add sbml2symbolics conversion

Project.toml

@@ -4,11 +4,13 @@ authors = ["Mirek Kratochvil <miroslav.kratochvil@uni.lu>", "LCSB R3 team <lcsb-
 version = "0.5.0"
 
 [deps]
+IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 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("sbml2symbolics.jl")
 
 sbml = (sym::Symbol) -> dlsym(SBML_jll.libsbml_handle, sym)
 

src/sbml2symbolics.jl

+@register Base.factorial(x)  # Todo: remove this line once factorial is registered per default
+
+function parse_piecewise(val, cond, other)
+    IfElse.ifelse(cond, val, other)
+end
+
+allowed_funs = Dict(
+    # Operators    
+    "+" => :+,
+    "-" => :-,
+    "*" => :*,
+    "/" => :/,
+    "power" => :^,
+
+    # Relational functions
+    "lt" => :<,
+    "leq" => :<=,
+    "geq" => :>=,
+    "gt" => :>,
+    
+    # Other
+    "factorial" => :factorial,
+    "ceiling" => :ceil,
+    "floor" => :floor,
+    "piecewise" => SBML.parse_piecewise,
+    #TODO add further translations of SBML functions to Julia
+)
+
+allowed_sym(x) = haskey(allowed_funs,x) ? allowed_funs[x] : throw(DomainError(x,"Unknown SBML function"))
+
+function Base.convert(::Type{Num}, x::SBML.Math)
+    conv(x::SBML.MathApply) =
+        eval(allowed_sym(x.fn))(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

@@ -8,4 +8,5 @@ import Pkg
     include("version.jl")
     include("ecoli_flux.jl")
     include("loadmodels.jl")
+    include("sbml2symbolics.jl")
 end