Merge pull request #931 from SciML/serialization_updates

`ReactionSystem` serialisation update

src/reactionsystem_serialisation/serialisation_support.jl

@@ -247,6 +247,8 @@ end
 function make_strip_call_dict(syms)
     return Dict([sym => strip_call(Symbolics.unwrap(sym)) for sym in syms])
 end
+
+# If the input is a `ReactionSystem`, extracts the unknowns (i.e. syms depending on another variable).
 function make_strip_call_dict(rn::ReactionSystem)
     return make_strip_call_dict(get_unknowns(rn))
 end

src/reactionsystem_serialisation/serialise_fields.jl

@@ -308,7 +308,7 @@ EQUATIONS_FS = (seri_has_equations, get_equations_string, get_equations_annotati
 
 # Checks if the reaction system has any observables.
 function seri_has_observed(rn::ReactionSystem)
-    return !isempty(observed(rn))
+    return !isempty(get_observed(rn))
 end
 
 # Extract a string which declares the system's observables.
@@ -354,6 +354,27 @@ end
 # Combines the 3 -related functions in a constant tuple.
 OBSERVED_FS = (seri_has_observed, get_observed_string, get_observed_annotation)
 
+### Handles Observables ###
+
+# Checks if the reaction system has any defaults.
+function seri_has_defaults(rn::ReactionSystem)
+    return !isempty(get_defaults(rn))
+end
+
+# Extract a string which declares the system's defaults.
+function get_defaults_string(rn::ReactionSystem)
+    defaults_string = "defaults = " * x_2_string(get_defaults(rn))
+    return defaults_string
+end
+
+# Creates an annotation for the system's defaults.
+function get_defaults_annotation(rn::ReactionSystem)
+    return "Defaults:"
+end
+
+# Combines the 3 defaults-related functions in a constant tuple.
+DEFAULTS_FS = (seri_has_defaults, get_defaults_string, get_defaults_annotation)
+
 ### Handles Continuous Events ###
 
 # Checks if the reaction system have has continuous events.

src/reactionsystem_serialisation/serialise_reactionsystem.jl

@@ -34,7 +34,13 @@ Notes:
 """
 function save_reactionsystem(filename::String, rn::ReactionSystem;
         annotate = true, safety_check = true)
+    # Error and warning checks.
     reactionsystem_uptodate_check()
+    if !isempty(get_networkproperties(rn))
+        @warn "The serialised network has cached network properties (e.g. computed conservation laws). This will not be saved as part of the network, and must be recomputed when it is loaded."
+    end
+
+    # Write model to file and performs a safety check.
     open(filename, "w") do file
         write(file, get_full_system_string(rn, annotate, true))
     end
@@ -65,6 +71,7 @@ function get_full_system_string(rn::ReactionSystem, annotate::Bool, top_level::B
     file_text, has_reactions = push_field(file_text, rn, annotate, top_level, REACTIONS_FS)
     file_text, has_equations = push_field(file_text, rn, annotate, top_level, EQUATIONS_FS)
     file_text, has_observed = push_field(file_text, rn, annotate, top_level, OBSERVED_FS)
+    file_text, has_defaults = push_field(file_text, rn, annotate, top_level, DEFAULTS_FS)
     file_text, has_continuous_events = push_field(file_text, rn, annotate,
         top_level, CONTINUOUS_EVENTS_FS)
     file_text, has_discrete_events = push_field(file_text, rn, annotate,
@@ -78,7 +85,7 @@ function get_full_system_string(rn::ReactionSystem, annotate::Bool, top_level::B
     rs_creation_code = make_reaction_system_call(
         rn, annotate, top_level, has_sivs, has_species,
         has_variables, has_parameters, has_reactions,
-        has_equations, has_observed, has_continuous_events,
+        has_equations, has_observed, has_defaults, has_continuous_events,
         has_discrete_events, has_systems, has_connection_type)
     annotate || (@string_prepend! "\n" file_text)
     @string_prepend! "let" file_text
@@ -89,11 +96,10 @@ end
 
 # Creates a ReactionSystem call for creating the model. Adds all the correct inputs to it. The input
 # `has_` `Bool`s described which inputs are used. If the model is `complete`, this is handled here.
-function make_reaction_system_call(
-        rs::ReactionSystem, annotate, top_level, has_sivs, has_species,
-        has_variables, has_parameters, has_reactions, has_equations,
-        has_observed, has_continuous_events, has_discrete_events,
-        has_systems, has_connection_type)
+function make_reaction_system_call(rs::ReactionSystem, annotate, top_level, has_sivs,
+        has_species, has_variables, has_parameters, has_reactions, has_equations,
+        has_observed, has_defaults, has_continuous_events, has_discrete_events, has_systems,
+        has_connection_type)
 
     # Gets the independent variable input.
     iv = x_2_string(get_iv(rs))
@@ -141,6 +147,7 @@ function make_reaction_system_call(
     # Goes through various fields that might exists, and if so, adds them to the string.
     has_sivs && (@string_append! reaction_system_string ", spatial_ivs")
     has_observed && (@string_append! reaction_system_string ", observed")
+    has_defaults && (@string_append! reaction_system_string ", defaults")
     has_continuous_events && (@string_append! reaction_system_string ", continuous_events")
     has_discrete_events && (@string_append! reaction_system_string ", discrete_events")
     has_systems && (@string_append! reaction_system_string ", systems")

test/miscellaneous_tests/reactionsystem_serialisation.jl

@@ -400,6 +400,30 @@ end
 
 ### Other Tests ###
 
+# Checks that systems with cached network properties yields a warning.
+# Checks that default values as saved properly (even if they have different types).
+let
+    # Prepares model inputs.
+    @species X1(t) X2(t)
+    @parameters k1 k2::Int64
+    rxs = [
+        Reaction(k1, [X1], [X2]),
+        Reaction(k2, [X2], [X1])
+    ]
+    defaults = Dict((X1 => 1.0, k2 => 2))
+
+    # Creates model and computes conservation laws.
+    @named rs = ReactionSystem(rxs, t; defaults)
+    conservationlaws(rs)
+
+    # Serialises model and then loads and checks it.
+    @test_logs (:warn, ) match_mode=:any save_reactionsystem("serialised_rs.jl", rs)
+    rs_loaded = include("../serialised_rs.jl")
+    @test rs == rs_loaded
+    @test ModelingToolkit.get_defaults(rs) == ModelingToolkit.get_defaults(rs_loaded)
+    rm("serialised_rs.jl")
+end
+
 # Tests that an error is generated when non-`ReactionSystem` subs-systems are used.
 let
     @variables V(t)
@@ -415,6 +439,7 @@ let
     @named osys = ODESystem([eq], t)
     @named rs = ReactionSystem(rxs, t; systems = [osys])
     @test_throws Exception save_reactionsystem("failed_serialisation.jl", rs)
+    rm("failed_serialisation.jl")
 end
 
 # Checks that completeness is recorded correctly.