Merge pull request #46 from LCSB-BioCore/mk-fix-nice-fba-variants

fix the nice FBA variants (again)

src/analysis/fba.jl

@@ -13,6 +13,35 @@ Returns a solved model from [`optimize_model`](@ref).
 flux_balance_analysis(model::M, optimizer) where {M<:MetabolicModel} =
     optimize_model(model, optimizer; sense = MOI.MAX_SENSE)
 
+"""
+    flux_balance_analysis_vec(args...)::Union{Vector{Float64},Nothing}
+
+A variant of FBA that returns a vector of fluxes in the same order as reactions
+of the model, if the solution is found.
+Arguments are passed to [`flux_balance_analysis`](@ref).
+"""
+function flux_balance_analysis_vec(args...)::Union{Vector{Float64},Nothing}
+    (optmodel, vars) = flux_balance_analysis(args...)
+
+    termination_status(optmodel) in [MOI.OPTIMAL, MOI.LOCALLY_SOLVED] || return nothing
+    value.(vars)
+end
+
+"""
+    flux_balance_analysis_dict(model::M, args...)::Union{Dict{String, Float64},Nothing} where {M <: MetabolicModel}
+
+A variant of FBA that returns a dictionary assigning fluxes to reactions, if
+the solution is found. Arguments are passed to [`flux_balance_analysis`](@ref).
+"""
+function flux_balance_analysis_dict(
+    model::M,
+    args...,
+)::Union{Dict{String,Float64},Nothing} where {M<:MetabolicModel}
+    v = flux_balance_analysis_vec(model, args...)
+    isnothing(v) && return nothing
+    Dict(zip(reactions(model), v))
+end
+
 """
     fba(model::CobraModel, optimizer; objective_func::Union{Reaction, Array{Reaction, 1}}=Reaction[], weights=Float64[], solver_attributes=Dict{Any, Any}(), constraints=Dict{String, Tuple{Float64,Float64}}())
 

test/analysis/fba.jl

@@ -34,12 +34,11 @@
     @test cp.c' * sol ≈ expected_optimum
 
     # test the "nicer output" variants
-    @test_broken false # reminder to implement these methods
-    # fluxes_vec = flux_balance_analysis_vec(cp, GLPK.Optimizer)
-    # @test_broken all(fluxes_vec .== sol)
-    # fluxes_dict = flux_balance_analysis_dict(cp, GLPK.Optimizer)
-    # rxns = reactions(cp)
-    # @test all([fluxes_dict[rxns[i]] == sol[i] for i in eachindex(rxns)])
+    fluxes_vec = flux_balance_analysis_vec(cp, GLPK.Optimizer)
+    @test all(fluxes_vec .== sol)
+    fluxes_dict = flux_balance_analysis_dict(cp, GLPK.Optimizer)
+    rxns = reactions(cp)
+    @test all([fluxes_dict[rxns[i]] == sol[i] for i in eachindex(rxns)])
 end
 
 @testset "Flux balance analysis with CobraModel" begin