remove the mandatory ID from the SBML events

Closes #254

SBML says that IDs on events are actually not mandatory, this softens the data
structure so that the ID-less events are supported. The vector-of-pairs
implementation is chosen for backwards compatibility (iteration through a
vector of pairs should work precisely like iteration through the dictionary
that was there before). Notably, this might look like a breaking change _but_
it is not -- the main use case that is broken by this commit is indexing the
events by ID, which was actually broken already.

Project.toml

@@ -1,7 +1,7 @@
 name = "SBML"
 uuid = "e5567a89-2604-4b09-9718-f5f78e97c3bb"
 authors = ["Mirek Kratochvil <[email protected]>", "LCSB R3 team <[email protected]>"]
-version = "1.4.1"
+version = "1.5.0"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

src/readsbml.jl

@@ -629,7 +629,7 @@ function get_model(mdl::VPtr)::SBML.Model
     end
 
     # events
-    events = Dict{String,Event}()
+    events = Pair{Maybe{String},Event}[]
     num_events = ccall(sbml(:Model_getNumEvents), Cuint, (VPtr,), mdl)
     for n = 0:(num_events-1)
         ev = ccall(sbml(:Model_getEvent), VPtr, (VPtr, Cuint), mdl, n)
@@ -662,8 +662,9 @@ function get_model(mdl::VPtr)::SBML.Model
             math = trig_math_ptr == C_NULL ? nothing : parse_math(trig_math_ptr),
         )
 
-        events[unsafe_string(ccall(sbml(:Event_getId), Cstring, (VPtr,), ev))] =
-            SBML.Event(;
+        push!(
+            events,
+            get_optional_string(ev, :Event_getId) => SBML.Event(;
                 use_values_from_trigger_time = ccall(
                     sbml(:Event_getUseValuesFromTriggerTime),
                     Cint,
@@ -673,7 +674,8 @@ function get_model(mdl::VPtr)::SBML.Model
                 name = get_optional_string(ev, :Event_getName),
                 trigger,
                 event_assignments,
-            )
+            ),
+        )
     end
 
     # Rules

src/structs.jl

@@ -466,7 +466,7 @@ Base.@kwdef struct Model
     active_objective::Maybe{String} = nothing
     gene_products::Dict{String,GeneProduct} = Dict()
     function_definitions::Dict{String,FunctionDefinition} = Dict()
-    events::Dict{String,Event} = Dict()
+    events::Vector{Pair{Maybe{String},Event}} = Pair{Maybe{String},Event}[]
     name::Maybe{String} = nothing
     id::Maybe{String} = nothing
     metaid::Maybe{String} = nothing

src/writesbml.jl

@@ -451,7 +451,7 @@ function model_to_sbml!(doc::VPtr, mdl::Model)::VPtr
     # Add events
     for (id, event) in mdl.events
         event_ptr = ccall(sbml(:Model_createEvent), VPtr, (VPtr,), model)
-        set_string!(event_ptr, :Event_setId, id)
+        isnothing(id) || set_string!(event_ptr, :Event_setId, id)
         set_bool!(
             event_ptr,
             :Event_setUseValuesFromTriggerTime,

test/loaddynamicmodels.jl

@@ -58,6 +58,28 @@ sbmlfiles = [
         ("reaction1", SBML.MathApply("*", [SBML.MathApply("*", [compartment, k2]), S1])),
         ("S1", 0.01125),
     ),
+    # case 00928 with an ID-less event
+    (
+        joinpath(@__DIR__, "data", "00928-sbml-l3v2.xml"),
+        SBML.test_suite_url(928, level = 3, version = 2),
+        "d2a95aee820712696a2056bb09fd7d3befcd99e331809105e12ee081073a4985",
+        x -> nothing,
+        1,
+        (
+            "reaction1",
+            SBML.MathApply(
+                "*",
+                SBML.Math[
+                    SBML.MathApply(
+                        "*",
+                        SBML.Math[SBML.MathIdent("C"), SBML.MathIdent("k1")],
+                    ),
+                    SBML.MathIdent("S1"),
+                ],
+            ),
+        ),
+        ("S1", 0.0),
+    ),
 ]
 
 @testset "Loading of models from sbml_test_suite" begin