matflow.ElementIteration#

class matflow.ElementIteration(id_, is_pending, index, element, data_idx, EARs_initialised, EAR_IDs, EARs, schema_parameters, loop_idx)#

Bases: ElementIteration

A particular iteration of an element.

Parameters:

id (int) – The ID of this iteration.
is_pending (bool) – Whether this iteration is pending execution.
index (int) – The index of this iteration in its parent element.
element (Element) – The element this is an iteration of.
data_idx (dict) – The overall element iteration data index, before resolution of EARs.
EARs_initialised (bool) – Whether EARs have been set up for the iteration.
EAR_IDs (dict[int, int]) – Mapping from iteration number to EAR ID, where known.
EARs (list[dict]) – Data about EARs.
schema_parameters (list[str]) – Parameters from the schema.
loop_idx (dict[str, int]) – Indexing information from the loop.
id_ (int) –

Methods

`get`	Get element data from the persistent store.
`get_EAR_dependencies`	Get EARs that this element iteration depends on (excluding EARs of this element iteration).
`get_data_idx`	Get the data index.
`get_dependent_EARs`	Get EARs of downstream iterations and tasks that depend on this element iteration.
`get_dependent_element_iterations`	Get elements iterations of downstream iterations and tasks that depend on this element iteration.
`get_dependent_elements`	Get elements of downstream tasks that depend on this element iteration.
`get_dependent_tasks`	Get downstream tasks that depend on this element iteration.
`get_element_dependencies`	Get elements that this element iteration depends on.
`get_element_iteration_dependencies`	Get element iterations that this element iteration depends on.
`get_input_dependencies`	Get locally defined inputs/sequences/defaults from other tasks that this element iteration depends on.
`get_parameter_names`	Get parameter types associated with a given prefix.
`get_parameter_sources`	Get the origin of parameters.
`get_resources`	Resolve specific resources for the specified action of this iteration, considering all applicable scopes.
`get_resources_obj`	Get the resources for an action (see `get_resources()`) as a searchable model.
`get_task_dependencies`	Get tasks (insert ID or WorkflowTask objects) that this element iteration depends on.
`get_template_resources`	Get template-level resources.

Attributes

`EAR_IDs`	Mapping from iteration number to EAR ID, where known.
`EAR_IDs_flat`	The EAR IDs.
`EARs_initialised`	Whether or not the EARs have been initialised.
`action_runs`	A list of element action runs, where only the final run is taken for each element action.
`actions`	The actions of this iteration.
`app`
`data_idx`	The overall element iteration data index, before resolution of EARs.
`element`	The element this is an iteration of.
`id_`	The ID of this iteration.
`index`	The index of this iteration in its parent element.
`input_files`	The input files to this element.
`inputs`	The inputs to this element.
`is_pending`	Whether this iteration is pending execution.
`loop_idx`	Indexing information from the loop.
`output_files`	The output files from this element.
`outputs`	The outputs from this element.
`schema_parameters`	Parameters from the schema.
`task`	The task this is an iteration of an element for.
`workflow`	The workflow this is a part of.

property EAR_IDs: Dict[int, int]#: Mapping from iteration number to EAR ID, where known.

property EAR_IDs_flat#: The EAR IDs.

property EARs_initialised#: Whether or not the EARs have been initialised.

property action_runs: List[ElementActionRun]#: A list of element action runs, where only the final run is taken for each element action.

property actions: Dict[app.ElementAction]#: The actions of this iteration.

app = App(name='MatFlow', version='0.3.0a132')#

property data_idx#: The overall element iteration data index, before resolution of EARs.

property element#: The element this is an iteration of.

get(path=None, action_idx=None, run_idx=-1, default=None, raise_on_missing=False, raise_on_unset=False)#

Get element data from the persistent store.

Parameters:

path (str) –
action_idx (int) –
run_idx (int) –
default (Any) –
raise_on_missing (bool) –
raise_on_unset (bool) –

Return type:

Any

get_EAR_dependencies(as_objects=False)#

Get EARs that this element iteration depends on (excluding EARs of this element iteration).

Parameters:: as_objects (bool | None) –
Return type:: List[int | ElementActionRun]

get_data_idx(path=None, action_idx=None, run_idx=-1)#

Get the data index.

Parameters:

path (str) – If specified, filters the data indices to the ones relevant to this path.
action_idx (int) – The index of the action within the schema.
run_idx (int) – The index of the run within the action.

Return type:

Dict[str, int]

get_dependent_EARs(as_objects=False)#

Get EARs of downstream iterations and tasks that depend on this element iteration.

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

get_dependent_element_iterations(as_objects=False)#

Get elements iterations of downstream iterations and tasks that depend on this element iteration.

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

get_dependent_elements(as_objects=False)#

Get elements of downstream tasks that depend on this element iteration.

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

get_dependent_tasks(as_objects=False)#

Get downstream tasks that depend on this element iteration.

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

get_element_dependencies(as_objects=False)#

Get elements that this element iteration depends on.

Parameters:: as_objects (bool | None) –
Return type:: List[int | Element]

get_element_iteration_dependencies(as_objects=False)#

Get element iterations that this element iteration depends on.

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

get_input_dependencies()#

Get locally defined inputs/sequences/defaults from other tasks that this element iteration depends on.

Return type:: Dict[str, Dict]

get_parameter_names(prefix)#

Get parameter types associated with a given prefix.

For example, with the prefix “inputs”, this would return [‘p1’, ‘p2’] for a task schema that has input types p1 and p2. For inputs, labels are ignored. For example, for a task schema that accepts two inputs of the same type p1, with labels one and two, this method would return (for the “inputs” prefix): [‘p1[one]’, ‘p1[two]’].

This method is distinct from Action.get_parameter_names in that it returns schema-level inputs/outputs, whereas Action.get_parameter_names returns action-level input/output/file types/labels.

Parameters:: prefix (str) – One of “inputs”, “outputs”.
Return type:: List[str]

get_parameter_sources(path=None, action_idx=None, run_idx=-1, typ=None, as_strings=False, use_task_index=False)#

Get the origin of parameters.

Parameters:

use_task_index (bool) – If True, use the task index within the workflow, rather than the task insert ID.
path (str) –
action_idx (int) –
run_idx (int) –
typ (str) –
as_strings (bool) –

Return type:

Dict[str, str | Dict[str, Any]]

get_resources(action, set_defaults=False)#

Resolve specific resources for the specified action of this iteration, considering all applicable scopes.

Parameters:

set_defaults (bool) – If True, include machine-defaults for os_name, shell and scheduler.
action (Action) –

Return type:

Dict

get_resources_obj(action, set_defaults=False)#

Get the resources for an action (see get_resources()) as a searchable model.

Parameters:

action (Action) –
set_defaults (bool) –

Return type:

ElementResources

get_task_dependencies(as_objects=False)#

Get tasks (insert ID or WorkflowTask objects) that this element iteration 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]

get_template_resources()#

Get template-level resources.

Return type:: Dict

property id_: int#: The ID of this iteration.

property index#: The index of this iteration in its parent element.

property input_files: ElementInputFiles#: The input files to this element.

property inputs: ElementInputs#: The inputs to this element.

property is_pending: bool#: Whether this iteration is pending execution.

property loop_idx: Dict[str, int]#: Indexing information from the loop.

property output_files: ElementOutputFiles#: The output files from this element.

property outputs: ElementOutputs#: The outputs from this element.

property schema_parameters: List[str]#: Parameters from the schema.

property task#: The task this is an iteration of an element for.

property workflow#: The workflow this is a part of.