Weird fix to problem where removing and re-adding the biomass reactio…

…n would raise an exception claiming that the reverse variable is already present in the solver variable container.

cameo/core/solver_based_model.py

@@ -229,6 +229,7 @@ def _populate_solver(self, reaction_list):
         if self.solver.objective is None:
             self.solver.objective = self.solver.interface.Objective(objective_expression, name='obj', direction='max')
         else:
+            self.solver.objective.variables  # TODO: remove this weird hack. Looks like some weird issue with lazy objective expressions in CPLEX and GLPK interface in optlang.
             self.solver.objective += objective_expression
 
     def add_reactions(self, reaction_list):
@@ -246,7 +247,8 @@ def add_reactions(self, reaction_list):
 
     def remove_reactions(self, the_reactions):
         for reaction in the_reactions:
-            self.solver.remove(reaction.id)
+            self.solver.remove(reaction.forward_variable)
+            self.solver.remove(reaction.reverse_variable)
         super(SolverBasedModel, self).remove_reactions(the_reactions)
 
     def add_demand(self, metabolite, prefix="DM_"):

tests/test_solver_based_model.py

@@ -564,6 +564,10 @@ def test_remove_reactions(self):
         for reaction in reactions_to_remove:
             self.assertNotIn(reaction.id, list(self.model.solver.variables.keys()))
 
+        self.model.add_reactions(reactions_to_remove)
+        for reaction in reactions_to_remove:
+            self.assertIn(reaction, self.model.reactions)
+
     def test_add_demand(self):
         for metabolite in self.model.metabolites:
             demand_reaction = self.model.add_demand(metabolite, prefix="DemandReaction_")