Merge pull request #55 from LCSB-BioCore/mk-conversions

add support for running SBML converters

src/SBML.jl

@@ -5,13 +5,15 @@ using SparseArrays
 
 include("structs.jl")
 include("version.jl")
+
 include("readsbml.jl")
+include("converters.jl")
 include("math.jl")
 include("utils.jl")
 
 sbml = (sym::Symbol) -> dlsym(SBML_jll.libsbml_handle, sym)
 
-export SBMLVersion,
-    readSBML, getS, getLBs, getUBs, getOCs
+export SBMLVersion, readSBML, getS, getLBs, getUBs, getOCs
+export convert_level_and_version, libsbml_convert, convert_simplify_math
 
 end # module

src/converters.jl

+
+"""
+    convert_level_and_version(level, version)
+
+A converter to pass into [`readSBML`](@ref) that enforces certain SBML level
+and version.
+"""
+convert_level_and_version(level, version) =
+    doc -> begin
+        ccall(
+            sbml(:SBMLDocument_setLevelAndVersion),
+            Cint,
+            (VPtr, Cint, Cint),
+            doc,
+            level,
+            version,
+        )
+    end
+
+"""
+    libsbml_convert(conversion_options::Vector{Pair{String, Dict{String, String}}})
+
+A converter that runs the SBML conversion routine, with specified conversion
+options. The argument is a vector of pairs to allow specifying the order of
+conversions.
+"""
+libsbml_convert(conversion_options::Vector{Pair{String,Dict{String,String}}}) =
+    doc -> begin
+        for (converter, options) in conversion_options
+            props = ccall(sbml(:ConversionProperties_create), VPtr, ())
+            opt = ccall(sbml(:ConversionOption_create), VPtr, (Cstring,), converter)
+            ccall(sbml(:ConversionProperties_addOption), Cvoid, (VPtr, VPtr), props, opt)
+            for (k, v) in options
+                opt = ccall(sbml(:ConversionOption_create), VPtr, (Cstring,), k)
+                ccall(sbml(:ConversionOption_setValue), Cvoid, (VPtr, Cstring), opt, v)
+                ccall(
+                    sbml(:ConversionProperties_addOption),
+                    Cvoid,
+                    (VPtr, VPtr),
+                    props,
+                    opt,
+                )
+            end
+            ccall(sbml(:SBMLDocument_convert), Cint, (VPtr, VPtr), doc, props)
+        end
+    end
+
+"""
+    convert_simplify_math
+
+Shortcut for [`libsbml_convert`](@ref) that expands functions, local
+parameters, and initial assignments in the SBML document.
+"""
+convert_simplify_math = libsbml_convert(
+    ["promoteLocalParameters", "expandFunctionDefinitions", "setLevelAndVersion"] .=>
+        Ref(Dict{String,String}()),
+)

src/readsbml.jl

@@ -75,11 +75,11 @@ function get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}
 end
 
 """
-    function readSBML(fn::String)::SBML.Model
+    function readSBML(fn::String, sbml_conversion = model->nothing)::SBML.Model
 
 Read the SBML from a XML file in `fn` and return the contained `SBML.Model`.
 """
-function readSBML(fn::String)::SBML.Model
+function readSBML(fn::String, sbml_conversion = document -> nothing)::SBML.Model
     doc = ccall(sbml(:readSBML), VPtr, (Cstring,), fn)
     try
         n_errs = ccall(sbml(:SBMLDocument_getNumErrors), Cuint, (VPtr,), doc)
@@ -92,6 +92,8 @@ function readSBML(fn::String)::SBML.Model
             throw(AssertionError("Opening SBML document has reported errors"))
         end
 
+        sbml_conversion(doc)
+
         if 0 == ccall(sbml(:SBMLDocument_isSetModel), Cint, (VPtr,), doc)
             throw(AssertionError("SBML document contains no model"))
         end