feat: separated simulation and pre-processing

Dockerfile

@@ -1,7 +1,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.0.5"
+ARG VERSION="0.0.6"
 ARG SIMULATOR_VERSION=8.0
 
 # metadata

biosimulators_xpp/_version.py

@@ -1 +1 @@
-__version__ = '0.0.5'
+__version__ = '0.0.6'

biosimulators_xpp/core.py

@@ -97,7 +97,7 @@ 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
@@ -127,36 +127,14 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
  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(model.language, ModelLanguage.XPP),
- error_summary='Language for model `{}` is not supported.'.format(model.id))
- 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))
- raise_errors_warnings(validation.validate_simulation_type(sim, (UniformTimeCourseSimulation, )),
- error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
- raise_errors_warnings(*validation.validate_simulation(sim),
- error_summary='Simulation `{}` is invalid.'.format(sim.id))
-
- if config.VALIDATE_SEDML_MODELS:
- 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
- _, _, xpp_sim = validate_model(model.source)
-
- # validate observables
- validate_variables(xpp_sim, variables)
+ xpp_sim = preprocessed_task['xpp_simulation']
 
  # model changes
  apply_model_changes(xpp_sim, model.changes)
 
  # setup simulation
- exec_kisao_id = set_up_simulation(sim, xpp_sim['simulation_method'], config=config)
+ exec_kisao_id = preprocessed_task['algorithm_kisao_id']
 
  # run simulation
  raw_results = exec_xpp_simulation(model.source, xpp_sim)
@@ -181,12 +159,46 @@ def preprocess_sed_task(task, variables, config=None):
  Args:
  task (:obj:`Task`): task
  variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
- preprocessed_task (:obj:`PreprocessedTask`, 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.
  config (:obj:`Config`, optional): BioSimulators common configuration
 
  Returns:
  :obj:`object`: preprocessed information about the task
  """
- pass
+ 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(model.language, ModelLanguage.XPP),
+ error_summary='Language for model `{}` is not supported.'.format(model.id))
+ 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))
+ raise_errors_warnings(validation.validate_simulation_type(sim, (UniformTimeCourseSimulation, )),
+ error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
+ raise_errors_warnings(*validation.validate_simulation(sim),
+ error_summary='Simulation `{}` is invalid.'.format(sim.id))
+
+ if config.VALIDATE_SEDML_MODELS:
+ 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
+ _, _, xpp_sim = validate_model(model.source)
+
+ # validate observables
+ validate_variables(xpp_sim, variables)
+
+ # setup simulation
+ exec_kisao_id = set_up_simulation(sim, xpp_sim['simulation_method'], config=config)
+
+ return {
+ 'xpp_simulation': xpp_sim,
+ 'algorithm_kisao_id': exec_kisao_id,
+ }