Fix label indexes.

Seemingly, when we added the rules and converted things through sets, the indexes of the labels can change from the indexes of the results that PySCeS exports.  Happily, the results come with labels already, so this switches things up to just use those labels.

biosimulators_pysces/core.py

@@ -156,15 +156,18 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
     model.Simulate()
 
     # extract results
-    results = model.data_sim.getAllSimData(lbls=False)
+    results, labels = model.data_sim.getAllSimData(lbls=True)
     variable_results = VariableResults()
     variable_results_model_attr_map = preprocessed_task['model']['variable_results_model_attr_map']
     for variable in variables:
-        i_results, model_attr_name = variable_results_model_attr_map[(variable.target, variable.symbol)]
-        if i_results is not None:
-            variable_results[variable.id] = results[:, i_results][-(sim.number_of_points + 1):]
+        label = variable_results_model_attr_map[(variable.target, variable.symbol)]
+        index = labels.index(label)
+
+        if index is not None:
+            variable_results[variable.id] = results[:, index][-(sim.number_of_points + 1):]
         else:
-            variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), getattr(model, model_attr_name))
+            raise ValueError("No variable " + variable.id + " found in simulation output.")
+            #variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), getattr(model, model_attr_name))
 
     # log action
     if config.LOG:
@@ -339,18 +342,18 @@ def preprocess_sed_task(task, variables, config=None):
     for variable in variables:
         if variable.symbol:
             if variable.symbol == Symbol.time.value:
-                variable_results_model_attr_map[(variable.target, variable.symbol)] = (0, None)
+                variable_results_model_attr_map[(variable.target, variable.symbol)] = "Time"
             else:
                 unpredicted_symbols.append(variable.symbol)
 
         else:
             sbml_id = variable_target_sbml_id_map[variable.target]
             try:
                 i_dynamic = dynamic_ids.index(sbml_id)
-                variable_results_model_attr_map[(variable.target, variable.symbol)] = (i_dynamic, None)
+                variable_results_model_attr_map[(variable.target, variable.symbol)] = sbml_id
             except ValueError:
                 if sbml_id in fixed_ids:
-                    variable_results_model_attr_map[(variable.target, variable.symbol)] = (None, sbml_id)
+                    variable_results_model_attr_map[(variable.target, variable.symbol)] = sbml_id
                 else:
                     unpredicted_targets.append(variable.target)