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test: add bad BMA input files
1 parent eb5ef56 commit 1e29ef0

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+333
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‎test/qn_test.jl‎

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@@ -145,9 +145,19 @@ end
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@testitem "Load from BMA" begin
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using JSON
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bma_models_path = joinpath(@__DIR__, "resources", "bma_models")
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good_models = joinpath(bma_models_path, "well_formed_examples")
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for model_path in readdir(bma_models_path; join = true)
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for model_path in readdir(good_models; join = true)
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qn = QN(model_path)
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@test qn isa GraphDynamicalSystem
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end
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bad_models = joinpath(bma_models_path, "error_examples")
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@test_throws "Neither alternative" QN(joinpath(bad_models, "bad_edge_key.json"))
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@test_throws "Failed to add" QN(joinpath(bad_models, "duplicate_entity_ids.json"))
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@test_throws "Error while constructing name for entity" QN(
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joinpath(bad_models, "multiple_incoming_edges_same_name.json"),
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)
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end

‎test/resources/bma_models/error_examples/bad_edge_key.json‎

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

‎test/resources/bma_models/error_examples/duplicate_entity_ids.json‎

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{
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}
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],
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"Description": "",
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"Variables": [
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{
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"Type": "Default"
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},
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{
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"Name": "b",
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"PositionX": 583.2,
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"PositionY": 178.77142857142857,
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"Type": "Default"
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},
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{
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"Angle": 0,
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"CellX": null,
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"CellY": null,
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"Description": "",
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"Id": 3,
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"Name": "c",
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"PositionX": 678.2,
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"PositionY": 162.34285714285716,
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"Type": "Default"
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}
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]
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},
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"Model": {
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"Name": "ToyModelStable",
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"Relationships": [
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{
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"FromVariable": 1,
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"Id": 1,
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"ToVariable": 2,
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"Type": "Activator"
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},
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{
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"FromVariable": 2,
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"Id": 2,
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"ToVariable": 3,
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"Type": "Activator"
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},
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{
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"FromVariable": 3,
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"Id": 3,
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"ToVariable": 1,
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"Type": "Inhibitor"
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}
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],
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"Variables": [
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{
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"Formula": "",
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"Id": 1,
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"Name": "a",
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"RangeFrom": 0,
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"RangeTo": 4
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},
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{
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"Formula": "",
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"Id": 1,
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"Name": "b",
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"RangeFrom": 0,
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"RangeTo": 4
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},
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{
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"Formula": "",
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"Id": 1,
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"Name": "c",
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"RangeFrom": 0,
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"RangeTo": 4
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}
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]
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},
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"ltl": {
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"operations": [],
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"states": []
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}
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}

‎test/resources/bma_models/error_examples/multiple_incoming_edges_same_name.json‎

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{
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"Layout": {
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"AnnotatedGridCells": [],
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"Containers": [
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{
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"Id": 1,
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"Name": "C0",
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"PositionX": 2,
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"PositionY": 0,
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"Size": 1
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}
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],
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"Description": "",
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"Variables": [
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{
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"Angle": 0,
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"CellY": null,
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"Type": "Default"
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},
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{
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"Angle": 0,
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"CellX": null,
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"Name": "b",
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},
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"Type": "Default"
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}
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]
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},
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"Model": {
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"Name": "ToyModelStable",
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"Relationships": [
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{
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"FromVariable": 1,
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"Id": 1,
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"ToVariable": 2,
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"Type": "Activator"
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},
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{
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"FromVariable": 2,
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"Id": 2,
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"ToVariable": 3,
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"Type": "Activator"
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},
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{
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"FromVariable": 3,
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"Type": "Inhibitor"
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},
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{
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"FromVariable": 4,
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"Id": 4,
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"ToVariable": 1,
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"Type": "Inhibitor"
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}
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],
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"Variables": [
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{
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"Formula": "min(var(c), var(c))",
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"Id": 1,
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"Name": "a",
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},
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{
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"Formula": "",
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},
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{
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"Formula": "",
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"RangeFrom": 0,
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{
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"Formula": "",
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"Id": 4,
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"Name": "c",
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"RangeFrom": 0,
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"RangeTo": 4
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}
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]
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},
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"ltl": {
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"operations": [],
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"states": []
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}
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}

test/resources/bma_models/RA_M1_macrophage_complex_corrected_phenotype_corrected_and_homogenized.json renamed to test/resources/bma_models/well_formed_examples/RA_M1_macrophage_complex_corrected_phenotype_corrected_and_homogenized.json

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test/resources/bma_models/RA_M2_macrophage_complex_corrected_phenotype_corrected_and_homogenized.json renamed to test/resources/bma_models/well_formed_examples/RA_M2_macrophage_complex_corrected_phenotype_corrected_and_homogenized.json

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test/resources/bma_models/RA_TH1_complex_corrected_phenotype_corrected_and_homogenized.json renamed to test/resources/bma_models/well_formed_examples/RA_TH1_complex_corrected_phenotype_corrected_and_homogenized.json

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test/resources/bma_models/RA_fibroblast_complex_corrected_phenotype_corrected_and_homogenized.json renamed to test/resources/bma_models/well_formed_examples/RA_fibroblast_complex_corrected_phenotype_corrected_and_homogenized.json

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test/resources/bma_models/RA_fixpoint.json renamed to test/resources/bma_models/well_formed_examples/RA_fixpoint.json

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test/resources/bma_models/Skin1D.json renamed to test/resources/bma_models/well_formed_examples/Skin1D.json

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