Merge pull request #24 from SciML/aj/wip

cleanup tests add script to clone the physiome

Project.toml

@@ -1,7 +1,7 @@
 name = "CellMLToolkit"
 uuid = "03cb29e0-1ef4-4721-aa24-cf58a006576f"
 authors = ["Shahriar Iravanian <siravan@svtsim.com>"]
-version = "2.1.1"
+version = "2.1.0"
 
 [deps]
 EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
@@ -12,16 +12,17 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
 EzXML = "1.1"
+JSON3 = "1.8"
 MathML = "0.1"
 ModelingToolkit = "5.13"
 SymbolicUtils = "0.9"
 julia = "1.5"
 
 [extras]
-Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "ModelingToolkit", "DifferentialEquations", "Plots"]
+test = ["Test", "ModelingToolkit", "OrdinaryDiffEq", "JSON3"]

src/CellMLToolkit.jl

@@ -6,6 +6,9 @@ using SymbolicUtils: FnType, Sym, operation, arguments
 using ModelingToolkit
 using EzXML
 
+include("utils.jl")
+export curl_exposures
+
 include("cellml.jl")
 
 """
@@ -97,7 +100,7 @@ end
     val is the new value
 """
 function update_list!(l, sym::Symbol, val)
-    for (i,x) in enumerate(l)
+    for (i, x) in enumerate(l)
         if first(x).name == sym
             l[i] = (first(x) => val)
             return

src/utils.jl

@@ -0,0 +1,23 @@
+"""queries the cellml repo api for links to cellml model repo"""
+function curl_exposures()
+    run(`curl -sL -H 'Accept: application/vnd.physiome.pmr2.json.1' 
+        https://models.physiomeproject.org/search -d '{
+        "template": {"data": [
+            {"name": "Subject", "value": "CellML Model"},
+            {"name": "portal_type", "value": "ExposureFile"}
+        ]}
+    }' -o cellml.json`)
+end
+
+"""
+downloads the cellml model repository
+todo use Base.Downloads to speed this up
+"""
+function grab(ls)
+    !ispath("data") && mkpath("data")
+    @sync Threads.@threads for l in ls 
+        fn = splitdir(l)[end]
+        download(l, "data/$(fn)")
+    end
+    nothing
+end

test/beeler.jl

@@ -0,0 +1,32 @@
+path = @__DIR__
+ml = CellModel(path * "/../models/beeler_reuter_1977.cellml.xml")
+
+# @test length(ml.eqs) == 8
+# @test ml.iv.op.name == :time
+
+# eqs, vs = CellMLToolkit.flat_equations(ml)
+# @test length(vs) == 8
+
+# @test find_V(ml).op.name == :V
+
+prob = ODEProblem(ml, (0,10000.0))
+sol1 = solve(prob, Euler(), dt=0.01, saveat=1.0)
+sol2 = solve(prob, TRBDF2(), dtmax=0.5, saveat=1.0)
+V1 = map(x -> x[1], sol1.u)
+V2 = map(x -> x[1], sol2.u)
+err = sum(abs.(V1 .- V2)) / length(V1)
+@test err < 0.1
+
+# prob = ODEProblem(ml, (0,10000.0); jac=true)
+# sol3 = solve(prob, TRBDF2(), dtmax=0.5, saveat=1.0)
+# V3 = map(x -> x[1], sol2.u)
+# err = sum(abs.(V1 .- V3)) / length(V1)
+# @test err < 0.1
+
+p = list_params(ml)
+update_list!(p, "IstimPeriod", 280.0)
+prob = ODEProblem(ml, (0,10000.0); jac=false, p=p)
+sol4 = solve(prob, TRBDF2(), dtmax=0.5, saveat=1.0)
+V4 = map(x -> x[1], sol2.u)
+err = sum(abs.(V1[1:250] .- V4[1:250])) / 250
+@test err < 0.1

test/runtests.jl

@@ -1,36 +1,12 @@
 using Test
 using CellMLToolkit
-using DifferentialEquations
+using OrdinaryDiffEq
+using JSON3, Base.Threads
+using ModelingToolkit
 
-path = @__DIR__
-ml = CellModel(path * "/../models/beeler_reuter_1977.cellml.xml")
+@testset "CellMLToolkit.jl" begin
+    @testset "beeler.jl" begin include("beeler.jl") end
 
-# @test length(ml.eqs) == 8
-# @test ml.iv.op.name == :time
-
-# eqs, vs = CellMLToolkit.flat_equations(ml)
-# @test length(vs) == 8
-
-# @test find_V(ml).op.name == :V
-
-prob = ODEProblem(ml, (0,10000.0))
-sol1 = solve(prob, Euler(), dt=0.01, saveat=1.0)
-sol2 = solve(prob, TRBDF2(), dtmax=0.5, saveat=1.0)
-V1 = map(x -> x[1], sol1.u)
-V2 = map(x -> x[1], sol2.u)
-err = sum(abs.(V1 .- V2)) / length(V1)
-@test err < 0.1
-
-# prob = ODEProblem(ml, (0,10000.0); jac=true)
-# sol3 = solve(prob, TRBDF2(), dtmax=0.5, saveat=1.0)
-# V3 = map(x -> x[1], sol2.u)
-# err = sum(abs.(V1 .- V3)) / length(V1)
-# @test err < 0.1
-
-p = list_params(ml)
-update_list!(p, "IstimPeriod", 280.0)
-prob = ODEProblem(ml, (0,10000.0); jac=false, p=p)
-sol4 = solve(prob, TRBDF2(), dtmax=0.5, saveat=1.0)
-V4 = map(x -> x[1], sol2.u)
-err = sum(abs.(V1[1:250] .- V4[1:250])) / 250
-@test err < 0.1
+    # mainly a used as a bin/ don't want to test every PR
+    # @testset "physiome.jl" begin include("test_physiome.jl") end
+end

test/test_physiome.jl

@@ -0,0 +1,63 @@
+"
+in place modifies a matrix with data about how far to `solve`
+we get for a given set of cellml files
+uses @threads
+"
+function test_cellmls!(mat, fns)
+    @sync Threads.@threads for i in eachindex(fns)
+        @show i fns[i]
+        mat[i, :] = test_cellml!(mat[i, :], fns[i])
+    end
+    mat
+end
+
+"
+in place modifies a row with data about how far to `solve`
+we get for a given cellml file
+"
+function test_cellml!(row, fn)
+    row[1] = fn
+    try
+        ml = CellModel(fn)
+        sys = ml.sys
+        row[2] = true
+        row[5] = length(states(sys))
+        row[6] = length(parameters(sys))
+        prob = ODEProblem(ml, tspan)
+        row[3] = true
+        sol = solve(prob)
+        row[4] = true
+    catch e 
+        row[end] = e
+    end
+    row
+end
+
+"""
+a
+"""
+function main(dir="data/")
+    tspan = (0., 1.)
+    fns = readdir(dir; join=true)
+    names = [:filename, :to_system, :to_problem, :to_solve, :states, :parameters, :error]
+    n = length(names)
+    mat = Array{Any,2}(nothing, length(fns), n)
+    test_cellmls!(mat, fns)
+    replace!(mat, nothing => missing)
+    names .=> eachcol(mat) # used with DataFrame()
+    # CSV.write("aggregate_stats.csv", df)
+    # print(df)
+end
+
+function json_to_cellml_links()
+    s = read("cellml.json", String);
+    j = JSON3.read(s);
+    x = j.collection.links
+    map(x -> x.href[1:end - 5], x) # remove `/view` from urls 
+end
+
+ls = json_to_cellml_links(curl_exposures())
+@test length(ls) == 2379
+CellMLToolkit.grab(ls[1:10])
+df = main()
+@test eltype(df) == Pair