AlgebraicJulia / AlgebraicJulia/StockFlow.jl

Serializing Stock & Flow objects fails

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Mô tả

Hi folks,

I tried serializing the StockFlow acset examples in https://github.com/AlgebraicJulia/StockFlow.jl/blob/master/examples/primitive_schema_examples/Covid19_composition_model_in_paper.ipynb

to json with:

```julia
using StockFlow

using Catlab.CategoricalAlgebra
using LabelledArrays
using OrdinaryDiffEq
using Plots

using Catlab.Graphics
using Catlab.Programs
using Catlab.WiringDiagrams

# define functions ϕ of flows in the SEIRH model
fNewIncidence(u,p,t)=p.β*u.S*u.I/p.N
fNewInfectious(u,p,t)=u.E*p.ri
fNewRecovery(u,p,t)=u.I/p.tr * (1.0-p.fH )
fWaningImmunityR(u,p,t)=u.R/p.tw
fHICUAdmission(u,p,t) = u.I/p.tr * p.fH * p.fICU
fHNICUAdmission(u,p,t) = u.I/p.tr * p.fH * (1.0-p.fICU)
fOutICU(u,p,t) = u.HICU/p.tICU
fRecoveryH(u,p,t)= u.HNICU/p.tH

# StockAndFlowp(stocks,
# (flow=>function, upstream=>downstream) => stocks linked)
seirh = StockAndFlowp((:S, :E, :I, :R, :HICU, :HNICU),
((:NewIncidence=>fNewIncidence, :S=>:E) => (:S, :I),
(:NewInfectious=>fNewInfectious, :E=>:I) => :E,
(:NewRecovery=>fNewRecovery, :I=>:R) => :I,
(:WaningImmunityR=>fWaningImmunityR, :R=>:S) => :R,
(:HICUAdmission=>fHICUAdmission, :I=>:HICU) => :I,
(:HNICUAdmission=>fHNICUAdmission, :I=>:HNICU) => :I,
(:OutICU=>fOutICU, :HICU=>:HNICU) => :HICU,
(:RecoveryH=>fRecoveryH, :HNICU=>:R) => :HNICU))

write_json_acset(seirh, "seirh.json")
```

But I got this error instead:

```julia
Cannot serialize type typeof(fNewIncidence)

Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] lower
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:47 [inlined]
[3] show_json(io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, a::Function)
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:348
[4] show_pair(io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, k::Symbol, v::Function)
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:257
[5] show_pair(io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, kv::Pair{Symbol, Any})
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:259
[6] (::JSON.Writer.var"#1#2"{JSON.Writer.CompactContext{IOBuffer}, JSON.Serializations.StandardSerialization, NamedTuple{(:_id, :u, :d, :fname, :ϕf), Tuple{Int64, Int64, Int64, Symbol, typeof(fNewIncidence)}}})()
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:300
[7] recursive_cycle_check(f::JSON.Writer.var"#1#2"{JSON.Writer.CompactContext{IOBuffer}, JSON.Serializations.StandardSerialization, NamedTuple{(:_id, :u, :d, :fname, :ϕf), Tuple{Int64, Int64, Int64, Symbol, typeof(fNewIncidence)}}}, io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, id::UInt64)
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:291
[8] show_json
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:297 [inlined]
[9] show_element(io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, x::NamedTuple{(:_id, :u, :d, :fname, :ϕf), Tuple{Int64, Int64, Int64, Symbol, typeof(fNewIncidence)}})
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:234
[10] (::JSON.Writer.var"#5#6"{JSON.Writer.CompactContext{IOBuffer}, JSON.Serializations.StandardSerialization, Vector{NamedTuple{(:_id, :u, :d, :fname, :ϕf)}}})()
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:326
[11] recursive_cycle_check(f::JSON.Writer.var"#5#6"{JSON.Writer.CompactContext{IOBuffer}, JSON.Serializations.StandardSerialization, Vector{NamedTuple{(:_id, :u, :d, :fname, :ϕf)}}}, io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, id::UInt64)
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:291
[12] show_json
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:323 [inlined]
[13] show_pair
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:257 [inlined]
[14] show_pair(io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, kv::Pair{Symbol, Vector{NamedTuple{(:_id, :u, :d, :fname, :ϕf)}}})
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:259
[15] (::JSON.Writer.var"#1#2"{JSON.Writer.CompactContext{IOBuffer}, JSON.Serializations.StandardSerialization, OrderedCollections.OrderedDict{Symbol, Any}})()
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:300
[16] recursive_cycle_check(f::JSON.Writer.var"#1#2"{JSON.Writer.CompactContext{IOBuffer}, JSON.Serializations.StandardSerialization, OrderedCollections.OrderedDict{Symbol, Any}}, io::JSON.Writer.CompactContext{IOBuffer}, s::JSON.Serializations.StandardSerialization, id::UInt64)
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:291
[17] show_json
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:297 [inlined]
[18] #show_json#9
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:359 [inlined]
[19] show_json
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:357 [inlined]
[20] print(io::IOBuffer, obj::OrderedCollections.OrderedDict{Symbol, Any})
@ JSON.Writer ~/.julia/packages/JSON/93Ea8/src/Writer.jl:383
[21] sprint(f::Function, args::OrderedCollections.OrderedDict{Symbol, Any}; context::Nothing, sizehint::Int64)
@ Base ./strings/io.jl:114
[22] sprint
@ ./strings/io.jl:107 [inlined]
[23] json
@ ~/.julia/packages/JSON/93Ea8/src/Writer.jl:399 [inlined]
[24] #7
@ ~/.julia/packages/ACSets/nILxS/src/JSONACSets.jl:91 [inlined]
[25] open(::ACSets.JSONACSets.var"#7#8"{StockAndFlowp}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Base ./io.jl:395
[26] open
@ ./io.jl:392 [inlined]
[27] write_json_acset(x::StockAndFlowp, fname::String)
@ ACSets.JSONACSets ~/.julia/packages/ACSets/nILxS/src/JSONACSets.jl:90
[28] top-level scope
@ In[5]:1
```

I got the same error with Vaccine model B, Persistent Asymptomaticity Model C, and the COVID19 model.

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