diff --git a/Project.toml b/Project.toml index 2aeac7c..7f71da5 100644 --- a/Project.toml +++ b/Project.toml @@ -13,6 +13,5 @@ JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" [compat] CSV = "0.10, 1" DataFrames = "1" -HTTP = "0.9, 1" JSON = "0.21, 1" julia = "1" diff --git a/docs/Project.toml b/docs/Project.toml new file mode 100644 index 0000000..dfa65cd --- /dev/null +++ b/docs/Project.toml @@ -0,0 +1,2 @@ +[deps] +Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" diff --git a/docs/make.jl b/docs/make.jl index 2e261fe..fa970ff 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -22,4 +22,4 @@ makedocs(; deploydocs(; repo="github.com/senresearch/GeneNetworkAPI.jl", devbranch="dev", -) +) \ No newline at end of file diff --git a/docs/src/functions.md b/docs/src/functions.md index f7d97dc..2441789 100644 --- a/docs/src/functions.md +++ b/docs/src/functions.md @@ -20,6 +20,7 @@ GeneNetworkAPI.check_gn GeneNetworkAPI.list_datasets GeneNetworkAPI.list_groups GeneNetworkAPI.list_species +GeneNetworkAPI.list_geno ``` ## Get data and information @@ -27,8 +28,33 @@ GeneNetworkAPI.list_species ```@docs GeneNetworkAPI.get_geno GeneNetworkAPI.get_pheno +GeneNetworkAPI.get_omics GeneNetworkAPI.info_dataset GeneNetworkAPI.info_pheno + +``` +## Download data + +```@docs +GeneNetworkAPI.download_geno +GeneNetworkAPI.download_pheno +GeneNetworkAPI.download_omics +``` + +## Display table + +```@docs +GeneNetworkAPI.show_table +``` + +## Utils + +```@docs +GeneNetworkAPI.make_rectangular +GeneNetworkAPI.has_error_500 +GeneNetworkAPI.parse_geno +GeneNetworkAPI.genofile_location +GeneNetworkAPI.has_genofile_meta ``` ## Run jobs on the server diff --git a/src/query.jl b/src/query.jl index 8f5b55e..1feb6f9 100644 --- a/src/query.jl +++ b/src/query.jl @@ -15,11 +15,11 @@ different instance of the server. ```jldoctest julia> gn_url() -"https://gn2.genenetwork.org/api/v_pre1/" +"https://genenetwork.org/api/v_pre1/" ``` """ function gn_url() - return url = "http://gn2.genenetwork.org/api/v_pre1/" + return url = "https://genenetwork.org/api/v_pre1/" end """ diff --git a/test/generate_ref.jl b/test/generate_ref.jl index 76a299c..9d3c5f6 100644 --- a/test/generate_ref.jl +++ b/test/generate_ref.jl @@ -139,5 +139,5 @@ dfCorrelation = GeneNetworkAPI.DataFrame( # Symbol("#_strains") = [25.100133], p_value = [0.00018929765647785504], sample_r = [-0.8756580854229329], - trait = string.([12762]) + trait = [12762] ) diff --git a/test/gnAPI_tests.jl b/test/gnAPI_tests.jl index 30b6baf..40e09bb 100644 --- a/test/gnAPI_tests.jl +++ b/test/gnAPI_tests.jl @@ -111,7 +111,7 @@ println("Get Gemma results test 9: ", @test (dfRslt1 == dfGemma)); ###################### dfRslt = run_correlation("1427571_at","HC_M2_0606_P","BXDPublish"); -dfRslt1 = GeneNetworkAPI.select(filter(row->row.trait == "12762", dfRslt), [2,3,4]); +dfRslt1 = GeneNetworkAPI.select(filter(row->row.trait == 12762, dfRslt), [2,3,4]); println("Get correlation test 10: ", @test (dfRslt1 == dfCorrelation));