Merge pull request #58 from LCSB-BioCore/mk-init-cs

add initial concentration, fix certainty of units

src/converters.jl

 
 """
-    convert_level_and_version(level, version)
+    set_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) =
+set_level_and_version(level, version) =
     doc -> begin
         ccall(
             sbml(:SBMLDocument_setLevelAndVersion),
@@ -45,6 +45,19 @@ libsbml_convert(conversion_options::Vector{Pair{String,Dict{String,String}}}) =
         end
     end
 
+"""
+    libsbml_convert(converter::String; kwargs...)
+
+Quickly construct a single run of a `libsbml` converter from keyword arguments.
+
+# Example
+```
+readSBML("example.xml", libsbml_convert("stripPackage", package="layout"))
+```
+"""
+libsbml_convert(converter::String; kwargs...) =
+    libsbml_convert([converter => Dict(string(k) => string(v) for (k, v) in kwargs)])
+
 """
     convert_simplify_math
 
@@ -52,6 +65,6 @@ 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"] .=>
+    ["promoteLocalParameters", "expandFunctionDefinitions"] .=>
         Ref(Dict{String,String}()),
 )

src/readsbml.jl

@@ -88,7 +88,7 @@ single parameter, which is the C pointer to the loaded SBML document (C type
 # Example
 ```
 m = readSBML("my_model.xml", doc -> begin
-    convert_level_and_version(3, 1)(doc)
+    set_level_and_version(3, 1)(doc)
     convert_simplify_math(doc)
 end)
 ```
@@ -240,7 +240,15 @@ function extractModel(mdl::VPtr)::SBML.Model
         if ccall(sbml(:Species_isSetInitialAmount), Cint, (VPtr,), sp) != 0
             ia = (
                 ccall(sbml(:Species_getInitialAmount), Cdouble, (VPtr,), sp),
-                get_string(sp, :Species_getSubstanceUnits),
+                get_optional_string(sp, :Species_getSubstanceUnits),
+            )
+        end
+
+        ic = nothing
+        if ccall(sbml(:Species_isSetInitialConcentration), Cint, (VPtr,), sp) != 0
+            ic = (
+                ccall(sbml(:Species_getInitialAmount), Cdouble, (VPtr,), sp),
+                get_optional_string(sp, :Species_getSubstanceUnits),
             )
         end
 
@@ -255,6 +263,7 @@ function extractModel(mdl::VPtr)::SBML.Model
             formula,
             charge,
             ia,
+            ic,
             get_optional_bool(
                 sp,
                 :Species_isSetHasOnlySubstanceUnits,

src/structs.jl

@@ -142,12 +142,13 @@ struct Species
     boundary_condition::Maybe{Bool}
     formula::Maybe{String}
     charge::Maybe{Int}
-    initial_amount::Maybe{Tuple{Float64,String}}
+    initial_amount::Maybe{Tuple{Float64,Maybe{String}}}
+    initial_concentration::Maybe{Tuple{Float64,Maybe{String}}}
     only_substance_units::Maybe{Bool}
     notes::Maybe{String}
     annotation::Maybe{String}
-    Species(na, co, b, f, ch, ia, osu, no = nothing, a = nothing) =
-        new(na, co, b, f, ch, ia, osu, no, a)
+    Species(na, co, b, f, ch, ia, ic, osu, no = nothing, a = nothing) =
+        new(na, co, b, f, ch, ia, ic, osu, no, a)
 end
 
 """