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Merge pull request #145 from biosimulators/implement-set-get-reset
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Add callbacks for setting, getting, and resetting.
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@luciansmith
luciansmith committed Jul 24, 2023
2 parents c911bf8 + b99416c commit a0486e7
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Showing 8 changed files with 221 additions and 107 deletions.
2 changes: 1 addition & 1 deletion biosimulators_utils/_version.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = '0.1.182'
__version__ = '0.1.183'
85 changes: 59 additions & 26 deletions biosimulators_utils/sedml/exec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
from lxml import etree # noqa: F401
import copy
import datetime
import functools
import numpy
import os
import sys
Expand All @@ -51,7 +52,8 @@ def exec_sed_doc(task_executer, doc, working_dir, base_out_path, rel_out_path=No
apply_xml_model_changes=False,
log=None, indent=0, pretty_print_modified_xml_models=False,
log_level=StandardOutputErrorCapturerLevel.c,
config=None):
config=None, get_value_executer=None, set_value_executer=None, preprocessed_task_executer=None,
reset_executer=None):
""" Execute the tasks specified in a SED document and generate the specified outputs
Args:
Expand Down Expand Up @@ -164,14 +166,24 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
original_model_changes = {}
temp_model_sources = []
model_etrees = {}
preprocessed_task = None

task_vars = get_variables_for_task(doc, task)
preprocessed_task_sub_executer = None
if preprocessed_task_executer:
preprocessed_task_sub_executer = functools.partial(preprocessed_task_executer,
task, task_vars,
config=config)

for original_model in original_models:
original_model_sources[original_model.id] = original_model.source
original_model_changes[original_model.id] = original_model.changes

temp_model, temp_model_source, model_etree = resolve_model_and_apply_xml_changes(
temp_model, temp_model_source, model_etree, preprocessed_task = resolve_model_and_apply_xml_changes(
original_model, doc, working_dir,
apply_xml_model_changes=apply_xml_model_changes,
pretty_print_modified_xml_models=pretty_print_modified_xml_models)
pretty_print_modified_xml_models=pretty_print_modified_xml_models,
set_value_executer=set_value_executer, preprocessed_task_sub_executer=preprocessed_task_sub_executer)

original_model.source = temp_model.source
original_model.changes = temp_model.changes
Expand All @@ -181,18 +193,24 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **

model_etrees[original_model.id] = model_etree

task_vars = get_variables_for_task(doc, task)
# The preprocessed task was not created if there was no set_value_executer, so create one now:
if not preprocessed_task and preprocessed_task_executer:
preprocessed_task = preprocessed_task_sub_executer()

# execute task
if isinstance(task, Task):
task_var_results = exec_task(task, task_executer, task_vars, doc, log=task_log, config=config)
task_var_results = exec_task(task, task_executer, task_vars, doc,
preprocessed_task=preprocessed_task, log=task_log, config=config)

elif isinstance(task, RepeatedTask):
task_var_results = exec_repeated_task(task, task_executer, task_vars, doc,
apply_xml_model_changes=apply_xml_model_changes,
model_etrees=model_etrees,
pretty_print_modified_xml_models=pretty_print_modified_xml_models,
config=config)
config=config, preprocessed_task=preprocessed_task,
get_value_executer=get_value_executer,
set_value_executer=set_value_executer,
reset_executer=reset_executer)

else: # pragma: no cover: already validated by :obj:`get_models_referenced_by_task`
raise NotImplementedError('Tasks of type {} are not supported.'.format(task.__class__.__name__))
Expand Down Expand Up @@ -363,7 +381,7 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
return report_results, log


def exec_task(task, task_executer, task_vars, doc, log=None, config=None):
def exec_task(task, task_executer, task_vars, doc, log=None, config=None, preprocessed_task=None):
""" Execute a basic SED task
Args:
Expand Down Expand Up @@ -401,7 +419,7 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
:obj:`VariableResults`: results of the variables
"""
# execute task
task_variable_results, _ = task_executer(task, task_vars, log=log, config=config)
task_variable_results, _ = task_executer(task, task_vars, log=log, config=config, preprocessed_task=preprocessed_task)

# check that the expected variables were recorded
variable_results = VariableResults()
Expand All @@ -413,7 +431,8 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **


def exec_repeated_task(task, task_executer, task_vars, doc, apply_xml_model_changes=False, model_etrees=None,
pretty_print_modified_xml_models=False, config=None):
pretty_print_modified_xml_models=False, config=None, preprocessed_task=None, get_value_executer=None,
set_value_executer=None, reset_executer=None):
""" Execute a repeated SED task
Args:
Expand Down Expand Up @@ -451,7 +470,7 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
:obj:`VariableResults`: results of the variables
"""
# warn about inability to not reset models
if not task.reset_model_for_each_iteration:
if not task.reset_model_for_each_iteration and not reset_executer:
models = get_first_last_models_executed_by_task(task)
if models[0] == models[-1]:
msg = (
Expand All @@ -462,7 +481,8 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **

sub_tasks = sorted(task.sub_tasks, key=lambda sub_task: sub_task.order)
for prev_sub_task, next_sub_task in zip(sub_tasks[0:-1], sub_tasks[1:]):
if get_first_last_models_executed_by_task(prev_sub_task.task)[-1] == get_first_last_models_executed_by_task(next_sub_task.task)[0]:
if get_first_last_models_executed_by_task(prev_sub_task.task)[-1] == get_first_last_models_executed_by_task(next_sub_task.task)[0] \
and not reset_executer:
msg = (
'Only independent execution of sub-tasks is supported. '
'Successive sub-tasks will not be executed starting from the end state of the previous sub-task.'
Expand Down Expand Up @@ -500,6 +520,8 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
doc = copy.deepcopy(original_doc)
task = next(task for task in doc.tasks if task.id == original_task.id)
model_etrees = copy.deepcopy(original_model_etrees)
if reset_executer:
reset_executer(preprocessed_task)

# get range values
current_range_values = {}
Expand All @@ -514,27 +536,35 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
for change in task.changes:
variable_values = {}
for variable in change.variables:
if not apply_xml_model_changes:
if get_value_executer and preprocessed_task:
value = get_value_executer(change.model, variable, preprocessed_task)
variable_values[variable.id] = value
elif not apply_xml_model_changes:
raise NotImplementedError('Set value changes that involve variables of non-XML-encoded models are not supported.')
variable_values[variable.id] = get_value_of_variable_model_xml_targets(variable, model_etrees)
else:
variable_values[variable.id] = get_value_of_variable_model_xml_targets(variable, model_etrees)

new_value = calc_compute_model_change_new_value(change, variable_values=variable_values, range_values=current_range_values)
if new_value == int(new_value):
new_value = str(int(new_value))

if set_value_executer:
set_value_executer(change.model, change.target, change.symbol, new_value, preprocessed_task)
else:
new_value = str(new_value)
if new_value == int(new_value):
new_value = str(int(new_value))
else:
new_value = str(new_value)

if change.symbol:
raise NotImplementedError('Set value changes of symbols is not supported.')
if change.symbol:
raise NotImplementedError('Set value changes of symbols is not supported.')

attr_change = ModelAttributeChange(target=change.target, target_namespaces=change.target_namespaces, new_value=new_value)
attr_change = ModelAttributeChange(target=change.target, target_namespaces=change.target_namespaces, new_value=new_value)

if apply_xml_model_changes and is_model_language_encoded_in_xml(change.model.language):
model = Model(changes=[attr_change])
apply_changes_to_xml_model(model, model_etrees[change.model.id], None, None)
if apply_xml_model_changes and is_model_language_encoded_in_xml(change.model.language):
model = Model(changes=[attr_change])
apply_changes_to_xml_model(model, model_etrees[change.model.id], None, None)

else:
change.model.changes.append(attr_change)
else:
change.model.changes.append(attr_change)

# sort the sub-tasks
sub_tasks = sorted(task.sub_tasks, key=lambda sub_task: sub_task.order)
Expand All @@ -554,7 +584,7 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
standalone=False,
pretty_print=pretty_print_modified_xml_models)

sub_task_var_results = exec_task(sub_task.task, task_executer, task_vars, doc, config=config)
sub_task_var_results = exec_task(sub_task.task, task_executer, task_vars, doc, config=config, preprocessed_task=preprocessed_task)

if apply_xml_model_changes and is_model_language_encoded_in_xml(model.language):
os.remove(model.source)
Expand All @@ -565,7 +595,10 @@ def exec_task(task, variables, preprocessed_task=None, log=None, config=None, **
apply_xml_model_changes=apply_xml_model_changes,
model_etrees=model_etrees,
pretty_print_modified_xml_models=pretty_print_modified_xml_models,
config=config)
config=config, preprocessed_task=preprocessed_task,
get_value_executer=get_value_executer,
set_value_executer=set_value_executer,
reset_executer=reset_executer)

else: # pragma: no cover: already validated by :obj:`get_first_last_models_executed_by_task`
raise NotImplementedError('Tasks of type {} are not supported.'.format(sub_task.task.__class__.__name__))
Expand Down

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