matflow.WorkflowTask#

class matflow.WorkflowTask(workflow, template, index, element_IDs)#

Bases: WorkflowTask

Class to represent a Task that is bound to a Workflow.

Methods

`add_elements`
`ensure_input_sources`	Check valid input sources are specified for a new task to be added to the workflow in a given position.
`generate_new_elements`
`get`
`get_all_element_iterations`
`get_dependent_elements`	Get elements from downstream tasks that depend on this task.
`get_dependent_tasks`	Get tasks (insert ID or WorkflowTask objects) that depends on this task.
`get_dir_name`
`get_element_dependencies`	Get elements from upstream tasks that this task depends on.
`get_task_dependencies`	Get tasks (insert ID or WorkflowTask objects) that this task depends on.
`initialise_EARs`	Try to initialise any uninitialised EARs of this task.
`new_empty_task`
`resolve_element_data_indices`	Find the index of the Zarr parameter group index list corresponding to each input data for all elements.

Attributes

`app`
`dir_name`
`downstream_tasks`	Get all workflow tasks that are downstream from this task.
`element_IDs`
`elements`
`index`
`inputs`
`insert_ID`
`name`
`num_actions`
`num_element_sets`
`num_elements`
`outputs`
`template`
`unique_name`
`upstream_tasks`	Get all workflow tasks that are upstream from this task.
`workflow`

Parameters:

workflow (app.Workflow) –
template (app.Task) –
index (int) –
element_IDs (List[int]) –

add_elements(base_element=None, inputs=None, input_files=None, sequences=None, resources=None, repeats=None, input_sources=None, nesting_order=None, element_sets=None, sourceable_elem_iters=None, propagate_to=None, return_indices=False)#

app = App(name='MatFlow', version='0.3.0a129')#

property dir_name#

property downstream_tasks#: Get all workflow tasks that are downstream from this task.

property element_IDs#

property elements#

ensure_input_sources(element_set)#

Check valid input sources are specified for a new task to be added to the workflow in a given position. If none are specified, set them according to the default behaviour.

This method mutates element_set.input_sources.

Return type:: Dict[str, List[int]]

generate_new_elements(input_data_indices, output_data_indices, element_data_indices, sequence_indices, source_indices)#

get(path, raise_on_missing=False, default=None)#

get_all_element_iterations()#

Return type:: Dict[int, ElementIteration]

get_dependent_elements(as_objects=False)#

Get elements from downstream tasks that depend on this task.

Parameters:: as_objects (bool) –
Return type:: List[int | Element]

get_dependent_tasks(as_objects=False)#

Get tasks (insert ID or WorkflowTask objects) that depends on this task.

Parameters:: as_objects (bool) –
Return type:: List[int | WorkflowTask]

get_dir_name(loop_idx=None)#

Parameters:: loop_idx (Dict[str, int]) –
Return type:: str

get_element_dependencies(as_objects=False)#

Get elements from upstream tasks that this task depends on.

Parameters:: as_objects (bool) –
Return type:: List[int | Element]

get_task_dependencies(as_objects=False)#

Get tasks (insert ID or WorkflowTask objects) that this task depends on.

Dependencies may come from either elements from upstream tasks, or from locally defined inputs/sequences/defaults from upstream tasks.

Parameters:: as_objects (bool) –
Return type:: List[int | WorkflowTask]

property index#

initialise_EARs(iter_IDs=None)#

Try to initialise any uninitialised EARs of this task.

Parameters:: iter_IDs (List[int] | None) –
Return type:: List[int]

property inputs#

property insert_ID#

property name#

classmethod new_empty_task(workflow, template, index)#

Parameters:

workflow (Workflow) –
template (Task) –
index (int) –

property num_actions#

property num_element_sets#

property num_elements#

property outputs#

static resolve_element_data_indices(multiplicities)#

Find the index of the Zarr parameter group index list corresponding to each input data for all elements.

# TODO: update docstring; shouldn’t reference Zarr.

Parameters:

multiplicities (list of dict) –

Each list item represents a sequence of values with keys:: multiplicity: int nesting_order: int path : str

Returns:

element_dat_idx – Each list item is a dict representing a single task element and whose keys are input data paths and whose values are indices that index the values of the dict returned by the task.make_persistent method.

Return type:

list of dict

property template#

property unique_name#

property upstream_tasks#: Get all workflow tasks that are upstream from this task.

property workflow#