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Intertypes, this time for real #31

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7b7fdc1
it might work?
olynch Jan 18, 2024
966eed4
intertypes loads, but some tests don't work
olynch Jan 18, 2024
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1 change: 1 addition & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ version = "0.1.0"
ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391"
DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
Expand Down
59 changes: 59 additions & 0 deletions src/amr.it
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@@ -0,0 +1,59 @@
@sum MathML begin
Math(str::String)
Presentation(str::String)
end

struct ExpressionFormula
expression::String
expression_mathml::MathML
end

struct Unit
expression::String
expression_mathml::MathML
end


@sum Distribution begin
StandardUniform()
Uniform(min::Float64, max::Float64)
StandardNormal()
Normal(mean::Float64, variance::Float64)
PointMass(value::Float64)
Undefined()
end

struct Observable
id::Symbol
name::String
states::Vector{Symbol}
f::ExpressionFormula
end

@sum Expression begin
Rate(target::Symbol, f::ExpressionFormula)
Initial(target::Symbol, f::ExpressionFormula)
Parameter(id::Symbol, name::String, description::String, units::Unit, value::Float64, distribution::Distribution)
Time(id::Symbol, units::Unit)
end

@sum Note begin
Name(str::String)
Description(str::String)
Grounding(ontology::String, identifier::String)
Units(expression::String)
end

struct Annotation
entity::Symbol
type::Symbol
note::Note
end

struct Header
name::String
schema::String
description::String
schema_name::String
model_version::String
end
89 changes: 14 additions & 75 deletions src/amr.jl
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Expand Up @@ -16,81 +16,20 @@ using StructTypes

using ..SyntacticModelsBase

@data MathML <: AbstractTerm begin
Math(String)
Presentation(String)
end

nomath = Math("")
@intertypes "amr.it" module amr end

@as_record struct ExpressionFormula{T} <: AbstractTerm
expression::T
expression_mathml::MathML
end

@as_record struct Unit <: AbstractTerm
expression::String
expression_mathml::MathML
end
using .amr

nomath = Math("")

nounit = Unit("", nomath)

@data Distribution <: AbstractTerm begin
StandardUniform
Uniform(min, max)
StandardNormal
Normal(mean, variance)
PointMass(value)
end

@as_record struct Observable{T <: AbstractTerm}
id::Symbol
name::String
states::Vector{Symbol}
f::ExpressionFormula
end

@data Expression <: AbstractTerm begin
Rate(target::Symbol, f::ExpressionFormula)
Initial(target::Symbol, f::ExpressionFormula)
Parameter(id::Symbol, name::String, description::String, units::Unit, value::Float64, distribution::Distribution)
Time(id::Symbol, units::Unit)
end

@data Semantic <: AbstractTerm begin
@data Semantic <: AbstractTerm begin
ODEList(statements::Vector{Expression})
ODERecord(rates::Vector{Rate}, initials::Vector{Initial}, parameters::Vector{Parameter}, time::Time)
# Metadata
Typing(system::ACSetSpec, map::Vector{Pair})
# Stratification
end

@data Note <: AbstractTerm begin
Name(str::String)
Description(str::String)
Grounding(ontology::String, identifier::String)
Units(expression::String)
Typing(system::ACSetSpec, map::Vector{Base.Pair})
end

StructTypes.StructType(::Type{Note}) = StructTypes.AbstractType()
StructTypes.subtypekey(::Type{Note}) = :_type
StructTypes.subtypes(::Type{Note}) =
(Name=Name,Description=Description,Grounding=Grounding,Units=Units,)

@as_record struct Annotation{E,T} <: AbstractTerm
entity::E
type::T
note::Note
end

@as_record struct Header <: AbstractTerm
name::String
schema::String
description::String
schema_name::String
model_version::String
end

@as_record struct ASKEModel <: AbstractTerm
header::Header
Expand Down Expand Up @@ -249,16 +188,16 @@ end

function load(::Type{Distribution}, d::AbstractDict)
@match d begin
Dict("type"=>"StandardUniform1") => StandardUniform
Dict("type"=>"StandardNormal") => StandardNormal
Dict("type"=>"StandardUniform1") => StandardUniform()
Dict("type"=>"StandardNormal") => StandardNormal()
Dict("type"=>"Uniform", "parameters"=>p) => Uniform(p["minimum"], p["maximum"])
Dict("type"=>"Uniform1", "parameters"=>p) => Uniform(p["minimum"], p["maximum"])
Dict("type"=>"Normal", "parameters"=>p) => Normal(p["mu"], p["var"])
Dict("type"=>"PointMass", "parameters"=>p) => PointMass(p["value"])
end
end

load(::Type{Distribution}, ::Nothing) = PointMass(missing)
load(::Type{Distribution}, ::Nothing) = Undefined()

function load(::Type{Note}, d::AbstractDict)
@match d begin
Expand All @@ -281,7 +220,7 @@ function load(::Type{Parameter}, d::AbstractDict)
u,
d["value"],
load(Distribution, get(d,"distribution", nothing))
)
)
end

function load(::Type{ODERecord}, d::AbstractDict)
Expand All @@ -297,10 +236,10 @@ function load(::Type{ODERecord}, d::AbstractDict)
end

function load(::Type{Header}, d::AbstractDict)
@match d begin
Dict("name"=>n, "schema"=>s, "description"=>d, "schema_name"=>sn, "model_version"=>mv) => Header(n,s,d,sn,mv)
_ => error("Information for Header was not found in $d")
end
@match d begin
Dict("name"=>n, "schema"=>s, "description"=>d, "schema_name"=>sn, "model_version"=>mv) => Header(n,s,d,sn,mv)
_ => error("Information for Header was not found in $d")
end
end

function load(::Type{Typing}, d::AbstractDict)
Expand Down Expand Up @@ -460,4 +399,4 @@ function load(::Type{ASKEModel}, ex::Expr)
end
ASKEModel(elts[2][1], elts[2][2], [elts[4], elts[6]])
end
end # module end
end # module end
4 changes: 4 additions & 0 deletions src/askemdecapodes.it
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@@ -0,0 +1,4 @@
@sum ASKEMDeca begin
ASKEMDecaExpr(header::amr.Header, model::decapodes.DecaExpr, annotations::Vector{amr.Annotation})
ASKEMDecapode(header::amr.Header, model::decapodeacset.SymSummationDecapode, annotations::Vector{amr.Annotation})
end
36 changes: 9 additions & 27 deletions src/decapodes.jl
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Expand Up @@ -4,16 +4,22 @@ export ASKEMDecaExpr, ASKEMDecapode

using ..SyntacticModelsBase
using ..AMR
import ..AMR: amr

using StructTypes
using Decapodes
using MLStyle
import DiagrammaticEquations: decapodes, decapodeacset

@data ASKEMDeca <: AbstractTerm begin
ASKEMDecaExpr(header::AMR.Header, model::Decapodes.DecaExpr, annotations::Vector{AMR.Annotation{Symbol,Symbol}})
ASKEMDecapode(header::AMR.Header, model::Decapodes.SummationDecapode, annotations::Vector{AMR.Annotation{Symbol,Symbol}})
@intertypes "askemdecapodes.it" module askemdecapodes
import ..amr
import ..decapodes
import ..decapodeacset
end

using .askemdecapodes
using .askemdecapodes: ASKEMDecaExpr, ASKEMDecapode

@doc """ ASKEMDeca

Stores a Decapode with the model metadata for ASKEM AMR conformance.
Expand All @@ -34,28 +40,4 @@ model metadata for ASKEM AMR conformance.
"""
ASKEMDecapode(header::AMR.Header, model::Decapodes.SummationDecapode) = ASKEMDecapode(header,model,Vector{AMR.Annotation{Symbol,Symbol}}())

StructTypes.StructType(::Type{ASKEMDeca}) = StructTypes.AbstractType()
StructTypes.subtypekey(::Type{ASKEMDeca}) = :_type
StructTypes.subtypes(::Type{ASKEMDeca}) = (ASKEMDecaExpr=ASKEMDecaExpr, ASKEMDecapode=ASKEMDecapode)

SyntacticModelsBase._dict(x::T) where {T<:Union{Decapodes.DecaExpr, Decapodes.Equation, Decapodes.Term}} = begin
Dict(:_type => typename_last(T), [k=>_dict(getfield(x, k)) for k in fieldnames(T)]...)
end

StructTypes.StructType(::Type{Decapodes.Equation}) = StructTypes.AbstractType()
StructTypes.subtypekey(::Type{Decapodes.Equation}) = :_type
StructTypes.subtypes(::Type{Decapodes.Equation}) = (Eq=Eq,)

StructTypes.StructType(::Type{Decapodes.Term}) = StructTypes.AbstractType()
StructTypes.subtypekey(::Type{Decapodes.Term}) = :_type
StructTypes.subtypes(::Type{Decapodes.Term}) = (Var=Decapodes.Var,
Lit=Decapodes.Lit,
Judgement=Decapodes.Judgement,
AppCirc1=Decapodes.AppCirc1,
App1=Decapodes.App1,
App2=Decapodes.App2,
Plus=Decapodes.Plus,
Mult=Decapodes.Mult,
Tan=Decapodes.Tan)

end
8 changes: 3 additions & 5 deletions test/core.jl
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@@ -1,7 +1,5 @@
include("../src/SyntacticModels.jl")

using .SyntacticModels
using .SyntacticModels.ASKEMDecapodes
using SyntacticModels
using SyntacticModels.ASKEMDecapodes

using Test
using JSON3
Expand Down Expand Up @@ -35,4 +33,4 @@ include("amr_examples.jl")
include("decapodes_examples.jl")
include("uwd_examples.jl")
include("composite_models_examples.jl")
include("serialization_mwe.jl")
include("serialization_mwe.jl")