Merge pull request #118 from LCSB-BioCore/mk-lenient-extensive-kinetic-math

Allow rescue in very deep failure with hOSU and extensive math

src/utils.jl

@@ -103,26 +103,42 @@ initial_concentrations(m::SBML.Model; convert_amounts = false) = (
 
 
 """
-    extensive_kinetic_math(m::SBML.Model, formula::SBML.Math)
+    function extensive_kinetic_math(
+        m::SBML.Model,
+        formula::SBML.Math;
+        handle_empty_compartment_size = (id::String) -> throw(
+            DomainError(
+                "Non-substance-only-unit reference to species `\$id' in an unsized compartment `\$(m.species[id].compartment)'",
+            ),
+        ),
+    )
 
 Convert a SBML math `formula` to "extensive" kinetic laws, where the references
 to species that are marked as not having only substance units are converted
 from amounts to concentrations.
 
+If the data is missing, you can supply a function that adds them. A common way
+to handle errors is to assume that unsized compartments have volume 1.0 (of
+whatever units), you can specify that behavior by supplying
+`handle_empty_compartment_size = _ -> 1.0`.
+
 Handling of units in the conversion process is ignored in this version.
 """
-function extensive_kinetic_math(m::SBML.Model, formula::SBML.Math)
+function extensive_kinetic_math(
+    m::SBML.Model,
+    formula::SBML.Math;
+    handle_empty_compartment_size = (id::String) -> throw(
+        DomainError(
+            "Non-substance-only-unit reference to species `$id' in an unsized compartment `$(m.species[id].compartment)'",
+        ),
+    ),
+)
     conv(x::SBML.MathIdent) = begin
         haskey(m.species, x.id) || return x
         sp = m.species[x.id]
         sp.only_substance_units && return x
         sz = m.compartments[sp.compartment].size
-        isnothing(sz) && throw(
-            DomainError(
-                formula,
-                "Non-substance-only-unit reference to species `$(x.id)' in an unsized compartment `$(sp.compartment)'.",
-            ),
-        )
+        isnothing(sz) && (sz = handle_empty_compartment_size(x.id))
         SBML.MathApply("/", [x, SBML.MathVal(sz)])
     end
     conv(x::SBML.MathApply) = SBML.MathApply(x.fn, conv.(x.args))