aim2dat.aiida_workflows.workflow_builder¶

WorkflowBuilder and auxiliary functions.

Module Contents¶

Classes¶

Attributes¶

exception aim2dat.aiida_workflows.workflow_builder.WorkflowProtocolError[source]¶

Bases: Exception

Error for incomplete or inconsistent workflow protocols.

class args¶

Overview

Methods¶

with_traceback()

Exception.with_traceback(tb) –

with_traceback()¶

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class aim2dat.aiida_workflows.workflow_builder.MultipleWorkflowBuilder(aiida_group=None, protocol=None, graph_attributes={'graph_attr': {'size': '10!,6'}}, use_uuid=False)[source]¶

Bases: _BaseWorkflowBuilder

Workflow builder that can manage a worklfow for several parent nodes at once.

Overview

Properties¶

aiida_group	Only consider processes in the AiiDA group.
graph_attributes	Graphiz graph attributes for the provenance graph.
protocol	Protocol used for the workflow.
task_queue	Return the task queue.
tasks	Return all tasks of the workflow.
use_uuid	Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key
user_input	Input parameters set by the user.

Methods¶

add_parent_node(parent_node)	Add new parent node.
add_to_task_queue(task_label, run_type)	Add a task to the task queue.
adopt_input_nodes_from_workflow(parent_node)	Import input parameters for the workflow based on another parent node.
execute_task_queue(interval, node_ids)	Execute a series of AiiDA processes for several tasks consecutively for all parent nodes
from_file(file_name)	class -
generate_inputs(parent_node, task)	Generate a dictionary or builder for a certain task of the workflow for a specific parent
generate_provenance_graph(parent_node_index)	Generate provenance graph of the workflow.
import_parent_nodes_from_aiida_db(group_labels)	Import parent nodes from the AiiDA database.
import_parent_nodes_from_pandas_df(data_frame, parent_node)	Extract parent nodes from a pandas data frame. The data frame needs to have a column
reset_task_queue()	Reset the task queue.
return_process_nodes()	Return a pandas data frame containing the process nodes of all completed tasks.
return_results(include, exclude)	Return a pandas data frame containing the calculated results of all completed tasks.
return_runtimes(unit)	Return a pandas data frame containing the runtimes of all completed tasks.
return_workflow_states(unformatted)	Return a pandas data frame containing the current state of workflow.
run_task(task_label, interval, node_ids)	Run the AiiDA processes of the task for all parent nodes.
set_user_input(input_port, value)	Set a user input parameter of the workflow for all parent nodes.
submit_task(task_label, interval, node_ids)	Submit the AiiDA processes of the task for all parent nodes.
to_file(file_name)	-

property aiida_group¶

Only consider processes in the AiiDA group.

Type:¶

str or aiida.orm.Group

property graph_attributes¶

Graphiz graph attributes for the provenance graph.

property protocol¶

Protocol used for the workflow.

property task_queue¶

Return the task queue.

property tasks¶

Return all tasks of the workflow.

property use_uuid¶

Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key (int).

Type:¶

bool

property user_input¶

Input parameters set by the user.

add_parent_node(parent_node)[source]¶

Add new parent node.

Parameters:¶

parent_node (aiida.orm.Node)

add_to_task_queue(task_label, run_type='run')[source]¶

Add a task to the task queue.

Parameters:¶

• task_label (str) – Label of the task.

• run_type (str (optional)) – Run type of the process, either run or submit. The default value is run.

adopt_input_nodes_from_workflow(parent_node)[source]¶

Import input parameters for the workflow based on another parent node.

Parameters:¶

parent_node (aiida.node) – Parent AiiDA node.

execute_task_queue(interval=None, node_ids=None)[source]¶

Execute a series of AiiDA processes for several tasks consecutively for all parent nodes as defined in the task_queue attribute.

Parameters:¶

• interval (tuple (optional)) – Lower and upper bound of the interval of workflows that are executed. None to run all workflows. The default value is None.

• node_ids (list (optional)) – List of primary keys or uuids of the parent nodes of the workflows that are started. None to run all workflows.

classmethod from_file(file_name='workflow.yaml')¶

generate_inputs(parent_node, task)[source]¶

Generate a dictionary or builder for a certain task of the workflow for a specific parent node.

Parameters:¶

• parent_node (aiida.orm.node or str or int) – Uuid, primary key or the AiiDA node itself.

• task (str) – Task label.

generate_provenance_graph(parent_node_index)[source]¶

Generate provenance graph of the workflow.

Returns:¶

aiida.tools.visualization.graph.Graph – Provenance graph.

import_parent_nodes_from_aiida_db(group_labels)[source]¶

Import parent nodes from the AiiDA database.

Parameters:¶

group_labels (str or list) – AiiDA group label or list of group labels.

import_parent_nodes_from_pandas_df(data_frame, parent_node='structure_node')[source]¶

Extract parent nodes from a pandas data frame. The data frame needs to have a column called ‘aiida_uuid’ with the universally unique identifier (uuid) of the nodes.

Parameters:¶

• data_frame (pandas.DataFrame) – Pandas data frame containing the uuids, primary keys of the AiiDA nodes or the AiiDA nodes themselves.

• parent_node (str (optional)) – Label of the column containing the parent nodes for the workflow. The default value is 'structure_node'.

reset_task_queue()[source]¶

Reset the task queue.

return_process_nodes()[source]¶

Return a pandas data frame containing the process nodes of all completed tasks.

Returns:¶

pandas.DataFrame – Pandas data frame.

return_results(include='all', exclude=[])[source]¶

Return a pandas data frame containing the calculated results of all completed tasks.

Parameters:¶

• include (list or str (optional)) – List of results that are included in the pandas data frame. The value 'all' returns all results. The default value is 'all'.

• exclude (list (optional)) – List of results that are excluded in the pandas data frame. The default value is [].

Returns:¶

pandas.DataFrame – Pandas data frame.

return_runtimes(unit=None)[source]¶

Return a pandas data frame containing the runtimes of all completed tasks.

Returns:¶

pandas.DataFrame – Pandas data frame.

return_workflow_states(unformatted=False)[source]¶

Return a pandas data frame containing the current state of workflow.

Paramters¶

unformattedbool (optional)

If set to True an unformatted pandas.DataFrame object is returned otherwise a pandas.Styler object is returned.

returns:

pandas.DataFrame or pandas.Styler – Pandas data frame.

run_task(task_label, interval=None, node_ids=None)[source]¶

Run the AiiDA processes of the task for all parent nodes.

Parameters:¶

• task_label (str) – Label of the workflow task.

• interval (tuple (optional)) – Lower and upper bound of the interval of workflows that are submitted. None to run all workflows. The default value is None.

• node_ids (list (optional)) – List of primary keys or uuids of the parent nodes of the workflows that are submitted. None to run all workflows.

set_user_input(input_port, value)[source]¶

Set a user input parameter of the workflow for all parent nodes.

Parameters:¶

• input_port (str) – Input port of the Parameter.

• value (variable) – Value of the input parameter.

submit_task(task_label, interval=None, node_ids=None)[source]¶

Submit the AiiDA processes of the task for all parent nodes.

Parameters:¶

• task_label (str) – Label of the workflow task.

• interval (tuple (optional)) – Lower and upper bound of the interval of workflows that are submitted. None to run all workflows. The default value is None.

• node_ids (list (optional)) – List of primary keys or uuids of the parent nodes of the workflows that are submitted. None to run all workflows.

to_file(file_name='workflow.yaml')¶

class aim2dat.aiida_workflows.workflow_builder.WorkflowBuilder(parent_node=None, protocol=None, graph_attributes={'graph_attr': {'size': '10!,6'}}, use_uuid=False)[source]¶

Bases: _BaseWorkflowBuilder

Class to manage complex AiiDA workflows.

Overview

Properties¶

aiida_group	Only consider processes in the AiiDA group.
completed_tasks	Completed tasks.
failed_tasks	Failed tasks.
parent_node	Parent AiiDA node.
protocol	Protocol used for the workflow.
results	Results of the workflow.
running_tasks	Tasks which have not yet finished.
tasks	Return all tasks of the workflow.
use_uuid	Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key
user_input	Input parameters set by the user.

Methods¶

adopt_input_nodes_from_workflow(parent_node)	Import input parameters for the workflow based on another parent node.
determine_workflow_state()	Determine which tasks of the workflow have been completed and which ones can be started
from_file(file_name)	class -
generate_inputs(task)	Generate a builder for an AiiDA work chain or calculation job.
generate_provenance_graph()	Generate provenance graph of the workflow.
run_task(task)	Run the underlying AiiDA process of the task.
set_user_input(input_port, value)	Set user input parameters of the workflow.
submit_task(task)	Submit the underlying AiiDA process of the task.
to_file(file_name)	-

property aiida_group¶

Only consider processes in the AiiDA group.

Type:¶

str or aiida.orm.Group

property completed_tasks¶

Completed tasks.

property failed_tasks¶

Failed tasks.

property parent_node¶

Parent AiiDA node.

property protocol¶

Protocol used for the workflow.

property results¶

Results of the workflow.

property running_tasks¶

Tasks which have not yet finished.

property tasks¶

Return all tasks of the workflow.

property use_uuid¶

Whether to use the uuid (str) to represent AiiDA nodes instead of the primary key (int).

Type:¶

bool

property user_input¶

Input parameters set by the user.

adopt_input_nodes_from_workflow(parent_node)[source]¶

Import input parameters for the workflow based on another parent node.

Parameters:¶

parent_node (aiida.node) – Parent AiiDA node.

determine_workflow_state()[source]¶

Determine which tasks of the workflow have been completed and which ones can be started next.

classmethod from_file(file_name='workflow.yaml')¶

generate_inputs(task)[source]¶

Generate a builder for an AiiDA work chain or calculation job.

Parameters:¶

task (str) – Workflow task.

Returns:¶

builder (aiida.work_chain or dict) – If the underlying AiiDA process is a work chain the builder of the work chain is returnedBuilder, otherwise a dictionary of the input parameters and the process is returned.

generate_provenance_graph()[source]¶

Generate provenance graph of the workflow.

Returns:¶

aiida.tools.visualization.graph.Graph – Provenance graph.

run_task(task)[source]¶

Run the underlying AiiDA process of the task.

Parameters:¶

task (str) – Workflow task.

Returns:¶

• proc_node (aiida.node) – AiiDA process node.

• result (aiida.node) – Results of the AiiDA process.

set_user_input(input_port, value)[source]¶

Set user input parameters of the workflow.

Parameters:¶

• input_port (str) – Input port of the parameter.

• value – Value.

submit_task(task)[source]¶

Submit the underlying AiiDA process of the task.

Parameters:¶

task (str) – Workflow task.

Returns:¶

proc_node (aiida.node) – AiiDA process node.

to_file(file_name='workflow.yaml')¶

aim2dat.aiida_workflows.workflow_builder.AiidaCode¶