Merge pull request #611 from LCSB-BioCore/mk-load-more-metadata

load more metadata from models
LCSB-BioCore · May 2, 2022 · 2b71b8f · 2b71b8f
2 parents 0138617 + 111073d
commit 2b71b8f
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Showing 3 changed files with 11 additions and 4 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
@@ -148,16 +148,16 @@ metabolite_formula(m::MATModel, mid::String) = _maybemap(
 )
 
 """
- metabolite_charge(m::MATModel, mid::String)
+ metabolite_charge(m::MATModel, mid::String)::Maybe{Int}
 
 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
@@ -114,6 +114,13 @@ Get [`MetaboliteFormula`](@ref) from a chosen metabolite from [`SBMLModel`](@ref
 metabolite_formula(model::SBMLModel, mid::String)::Maybe{MetaboliteFormula} =
  _maybemap(_parse_formula, model.sbml.species[mid].formula)
 
+"""
+ metabolite_compartment(model::SBMLModel, mid::String)::Maybe{String}
+
+Get the compartment of a chosen metabolite from [`SBMLModel`](@ref).
+"""
+metabolite_compartment(model::SBMLModel, mid::String) = model.sbml.species[mid].compartment
+
 """
  metabolite_charge(model::SBMLModel, mid::String)::Maybe{Int}