support parsing out function definitions

src/math.jl

@@ -6,6 +6,16 @@ Helper for quickly recognizing kinds of ASTs
 """
 ast_is(ast::VPtr, what::Symbol)::Bool = ccall(sbml(what), Cint, (VPtr,), ast) != 0
 
+"""
+    parse_math_children(ast::VPtr)::Vector{Math}
+
+Recursively parse all children of an AST node.
+"""
+parse_math_children(ast::VPtr)::Vector{Math} = [
+    parse_math(ccall(sbml(:ASTNode_getChild), VPtr, (VPtr, Cuint), ast, i - 1)) for
+    i = 1:ccall(sbml(:ASTNode_getNumChildren), Cuint, (VPtr,), ast)
+]
+
 """
     parse_math(ast::VPtr)::Math
 
@@ -15,26 +25,28 @@ pointer to `ASTNode_t`.
 function parse_math(ast::VPtr)::Math
     if ast_is(ast, :ASTNode_isName) || ast_is(ast, :ASTNode_isConstant)
         return MathIdent(get_string(ast, :ASTNode_getName))
-    elseif ast_is(ast, :ASTNode_isConstantNumber)
-        return MathVal(ccall_sbml(:ASTNode_getValue), Cdouble, (VPtr,), ast)
+    elseif ast_is(ast, :ASTNode_isInteger)
+        return MathVal(ccall(sbml(:ASTNode_getInteger), Cint, (VPtr,), ast))
+    elseif ast_is(ast, :ASTNode_isReal)
+        return MathVal(ccall(sbml(:ASTNode_getReal), Cdouble, (VPtr,), ast))
     elseif ast_is(ast, :ASTNode_isFunction)
-        return MathApply(
-            get_string(ast, :ASTNode_getName),
-            [
-                parse_math(ccall(sbml(:ASTNode_getChild), VPtr, (VPtr, Cuint), ast, i - 1))
-                for i = 1:ccall(sbml(:ASTNode_getNumChildren), Cuint, (VPtr,), ast)
-            ],
-        )
+        return MathApply(get_string(ast, :ASTNode_getName), parse_math_children(ast))
     elseif ast_is(ast, :ASTNode_isOperator)
         return MathApply(
             string(Char(ccall(sbml(:ASTNode_getCharacter), Cchar, (VPtr,), ast))),
-            [
-                parse_math(ccall(sbml(:ASTNode_getChild), VPtr, (VPtr, Cuint), ast, i - 1))
-                for i = 1:ccall(sbml(:ASTNode_getNumChildren), Cuint, (VPtr,), ast)
-            ],
+            parse_math_children(ast),
         )
+    elseif ast_is(ast, :ASTNode_isLambda)
+        children = parse_math_children(ast)
+        if !isempty(children)
+            body = pop!(children)
+            return MathLambda(broadcast((x::MathIdent) -> x.id, children), body)
+        else
+            @warn "invalid function definition found"
+            return MathIdent("?invalid?")
+        end
     else
-        @warn "unsupported math element at $ast"
+        @warn "unsupported math element found"
         return MathIdent("?unsupported?")
     end
 end

src/readsbml.jl

@@ -331,6 +331,23 @@ function extractModel(mdl::VPtr)::Model
         end
     end
 
+    function_definitions = Dict{String,FunctionDefinition}()
+    for i = 1:ccall(sbml(:Model_getNumFunctionDefinitions), Cuint, (VPtr,), mdl)
+        fd = ccall(sbml(:Model_getFunctionDefinition), VPtr, (VPtr, Cuint), mdl, i - 1)
+        def = nothing
+        if ccall(sbml(:FunctionDefinition_isSetMath), Cint, (VPtr,), fd) != 0
+            def = parse_math(ccall(sbml(:FunctionDefinition_getMath), VPtr, (VPtr,), fd))
+        end
+
+        function_definitions[get_string(fd, :FunctionDefinition_getId)] =
+            FunctionDefinition(
+                get_optional_string(fd, :FunctionDefinition_getName),
+                def,
+                getNotes(fd),
+                getAnnotation(fd),
+            )
+    end
+
     return Model(
         parameters,
         units,

src/structs.jl

@@ -82,6 +82,14 @@ struct MathApply <: Math
     args::Vector{Math}
 end
 
+"""
+Function definition (aka "lambda") in mathematical expression
+"""
+struct MathLambda <: Math
+    args::Vector{String}
+    body::Math
+end
+
 """
 Reaction with stoichiometry that assigns reactants and products their relative
 consumption/production rates (accessible in field `stoichiometry`), lower/upper
@@ -128,6 +136,17 @@ struct GeneProduct
     GeneProduct(na, l, no = nothing, a = nothing) = new(na, l, no, a)
 end
 
+"""
+Custom function definition.
+"""
+struct FunctionDefinition
+    name::Maybe{String}
+    body::Maybe{Math}
+    notes::Maybe{String}
+    annotation::Maybe{String}
+    FunctionDefinition(na, b, no = nothing, a = nothing) = new(na, b, no, a)
+end
+
 """
 Structure that collects the model-related data. Contains `parameters`, `units`,
 `compartments`, `species` and `reactions` and `gene_products`, and additional
@@ -142,7 +161,8 @@ struct Model
     species::Dict{String,Species}
     reactions::Dict{String,Reaction}
     gene_products::Dict{String,GeneProduct}
+    function_definitions::Dict{String,FunctionDefinition}
     notes::Maybe{String}
     annotation::Maybe{String}
-    Model(p, u, c, s, r, g, n = nothing, a = nothing) = new(p, u, c, s, r, g, n, a)
+    Model(p, u, c, s, r, g, f, n = nothing, a = nothing) = new(p, u, c, s, r, g, f, n, a)
 end