matflow.WorkflowTask#

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

Bases: WorkflowTask

Represents a Task that is bound to a Workflow.

Parameters:

workflow (app.Workflow) – The workflow that the task is bound to.
template (app.Task) – The task template that this binds.
index (int) – Where in the workflow’s list of tasks is this one.
element_IDs (List[int]) – The IDs of the elements of this task.

Methods

`add_elements`	Add elements to this task.
`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`	Create information about new elements in this task.
`get`	Get a parameter known to this task by its path.
`get_all_element_iterations`	Get the iterations known by the task's elements.
`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 the directory name for a particular iteration.
`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`	Make a new instance without any elements set up yet.
`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`	The name of the directory for the task's temporary files.
`downstream_tasks`	All workflow tasks that are downstream from this task.
`element_IDs`	The IDs of elements associated with this task.
`elements`	The elements associated with this task.
`index`	The index of this task within its workflow.
`inputs`	Inputs to this task.
`insert_ID`	The insertion ID of the template task.
`name`	The name of this task based on its template.
`num_actions`	The number of actions in this task.
`num_element_sets`	The number of element sets associated with this task.
`num_elements`	The number of elements associated with this task.
`outputs`	Outputs from this task.
`template`	The template for this task.
`unique_name`	The unique name for this task specifically.
`upstream_tasks`	All workflow tasks that are upstream from this task.
`workflow`	The workflow this task is bound to.

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)#

Add elements to this task.

Parameters:

sourceable_elem_iters (list of int, optional) – If specified, a list of global element iteration indices from which inputs may be sourced. If not specified, all workflow element iterations are considered sourceable.
propagate_to (dict[str, ElementPropagation]) – Propagate the new elements downstream to the specified tasks.
return_indices (bool) – If True, return the list of indices of the newly added elements. False by default.

app = App(name='MatFlow', version='0.3.0a131')#

property dir_name#: The name of the directory for the task’s temporary files.

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

property element_IDs#: The IDs of elements associated with this task.

property elements#: The elements associated with this task.

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)#: Create information about new elements in this task.

get(path, raise_on_missing=False, default=None)#: Get a parameter known to this task by its path.

get_all_element_iterations()#

Get the iterations known by the task’s elements.

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)#

Get the directory name for a particular iteration.

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#: The index of this task within its workflow.

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#: Inputs to this task.

property insert_ID#: The insertion ID of the template task.

property name#: The name of this task based on its template.

classmethod new_empty_task(workflow, template, index)#

Make a new instance without any elements set up yet.

Parameters:

workflow (Workflow) – The workflow that the task is bound to.
template (Task) – The task template that this binds.
index (int) – Where in the workflow’s list of tasks is this one.

property num_actions#: The number of actions in this task.

property num_element_sets#: The number of element sets associated with this task.

property num_elements#: The number of elements associated with this task.

property outputs#: Outputs from this task.

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#: The template for this task.

property unique_name#: The unique name for this task specifically.

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

property workflow#: The workflow this task is bound to.