updated genetwork link and correlation return trait as numeric not as…

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"

docs/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -22,4 +22,4 @@ makedocs(;
 deploydocs(;
    repo="github.com/senresearch/GeneNetworkAPI.jl",
    devbranch="dev",
-)
+)

docs/src/functions.md

@@ -20,15 +20,41 @@ GeneNetworkAPI.check_gn
 GeneNetworkAPI.list_datasets
 GeneNetworkAPI.list_groups
 GeneNetworkAPI.list_species
+GeneNetworkAPI.list_geno
 ```
 
 ## Get data and information
 
 ```@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

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
 
 """

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]
 )

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));