idmtools_models.r.r_task module¶

idmtools rtask.

class idmtools_models.r.r_task.RTask(command: typing.Union[str, idmtools.entities.command_line.CommandLine] = <property object>, platform_requirements: typing.Set[idmtools.entities.platform_requirements.PlatformRequirements] = <factory>, _ITask__pre_creation_hooks: typing.List[typing.Callable[[typing.Union[Simulation, IWorkflowItem], IPlatform], typing.NoReturn]] = <factory>, _ITask__post_creation_hooks: typing.List[typing.Callable[[typing.Union[Simulation, IWorkflowItem], IPlatform], typing.NoReturn]] = <factory>, common_assets: idmtools.assets.asset_collection.AssetCollection = <factory>, transient_assets: idmtools.assets.asset_collection.AssetCollection = <factory>, image_name: str = None, build: bool = False, build_path: typing.Optional[str] = None, Dockerfile: typing.Optional[str] = None, pull_before_build: bool = True, use_nvidia_run: bool = False, _DockerTask__image_built: bool = False, script_path: str = None, r_path: str = 'Rscript')¶

Bases: idmtools.core.docker_task.DockerTask

Defines an RTask for idmtools. Currently only useful for local platform.

Notes

TODO rework this to be non-docker

script_path: str = None¶

r_path: str = 'Rscript'¶

reload_from_simulation(simulation: idmtools.entities.simulation.Simulation, **kwargs)¶

Reload RTask from a simulation. Used when fetching an simulation to do a recreation.

Parameters:

simulation – Simulation object containing our metadata to rebuild task
**kwargs –

Returns:

None

gather_common_assets() → idmtools.assets.asset_collection.AssetCollection¶

Gather R Assets.

Returns:: Common assets

gather_transient_assets() → idmtools.assets.asset_collection.AssetCollection¶

Gather transient assets. Generally this is the simulation level assets.

Returns:: Transient assets(Simulation level Assets)

pre_creation(parent: Union[idmtools.entities.simulation.Simulation, idmtools.entities.iworkflow_item.IWorkflowItem], platform: IPlatform)¶

Called before creation of parent.

Parameters:

parent – Parent
platform – Platform R Task is executing on

Returns:

None

Raises:

ValueError if script name is not provided –

__init__(command: typing.Union[str, idmtools.entities.command_line.CommandLine] = <property object>, platform_requirements: typing.Set[idmtools.entities.platform_requirements.PlatformRequirements] = <factory>, _ITask__pre_creation_hooks: typing.List[typing.Callable[[typing.Union[Simulation, IWorkflowItem], IPlatform], typing.NoReturn]] = <factory>, _ITask__post_creation_hooks: typing.List[typing.Callable[[typing.Union[Simulation, IWorkflowItem], IPlatform], typing.NoReturn]] = <factory>, common_assets: idmtools.assets.asset_collection.AssetCollection = <factory>, transient_assets: idmtools.assets.asset_collection.AssetCollection = <factory>, image_name: str = None, build: bool = False, build_path: typing.Optional[str] = None, Dockerfile: typing.Optional[str] = None, pull_before_build: bool = True, use_nvidia_run: bool = False, _DockerTask__image_built: bool = False, script_path: str = None, r_path: str = 'Rscript') → None¶

class idmtools_models.r.r_task.RTaskSpecification¶

Bases: idmtools.registry.task_specification.TaskSpecification

RTaskSpecification defines plugin specification for RTask.

get(configuration: dict) → idmtools_models.r.r_task.RTask¶

Get instance of RTask.

Parameters:: configuration – configuration for task
Returns:: RTask with configuration

get_description() → str¶

Returns the Description of the plugin.

Returns:: Plugin Description

get_type() → Type[idmtools_models.r.r_task.RTask]¶

Get Type for Plugin.

Returns:: RTask

get_version() → str¶

Returns the version of the plugin.

Returns:: Plugin Version