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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)

Bases: object

__init__(raw_workflow_description, workflow, module_injector)

refactor(refactor_request: RefactorActions)

static normalize_input_connections_to_list(all_input_connections, input_name, add_if_missing=False)

galaxy.workflow.refactor.schema module

class galaxy.workflow.refactor.schema.StepReferenceByOrderIndex(*, order_index: int)

Bases: BaseModel

order_index: int

class galaxy.workflow.refactor.schema.StepReferenceByLabel(*, label: str)

Bases: BaseModel

label: str

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

Bases: StepReferenceByOrderIndex

input_name: str

class galaxy.workflow.refactor.schema.InputReferenceByLabel(*, label: str, input_name: str)

Bases: StepReferenceByLabel

input_name: str

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

Bases: StepReferenceByOrderIndex

output_name: Optional[str]

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

Bases: StepReferenceByLabel

output_name: Optional[str]

class galaxy.workflow.refactor.schema.Position(*, left: float, top: float)

Bases: BaseModel

left: float

top: float

to_dict()

class galaxy.workflow.refactor.schema.BaseAction

Bases: BaseModel

Refactoring actions.

class galaxy.workflow.refactor.schema.Action(*, action_type: str)

Bases: BaseAction

action_type: str

classmethod return_action(values)

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

Bases: BaseAction

action_type: typing_extensions.Literal[update_step_label]

label: str

step: Union[StepReferenceByOrderIndex, StepReferenceByLabel]

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

Bases: BaseAction

action_type: typing_extensions.Literal[update_step_position]

step: Union[StepReferenceByOrderIndex, StepReferenceByLabel]

position_shift: 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: Position = None)

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]

type: str

tool_state: Optional[Dict[str, Any]]

label: Optional[str]

position: Optional[Position]

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

Bases: BaseAction

action_type: typing_extensions.Literal[connect]

input: Union[InputReferenceByOrderIndex, InputReferenceByLabel]

output: Union[OutputReferenceByOrderIndex, OutputReferenceByLabel]

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

Bases: BaseAction

action_type: typing_extensions.Literal[disconnect]

input: Union[InputReferenceByOrderIndex, InputReferenceByLabel]

output: Union[OutputReferenceByOrderIndex, OutputReferenceByLabel]

class galaxy.workflow.refactor.schema.AddInputAction(*, action_type: typing_extensions.Literal[add_input], type: str, label: str = None, position: 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)

Bases: BaseAction

action_type: typing_extensions.Literal[add_input]

type: str

label: Optional[str]

position: Optional[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[InputReferenceByOrderIndex, InputReferenceByLabel], label: str = None, position: Position = None)

Bases: BaseAction

action_type: typing_extensions.Literal[extract_input]

input: Union[InputReferenceByOrderIndex, InputReferenceByLabel]

label: Optional[str]

position: Optional[Position]

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

Bases: BaseAction

action_type: typing_extensions.Literal[extract_untyped_parameter]

name: str

label: Optional[str]

position: Optional[Position]

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

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)

Bases: 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)

Bases: 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)

Bases: 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)

Bases: BaseAction

action_type: typing_extensions.Literal[update_creator]

creator: Any

class galaxy.workflow.refactor.schema.Report(*, markdown: str)

Bases: BaseModel

markdown: str

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

Bases: BaseAction

action_type: typing_extensions.Literal[update_report]

report: Report

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

Bases: BaseAction

action_type: typing_extensions.Literal[update_output_label]

output: Union[OutputReferenceByOrderIndex, OutputReferenceByLabel]

output_label: str

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

Bases: BaseAction

action_type: typing_extensions.Literal[fill_step_defaults]

step: Union[StepReferenceByOrderIndex, StepReferenceByLabel]

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

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: str = None)

Bases: BaseAction

action_type: typing_extensions.Literal[upgrade_subworkflow]

step: Union[StepReferenceByOrderIndex, StepReferenceByLabel]

content_id: Optional[str]

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

Bases: BaseAction

action_type: typing_extensions.Literal[upgrade_tool]

step: Union[StepReferenceByOrderIndex, StepReferenceByLabel]

tool_version: Optional[str]

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

Bases: BaseAction

action_type: typing_extensions.Literal[upgrade_all_steps]

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

Bases: BaseModel

actions: List[Action]

dry_run: bool

class galaxy.workflow.refactor.schema.RefactorActionExecutionMessageTypeEnum(value)

Bases: str, 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: 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)

Bases: BaseModel

message: str

message_type: 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: Action, messages: List[RefactorActionExecutionMessage])

Bases: BaseModel

action: Action

messages: List[RefactorActionExecutionMessage]

galaxy.workflow.refactor.schema.action_class

alias of RemoveUnlabeledWorkflowOutputs