feat: added recording parameter values, reaction fluxes, compartment …

…sizes

Dockerfile

@@ -1,7 +1,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.15"
+ARG VERSION="0.1.16"
 ARG SIMULATOR_VERSION="0.11.18"
 
 # metadata

biosimulators.json

@@ -261,7 +261,15 @@
         {
           "variables": "parameter values",
           "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter/@value"
-        }
+        },
+        {
+          "variables": "reaction fluxes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction"
+        },
+        {
+          "variables": "compartment sizes",
+          "targetPattern": "/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment"
+        }        
       ],
       "availableSoftwareInterfaceTypes": [
         "library",

biosimulators_amici/_version.py

@@ -1 +1 @@
-__version__ = '0.1.15'
+__version__ = '0.1.16'

biosimulators_amici/core.py

@@ -319,7 +319,7 @@ def extract_variables_from_results(model, sbml_model, variables, target_x_paths_
         :obj:`NotImplementedError`: if a symbol could not be recorded
         :obj:`ValueError`: if a target could not be recorded
     """
-    var_id_to_state_index = {id: index for index, id in enumerate(model.getStateIds())}
+    sbml_id_to_obs_index = {id: index for index, id in enumerate(model.getObservableIds())}
 
     variable_results = VariableResults()
     unpredicted_symbols = []
@@ -332,12 +332,12 @@ def extract_variables_from_results(model, sbml_model, variables, target_x_paths_
                 unpredicted_symbols.append(variable.symbol)
 
         else:
-            var_id = target_x_paths_ids.get(variable.target, None)
-            i_state = var_id_to_state_index.get(var_id, None)
-            if i_state is None:
+            sbml_id = target_x_paths_ids.get(variable.target, None)
+            i_obs = sbml_id_to_obs_index.get(sbml_id, None)
+            if i_obs is None:
                 unpredicted_targets.append(variable.target)
             else:
-                variable_results[variable.id] = results['x'][:, i_state]
+                variable_results[variable.id] = results['y'][:, i_obs]
 
     if unpredicted_symbols:
         raise NotImplementedError("".join([
@@ -353,10 +353,7 @@ def extract_variables_from_results(model, sbml_model, variables, target_x_paths_
                 '\n  - '.join(sorted(unpredicted_targets)),
             ),
             'Targets must have one of the following ids:\n  - {}'.format(
-                '\n  - '.join(sorted((
-                    [s.getId() for s in sbml_model.species]
-                    + [p.getId() for p in sbml_model.parameters]
-                ))),
+                '\n  - '.join(sorted(model.getObservableIds())),
             ),
         ]))
 

tests/test_core_main.py

@@ -87,6 +87,86 @@ def test_exec_sed_task_successfully(self):
                 target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='IL']",
                 target_namespaces=self.NAMESPACES,
                 task=task),
+            sedml_data_model.Variable(
+                id='kf_0',
+                target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='kf_0']",
+                target_namespaces=self.NAMESPACES,
+                task=task),
+            sedml_data_model.Variable(
+                id='comp1',
+                target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='comp1']",
+                target_namespaces=self.NAMESPACES,
+                task=task),
+            sedml_data_model.Variable(
+                id='React0',
+                target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='React0']",
+                target_namespaces=self.NAMESPACES,
+                task=task),
+        ]
+
+        variable_results, _ = core.exec_sed_task(task, variables)
+
+        self.assertTrue(sorted(variable_results.keys()), sorted([var.id for var in variables]))
+        self.assertEqual(variable_results[variables[0].id].shape, (task.simulation.number_of_points + 1,))
+        numpy.testing.assert_almost_equal(
+            variable_results['time'],
+            numpy.linspace(task.simulation.output_start_time, task.simulation.output_end_time, task.simulation.number_of_points + 1),
+        )
+
+        for results in variable_results.values():
+            self.assertFalse(numpy.any(numpy.isnan(results)))
+        numpy.testing.assert_almost_equal(
+            variable_results['kf_0'],
+            numpy.full((task.simulation.number_of_points + 1), 300000000.),
+        )
+        numpy.testing.assert_almost_equal(
+            variable_results['comp1'],
+            numpy.full((task.simulation.number_of_points + 1), 1E-16),
+        )
+
+    def test_exec_sed_task_successfully_with_assignment_rule(self):
+        task = sedml_data_model.Task(
+            model=sedml_data_model.Model(
+                source=os.path.join(os.path.dirname(__file__), 'fixtures', 'BIOMD0000000297_url.xml'),
+                language=sedml_data_model.ModelLanguage.SBML.value,
+                changes=[],
+            ),
+            simulation=sedml_data_model.UniformTimeCourseSimulation(
+                algorithm=sedml_data_model.Algorithm(
+                    kisao_id='KISAO_0000496',
+                ),
+                initial_time=0.,
+                output_start_time=0.,
+                output_end_time=10.,
+                number_of_points=10,
+            ),
+        )
+
+        variables = [
+            sedml_data_model.Variable(
+                id='time',
+                symbol=sedml_data_model.Symbol.time,
+                task=task),
+            sedml_data_model.Variable(
+                id='kswe',
+                target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='kswe']",
+                target_namespaces=self.NAMESPACES,
+                task=task),
+            sedml_data_model.Variable(
+                id='kswe_prime',
+                target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='kswe_prime']",
+                target_namespaces=self.NAMESPACES,
+                task=task),
+            sedml_data_model.Variable(
+                id='compartment',
+                target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']",
+                target_namespaces=self.NAMESPACES,
+                task=task),
+            sedml_data_model.Variable(
+                id='R1',
+                target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='R1']",
+                target_namespaces=self.NAMESPACES,
+                task=task),
         ]
 
         variable_results, _ = core.exec_sed_task(task, variables)
@@ -100,6 +180,14 @@ def test_exec_sed_task_successfully(self):
 
         for results in variable_results.values():
             self.assertFalse(numpy.any(numpy.isnan(results)))
+        numpy.testing.assert_almost_equal(
+            variable_results['kswe_prime'],
+            numpy.full((task.simulation.number_of_points + 1), 2.),
+        )
+        numpy.testing.assert_almost_equal(
+            variable_results['compartment'],
+            numpy.full((task.simulation.number_of_points + 1), 1.),
+        )
 
     def test_exec_sed_task_error_handling(self):
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'NONE'}):