load and test models from multiple sources

(Uses a few new models from EBI repository.)

test/ecoli_flux.jl

@@ -15,6 +15,7 @@ end
 
     @test typeof(mdl) == Model
 
+    @info "The next warning is an expected side-effect of testing an error condition"
     @test_throws AssertionError readSBML(sbmlfile * ".does.not.really.exist")
 
     @test length(mdl.compartments) == 2

test/ecoli_modelonly.jl

-
-sbmlfile = "e_coli_core.xml"
-
-if !isfile(sbmlfile)
-    download("http://bigg.ucsd.edu/static/models/e_coli_core.xml", sbmlfile)
-end
-
-cksum = bytes2hex(sha256(open(sbmlfile)))
-if cksum != "b4db506aeed0e434c1f5f1fdd35feda0dfe5d82badcfda0e9d1342335ab31116"
-    @warn "The downloaded E Coli core model seems to be different from the expected one. Tests will likely fail." cksum
-end
-
-@testset "SBML model-only file loading" begin
-    mdl = readSBML(sbmlfile)
-
-    @test typeof(mdl) == Model
-
-    mets, rxns, _ = getS(mdl)
-
-    @test length(mets) == 72
-    @test length(rxns) == 95
-end

test/loadmodels.jl

+
+sbmlfiles = [
+    # a test model from BIGG
+    ("e_coli_core.xml",
+     "http://bigg.ucsd.edu/static/models/e_coli_core.xml",
+     "b4db506aeed0e434c1f5f1fdd35feda0dfe5d82badcfda0e9d1342335ab31116",
+     72,
+     95),
+    # a relatively new non-curated model from biomodels
+    ("T1M1133.xml",
+     "https://www.ebi.ac.uk/biomodels/model/download/MODEL1909260004.4?filename=T1M1133.xml",
+     "2b1e615558b6190c649d71052ac9e0dc1635e3ad281e541bc7d4fdf2892a5967",
+     2517,
+     3956),
+    # a curated model from biomodels
+    ("Dasgupta2020.xml",
+     "https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000973.3?filename=Dasgupta2020.xml",
+     "958b131d4df2f215dae68255433542f228601db0326d26a54efd08ddcf823489",
+     2, 6),
+]
+
+@testset "Loading of models from various sources" begin
+    for (sbmlfile, url, hash, expected_mets, expected_rxns) in sbmlfiles
+        if !isfile(sbmlfile)
+            download(url, sbmlfile)
+        end
+
+        cksum = bytes2hex(sha256(open(sbmlfile)))
+        if cksum != hash
+            @warn "The downloaded model `$sbmlfile' seems to be different from the expected one. Tests will likely fail." cksum
+        end
+
+        @testset "Loading of $sbmlfile" begin
+            mdl = readSBML(sbmlfile)
+
+            @test typeof(mdl) == Model
+
+            mets, rxns, _ = getS(mdl)
+
+            @test length(mets) == expected_mets
+            @test length(rxns) == expected_rxns
+        end
+    end
+end

test/runtests.jl

@@ -6,5 +6,5 @@ import Pkg
 @testset "SBML test suite" begin
     include("version.jl")
     include("ecoli_flux.jl")
-    include("ecoli_modelonly.jl")
+    include("loadmodels.jl")
 end