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feat: separated task preprocessing from simulation
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@jonrkarr
jonrkarr committed Sep 16, 2021
1 parent c06277b commit d615b24
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Showing 8 changed files with 1,033 additions and 70 deletions.
2 changes: 1 addition & 1 deletion Dockerfile
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# Base OS
FROM python:3.9-slim-buster

ARG VERSION="0.0.6"
ARG VERSION="0.0.7"
ARG SIMULATOR_VERSION=3.0.0b

# metadata
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2 changes: 1 addition & 1 deletion biosimulators_ginsim/_version.py
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@@ -1 +1 @@
__version__ = '0.0.6'
__version__ = '0.0.7'
161 changes: 117 additions & 44 deletions biosimulators_ginsim/core.py
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Expand Up @@ -6,7 +6,7 @@
:License: MIT
"""

from .utils import (validate_simulation, get_variable_target_xpath_ids,
from .utils import (validate_simulation, get_variable_target_xpath_ids, validate_variables,
read_model, set_up_simulation, exec_simulation, get_variable_results)
from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
from biosimulators_utils.config import get_config, Config # noqa: F401
Expand All @@ -18,9 +18,12 @@
SteadyStateSimulation, UniformTimeCourseSimulation,
Variable, Symbol)
from biosimulators_utils.sedml.exec import exec_sed_doc as base_exec_sed_doc
from biosimulators_utils.sedml.utils import apply_changes_to_xml_model
from biosimulators_utils.utils.core import raise_errors_warnings
import copy
import lxml.etree
import os
import tempfile

__all__ = ['exec_sedml_docs_in_combine_archive', 'exec_sed_doc', 'exec_sed_task', 'preprocess_sed_task']

Expand Down Expand Up @@ -129,83 +132,153 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
model = task.model
sim = task.simulation

# read model
biolqm_model = preprocessed_task['model']
variable_target_sbml_id_map = preprocessed_task['variable_target_sbml_id_map']

# modify model
if model.changes:
if model.language == ModelLanguage.SBML.value:
allowed_change_types = ()
# allowed_change_types = (ModelAttributeChange,) # TODO: uncomment when bioLQM recognizes initial state
raise_errors_warnings(
validation.validate_model_change_types(model.changes, allowed_change_types),
error_summary='Changes for model `{}` are not supported.'.format(model.id))

model_etree = preprocessed_task['model_etree']

model = copy.deepcopy(model)
for change in model.changes:
change.new_value = str(int(float(change.new_value)))

apply_changes_to_xml_model(model, model_etree, sed_doc=None, working_dir=None)

model_file, model_filename = tempfile.mkstemp(suffix='.xml')
os.close(model_file)

model_etree.write(model_filename,
xml_declaration=True,
encoding="utf-8",
standalone=False,
pretty_print=False)

biolqm_model = read_model(model_filename, model.language)

os.remove(model_filename)

else:
raise_errors_warnings(
validation.validate_model_change_types(model.changes, ()),
error_summary='Changes for model `{}` are not supported.'.format(model.id))

# setup simulation
raise_errors_warnings(
*validate_simulation(sim),
error_summary='Simulation `{}` is invalid.'.format(sim.id))

alg_method_name = preprocessed_task['algorithm_method_name']
alg_method_args = preprocessed_task['algorithm_method_args'](sim)

# run simulation
raw_results = exec_simulation(alg_method_name, biolqm_model, alg_method_args)

# transform results
variable_results = get_variable_results(variables, model.language, variable_target_sbml_id_map, sim, raw_results)

# log action
if config.LOG:
log.algorithm = preprocessed_task['algorithm_kisao_id']
log.simulator_details = {
'method': alg_method_name,
'arguments': alg_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
"""
config = config or get_config()

# validate task
model = task.model
sim = task.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,
model.language,
(ModelLanguage.SBML, ModelLanguage.ZGINML)),
error_summary='Language for model `{}` is not supported.'.format(model.id))

if model.language == ModelLanguage.SBML.value:
allowed_change_types = (ModelAttributeChange,)
else:
allowed_change_types = ()
raise_errors_warnings(
validation.validate_model_change_types(task.model.changes, ()),
validation.validate_model_change_types(model.changes, allowed_change_types),
error_summary='Changes for model `{}` are not supported.'.format(model.id))
raise_errors_warnings(
*validation.validate_model_changes(task.model),
*validation.validate_model_changes(model),
error_summary='Changes for model `{}` are invalid.'.format(model.id))
raise_errors_warnings(
validation.validate_simulation_type(task.simulation,
validation.validate_simulation_type(sim,
(UniformTimeCourseSimulation, SteadyStateSimulation)),
error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
raise_errors_warnings(
*validation.validate_simulation(task.simulation),
*validation.validate_simulation(sim),
error_summary='Simulation `{}` is invalid.'.format(sim.id))
raise_errors_warnings(
*validate_simulation(task.simulation),
*validate_simulation(sim),
error_summary='Simulation `{}` is invalid.'.format(sim.id))

if not os.path.isfile(task.model.source):
raise FileNotFoundError('`{}` is not a file.'.format(task.model.source))
if not os.path.isfile(model.source):
raise FileNotFoundError('`{}` is not a file.'.format(model.source))

if model.language == ModelLanguage.SBML.value:
model_etree = lxml.etree.parse(task.model.source)
target_xpath_ids = get_variable_target_xpath_ids(variables, model_etree)
model_etree = lxml.etree.parse(model.source)
variable_target_sbml_id_map = get_variable_target_xpath_ids(variables, model_etree)
else:
model_etree = None
target_xpath_ids = None
variable_target_sbml_id_map = None

# validate model
if config.VALIDATE_SEDML_MODELS:
raise_errors_warnings(*validation.validate_model(task.model, [], working_dir='.'),
raise_errors_warnings(*validation.validate_model(model, [], working_dir='.'),
error_summary='Model `{}` is invalid.'.format(model.id),
warning_summary='Model `{}` may be invalid.'.format(model.id))

# read model
biolqm_model = read_model(model.source, model.language)

# validate variables
validate_variables(variables, biolqm_model, model.language, variable_target_sbml_id_map, sim)

# setup simulation
alg_kisao_id, method_name, method_args = set_up_simulation(sim, config=config)

# run simulation
raw_results = exec_simulation(method_name, biolqm_model, method_args)

# transform results
variable_results = get_variable_results(variables, model.language, target_xpath_ids, sim, raw_results)

# log action
if config.LOG:
log.algorithm = alg_kisao_id
log.simulator_details = {
'method': method_name,
'arguments': 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
# return preprocessed information
return {
'model': biolqm_model,
'model_etree': model_etree,
'variable_target_sbml_id_map': variable_target_sbml_id_map,
'algorithm_kisao_id': alg_kisao_id,
'algorithm_method_name': method_name,
'algorithm_method_args': method_args,
}
79 changes: 64 additions & 15 deletions biosimulators_ginsim/utils.py
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Expand Up @@ -24,11 +24,13 @@
import numpy
import os
import py4j.java_gateway # noqa: F401
import types # noqa: F401

__all__ = [
'validate_simulation',
'validate_time_course',
'get_variable_target_xpath_ids',
'validate_variables',
'read_model',
'set_up_simulation',
'exec_simulation',
Expand Down Expand Up @@ -123,6 +125,59 @@ def get_variable_target_xpath_ids(variables, model_etree):
)


def validate_variables(variables, model, model_language, target_xpath_ids, simulation):
""" Get the result of each SED-ML variable
Args:
variables (:obj:`list` of :obj:`Variable`): variables
model (:obj:`py4j.java_gateway.JavaObject`): bioLQM model
model_language (:obj:`str`): model language
target_xpath_ids (:obj:`dict`): dictionary that maps XPaths to the SBML qualitative ids
of the corresponding objects
simulation (:obj:`Simulation`): analysis
"""
component_ids = set(component.getNodeID() for component in model.getComponents())
invalid_variables = []

for variable in variables:
if variable.symbol:
if not (isinstance(simulation, UniformTimeCourseSimulation) and variable.symbol == Symbol.time.value):
invalid_variables.append('{}: symbol: {}'.format(variable.id, variable.symbol))
else:
if model_language == ModelLanguage.SBML.value:
id = target_xpath_ids[variable.target]
else:
id = variable.target

if id not in component_ids:
invalid_variables.append('{}: target: {}'.format(variable.id, variable.target))

if invalid_variables:
valid_variables = []

if isinstance(simulation, UniformTimeCourseSimulation):
valid_variables.append('symbol: {}'.format(Symbol.time.value))

for component_id in component_ids:
if model_language == ModelLanguage.SBML.value:
valid_variables.append(
"target: /sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@id='{}']".format(component_id))
else:
valid_variables.append(
'target: {}'.format(component_id))

raise ValueError((
'The following variables cannot be recorded:\n'
' {}\n'
'\n'
'Variables with the following symbols and targets can be recorded:\n'
' {}'
).format(
'\n '.join(sorted(invalid_variables)),
'\n '.join(sorted(valid_variables)),
))


def read_model(filename, language):
""" Read a model
Expand Down Expand Up @@ -160,7 +215,7 @@ def set_up_simulation(simulation, config=None):
* :obj:`str`: KiSAO of algorithm to execute
* :obj:`str`: name of the :obj:`biolqm` simulation/analysis method
* :obj:`list` of :obj:`str`: arguments for simulation method
* :obj:`types.LambdaType` of :obj:`Simulation` -> :obj:`list` of :obj:`str`: arguments for simulation method
"""
# simulation algorithm
alg_kisao_id = simulation.algorithm.kisao_id
Expand All @@ -174,7 +229,7 @@ def set_up_simulation(simulation, config=None):
simulation.__class__.__name__, exec_kisao_id, alg_props['name']))

method = alg_props['method']
method_args = alg_props['method_args'](simulation)
method_args = []

# Apply the algorithm parameter changes specified by `simulation.algorithm.parameter_changes`
if exec_kisao_id == alg_kisao_id:
Expand Down Expand Up @@ -211,7 +266,11 @@ def set_up_simulation(simulation, config=None):
warn('Unsuported algorithm parameter `{}` was ignored.'.format(change.kisao_id), BioSimulatorsWarning)

# return
return (exec_kisao_id, method, method_args)
return (
exec_kisao_id,
method,
lambda simulation: alg_props['method_args'](simulation) + method_args,
)


def exec_simulation(method_name, model, args=None):
Expand Down Expand Up @@ -253,28 +312,18 @@ def get_variable_results(variables, model_language, target_xpath_ids, simulation
for variable in variables:
variable_results[variable.id] = numpy.full((n_states,), numpy.nan)

invalid_variables = []
for i_state, state in enumerate(raw_results):
for variable in variables:
if variable.symbol:
if isinstance(simulation, UniformTimeCourseSimulation) and variable.symbol == Symbol.time.value:
variable_results[variable.id][i_state] = i_state
else:
invalid_variables.append('{}: symbol: {}'.format(variable.id, variable.symbol))
variable_results[variable.id][i_state] = i_state

else:
if model_language == ModelLanguage.SBML.value:
id = target_xpath_ids[variable.target]
else:
id = variable.target

variable_results[variable.id][i_state] = state.get(id, numpy.nan)
if i_state == 0 and numpy.isnan(variable_results[variable.id][i_state]):
invalid_variables.append('{}: target: {}'.format(variable.id, variable.target))

if invalid_variables:
raise ValueError('The following variables could not recorded:\n {}'.format(
'\n '.join(sorted(invalid_variables))))
variable_results[variable.id][i_state] = state[id]

if isinstance(simulation, UniformTimeCourseSimulation):
for key in variable_results.keys():
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
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@@ -1,4 +1,4 @@
biosimulators_utils[logging,sbml] >= 0.1.116
biosimulators_utils[logging,sbml] >= 0.1.120
ginsim >= 0.4.4
kisao >= 2.28
lxml
Expand Down
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