galaxy.workflow.refactor package

Submodules

galaxy.workflow.refactor.execute module

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

Bases: object

__init__(raw_workflow_description, workflow, module_injector: WorkflowModuleInjector)[source]

refactor(refactor_request: 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: BaseModel

order_index: int

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseModel

label: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: StepReferenceByOrderIndex

input_name: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: StepReferenceByLabel

input_name: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class galaxy.workflow.refactor.schema.OutputReferenceByOrderIndex(*, order_index: int, output_name: str | None = 'output')[source]

Bases: StepReferenceByOrderIndex

output_name: str | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class galaxy.workflow.refactor.schema.OutputReferenceByLabel(*, label: str, output_name: str | None = 'output')[source]

Bases: StepReferenceByLabel

output_name: str | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseModel

left: float

top: float

to_dict()[source]

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseModel

Refactoring actions.

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: str

classmethod return_action(values)[source]

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[update_step_label]

label: str

step: StepReferenceByOrderIndex | StepReferenceByLabel

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[update_step_position]

step: StepReferenceByOrderIndex | StepReferenceByLabel

position_shift: Position

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

type: str

tool_state: Dict[str, Any] | None

label: str | None

position: Position | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[connect]

input: InputReferenceByOrderIndex | InputReferenceByLabel

output: OutputReferenceByOrderIndex | OutputReferenceByLabel

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[disconnect]

input: InputReferenceByOrderIndex | InputReferenceByLabel

output: OutputReferenceByOrderIndex | OutputReferenceByLabel

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

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 | None

default: Any | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[extract_input]

input: InputReferenceByOrderIndex | InputReferenceByLabel

label: str | None

position: Position | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[extract_untyped_parameter]

name: str

label: str | None

position: Position | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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]

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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]

name: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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]

annotation: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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]

license: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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]

creator: Any

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseModel

markdown: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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]

report: Report

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[update_output_label]

output: OutputReferenceByOrderIndex | OutputReferenceByLabel

output_label: str

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[fill_step_defaults]

step: StepReferenceByOrderIndex | StepReferenceByLabel

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[fill_defaults]

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[upgrade_subworkflow]

step: StepReferenceByOrderIndex | StepReferenceByLabel

content_id: str | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

Bases: BaseAction

action_type: typing_extensions.Literal[upgrade_tool]

step: StepReferenceByOrderIndex | StepReferenceByLabel

tool_version: str | None

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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]

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

Bases: BaseModel

actions: List[Annotated[AddInputAction | AddStepAction | ConnectAction | DisconnectAction | ExtractInputAction | ExtractUntypedParameter | FileDefaultsAction | FillStepDefaultsAction | UpdateAnnotationAction | UpdateCreatorAction | UpdateNameAction | UpdateLicenseAction | UpdateOutputLabelAction | UpdateReportAction | UpdateStepLabelAction | UpdateStepPositionAction | UpgradeSubworkflowAction | UpgradeToolAction | UpgradeAllStepsAction | RemoveUnlabeledWorkflowOutputs, FieldInfo(annotation=NoneType, required=True, discriminator='action_type')]]

dry_run: bool

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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

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 = None, order_index: int | None = None, input_name: str | None = None, output_name: str | None = None, from_step_label: str | None = None, from_order_index: int | None = None, output_label: str | None = None)[source]

Bases: BaseModel

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

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

Bases: BaseModel

messages: List[RefactorActionExecutionMessage]

model_config: ClassVar[ConfigDict] = {}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

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