Merge pull request #683 from LCSB-BioCore/mk-fix-mergeability

backmerge `master` changes to `develop` to resolve merge conflicts
LCSB-BioCore · Oct 14, 2022 · 677b099 · 677b099
2 parents cfaed93 + 40c15f8
commit 677b099
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/src/base/constants.jl b/src/base/constants.jl
@@ -26,7 +26,7 @@ const _constants = (
         ids = ["id", "description"],
         metformulas = ["metFormula", "metFormulas"],
         metcharges = ["metCharge", "metCharges"],
-        metcompartments = ["metCompartment", "metCompartments"],
+        metcompartments = ["metCompartment", "metCompartments", "metComp", "metComps"],
         rxnnames = ["rxnNames"],
         metnames = ["metNames"],
     ),

diff --git a/src/base/types/MATModel.jl b/src/base/types/MATModel.jl
@@ -155,12 +155,12 @@ $(TYPEDSIGNATURES)
 
 Extract metabolite charge from `metCharge` or `metCharges`.
 """
-function metabolite_charge(m::MATModel, mid::String)
+function metabolite_charge(m::MATModel, mid::String)::Maybe{Int}
     met_charge = _maybemap(
         x -> x[findfirst(==(mid), metabolites(m))],
         gets(m.mat, nothing, _constants.keynames.metcharges),
     )
-    isnan(met_charge) ? 0 : met_charge
+    _maybemap(Int, isnan(met_charge) ? nothing : met_charge)
 end
 
 """

diff --git a/src/base/types/SBMLModel.jl b/src/base/types/SBMLModel.jl
@@ -120,6 +120,13 @@ metabolite_formula(model::SBMLModel, mid::String)::Maybe{MetaboliteFormula} =
 """
 $(TYPEDSIGNATURES)
 
+Get the compartment of a chosen metabolite from [`SBMLModel`](@ref).
+"""
+metabolite_compartment(model::SBMLModel, mid::String) = model.sbml.species[mid].compartment
+
+"""
+$(TYPEDSIGNATURES)
+
 Get charge of a chosen metabolite from [`SBMLModel`](@ref).
 """
 metabolite_charge(model::SBMLModel, mid::String)::Maybe{Int} =