From 5e24202257d1cac3199748e134e60a11368e958a Mon Sep 17 00:00:00 2001
From: Luke Morris <lukelukemorrismorris@gmail.com>
Date: Tue, 31 Oct 2023 10:21:59 -0400
Subject: [PATCH 1/3] Read and write FinFunction JSON

---
 src/categorical_algebra/CategoricalAlgebra.jl |   3 +
 .../JSONCSetTransformations.jl                | 136 ++++++++++++++++++
 .../categorical_algebra/CategoricalAlgebra.jl |   4 +
 .../JSONCSetTransformations.jl                |  33 +++++
 4 files changed, 176 insertions(+)
 create mode 100644 src/categorical_algebra/JSONCSetTransformations.jl
 create mode 100644 test/categorical_algebra/JSONCSetTransformations.jl

diff --git a/src/categorical_algebra/CategoricalAlgebra.jl b/src/categorical_algebra/CategoricalAlgebra.jl
index 1f4c9aee9..d672e48b2 100644
--- a/src/categorical_algebra/CategoricalAlgebra.jl
+++ b/src/categorical_algebra/CategoricalAlgebra.jl
@@ -22,6 +22,7 @@ include("Chase.jl")
 include("FunctorialDataMigrations.jl")
 include("StructuredCospans.jl")
 include("Slices.jl")
+include("JSONCSetTransformations.jl")
 
 @reexport using .Categories
 @reexport using .FinCats
@@ -43,4 +44,6 @@ include("Slices.jl")
 @reexport using .StructuredCospans
 @reexport using .Slices
 
+@reexport using .JSONCSetTransformations
+
 end
diff --git a/src/categorical_algebra/JSONCSetTransformations.jl b/src/categorical_algebra/JSONCSetTransformations.jl
new file mode 100644
index 000000000..6547ea95d
--- /dev/null
+++ b/src/categorical_algebra/JSONCSetTransformations.jl
@@ -0,0 +1,136 @@
+""" JSON serialization of acset transformations.
+"""
+module JSONCSetTransformations
+export generate_json_fin_function, parse_json_fin_function,
+  read_json_fin_function, write_json_fin_function#=,
+  generate_json_acset_transformation, parse_json_acset_transformation,
+  read_json_acset_transformation, write_json_acset_transformation=#
+
+import JSON
+using DataStructures: OrderedDict
+#import Pkg
+#import Tables
+
+using ..FinSets, ..CSets
+# TODO: Some of these `using`s might not be necessary.
+using ACSets.ACSetInterface, ACSets.Schemas, ACSets.DenseACSets
+using ACSets.DenseACSets: attr_type
+using ACSets.ColumnImplementations: AttrVar
+
+# ACSetTransformation serialization
+#####################
+
+""" Generate JSON-able object representing a FinFunction.
+
+Inverse to [`parse_json_fin_function`](@ref).
+"""
+function generate_json_fin_function(F::FinFunction)
+  OrderedDict{Symbol,Any}(
+    :dom        => dom(    F),
+    :codom      => codom(  F),
+    :map => collect(F))
+end
+
+""" Serialize a FinFunction object to a JSON file.
+
+Inverse to [`read_json_fin_function`](@ref).
+"""
+function write_json_fin_function(x::FinFunction, fname::AbstractString)
+  open(fname, "w") do f
+    write(f, JSON.json(generate_json_fin_function(x)))
+  end
+end
+
+function parse_json_fin_function(input::AbstractDict)
+  FinFunction(
+              Int.(input["map"]), 
+              input["dom"]["n"], 
+              input["codom"]["n"])
+end
+
+""" Deserialize a FinFunction object from a JSON file.
+
+Inverse to [`write_json_fin_function`](@ref).
+"""
+function read_json_fin_function(fname::AbstractString)
+  parse_json_fin_function(JSON.parsefile(fname))
+end
+
+""" Generate JSON-able object representing an ACSetTransformation.
+
+Inverse to [`parse_json_acset_transformation`](@ref).
+"""
+function generate_json_acset_transformation(X::ACSetTransformation)
+  OrderedDict{Symbol,Any}(
+    :dom   => (generate_json_acset ∘   dom)(X),
+    :codom => (generate_json_acset ∘ codom)(X),
+    :components => OrderedDict{Symbol,Any}(
+      Iterators.map((keys ∘ components)(X), (values ∘ components)(X)) do (k,v)
+        k => k ∈ (attrtypes ∘ acset_schema ∘ dom)(X) ?
+          "foo" :
+          generate_json_fin_function(k)
+      end))
+end
+
+
+#attr_to_json(var::AttrVar) = (_var = var.val,)
+#attr_to_json(val) = val
+#
+#""" Parse JSON-able object or JSON string representing an ACSet.
+#
+#Inverse to [`generate_json_acset`](@ref).
+#"""
+#parse_json_acset_transformation(cons, input::AbstractDict) =
+#  parse_json_acset!(cons(), input)
+#parse_json_acset_transformation(cons, input::AbstractString) =
+#  parse_json_acset_transformation(cons, JSON.parse(input))
+#parse_json_acset_transformation(acs::ACSet, input::AbstractDict) =
+#  parse_json_acset_transformation(constructor(acs), input)
+#
+## TODO
+#function parse_json_acset_transformation!(out::ACSetTransformation, input::AbstractDict)
+#  schema = acset_schema(out)
+#  parts = Iterators.map(input) do (type, rows)
+#    Symbol(type) => add_parts!(out, Symbol(type), length(rows))
+#  end |> Dict
+#  for rows ∈ values(input)
+#    for (rownum, row) ∈ enumerate(rows)
+#      for (k, v) ∈ pairs(row)
+#        k = Symbol(k)
+#        if k == :_id
+#          # For now, IDs are assumed to coincide with row number.
+#          @assert rownum == v
+#          continue
+#        end
+#        if k ∈ attrs(schema; just_names=true)
+#          vtype = attr_type(out, k)
+#          v = v isa AbstractDict && haskey(v, "_var") ?
+#            AttrVar(v["_var"]) : vtype(v)
+#        end
+#        set_subpart!(out, parts[dom(schema, k)][rownum], k, v)
+#      end
+#    end
+#  end
+#  out
+#end
+#
+#""" Deserialize an ACSetTransformation object from a JSON file.
+#
+#Inverse to [`write_json_acset_transformation`](@ref).
+#"""
+#function read_json_acset_transformation(ty, fname::AbstractString)
+#  parse_json_acset_transformation(ty, JSON.parsefile(fname))
+#end
+#
+#""" Serialize an ACSetTransformation object to a JSON file.
+#
+#Inverse to [`read_json_acset_transformation`](@ref).
+#"""
+#function write_json_acset_transformation(x::ACSetTransformation, fname::AbstractString)
+#  open(fname, "w") do f
+#    write(f, JSON.json(generate_json_acset_transformation(x)))
+#  end
+#end
+
+end # module
+
diff --git a/test/categorical_algebra/CategoricalAlgebra.jl b/test/categorical_algebra/CategoricalAlgebra.jl
index 40e3d64f9..dfe6abf05 100644
--- a/test/categorical_algebra/CategoricalAlgebra.jl
+++ b/test/categorical_algebra/CategoricalAlgebra.jl
@@ -60,5 +60,9 @@ end
   include("Slices.jl")
 end
 
+@testset "JSONCSetTransformations" begin
+  include("JSONCSetTransformations.jl")
+end
+
 
 end
diff --git a/test/categorical_algebra/JSONCSetTransformations.jl b/test/categorical_algebra/JSONCSetTransformations.jl
new file mode 100644
index 000000000..dfc60bef1
--- /dev/null
+++ b/test/categorical_algebra/JSONCSetTransformations.jl
@@ -0,0 +1,33 @@
+# FinFunction serialization
+###########################
+function roundtrip_json_fin_function(f::T) where T <: FinFunction
+  mktempdir() do dir
+    path = joinpath(dir, "fin_function.json")
+    write_json_fin_function(f, path)
+    read_json_fin_function(path)
+  end
+end
+
+f = FinFunction([2,3], 2, 4)
+g = FinFunction([2],   1, 3)
+
+for ϕ in [f,g]
+  @test roundtrip_json_fin_function(ϕ) == ϕ
+end
+
+# ACSetTransformation serialization
+###################################
+
+function roundtrip_json_acset_transformation(x::T) where T <: ACSetTransformation
+  mktempdir() do dir
+    path = joinpath(dir, "acset_transformation.json")
+    write_json_acset_transformation(x, path)
+    read_json_acset_transformation(T, path)
+  end
+end
+
+g = path_graph(WeightedGraph{Float64}, 2, E=(weight=2,))
+h = path_graph(WeightedGraph{Float64}, 4, E=(weight=[1,2,3],))
+α = ACSetTransformation((V=[2,3], E=[2]), g, h)
+@test_broken roundtrip_json_acset_transformation(g) == g
+

From 8ff21ea2ecd4793b3908d6bfa7115be660f065ba Mon Sep 17 00:00:00 2001
From: Luke Morris <lukelukemorrismorris@gmail.com>
Date: Tue, 31 Oct 2023 12:16:14 -0400
Subject: [PATCH 2/3] Read and Write JSON ACSetTransformations

---
 .../JSONCSetTransformations.jl                | 118 +++++++-----------
 .../JSONCSetTransformations.jl                |   6 +-
 2 files changed, 51 insertions(+), 73 deletions(-)

diff --git a/src/categorical_algebra/JSONCSetTransformations.jl b/src/categorical_algebra/JSONCSetTransformations.jl
index 6547ea95d..39188ba83 100644
--- a/src/categorical_algebra/JSONCSetTransformations.jl
+++ b/src/categorical_algebra/JSONCSetTransformations.jl
@@ -2,20 +2,14 @@
 """
 module JSONCSetTransformations
 export generate_json_fin_function, parse_json_fin_function,
-  read_json_fin_function, write_json_fin_function#=,
+  read_json_fin_function, write_json_fin_function,
   generate_json_acset_transformation, parse_json_acset_transformation,
-  read_json_acset_transformation, write_json_acset_transformation=#
+  read_json_acset_transformation, write_json_acset_transformation
 
 import JSON
 using DataStructures: OrderedDict
-#import Pkg
-#import Tables
 
 using ..FinSets, ..CSets
-# TODO: Some of these `using`s might not be necessary.
-using ACSets.ACSetInterface, ACSets.Schemas, ACSets.DenseACSets
-using ACSets.DenseACSets: attr_type
-using ACSets.ColumnImplementations: AttrVar
 
 # ACSetTransformation serialization
 #####################
@@ -65,72 +59,56 @@ function generate_json_acset_transformation(X::ACSetTransformation)
     :dom   => (generate_json_acset ∘   dom)(X),
     :codom => (generate_json_acset ∘ codom)(X),
     :components => OrderedDict{Symbol,Any}(
-      Iterators.map((keys ∘ components)(X), (values ∘ components)(X)) do (k,v)
-        k => k ∈ (attrtypes ∘ acset_schema ∘ dom)(X) ?
-          "foo" :
-          generate_json_fin_function(k)
+      Iterators.map((keys ∘ components)(X), (values ∘ components)(X)) do k,v
+        k , k ∈ (attrtypes ∘ acset_schema ∘ dom)(X) ?
+          # TODO: Support VarFunctions that are not empty.
+          "TODO: VarFunctions are current not supported." :
+          generate_json_fin_function(v)
       end))
 end
 
+""" Serialize an ACSetTransformation object to a JSON file.
 
-#attr_to_json(var::AttrVar) = (_var = var.val,)
-#attr_to_json(val) = val
-#
-#""" Parse JSON-able object or JSON string representing an ACSet.
-#
-#Inverse to [`generate_json_acset`](@ref).
-#"""
-#parse_json_acset_transformation(cons, input::AbstractDict) =
-#  parse_json_acset!(cons(), input)
-#parse_json_acset_transformation(cons, input::AbstractString) =
-#  parse_json_acset_transformation(cons, JSON.parse(input))
-#parse_json_acset_transformation(acs::ACSet, input::AbstractDict) =
-#  parse_json_acset_transformation(constructor(acs), input)
-#
-## TODO
-#function parse_json_acset_transformation!(out::ACSetTransformation, input::AbstractDict)
-#  schema = acset_schema(out)
-#  parts = Iterators.map(input) do (type, rows)
-#    Symbol(type) => add_parts!(out, Symbol(type), length(rows))
-#  end |> Dict
-#  for rows ∈ values(input)
-#    for (rownum, row) ∈ enumerate(rows)
-#      for (k, v) ∈ pairs(row)
-#        k = Symbol(k)
-#        if k == :_id
-#          # For now, IDs are assumed to coincide with row number.
-#          @assert rownum == v
-#          continue
-#        end
-#        if k ∈ attrs(schema; just_names=true)
-#          vtype = attr_type(out, k)
-#          v = v isa AbstractDict && haskey(v, "_var") ?
-#            AttrVar(v["_var"]) : vtype(v)
-#        end
-#        set_subpart!(out, parts[dom(schema, k)][rownum], k, v)
-#      end
-#    end
-#  end
-#  out
-#end
-#
-#""" Deserialize an ACSetTransformation object from a JSON file.
-#
-#Inverse to [`write_json_acset_transformation`](@ref).
-#"""
-#function read_json_acset_transformation(ty, fname::AbstractString)
-#  parse_json_acset_transformation(ty, JSON.parsefile(fname))
-#end
-#
-#""" Serialize an ACSetTransformation object to a JSON file.
-#
-#Inverse to [`read_json_acset_transformation`](@ref).
-#"""
-#function write_json_acset_transformation(x::ACSetTransformation, fname::AbstractString)
-#  open(fname, "w") do f
-#    write(f, JSON.json(generate_json_acset_transformation(x)))
-#  end
-#end
+Inverse to [`read_json_acset_transformation`](@ref).
+"""
+function write_json_acset_transformation(x::ACSetTransformation, fname::AbstractString)
+  open(fname, "w") do f
+    write(f, JSON.json(generate_json_acset_transformation(x)))
+  end
+end
+
+""" Parse JSON-able object or JSON string representing an ACSetTransformation.
+
+Inverse to [`generate_json_acset_transformation`](@ref).
+"""
+parse_json_acset_transformation(cons, input::AbstractString) =
+  parse_json_acset_transformation(cons, JSON.parse(input))
+parse_json_acset_transformation(acs::ACSet, input::AbstractDict) =
+  parse_json_acset_transformation(constructor(acs), input)
+
+function parse_json_acset_transformation(cons, input::AbstractDict)
+  domain   = parse_json_acset(cons(), input["dom"])
+  codomain = parse_json_acset(cons(), input["codom"])
+  hom_keys = filter(keys(input["components"])) do k
+    Symbol(k) ∉ (attrtypes ∘ acset_schema)(domain)
+  end
+  # TODO: Support VarFunctions that are not empty.
+  ACSetTransformation(
+    NamedTuple{Tuple(Symbol.(hom_keys))}(
+      Iterators.map(hom_keys) do k
+        parse_json_fin_function(input["components"][k])
+      end),
+    domain,
+    codomain)
+end
+
+""" Deserialize an ACSetTransformation object from a JSON file.
+
+Inverse to [`write_json_acset_transformation`](@ref).
+"""
+function read_json_acset_transformation(ty, fname::AbstractString)
+  parse_json_acset_transformation(ty, JSON.parsefile(fname))
+end
 
 end # module
 
diff --git a/test/categorical_algebra/JSONCSetTransformations.jl b/test/categorical_algebra/JSONCSetTransformations.jl
index dfc60bef1..2c9efc590 100644
--- a/test/categorical_algebra/JSONCSetTransformations.jl
+++ b/test/categorical_algebra/JSONCSetTransformations.jl
@@ -18,16 +18,16 @@ end
 # ACSetTransformation serialization
 ###################################
 
-function roundtrip_json_acset_transformation(x::T) where T <: ACSetTransformation
+function roundtrip_json_acset_transformation(x, t)
   mktempdir() do dir
     path = joinpath(dir, "acset_transformation.json")
     write_json_acset_transformation(x, path)
-    read_json_acset_transformation(T, path)
+    read_json_acset_transformation(t, path)
   end
 end
 
 g = path_graph(WeightedGraph{Float64}, 2, E=(weight=2,))
 h = path_graph(WeightedGraph{Float64}, 4, E=(weight=[1,2,3],))
 α = ACSetTransformation((V=[2,3], E=[2]), g, h)
-@test_broken roundtrip_json_acset_transformation(g) == g
+@test roundtrip_json_acset_transformation(α, WeightedGraph{Float64}) == α
 

From a02baa5731c0610b0b961c4586aaa4b1d43e6261 Mon Sep 17 00:00:00 2001
From: Luke Morris <lukelukemorrismorris@gmail.com>
Date: Tue, 31 Oct 2023 14:39:07 -0400
Subject: [PATCH 3/3] Parse FinFunctions of domain 0

---
 .../JSONCSetTransformations.jl                | 10 ++--
 .../JSONCSetTransformations.jl                | 57 +++++++++++++++++++
 2 files changed, 62 insertions(+), 5 deletions(-)

diff --git a/src/categorical_algebra/JSONCSetTransformations.jl b/src/categorical_algebra/JSONCSetTransformations.jl
index 39188ba83..c10847c2d 100644
--- a/src/categorical_algebra/JSONCSetTransformations.jl
+++ b/src/categorical_algebra/JSONCSetTransformations.jl
@@ -20,9 +20,9 @@ Inverse to [`parse_json_fin_function`](@ref).
 """
 function generate_json_fin_function(F::FinFunction)
   OrderedDict{Symbol,Any}(
-    :dom        => dom(    F),
-    :codom      => codom(  F),
-    :map => collect(F))
+    :dom   => dom(F),
+    :codom => codom(F),
+    :map   => collect(F))
 end
 
 """ Serialize a FinFunction object to a JSON file.
@@ -37,8 +37,8 @@ end
 
 function parse_json_fin_function(input::AbstractDict)
   FinFunction(
-              Int.(input["map"]), 
-              input["dom"]["n"], 
+              input["dom"]["n"] != 0 ? Int.(input["map"]) : 1:0,
+              input["dom"]["n"],
               input["codom"]["n"])
 end
 
diff --git a/test/categorical_algebra/JSONCSetTransformations.jl b/test/categorical_algebra/JSONCSetTransformations.jl
index 2c9efc590..39a0852fb 100644
--- a/test/categorical_algebra/JSONCSetTransformations.jl
+++ b/test/categorical_algebra/JSONCSetTransformations.jl
@@ -1,3 +1,8 @@
+module TestJSONCSetTransformations
+using Test
+
+using Catlab.CategoricalAlgebra, Catlab.Graphs
+
 # FinFunction serialization
 ###########################
 function roundtrip_json_fin_function(f::T) where T <: FinFunction
@@ -31,3 +36,55 @@ h = path_graph(WeightedGraph{Float64}, 4, E=(weight=[1,2,3],))
 α = ACSetTransformation((V=[2,3], E=[2]), g, h)
 @test roundtrip_json_acset_transformation(α, WeightedGraph{Float64}) == α
 
+@present SchFalseDecapode(FreeSchema) begin
+  (Var, TVar, Op1, Op2)::Ob
+  (Type, Operator)::AttrType
+  src::Hom(Op1, Var)
+  tgt::Hom(Op1, Var)
+  proj1::Hom(Op2, Var)
+  proj2::Hom(Op2, Var)
+  res::Hom(Op2, Var)
+  incl::Hom(TVar, Var)
+  
+  op1::Attr(Op1, Operator)
+  op2::Attr(Op2, Operator)
+  type::Attr(Var, Type)
+
+  Name::AttrType
+  name::Attr(Var, Name)
+
+  (Σ, Summand)::Ob
+  summand::Hom(Summand, Var)
+  summation::Hom(Summand, Σ)
+  sum::Hom(Σ, Var)
+end
+
+@acset_type FalseDecapode(SchFalseDecapode,
+  index=[:src, :tgt, :res, :incl, :op1, :op2, :type])
+
+dynamics = @acset FalseDecapode{Symbol,Symbol,Symbol} begin
+  Var = 2
+  name = [:Q, :Qᵤ]
+  type = [:Form0, :Form0]
+  Op1 = 2
+  src = [1,1]
+  tgt = [2,2]
+  op1 = [:dt,:Δ]
+  TVar = 1
+  incl = [2]
+end
+boundaries = @acset FalseDecapode{Symbol,Symbol,Symbol} begin
+  Var = 1
+  name = [:Q]
+  type = [:Form0]
+end
+
+boundary_conditions = ACSetTransformation(
+  (Var=[1],),
+  boundaries, dynamics)
+
+@test roundtrip_json_acset_transformation(boundary_conditions,
+  FalseDecapode{Symbol,Symbol,Symbol}()) == boundary_conditions
+
+end
+