-stage implementation and attach artifacts/metadata to scaffold.

Parameters:

• scaffold (Scaffold) – Shared pipeline scaffold.

• config (APIConfig) – Root API configuration.

Returns:

Scaffold – Updated scaffold with model-stage payload.

Raises:

ConfigurationError – When no model path or search roots are configured.

Modifies:

scaffold[“artifacts”] and scaffold[“metadata”].

_build_transcript_artifacts_for_model(*, model: Model, config: APIConfig) → dict[str, Any]

Generated: validation needed.

Description:

Build transcript metadata artifacts for model genes when transcript target level is requested.

Parameters:

• model (Model) – Irreversible cobra model.

• config (APIConfig) – Root API configuration.

Returns:

dict[str, Any] – Transcript metadata and mapping artifacts.

static _build_id_type_name(provider: str | None, level: str) → str | None

Generated: validation needed.

Description:

Build full identifier type name from provider and granularity level.

Parameters:

• provider (str | None) – Identifier provider value.

• level (str) – Gene/transcript level.

Returns:

str | None – Full identifier type name or None when provider missing.

_resolve_model_input(config: APIConfig, scaffold: Scaffold) → tuple[Model, dict[str, Any]]

Generated: validation needed.

Description:

Resolve model reference from explicit path or configured discovery roots.

Parameters:

• config (APIConfig) – Root API configuration.

• scaffold (Scaffold) – Shared pipeline scaffold.

Returns:

tuple[cobra.Model, dict[str, Any]] – Loaded model object and model reference metadata.

Raises:

ConfigurationError – When explicit path and discovery roots are both absent.

_resolve_model_file_path(model_path: Path, config: APIConfig) → Path

Generated: validation needed.

Description:

Resolve a model file path from file or directory input.

Parameters:

• model_path (Path) – Candidate model file or directory path.

• config (APIConfig) – Root API configuration.

Returns:

Path – Resolved model file path.

Raises:

ConfigurationError – When no supported model file can be resolved.

_load_model_from_path(model_path: Path) → Model

Generated: validation needed.

Description:

Load cobra model from path using extension-aware loader.

Parameters:

model_path (Path) – Model file path.

Returns:

cobra.Model – Loaded cobra model.

Raises:

ConfigurationError – When loaded object is not a cobra model.