Merge pull request #41 from senresearch/dev

v0.3.1

Project.toml

@@ -1,7 +1,7 @@
 name = "GeneNetworkAPI"
 uuid = "5ef98721-7938-4c15-bad2-60f0fa16d62a"
 authors = ["Chelsea Trotter <chelsea.xhu@gmail.com>", "Gregory Farage <gfarage@uthsc.edu>", "Saunak Sen <sen@uthsc.edu>"]
-version = "0.3.0"
+version = "0.3.1"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -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()
-"http://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

@@ -126,11 +126,11 @@ dfInfoPheno3 = GeneNetworkAPI.DataFrame(
 
 dfGemma = GeneNetworkAPI.DataFrame( 
     Mb = [24.916883],
-    additive = [-2.292895],
-    chr = [2],
-    lod_score = [15.186008593663088],
+    additive = [-2.292896],
+    chr = Vector{Any}([2]),
+    lod_score = [15.186000529222568],
     name = ["rs32869517"],
-    p_value = [6.516155e-16]
+    p_value = [6.516276e-16]
 )
 
 # TEST 10 - refs
@@ -140,4 +140,4 @@ dfCorrelation = GeneNetworkAPI.DataFrame(
     p_value = [0.00018929765647785504],
     sample_r = [-0.8756580854229329],
     trait = [12762]
-)
+)