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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'order_index': FieldInfo(annotation=int, required=True, description='The order_index of the step being referenced. The order indices of a workflow start at 0.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: BaseModel

label: str

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'label': FieldInfo(annotation=str, required=True, description='The unique label of the step being referenced.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: StepReferenceByOrderIndex

input_name: str

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'input_name': FieldInfo(annotation=str, required=True, description="The input name as defined by the workflow module corresponding to the step being referenced. For Galaxy tool steps these inputs should be normalized using '|' (e.g. 'cond|repeat_0|input')."), 'order_index': FieldInfo(annotation=int, required=True, description='The order_index of the step being referenced. The order indices of a workflow start at 0.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: StepReferenceByLabel

input_name: str

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'input_name': FieldInfo(annotation=str, required=True, description="The input name as defined by the workflow module corresponding to the step being referenced. For Galaxy tool steps these inputs should be normalized using '|' (e.g. 'cond|repeat_0|input')."), 'label': FieldInfo(annotation=str, required=True, description='The unique label of the step being referenced.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: StepReferenceByOrderIndex

output_name: str | None

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'order_index': FieldInfo(annotation=int, required=True, description='The order_index of the step being referenced. The order indices of a workflow start at 0.'), 'output_name': FieldInfo(annotation=Union[str, NoneType], required=False, default='output', description="The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.")}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: StepReferenceByLabel

output_name: str | None

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'label': FieldInfo(annotation=str, required=True, description='The unique label of the step being referenced.'), 'output_name': FieldInfo(annotation=Union[str, NoneType], required=False, default='output', description="The output name as defined by the workflow module corresponding to the step being referenced. The default is 'output', corresponding to the output defined by input step types.")}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: BaseModel

left: float

top: float

to_dict()[source]

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'left': FieldInfo(annotation=float, required=True), 'top': FieldInfo(annotation=float, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: BaseModel

Refactoring actions.

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: BaseAction

action_type: str

classmethod return_action(values)[source]

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_step_label'], required=True), 'label': FieldInfo(annotation=str, required=True, description='The unique label of the step being referenced.'), 'step': FieldInfo(annotation=Union[StepReferenceByOrderIndex, StepReferenceByLabel], required=True, description='The target step for this action.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_step_position'], required=True), 'position_shift': FieldInfo(annotation=Position, required=True), 'step': FieldInfo(annotation=Union[StepReferenceByOrderIndex, StepReferenceByLabel], required=True, description='The target step for this action.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['add_step'], required=True), 'label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='A unique label for the step being added, must be distinct from the labels already present in the workflow.'), 'position': FieldInfo(annotation=Union[Position, NoneType], required=False, default=None, description='The location of the step in the Galaxy workflow editor.'), 'tool_state': FieldInfo(annotation=Union[Dict[str, Any], NoneType], required=False, default=None), 'type': FieldInfo(annotation=str, required=True, description='Module type of the step to add, see galaxy.workflow.modules for available types.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['connect'], required=True), 'input': FieldInfo(annotation=Union[InputReferenceByOrderIndex, InputReferenceByLabel], required=True), 'output': FieldInfo(annotation=Union[OutputReferenceByOrderIndex, OutputReferenceByLabel], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['disconnect'], required=True), 'input': FieldInfo(annotation=Union[InputReferenceByOrderIndex, InputReferenceByLabel], required=True), 'output': FieldInfo(annotation=Union[OutputReferenceByOrderIndex, OutputReferenceByLabel], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['add_input'], required=True), 'collection_type': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'default': FieldInfo(annotation=Union[Any, NoneType], required=False, default=None), 'label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'optional': FieldInfo(annotation=Union[bool, NoneType], required=False, default=False), 'position': FieldInfo(annotation=Union[Position, NoneType], required=False, default=None), 'restrict_on_connections': FieldInfo(annotation=Union[bool, NoneType], required=False, default=None), 'restrictions': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None), 'suggestions': FieldInfo(annotation=Union[List[str], NoneType], required=False, default=None), 'type': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['extract_input'], required=True), 'input': FieldInfo(annotation=Union[InputReferenceByOrderIndex, InputReferenceByLabel], required=True), 'label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'position': FieldInfo(annotation=Union[Position, NoneType], required=False, default=None)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['extract_untyped_parameter'], required=True), 'label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'name': FieldInfo(annotation=str, required=True), 'position': FieldInfo(annotation=Union[Position, NoneType], required=False, default=None)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['remove_unlabeled_workflow_outputs'], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_name'], required=True), 'name': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_annotation'], required=True), 'annotation': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_license'], required=True), 'license': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_creator'], required=True), 'creator': FieldInfo(annotation=Any, required=False, default=None)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: BaseModel

markdown: str

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'markdown': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_report'], required=True), 'report': FieldInfo(annotation=Report, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['update_output_label'], required=True), 'output': FieldInfo(annotation=Union[OutputReferenceByOrderIndex, OutputReferenceByLabel], required=True), 'output_label': FieldInfo(annotation=str, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['fill_step_defaults'], required=True), 'step': FieldInfo(annotation=Union[StepReferenceByOrderIndex, StepReferenceByLabel], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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

Bases: BaseAction

action_type: typing_extensions.Literal[fill_defaults]

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['fill_defaults'], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['upgrade_subworkflow'], required=True), 'content_id': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'step': FieldInfo(annotation=Union[StepReferenceByOrderIndex, StepReferenceByLabel], required=True, description='The target step for this action.')}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['upgrade_tool'], required=True), 'step': FieldInfo(annotation=Union[StepReferenceByOrderIndex, StepReferenceByLabel], required=True, description='The target step for this action.'), 'tool_version': FieldInfo(annotation=Union[str, NoneType], required=False, default=None)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action_type': FieldInfo(annotation=Literal['upgrade_all_steps'], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

Bases: BaseModel

actions: List[AddInputAction | galaxy.workflow.refactor.schema.AddStepAction | galaxy.workflow.refactor.schema.ConnectAction | galaxy.workflow.refactor.schema.DisconnectAction | galaxy.workflow.refactor.schema.ExtractInputAction | galaxy.workflow.refactor.schema.ExtractUntypedParameter | galaxy.workflow.refactor.schema.FileDefaultsAction | galaxy.workflow.refactor.schema.FillStepDefaultsAction | galaxy.workflow.refactor.schema.UpdateAnnotationAction | galaxy.workflow.refactor.schema.UpdateCreatorAction | galaxy.workflow.refactor.schema.UpdateNameAction | galaxy.workflow.refactor.schema.UpdateLicenseAction | galaxy.workflow.refactor.schema.UpdateOutputLabelAction | galaxy.workflow.refactor.schema.UpdateReportAction | galaxy.workflow.refactor.schema.UpdateStepLabelAction | galaxy.workflow.refactor.schema.UpdateStepPositionAction | galaxy.workflow.refactor.schema.UpgradeSubworkflowAction | galaxy.workflow.refactor.schema.UpgradeToolAction | galaxy.workflow.refactor.schema.UpgradeAllStepsAction | galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs[AddInputAction | AddStepAction | ConnectAction | DisconnectAction | ExtractInputAction | ExtractUntypedParameter | FileDefaultsAction | FillStepDefaultsAction | UpdateAnnotationAction | UpdateCreatorAction | UpdateNameAction | UpdateLicenseAction | UpdateOutputLabelAction | UpdateReportAction | UpdateStepLabelAction | UpdateStepPositionAction | UpgradeSubworkflowAction | UpgradeToolAction | UpgradeAllStepsAction | RemoveUnlabeledWorkflowOutputs]]

dry_run: bool

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'actions': FieldInfo(annotation=List[Annotated[Union[galaxy.workflow.refactor.schema.AddInputAction, galaxy.workflow.refactor.schema.AddStepAction, galaxy.workflow.refactor.schema.ConnectAction, galaxy.workflow.refactor.schema.DisconnectAction, galaxy.workflow.refactor.schema.ExtractInputAction, galaxy.workflow.refactor.schema.ExtractUntypedParameter, galaxy.workflow.refactor.schema.FileDefaultsAction, galaxy.workflow.refactor.schema.FillStepDefaultsAction, galaxy.workflow.refactor.schema.UpdateAnnotationAction, galaxy.workflow.refactor.schema.UpdateCreatorAction, galaxy.workflow.refactor.schema.UpdateNameAction, galaxy.workflow.refactor.schema.UpdateLicenseAction, galaxy.workflow.refactor.schema.UpdateOutputLabelAction, galaxy.workflow.refactor.schema.UpdateReportAction, galaxy.workflow.refactor.schema.UpdateStepLabelAction, galaxy.workflow.refactor.schema.UpdateStepPositionAction, galaxy.workflow.refactor.schema.UpgradeSubworkflowAction, galaxy.workflow.refactor.schema.UpgradeToolAction, galaxy.workflow.refactor.schema.UpgradeAllStepsAction, galaxy.workflow.refactor.schema.RemoveUnlabeledWorkflowOutputs], FieldInfo(annotation=NoneType, required=True, discriminator='action_type')]], required=True), 'dry_run': FieldInfo(annotation=bool, required=False, default=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'from_order_index': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description='For dropped connections these optional attributes refer to the output\nside of the connection that was dropped.'), 'from_step_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='For dropped connections these optional attributes refer to the output\nside of the connection that was dropped.'), 'input_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description="If this message is about an input to a step,\nthis field describes the target input name. $The input name as defined by the workflow module corresponding to the step being referenced. For Galaxy tool steps these inputs should be normalized using '|' (e.g. 'cond|repeat_0|input')."), 'message': FieldInfo(annotation=str, required=True), 'message_type': FieldInfo(annotation=RefactorActionExecutionMessageTypeEnum, required=True), 'order_index': FieldInfo(annotation=Union[int, NoneType], required=False, default=None, description="Reference to the step the message refers to. $\n\nMessages don't have to be bound to a step, but if they are they will\nhave a step_label and order_index included in the execution message.\nThese are the label and order_index before applying the refactoring,\nthe result of applying the action may change one or both of these.\nIf connections are dropped this step reference will refer to the\nstep with the previously connected input.\n"), 'output_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='If the message_type is workflow_output_drop_forced, this is the output label dropped.'), 'output_name': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description='If this message is about an output to a step,\nthis field describes the target output name. The output name as defined by the workflow module corresponding to the step being referenced.\n'), 'step_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None, description="Reference to the step the message refers to. $\n\nMessages don't have to be bound to a step, but if they are they will\nhave a step_label and order_index included in the execution message.\nThese are the label and order_index before applying the refactoring,\nthe result of applying the action may change one or both of these.\nIf connections are dropped this step reference will refer to the\nstep with the previously connected input.\n")}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

Bases: BaseModel

messages: List[RefactorActionExecutionMessage]

model_computed_fields: ClassVar[Dict[str, ComputedFieldInfo]] = {}: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_fields: ClassVar[Dict[str, FieldInfo]] = {'action': FieldInfo(annotation=Union[AddInputAction, AddStepAction, ConnectAction, DisconnectAction, ExtractInputAction, ExtractUntypedParameter, FileDefaultsAction, FillStepDefaultsAction, UpdateAnnotationAction, UpdateCreatorAction, UpdateNameAction, UpdateLicenseAction, UpdateOutputLabelAction, UpdateReportAction, UpdateStepLabelAction, UpdateStepPositionAction, UpgradeSubworkflowAction, UpgradeToolAction, UpgradeAllStepsAction, RemoveUnlabeledWorkflowOutputs], required=True), 'messages': FieldInfo(annotation=List[galaxy.workflow.refactor.schema.RefactorActionExecutionMessage], required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

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