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feat: separated task processing from simulation
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@jonrkarr
jonrkarr committed Sep 18, 2021
1 parent 7e63500 commit 17fa565
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Showing 8 changed files with 409 additions and 139 deletions.
2 changes: 1 addition & 1 deletion Dockerfile
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# Base OS
FROM python:3.9-slim-buster

ARG VERSION="0.1.12"
ARG VERSION="0.1.13"
ARG SIMULATOR_VERSION=0.7.25

# metadata
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2 changes: 1 addition & 1 deletion biosimulators_cbmpy/_version.py
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__version__ = '0.1.12'
__version__ = '0.1.13'
190 changes: 137 additions & 53 deletions biosimulators_cbmpy/core.py
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Expand Up @@ -10,14 +10,15 @@
from .utils import (apply_algorithm_change_to_simulation_module_method_args,
apply_variables_to_simulation_module_method_args,
get_simulation_method_args, validate_variables,
get_results_of_variables,
get_results_paths_for_variables, get_results_of_variables,
get_default_solver_module_function_args)
from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
from biosimulators_utils.config import get_config, Config # noqa: F401
from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog, StandardOutputErrorCapturerLevel # noqa: F401
from biosimulators_utils.model_lang.sbml.utils import get_package_namespace as get_sbml_package_namespace
from biosimulators_utils.viz.data_model import VizFormat # noqa: F401
from biosimulators_utils.report.data_model import ReportFormat, VariableResults, SedDocumentResults # noqa: F401
from biosimulators_utils.sedml.data_model import (Task, ModelLanguage, SteadyStateSimulation, # noqa: F401
from biosimulators_utils.sedml.data_model import (Task, ModelLanguage, ModelAttributeChange, SteadyStateSimulation, # noqa: F401
Variable)
from biosimulators_utils.sedml import validation
from biosimulators_utils.sedml.exec import exec_sed_doc as base_exec_sed_doc
Expand All @@ -29,6 +30,7 @@
from kisao.utils import get_preferred_substitute_algorithm_by_ids
from lxml import etree
import cbmpy
import copy

__all__ = [
'exec_sedml_docs_in_combine_archive',
Expand Down Expand Up @@ -112,7 +114,7 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
Args:
task (:obj:`Task`): task
variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
preprocessed_task (:obj:`object`, optional): preprocessed information about the task, including possible
preprocessed_task (:obj:`dict`, optional): preprocessed information about the task, including possible
model changes and variables. This can be used to avoid repeatedly executing the same initialization
for repeated calls to this method.
log (:obj:`TaskLog`, optional): log for the task
Expand All @@ -130,12 +132,73 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
:obj:`NotImplementedError`: if the task is not of a supported type or involves an unsuported feature
'''
config = config or get_config()

if config.LOG and not log:
log = TaskLog()

if preprocessed_task is None:
preprocessed_task = preprocess_sed_task(task, variables, config=config)

model = task.model

# Read the model
cbmpy_model = preprocessed_task['model']['model']

# modify model
if model.changes:
raise_errors_warnings(validation.validate_model_change_types(model.changes, (ModelAttributeChange,)),
error_summary='Changes for model `{}` are not supported.'.format(model.id))
model_change_setter_map = preprocessed_task['model']['model_change_setter_map']
for change in model.changes:
new_value = float(change.new_value)
model_change_setter_map[change.target](new_value)

# Set up simulation function and its keyword arguments
variable_target_sbml_id_map = preprocessed_task['model']['variable_target_sbml_id_map']
method_props = preprocessed_task['simulation']['method_props']
simulation_method_args = copy.copy(preprocessed_task['simulation']['method_args'])
apply_variables_to_simulation_module_method_args(variable_target_sbml_id_map, method_props, variables, simulation_method_args)

# Simulate the model
simulation_method = preprocessed_task['simulation']['method']
solution = simulation_method(cbmpy_model, **simulation_method_args)

# throw error if status isn't optimal
module_method_args = preprocessed_task['simulation']['module_method_args']
method_props['raise_if_simulation_error'](module_method_args, solution)

# get the result of each variable
variable_results = get_results_of_variables(
preprocessed_task['model']['variable_target_results_path_map'],
method_props, module_method_args['solver'],
variables, cbmpy_model, solution)

# log action
if config.LOG:
log.algorithm = preprocessed_task['simulation']['algorithm_kisao_id']
log.simulator_details = {
'method': simulation_method.__module__ + '.' + simulation_method.__name__,
'arguments': simulation_method_args,
}

# return the result of each variable and log
return variable_results, log


def preprocess_sed_task(task, variables, config=None):
""" Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
repeatedly initializing tasks on repeated calls of :obj:`exec_sed_task`.
Args:
task (:obj:`Task`): task
variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
config (:obj:`Config`, optional): BioSimulators common configuration
Returns:
:obj:`dict`: preprocessed information about the task
"""
config = config or get_config()

model = task.model
sim = task.simulation

Expand All @@ -144,7 +207,7 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
error_summary='Task `{}` is invalid.'.format(task.id))
raise_errors_warnings(validation.validate_model_language(model.language, ModelLanguage.SBML),
error_summary='Language for model `{}` is not supported.'.format(model.id))
raise_errors_warnings(validation.validate_model_change_types(model.changes, ()),
raise_errors_warnings(validation.validate_model_change_types(model.changes, (ModelAttributeChange,)),
error_summary='Changes for model `{}` are not supported.'.format(model.id))
raise_errors_warnings(*validation.validate_model_changes(model),
error_summary='Changes for model `{}` are invalid.'.format(model.id))
Expand All @@ -156,38 +219,78 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
error_summary='Data generator variables for task `{}` are invalid.'.format(task.id))

model_etree = etree.parse(model.source)
target_x_paths_ids = validation.validate_target_xpaths(
model_change_sbml_id_map = validation.validate_target_xpaths(
model.changes, model_etree, attr='id')
variable_target_sbml_id_map = validation.validate_target_xpaths(
variables, model_etree, attr='id')
namespaces = get_namespaces_for_xml_doc(model_etree)
target_x_paths_fbc_ids = validation.validate_target_xpaths(
sbml_fbc_prefix, sbml_fbc_uri = get_sbml_package_namespace('fbc', namespaces)
variable_target_sbml_fbc_id_map = validation.validate_target_xpaths(
variables,
model_etree,
attr={
'namespace': {
'prefix': 'fbc',
'uri': namespaces['fbc'],
'prefix': sbml_fbc_prefix,
'uri': sbml_fbc_uri,
},
'name': 'id',
}
)

# Read the model
model = cbmpy.CBRead.readSBML3FBC(model.source)
cbmpy_model = cbmpy.CBRead.readSBML3FBC(model.source)

# preprocess model changes
model_change_setter_map = {}
sbml_id_reaction_map = {rxn.id: rxn for rxn in cbmpy_model.reactions}
invalid_changes = []
for change in model.changes:
target = change.target
sbml_id = model_change_sbml_id_map[target]
reaction = sbml_id_reaction_map.get(sbml_id, None)
setter = None
if reaction:
attr = target.partition('/@')[2]
ns, _, attr = attr.partition(':')
ns = change.target_namespaces.get(ns, None)

if ns == sbml_fbc_uri:
if attr == 'lowerFluxBound':
setter = reaction.setLowerBound
elif attr == 'upperFluxBound':
setter = reaction.setUpperBound
if setter:
model_change_setter_map[change.target] = setter
else:
invalid_changes.append(change.target)

if invalid_changes:
valid_changes = []
for reaction in cbmpy_model.reactions:
valid_changes.append(
"/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='{}']/@fbc:lowerFluxBound".format(reaction.id))
valid_changes.append(
"/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='{}']/@fbc:upperFluxBound".format(reaction.id))

msg = 'The following changes are invalid:\n {}\n\nThe following targets are valid:\n {}'.format(
'\n '.join(sorted(invalid_changes)),
'\n '.join(sorted(valid_changes)),
)
raise ValueError(msg)

# Set up the algorithm specified by :obj:`task.simulation.algorithm.kisao_id`
algorithm_kisao_id = sim.algorithm.kisao_id
alg_substitution_policy = get_algorithm_substitution_policy(config=config)
exec_kisao_id = get_preferred_substitute_algorithm_by_ids(
algorithm_kisao_id, KISAO_ALGORITHMS_PARAMETERS_MAP.keys(),
sim.algorithm.kisao_id, KISAO_ALGORITHMS_PARAMETERS_MAP.keys(),
substitution_policy=alg_substitution_policy)
method_props = KISAO_ALGORITHMS_PARAMETERS_MAP[exec_kisao_id]

# Set up the the parameters of the algorithm
module_method_args = get_default_solver_module_function_args(exec_kisao_id)
if exec_kisao_id == algorithm_kisao_id:
if exec_kisao_id == sim.algorithm.kisao_id:
for change in sim.algorithm.changes:
try:
apply_algorithm_change_to_simulation_module_method_args(method_props, change, model, module_method_args)
apply_algorithm_change_to_simulation_module_method_args(method_props, change, cbmpy_model, module_method_args)
except NotImplementedError as exception:
if (
ALGORITHM_SUBSTITUTION_POLICY_LEVELS[alg_substitution_policy]
Expand All @@ -209,50 +312,31 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
else:
raise

# validate variables
validate_variables(method_props, variables)

# set keyword arguments based on desired outputs
apply_variables_to_simulation_module_method_args(target_x_paths_ids, method_props, variables, module_method_args)
# validate selected solver is available
if not module_method_args['solver']['module']:
raise ModuleNotFoundError('{} solver is not available.'.format(module_method_args['solver']['name']))

# Setup simulation function and its keyword arguments
simulation_method, simulation_method_args = get_simulation_method_args(method_props, module_method_args)

# Simulate the model
solution = simulation_method(model, **simulation_method_args)

# throw error if status isn't optimal
method_props['raise_if_simulation_error'](module_method_args, solution)

# get the result of each variable
variable_results = get_results_of_variables(target_x_paths_ids, target_x_paths_fbc_ids,
method_props, module_method_args['solver'],
variables, model, solution)

# log action
if config.LOG:
log.algorithm = exec_kisao_id
log.simulator_details = {
'method': simulation_method.__module__ + '.' + simulation_method.__name__,
'arguments': simulation_method_args,
# validate and preprocess variables
validate_variables(cbmpy_model, method_props, variables, variable_target_sbml_id_map, variable_target_sbml_fbc_id_map, sbml_fbc_uri)
variable_target_results_path_map = get_results_paths_for_variables(
cbmpy_model, method_props, variables, variable_target_sbml_id_map, variable_target_sbml_fbc_id_map)

# return preprocessed information
return {
'model': {
'model': cbmpy_model,
'model_change_setter_map': model_change_setter_map,
'variable_target_sbml_id_map': variable_target_sbml_id_map,
'variable_target_results_path_map': variable_target_results_path_map,
},
'simulation': {
'algorithm_kisao_id': exec_kisao_id,
'method': simulation_method,
'method_props': method_props,
'method_args': simulation_method_args,
'module_method_args': module_method_args,
}

# return the result of each variable and log
return variable_results, log


def preprocess_sed_task(task, variables, config=None):
""" Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
repeatedly initializing tasks on repeated calls of :obj:`exec_sed_task`.
Args:
task (:obj:`Task`): task
variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
config (:obj:`Config`, optional): BioSimulators common configuration
Returns:
:obj:`object`: preprocessed information about the task
"""
pass
}
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