Error for species in TR rate added and tested

Author: TorkelE

src/spatial_reaction_systems/spatial_reactions.jl

@@ -29,6 +29,9 @@ struct TransportReaction <: AbstractSpatialReaction
 
     # Creates a diffusion reaction.
     function TransportReaction(rate, species)
+        if any(!ModelingToolkit.isparameter(var) for var in ModelingToolkit.get_variables(rate)) 
+            error("TransportReaction rate contain variables: $(filter(var -> !ModelingToolkit.isparameter(var), ModelingToolkit.get_variables(rate))). The rate must consist of parameters only.")
+        end
         new(rate, species.val)
     end
 end
@@ -76,15 +79,29 @@ spatial_species(tr::TransportReaction) = [tr.species]
 
 # Checks that a transport reaction is valid for a given reaction system.
 function check_spatial_reaction_validity(rs::ReactionSystem, tr::TransportReaction; edge_parameters=[])
-    # Checks that the species exist in the reaction system (ODE simulation code becomes difficult if this is not required, as non-spatial jacobian and f function generated from rs is of wrong size).  
-    any(isequal(tr.species), species(rs)) || error("Currently, species used in TransportReactions must have previously been declared within the non-spatial ReactionSystem. This is not the case for $(tr.species).")
+    # Checks that the species exist in the reaction system.
+    # (ODE simulation code becomes difficult if this is not required, as non-spatial jacobian and f function generated from rs is of wrong size).  
+    if !any(isequal(tr.species), species(rs)) 
+        error("Currently, species used in TransportReactions must have previously been declared within the non-spatial ReactionSystem. This is not the case for $(tr.species).")
+    end
+
     # Checks that the rate does not depend on species.    
-    isempty(intersect(ModelingToolkit.getname.(species(rs)), ModelingToolkit.getname.(Symbolics.get_variables(tr.rate)))) || error("The following species were used in rates of a transport reactions: $(setdiff(ModelingToolkit.getname.(species(rs)), ModelingToolkit.getname.(Symbolics.get_variables(tr.rate)))).")
+    if !isempty(intersect(ModelingToolkit.getname.(species(rs)), ModelingToolkit.getname.(Symbolics.get_variables(tr.rate)))) 
+        error("The following species were used in rates of a transport reactions: $(setdiff(ModelingToolkit.getname.(species(rs)), ModelingToolkit.getname.(Symbolics.get_variables(tr.rate)))).")
+    end
+
     # Checks that the species does not exist in the system with different metadata.
-    any([isequal(tr.species, s) && !isequivalent(tr.species, s) for s in species(rs)]) && error("A transport reaction used a species, $(tr.species), with metadata not matching its lattice reaction system. Please fetch this species from the reaction system and used in transport reaction creation.")
-    any([isequal(rs_p, tr_p) && !equivalent_metadata(rs_p, tr_p) for rs_p in parameters(rs), tr_p in Symbolics.get_variables(tr.rate)]) && error("A transport reaction used a parameter with metadata not matching its lattice reaction system. Please fetch this parameter from the reaction system and used in transport reaction creation.")
+    if any([isequal(tr.species, s) && !isequivalent(tr.species, s) for s in species(rs)]) 
+        error("A transport reaction used a species, $(tr.species), with metadata not matching its lattice reaction system. Please fetch this species from the reaction system and used in transport reaction creation.")
+    end
+    if any([isequal(rs_p, tr_p) && !equivalent_metadata(rs_p, tr_p) for rs_p in parameters(rs), tr_p in Symbolics.get_variables(tr.rate)]) 
+        error("A transport reaction used a parameter with metadata not matching its lattice reaction system. Please fetch this parameter from the reaction system and used in transport reaction creation.")
+    end
+
     # Checks that no edge parameter occur among rates of non-spatial reactions.
-    any([!isempty(intersect(Symbolics.get_variables(r.rate), edge_parameters)) for r in reactions(rs)]) && error("Edge paramter(s) were found as a rate of a non-spatial reaction.")
+    if any([!isempty(intersect(Symbolics.get_variables(r.rate), edge_parameters)) for r in reactions(rs)])
+        error("Edge paramter(s) were found as a rate of a non-spatial reaction.")
+    end
 end
 equivalent_metadata(p1, p2) = isempty(setdiff(p1.metadata, p2.metadata, [Catalyst.EdgeParameter => true]))
 

test/spatial_reaction_systems/lattice_reaction_systems.jl

@@ -242,6 +242,16 @@ end
 
 ### Tests Error generation ###
 
+# Test creation of TransportReaction with non-parameters in rate.
+# Tests that it works even when rate is highly nested.
+let 
+    @variables t
+    @species X(t) Y(t)
+    @parameters D1 D2 D3
+    @test_throws ErrorException TransportReaction(D1 + D2*(D3 + Y), X)
+    @test_throws ErrorException TransportReaction(Y, X)
+end
+
 # Network where diffusion species is not declared in non-spatial network.
 let 
     rs = @reaction_network begin