read notes from species, reactions and models

Co-authored-by: Mirek Kratochvil <miroslav.kratochvil@uni.lu>

src/SBML.jl

@@ -11,6 +11,6 @@ include("utils.jl")
 sbml = (sym::Symbol) -> dlsym(SBML_jll.libsbml_handle, sym)
 
 export SBMLVersion,
-    readSBML, Model, UnitPart, Species, Reaction, getS, getLBs, getUBs, getOCs
+    readSBML, Model, Maybe, UnitPart, Species, Reaction, getS, getLBs, getUBs, getOCs
 
 end # module

src/readsbml.jl

@@ -31,6 +31,15 @@ function readSBML(fn::String)::Model
     end
 end
 
+function getNotes(x::VPtr)::Maybe{String}
+    str = ccall(sbml(:SBase_getNotesString), Cstring, (VPtr,), x)
+    if str != C_NULL
+        return unsafe_string(str)
+    else
+        return nothing
+    end
+end
+
 function extractModel(mdl::VPtr)::Model
     mdl_fbc = ccall(sbml(:SBase_getPlugin), VPtr, (VPtr, Cstring), mdl, "fbc")
 
@@ -104,6 +113,7 @@ function extractModel(mdl::VPtr)::Model
             unsafe_string(ccall(sbml(:Species_getCompartment), Cstring, (VPtr,), sp)),
             formula,
             charge,
+            getNotes(sp),
         )
     end
 
@@ -193,9 +203,14 @@ function extractModel(mdl::VPtr)::Model
         end
 
         reid = unsafe_string(ccall(sbml(:Reaction_getId), Cstring, (VPtr,), re))
-        reactions[reid] =
-            Reaction(stoi, lb, ub, haskey(objectives_fbc, reid) ? objectives_fbc[reid] : oc)
+        reactions[reid] = Reaction(
+            stoi,
+            lb,
+            ub,
+            haskey(objectives_fbc, reid) ? objectives_fbc[reid] : oc,
+            getNotes(re),
+        )
     end
 
-    return Model(parameters, units, compartments, species, reactions)
+    return Model(parameters, units, compartments, species, reactions, getNotes(mdl))
 end

src/structs.jl

 
+const Maybe{X} = Union{Nothing,X}
+
 """
 Part of a measurement unit definition that corresponds to the SBML definition
 of `Unit`. For example, the unit "per square megahour", Mh^(-2), is written as:
@@ -31,7 +33,8 @@ struct Reaction
     lb::Tuple{Float64,String}
     ub::Tuple{Float64,String}
     oc::Float64
-    Reaction(s, l, u, o) = new(s, l, u, o)
+    notes::Maybe{String}
+    Reaction(s, l, u, o, n) = new(s, l, u, o, n)
 end
 
 """
@@ -42,8 +45,9 @@ struct Species
     name::String
     compartment::String
     formula::String
-    charge::Union{Nothing,Int}
-    Species(n, co, f, ch) = new(n, co, f, ch)
+    charge::Maybe{Int}
+    notes::Maybe{String}
+    Species(na, co, f, ch, no) = new(na, co, f, ch, no)
 end
 
 """
@@ -57,5 +61,6 @@ struct Model
     compartments::Vector{String}
     species::Dict{String,Species}
     reactions::Dict{String,Reaction}
-    Model(p, u, c, s, r) = new(p, u, c, s, r)
+    notes::Maybe{String}
+    Model(p, u, c, s, r, n) = new(p, u, c, s, r, n)
 end