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feat: added support for observables for parameters, compartments not …
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…set via assignment rules; separated task preprocessing; added test for negative initial times
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@jonrkarr
jonrkarr committed Sep 12, 2021
1 parent 53f26ed commit adebb75
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23 changes: 23 additions & 0 deletions biosimulators.json
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Expand Up @@ -298,9 +298,17 @@
"variables": "species concentrations",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
},
{
"variables": "constant parameter values",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@constant!='false']"
},
{
"variables": "reaction fluxes",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
},
{
"variables": "constant compartment sizes",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@constant!='false']"
}
],
"availableSoftwareInterfaceTypes": [
Expand Down Expand Up @@ -464,9 +472,17 @@
"variables": "species concentrations",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species"
},
{
"variables": "constant parameter values",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@constant!='false']"
},
{
"variables": "reaction fluxes",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
},
{
"variables": "constant compartment sizes",
"targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@constant!='false']"
}
],
"availableSoftwareInterfaceTypes": [
Expand All @@ -476,6 +492,13 @@
"BioSimulators Docker image"
],
"dependencies": [
{
"name": "Assimulo",
"version": null,
"required": true,
"freeNonCommercialLicense": true,
"url": "https://jmodelica.org/assimulo/"
},
{
"name": "SUNDIALS",
"version": null,
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210 changes: 121 additions & 89 deletions biosimulators_pysces/core.py
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Expand Up @@ -12,7 +12,7 @@
from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog, StandardOutputErrorCapturerLevel # noqa: F401
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, UniformTimeCourseSimulation, # noqa: F401
from biosimulators_utils.sedml.data_model import (Task, ModelLanguage, ModelAttributeChange, UniformTimeCourseSimulation, # noqa: F401
Variable, Symbol)
from biosimulators_utils.utils.core import validate_str_value, parse_value
from biosimulators_utils.sedml import validation
Expand Down Expand Up @@ -126,43 +126,115 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
if preprocessed_task is None:
preprocessed_task = preprocess_sed_task(task, variables, config=config)

model = task.model
# get the model configured with simulation algorithm and its parameters
model = preprocessed_task['model']['model']

# modify model
raise_errors_warnings(validation.validate_model_change_types(task.model.changes, (ModelAttributeChange, )),
error_summary='Changes for model `{}` are not supported.'.format(task.model.id))
model_change_target_sbml_id_map = preprocessed_task['model']['change_target_sbml_id_map']
for change in task.model.changes:
sbml_id = model_change_target_sbml_id_map[change.target]
new_value = float(change.new_value)
setattr(model, sbml_id + '_init', new_value)

# setup time course
sim = task.simulation
model.sim_start = sim.initial_time
model.sim_end = sim.output_end_time
model.sim_points = (
sim.number_of_points
* (sim.output_end_time - sim.initial_time)
/ (sim.output_end_time - sim.output_start_time)
+ 1
)
if model.sim_points != int(model.sim_points):
raise NotImplementedError('Time course must specify an integer number of time points')

# execute simulation
model.Simulate()

# extract results
results = model.data_sim.getAllSimData(lbls=False)
variable_results = VariableResults()
variable_results_model_attr_map = preprocessed_task['model']['variable_results_model_attr_map']
for variable in variables:
i_results, model_attr_name = variable_results_model_attr_map[(variable.target, variable.symbol)]
if i_results is not None:
variable_results[variable.id] = results[:, i_results][-(sim.number_of_points + 1):]
else:
variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), getattr(model, model_attr_name))

# log action
if config.LOG:
log.algorithm = preprocessed_task['simulation']['algorithm_kisao_id']

arguments = {}
for key, val in model.__settings__.items():
if model.mode_integrator == 'CVODE':
if key.startswith('cvode_'):
arguments[key] = val
else:
if key.startswith('lsoda_'):
arguments[key] = val

log.simulator_details = {
'method': model.Simulate.__module__ + '.' + model.Simulate.__name__,
'arguments': arguments,
}

# return results 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
"""
config = config or get_config()

# validate simulation
if config.VALIDATE_SEDML:
raise_errors_warnings(validation.validate_task(task),
error_summary='Task `{}` is invalid.'.format(task.id))
raise_errors_warnings(validation.validate_model_language(task.model.language, ModelLanguage.SBML),
error_summary='Language for model `{}` is not supported.'.format(model.id))
raise_errors_warnings(validation.validate_model_change_types(task.model.changes, ()),
error_summary='Changes for model `{}` are not supported.'.format(model.id))
error_summary='Language for model `{}` is not supported.'.format(task.model.id))
raise_errors_warnings(validation.validate_model_change_types(task.model.changes, (ModelAttributeChange, )),
error_summary='Changes for model `{}` are not supported.'.format(task.model.id))
raise_errors_warnings(*validation.validate_model_changes(task.model),
error_summary='Changes for model `{}` are invalid.'.format(model.id))
error_summary='Changes for model `{}` are invalid.'.format(task.model.id))
raise_errors_warnings(validation.validate_simulation_type(task.simulation, (UniformTimeCourseSimulation, )),
error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
error_summary='{} `{}` is not supported.'.format(task.simulation.__class__.__name__, task.simulation.id))
raise_errors_warnings(*validation.validate_simulation(task.simulation),
error_summary='Simulation `{}` is invalid.'.format(sim.id))
error_summary='Simulation `{}` is invalid.'.format(task.simulation.id))
raise_errors_warnings(*validation.validate_data_generator_variables(variables),
error_summary='Data generator variables for task `{}` are invalid.'.format(task.id))

model_etree = lxml.etree.parse(task.model.source)
target_x_paths_to_sbml_ids = validation.validate_target_xpaths(variables, model_etree, attr='id')

# Get the current working directory because PySCeS opaquely changes it
cwd = os.getcwd()
change_target_sbml_id_map = validation.validate_target_xpaths(task.model.changes, model_etree, attr='id')
variable_target_sbml_id_map = validation.validate_target_xpaths(variables, model_etree, attr='id')

# Read the model
interfaces = pysces.PyscesInterfaces.Core2interfaces()
fid, model_filename = tempfile.mkstemp(suffix='.psc')
os.close(fid)
sbml_model_filename = task.model.source
pysces_interface = pysces.PyscesInterfaces.Core2interfaces()
pysces_model_file, pysces_model_filename = tempfile.mkstemp(suffix='.psc')
os.close(pysces_model_file)
try:
interfaces.convertSBML2PSC(sbmlfile=task.model.source, pscfile=model_filename)
pysces_interface.convertSBML2PSC(sbmlfile=sbml_model_filename, pscfile=pysces_model_filename)
except Exception as exception:
os.remove(model_filename)
os.remove(pysces_model_filename)
raise ValueError('Model at {} could not be imported:\n {}'.format(
task.model.source, str(exception).replace('\n', '\n ')))
model = pysces.model(model_filename)
os.remove(model_filename)
model = pysces.model(pysces_model_filename)
os.remove(pysces_model_filename)

# Load the algorithm specified by `simulation.algorithm.kisao_id`
sim = task.simulation
Expand Down Expand Up @@ -233,99 +305,59 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
if model.mode_integrator == 'CVODE':
model.__settings__['cvode_return_event_timepoints'] = False

# setup time course
model.sim_start = sim.initial_time
model.sim_end = sim.output_end_time
model.sim_points = (
sim.number_of_points
* (sim.output_end_time - sim.initial_time)
/ (sim.output_end_time - sim.output_start_time)
+ 1
)
if model.sim_points != int(model.sim_points):
raise NotImplementedError('Time course must specify an integer number of time points')
# validate and preprocess variables
dynamic_ids = ['Time'] + list(model.species) + list(model.reactions)
fixed_ids = (set(model.parameters) | set(model.__compartments__.keys())).difference(set(model.__rules__.keys()))

# execute simulation
model.Simulate()
variable_results_model_attr_map = {}

# extract results
variable_results = VariableResults()
unpredicted_symbols = []
unpredicted_targets = []
results, labels = model.data_sim.getAllSimData(lbls=True)
labels = {label: i_label for i_label, label in enumerate(labels)}

for variable in variables:
if variable.symbol:
if variable.symbol == Symbol.time:
i_result = labels['Time']
variable_results[variable.id] = results[:, i_result][-(sim.number_of_points + 1):]
if variable.symbol == Symbol.time.value:
variable_results_model_attr_map[(variable.target, variable.symbol)] = (0, None)
else:
unpredicted_symbols.append(variable.symbol)

else:
sbml_id = target_x_paths_to_sbml_ids[variable.target]
i_result = labels.get(sbml_id, None)
if i_result is not None:
variable_results[variable.id] = results[:, i_result][-(sim.number_of_points + 1):]
elif sbml_id in model.fixed_species:
variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), getattr(model, sbml_id))
else:
unpredicted_targets.append(variable.target)
sbml_id = variable_target_sbml_id_map[variable.target]
try:
i_dynamic = dynamic_ids.index(sbml_id)
variable_results_model_attr_map[(variable.target, variable.symbol)] = (i_dynamic, None)
except ValueError:
if sbml_id in fixed_ids:
variable_results_model_attr_map[(variable.target, variable.symbol)] = (None, sbml_id)
else:
unpredicted_targets.append(variable.target)

if unpredicted_symbols:
raise NotImplementedError("".join([
"The following variable symbols are not supported:\n - {}\n\n".format(
'\n - '.join(sorted(unpredicted_symbols)),
),
"Symbols must be one of the following:\n - {}".format(Symbol.time),
"Symbols must be one of the following:\n - {}".format(Symbol.time.value),
]))

if unpredicted_targets:
raise ValueError(''.join([
'The following variable targets could not be recorded:\n - {}\n\n'.format(
'The following variable targets cannot not be recorded:\n - {}\n\n'.format(
'\n - '.join(sorted(unpredicted_targets)),
),
'Targets must have one of the following ids:\n - {}'.format(
'\n - '.join(sorted(set(labels.keys()).difference(set(['Time'])))),
'Targets must have one of the following SBML ids:\n - {}'.format(
'\n - '.join(sorted(dynamic_ids + list(fixed_ids))),
),
]))

# restore working directory
os.chdir(cwd)

# log action
if config.LOG:
log.algorithm = 'KISAO_0000019' if model.mode_integrator == 'CVODE' else 'KISAO_0000088'

arguments = {}
for key, val in model.__settings__.items():
if model.mode_integrator == 'CVODE':
if key.startswith('cvode_'):
arguments[key] = val
else:
if key.startswith('lsoda_'):
arguments[key] = val

log.simulator_details = {
'method': model.Simulate.__module__ + '.' + model.Simulate.__name__,
'arguments': arguments,
}

# return results 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
# return preprocessed information
return {
'model': {
'model': model,
'change_target_sbml_id_map': change_target_sbml_id_map,
'variable_results_model_attr_map': variable_results_model_attr_map,
},
'simulation': {
'algorithm_kisao_id': 'KISAO_0000019' if model.mode_integrator == 'CVODE' else 'KISAO_0000088',
},
}

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