Merge pull request #128 from LCSB-BioCore/mk-relational-ops

fix parsing of relational operators

src/math.jl

@@ -16,6 +16,25 @@ parse_math_children(ast::VPtr)::Vector{Math} = [
     i = 1:ccall(sbml(:ASTNode_getNumChildren), Cuint, (VPtr,), ast)
 ]
 
+
+
+# Mapping of AST node type value subset to relational operations. Depends on
+# `ASTNodeType.h` (also see below the case with AST_NAME_TIME)
+const relational_opers = Dict{Int32,String}(
+    308 => "eq",
+    309 => "geq",
+    310 => "gt",
+    311 => "leq",
+    312 => "lt",
+    313 => "neq",
+)
+
+function relational_oper(t::Int)
+    haskey(relational_opers, t) ||
+        throw(DomainError(t, "Unknown ASTNodeType value for relational operator"))
+    relational_opers[t]
+end
+
 """
     parse_math(ast::VPtr)::Math
 
@@ -42,11 +61,16 @@ function parse_math(ast::VPtr)::Math
         return MathVal(ccall(sbml(:ASTNode_getReal), Cdouble, (VPtr,), ast))
     elseif ast_is(ast, :ASTNode_isFunction)
         return MathApply(get_string(ast, :ASTNode_getName), parse_math_children(ast))
-    elseif ast_is(ast, :ASTNode_isOperator) || ast_is(ast, :ASTNode_isRelational)
+    elseif ast_is(ast, :ASTNode_isOperator)
         return MathApply(
             string(Char(ccall(sbml(:ASTNode_getCharacter), Cchar, (VPtr,), ast))),
             parse_math_children(ast),
         )
+    elseif ast_is(ast, :ASTNode_isRelational)
+        return MathApply(
+            relational_oper(Int(ccall(sbml(:ASTNode_getType), Cint, (VPtr,), ast))),
+            parse_math_children(ast),
+        )
     elseif ast_is(ast, :ASTNode_isLambda)
         children = parse_math_children(ast)
         if !isempty(children)

src/symbolics.jl

@@ -45,6 +45,7 @@ const default_symbolics_mapping = Dict{String,Any}(
     "ln" => :log,
     "log" => :sbmlLog,
     "lt" => :<,
+    "neq" => :(sbmlNeq),
     "piecewise" => :(sbmlPiecewise),
     "power" => :^,
     "root" => :sbmlRoot,
@@ -66,6 +67,7 @@ function sbmlPiecewise(args...)
     end
 end
 
+sbmlNeq(a, b) = !isequal(a, b)
 
 sbmlLog(x) = log(x, 10)
 sbmlLog(base, x) = log(base, x)

test/loadmodels.jl

@@ -56,6 +56,14 @@ sbmlfiles = [
         0,
         0,
     ),
+    # this contains a relational operator
+    (
+        joinpath(@__DIR__, "data", "sbml00191.xml"),
+        "https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/master/cases/semantic/00191/00191-sbml-l3v2.xml",
+        "c474e94888767d70f9e9e03b32778f18069641563953de60dabac7daa7f481ce",
+        4,
+        2,
+    ),
 ]
 
 @testset "Loading of models from various sources" begin
@@ -163,3 +171,10 @@ end
     @test test_math.args[2].fn == "sin"
     @test test_math.args[2].args[1].val == 2.1
 end
+
+@testset "relational operators are decoded correctly" begin
+    test_math =
+        readSBML(joinpath(@__DIR__, "data", "sbml00191.xml")).reactions["reaction2"].kinetic_math
+
+    @test test_math.args[2].fn == "geq"
+end