extract freetext annotations

src/readsbml.jl

@@ -31,8 +31,8 @@ function readSBML(fn::String)::Model
     end
 end
 
-function getNotes(x::VPtr)::Maybe{String}
-    str = ccall(sbml(:SBase_getNotesString), Cstring, (VPtr,), x)
+function getOptionalString(x::VPtr, fn_sym)::Maybe{String}
+    str = ccall(sbml(fn_sym), Cstring, (VPtr,), x)
     if str != C_NULL
         return unsafe_string(str)
     else
@@ -40,6 +40,9 @@ function getNotes(x::VPtr)::Maybe{String}
     end
 end
 
+getNotes(x::VPtr)::Maybe{String} = getOptionalString(x, :SBase_getNotesString)
+getAnnotation(x::VPtr)::Maybe{String} = getOptionalString(x, :SBase_getAnnotationString)
+
 function extractModel(mdl::VPtr)::Model
     mdl_fbc = ccall(sbml(:SBase_getPlugin), VPtr, (VPtr, Cstring), mdl, "fbc")
 
@@ -114,6 +117,7 @@ function extractModel(mdl::VPtr)::Model
             formula,
             charge,
             getNotes(sp),
+            getAnnotation(sp),
         )
     end
 
@@ -209,8 +213,17 @@ function extractModel(mdl::VPtr)::Model
             ub,
             haskey(objectives_fbc, reid) ? objectives_fbc[reid] : oc,
             getNotes(re),
+            getAnnotation(re),
         )
     end
 
-    return Model(parameters, units, compartments, species, reactions, getNotes(mdl))
+    return Model(
+        parameters,
+        units,
+        compartments,
+        species,
+        reactions,
+        getNotes(mdl),
+        getAnnotation(mdl),
+    )
 end

src/structs.jl

@@ -40,7 +40,8 @@ struct Reaction
     ub::Tuple{Float64,String}
     oc::Float64
     notes::Maybe{String}
-    Reaction(s, l, u, o, n) = new(s, l, u, o, n)
+    annotation::Maybe{String}
+    Reaction(s, l, u, o, n = nothing, a = nothing) = new(s, l, u, o, n, a)
 end
 
 """
@@ -53,7 +54,8 @@ struct Species
     formula::String
     charge::Maybe{Int}
     notes::Maybe{String}
-    Species(na, co, f, ch, no) = new(na, co, f, ch, no)
+    annotation::Maybe{String}
+    Species(na, co, f, ch, no = nothing, a = nothing) = new(na, co, f, ch, no, a)
 end
 
 """
@@ -68,5 +70,6 @@ struct Model
     species::Dict{String,Species}
     reactions::Dict{String,Reaction}
     notes::Maybe{String}
-    Model(p, u, c, s, r, n) = new(p, u, c, s, r, n)
+    annotation::Maybe{String}
+    Model(p, u, c, s, r, n = nothing, a = nothing) = new(p, u, c, s, r, n, a)
 end