Merge pull request #3 from LCSB-BioCore/tests

tests

.github/workflows/ci.yml

+name: CI
+
+on:
+  push:
+    branches:
+      - master
+      - develop
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - 'nightly'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@latest
+      - run: |
+          git config --global user.name Tester
+          git config --global user.email te@st.er
+      - uses: julia-actions/julia-runtest@latest
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

Project.toml

 name = "SBML"
 uuid = "e5567a89-2604-4b09-9718-f5f78e97c3bb"
-authors = ["Mirek Kratochvil <miroslav.kratochvil@uni.lu>",
-           "LCSB R3 team <lcsb-r3@uni.lu>"]
+authors = ["Mirek Kratochvil <miroslav.kratochvil@uni.lu>", "LCSB R3 team <lcsb-r3@uni.lu>"]
 version = "0.1.0"
 
 [deps]
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 SBML_jll = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1"
+SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

src/readsbml.jl

@@ -11,13 +11,11 @@ function readSBML(fn::String)::Model
     try
         n_errs = ccall(sbml(:SBMLDocument_getNumErrors), Cuint, (VPtr,), doc)
         if n_errs > 0
-            @error "SBML loading failed"
-            throw(:IOError)
+            throw(SystemError("Opening SBML document has failed"))
         end
 
         if 0 == ccall(sbml(:SBMLDocument_isSetModel), Cint, (VPtr,), doc)
-            @error "SBML document does not contain a model"
-            throw(:ValueError)
+            throw(AssertionError("SBML document contains no model"))
         end
 
         model = ccall(sbml(:SBMLDocument_getModel), VPtr, (VPtr,), doc)

test/loadEColi.jl

+
+sbmlfile = "EColi.xml"
+
+if !isfile(sbmlfile)
+    download("https://systemsbiology.ucsd.edu/sites/systemsbiology.ucsd.edu/files/Attachments/Images/InSilicoOrganisms/Ecoli/Ecoli_SBML/Ec_core_flux1.xml", sbmlfile)
+end
+
+if bytes2hex(sha256(sbmlfile)) != "e3d18499660a0f7fc15a5a44f33f001c7881ac99a2e8a6a461edf1cf3d69a537"
+    @warn "The downloaded E Coli core flux model seems to be different from the expected one. Tests will likely fail."
+end
+
+@testset "SBML model loading" begin
+    mdl = readSBML(sbmlfile)
+
+    @test typeof(mdl) == Model
+    
+    @test_throws SystemError readSBML(sbmlfile * ".does.not.really.exist")
+
+    @test length(mdl.compartments) == 2
+    
+    mets, rxns, S = getS(mdl)
+
+    @test length(mets) == 77
+    @test length(rxns) == 77
+    @test size(S) == (length(mets),length(rxns))
+
+    # totally arbitrary value tests
+    @test isapprox(sum(S), 42.1479)
+    @test mets[10:12] == ["M_akg_e", "M_fum_c", "M_pyr_c"]
+    @test rxns[10:12] == ["R_H2Ot", "R_PGL", "R_EX_glc_e_"]
+
+    lbs = getLBs(mdl)
+    ubs = getUBs(mdl)
+    ocs = getOCs(mdl)
+
+    @test length(ocs) == length(mets)
+    @test ocs[40] == 1.0
+    deleteat!(ocs, 40)
+    @test all(ocs .== 0.0)
+
+    @test length(getLBs(mdl)) == length(rxns)
+    @test length(getUBs(mdl)) == length(rxns)
+
+    getunit = (val,unit)::Tuple -> unit
+    @test all([broadcast(getunit, lbs) broadcast(getunit, ubs)] .== "mmol_per_gDW_per_hr")
+
+    getval = (val,unit)::Tuple -> val
+    lvals = broadcast(getval, lbs)
+    uvals = broadcast(getval, ubs)
+    @test isapprox(lvals[27], uvals[27])
+    @test isapprox(lvals[27], 7.6)
+    @test isapprox(lvals[12], -10)
+
+    @test count(isapprox.(lvals, -999999)) == 40
+    @test count(isapprox.(lvals, 0)) == 35
+    @test count(isapprox.(uvals, 999999)) == 76
+end

test/runtests.jl

+
+using Test, SHA
+using SBML
+import Pkg
+
+@testset "SBML test suite" begin
+    include("version.jl")
+    include("loadEColi.jl")
+end

test/version.jl

+
+@testset "CCall to SBML works and SBML returns a version" begin
+    @test typeof(SBMLVersion())==Pkg.VersionNumber
+end