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galaxy.workflow.refactor package¶
Submodules¶
galaxy.workflow.refactor.execute module¶
galaxy.workflow.refactor.schema module¶
- class galaxy.workflow.refactor.schema.StepReferenceByOrderIndex(*, order_index: int)[source]¶
Bases:
BaseModel
- class galaxy.workflow.refactor.schema.InputReferenceByOrderIndex(*, order_index: int, input_name: str)[source]¶
Bases:
StepReferenceByOrderIndex
- class galaxy.workflow.refactor.schema.InputReferenceByLabel(*, label: str, input_name: str)[source]¶
Bases:
StepReferenceByLabel
- class galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex(*, order_index: int, output_name: Optional[str] = 'output')[source]¶
Bases:
StepReferenceByOrderIndex
- class galaxy.workflow.refactor.schema.OutputReferenceByLabel(*, label: str, output_name: Optional[str] = 'output')[source]¶
Bases:
StepReferenceByLabel
- class galaxy.workflow.refactor.schema.Position(*, left: float, top: float)[source]¶
Bases:
BaseModel
- class galaxy.workflow.refactor.schema.Action(*, action_type: str)[source]¶
Bases:
BaseAction
- class galaxy.workflow.refactor.schema.UpdateStepLabelAction(*, action_type: typing_extensions.Literal[update_step_label], label: str, step: Union[StepReferenceByOrderIndex, StepReferenceByLabel])[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_step_label]¶
- class galaxy.workflow.refactor.schema.UpdateStepPositionAction(*, action_type: typing_extensions.Literal[update_step_position], step: Union[StepReferenceByOrderIndex, StepReferenceByLabel], position_shift: Position)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_step_position]¶
- class galaxy.workflow.refactor.schema.AddStepAction(*, action_type: typing_extensions.Literal[add_step], type: str, tool_state: Optional[Dict[str, Any]] = None, label: Optional[str] = None, position: Optional[Position] = None)[source]¶
Bases:
BaseAction
Add a new action to the workflow.
After the workflow is updated, an order_index will be assigned and this step may cause other steps to have their output_index adjusted.
- action_type: typing_extensions.Literal[add_step]¶
- class galaxy.workflow.refactor.schema.ConnectAction(*, action_type: typing_extensions.Literal[connect], input: Union[InputReferenceByOrderIndex, InputReferenceByLabel], output: Union[OutputReferenceByOrderIndex, OutputReferenceByLabel])[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[connect]¶
- class galaxy.workflow.refactor.schema.DisconnectAction(*, action_type: typing_extensions.Literal[disconnect], input: Union[InputReferenceByOrderIndex, InputReferenceByLabel], output: Union[OutputReferenceByOrderIndex, OutputReferenceByLabel])[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[disconnect]¶
- class galaxy.workflow.refactor.schema.AddInputAction(*, action_type: typing_extensions.Literal[add_input], type: str, label: Optional[str] = None, position: Optional[Position] = None, collection_type: Optional[str] = None, restrictions: Optional[List[str]] = None, restrict_on_connections: Optional[bool] = None, suggestions: Optional[List[str]] = None, optional: Optional[bool] = False, default: Optional[Any] = None)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[add_input]¶
- class galaxy.workflow.refactor.schema.ExtractInputAction(*, action_type: typing_extensions.Literal[extract_input], input: Union[InputReferenceByOrderIndex, InputReferenceByLabel], label: Optional[str] = None, position: Optional[Position] = None)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[extract_input]¶
- class galaxy.workflow.refactor.schema.ExtractUntypedParameter(*, action_type: typing_extensions.Literal[extract_untyped_parameter], name: str, label: Optional[str] = None, position: Optional[Position] = None)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[extract_untyped_parameter]¶
- class galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs(*, action_type: typing_extensions.Literal[remove_unlabeled_workflow_outputs])[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[remove_unlabeled_workflow_outputs]¶
- class galaxy.workflow.refactor.schema.UpdateNameAction(*, action_type: typing_extensions.Literal[update_name], name: str)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_name]¶
- class galaxy.workflow.refactor.schema.UpdateAnnotationAction(*, action_type: typing_extensions.Literal[update_annotation], annotation: str)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_annotation]¶
- class galaxy.workflow.refactor.schema.UpdateLicenseAction(*, action_type: typing_extensions.Literal[update_license], license: str)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_license]¶
- class galaxy.workflow.refactor.schema.UpdateCreatorAction(*, action_type: typing_extensions.Literal[update_creator], creator: Any = None)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_creator]¶
- class galaxy.workflow.refactor.schema.UpdateReportAction(*, action_type: typing_extensions.Literal[update_report], report: Report)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_report]¶
- class galaxy.workflow.refactor.schema.UpdateOutputLabelAction(*, action_type: typing_extensions.Literal[update_output_label], output: Union[OutputReferenceByOrderIndex, OutputReferenceByLabel], output_label: str)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[update_output_label]¶
- class galaxy.workflow.refactor.schema.FillStepDefaultsAction(*, action_type: typing_extensions.Literal[fill_step_defaults], step: Union[StepReferenceByOrderIndex, StepReferenceByLabel])[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[fill_step_defaults]¶
- class galaxy.workflow.refactor.schema.FileDefaultsAction(*, action_type: typing_extensions.Literal[fill_defaults])[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[fill_defaults]¶
- class galaxy.workflow.refactor.schema.UpgradeSubworkflowAction(*, action_type: typing_extensions.Literal[upgrade_subworkflow], step: Union[StepReferenceByOrderIndex, StepReferenceByLabel], content_id: Optional[str] = None)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[upgrade_subworkflow]¶
- class galaxy.workflow.refactor.schema.UpgradeToolAction(*, action_type: typing_extensions.Literal[upgrade_tool], step: Union[StepReferenceByOrderIndex, StepReferenceByLabel], tool_version: Optional[str] = None)[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[upgrade_tool]¶
- class galaxy.workflow.refactor.schema.UpgradeAllStepsAction(*, action_type: typing_extensions.Literal[upgrade_all_steps])[source]¶
Bases:
BaseAction
- action_type: typing_extensions.Literal[upgrade_all_steps]¶
- class galaxy.workflow.refactor.schema.RefactorActions(*, actions: List[Action], dry_run: bool = False)[source]¶
Bases:
BaseModel
- class galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum(value)[source]¶
-
An enumeration.
- tool_version_change = 'tool_version_change'¶
- tool_state_adjustment = 'tool_state_adjustment'¶
- connection_drop_forced = 'connection_drop_forced'¶
- workflow_output_drop_forced = 'workflow_output_drop_forced'¶
- class galaxy.workflow.refactor.schema.RefactorActionExecutionMessage(*, message: str, message_type: RefactorActionExecutionMessageTypeEnum, step_label: Optional[str] = None, order_index: Optional[int] = None, input_name: Optional[str] = None, output_name: Optional[str] = None, from_step_label: Optional[str] = None, from_order_index: Optional[int] = None, output_label: Optional[str] = None)[source]¶
Bases:
BaseModel
- message_type: RefactorActionExecutionMessageTypeEnum¶
- class galaxy.workflow.refactor.schema.RefactorActionExecution(*, action: Action, messages: List[RefactorActionExecutionMessage])[source]¶
Bases:
BaseModel
- messages: List[RefactorActionExecutionMessage]¶
- galaxy.workflow.refactor.schema.action_class¶
alias of
RemoveUnlabeledWorkflowOutputs