Merge pull request #20 from biosimulators/flexible-steady-state

Try presimulation with steady state algorithms.

biosimulators_tellurium/_version.py

@@ -1 +1 @@
-__version__ = '0.1.41'
+__version__ = '0.1.42'

biosimulators_tellurium/core.py

@@ -273,12 +273,41 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
 
  results = numpy.array(road_runner.simulate(sim.output_start_time, sim.output_end_time, sim.number_of_steps+1).tolist()).transpose()
  else:
- road_runner.steadyState()
- results = road_runner.getSteadyStateValues()
+ results = None
+ simdists = [0, 0.1, 1, 10, 100, 1000]
+ sd = 0
+ lasterr = ""
+ while sd < len(simdists) and results is None:
+ try:
+ if simdists[sd] > 0:
+ road_runner.resetAll()
+ if model.changes:
+ for change in model.changes:
+ component_id = preprocessed_task.model_change_target_tellurium_id_maps[task.id][(change.model,
+ change.target,
+ change.symbol)]
+ new_value = float(change.new_value)
+ road_runner[component_id] = new_value
+ road_runner.simulate(end=simdists[sd])
+ road_runner.steadyState()
+ results = road_runner.getSteadyStateValues()
+ except Exception as e:
+ lasterr = str(e)
+ sd += 1
+ if results is None:
+ msg = 'Steady state analysis failed with algorithm `{}` ({}):'.format(
+ preprocessed_task.algorithm_kisao_ids[task.id],
+ KISAO_ALGORITHM_MAP[preprocessed_task.algorithm_kisao_ids[task.id]]['id'])
+ msg += "\n '" + lasterr + "'"
+ for i_param in range(preprocessed_task.solvers[task.id].getNumParams()):
+ param_name = preprocessed_task.solvers[task.id].getParamName(i_param)
+ msg += '\n - {}: {}'.format(param_name, getattr(preprocessed_task.solvers[task.id], param_name))
+ raise ValueError(msg)
 
  # check simulation succeeded
  if config.VALIDATE_RESULTS and numpy.any(numpy.isnan(results)):
- msg = 'Simulation failed with algorithm `{}` ({})'.format(
+ msg = 'Simulation failed: ' + str(numpy.count_nonzero(numpy.isnan(results))) +\
+ ' nan value(s) found in results with algorithm `{}` ({})'.format(
  preprocessed_task.algorithm_kisao_ids[task.id],
  KISAO_ALGORITHM_MAP[preprocessed_task.algorithm_kisao_ids[task.id]]['id'])
  for i_param in range(preprocessed_task.solvers[task.id].getNumParams()):
@@ -425,51 +454,52 @@ def preprocess_sed_task(task, variables, config=None, simulator_config=None):
  error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
 
  # set the parameters of the solver
- if exec_alg_kisao_id == sim.algorithm.kisao_id:
- for change in sim.algorithm.changes:
- param_props = alg_props['parameters'].get(change.kisao_id, None)
- if not config.VALIDATE_SEDML or param_props:
- if not config.VALIDATE_SEDML or validate_str_value(change.new_value, param_props['type']):
- new_value = parse_value(change.new_value, param_props['type'])
- att = param_props['id']
- if "roadrunner_attribute" in param_props:
- att = param_props['roadrunner_attribute']
- setattr(solver, att, new_value)
-
- else:
- if (
- ALGORITHM_SUBSTITUTION_POLICY_LEVELS[algorithm_substitution_policy]
- <= ALGORITHM_SUBSTITUTION_POLICY_LEVELS[AlgorithmSubstitutionPolicy.NONE]
- ):
- msg = "'{}' is not a valid {} value for parameter {}".format(
- change.new_value, param_props['type'].name, change.kisao_id)
- raise ValueError(msg)
- else:
- msg = "'{}' was ignored because it is not a valid {} value for parameter {}".format(
- change.new_value, param_props['type'].name, change.kisao_id)
- warn(msg, BioSimulatorsWarning)
+ for change in sim.algorithm.changes:
+ param_props = alg_props['parameters'].get(change.kisao_id, None)
+ if not config.VALIDATE_SEDML or param_props:
+ if not config.VALIDATE_SEDML or validate_str_value(change.new_value, param_props['type']):
+ new_value = parse_value(change.new_value, param_props['type'])
+ att = param_props['id']
+ if "roadrunner_attribute" in param_props:
+ att = param_props['roadrunner_attribute']
+ setattr(solver, att, new_value)
 
  else:
  if (
+ exec_alg_kisao_id == sim.algorithm.kisao_id and
  ALGORITHM_SUBSTITUTION_POLICY_LEVELS[algorithm_substitution_policy]
  <= ALGORITHM_SUBSTITUTION_POLICY_LEVELS[AlgorithmSubstitutionPolicy.NONE]
  ):
- msg = "".join([
- "Algorithm parameter with KiSAO id '{}' is not supported. ".format(change.kisao_id),
- "Parameter must have one of the following KiSAO ids:\n - {}".format('\n - '.join(
- '{}: {} ({})'.format(kisao_id, param_props['id'], param_props['name'])
- for kisao_id, param_props in alg_props['parameters'].items())),
- ])
- raise NotImplementedError(msg)
+ msg = "'{}' is not a valid {} value for parameter {}".format(
+ change.new_value, param_props['type'].name, change.kisao_id)
+ raise ValueError(msg)
  else:
- msg = "".join([
- "Algorithm parameter with KiSAO id '{}' was ignored because it is not supported. ".format(change.kisao_id),
- "Parameter must have one of the following KiSAO ids:\n - {}".format('\n - '.join(
- '{}: {} ({})'.format(kisao_id, param_props['id'], param_props['name'])
- for kisao_id, param_props in alg_props['parameters'].items())),
- ])
+ msg = "'{}' was ignored because it is not a valid {} value for parameter {}".format(
+ change.new_value, param_props['type'].name, change.kisao_id)
  warn(msg, BioSimulatorsWarning)
 
+ else:
+ if (
+ exec_alg_kisao_id == sim.algorithm.kisao_id and
+ ALGORITHM_SUBSTITUTION_POLICY_LEVELS[algorithm_substitution_policy]
+ <= ALGORITHM_SUBSTITUTION_POLICY_LEVELS[AlgorithmSubstitutionPolicy.NONE]
+ ):
+ msg = "".join([
+ "Algorithm parameter with KiSAO id '{}' is not supported. ".format(change.kisao_id),
+ "Parameter must have one of the following KiSAO ids:\n - {}".format('\n - '.join(
+ '{}: {} ({})'.format(kisao_id, param_props['id'], param_props['name'])
+ for kisao_id, param_props in alg_props['parameters'].items())),
+ ])
+ raise NotImplementedError(msg)
+ else:
+ msg = "".join([
+ "Algorithm parameter with KiSAO id '{}' was ignored because it is not supported. ".format(change.kisao_id),
+ "Parameter must have one of the following KiSAO ids:\n - {}".format('\n - '.join(
+ '{}: {} ({})'.format(kisao_id, param_props['id'], param_props['name'])
+ for kisao_id, param_props in alg_props['parameters'].items())),
+ ])
+ warn(msg, BioSimulatorsWarning)
+
  # validate model changes and build map
  if isinstance(subtask, RepeatedTask):
  allchanges = allchanges + subtask.changes