Merge pull request #48 from LCSB-BioCore/mk-clean-downloads

clean-up downloading of files for testing

.gitignore

 .DS_Store
 test/data/*.xml
+test/data/*.mat
+test/data/*.json
 
 # ignore VScode clutter
 /.vscode

test/analysis/fba.jl

@@ -43,9 +43,10 @@ end
 
 @testset "Flux balance analysis with CobraModel" begin
     model = read_model(
-        Downloads.download(
+        download_data_file(
             "http://bigg.ucsd.edu/static/models/e_coli_core.json",
             joinpath("data", "e_coli_core.json"),
+            "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
         ),
     )
     @test length(model.reactions) == 95 # read in correctly

test/analysis/fva.jl

@@ -62,9 +62,10 @@ end
 
 @testset "Flux variability analysis with CobraModel" begin
     model = read_model(
-        Downloads.download(
+        download_data_file(
             "http://bigg.ucsd.edu/static/models/e_coli_core.json",
             joinpath("data", "e_coli_core.json"),
+            "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
         ),
     )
     @test length(model.reactions) == 95 # read in correctly

test/analysis/pfba.jl

 @testset "Parsimonious flux balance analysis with CobraModel" begin
+
     model = read_model(
-        Downloads.download(
+        download_data_file(
             "http://bigg.ucsd.edu/static/models/e_coli_core.json",
             joinpath("data", "e_coli_core.json"),
+            "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
         ),
     )
-    @test length(model.reactions) == 95 # read in correctly
 
     biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
     cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
 
     # pFBA
-    optimizer = OSQP.Optimizer
     atts = Dict(
         "eps_abs" => 5e-4,
         "eps_rel" => 5e-4,
@@ -20,7 +20,7 @@
     )
     solworks = pfba(
         model,
-        optimizer;
+        OSQP.Optimizer;
         objective_func = biomass,
         solver_attributes = atts,
         constraints = cons,
@@ -34,5 +34,4 @@
 
     @test !isempty(solworks)
     @test isapprox(sol["PGM"], -14.737442319041387, atol = 1e-3)
-
 end

test/io/io_test.jl

 @testset "IO" begin
 
     # E. coli models - realistic size models
-    iJO1366_xml = Downloads.download(
+    iJO1366_xml = download_data_file(
         "http://bigg.ucsd.edu/static/models/iJO1366.xml",
         joinpath("data", "iJO1366.xml"),
+        "d6d9ec61ef6f155db5bb2f49549119dc13b96f6098b403ef82ea4240b27232eb",
     )
     sbmlmodel_ecoli = read_model(iJO1366_xml)
     @test_broken length(sbmlmodel_ecoli.reactions) == 2583
 
-    iJO1366_mat = Downloads.download(
+    iJO1366_mat = download_data_file(
         "http://bigg.ucsd.edu/static/models/iJO1366.mat",
         joinpath("data", "iJO1366.mat"),
+        "b5cfe21b6369a00e45d600b783f89521f5cc953e25ee52c5f1d0a3f83743be30",
     )
     matlabmodel_ecoli = read_model(iJO1366_mat)
     @test length(matlabmodel_ecoli.reactions) == 2583
 
-    iJO1366_json = Downloads.download(
+    iJO1366_json = download_data_file(
         "http://bigg.ucsd.edu/static/models/iJO1366.json",
         joinpath("data", "iJO1366.json"),
+        "9376a93f62ad430719f23e612154dd94c67e0d7c9545ed9d17a4d0c347672313",
     )
     jsonmodel_ecoli = read_model(iJO1366_json)
     @test length(jsonmodel_ecoli.reactions) == 2583

test/io/sbml.jl

 
 sbmlfile = joinpath("data", "ecoli_core.xml")
-if !isfile(sbmlfile)
-    Downloads.download(
-        "http://systemsbiology.ucsd.edu/sites/systemsbiology.ucsd.edu/files/Attachments/Images/downloads/Ecoli_core/ecoli_core_model.xml",
-        sbmlfile,
-    )
-end
-
-cksum = bytes2hex(sha256(open(sbmlfile)))
-if cksum != "78692f8509fb36534f4f9b6ade23b23552044f3ecd8b48d84d484636922ae907"
-    @warn "The downloaded E Coli core model seems to be different from the expected one. Tests may fail." cksum
-end
+download_data_file(
+    "http://systemsbiology.ucsd.edu/sites/systemsbiology.ucsd.edu/files/Attachments/Images/downloads/Ecoli_core/ecoli_core_model.xml",
+    sbmlfile,
+    "78692f8509fb36534f4f9b6ade23b23552044f3ecd8b48d84d484636922ae907",
+)
 
 @testset "SBML import and conversion" begin
     sbmlm = load_sbml_model(sbmlfile)

test/runtests.jl

@@ -14,7 +14,7 @@ using OSQP
 using Statistics
 using JSON
 using Measurements
-using Downloads # need this for download(...), depr warning
+using Downloads
 
 function run_test_file(path...)
     fn = joinpath(path...)
@@ -38,6 +38,7 @@ end
 function download_data_file(url, path, hash)
     if isfile(path)
         check_data_file_hash(path, hash)
+        @info "using cached `$path'"
         return path
     end
 

test/sampling/sampling_tools_test.jl

 @testset "Sampling Tests" begin
     # these tests are not very good - sampling needs work
     model = read_model(
-        Downloads.download(
+        download_data_file(
             "http://bigg.ucsd.edu/static/models/e_coli_core.json",
             joinpath("data", "e_coli_core.json"),
+            "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
         ),
     )
-    @test length(model.reactions) == 95 # read in correctly
-
 
     optimizer = Tulip.Optimizer
     biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
     cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
     atts = Dict("IPM_IterationsLimit" => 110)
+
     sol = fba(model, optimizer; objective_func = biomass, constraints = cons)
+
     cons["BIOMASS_Ecoli_core_w_GAM"] =
         (sol["BIOMASS_Ecoli_core_w_GAM"] * 0.99, sol["BIOMASS_Ecoli_core_w_GAM"])
 
@@ -27,6 +28,7 @@
         solver_attributes = atts,
     )
 
+    # TODO
     # @test isapprox(mean(samples[64, :]), 8.9, atol = 0.5) # only tests if the sampler approximately converged
 
     # samples = achr(
@@ -38,5 +40,4 @@
     #     constraints = cons,
     # )
     # @test isapprox(mean(samples[64, :]), 8.9, atol = 0.5) # only tests if the sampler approximately converged
-
 end