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

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

Author: luciansmith

biosimulators_tellurium/_version.py

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

biosimulators_tellurium/core.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

biosimulators_tellurium/data_model.py

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

requirements.txt

@@ -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 {