support SBML writing

.github/workflows/pr-format.yml

@@ -57,6 +57,6 @@ jobs:
               ":x: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) failed, perhaps someone pushed to the PR in the meantime?"
             fi
           else
-            then gh pr comment ${{ github.event.issue.number }} --body \
+            gh pr comment ${{ github.event.issue.number }} --body \
               ":sunny: Auto-formatting triggered by [this comment](${{ github.event.comment.html_url }}) succeeded, but the code was already formatted correctly."
           fi

Project.toml

@@ -28,7 +28,7 @@ MAT = "0.10"
 MacroTools = "0.5.6"
 OSQP = "0.6"
 OrderedCollections = "1.4"
-SBML = "0.10.0"
+SBML = "~1.1"
 StableRNGs = "1.0"
 Tulip = "0.7.0, 0.8.0, 0.9.2"
 julia = "1.5"

src/base/types/SBMLModel.jl

@@ -126,9 +126,10 @@ function _sbml_export_annotation(annotation)::Maybe{String}
     if isnothing(annotation) || isempty(annotation)
         nothing
     elseif length(annotation) != 1 || first(annotation).first != ""
-        @_io_log @warn "Possible data loss: annotation cannot be exported to SBML" annotation
+        @_io_log @warn "Possible data loss: multiple annotations converted to text for SBML" annotation
         join(["$k: $v" for (k, v) in annotation], "\n")
     else
+        @_io_log @warn "Possible data loss: trying to represent annotation in SBML is unlikely to work " annotation
         first(annotation).second
     end
 end
@@ -142,11 +143,12 @@ Return the stoichiometry of reaction with ID `rid`.
 """
 function reaction_stoichiometry(m::SBMLModel, rid::String)::Dict{String,Float64}
     s = Dict{String,Float64}()
-    for (mid, x) in m.sbml.reactions[rid].reactants
-        s[mid] = get(s, mid, 0.0) - x
+    default1(x) = isnothing(x) ? 1 : x
+    for sr in m.sbml.reactions[rid].reactants
+        s[sr.species] = get(s, sr.species, 0.0) - default1(sr.stoichiometry)
     end
-    for (mid, x) in m.sbml.reactions[rid].products
-        s[mid] = get(s, mid, 0.0) + x
+    for sr in m.sbml.reactions[rid].products
+        s[sr.species] = get(s, sr.species, 0.0) + default1(sr.stoichiometry)
     end
     return s
 end
@@ -186,37 +188,52 @@ function Base.convert(::Type{SBMLModel}, mm::MetabolicModel)
     rxns = reactions(mm)
     stoi = stoichiometry(mm)
     (lbs, ubs) = bounds(mm)
-    comps = _default.("", metabolite_compartment.(Ref(mm), mets))
+    comps = _default.("compartment", metabolite_compartment.(Ref(mm), mets))
     compss = Set(comps)
 
     return SBMLModel(
         SBML.Model(
-            compartments = Dict(comp => SBML.Compartment() for comp in compss),
+            compartments = Dict(
+                comp => SBML.Compartment(constant = true) for comp in compss
+            ),
             species = Dict(
                 mid => SBML.Species(
                     name = metabolite_name(mm, mid),
-                    compartment = _default("", comps[mi]),
+                    compartment = _default("compartment", comps[mi]),
                     formula = metabolite_formula(mm, mid),
                     charge = metabolite_charge(mm, mid),
+                    constant = false,
+                    boundary_condition = false,
+                    only_substance_units = false,
                     notes = _sbml_export_notes(metabolite_notes(mm, mid)),
                     annotation = _sbml_export_annotation(metabolite_annotations(mm, mid)),
                 ) for (mi, mid) in enumerate(mets)
             ),
             reactions = Dict(
                 rid => SBML.Reaction(
                     name = reaction_name(mm, rid),
-                    reactants = Dict(
-                        mets[i] => -stoi[i, ri] for
+                    reactants = [
+                        SBML.SpeciesReference(
+                            species = mets[i],
+                            stoichiometry = -stoi[i, ri],
+                            constant = true,
+                        ) for
                         i in SparseArrays.nonzeroinds(stoi[:, ri]) if stoi[i, ri] <= 0
-                    ),
-                    products = Dict(
-                        mets[i] => stoi[i, ri] for
+                    ],
+                    products = [
+                        SBML.SpeciesReference(
+                            species = mets[i],
+                            stoichiometry = stoi[i, ri],
+                            constant = true,
+                        ) for
                         i in SparseArrays.nonzeroinds(stoi[:, ri]) if stoi[i, ri] > 0
-                    ),
+                    ],
                     kinetic_parameters = Dict(
                         "LOWER_BOUND" => SBML.Parameter(value = lbs[ri]),
                         "UPPER_BOUND" => SBML.Parameter(value = ubs[ri]),
                     ),
+                    lower_bound = "LOWER_BOUND",
+                    upper_bound = "UPPER_BOUND",
                     gene_product_association = _maybemap(
                         x -> _unparse_grr(SBML.GeneProductAssociation, x),
                         reaction_gene_association(mm, rid),
@@ -228,13 +245,18 @@ function Base.convert(::Type{SBMLModel}, mm::MetabolicModel)
             ),
             gene_products = Dict(
                 gid => SBML.GeneProduct(
+                    label = gid,
                     name = gene_name(mm, gid),
                     notes = _sbml_export_notes(gene_notes(mm, gid)),
                     annotation = _sbml_export_annotation(gene_annotations(mm, gid)),
                 ) for gid in genes(mm)
             ),
-            objective = Dict(
-                rid => oc for (rid, oc) in zip(rxns, objective(mm)) if oc != 0
+            active_objective = "objective",
+            objectives = Dict(
+                "objective" => SBML.Objective(
+                    "maximize",
+                    Dict(rid => oc for (rid, oc) in zip(rxns, objective(mm)) if oc != 0),
+                ),
             ),
         ),
     )

src/base/utils/Reaction.jl

@@ -12,7 +12,7 @@ See also: [`reaction_mass_balanced`](@ref)
 function check_duplicate_reaction(
     crxn::Reaction,
     rxns::OrderedDict{String,Reaction};
-    only_metabolites=true
+    only_metabolites = true,
 )
     for (k, rxn) in rxns
         if rxn.id != crxn.id # skip if same ID
@@ -120,7 +120,7 @@ julia> stoichiometry_string(req; format_id = x -> x[1:end-2])
 "coa + pyr = for + accoa"
 ```
 """
-function stoichiometry_string(req; format_id=x -> x)
+function stoichiometry_string(req; format_id = x -> x)
     count_prefix(n) = abs(n) == 1 ? "" : string(abs(n), " ")
     substrates =
         join((string(count_prefix(n), format_id(met)) for (met, n) in req if n < 0), " + ")

src/base/utils/gene_associations.jl

@@ -30,7 +30,7 @@ Convert a GeneAssociation to the corresponding `SBML.jl` structure.
 function _unparse_grr(
     ::Type{SBML.GeneProductAssociation},
     x::GeneAssociation,
-)::SBML.GeneAssociation
+)::SBML.GeneProductAssociation
     SBML.GPAOr([SBML.GPAAnd([SBML.GPARef(j) for j in i]) for i in x])
 end
 

src/io/io.jl

@@ -52,6 +52,8 @@ Currently, these model types are supported:
 function save_model(model::MetabolicModel, file_name::String)
     if endswith(file_name, ".json")
         return save_json_model(model, file_name)
+    elseif endswith(file_name, ".xml")
+        return save_sbml_model(model, file_name)
     elseif endswith(file_name, ".mat")
         return save_mat_model(model, file_name)
     else

src/io/sbml.jl

@@ -7,3 +7,19 @@ Load and return a SBML XML model in `file_name`.
 function load_sbml_model(file_name::String)::SBMLModel
     return SBMLModel(SBML.readSBML(file_name))
 end
+
+"""
+    write_sbml_model(model::MetabolicModel, file_name::String)
+
+Write a given SBML model to `file_name`.
+"""
+function save_sbml_model(model::MetabolicModel, file_name::String)
+    m =
+        typeof(model) == SBMLModel ? model :
+        begin
+            @_io_log @warn "Automatically converting $(typeof(model)) to SBMLModel for saving, information may be lost."
+            convert(SBMLModel, model)
+        end
+
+    SBML.writeSBML(m.sbml, file_name)
+end

test/base/types/SBMLModel.jl

@@ -7,10 +7,25 @@
     @test Set(reactions(sbmlm)) == Set(reactions(sbmlm2))
     @test Set(reactions(sbmlm)) == Set(reactions(sm))
     @test Set(metabolites(sbmlm)) == Set(metabolites(sbmlm2))
+    sp(x) = x.species
     @test all([
-        sbmlm.sbml.reactions[i].reactants == sbmlm2.sbml.reactions[i].reactants &&
-        sbmlm.sbml.reactions[i].products == sbmlm2.sbml.reactions[i].products for
-        i in reactions(sbmlm2)
+        issetequal(
+            sp.(sbmlm.sbml.reactions[i].reactants),
+            sp.(sbmlm2.sbml.reactions[i].reactants),
+        ) && issetequal(
+            sp.(sbmlm.sbml.reactions[i].products),
+            sp.(sbmlm2.sbml.reactions[i].products),
+        ) for i in reactions(sbmlm2)
+    ])
+    st(x) = isnothing(x.stoichiometry) ? 1.0 : x.stoichiometry
+    @test all([
+        issetequal(
+            st.(sbmlm.sbml.reactions[i].reactants),
+            st.(sbmlm2.sbml.reactions[i].reactants),
+        ) && issetequal(
+            st.(sbmlm.sbml.reactions[i].products),
+            st.(sbmlm2.sbml.reactions[i].products),
+        ) for i in reactions(sbmlm2)
     ])
 end
 

test/io/json.jl

@@ -14,3 +14,11 @@
     @test sum(jlbs) == sum(slbs)
     @test sum(jubs) == sum(subs)
 end
+
+@testset "Save JSON model" begin
+    model = load_model(CoreModel, model_paths["e_coli_core.json"])
+    testpath = tmpfile("modeltest.json")
+    save_model(model, testpath)
+    wrote = convert(CoreModel, load_json_model(testpath))
+    @test isequal(model, wrote)
+end

test/io/mat.jl

@@ -6,8 +6,8 @@
 end
 
 @testset "Save MAT model" begin
-    testpath = tmpfile("iJR904-clone.mat")
     loaded = load_model(CoreModel, model_paths["iJR904.mat"])
+    testpath = tmpfile("iJR904-clone.mat")
     save_model(loaded, testpath)
     wrote = load_model(CoreModel, testpath)
     @test wrote isa CoreModel

test/io/sbml.jl

@@ -16,3 +16,11 @@
     cm = convert(CoreModelCoupled, sbmlm)
     @test n_coupling_constraints(cm) == 0
 end
+
+@testset "Save SBML model" begin
+    model = load_model(CoreModel, model_paths["e_coli_core.xml"])
+    testpath = tmpfile("modeltest.xml")
+    save_model(convert(SBMLModel, model), testpath)
+    wrote = convert(CoreModel, load_sbml_model(testpath))
+    @test isequal(model, wrote)
+end