MAT model not converting to CanonicalModel

[HettieC]

Next issue... the yeast-GEM downloaded from here errors when converted to a CanonicalModel

using MATFBCModels, COBREXA
import AbstractFBCModels.CanonicalModel as CM
model = convert(CM.Model,load_model("yeast-GEM.mat"))

Think it was initially a problem in v1 as well but can't remember what the problem actually was!

[exaexa]

@HettieC can you please paste the error?

[exaexa]

ah OK found it here: LCSB-BioCore/COBREXA.jl#691

There's a workaround in the issue. Looks like the fix we applied somehow didn't make it to MATFBCModels, I'll check where it got dropped. Thanks for spotting this!

[HettieC]

Here is the error in case still needed:

ERROR: InexactError: Int64(NaN)
Stacktrace:
  [1] Int64
    @ Base ./float.jl:909 [inlined]
  [2] parse_charge(x::Float64)
    @ MATFBCModels ~/.julia/packages/MATFBCModels/pA6WE/src/utils.jl:20
  [3] metabolite_charge(m::MATFBCModel, mid::String)
    @ MATFBCModels ~/.julia/packages/MATFBCModels/pA6WE/src/interface.jl:108
  [4] (::AbstractFBCModels.CanonicalModel.var"#19#23"{MATFBCModel})(::Tuple{String, Float64})
    @ AbstractFBCModels.CanonicalModel ./none:0
  [5] iterate(g::Base.Generator, s::Vararg{Any})
    @ Base ./generator.jl:47 [inlined]
  [6] _all(f::Base.var"#384#386", itr::Base.Generator{…}, ::Colon)
    @ Base ./reduce.jl:1297
  [7] all
    @ ./reduce.jl:1283 [inlined]
  [8] Dict(kv::Base.Generator{Base.Iterators.Zip{Tuple{…}}, AbstractFBCModels.CanonicalModel.var"#19#23"{MATFBCModel}})
    @ Base ./dict.jl:111
  [9] convert(::Type{AbstractFBCModels.CanonicalModel.Model}, x::MATFBCModel)
    @ AbstractFBCModels.CanonicalModel ~/.julia/packages/AbstractFBCModels/UeDEO/src/canonical.jl:197
 [10] top-level scope
    @ ~/Documents/Projects/DifferentiableEFMPaper/src/yeastGEM/gecko_setup.jl:26

caused by: InexactError: Int64(NaN)
Stacktrace:
  [1] Int64
    @ Base ./float.jl:909 [inlined]
  [2] parse_charge(x::Float64)
    @ MATFBCModels ~/.julia/packages/MATFBCModels/pA6WE/src/utils.jl:20
  [3] metabolite_charge(m::MATFBCModel, mid::String)
    @ MATFBCModels ~/.julia/packages/MATFBCModels/pA6WE/src/interface.jl:108
  [4] (::AbstractFBCModels.CanonicalModel.var"#19#23"{MATFBCModel})(::Tuple{String, Float64})
    @ AbstractFBCModels.CanonicalModel ./none:0
  [5] iterate
    @ ./generator.jl:47 [inlined]
  [6] Dict{…}(kv::Base.Generator{…})
    @ Base ./dict.jl:85
  [7] dict_with_eltype
    @ ./abstractdict.jl:581 [inlined]
  [8] dict_with_eltype
    @ ./abstractdict.jl:588 [inlined]
  [9] Dict(kv::Base.Generator{Base.Iterators.Zip{Tuple{…}}, AbstractFBCModels.CanonicalModel.var"#19#23"{MATFBCModel}})
    @ Base ./dict.jl:109
 [10] convert(::Type{AbstractFBCModels.CanonicalModel.Model}, x::MATFBCModel)
    @ AbstractFBCModels.CanonicalModel ~/.julia/packages/AbstractFBCModels/UeDEO/src/canonical.jl:197
 [11] top-level scope
    @ ~/Documents/Projects/DifferentiableEFMPaper/src/yeastGEM/gecko_setup.jl:26
Some type information was truncated. Use `show(err)` to see complete types.

[exaexa]

ok wait this is another one. NaN's in charges. :D

[exaexa]

@HettieC should be fixed by #9 , I'll try to release that ASAP.