chore: debugged model changing

Dockerfile

@@ -22,7 +22,7 @@
 
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.14"
+ARG VERSION="0.1.15"
 ARG SIMULATOR_VERSION=2.6.0
 
 # metadata

biosimulators_bionetgen/_version.py

@@ -1 +1 @@
-__version__ = '0.1.14'
+__version__ = '0.1.15'

biosimulators_bionetgen/core.py

@@ -8,7 +8,8 @@
 """
 
 from .io import read_task
-from .utils import (exec_bionetgen_task, preprocess_model_attribute_change, add_model_attribute_change_to_task, add_simulation_to_task,
+from .utils import (exec_bionetgen_task, preprocess_model_attribute_change, add_model_attribute_change_to_task,
+                    create_actions_for_simulation,
                     get_variables_results_from_observable_results, add_variables_to_model)
 from .warnings import IgnoredBnglFileContentWarning
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
@@ -21,6 +22,7 @@
                                                   UniformTimeCourseSimulation, Variable)
 from biosimulators_utils.sedml.exec import exec_sed_doc as base_exec_sed_doc
 from biosimulators_utils.utils.core import raise_errors_warnings
+import copy
 import warnings
 
 __all__ = ['exec_sedml_docs_in_combine_archive', 'exec_sed_doc', 'exec_sed_task', 'preprocess_sed_task']
@@ -145,6 +147,8 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
 
     # read the model from the BNGL file
     bionetgen_task = preprocessed_task['bionetgen_task']
+    preprocessed_actions = bionetgen_task.actions
+    bionetgen_task.actions = copy.deepcopy(preprocessed_actions)
 
     # validate and apply the model attribute changes to the BioNetGen task
     for change in task.model.changes:
@@ -154,6 +158,8 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     alg_kisao_id = preprocessed_task['algorithm_kisao_id']
 
     # execute the task
+    bionetgen_task.actions.extend(preprocessed_task['simulation_actions'])
+
     observable_results = exec_bionetgen_task(bionetgen_task)
 
     # get predicted values of the variables
@@ -168,6 +174,9 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
             'actions': bionetgen_task.actions,
         }
 
+    # clean up
+    bionetgen_task.actions = preprocessed_actions
+
     # return the values of the variables and log
     return variable_results, log
 
@@ -226,11 +235,12 @@ def preprocess_sed_task(task, variables, config=None):
     add_variables_to_model(bionetgen_task.model, variables)
 
     # apply the SED algorithm and its parameters to the BioNetGen task
-    alg_kisao_id = add_simulation_to_task(bionetgen_task, task.simulation)
+    simulation_actions, alg_kisao_id = create_actions_for_simulation(task.simulation)
 
     # return the values of the variables and log
     return {
         'bionetgen_task': bionetgen_task,
         'model_changes': model_changes,
+        'simulation_actions': simulation_actions,
         'algorithm_kisao_id': alg_kisao_id,
     }

biosimulators_bionetgen/utils.py

@@ -29,7 +29,7 @@
     'preprocess_model_attribute_change',
     'add_model_attribute_change_to_task',
     'add_variables_to_model',
-    'add_simulation_to_task',
+    'create_actions_for_simulation',
     'exec_bionetgen_task',
     'get_variables_results_from_observable_results',
 ]
@@ -70,7 +70,8 @@ def preprocess_model_attribute_change(task, change):
                     'type': 'replace_line_in_block',
                     'block': block,
                     'i_line': i_line,
-                    'new_line': lambda new_value: '{} {} {} {}'.format(obj_id, match.group(1), new_value, (match.group(3) or '').strip()).strip(),
+                    'new_line': lambda new_value: '{} {} {} {}'.format(
+                        obj_id, match.group(1), new_value, (match.group(3) or '').strip()).strip(),
                 }
 
         if not comp_changed:
@@ -241,11 +242,10 @@ def add_variables_to_model(model, variables):
         raise NotImplementedError(msg)
 
 
-def add_simulation_to_task(task, simulation, config=None):
-    """ Add a SED simulation to a BioNetGen task
+def create_actions_for_simulation(simulation, config=None):
+    """ Create BioNetGen actions for a SED simulation
 
     Args:
-        task (:obj:`Task`): BioNetGen task
         simulation (:obj:`UniformTimeCourseSimulation`): SED simulation
         config (:obj:`Config`, optional): configuration
 
@@ -254,7 +254,10 @@ def add_simulation_to_task(task, simulation, config=None):
             algorithm parameters
 
     Returns:
-        :obj:`str`: KiSAO id of the algorithm that will be executed
+        :obj:`tuple`:
+
+            * :obj:`list` of :obj:`str`: actions for SED simulation
+            * :obj:`str`: KiSAO id of the algorithm that will be executed
     """
     simulate_args = OrderedDict()
 
@@ -311,15 +314,17 @@ def add_simulation_to_task(task, simulation, config=None):
                     ])
                     warn(msg, BioSimulatorsWarning)
 
-    # if necessary add network generation to the BioNetGen task
+    # if necessary create a network generation action
+    actions = []
+
     if simulation_method['generate_network']:
-        task.actions.append("generate_network({overwrite => 1})")
+        actions.append("generate_network({overwrite => 1})")
 
-    # add the simulation to the BioNetGen task
-    task.actions.append('simulate({{{}}})'.format(', '.join('{} => {}'.format(key, val) for key, val in simulate_args.items())))
+    # create a simulation action
+    actions.append('simulate({{{}}})'.format(', '.join('{} => {}'.format(key, val) for key, val in simulate_args.items())))
 
-    # return the KiSAO id of the algorithm that will be executed
-    return exec_kisao_id
+    # return actions and the KiSAO id of the algorithm that will be executed
+    return actions, exec_kisao_id
 
 
 def exec_bionetgen_task(task):

tests/test_core_main.py

@@ -20,6 +20,7 @@
 from biosimulators_utils.simulator.exec import exec_sedml_docs_in_archive_with_containerized_simulator
 from biosimulators_utils.simulator.specs import gen_algorithms_from_specs
 from unittest import mock
+import copy
 import datetime
 import dateutil.tz
 import numpy
@@ -52,6 +53,25 @@ def test_exec_sed_task(self):
         self.assertEqual(variable_results['var_time'].size, sim.number_of_points + 1)
         numpy.testing.assert_allclose(variable_results['var_time'],
                                       numpy.linspace(sim.output_start_time, sim.output_end_time, sim.number_of_points + 1))
+        numpy.testing.assert_allclose(variable_results['var_A'][0], 4, rtol=1e-1)
+
+        doc2 = copy.deepcopy(doc)
+        doc2.tasks[0].model.changes.append(sedml_data_model.ModelAttributeChange(
+            target='species.A().initialCount',
+            new_value='5',
+        ))
+        variable_results_2, _ = exec_sed_task(doc2.tasks[0], variables)
+        numpy.testing.assert_allclose(variable_results_2['var_A'][0], 5, rtol=1e-1)
+        self.assertGreater(variable_results_2['var_A'][0], variable_results['var_A'][0])
+
+        doc3 = copy.deepcopy(doc)
+        doc3.tasks[0].model.changes.append(sedml_data_model.ModelAttributeChange(
+            target='species.A().initialCount',
+            new_value=6,
+        ))
+        variable_results_3, _ = exec_sed_task(doc3.tasks[0], variables)
+        numpy.testing.assert_allclose(variable_results_3['var_A'][0], 6, rtol=1e-1)
+        self.assertGreater(variable_results_3['var_A'][0], variable_results_2['var_A'][0])
 
     def test_exec_sed_task_non_zero_initial_time(self):
         doc = self._build_sed_doc()
@@ -75,7 +95,7 @@ def test_exec_sedml_docs_in_combine_archive(self):
         out_dir = os.path.join(self.dirname, 'out')
 
         config = get_config()
-        config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv,]
+        config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
         config.BUNDLE_OUTPUTS = True
         config.KEEP_INDIVIDUAL_OUTPUTS = True
 
@@ -92,7 +112,7 @@ def test_exec_sedml_docs_in_combine_archive_with_all_algorithms(self):
             out_dir = os.path.join(self.dirname, alg.kisao_id)
 
             config = get_config()
-            config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv,]
+            config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
             config.BUNDLE_OUTPUTS = True
             config.KEEP_INDIVIDUAL_OUTPUTS = True
 
@@ -171,8 +191,8 @@ def _build_sed_doc(self, algorithm=None):
             changes=[
                 sedml_data_model.ModelAttributeChange(target='functions.gfunc.expression', new_value='0.5*Atot^2/(10 + Atot^2)'),
                 sedml_data_model.ModelAttributeChange(target='functions.gfunc().expression', new_value='0.5*Atot^2/(10 + Atot^2)'),
-                sedml_data_model.ModelAttributeChange(target='species.A().initialCount', new_value='5'),
-                sedml_data_model.ModelAttributeChange(target='parameters.g1.value', new_value='16.0'),
+                sedml_data_model.ModelAttributeChange(target='species.A().initialCount', new_value='4'),
+                sedml_data_model.ModelAttributeChange(target='parameters.g1.value', new_value='18.0'),
             ],
         ))
         doc.simulations.append(sedml_data_model.UniformTimeCourseSimulation(

tests/test_utils.py

@@ -3,7 +3,7 @@
 from biosimulators_bionetgen.data_model import Task
 from biosimulators_bionetgen.utils import (add_model_attribute_change_to_task,
                                            add_variables_to_model,
-                                           add_simulation_to_task,
+                                           create_actions_for_simulation,
                                            exec_bionetgen_task,
                                            get_variables_results_from_observable_results,)
 from biosimulators_bionetgen.io import read_task, read_simulation_results, write_task
@@ -63,6 +63,10 @@ def test_add_model_attribute_change_to_task(self):
         add_model_attribute_change_to_task(task, change)
         self.assertEqual(task.actions[-1], 'setParameter("k_1", 1.0)')
 
+        change = ModelAttributeChange(target='parameters.k_1.value', new_value=2.0)
+        add_model_attribute_change_to_task(task, change)
+        self.assertEqual(task.actions[-1], 'setParameter("k_1", 2.0)')
+
         change = ModelAttributeChange(target='species.GeneA_00().initialCount', new_value='1')
         add_model_attribute_change_to_task(task, change)
         self.assertEqual(task.actions[-1], 'setConcentration("GeneA_00()", 1)')
@@ -140,9 +144,8 @@ def test_add_variables_to_task(self):
         with self.assertRaisesRegex(NotImplementedError, 'targets are not supported'):
             add_variables_to_model(task.model, [Variable(id='X', target='x')])
 
-    def test_add_simulation_to_task(self):
+    def test_create_actions_for_simulation(self):
         # CVODE
-        task = Task()
         simulation = UniformTimeCourseSimulation(
             initial_time=0.,
             output_start_time=10.,
@@ -155,44 +158,44 @@ def test_add_simulation_to_task(self):
                 ]
             ),
         )
-        add_simulation_to_task(task, simulation)
-        self.assertEqual(task.actions, [
+        actions, _ = create_actions_for_simulation(simulation)
+        self.assertEqual(actions, [
             'generate_network({overwrite => 1})',
             'simulate({t_start => 0.0, t_end => 20.0, n_steps => 20, method => "ode", atol => 1e-6})',
         ])
 
         # Error handling: non-integer steps
         simulation.output_end_time = 20.1
         with self.assertRaisesRegex(NotImplementedError, 'must specify an integer number of steps'):
-            add_simulation_to_task(task, simulation)
+            create_actions_for_simulation(simulation)
 
         # Error handling: non-zero initial time
         simulation.output_end_time = 20.0
         simulation.initial_time = 5.
         simulation.algorithm.kisao_id = 'KISAO_0000019'
-        add_simulation_to_task(task, simulation)
+        create_actions_for_simulation(simulation)
 
         simulation.initial_time = 5.
         simulation.algorithm.kisao_id = 'KISAO_0000263'
         with self.assertRaisesRegex(NotImplementedError, 'must be 0'):
-            add_simulation_to_task(task, simulation)
+            create_actions_for_simulation(simulation)
 
         # Error handling: unknown algorithm
         simulation.algorithm.kisao_id = 'KISAO_0000448'
         with self.assertRaisesRegex(AlgorithmCannotBeSubstitutedException, 'No algorithm can be substituted'):
-            add_simulation_to_task(task, simulation)
+            create_actions_for_simulation(simulation)
 
         # Error handling: unknown algorithm parameter
         simulation.algorithm.kisao_id = 'KISAO_0000019'
         simulation.algorithm.changes[0].kisao_id = 'KISAO_0000001'
 
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'NONE'}):
             with self.assertRaisesRegex(NotImplementedError, 'is not supported. Parameter must have'):
-                add_simulation_to_task(task, simulation)
+                create_actions_for_simulation(simulation)
 
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'SIMILAR_VARIABLES'}):
             with pytest.warns(BioSimulatorsWarning, match='is not supported. Parameter must have'):
-                add_simulation_to_task(task, simulation)
+                create_actions_for_simulation(simulation)
 
     def test_exec_bionetgen_task(self):
         model_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'test.bngl')
@@ -273,7 +276,7 @@ def test_get_parameters_variables_outputs_for_simulation(self):
             model_filename_2 = os.path.join(self.dirname, 'task.bngl')
             write_task(task, model_filename_2)
 
-            changes_2, sim, variables_2,plots_2 = get_parameters_variables_outputs_for_simulation(
+            changes_2, sim, variables_2, plots_2 = get_parameters_variables_outputs_for_simulation(
                 model_filename_2, None, UniformTimeCourseSimulation, None)
             for change, change_2 in zip(changes, changes_2):
                 self.assertTrue(change_2.is_equal(change))