fix null kinetic law

src/readsbml.jl

@@ -33,12 +33,12 @@ end
 
 function extractModel(mdl::VPtr)::Model
     units = Dict{String,Vector{UnitPart}}()
-    for i = 0:ccall(sbml(:Model_getNumUnitDefinitions), Cuint, (VPtr,), mdl)-1
-        ud = ccall(sbml(:Model_getUnitDefinition), VPtr, (VPtr, Cuint), mdl, i)
+    for i = 1:ccall(sbml(:Model_getNumUnitDefinitions), Cuint, (VPtr,), mdl)
+        ud = ccall(sbml(:Model_getUnitDefinition), VPtr, (VPtr, Cuint), mdl, i - 1)
         id = unsafe_string(ccall(sbml(:UnitDefinition_getId), Cstring, (VPtr,), ud))
         units[id] = [
             begin
-                u = ccall(sbml(:UnitDefinition_getUnit), VPtr, (VPtr, Cuint), ud, j)
+                u = ccall(sbml(:UnitDefinition_getUnit), VPtr, (VPtr, Cuint), ud, j - 1)
                 UnitPart(
                     unsafe_string(
                         ccall(
@@ -52,7 +52,7 @@ function extractModel(mdl::VPtr)::Model
                     ccall(sbml(:Unit_getScale), Cint, (VPtr,), u),
                     ccall(sbml(:Unit_getMultiplier), Cdouble, (VPtr,), u),
                 )
-            end for j = 0:ccall(sbml(:UnitDefinition_getNumUnits), Cuint, (VPtr,), ud)-1
+            end for j = 1:ccall(sbml(:UnitDefinition_getNumUnits), Cuint, (VPtr,), ud)
         ]
     end
 
@@ -62,14 +62,14 @@ function extractModel(mdl::VPtr)::Model
                 sbml(:Compartment_getId),
                 Cstring,
                 (VPtr,),
-                ccall(sbml(:Model_getCompartment), VPtr, (VPtr, Cuint), mdl, i),
+                ccall(sbml(:Model_getCompartment), VPtr, (VPtr, Cuint), mdl, i - 1),
             ),
-        ) for i = 0:ccall(sbml(:Model_getNumCompartments), Cuint, (VPtr,), mdl)-1
+        ) for i = 1:ccall(sbml(:Model_getNumCompartments), Cuint, (VPtr,), mdl)
     ]
 
     species = Dict{String,Species}()
-    for i = 0:ccall(sbml(:Model_getNumSpecies), Cuint, (VPtr,), mdl)-1
-        sp = ccall(sbml(:Model_getSpecies), VPtr, (VPtr, Cuint), mdl, i)
+    for i = 1:ccall(sbml(:Model_getNumSpecies), Cuint, (VPtr,), mdl)
+        sp = ccall(sbml(:Model_getSpecies), VPtr, (VPtr, Cuint), mdl, i - 1)
         species[unsafe_string(ccall(sbml(:Species_getId), Cstring, (VPtr,), sp))] = Species(
             unsafe_string(ccall(sbml(:Species_getName), Cstring, (VPtr,), sp)),
             unsafe_string(ccall(sbml(:Species_getCompartment), Cstring, (VPtr,), sp)),
@@ -77,24 +77,29 @@ function extractModel(mdl::VPtr)::Model
     end
 
     reactions = Dict{String,Reaction}()
-    for i = 0:ccall(sbml(:Model_getNumReactions), Cuint, (VPtr,), mdl)-1
-        re = ccall(sbml(:Model_getReaction), VPtr, (VPtr, Cuint), mdl, i)
-        kl = ccall(sbml(:Reaction_getKineticLaw), VPtr, (VPtr,), re)
+
+    for i = 1:ccall(sbml(:Model_getNumReactions), Cuint, (VPtr,), mdl)
+        re = ccall(sbml(:Model_getReaction), VPtr, (VPtr, Cuint), mdl, i - 1)
         lb = (-Inf, "")
         ub = (Inf, "")
         oc = 0.0
-        for j = 0:ccall(sbml(:KineticLaw_getNumParameters), Cuint, (VPtr,), kl)-1
-            p = ccall(sbml(:KineticLaw_getParameter), VPtr, (VPtr, Cuint), kl, j)
-            id = unsafe_string(ccall(sbml(:Parameter_getId), Cstring, (VPtr,), p))
-            pval = () -> ccall(sbml(:Parameter_getValue), Cdouble, (VPtr,), p)
-            punit =
-                () -> unsafe_string(ccall(sbml(:Parameter_getUnits), Cstring, (VPtr,), p))
-            if id == "LOWER_BOUND"
-                lb = (pval(), punit())
-            elseif id == "UPPER_BOUND"
-                ub = (pval(), punit())
-            elseif id == "OBJECTIVE_COEFFICIENT"
-                oc = pval()
+
+        kl = ccall(sbml(:Reaction_getKineticLaw), VPtr, (VPtr,), re)
+        if kl != C_NULL
+            for j = 1:ccall(sbml(:KineticLaw_getNumParameters), Cuint, (VPtr,), kl)
+                p = ccall(sbml(:KineticLaw_getParameter), VPtr, (VPtr, Cuint), kl, j - 1)
+                id = unsafe_string(ccall(sbml(:Parameter_getId), Cstring, (VPtr,), p))
+                pval = () -> ccall(sbml(:Parameter_getValue), Cdouble, (VPtr,), p)
+                punit =
+                    () ->
+                        unsafe_string(ccall(sbml(:Parameter_getUnits), Cstring, (VPtr,), p))
+                if id == "LOWER_BOUND"
+                    lb = (pval(), punit())
+                elseif id == "UPPER_BOUND"
+                    ub = (pval(), punit())
+                elseif id == "OBJECTIVE_COEFFICIENT"
+                    oc = pval()
+                end
             end
         end
 
@@ -107,13 +112,13 @@ function extractModel(mdl::VPtr)::Model
                     ccall(sbml(:SpeciesReference_getStoichiometry), Cdouble, (VPtr,), sr) *
                     factor
 
-        for j = 0:ccall(sbml(:Reaction_getNumReactants), Cuint, (VPtr,), re)-1
-            sr = ccall(sbml(:Reaction_getReactant), VPtr, (VPtr, Cuint), re, j)
+        for j = 1:ccall(sbml(:Reaction_getNumReactants), Cuint, (VPtr,), re)
+            sr = ccall(sbml(:Reaction_getReactant), VPtr, (VPtr, Cuint), re, j - 1)
             add_stoi(sr, -1)
         end
 
-        for j = 0:ccall(sbml(:Reaction_getNumProducts), Cuint, (VPtr,), re)-1
-            sr = ccall(sbml(:Reaction_getProduct), VPtr, (VPtr, Cuint), re, j)
+        for j = 1:ccall(sbml(:Reaction_getNumProducts), Cuint, (VPtr,), re)
+            sr = ccall(sbml(:Reaction_getProduct), VPtr, (VPtr, Cuint), re, j - 1)
             add_stoi(sr, 1)
         end