Merge pull request #255 from LCSB-BioCore/mk-fix-event-ids

Fix non-mandatory event IDs
LCSB-BioCore · Aug 30, 2023 · 1c7c5e3 · 1c7c5e3 · exaexa · Aug 30, 2023
2 parents a30bd51 + df38e09
commit 1c7c5e3
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Showing 6 changed files with 62 additions and 15 deletions.
diff --git a/Project.toml b/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 = "1.4.4"
+version = "1.5.0"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

diff --git a/docs/src/assets/unilu.svg b/docs/src/assets/unilu.svg
diff --git a/src/readsbml.jl b/src/readsbml.jl
@@ -630,7 +630,7 @@ 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)
@@ -663,8 +663,9 @@ 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,
@@ -674,7 +675,8 @@ function get_model(mdl::VPtr)::SBML.Model
                 name = get_optional_string(ev, :Event_getName),
                 trigger,
                 event_assignments,
-            )
+            ),
+        )
     end
 
     # Rules

diff --git a/src/structs.jl b/src/structs.jl
@@ -471,7 +471,7 @@ 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

diff --git a/src/writesbml.jl b/src/writesbml.jl
@@ -456,7 +456,7 @@ 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,

diff --git a/test/loaddynamicmodels.jl b/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