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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]¶: Initialize self. See help(type(self)) for accurate signature.

refactor(refactor_request: galaxy.workflow.refactor.schema.RefactorActions)[source]¶

static normalize_input_connections_to_list(all_input_connections, input_name, add_if_missing=False)[source]¶

galaxy.workflow.refactor.schema module¶

class galaxy.workflow.refactor.schema.StepReferenceByOrderIndex(*, order_index: int)[source]¶

Bases: pydantic.main.BaseModel

order_index: int¶

class galaxy.workflow.refactor.schema.StepReferenceByLabel(*, label: str)[source]¶

Bases: pydantic.main.BaseModel

label: str¶

class galaxy.workflow.refactor.schema.InputReferenceByOrderIndex(*, order_index: int, input_name: str)[source]¶

Bases: galaxy.workflow.refactor.schema.StepReferenceByOrderIndex

input_name: str¶

class galaxy.workflow.refactor.schema.InputReferenceByLabel(*, label: str, input_name: str)[source]¶

Bases: galaxy.workflow.refactor.schema.StepReferenceByLabel

input_name: str¶

class galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex(*, order_index: int, output_name: str = 'output')[source]¶

Bases: galaxy.workflow.refactor.schema.StepReferenceByOrderIndex

output_name: Optional[str]¶

class galaxy.workflow.refactor.schema.OutputReferenceByLabel(*, label: str, output_name: str = 'output')[source]¶

Bases: galaxy.workflow.refactor.schema.StepReferenceByLabel

output_name: Optional[str]¶

class galaxy.workflow.refactor.schema.Position(*, left: float, top: float)[source]¶

Bases: pydantic.main.BaseModel

left: float¶

top: float¶

to_dict()[source]¶

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

Bases: pydantic.main.BaseModel

Refactoring actions.

class galaxy.workflow.refactor.schema.Action(*, action_type: str)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: str¶

classmethod return_action(values)[source]¶

class galaxy.workflow.refactor.schema.UpdateStepLabelAction(*, action_type: typing_extensions.Literal[update_step_label], label: str, step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel])[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_step_label]¶

label: str¶

step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel]¶

class galaxy.workflow.refactor.schema.UpdateStepPositionAction(*, action_type: typing_extensions.Literal[update_step_position], step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel], position: galaxy.workflow.refactor.schema.Position)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_step_position]¶

step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel]¶

position: galaxy.workflow.refactor.schema.Position¶

class galaxy.workflow.refactor.schema.AddStepAction(*, action_type: typing_extensions.Literal[add_step], type: str, tool_state: Dict[str, Any] = None, label: str = None, position: galaxy.workflow.refactor.schema.Position = None)[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.

action_type: typing_extensions.Literal[add_step]¶

type: str¶

tool_state: Optional[Dict[str, Any]]¶

label: Optional[str]¶

position: Optional[galaxy.workflow.refactor.schema.Position]¶

class galaxy.workflow.refactor.schema.ConnectAction(*, action_type: typing_extensions.Literal[connect], input: Union[galaxy.workflow.refactor.schema.InputReferenceByOrderIndex, galaxy.workflow.refactor.schema.InputReferenceByLabel], output: Union[galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex, galaxy.workflow.refactor.schema.OutputReferenceByLabel])[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[connect]¶

input: Union[galaxy.workflow.refactor.schema.InputReferenceByOrderIndex, galaxy.workflow.refactor.schema.InputReferenceByLabel]¶

output: Union[galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex, galaxy.workflow.refactor.schema.OutputReferenceByLabel]¶

class galaxy.workflow.refactor.schema.DisconnectAction(*, action_type: typing_extensions.Literal[disconnect], input: Union[galaxy.workflow.refactor.schema.InputReferenceByOrderIndex, galaxy.workflow.refactor.schema.InputReferenceByLabel], output: Union[galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex, galaxy.workflow.refactor.schema.OutputReferenceByLabel])[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[disconnect]¶

input: Union[galaxy.workflow.refactor.schema.InputReferenceByOrderIndex, galaxy.workflow.refactor.schema.InputReferenceByLabel]¶

output: Union[galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex, galaxy.workflow.refactor.schema.OutputReferenceByLabel]¶

class galaxy.workflow.refactor.schema.AddInputAction(*, action_type: typing_extensions.Literal[add_input], type: str, label: str = None, position: galaxy.workflow.refactor.schema.Position = None, collection_type: str = None, restrictions: List[str] = None, restrict_on_connections: bool = None, suggestions: List[str] = None, optional: bool = False, default: Any = None)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[add_input]¶

type: str¶

label: Optional[str]¶

position: Optional[galaxy.workflow.refactor.schema.Position]¶

collection_type: Optional[str]¶

restrictions: Optional[List[str]]¶

restrict_on_connections: Optional[bool]¶

suggestions: Optional[List[str]]¶

optional: Optional[bool]¶

default: Optional[Any]¶

class galaxy.workflow.refactor.schema.ExtractInputAction(*, action_type: typing_extensions.Literal[extract_input], input: Union[galaxy.workflow.refactor.schema.InputReferenceByOrderIndex, galaxy.workflow.refactor.schema.InputReferenceByLabel], label: str = None, position: galaxy.workflow.refactor.schema.Position = None)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[extract_input]¶

input: Union[galaxy.workflow.refactor.schema.InputReferenceByOrderIndex, galaxy.workflow.refactor.schema.InputReferenceByLabel]¶

label: Optional[str]¶

position: Optional[galaxy.workflow.refactor.schema.Position]¶

class galaxy.workflow.refactor.schema.ExtractUntypedParameter(*, action_type: typing_extensions.Literal[extract_untyped_parameter], name: str, label: str = None, position: galaxy.workflow.refactor.schema.Position = None)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[extract_untyped_parameter]¶

name: str¶

label: Optional[str]¶

position: Optional[galaxy.workflow.refactor.schema.Position]¶

class galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs(*, action_type: typing_extensions.Literal[remove_unlabeled_workflow_outputs])[source]¶

Bases: galaxy.workflow.refactor.schema.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: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_name]¶

name: str¶

class galaxy.workflow.refactor.schema.UpdateAnnotationAction(*, action_type: typing_extensions.Literal[update_annotation], annotation: str)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_annotation]¶

annotation: str¶

class galaxy.workflow.refactor.schema.UpdateLicenseAction(*, action_type: typing_extensions.Literal[update_license], license: str)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_license]¶

license: str¶

class galaxy.workflow.refactor.schema.UpdateCreatorAction(*, action_type: typing_extensions.Literal[update_creator], creator: Any = None)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_creator]¶

creator: Any¶

class galaxy.workflow.refactor.schema.Report(*, markdown: str)[source]¶

Bases: pydantic.main.BaseModel

markdown: str¶

class galaxy.workflow.refactor.schema.UpdateReportAction(*, action_type: typing_extensions.Literal[update_report], report: galaxy.workflow.refactor.schema.Report)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_report]¶

report: galaxy.workflow.refactor.schema.Report¶

class galaxy.workflow.refactor.schema.UpdateOutputLabelAction(*, action_type: typing_extensions.Literal[update_output_label], output: Union[galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex, galaxy.workflow.refactor.schema.OutputReferenceByLabel], output_label: str)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[update_output_label]¶

output: Union[galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex, galaxy.workflow.refactor.schema.OutputReferenceByLabel]¶

output_label: str¶

class galaxy.workflow.refactor.schema.FillStepDefaultsAction(*, action_type: typing_extensions.Literal[fill_step_defaults], step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel])[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[fill_step_defaults]¶

step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel]¶

class galaxy.workflow.refactor.schema.FileDefaultsAction(*, action_type: typing_extensions.Literal[fill_defaults])[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[fill_defaults]¶

class galaxy.workflow.refactor.schema.UpgradeSubworkflowAction(*, action_type: typing_extensions.Literal[upgrade_subworkflow], step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel], content_id: str = None)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[upgrade_subworkflow]¶

step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel]¶

content_id: Optional[str]¶

class galaxy.workflow.refactor.schema.UpgradeToolAction(*, action_type: typing_extensions.Literal[upgrade_tool], step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel], tool_version: str = None)[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[upgrade_tool]¶

step: Union[galaxy.workflow.refactor.schema.StepReferenceByOrderIndex, galaxy.workflow.refactor.schema.StepReferenceByLabel]¶

tool_version: Optional[str]¶

class galaxy.workflow.refactor.schema.UpgradeAllStepsAction(*, action_type: typing_extensions.Literal[upgrade_all_steps])[source]¶

Bases: galaxy.workflow.refactor.schema.BaseAction

action_type: typing_extensions.Literal[upgrade_all_steps]¶

class galaxy.workflow.refactor.schema.RefactorActions(*, actions: List[galaxy.workflow.refactor.schema.Action], dry_run: bool = False)[source]¶

Bases: pydantic.main.BaseModel

actions: List[galaxy.workflow.refactor.schema.Action]¶

dry_run: bool¶

class galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum(value)[source]¶

Bases: str, enum.Enum

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: galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum, step_label: str = None, order_index: int = None, input_name: str = None, output_name: str = None, from_step_label: str = None, from_order_index: int = None, output_label: str = None)[source]¶

Bases: pydantic.main.BaseModel

message: str¶

message_type: galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum¶

step_label: Optional[str]¶

order_index: Optional[int]¶

input_name: Optional[str]¶

output_name: Optional[str]¶

from_step_label: Optional[str]¶

from_order_index: Optional[int]¶

output_label: Optional[str]¶

class galaxy.workflow.refactor.schema.RefactorActionExecution(*, action: galaxy.workflow.refactor.schema.Action, messages: List[galaxy.workflow.refactor.schema.RefactorActionExecutionMessage])[source]¶

Bases: pydantic.main.BaseModel

action: galaxy.workflow.refactor.schema.Action¶

messages: List[galaxy.workflow.refactor.schema.RefactorActionExecutionMessage]¶

galaxy.workflow.refactor.schema.action_class¶: alias of galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs