Merge pull request #47 from sebapersson/Refactor_tests

Refactor tests

README.md

@@ -83,9 +83,8 @@ The key differences between SBMLToolkit and SBMLImporter are:
 
 ## Supported SBML Features
 
-SBMLImporter supports many SBML features for SBML models (level 2 or higher). Currently, excluding FBA models, it successfully passes 1257 out of 1785 test cases. The failed test cases cover features currently not supported. If SBMLImporter lacks support for a feature you would like, please file an issue on GitHub. Currently unsupported features are:
+SBMLImporter supports many SBML features for SBML models (level 2 or higher). Currently, excluding FBA models, it successfully passes 1265 out of 1785 test cases. The failed test cases cover features currently not supported. If SBMLImporter lacks support for a feature you would like, please file an issue on GitHub. Currently unsupported features are:
 
-* Models with empty SBML reactions.
 * Delay (creating a delay-differential-equations).
 * Events with delay.
 * Events with priority.

docs/src/Support.md

@@ -1,6 +1,6 @@
 # [Supported SBML Features](@id support)
 
-SBMLImporter supports many SBML features for models of level 2 or higher. Currently, excluding FBA models it successfully passes 1257 out of 1785 test cases. The failed test cases cover features currently not supported. Key features supported include:
+SBMLImporter supports many SBML features for models of level 2 or higher. Currently, excluding FBA models it successfully passes 1265 out of 1785 test cases. The failed test cases cover features currently not supported. Key features supported include:
 
 - Events.
 - Rate rules.
@@ -17,7 +17,6 @@ Species can be specified in either concentrations or amounts. The unit is determ
 
 Currently SBMLImporter does not support the following features:
 
-* Models with empty SBML reactions.
 * Delay (creating a delay-differential-equations).
 * Events with delay.
 * Events with priority.

src/Build_model.jl

@@ -13,6 +13,9 @@ function build_SBML_model(path_SBML::String; ifelse_to_callback::Bool = true,
                           model_as_string = true, inline_assignment_rules::Bool = true,
                           mass_action::Bool = false)::ModelSBML
     if model_as_string == false
+        if !isfile(path_SBML)
+            throw(SBMLSupport("$path_SBML is not the path to a SBML file"))
+        end
         f = open(path_SBML, "r")
         model_str = read(f, String)
         close(f)

test/Large_model.jl

@@ -14,7 +14,7 @@ sbml_string = String(take!(Downloads.download(sbml_url, IOBuffer())))
 b1 = @elapsed parsed_rn, cb = load_SBML(sbml_string; model_as_string = true)
 
 # Usually takes around 4s locally, but better to brace for GitHub CI
-@test b1 ≤ 20
+@test b1 ≤ 40
 
 # Large fceri-γ model with ≈ 58,000 reactions. Should take around 4min locally, but it
 # is always good to brace for GitHub CI
@@ -24,17 +24,18 @@ b2 = @elapsed parsed_rn, cb = load_SBML(path_SBML)
 
 # Test that SBMLImporter correctly enforces mass action
 path_SBML = joinpath(@__DIR__, "Models", "egfr_net.xml")
-b3 = @elapsed model, cb = load_SBML(path_SBML; mass_action=true)
-dprob = DiscreteProblem(model.rn, model.u₀, (0.0,0.0), model.p)
+b3 = @elapsed model, cb = load_SBML(path_SBML; mass_action = true)
+dprob = DiscreteProblem(model.rn, model.u₀, (0.0, 0.0), model.p)
 dprob = remake(dprob, u0 = Int64.(dprob.u0));
-jprob = JumpProblem(model.rn, dprob, RSSA(), save_positions=(false,false))
+jprob = JumpProblem(model.rn, dprob, RSSA(), save_positions = (false, false))
 @test b3 ≤ 20
 @test length(jprob.massaction_jump.net_stoch) == 3749
 
 # Lots of edge cases
 sbml_url = "https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000627.3?filename=BIOMD0000000627_url.xml"
 sbml_string = String(take!(Downloads.download(sbml_url, IOBuffer())))
-mdl, cb = load_SBML(sbml_string; inline_assignment_rules=true, ifelse_to_callback=true, check_massaction=false,
-                    model_as_string=true)
+mdl, cb = load_SBML(sbml_string; inline_assignment_rules = true, ifelse_to_callback = true,
+                    check_massaction = false,
+                    model_as_string = true)
 sys = structural_simplify(convert(ODESystem, mdl.rn))
 @test length(states(sys)) == 66

test/Stochastic_tests.jl

@@ -9,33 +9,7 @@ using Downloads
 using Catalyst
 using JumpProcesses
 
-function get_sbml_urls(base_url::String)
-    levels = ["2", "3"]
-    sublevels = ["1", "2", "3", "4", "5"]
-    sbml_urls = Vector{String}(undef, 0)
-
-    for level in levels
-        for sublevel in sublevels
-            sbml_url = base_url * "-sbml-l" * level * "v" * sublevel * ".xml"
-            try
-                sbml = String(take!(Downloads.download(sbml_url, IOBuffer())))
-                push!(sbml_urls, sbml_url)
-            catch
-            end
-        end
-    end
-    return sbml_urls
-end
-
-function get_model_str(test_case)
-    base_url = "https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/master/cases/stochastic/$test_case/$test_case"
-    sbml_urls = get_sbml_urls(base_url)
-    sbml_url = sbml_urls[end]
-    sbml_string = String(take!(Downloads.download(sbml_url, IOBuffer())))
-    model_SBML = SBMLImporter.build_SBML_model(sbml_string, model_as_string = true)
-    reaction_system = SBMLImporter.reactionsystem_from_SBML(model_SBML, "", false)
-    return reaction_system, model_SBML
-end
+include(joinpath(@__DIR__, "common.jl"))
 
 function read_settings(settings_url::String)
     settings = String(take!(Downloads.download(settings_url, IOBuffer())))
@@ -132,16 +106,16 @@ end
 @testset "Stochastic tests" begin
     for i in 1:39
 
-        # 19 has assignment rule 
-        # 33 has continious callback
+        # 19 has assignment rule
+        # 33 has continous callback
         if i ∈ [19, 33]
             continue
         end
 
         @info "Test case $i"
         test_case = repeat("0", 5 - length(string(i))) * string(i)
 
-        # i = 5 nast test case were many simulations must be run to get a 
+        # i = 5 nast test case were many simulations must be run to get a
         # good mean estimate (as amounts are large)
         if i == 5
             test_stochastic_testcase(test_case; nsolve = 70000)

test/Write_model.jl

@@ -6,18 +6,18 @@ isfile(path_model) && rm(path_model)
 isfile(path_cb) && rm(path_cb)
 
 path_SBML = joinpath(@__DIR__, "Models", "model_Boehm_JProteomeRes2014.xml")
-parsed_rn, cb = load_SBML(path_SBML; write_to_file=true)
+parsed_rn, cb = load_SBML(path_SBML; write_to_file = true)
 sys_ref = structural_simplify(convert(ODESystem, parsed_rn.rn))
 oprob_ref = ODEProblem(sys_ref, parsed_rn.u₀, (0.0, 5.0), parsed_rn.p, jac = true)
-sol_ref = solve(oprob_ref, Rodas4P(), saveat=1:5)
+sol_ref = solve(oprob_ref, Rodas4P(), saveat = 1:5)
 
 include(path_model)
 include(path_cb)
 
 rn, u0map, pmap = get_reaction_system([])
 sys_check = structural_simplify(convert(ODESystem, rn))
 oprob_check = ODEProblem(sys_ref, u0map, (0.0, 5.0), pmap, jac = true)
-sol_check = solve(oprob_check, Rodas4P(), saveat=1:5)
+sol_check = solve(oprob_check, Rodas4P(), saveat = 1:5)
 
 @test oprob_check.u0 == oprob_ref.u0
 @test oprob_check.p == oprob_ref.p

test/common.jl

@@ -0,0 +1,32 @@
+function get_sbml_urls(base_url::String)
+    levels = ["2", "3"]
+    sublevels = ["1", "2", "3", "4", "5"]
+    sbml_urls = Vector{String}(undef, 0)
+    for level in levels
+        for sublevel in sublevels
+            sbml_url = base_url * "-sbml-l" * level * "v" * sublevel * ".xml"
+            try
+                sbml = String(take!(Downloads.download(sbml_url, IOBuffer())))
+                push!(sbml_urls, sbml_url)
+            catch
+            end
+        end
+    end
+    return sbml_urls
+end
+
+# Function to get model-str
+function get_model_str(test_case)
+    base_url = "https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/master/cases/semantic/$test_case/$test_case"
+    sbml_urls = get_sbml_urls(base_url)
+    sbml_url = sbml_urls[end]
+    sbml_string = String(take!(Downloads.download(sbml_url, IOBuffer())))
+    model_SBML = SBMLImporter.build_SBML_model(sbml_string, model_as_string = true,
+                                               inline_assignment_rules = false)
+
+    parsed_model_SBML = SBMLImporter._reactionsystem_from_SBML(model_SBML)
+    model_str = SBMLImporter.reactionsystem_to_string(parsed_model_SBML, false, "",
+                                                      model_SBML)
+
+    return model_str, model_SBML
+end

test/curated_jump_test.jl

@@ -50,7 +50,7 @@ sol_catalyst = solve(jprob_catalyst, SSAStepper(); seed = 1234)
 # Catalyst mass-action format
 path_SBML = joinpath(@__DIR__, "Models", "brusselator.xml")
 parsed_rn1, cb1 = load_SBML(path_SBML)
-parsed_rn2, cb2 = load_SBML(path_SBML; check_massaction=false)
+parsed_rn2, cb2 = load_SBML(path_SBML; check_massaction = false)
 @test reactions(parsed_rn1.rn)[1].only_use_rate == false
 @test reactions(parsed_rn2.rn)[1].only_use_rate == true
 oprob1 = ODEProblem(parsed_rn1.rn, parsed_rn1.u0, (0.0, 10.0), parsed_rn1.p)