reach a pretty good coverage

docs/src/canonical.jl

@@ -64,21 +64,34 @@ A.run_fbcmodel_type_tests(Model);
 # For testing the values, you need to provide an existing file that contains
 # the model. Let's create some contents first:
 
-import AbstractFBCModels.CanonicalModel: Reaction, Metabolite
+import AbstractFBCModels.CanonicalModel: Reaction, Metabolite, Gene
 
 m = Model()
-m.reactions["forward"] =
-    Reaction(name = "import", stoichiometry = Dict("m1" => -1.0, "m2" => 1.0))
-m.reactions["and_back"] =
-    Reaction(name = "export", stoichiometry = Dict("m2" => -1.0, "m1" => 1.0))
 m.metabolites["m1"] = Metabolite(compartment = "inside")
 m.metabolites["m2"] = Metabolite(compartment = "outside")
+m.genes["g1"] = Gene()
+m.genes["g2"] = Gene()
+m.reactions["forward"] = Reaction(
+    name = "import",
+    stoichiometry = Dict("m1" => -1.0, "m2" => 1.0),
+    gene_association_dnf = [["g1"], ["g2"]],
+)
+m.reactions["and_back"] =
+    Reaction(name = "export", stoichiometry = Dict("m2" => -1.0, "m1" => 1.0))
 nothing #hide
 
 # We should immediately find the basic accessors working:
 A.stoichiometry(m)
 
-# We can now write the model to disk and try to load it with the default
+# We can check various side things, such as which reactions would and would not work given all gene products disappear:
+products_available = [
+    A.reaction_gene_products_available(m, rid, _ -> false) for
+    rid in ["forward", "and_back"]
+]
+
+@test products_available == [false, nothing] #src
+
+# We can now also write the model to disk and try to load it with the default
 # loading function:
 mktempdir() do dir
     path = joinpath(dir, "model.canonical-serialized-fbc")

docs/src/utilities.jl

@@ -12,7 +12,7 @@ import AbstractFBCModels as A
 
 A.accessors()
 
-@test length(A.accessors) == 27 #src
+@test length(A.accessors()) == 27 #src
 
 # You do not need to overload all of them (e.g., if you model does not have any
 # genes you can completely omit all gene-related functions). The main required
@@ -57,6 +57,36 @@ A.accessors()
 #
 # ## Downloading models for testing
 #
-# For reproducibility,
+# For reproducibility, it is often viable to check downloaded files for
+# validity, using e.g. checksums. Since this is a common operation, we provide
+# `download_data_file`, which is an appropriate wrapper for
+# `Downloads.download`:
 
-#TODO download file:///something
+mktempdir() do dir
+    origin = joinpath(dir, "origin")
+    url = "file://$origin"
+    dest = joinpath(dir, "model")
+    open(origin, "w") do f
+        write(f, "hello")
+    end
+    A.download_data_file( #src
+        url, #src
+        dest, #src
+        "2cf24dba5fb0a30e26e83b2ac5b9e29e1b161e5c1fa7425e73043362938b9824", #src
+    ) #src
+    x = A.download_data_file( #src
+        url, #src
+        dest, #src
+        "2cf24dba5fb0a30e26e83b2ac5b9e29e1b161e5c1fa7425e73043362938b9824", #src
+    ) # src
+    @test x == dest #src
+    @test read(origin) == read(dest) #src
+    open(dest, "w") do f #src
+        write(f, "olleh") #src
+    end #src
+    @test_warn "different" A.download_data_file( #src
+        url, #src
+        dest, #src
+        "2cf24dba5fb0a30e26e83b2ac5b9e29e1b161e5c1fa7425e73043362938b9824", #src
+    ) #src
+end

src/accessors.jl

@@ -49,7 +49,7 @@ Return identifiers of all genes contained in the model. Empty if none.
 Genes are also sometimes called "gene products" but we write genes for
 simplicity.
 """
-genes(::AbstractFBCModel)::Vector{String} = unimplemented(typeof(a), :genes)
+genes(a::AbstractFBCModel)::Vector{String} = unimplemented(typeof(a), :genes)
 
 """
 $(TYPEDSIGNATURES)
@@ -60,7 +60,7 @@ by [`genes`](@ref)).
 This may be more efficient than calling [`genes`](@ref) and measuring the
 array.
 """
-n_genes(::AbstractFBCModel)::Int = unimplemented(typeof(a), :n_genes)
+n_genes(a::AbstractFBCModel)::Int = unimplemented(typeof(a), :n_genes)
 
 """
 $(TYPEDSIGNATURES)
@@ -86,7 +86,7 @@ $(TYPEDSIGNATURES)
 Get the sparse balance vector of a model, which usually corresponds to the
 accumulation term associated with stoichiometric matrix.
 """
-balance(a::AbstractFBCModel)::SparseVec = spzeros(length(n_metabolites(a)))
+balance(a::AbstractFBCModel)::SparseVec = spzeros(n_metabolites(a))
 
 """
 $(TYPEDSIGNATURES)

src/utils.jl

@@ -55,7 +55,7 @@ function download_data_file(url, path, hash)
         return path
     end
 
-    Downloads.download(url, path)
+    path = download(url, path)
     check_cached_file_hash(path, hash)
     return path
 end

test/defaults.jl

@@ -0,0 +1,42 @@
+
+@testset "behavior of accessors on abstract type" begin
+
+    import AbstractFBCModels as A
+
+    struct NotAModel <: A.AbstractFBCModel end
+
+    m = NotAModel()
+
+    @test_throws ErrorException A.reactions(m)
+    @test_throws ErrorException A.metabolites(m)
+    @test_throws ErrorException A.genes(m)
+    @test_throws ErrorException A.n_reactions(m)
+    @test_throws ErrorException A.n_metabolites(m)
+    @test_throws ErrorException A.n_genes(m)
+    @test_throws ErrorException A.stoichiometry(m)
+    @test_throws ErrorException A.balance(m)
+    @test_throws ErrorException A.bounds(m)
+    @test_throws ErrorException A.objective(m)
+
+    @test isnothing(A.reaction_gene_products_available(m, "", _ -> True))
+    @test isnothing(A.reaction_gene_association_dnf(m, ""))
+    @test_throws ErrorException A.reaction_stoichiometry(m, "")
+    @test isnothing(A.metabolite_formula(m, ""))
+    @test isnothing(A.metabolite_charge(m, ""))
+    @test isnothing(A.metabolite_compartment(m, ""))
+
+    @test isempty(A.reaction_annotations(m, ""))
+    @test isempty(A.metabolite_annotations(m, ""))
+    @test isempty(A.gene_annotations(m, ""))
+    @test isempty(A.reaction_notes(m, ""))
+    @test isempty(A.metabolite_notes(m, ""))
+    @test isempty(A.gene_notes(m, ""))
+    @test isnothing(A.reaction_name(m, ""))
+    @test isnothing(A.metabolite_name(m, ""))
+    @test isnothing(A.gene_name(m, ""))
+
+    @test_throws ErrorException A.load(NotAModel, ".")
+    @test_throws ErrorException A.save(m, ".")
+    @test_throws ErrorException A.filename_extensions(NotAModel)
+    @test_throws ErrorException show(stdout, MIME"text/plain"(), m)
+end

test/runtests.jl

@@ -8,6 +8,8 @@ import AbstractFBCModels as A
         include("../docs/src/canonical.jl")
     end
     @testset "Utilities" begin
-        include("../docs/src/canonical.jl")
+        include("../docs/src/utilities.jl")
     end
+
+    include("defaults.jl")
 end