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galaxy.workflow.refactor package

Submodules

galaxy.workflow.refactor.execute module

class galaxy.workflow.refactor.execute.WorkflowRefactorExecutor(raw_workflow_description, workflow, module_injector)[source]

Bases: object

__init__(raw_workflow_description, workflow, module_injector)[source]
static normalize_input_connections_to_list(all_input_connections, input_name, add_if_missing=False)[source]
refactor(refactor_request: galaxy.workflow.refactor.schema.RefactorActions)[source]

galaxy.workflow.refactor.schema module

class galaxy.workflow.refactor.schema.Action[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

classmethod return_action(values)[source]
class galaxy.workflow.refactor.schema.AddInputAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.AddStepAction[source]

Bases: galaxy.workflow.refactor.schema.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.

class galaxy.workflow.refactor.schema.BaseAction[source]

Bases: pydantic.main.BaseModel

Refactoring actions.

class galaxy.workflow.refactor.schema.ConnectAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.DisconnectAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.ExtractInputAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.ExtractUntypedParameter[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.FileDefaultsAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.FillStepDefaultsAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.InputReferenceByLabel[source]

Bases: galaxy.workflow.refactor.schema.StepReferenceByLabel

class galaxy.workflow.refactor.schema.InputReferenceByOrderIndex[source]

Bases: galaxy.workflow.refactor.schema.StepReferenceByOrderIndex

class galaxy.workflow.refactor.schema.OutputReferenceByLabel[source]

Bases: galaxy.workflow.refactor.schema.StepReferenceByLabel

class galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex[source]

Bases: galaxy.workflow.refactor.schema.StepReferenceByOrderIndex

class galaxy.workflow.refactor.schema.Position[source]

Bases: pydantic.main.BaseModel

to_dict()[source]
class galaxy.workflow.refactor.schema.RefactorActionExecution[source]

Bases: pydantic.main.BaseModel

class galaxy.workflow.refactor.schema.RefactorActionExecutionMessage[source]

Bases: pydantic.main.BaseModel

class galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum[source]

Bases: str, enum.Enum

An enumeration.

connection_drop_forced = 'connection_drop_forced'
tool_state_adjustment = 'tool_state_adjustment'
tool_version_change = 'tool_version_change'
workflow_output_drop_forced = 'workflow_output_drop_forced'
class galaxy.workflow.refactor.schema.RefactorActions[source]

Bases: pydantic.main.BaseModel

class galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.Report[source]

Bases: pydantic.main.BaseModel

class galaxy.workflow.refactor.schema.StepReferenceByLabel[source]

Bases: pydantic.main.BaseModel

class galaxy.workflow.refactor.schema.StepReferenceByOrderIndex[source]

Bases: pydantic.main.BaseModel

class galaxy.workflow.refactor.schema.UpdateAnnotationAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpdateCreatorAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpdateLicenseAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpdateNameAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpdateOutputLabelAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpdateReportAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpdateStepLabelAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpdateStepPositionAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpgradeAllStepsAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpgradeSubworkflowAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

class galaxy.workflow.refactor.schema.UpgradeToolAction[source]

Bases: galaxy.workflow.refactor.schema.BaseAction

galaxy.workflow.refactor.schema.action_class

alias of galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs