feat: load BMA models

Project.toml

@@ -1,7 +1,7 @@
 name = "GraphDynamicalSystems"
 uuid = "13529e2e-ed53-56b1-bd6f-420b01fca819"
 authors = ["Reuben Gardos Reid <[email protected]>"]
-version = "0.0.3"
+version = "0.0.4"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -18,6 +18,13 @@ 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"]
+
 [compat]
 AbstractTrees = "0.4.5"
 DocStringExtensions = "0.9.3"
@@ -27,6 +34,8 @@ HerbConstraints = "0.4"
 HerbCore = "0.3.4"
 HerbGrammar = "0.6"
 HerbSearch = "0.4.1"
+JSON = "0.21.4"
+MacroTools = "0.5.16"
 MLStyle = "0.4.17"
 MetaGraphsNext = "0.7"
 Random = "1.10"

docs/src/91-developer.md

@@ -68,6 +68,24 @@ pkg> activate .
 pkg> test
 ```
 
+Alternatively, if you have
+[`ReTestItems.jl`](https://github.com/JuliaTesting/ReTestItems.jl),
+[`TestEnv.jl`](https://github.com/JuliaTesting/TestEnv.jl), and
+[`Revise.jl`](https://timholy.github.io/Revise.jl/stable) installed, you can use the script
+at `test/quick.jl` for rapid testing. This allows you to make changes and immediately run the entire test
+suite with those changes. The upside to this setup is that the tests will fail fast, and if
+you re-run, the tests that failed on the most recent run will run first. This is great if
+you're just iterating on one part of the package and trying to get a handful of tests to
+pass. You won't waste time on waiting for other tests to pass and you don't have to manually
+select which tests you're actively working on.
+
+```julia-repl
+julia> include("test/quick.jl")
+```
+
+is all you need to get up and running. Rerunning `include` will rerun the tests as described
+above.
+
 ## Working on a new issue
 
 We try to keep a linear history in this repo, so it is important to keep your branches up-to-date.

ext/JSONExt.jl

@@ -0,0 +1,159 @@
+module JSONExt
+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 = "$(from_to)variable"
+    k_w_id = k * "id"
+
+    if haskey(r, k)
+        return r[k]
+    elseif haskey(r, k_w_id)
+        return r[k_w_id]
+    else
+        error("""
+              Neither alternative key was found to retrieve the edge variable id. The \
+              model file is not using the expected structure for BMA models.
+              """)
+    end
+end
+
+function QualitativeNetwork(bma_file_path::AbstractString)
+    json_def = JSON.parse(read(bma_file_path, String))
+
+    json_def = nested_dicts_keys_to_lowercase(json_def)
+    model = json_def["model"]
+    variables = model["variables"]
+    relationships = model["relationships"]
+
+    id_to_name = Dict([v["id"] => v["name"] for v in variables])
+    names = [Symbol("$(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
+    ]
+
+    # @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)
+end
+end

test/Project.toml

@@ -5,6 +5,7 @@ DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReTestItems = "817f1d60-ba6b-4fd5-9520-3cf149f6a823"

test/qn_test.jl

@@ -141,3 +141,23 @@ end
 
     @test_throws r"no activators or inhibitors" default_target_function(0, 4)
 end
+
+@testitem "Load from BMA" begin
+    using JSON
+    bma_models_path = joinpath(@__DIR__, "resources", "bma_models")
+    good_models = joinpath(bma_models_path, "well_formed_examples")
+
+    for model_path in readdir(good_models; join = true)
+        qn = QN(model_path)
+        @test qn isa GraphDynamicalSystem
+    end
+
+    bad_models = joinpath(bma_models_path, "error_examples")
+
+    @test_throws "Neither alternative" QN(joinpath(bad_models, "bad_edge_key.json"))
+    @test_throws "Failed to add" QN(joinpath(bad_models, "duplicate_entity_ids.json"))
+    @test_throws "Error while constructing name for entity" QN(
+        joinpath(bad_models, "multiple_incoming_edges_same_name.json"),
+    )
+
+end

test/quick.jl

@@ -0,0 +1,18 @@
+#
+# `include("test/quick.jl")` for quick testing
+#
+# Assumes you have TestEnv and ReTestItems installed in your
+# global Julia environment.
+#
+using TestEnv
+using ReTestItems
+using GraphDynamicalSystems
+
+TestEnv.activate() do
+    runtests(
+        GraphDynamicalSystems,
+        name = r"^(?!Code).+$",
+        failfast = true,
+        failures_first = true,
+    )
+end

test/resources/bma_models/error_examples/bad_edge_key.json

@@ -0,0 +1,103 @@
+{
+    "Layout": {
+        "AnnotatedGridCells": [],
+        "Containers": [
+            {
+                "Id": 1,
+                "Name": "C0",
+                "PositionX": 2,
+                "PositionY": 0,
+                "Size": 1
+            }
+        ],
+        "Description": "",
+        "Variables": [
+            {
+                "Angle": 0,
+                "CellX": null,
+                "CellY": null,
+                "ContainerId": 1,
+                "Description": "",
+                "Id": 1,
+                "Name": "a",
+                "PositionX": 630.7,
+                "PositionY": 47.34285714285714,
+                "Type": "Default"
+            },
+            {
+                "Angle": 0,
+                "CellX": null,
+                "CellY": null,
+                "ContainerId": 1,
+                "Description": "",
+                "Id": 2,
+                "Name": "b",
+                "PositionX": 583.2,
+                "PositionY": 178.77142857142857,
+                "Type": "Default"
+            },
+            {
+                "Angle": 0,
+                "CellX": null,
+                "CellY": null,
+                "ContainerId": 1,
+                "Description": "",
+                "Id": 3,
+                "Name": "c",
+                "PositionX": 678.2,
+                "PositionY": 162.34285714285716,
+                "Type": "Default"
+            }
+        ]
+    },
+    "Model": {
+        "Name": "ToyModelStable",
+        "Relationships": [
+            {
+                "FromVariableError": 1,
+                "Id": 1,
+                "ToVariableError": 2,
+                "Type": "Activator"
+            },
+            {
+                "ErrorFromVariable": 2,
+                "ErrorToVariable": 3,
+                "Id": 2,
+                "Type": "Activator"
+            },
+            {
+                "FromErrorVariable": 3,
+                "Id": 3,
+                "ToErrorVariable": 1,
+                "Type": "Inhibitor"
+            }
+        ],
+        "Variables": [
+            {
+                "Formula": "",
+                "Id": 1,
+                "Name": "a",
+                "RangeFrom": 0,
+                "RangeTo": 4
+            },
+            {
+                "Formula": "",
+                "Id": 2,
+                "Name": "b",
+                "RangeFrom": 0,
+                "RangeTo": 4
+            },
+            {
+                "Formula": "",
+                "Id": 3,
+                "Name": "c",
+                "RangeFrom": 0,
+                "RangeTo": 4
+            }
+        ]
+    },
+    "ltl": {
+        "operations": [],
+        "states": []
+    }
+}