diff --git a/Project.toml b/Project.toml index d39c72a..4990f11 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "GraphDynamicalSystems" uuid = "13529e2e-ed53-56b1-bd6f-420b01fca819" authors = ["Reuben Gardos Reid <5456207+ReubenJ@users.noreply.github.com>"] -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" diff --git a/docs/src/91-developer.md b/docs/src/91-developer.md index 41f0cb9..57e0331 100644 --- a/docs/src/91-developer.md +++ b/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. diff --git a/ext/JSONExt.jl b/ext/JSONExt.jl new file mode 100644 index 0000000..96ff154 --- /dev/null +++ b/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 diff --git a/test/Project.toml b/test/Project.toml index fe534bd..55eba4e 100644 --- a/test/Project.toml +++ b/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" diff --git a/test/qn_test.jl b/test/qn_test.jl index 3819732..5a0f74b 100644 --- a/test/qn_test.jl +++ b/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 diff --git a/test/quick.jl b/test/quick.jl new file mode 100644 index 0000000..b99bb1b --- /dev/null +++ b/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 diff --git a/test/resources/bma_models/error_examples/bad_edge_key.json b/test/resources/bma_models/error_examples/bad_edge_key.json new file mode 100644 index 0000000..a812edc --- /dev/null +++ b/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": [] + } +} diff --git a/test/resources/bma_models/error_examples/duplicate_entity_ids.json b/test/resources/bma_models/error_examples/duplicate_entity_ids.json new file mode 100644 index 0000000..20ad390 --- /dev/null +++ b/test/resources/bma_models/error_examples/duplicate_entity_ids.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": [ + { + "FromVariable": 1, + "Id": 1, + "ToVariable": 2, + "Type": "Activator" + }, + { + "FromVariable": 2, + "Id": 2, + "ToVariable": 3, + "Type": "Activator" + }, + { + "FromVariable": 3, + "Id": 3, + "ToVariable": 1, + "Type": "Inhibitor" + } + ], + "Variables": [ + { + "Formula": "", + "Id": 1, + "Name": "a", + "RangeFrom": 0, + "RangeTo": 4 + }, + { + "Formula": "", + "Id": 1, + "Name": "b", + "RangeFrom": 0, + "RangeTo": 4 + }, + { + "Formula": "", + "Id": 1, + "Name": "c", + "RangeFrom": 0, + "RangeTo": 4 + } + ] + }, + "ltl": { + "operations": [], + "states": [] + } +} diff --git a/test/resources/bma_models/error_examples/multiple_incoming_edges_same_name.json b/test/resources/bma_models/error_examples/multiple_incoming_edges_same_name.json new file mode 100644 index 0000000..f162244 --- /dev/null +++ b/test/resources/bma_models/error_examples/multiple_incoming_edges_same_name.json @@ -0,0 +1,116 @@ +{ + "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": [ + { + "FromVariable": 1, + "Id": 1, + "ToVariable": 2, + "Type": "Activator" + }, + { + "FromVariable": 2, + "Id": 2, + "ToVariable": 3, + "Type": "Activator" + }, + { + "FromVariable": 3, + "Id": 3, + "ToVariable": 1, + "Type": "Inhibitor" + }, + { + "FromVariable": 4, + "Id": 4, + "ToVariable": 1, + "Type": "Inhibitor" + } + ], + "Variables": [ + { + "Formula": "min(var(c), var(c))", + "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 + }, + { + "Formula": "", + "Id": 4, + "Name": "c", + "RangeFrom": 0, + "RangeTo": 4 + } + ] + }, + "ltl": { + "operations": [], + "states": [] + } +} diff --git a/test/resources/bma_models/well_formed_examples/RA_M1_macrophage_complex_corrected_phenotype_corrected_and_homogenized.json b/test/resources/bma_models/well_formed_examples/RA_M1_macrophage_complex_corrected_phenotype_corrected_and_homogenized.json new file mode 100644 index 0000000..937680c --- /dev/null +++ b/test/resources/bma_models/well_formed_examples/RA_M1_macrophage_complex_corrected_phenotype_corrected_and_homogenized.json @@ -0,0 +1,9928 @@ +{ + "Layout": { + "Containers": [], + "Description": "", + "Variables": [ + { + "Angle": 0, + "CellX": 0, + "CellY": 0, + "ContainerId": 0, + "Description": "M1 macrophage: Cytoplasmic membrane up", + "Fill": 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}, + { + "Formula": "(max((min(1,1)),0))", + "Id": 25, + "Name": "IL11Ra_IL6ST_IL11_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min((min(var(180),(min(var(178),1)))),1)),0))", + "Id": 26, + "Name": "VegfR1_vegfa_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min(1,1)),0))", + "Id": 27, + "Name": "LIFR_IL6ST_CTF1_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min((min(var(216),(min(var(219),1)))),1)),0))", + "Id": 28, + "Name": "IKK1_IKK2_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min((min(var(108),1)),1)),0))", + "Id": 29, + "Name": "VegfR2_vegfc_nrp2_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min((min(var(108),1)),1)),0))", + "Id": 30, + "Name": "vegfc_vegfr3_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "1", + "Id": 31, + "Name": "GSK3b_APC_AXIN1_CTNNB1_CK1A_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": 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{ + "Formula": "(max((min((min(var(31),1)),(min((max(var(184),0)),1)))),0))", + "Id": 38, + "Name": "GSK3b_APC_AXIN1_CK1A_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "1", + "Id": 39, + "Name": "EFNB1_EPHB1_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min(1,1)),0))", + "Id": 40, + "Name": "ARI_ARII_bmp6_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "1", + "Id": 41, + "Name": "RELA_NFKB1_NFKBIE_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min((min(var(230),1)),1)),0))", + "Id": 42, + "Name": "GAS6_MERTK_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "(max((min((min(var(118),(min(var(12),1)))),1)),0))", + "Id": 43, + "Name": "immune_complex_complex_M2_macrophage__cytoplasmic_membrane_up", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": "1", + "Id": 44, + "Name": "IL10R1_IL10R2_complex", + "RangeFrom": 0, + "RangeTo": 1 + }, + { + "Formula": 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