Merge pull request #68 from LCSB-BioCore/mk-merge-65

Minor cleaning&merge of #65

Project.toml

@@ -9,6 +9,7 @@ Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 SBML_jll = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1"
 SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]

src/SBML.jl

@@ -2,6 +2,7 @@ module SBML
 
 using SBML_jll, Libdl, Pkg
 using SparseArrays
+using Symbolics
 
 include("structs.jl")
 include("version.jl")
@@ -10,6 +11,7 @@ include("readsbml.jl")
 include("converters.jl")
 include("math.jl")
 include("utils.jl")
+include("symbolics.jl")
 
 sbml = (sym::Symbol) -> dlsym(SBML_jll.libsbml_handle, sym)
 

src/symbolics.jl

+
+default_symbolics_mapping = Dict(
+    "+" => :+,
+    "-" => :-,
+    "*" => :*,
+    "/" => :/,
+    "power" => :^,
+    "lt" => :<,
+    "leq" => :<=,
+    "geq" => :>=,
+    "gt" => :>,
+    "ceiling" => :ceil,
+    "floor" => :floor,
+    "piecewise" => :(Core.ifelse),
+    #TODO extend this in the future
+)
+
+allowed_sym(x, allowed_funs) =
+    haskey(allowed_funs, x) ? allowed_funs[x] :
+    throw(DomainError(x, "Unknown SBML function"))
+
+function Base.convert(::Type{Num}, x::SBML.Math; mapping = default_symbolics_mapping)
+    conv(x::SBML.MathApply) = eval(allowed_sym(x.fn, mapping))(conv.(x.args)...)
+    conv(x::SBML.MathIdent) = Num(Variable(Symbol(x.id))).val
+    conv(x::SBML.MathVal) = x.val
+    conv(x::SBML.MathLambda) = throw(DomainError(x, "can't translate lambdas to symbolics"))
+    conv(x)
+end

test/runtests.jl

@@ -2,10 +2,12 @@
 using Test, SHA, SparseArrays, Downloads
 using SBML
 using SBML: Model, Reaction, Species
+using Symbolics
 import Pkg
 
 @testset "SBML test suite" begin
     include("version.jl")
     include("ecoli_flux.jl")
     include("loadmodels.jl")
+    include("symbolics.jl")
 end

test/symbolics.jl

+
+@testset "Math to Symbolics conversions" begin
+    @variables A B C D E
+
+    test = SBML.MathApply(
+        "*",
+        SBML.Math[
+            SBML.MathApply(
+                "+",
+                SBML.Math[
+                    SBML.MathApply(
+                        "*",
+                        SBML.Math[SBML.MathIdent("A"), SBML.MathIdent("B")],
+                    ),
+                    SBML.MathApply(
+                        "-",
+                        SBML.Math[SBML.MathApply(
+                            "*",
+                            SBML.Math[SBML.MathIdent("C"), SBML.MathIdent("D")],
+                        )],
+                    ),
+                ],
+            ),
+            SBML.MathIdent("E"),
+        ],
+    )
+
+    @test isequal(convert(Num, test), (A * B - C * D) * E)
+
+    test = SBML.MathApply(
+        "piecewise",
+        SBML.Math[
+            SBML.MathApply("lt", SBML.Math[SBML.MathVal(1), SBML.MathVal(0)]),
+            SBML.MathVal(123),
+            SBML.MathVal(456),
+        ],
+    )
+
+    @test isequal(convert(Num, test), 456)
+end