save progress

Author: TorkelE

src/reactionsystem_serialisation/serialisation_support.jl

@@ -21,6 +21,13 @@ macro string_prepend!(input1, input2, string)
     return esc(:($string = $rhs))
 end
 
+# Gets the character at a specific index.
+get_char(str, idx) = collect(str)[idx]
+get_char_end(str, offset) = collect(str)[end - offset]
+# Gets a substring (which is robust to unicode characters like η).
+get_substring(str, idx1, idx2) = String(collect(str)[idx1, idx2])
+get_substring_end(str, idx1, offset) = String(collect(str)[idx1, end - offset])
+
 
 ### Field Serialisation Support Functions ###
 
@@ -72,7 +79,7 @@ end
 # any calls (e.g. X(t) becomes X). E.g. a species vector [X, Y, Z] is converted to "[X, Y, Z]".
 function syms_2_strings(syms)
     strip_called_syms = [strip_call(Symbolics.unwrap(sym)) for sym in syms]
-    return "$(convert(Vector{Any}, strip_called_syms))"[4:end]
+    return get_substring("$(convert(Vector{Any}, strip_called_syms))", 4)
 end    
 
 # Converts a vector of symbolics (e.g. the species or parameter vectors) to a string corresponding to 
@@ -100,10 +107,10 @@ function sym_2_declaration_string(sym; multiline_format = false)
     # to ensure that this is the case.
     if !(sym isa SymbolicUtils.BasicSymbolic{Real})
         sym_type = String(Symbol(typeof(Symbolics.unwrap(sym))))
-        if (sym_type[1:28] != "SymbolicUtils.BasicSymbolic{") || (sym_type[end] != '}')
+        if (get_substring(sym_type, 1, 28) != "SymbolicUtils.BasicSymbolic{") || (get_char_end(sym_type, 0) != '}')
             error("Encountered symbolic of unexpected type: $sym_type.")
         end
-        @string_append! dec_string "::" sym_type[29:end-1]
+        @string_append! dec_string "::" get_substring_end(sym_type, 29, -1)
     end
 
     # If there is a default value, adds this to the declaration.
@@ -120,7 +127,7 @@ function sym_2_declaration_string(sym; multiline_format = false)
         for metadata in metadata_to_declare
             @string_append! metadata_string metadata_2_string(sym, metadata) ", "
         end
-        @string_append! dec_string metadata_string[1:end-2] "]"
+        @string_append! dec_string $(get_substring_end(metadata_string, 1, -2)) "]"
     end
 
     # Returns the declaration entry for the symbol.
@@ -145,31 +152,31 @@ function x_2_string(x::Vector)
     for val in x
         @string_append! output x_2_string(val) ", "
     end
-    return output[1:end-2] * "]"
+    return get_substring_end(output, 1, -2) * "]"
 end 
 function x_2_string(x::Tuple)
     output = "("
     for val in x
         @string_append! output x_2_string(val) ", "
     end
-    return output[1:end-2] * ")"
+    return get_substring_end(output, 1, -2) * ")"
 end 
 function x_2_string(x::Dict)
     output = "Dict(["
     for key in keys(x)
         @string_append! output x_2_string(key) " => " x_2_string(x[key]) ", "
     end
-    return output[1:end-2] * "])"
+    return get_substring_end(output, 1, -2) * "])"
 end
 function x_2_string(x::Union{Matrix, Symbolics.Arr{Any, 2}})
     output = "["
     for j = 1:size(x)[1]
         for i = 1:size(x)[2]
             @string_append! output x_2_string(x[j,i]) " "
         end
-        output = output[1:end-1] * "; "
+        output = get_substring_end(output, 1, -1) * "; "
     end
-    return output[1:end-2] *"]"
+    return get_substring_end(output, 1, -2) *"]"
 end 
 
 

src/reactionsystem_serialisation/serialise_fields.jl

@@ -87,7 +87,7 @@ function handle_us_n_ps(file_text::String, rn::ReactionSystem, annotate::Bool, t
             p_deps && (@string_append! us_n_ps_string "parameters, ")
             sp_deps && (@string_append! us_n_ps_string "species, ")
             var_deps && (@string_append! us_n_ps_string "variables, ")
-            us_n_ps_string = us_n_ps_string[1:end-2]
+            us_n_ps_string = get_substring_end(us_n_ps_string, 1, -2)
             @string_append! us_n_ps_string " depends on the declaration of other parameters, species, and/or variables.\n# These are specially handled here.\n"
         end
 
@@ -117,7 +117,7 @@ function handle_us_n_ps(file_text::String, rn::ReactionSystem, annotate::Bool, t
         p_deps && (@string_append! us_n_ps_string "ps = " syms_2_strings(ps_all) "\n")
         sp_deps && (@string_append! us_n_ps_string "sps = " syms_2_strings(sps_all) "\n")
         var_deps && (@string_append! us_n_ps_string "vars = " syms_2_strings(vars_all) "\n")
-        us_n_ps_string = us_n_ps_string[1:end-1]
+        us_n_ps_string = get_substring_end(us_n_ps_string, 1, -1)
     end
 
     # If this is not a top-level system, `local ` must be added to all declarations.
@@ -217,7 +217,9 @@ function get_reactions_string(rn::ReactionSystem)
     strip_call_dict = make_strip_call_dict(rn)
 
     # Handles the case with one reaction separately. Only effect is nicer formatting.
-    (length(get_rxs(rn)) == 1) && (return "rxs = [$(reaction_string(rx, strip_call_dict))]")
+    if length(get_rxs(rn)) == 1
+        return "rxs = [$(reaction_string(get_rxs(rn)[1], strip_call_dict))]"
+    end
 
     # Creates the string corresponding to the code which generates the system's reactions. 
     rxs_string = "rxs = ["
@@ -226,7 +228,7 @@ function get_reactions_string(rn::ReactionSystem)
     end
 
     # Updates the string (including removing the last `,`) and returns it.
-    return rxs_string[1:end-1] * "\n]"
+    return get_substring_end(rxs_string, 1, -1) * "\n]"
 end
 
 # Creates a string that corresponds to the declaration of a single `Reaction`.
@@ -251,7 +253,7 @@ function reaction_string(rx::Reaction, strip_call_dict)
             metadata_entry = "$(x_2_string(entry)), "
             @string_append! rx_string metadata_entry
         end
-        rx_string = rx_string[1:end-2] * "]"
+        rx_string = get_substring_end(rx_string, 1, -2) * "]"
     end
 
     # Returns the Reaction string.
@@ -291,7 +293,7 @@ function get_equations_string(rn::ReactionSystem)
     end
 
     # Updates the string (including removing the last `,`) and returns it.
-    return eqs_string[1:end-1] * "\n]"
+    return get_substring_end(eqs_string, 1, -1) * "\n]"
 end
 
 # Creates an annotation for the system's equations.
@@ -378,7 +380,7 @@ function get_continuous_events_string(rn::ReactionSystem)
     end
 
     # Updates the string (including removing the last `,`) and returns it.
-    return continuous_events_string[1:end-1] * "\n]"
+    return get_substring_end(continuous_events_string, 1, -1) * "\n]"
 end
 
 # Creates a string that corresponds to the declaration of a single continuous event.
@@ -388,7 +390,7 @@ function continuous_event_string(continuous_event, strip_call_dict)
     for eq in continuous_event.eqs
         @string_append! eqs_string expression_2_string(eq; strip_call_dict) ", "
     end
-    eqs_string = eqs_string[1:end-2] * "]"
+    eqs_string = get_substring_end(eqs_string, 1, -2) * "]"
 
     # Creates the string corresponding to the affects.
     # Continuous events' `affect` field should probably be called `affects`. Likely the `s` was
@@ -397,7 +399,7 @@ function continuous_event_string(continuous_event, strip_call_dict)
     for affect in continuous_event.affect
         @string_append! affects_string expression_2_string(affect; strip_call_dict) ", "
     end
-    affects_string = affects_string[1:end-2] * "]"
+    affects_string = get_substring_end(affects_string, 1, -2) * "]"
 
     return eqs_string * " => " * affects_string
 end
@@ -435,7 +437,7 @@ function get_discrete_events_string(rn::ReactionSystem)
     end
 
     # Updates the string (including removing the last `,`) and returns it.
-    return discrete_events_string[1:end-1] * "\n]"
+    return get_substring_end(discrete_events_string, 1, -1) * "\n]"
 end
 
 # Creates a string that corresponds to the declaration of a single discrete event.
@@ -453,7 +455,7 @@ function discrete_event_string(discrete_event, strip_call_dict)
     for affect in discrete_event.affects
         @string_append! affects_string expression_2_string(affect; strip_call_dict) ", "
     end
-    affects_string = affects_string[1:end-2] * "]"
+    affects_string = get_substring_end(affects_string, 1, -2) * "]"
 
     return condition_string * " => " * affects_string
 end
@@ -504,7 +506,7 @@ function get_systems_string(rn::ReactionSystem, annotate::Bool)
         # Manipulates the subsystem declaration to make it nicer.
         subsystem_string = get_full_system_string(system, annotate, false)
         subsystem_string = replace(subsystem_string, "\n" => "\n\t")
-        subsystem_string = "let\n" * subsystem_string[7:end-6] * "end"
+        subsystem_string = "let\n" * get_substring_end(subsystem_string, 7, -6) * "end"
         @string_append! systems_string "\nsystems[$idx] = " subsystem_string
     end
 

test/miscellaneous_tests/reactionsystem_serialisation.jl

@@ -2,6 +2,7 @@
 
 # Fetch packages.
 using Catalyst
+using Catalyst: get_rxs
 using ModelingToolkit: getdefault, getdescription, get_metadata
 
 # Creates missing getters for MTK metadata (can be removed once added to MTK).
@@ -20,21 +21,63 @@ D = default_time_deriv()
 # Checks annotated and non-annotated files against manually written ones.
 let 
     # Creates and serialises the model.
-    rn = @reaction_system begin
+    rn = @reaction_network rn begin
         @observables X2 ~ 2X
         @equations D(V) ~ 1 - V
-        (p,d), 0 <--> X
+        d, X --> 0
     end
     save_reaction_network("test_serialisation_annotated.jl", rn; safety_check = false)
     save_reaction_network("test_serialisation.jl", rn; annotate = false, safety_check = false)
 
     # Checks equivalence.
     file_string_annotated = read("test_serialisation_annotated.jl", String)
     file_string = read("test_serialisation.jl", String)
-    file_string_annotated_real = ""
-    file_string_real = ""
+    file_string_annotated_real = """let
+
+    # Independent variable:
+    @variables t
+
+    # Parameters:
+    ps = @parameters d
+
+    # Species:
+    sps = @species X(t)
+
+    # Variables:
+    vars = @variables V(t)
+
+    # Reactions:
+    rxs = [Reaction(d, [X], nothing, [1], nothing)]
+
+    # Equations:
+    eqs = [Differential(t)(V) ~ 1 - V]
+
+    # Observables:
+    @variables X2(t)
+    observed = [X2 ~ 2X]
+
+    # Declares ReactionSystem model:
+    rs = ReactionSystem([rxs; eqs], t, [sps; vars], ps; name = :rn, observed)
+    complete(rs)
+
+    end"""
+    file_string_real = """let
+
+    @variables t
+    ps = @parameters d
+    sps = @species X(t)
+    vars = @variables V(t)
+    rxs = [Reaction(d, [X], nothing, [1], nothing)]
+    eqs = [Differential(t)(V) ~ 1 - V]
+    @variables X2(t)
+    observed = [X2 ~ 2X]
+
+    rs = ReactionSystem([rxs; eqs], t, [sps; vars], ps; name = :rn, observed)
+    complete(rs)
+
+    end"""
     @test file_string_annotated == file_string_annotated_real
-    @test file == file_string_real
+    @test file_string == file_string_real
 
     # Deletes the files.
     rm("test_serialisation_annotated.jl")
@@ -95,8 +138,10 @@ let
     end
 
     # Creates the hierarchical model. Adds metadata to both reactions and the systems.
+    # First reaction has `+ s + r` as that is easier than manually listing all symbolics.
+    # (These needs to be part of the system somehow, as they are only added through the `misc` metadata)
     rxs1 = [
-        Reaction(a + A, [X], [], metadata = [:misc => bool_md])
+        Reaction(a + A + s + r, [X], [], metadata = [:misc => bool_md])
         Reaction(b + B, [Y], [], metadata = [:misc => int_md])
         Reaction(c + C, [Z], [], metadata = [:misc => sym_md])
         Reaction(d1 + D1, [V1], [], metadata = [:misc => str_md])
@@ -329,15 +374,15 @@ let
             X3 ~ 3*X
         end
         @continuous_events begin
-            X2 < 5.0 => [X ~ X + 1.0]
-            X3 > 20.0 => [X ~ X - 1.0]
+            [X ~ 5.0] => [X ~ X + 1.0]
+            [X ~ 20.0] => [X ~ X - 1.0]
         end
-        @discrete_events [5.0 => d ~ d/2]
+        @discrete_events 5.0 => [d ~ d/2]
         d, X --> 0
     end
 
     # Checks that serialisation works.
-    save_reaction_network("serialised_rs", rs; safety_check = false)
+    save_reaction_network("serialised_rs.jl", rs; safety_check = false)
     @test isequal(rs, include("serialised_rs.jl"))
     rm("serialised_rs.jl")
 end
@@ -371,7 +416,7 @@ let
     save_reaction_network("serialised_rs_complete.jl", rs_complete)
     rs_complete_loaded = include("serialised_rs_complete.jl")
     @test ModelingToolkit.iscomplete(rs_complete_loaded)
-    rn("serialised_rs_complete.jl")
+    rm("serialised_rs_complete.jl")
 
     # Checks for non-complete system.
     rs_incomplete = @network_component begin
@@ -380,5 +425,5 @@ let
     save_reaction_network("serialised_rs_incomplete.jl", rs_incomplete)
     rs_incomplete_loaded = include("serialised_rs_incomplete.jl")
     @test !ModelingToolkit.iscomplete(rs_incomplete_loaded)
-    rn("serialised_rs_incomplete.jl")
+    rm("serialised_rs_incomplete.jl")
 end