diff --git a/Project.toml b/Project.toml index 6e55b3f..d207a25 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "SimulationService" uuid = "e66378d9-a322-4933-8764-0ce0bcab4993" authors = ["Five Grant <5@fivegrant.com>"] -version = "0.13.0" +version = "0.14.0" [deps] AMQPClient = "79c8b4cd-a41a-55fa-907c-fab5288e1383" diff --git a/examples/BIOMD0000000955_askenet.json b/examples/calibrate_example1/BIOMD0000000955_askenet.json similarity index 100% rename from examples/BIOMD0000000955_askenet.json rename to examples/calibrate_example1/BIOMD0000000955_askenet.json diff --git a/examples/dataset.csv b/examples/calibrate_example1/dataset.csv similarity index 100% rename from examples/dataset.csv rename to examples/calibrate_example1/dataset.csv diff --git a/examples/request-calibrate-no-integration.json b/examples/calibrate_example1/request-calibrate-no-integration.json similarity index 100% rename from examples/request-calibrate-no-integration.json rename to examples/calibrate_example1/request-calibrate-no-integration.json diff --git a/examples/calibrate_example2/SIRModelConfiguartion.json b/examples/calibrate_example2/SIRModelConfiguartion.json new file mode 100644 index 0000000..f37f678 --- /dev/null +++ b/examples/calibrate_example2/SIRModelConfiguartion.json @@ -0,0 +1,642 @@ +{ + "id": "55ca595f-940d-458c-9c73-7c315a10b559", + "name": "Default config", + "description": "Default config", + "timestamp": "2023-07-13T20:18:12", + "model_id": "0984a5a9-6438-4041-aa11-2f9ea8fc9d4a", + "configuration": { + "id": "0984a5a9-6438-4041-aa11-2f9ea8fc9d4a", + "name": "SIRs", + "description": "SIR model", + "model_version": "0.1", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/petrinet_v0.5/petrinet/petrinet_schema.json", + "schema_name": "petrinet", + "model": { + "states": [ + { + "id": "S", + "name": "Susceptible", + "description": "Number of individuals that are 'susceptible' to a disease infection", + 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a/examples/calibrate_example2/request-calibrate2.json b/examples/calibrate_example2/request-calibrate2.json new file mode 100644 index 0000000..960d120 --- /dev/null +++ b/examples/calibrate_example2/request-calibrate2.json @@ -0,0 +1,15 @@ +{ + "modelConfigId": "55ca595f-940d-458c-9c73-7c315a10b559", + "dataset": { + "id": "a3365ea8-a199-49e1-b634-a1b3f8635731", + "filename": "sirFixed.csv", + "mappings": { + "t": "timestep", + "s": "S", + "i": "I", + "r": "R" + } + }, + "extra": {}, + "engine": "sciml" +} \ No newline at end of file diff --git a/examples/calibrate_example2/sirFixed.csv b/examples/calibrate_example2/sirFixed.csv new file mode 100644 index 0000000..71926ba --- /dev/null +++ b/examples/calibrate_example2/sirFixed.csv @@ -0,0 +1,201 @@ +t,s,i,r +0.0,0.99995,5E-05,0.0 +0.9045226130653270,0.9999360401998250,5.81428837853521E-05,5.81691638943948E-06 +1.8090452261306500,0.9999198054491840,6.76126650732997E-05,1.25818857422612E-05 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-70,10 +70,10 @@ end # data function amr_get(df::DataFrame, sys::ODESystem, ::Val{:data}) - + @info "parse dataset into calibrate format" statelist = states(sys) statenames = string.(statelist) - statenames = map(statenames) do n; n[1:end-3]; end # there's a better way to do this + statenames = [replace(nm, "(t)" => "") for nm in statenames] tvals = df[:,"timestamp"] map(statelist, statenames) do s,n @@ -128,8 +128,8 @@ end function solve(op::Simulate; kw...) # joshday: What does providing `u0 = []` do? Don't we know what u0 is from AMR? - prob = ODEProblem(op.sys, [], op.timespan, saveat=1) - sol = solve(prob; progress = true, progress_steps = 1, kw...) + prob = ODEProblem(op.sys, [], op.timespan) + sol = solve(prob; progress = true, progress_steps = 1, saveat=1, kw...) @info "Timesteps returned are: $(sol.t)" dataframe_with_observables(sol) end @@ -198,11 +198,11 @@ function solve(o::Calibrate; callback) fit = EasyModelAnalysis.datafit(prob, init_params, o.data) else init_params = Pair.(EasyModelAnalysis.ModelingToolkit.Num.(first.(o.priors)), tuple.(minimum.(last.(o.priors)), maximum.(last.(o.priors)))) - fit = global_datafit(prob, init_params, o.data) + fit = EasyModelAnalysis.global_datafit(prob, init_params, o.data) end - newprob = remake(prob, p=fit) - sol = solve(newprob) + newprob = EasyModelAnalysis.DifferentialEquations.remake(prob, p=fit) + sol = EasyModelAnalysis.DifferentialEquations.solve(newprob; saveat = 1) dfsim = DataFrame(hcat(sol.t,stack(sol[statenames])'), :auto) rename!(dfsim, ["timestamp";string.(statenames)]) diff --git a/test/runtests.jl b/test/runtests.jl index 75f8d28..280f964 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -21,15 +21,15 @@ here(x...) = joinpath(dirname(pathof(SimulationService)), "..", x...) #-----------------------------------------------------------------------# JSON payloads for testing # route => payload simulate_payloads = JSON3.write.([ - (local_model_file=here("examples", "BIOMD0000000955_askenet.json"), timespan = (; start=0, var"end"=100)), + (local_model_file=here("examples", "calibrate_example1", "BIOMD0000000955_askenet.json"), timespan = (; start=0, var"end"=100)), ]) calibrate_payloads = JSON3.write.([ let - (; engine, timespan, extra) = JSON3.read(read(here("examples", "request-calibrate-no-integration.json"))) + (; engine, timespan, extra) = JSON3.read(read(here("examples", "calibrate_example1", "request-calibrate-no-integration.json"))) (; - local_csv_file = here("examples", "dataset.csv"), - local_model_file = here("examples", "BIOMD0000000955_askenet.json"), + local_csv_file = here("examples", "calibrate_example1", "dataset.csv"), + local_model_file = here("examples", "calibrate_example1", "BIOMD0000000955_askenet.json"), engine, timespan, extra ) @@ -46,7 +46,7 @@ end #-----------------------------------------------------------------------------# AMR parsing @testset "AMR parsing" begin - file = here("examples", "BIOMD0000000955_askenet.json") + file = here("examples", "calibrate_example1", "BIOMD0000000955_askenet.json") amr = JSON3.read(read(file)) sys = SimulationService.amr_get(amr, ODESystem) @test string.(states(sys)) == ["Susceptible(t)", "Diagnosed(t)", "Infected(t)", "Ailing(t)", "Recognized(t)", "Healed(t)", "Threatened(t)", "Extinct(t)"] @@ -58,7 +58,7 @@ end @test string.(first.(priors)) == string.(parameters(sys)) @test last.(priors) isa Vector{Uniform{Float64}} - df = CSV.read(here("examples", "dataset.csv"), DataFrame) + df = CSV.read(here("examples", "calibrate_example1", "dataset.csv"), DataFrame) data = SimulationService.amr_get(df, sys, Val(:data)) @test data isa Vector{Pair{SymbolicUtils.BasicSymbolic{Real}, Tuple{Vector{Int64}, Vector{Float64}}}} @test string.(first.(data)) == string.(states(sys)) @@ -129,11 +129,11 @@ end @test extrema(df.timestamp) == (0.0, 99.0) end @testset "calibrate" begin - file = here("examples", "BIOMD0000000955_askenet.json") + file = here("examples", "calibrate_example1", "BIOMD0000000955_askenet.json") amr = JSON3.read(read(file)) sys = SimulationService.amr_get(amr, ODESystem) priors = SimulationService.amr_get(amr, sys, Val(:priors)) - df = CSV.read(here("examples", "dataset.csv"), DataFrame) + df = CSV.read(here("examples", "calibrate_example1", "dataset.csv"), DataFrame) data = SimulationService.amr_get(df, sys, Val(:data)) num_chains = 4 num_iterations = 100 @@ -146,6 +146,18 @@ end statenames = [states(o.sys);getproperty.(observed(o.sys), :lhs)] @test names(dfsim) == vcat("timestamp",reduce(vcat,[string.("ensemble",i,"_", statenames) for i in 1:size(dfsim,2)÷length(statenames)])) @test names(dfparam) == string.(parameters(sys)) + + #calibrate_method = "local" + #o = SimulationService.Calibrate(sys, (0.0, 89.0), priors, data, num_chains, num_iterations, calibrate_method, ode_method) + #dfsim, dfparam = SimulationService.solve(o; callback = nothing) + + calibrate_method = "global" + o = SimulationService.Calibrate(sys, (0.0, 89.0), priors, data, num_chains, num_iterations, calibrate_method, ode_method) + dfsim, dfparam = SimulationService.solve(o; callback = nothing) + + statenames = [states(o.sys);getproperty.(observed(o.sys), :lhs)] + @test names(dfsim) == vcat("timestamp",string.(statenames)) + @test names(dfparam) == string.(parameters(sys)) end end diff --git a/test/tds.jl b/test/tds.jl index 1628b28..cccba2b 100644 --- a/test/tds.jl +++ b/test/tds.jl @@ -35,7 +35,8 @@ datasets = get_json("$(TDS_URL[])/datasets") data_obj = JSON3.read(JSON3.write((; id = datasets[1].id, name = datasets[1].name, - filename = datasets[1].file_names[1] + filename = datasets[1].file_names[1], + mappings = (; Ailing = "A") ))) get_dataset(data_obj)