#61: expose the collect_data method

basico/model_info.py

@@ -5113,13 +5113,24 @@ def _get_cn_string(cn):
         return cn.getString()
     return str(cn)
 
-def _collect_data(names=None, cns=None, **kwargs):
+def collect_data(names=None, cns=None, **kwargs):
     """Collects data from the model, returning it as dataframe
 
-    :param names: list of names of elements to return
+    :param names: list of display names of elements to return
     :type names: list or None
+    
     :param cns: list of common names of references for which to return the results
     :type cns: list or None
+
+    :param kwargs: optional parameters
+
+        - | `model`: to specify the data model to be used (if not specified
+          | the one from :func:`.get_current_model` will be taken)
+
+        - `preserve_names`: if set to True, the names will be preserved in the output
+                            otherwise the display name of the object will be used. Default is True 
+                            for names. It does not apply to cns.
+    
     :return: data frame with the results
     :rtype: pd.DataFrame
     """
@@ -5143,8 +5154,18 @@ def _collect_data(names=None, cns=None, **kwargs):
             data.append({'name': obj.getObjectDisplayName(), 'value': value})
 
     if names:
+        preseve_names = kwargs.get('preserve_names', True)
         for name in names:
-            obj = model.findObjectByDisplayName(name)
+            obj = None
+            if name == '[Time]':
+                # workaround for a bug in the python bindings
+                # where Time would always return the models time instead of potentially
+                # existing species called Time
+                obj = model.getModel().getMetabolite(name[1:-1])
+
+            if obj is None:
+                obj = model.findObjectByDisplayName(name)
+
             if obj is None:
                 # couldn't find that object in the model
                 logger.warning('No object for name: {0}'.format(name))
@@ -5165,7 +5186,7 @@ def _collect_data(names=None, cns=None, **kwargs):
                 else:
                     value = None
 
-            data.append({'name': obj.getObjectDisplayName(), 'value': value})
+            data.append({'name': name if preseve_names else obj.getObjectDisplayName(), 'value': value})
 
     return pandas.DataFrame(data=data).set_index('name')
 

basico/task_parameterestimation.py

@@ -1300,7 +1300,7 @@ def get_simulation_results(values_only=False, update_parameters=True, **kwargs):
             # run steady state
             steady_state_task.initializeRaw(COPASI.CCopasiTask.OUTPUT_UI)
             steady_state_task.processRaw(True)
-            data = basico.model_info._collect_data(cns=mapping[mapping.type == 'dependent']['cn'].to_list()).transpose()
+            data = basico.model_info.collect_data(cns=mapping[mapping.type == 'dependent']['cn'].to_list()).transpose()
 
             for j in range(1, num_independent_points):
                 container.applyInitialValues()
@@ -1314,7 +1314,7 @@ def get_simulation_results(values_only=False, update_parameters=True, **kwargs):
                     _update_fit_parameters_from(dm, solution, exp_name)
                 steady_state_task.processRaw(True)
 
-                new_row = basico.model_info._collect_data(
+                new_row = basico.model_info.collect_data(
                     cns=mapping[mapping.type == 'dependent']['cn'].to_list()).transpose()
                 data = pd.concat([data, new_row], ignore_index=True)
 

tests/test_basico_info.py

@@ -181,7 +181,7 @@ def test_collect_data(self):
         mod = basico.get_current_model().getModel()
         assert (isinstance(mod, COPASI.CModel))
         mod.applyInitialValues()
-        data = basico.model_info._collect_data(cns=[
+        data = basico.model_info.collect_data(cns=[
             'CN=Root,Model=The Brusselator,Reference=Time',
             'CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Reference=InitialVolume',
             'CN=Root,Model=The Brusselator,Vector=Compartments[compartment],Reference=Rate',
@@ -200,7 +200,7 @@ def test_collect_data(self):
             'CN=Root,Model=The Brusselator,Vector=Reactions[R1],ParameterGroup=Parameters,Parameter=k1,Reference=Value'
         ])
 
-        data2 = basico.model_info._collect_data(names=[
+        data2 = basico.model_info.collect_data(names=[
             'Time',
             'Compartments[compartment].InitialVolume',
             'Compartments[compartment].Rate',
@@ -643,6 +643,12 @@ def test_multiple_elements_with_same_name(self):
         result2 = basico.run_time_course_with_output(['Time', '[Time]'])
         self.assertListEqual(result2.columns.tolist(), ['Time', '[Time]'])
 
+        # test using collect:
+        data = basico.model_info.collect_data(names=['Time', '[Time]'])
+        self.assertTrue(data is not None)
+        self.assertListEqual(data.index.to_list(), ['Time', '[Time]'])
+
+
         names = basico.model_info._get_name_map(dm)
         self.assertGreater(len(names['Time']), 1)
 
@@ -651,6 +657,7 @@ def test_multiple_elements_with_same_name(self):
 
         names2 = basico.model_info._get_name_map(dm)
         self.assertEqual(len(names2['Time']), 1)
+
 
         basico.remove_datamodel(dm);