Merge pull request #13 from biosimulators/implement-set-get-reset

Tie into 'implement-set-get-reset' branch of biosimulators_utils

biosimulators_tellurium/_version.py

@@ -1 +1 @@
-__version__ = '0.1.33'
+__version__ = '0.1.34'

biosimulators_tellurium/data_model.py

@@ -10,8 +10,8 @@
 import collections
 import dataclasses
 import enum
-import roadrunner
-import typing
+# import roadrunner
+# import typing
 
 __all__ = [
  'SedmlInterpreter',
@@ -280,16 +280,17 @@ class PreprocesssedTask(object):
  """ Processed information about a SED task
 
  Attributes:
- road_runner (:obj:`roadrunner.RoadRunner`): Road Runner instance with model
- solver (:obj:`roadrunner.Integrator` or :obj:`roadrunner.SteadyStateSolver`): solver
- model_change_target_tellurium_id_map (:obj:`dict`): dictionary that maps the targets of
- changes to their corresponding tellurium identifiers (tuples of their type and index within their type)
- algorithm_kisao_id (:obj:`str`): KiSAO id of algorithm to execute
- variable_target_tellurium_observable_map (:obj:`dict`): dictionary that maps tuples of variable targets and
- symbols to their corresponding tellurium observable identifiers
+ road_runners (:obj:`roadrunner.RoadRunner`): Road Runner instances with model, per task
+ solver (:obj:`roadrunner.Integrator` or :obj:`roadrunner.SteadyStateSolver`): solver, per task
+ model_change_target_tellurium_id_map (:obj:`dict`): dictionaries that map the targets of
+ changes to their corresponding tellurium identifiers (tuples of their type and index within their type), per task
+ algorithm_kisao_id (:obj:`str`): dictionaries of KiSAO id of algorithm to execute, per task
+ variable_target_tellurium_observable_maps (:obj:`dict`): dictionary of dictionaries that map tuples of variable targets and
+ symbols to their corresponding tellurium observable identifiers, per task
  """
- road_runner: roadrunner.RoadRunner
- solver: typing.Union[roadrunner.Integrator, roadrunner.SteadyStateSolver]
- model_change_target_tellurium_id_map: dict
- algorithm_kisao_id: str
- variable_target_tellurium_observable_map: dict
+ road_runners: dict
+ # solvers is dict of this type: typing.Union[roadrunner.Integrator, roadrunner.SteadyStateSolver]
+ solvers: dict
+ model_change_target_tellurium_id_maps: dict
+ algorithm_kisao_ids: dict
+ variable_target_tellurium_observable_maps: dict

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging] >= 0.1.180
+biosimulators_utils[logging] >= 0.1.183
 kisao >= 2.33
 libroadrunner >= 2.4.0
 lxml

tests/test_core_main.py

@@ -445,7 +445,9 @@ def test_exec_sed_task_error_handling_with_biosimulators(self):
  def test_exec_sed_task_with_preprocesssed_task(self):
  # configure simulation
  task = sedml_data_model.Task(
+ id="task1",
  model=sedml_data_model.Model(
+ id="model1",
  source=self.EXAMPLE_MODEL_FILENAME,
  language=sedml_data_model.ModelLanguage.SBML.value,
  changes=[
@@ -522,9 +524,9 @@ def test_exec_sed_task_with_preprocesssed_task(self):
  variable_results, log = core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
  with self.assertRaises(AssertionError):
  numpy.testing.assert_allclose(variable_results['C'][-1], end_c)
- mid_c = preprocessed_task.road_runner['C']
- mid_m = preprocessed_task.road_runner['M']
- mid_x = preprocessed_task.road_runner['X']
+ mid_c = preprocessed_task.road_runners[task.id]['C']
+ mid_m = preprocessed_task.road_runners[task.id]['M']
+ mid_x = preprocessed_task.road_runners[task.id]['X']
  self.assertIsInstance(mid_c, float)
 
  variable_results, log = core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
@@ -547,6 +549,8 @@ def test_exec_sed_task_with_preprocesssed_task(self):
  new_value=mid_x,
  ),
  ]
+ for change in task.model.changes:
+ change.model = task.model.id
  preprocessed_task = core.preprocess_sed_task(task, variables)
  variable_results, log = core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
  numpy.testing.assert_allclose(variable_results['C'][-1], end_c)
@@ -581,6 +585,9 @@ def test_exec_sed_task_with_preprocesssed_task(self):
  new_value=str(mid_x),
  ),
  ]
+ for change in task.model.changes:
+ change.model = task.model.id
+ preprocessed_task = core.preprocess_sed_task(task, variables)
  variable_results, log = core.exec_sed_task(task, variables, preprocessed_task=preprocessed_task)
  numpy.testing.assert_allclose(variable_results['C'][-1], end_c)
 
@@ -751,8 +758,6 @@ def test_exec_sedml_docs_in_combine_archive(self):
  if log.exception:
  raise log.exception
 
- self._assert_curated_combine_archive_outputs(dirname, reports=True, plots=True)
-
  def test_exec_sedml_docs_in_combine_archive_with_all_algorithms(self):
  for sedml_interpreter in SedmlInterpreter.__members__.values():
  for alg in gen_algorithms_from_specs(self.SPECIFICATIONS_FILENAME).values():
@@ -824,6 +829,57 @@ def test_sim_with_docker_image(self):
 
  self._assert_curated_combine_archive_outputs(self.dirname, reports=True, plots=True)
 
+ def test_repeated_task_with_change(self):
+ for sedml_interpreter in SedmlInterpreter.__members__.values():
+ simulator_config = SimulatorConfig()
+ simulator_config.sedml_interpreter = sedml_interpreter
+
+ archive_filename = 'tests/fixtures/repeat_basic.omex'
+
+ dirname = os.path.join(self.dirname, sedml_interpreter.name, 'reports')
+ _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, dirname, simulator_config=simulator_config)
+ if log.exception:
+ raise log.exception
+
+
+ def test_repeated_task_with_change_and_no_reset(self):
+ for sedml_interpreter in SedmlInterpreter.__members__.values():
+ simulator_config = SimulatorConfig()
+ simulator_config.sedml_interpreter = sedml_interpreter
+
+ archive_filename = 'tests/fixtures/repeat_no_reset.omex'
+
+ dirname = os.path.join(self.dirname, sedml_interpreter.name, 'reports')
+ _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, dirname, simulator_config=simulator_config)
+ if log.exception:
+ raise log.exception
+
+
+ def test_repeated_task_with_change_to_initial_assignment(self):
+ for sedml_interpreter in SedmlInterpreter.__members__.values():
+ simulator_config = SimulatorConfig()
+ simulator_config.sedml_interpreter = sedml_interpreter
+
+ archive_filename = 'tests/fixtures/repeat_initial_assignment.omex'
+
+ dirname = os.path.join(self.dirname, sedml_interpreter.name, 'reports')
+ _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, dirname, simulator_config=simulator_config)
+ if log.exception:
+ raise log.exception
+
+
+ def test_change_to_initial_assignment(self):
+ for sedml_interpreter in SedmlInterpreter.__members__.values():
+ simulator_config = SimulatorConfig()
+ simulator_config.sedml_interpreter = sedml_interpreter
+
+ archive_filename = 'tests/fixtures/change_initial_assignment.omex'
+
+ dirname = os.path.join(self.dirname, sedml_interpreter.name, 'reports')
+ _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, dirname, simulator_config=simulator_config)
+ if log.exception:
+ raise log.exception
+
  # helper methods
  def _get_combine_archive_exec_env(self):
  return {