Dataflows Components: Task and Workflow

A Task is the basic runnable component of Pydra and is described by the class TaskBase. A Task has named inputs and outputs, thus allowing construction of dataflows. It can be hashed and executes in a specific working directory. Any Pydra’s Task can be used as a function in a script, thus allowing dual use in Pydra’s Workflows and in standalone scripts. There are several classes that inherit from TaskBase and each has a different application:

Function Tasks

  • FunctionTask is a Task that executes Python functions. Most Python functions declared in an existing library, package, or interactively in a terminal can be converted to a FunctionTask by using Pydra’s decorator - mark.task.

    import numpy as np
    from pydra import mark
    fft = mark.annotate({'a': np.ndarray,
                     'return': float})(np.fft.fft)
    fft_task = mark.task(fft)()
    result = fft_task(a=np.random.rand(512))

    fft_task is now a Pydra Task and result will contain a Pydra’s Result object. In addition, the user can use Python’s function annotation or another Pydra decorator — mark.annotate in order to specify the output. In the following example, we decorate an arbitrary Python function to create named outputs:

        {"return": {"mean": float, "std": float}}
    def mean_dev(my_data):
        import statistics as st
        return st.mean(my_data), st.stdev(my_data)
    result = mean_dev(my_data=[...])()

    When the Task is executed result.output will contain two attributes: mean and std. Named attributes facilitate passing different outputs to different downstream nodes in a dataflow.

Shell Command Tasks

  • ShellCommandTask is a Task used to run shell commands and executables. It can be used with a simple command without any arguments, or with specific set of arguments and flags, e.g.:

    ShellCommandTask(executable="ls", args="my_dir")

    The Task can accommodate more complex shell commands by allowing the user to customize inputs and outputs of the commands. One can generate an input specification to specify names of inputs, positions in the command, types of the inputs, and other metadata. As a specific example, FSL’s BET command (Brain Extraction Tool) can be called on the command line as:

    bet input_file output_file -m

    Each of the command argument can be treated as a named input to the ShellCommandTask, and can be included in the input specification. As shown next, even an output is specified by constructing the out_file field form a template:

    bet_input_spec = SpecInfo(
        ( "in_file", File,
          { "help_string": "input file ...",
            "position": 1,
            "mandatory": True } ),
        ( "out_file", str,
          { "help_string": "name of output ...",
            "position": 2,
                              "{in_file}_br" } ),
        ( "mask", bool,
          { "help_string": "create binary mask",
            "argstr": "-m", } ) ],
        bases=(ShellSpec,) )

    More details are in the Input Specification.

Container Tasks

  • ContainerTask class is a child class of ShellCommandTask and serves as a parent class for DockerTask and SingularityTask. Both Container Tasks run shell commands or executables within containers with specific user defined environments using Docker and Singularity software respectively. This might be extremely useful for users and projects that require environment encapsulation and sharing. Using container technologies helps improve scientific workflows reproducibility, one of the key concept behind Pydra.

    These Container Tasks can be defined by using DockerTask and SingularityTask classes directly, or can be created automatically from ShellCommandTask, when an optional argument container_info is used when creating a Shell Task. The following two types of syntax are equivalent:

    DockerTask(executable="pwd", image="busybox")
         container_info=("docker", "busybox"))


  • Workflow - is a subclass of Task that provides support for creating Pydra dataflows. As a subclass, a Workflow acts like a Task and has inputs, outputs, is hashable, and is treated as a single unit. Unlike Tasks, workflows embed a directed acyclic graph. Each node of the graph contains a Task of any type, including another Workflow, and can be added to the Workflow simply by calling the add method. The connections between Tasks are defined by using so called Lazy Inputs or Lazy Outputs. These are special attributes that allow assignment of values when a Workflow is executed rather than at the point of assignment. The following example creates a Workflow from two Pydra Tasks.

    # creating workflow with two input fields
    wf = Workflow(input_spec=["x", "y"])
    # adding a task and connecting task's input
    # to the workflow input
                   x=wf.lzin.x, y=wf.lzin.y))
    # adding another task and connecting
    # task's input to the "mult" task's output
    wf.add(add2(name="add", x=wf.mlt.lzout.out))
    # setting workflow output
    wf.set_output([("out", wf.add.lzout.out)])

Task’s State

All Tasks, including Workflows, can have an optional attribute representing an instance of the State class. This attribute controls the execution of a Task over different input parameter sets. This class is at the heart of Pydra’s powerful Map-Reduce over arbitrary inputs of nested dataflows feature. The State class formalizes how users can specify arbitrary combinations. Its functionality is used to create and track different combinations of input parameters, and optionally allow limited or complete recombinations. In order to specify how the inputs should be split into parameter sets, and optionally combined after the Task execution, the user can set splitter and combiner attributes of the State class.

task_with_state =
      add2().split(x=[1, 5]).combine("x")

In this example, the State class is responsible for creating a list of two separate inputs, [{x: 1}, {x:5}], each run of the Task should get one element from the list. Note that in this case the value for x is set in the split() method, not at the task’s initialisation. The combine() method, specifies that the results are grouped back when returning the result from the Task.

While this example illustrates mapping and grouping of results over a single parameter, Pydra extends this to arbitrary combinations of input fields and downstream grouping over nested dataflows. Details of how splitters and combiners power Pydra’s scalable dataflows are described in the next section.