Created Stratification DSL. Required adding getter methods for lss, …

src/StockFlow.jl

@@ -9,7 +9,9 @@ funcDynam, flowVariableIndex, funcFlow, funcFlows, funcSV, funcSVs, TransitionMa
 vectorfield, funcFlowsRaw, funcFlowRaw, inflowsAll, outflowsAll,instock,outstock, stockssv, stocksv, svsv, svsstock,
 vsstock, vssv, svsstockAllF, vsstockAllF, vssvAllF, StockAndFlowUntyped, StockAndFlowFUntyped, StockAndFlowStructureUntyped, StockAndFlowStructureFUntyped, StockAndFlowUntyped0, Open, snames, fnames, svnames, vnames,
 object_shift_right, foot, leg, lsnames, OpenStockAndFlow, OpenStockAndFlowOb, fv, fvs, nlvv, nlpv, vtgt, vsrc, vpsrc, vptgt, pname, pnames, make_v_expr,
-vop, lvvposition, lvtgtposition, lsvvposition, lpvvposition, recreate_stratified, set_snames!, set_fnames!, set_svnames!, set_vnames!, set_pnames!, set_sname!, set_fname!, set_svname!, set_vname!, set_pname!
+vop, lvvposition, lvtgtposition, lsvvposition, lpvvposition, recreate_stratified, set_snames!, set_fnames!, set_svnames!, set_vnames!, set_pnames!, set_sname!, set_fname!, set_svname!, set_vname!, set_pname!,
+get_lss, get_lssv, get_lsvsv, get_lsvv, get_lvs, get_lvv, get_is, get_ifn, get_os, get_ofn, get_lpvp, get_lpvv, get_lvsrc, get_lvtgt, get_links
+
 
 using Catlab
 using Catlab.CategoricalAlgebra
@@ -252,6 +254,23 @@ nlvv(p::AbstractStockAndFlowStructureF) = nparts(p,:LVV) #links from dynamic var
 nlpv(p::AbstractStockAndFlowStructureF) = nparts(p,:LPV) #links from dynamic variable to dynamic varibale
 np(p::AbstractStockAndFlowStructureF) = nparts(p,:P) #parameters
 
+
+get_lss(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lss].m))
+get_lssv(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lssv].m))
+get_lsvsv(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lsvsv].m))
+get_lsvv(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lsvv].m))
+get_lvs(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lvs].m))
+get_lvv(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lvv].m))
+get_is(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:is].m))
+get_ifn(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:ifn].m))
+get_os(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:os].m))
+get_ofn(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:ofn].m))
+get_lpvp(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lpvp].m))
+get_lpvv(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lpvv].m))
+get_lvsrc(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lvsrc].m))
+get_lvtgt(sf::AbstractStockAndFlowF) = collect(values(sf.subparts[:lvtgt].m))
+
+
 #EXAMPLE:
 #sir_StockAndFlow=StockAndFlow(((:S, 990)=>(:birth,(:inf,:deathS),(:v_inf,:v_deathS),:N), (:I, 10)=>(:inf,(:rec,:deathI),(:v_rec,:v_deathI,:v_fractionNonS),:N),(:R, 0)=>(:rec,:deathR,(:v_deathR,:v_fractionNonS),:N)),
 #  (:birth=>:v_birth,:inf=>:v_inf,:rec=>:v_rec,:deathS=>:v_deathS,:deathI=>:v_deathI,:deathR=>:v_deathR),

src/Syntax.jl

@@ -103,11 +103,13 @@ end
 ```
 """
 module Syntax
-export @stock_and_flow, @foot, @feet
+export @stock_and_flow, @foot, @feet, infer_links
 
 using ..StockFlow
 using MLStyle
 
+import Base: ==, Iterators.flatmap
+
 """
     stock_and_flow(block :: Expr)
 
@@ -1030,6 +1032,214 @@ function match_foot_format(footblock::Expr)
     end
 end
 
+#############################################
+
+"""
+    infer_particular_link!(sfsrc, sftgt, f1, f2, map1, map2, destination_vector, posf=nothing)
+
+infer_particular_link!(sfsrc, sftgt, get_lvs, get_lvv, stockmaps, dyvarmaps, lvmaps, get_lvvposition) # LV
+
+If we're mapping the same value to multiple positions, it doesn't matter which one goes where.
+We have a few options, on how we want to distribute mappings.  Way it's done here, always goes to the last position.
+
+"""
+function infer_particular_link!(sfsrc, sftgt, f1, f2, map1, map2, destination_vector)
+
+    hom1′_mappings = f1(sftgt)
+    hom2′_mappings = f2(sftgt)
 
+    tgt::Dict{Tuple{Int, Int}, Int} = Dict((hom1′, hom2′) => i for (i, (hom1′, hom2′)) in enumerate(zip(hom1′_mappings, hom2′_mappings))) # ISSUE: If there are two matches, second one overwrites the first.
+    # SOLUTION: Who cares.  Just map to the last.
+    for (i, (hom1, hom2)) in enumerate(zip(f1(sfsrc), f2(sfsrc)))
+        mapped_index1 = map1[hom1]
+        mapped_index2 = map2[hom2]
+
+        linkmap = tgt[(mapped_index1, mapped_index2)]
+
+
+
+        destination_vector[i] = linkmap # updated
+    end
+    return destination_vector
 
 end
+
+
+"""
+    infer_links(sfsrc :: StockAndFlowF, sftgt :: StockAndFlowF, NecMaps :: Dict{Symbol, Vector{Int64}})
+
+Infer LS, I, O, LV, LSV, LVV, LPV mappings for an ACSetTransformation.
+Returns dictionary of Symbols to lists of indices, corresponding to an ACSetTransformation argument.
+If there exist no such mappings (eg, no LVV), that pairing will not be included in the returned dictionary.
+
+If A <- C -> B, and we have A -> A' and B -> B' and a unique C' such that A' <- C' -> B', we can assume C -> C'.
+
+:S => [2,4,1,3], :F => [1,2,4,3], ...
+
+NecMaps must contain keys S, F, SV, P, V, each pointing to a (possibly empty) array of indices
+"""
+function infer_links(sfsrc :: StockAndFlowF, sftgt :: StockAndFlowF, NecMaps :: Dict{Symbol, Vector{Int64}})
+
+
+    stockmaps = NecMaps[:S]
+    flowmaps = NecMaps[:F]
+    summaps = NecMaps[:SV]
+    parammaps = NecMaps[:P]
+    dyvarmaps = NecMaps[:V]
+
+    lsmaps = zeros(Int, nls(sfsrc))
+    imaps = zeros(Int, ni(sfsrc))
+    omaps = zeros(Int, no(sfsrc))
+    lvmaps = zeros(Int, nlv(sfsrc))
+    lsvmaps = zeros(Int, nlsv(sfsrc))
+    lvvmaps = zeros(Int, nlvv(sfsrc))
+    lpvmaps = zeros(Int, nlpv(sfsrc))
+    # After the following calls, there should be no zeroes.
+
+
+    infer_particular_link!(sfsrc, sftgt, get_lss, get_lssv, stockmaps, summaps, lsmaps) # LS
+    infer_particular_link!(sfsrc, sftgt, get_ifn, get_is, flowmaps, stockmaps, imaps) # I
+    infer_particular_link!(sfsrc, sftgt, get_ofn, get_os, flowmaps, stockmaps, omaps) # O
+    infer_particular_link!(sfsrc, sftgt, get_lvs, get_lvv, stockmaps, dyvarmaps, lvmaps) # LV
+    infer_particular_link!(sfsrc, sftgt, get_lsvsv, get_lsvv, summaps, dyvarmaps, lsvmaps) # LSV
+    infer_particular_link!(sfsrc, sftgt, get_lvsrc, get_lvtgt, dyvarmaps, dyvarmaps, lvvmaps) # LVV
+    infer_particular_link!(sfsrc, sftgt, get_lpvp, get_lpvv, parammaps, dyvarmaps, lpvmaps) # LPV
+
+    return Dict(:LS => lsmaps, :LSV => lsvmaps, :LV => lvmaps, :I => imaps, :O => omaps, :LPV => lpvmaps, :LVV => lvvmaps)
+
+
+end
+
+
+struct DSLArgument
+    key::Symbol
+    value::Symbol
+    flags::Set{Symbol} # At present, the only flag that exists is ~
+    DSLArgument(kv::Pair{Union{Expr, Symbol}, Symbol}) = begin # this constructor seemed to fail... need to figure out why.  Maybe it can't call other constructors.
+        key, flags = unwrap_expression(first(kv))
+        new(key, second(kv), flags)
+    end
+    DSLArgument(k::Union{Expr, Symbol}, v::Symbol) = begin
+        key, flags = unwrap_expression(k)
+        new(key, v, flags)
+    end
+    DSLArgument(k::Symbol, v::Symbol, f::Set{Symbol}) = new(k, v, f)
+end
+
+==(a::DSLArgument, b::DSLArgument) = a.key == b.key && a.value == b.value && a.flags == b.flags
+
+
+function unwrap_expression(x::Union{Symbol, Expr}, flags::Set{Symbol}=Set{Symbol}())::Tuple{Symbol, Set{Symbol}} # No mutable default arguments.
+    if typeof(x) == Symbol
+        return (x, flags)
+    else
+        return unwrap_expression(x.args[2], push!(flags, x.args[1]))
+    end
+end
+
+
+"""
+S₁ => I₁
+S₂ => I₂
+S₁ => S₂
+
+⊢
+
+I₁ => I₂
+
+Determine what index an element e maps to based upon what f we have in the mapping such that e -> f
+"""
+function connect_by_value(; src::Dict{T,U}, mapping::Dict{T,T}, tgt::Dict{T,U})::Dict{U, U}  where {T, U}
+    @assert allunique(values(src))
+
+    @assert all(x -> x ∈ keys(mapping), keys(src))
+    @assert all(x -> x ∈ keys(tgt), values(mapping))
+
+    return Dict(src[key] => tgt[value] for (key, value) in mapping)
+
+end
+
+
+"""
+Filter a vector for all elements with substr as a substring.
+"""
+function substring_matches(v::Vector, substr::String)::Vector
+    return filter(x -> occursin(substr, string(x)), v)
+end
+
+
+"""
+Takes a symbol 'key', applys flags, finds matches in s, and returns a vector of matching keys.
+Currently, there are two options: no flags, in which case [key] is returned, or ~ is the only flag, in which case all Symbols with matching substrings are returned.
+"""
+function apply_flags(key::Symbol, flags::Set{Symbol}, s::Vector{Symbol})::Vector{Symbol} # Could make this a generator?
+
+    if isempty(flags)
+        @assert (key ∈ s) "$s does not contain key $key !  Did you forget to prefix ~?"
+        return [key] # potentially inefficient
+    elseif :~ ∈ flags
+
+        matches = collect(substring_matches(s, string(key)))
+
+        new_flags = copy(flags) # copy isn't necessary, probably
+        pop!(new_flags, :~) 
+
+        return collect(flatmap(x -> apply_flags(x, new_flags, s), matches)) # this is just in case we add additional flags.  As is, the recursion is unnecessary.
+    else
+        error("Unknown flag found!  $(flags)")
+    end
+end
+
+"""
+    substitute_symbols(s::Dict{Symbol, Int}, t::Dict{Symbol, Int}, m::Vector{DSLArgument} ; use_flags::Bool=true)::Dict{Int, Int}
+
+Convert Dict(SymA => IntA), Dict(SymB => IntB), Dict(SymA => SymB) into Dict{IntA => IntB}
+Using original sf defintions, and the user defined mappings, transform user defined symbol mappings to index mappings.
+"""
+function substitute_symbols(s::Dict{Symbol, Int}, t::Dict{Symbol, Int}, m::Vector{DSLArgument} ; use_flags::Bool=true)::Dict{Int, Int}
+    if !use_flags
+        mapping = Dict(arg.key => arg.value for arg in m)
+        return connect_by_value(src=s, mapping=mapping, tgt=t)
+    else
+        master_dict::Dict{Int, Int} = Dict()
+        for statement in m
+            key_matches = apply_flags(statement.key, statement.flags, collect(keys(s))) # Vector of Symbol
+            if isempty(key_matches)
+                println("WARNING!  No matches on $(statement.key) with flags $(statement.flags)")
+            else
+                mergewith!((x...) -> first(x), master_dict, Dict(s[match] => t[statement.value] for match ∈ key_matches))
+            end
+        end
+        return master_dict
+    end
+end
+
+
+"""
+Convert a vector of unique elements to a dictionary with each element pointing to their original index.
+"""
+function invert_vector(v::Vector{K})::Dict{K, Int} where {K} # Elements of v must be hashable
+    new_dict = Dict(val => i for (i, val) ∈ enumerate(v))
+    @assert length(new_dict) == length(v) "Nonunique key in vector v: $v"
+    return new_dict
+end
+
+
+"""
+Takes any arguments and returns nothing.
+Used so we can maintain equality when making ACSetTransformations.
+"""
+NothingFunction(x...)::Nothing = nothing;
+
+
+
+
+
+include("syntax/Stratification.jl")
+
+end
+
+
+
+
+