feat: save to BMA json format

Author: ReubenJ

Project.toml

@@ -13,14 +13,14 @@ HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
 HerbGrammar = "4ef9e186-2fe5-4b24-8de7-9f7291f24af7"
 HerbSearch = "3008d8e8-f9aa-438a-92ed-26e9c7b4829f"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
+MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [weakdeps]
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 
 [extensions]
 JSONExt = ["JSON", "MacroTools"]
@@ -35,8 +35,8 @@ HerbCore = "0.3.4"
 HerbGrammar = "0.6"
 HerbSearch = "0.4.1"
 JSON = "0.21.4"
-MacroTools = "0.5.16"
 MLStyle = "0.4.17"
+MacroTools = "0.5.16"
 MetaGraphsNext = "0.7"
 Random = "1.10"
 SciMLBase = "2.74.1"

ext/JSONExt.jl

@@ -1,159 +1,18 @@
 module JSONExt
+import GraphDynamicalSystems.QualitativeNetwork
 import JSON
 
-using GraphDynamicalSystems: Asynchronous, QualitativeNetwork, default_target_function
-using Graphs: SimpleDiGraph, add_edge!, add_vertex!
-using MacroTools: @capture, postwalk
-using MetaGraphsNext: MetaGraph, inneighbor_labels
-
-function nested_dicts_keys_to_lowercase(d)
-    if d isa AbstractDict
-        return Dict([lowercase(k) => nested_dicts_keys_to_lowercase(v) for (k, v) in d])
-    elseif d isa AbstractVector
-        return [nested_dicts_keys_to_lowercase(v) for v in d]
-    else
-        return d
-    end
-end
-
-function sanitize_formula(f)
-    # surround variable names with quotes
-    return replace(f, r"var\(([^\)]+)\)" => s"var(\"\1\")")
-end
-
-function entity_name_from_in_neighbors(entity, in_neighbors)
-    # the formulas can reference their incoming edges
-    # with either the name of the neighbor entity or
-    # its id
-    e_id = tryparse(Int, entity)
-
-    entity_name = [
-        Symbol("$(name)_$id") for
-        (id, name, _) in in_neighbors if isnothing(e_id) ? name == entity : id == e_id
-    ]
-
-    if length(entity_name) != 1
-        error(
-            """
-            Error while constructing name for entity: $entity, with in neighbors: \
-            $in_neighbors. There are more than one incoming neighbor entities with the same \
-            name. To fix this error, remove the erroneous relationships from the JSON file, \
-            or reference the entity by id (like `var(3)`).
-            """,
-        )
-    end
-    return only(entity_name)
-end
-
-function create_target_function(
-    variable::Dict,
-    in_neighbor_ids::Vector{Int},
-    id_to_name::Dict,
-    mg::MetaGraph,
-)
-    formula = Meta.parse(sanitize_formula(variable["formula"]))
-    in_neighbor_names = getindex.((id_to_name,), in_neighbor_ids)
-    in_neighbor_types = getindex.((mg.edge_data,), in_neighbor_ids, (variable["id"],))
-    in_neighbors = zip(in_neighbor_ids, in_neighbor_names, in_neighbor_types)
-
-    if isnothing(formula) # default target function
-        if length(in_neighbor_ids) == 0
-            @warn "$(variable["name"]) has no inputs, defaulting formula to lowest value ($(variable["rangefrom"]))."
-            return variable["rangefrom"]
-        else
-            activators = [
-                Symbol("$(name)_$id") for
-                (id, name, ty) in in_neighbors if ty == "Activator"
-            ]
-            inhibitors = [
-                Symbol("$(name)_$id") for
-                (id, name, ty) in in_neighbors if ty == "Inhibitor"
-            ]
-            return default_target_function(
-                variable["rangefrom"],
-                variable["rangeto"],
-                activators,
-                inhibitors,
-            )
-        end
-    else # custom target function
-        return postwalk(
-            x ->
-                @capture(x, var(v_String)) ?
-                :($(entity_name_from_in_neighbors(v, in_neighbors))) : x,
-            formula,
-        )
-    end
-end
-
-function to_from_variable_id(r, from_to)
-    k = "$(from_to)variable"
-    k_w_id = k * "id"
-
-    if haskey(r, k)
-        return r[k]
-    elseif haskey(r, k_w_id)
-        return r[k_w_id]
-    else
-        error("""
-              Neither alternative key was found to retrieve the edge variable id. The \
-              model file is not using the expected structure for BMA models.
-              """)
-    end
-end
+using AbstractTrees: PostOrderDFS
+using GraphDynamicalSystems: QualitativeNetwork, bma_dict_to_qn, qn_to_bma_dict
 
 function QualitativeNetwork(bma_file_path::AbstractString)
     json_def = JSON.parse(read(bma_file_path, String))
 
-    json_def = nested_dicts_keys_to_lowercase(json_def)
-    model = json_def["model"]
-    variables = model["variables"]
-    relationships = model["relationships"]
-
-    id_to_name = Dict([v["id"] => v["name"] for v in variables])
-    names = [Symbol("$(v["name"])_$(v["id"])") for v in variables]
-    mg = MetaGraph(SimpleDiGraph(), Int, Union{Expr,Integer,Symbol}, String)
-
-    foreach(variables) do v
-        id = v["id"]
-        name = v["name"]
-        # adding an empty expression: :()
-        # because we need to construct the interaction graph
-        # first before parsing the functions correctly
-        added = add_vertex!(mg, id, :())
-        if !added
-            error(
-                """
-                Failed to add the entity (\"$name\", id: #$id) from the input file while \
-                constructing the QN. Check that there is only one entity in the model with \
-                the id #$id.
-                """,
-            )
-        end
-    end
-
-    foreach(relationships) do r
-        from = to_from_variable_id(r, "from")
-        to = to_from_variable_id(r, "to")
-        type_of_edge = r["type"]
-        added = add_edge!(mg, from, to, type_of_edge)
-        if !added
-            @warn """
-            Encountered a duplicate relationship between entities (from: \
-            $(id_to_name[from]), #$from; to: $(id_to_name[to]), #$to) while constructing \
-            the QN.
-            """
-        end
-    end
-
-    formulas = Union{Expr,Integer,Symbol}[
-        create_target_function(v, collect(inneighbor_labels(mg, v["id"])), id_to_name, mg) for v in variables
-    ]
+    return bma_dict_to_qn(json_def)
+end
 
-    # @show formulas
-    # formulas = Union{Expr,Integer,Symbol}[v["formula"] for v in variables]
-    domains = [v["rangefrom"]:v["rangeto"] for v in variables]
-    #
-    return QualitativeNetwork(names, formulas, domains; schedule = Asynchronous)
+function JSON.json(qn::QualitativeNetwork)
+    return JSON.json(qn_to_bma_dict(qn))
 end
+
 end