Merge branch 'master' of github.com:genenetwork/genenetwork2 into development

4 files changed, 196 insertions, 46 deletions

diff --git a/bin/test-website b/bin/test-website
index 24274713..aeab459b 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -25,6 +25,10 @@ opts = OptionParser.new do |o|
   o.on('-l','--link-checker', 'Check for dead links') do
     options[:link_checker] = true
   end
+  
+  o.on('-n','--navigation-test', 'Check for navigation test results') do
+    options[:navigation_test] = true
+  end
 
   o.separator ""
   o.on_tail('-h', '--help', 'display this help and exit') do
@@ -63,4 +67,7 @@ else
   require 'main_web_functionality'
 end
   
+if options[:navigation_test]
+  require 'NavigationTest'
+end
 
diff --git a/test/lib/NavigationTest.rb b/test/lib/NavigationTest.rb
new file mode 100644
index 00000000..26080d28
--- /dev/null
+++ b/test/lib/NavigationTest.rb
@@ -0,0 +1,46 @@
+# In these tests we navigate from the main page to a specific trait then hit the different mapping tool buttons (In this case pylMM and r/qtl) followed by computing the results (marker regressions).
+
+class NavigationTest
+end
+
+describe NavigationTest do
+  before do
+    @agent = Mechanize.new
+    @agent.agent.http.ca_file = '/etc/ssl/certs/ca-certificates.crt'
+  end
+
+  describe NavigationTest do
+    it "pyLMM mapping tool selection" do
+      page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P')
+#Navigates to http://localhost:5003/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P and clicks respective buttons.
+      link = page.link_with(text: 'pyLMM')
+      page = link.click
+      puts page.uri
+      link = page.link_with(text: 'Compute')
+      page = link.click
+      puts page.uri
+      probe_link.uri.to_s.must_equal "/marker_regression"
+      
+       
+        end
+      end
+
+end
+
+describe NavigationTest do
+    it "R/qtl mapping tool selection" do
+      page = @agent.get($host+'/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P')
+      link = page.link_with(text: 'R/qtl')
+      page = link.click
+      puts page.uri
+      form.field_with(:name => 'Methods').options[2].select
+      link = page.link_with(text: 'Compute')
+      page = link.click
+      puts page.uri
+      probe_link.uri.to_s.must_equal "/marker_regression"
+      
+       
+        end
+      end
+
+
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 4fc95a60..d1c0be83 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -331,7 +331,7 @@ class GeneralTrait(object):
                     #        
                     #    description = self.pre_publication_description
                 
-                if len(description) > 0:
+                if description:
                     self.description_display = description.strip()
                 else:
                     self.description_display = ""
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 2b16383f..12a30e84 100755
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1596,6 +1596,11 @@
          "B6D2F2": {
             "Brain mRNA": [
                [
+                  "76",
+                  "BRF2_M_0805_M",
+                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
+               ],
+               [
                   "78",
                   "BRF2_M_0805_P",
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
@@ -1606,11 +1611,6 @@
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
                ],
                [
-                  "76",
-                  "BRF2_M_0805_M",
-                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
-               ],
-               [
                   "33",
                   "BRF2_M_0304_P",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
@@ -1846,6 +1846,18 @@
             ]
          },
          "BXD": {
+            "Adipose Proteome": [
+               [
+                  "797",
+                  "EPFL_AdiPro0416",
+                  "EPFL/ETHZ BXD Brown Adipose, Total Tissue Proteome, Chow Diet (Apr16) Light SWATH **"
+               ],
+               [
+                  "798",
+                  "EPFL_AdiMitPro0416",
+                  "EPFL/ETHZ BXD Brown Adipose, Isolated Mitochondria Proteome, Chow Diet (Apr16) Light SWATH **"
+               ]
+            ],
             "Adipose mRNA": [
                [
                   "469",
@@ -1916,21 +1928,21 @@
                [
                   "414",
                   "UCLA_BXD-on_Femur_0113_RSN",
-                  "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v2.0 (Jan13) RSN"
+                  "UCLA GSE27483 BXD Only Bone Femur ILM Mouse WG-6 v1.1 (Jan13) RSN"
                ]
             ],
             "Brain mRNA": [
                [
-                  "164",
-                  "UTHSC_BXD_WB_RNASeq1112",
-                  "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed"
-               ],
-               [
                   "590",
                   "UTHSC_BXD_WB_RNASeqtrim1_1112",
                   "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Trimmed 1.0"
                ],
                [
+                  "164",
+                  "UTHSC_BXD_WB_RNASeq1112",
+                  "UTHSC Mouse BXD Whole Brain RNA Sequence (Nov12) RPKM Untrimmed"
+               ],
+               [
                   "394",
                   "UTHSC_BXD_WB_RNASeqEx1112",
                   "UTHSC Mouse BXD Whole Brain RNA Sequence Exon Level (Nov12) RPKM"
@@ -1946,6 +1958,11 @@
                   "UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
                ],
                [
+                  "82",
+                  "BR_U_0805_R",
+                  "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
+               ],
+               [
                   "81",
                   "BR_U_0805_P",
                   "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
@@ -1956,11 +1973,6 @@
                   "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
                ],
                [
-                  "82",
-                  "BR_U_0805_R",
-                  "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
-               ],
-               [
                   "42",
                   "CB_M_0204_P",
                   "INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2027,6 +2039,11 @@
                   "Eye M430v2 WT Gpnmb (Sep08) RMA"
                ],
                [
+                  "278",
+                  "Eye_M2_0908_R_MT",
+                  "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
+               ],
+               [
                   "382",
                   "Eye_M2_0908_WTWT",
                   "Eye M430v2 WT WT (Sep08) RMA"
@@ -2037,11 +2054,6 @@
                   "Eye M430v2 WT Tyrp1 (Sep08) RMA"
                ],
                [
-                  "278",
-                  "Eye_M2_0908_R_MT",
-                  "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
-               ],
-               [
                   "400",
                   "DBA2J-ONH-1212",
                   "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
@@ -2557,29 +2569,29 @@
             ],
             "Retina mRNA": [
                [
+                  "267",
+                  "Illum_Retina_BXD_RankInv0410",
+                  "Full HEI Retina Illumina V6.2 (Apr10) RankInv"
+               ],
+               [
+                  "302",
+                  "G2NEI_ILM_Retina_BXD_RI0410",
+                  "HEI Retina Normal Illumina V6.2 (Apr10) RankInv"
+               ],
+               [
                   "709",
                   "DoDCMMRPRetMoGene2_0515",
-                  "DoD CDMRP Retina Affy MoGene 2.0 ST (May15) RMA Gene Level"
+                  "DoD Retina Normal Affy MoGene 2.0 ST (May15) RMA Gene Level"
                ],
                [
                   "710",
                   "DoDCMMRPRetMoGene2Ex_0515",
-                  "DoD CDMRP Retina Affy MoGene 2.0 ST (May15) RMA Exon Level"
+                  "DoD Retina Normal Affy MoGene 2.0 ST (May15) RMA Exon Level"
                ],
                [
                   "385",
                   "ONCRetILM6_0412",
                   "ONC HEI Retina (April 2012) RankInv"
-               ],
-               [
-                  "302",
-                  "G2NEI_ILM_Retina_BXD_RI0410",
-                  "Normal HEI Retina (April 2010) RankInv"
-               ],
-               [
-                  "267",
-                  "Illum_Retina_BXD_RankInv0410",
-                  "Full HEI Retina (April 2010) RankInv"
                ]
             ],
             "Spleen mRNA": [
@@ -2704,6 +2716,23 @@
                   "RTC_1106_R",
                   "HZI Treg M430v2 (Feb11) RMA"
                ]
+            ],
+            "Ventral Tegmental Area mRNA": [
+               [
+                  "228",
+                  "VCUSal_0609_R",
+                  "VCU BXD VTA Sal M430 2.0 (Jun09) RMA"
+               ],
+               [
+                  "230",
+                  "VCUEtvsSal_0609_R",
+                  "VCU BXD VTA Et vs Sal M430 2.0 (Jun09) RMA"
+               ],
+               [
+                  "229",
+                  "VCUEtOH_0609_R",
+                  "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA"
+               ]
             ]
          },
          "BXH": {
@@ -2810,6 +2839,16 @@
                   "170",
                   "UCLA_CTB6B6CTF2_ADIPOSE_2005",
                   "UCLA CTB6/B6CTF2 Adipose (2005) mlratio"
+               ],
+               [
+                  "189",
+                  "UCLA_CTB6B6CTF2_ADIPOSE_FEMALE",
+                  "UCLA CTB6B6CTF2 Adipose Female mlratio"
+               ],
+               [
+                  "188",
+                  "UCLA_CTB6B6CTF2_ADIPOSE_MALE",
+                  "UCLA CTB6B6CTF2 Adipose Male mlratio"
                ]
             ],
             "Brain mRNA": [
@@ -2841,6 +2880,16 @@
                   "172",
                   "UCLA_CTB6B6CTF2_LIVER_2005",
                   "UCLA CTB6/B6CTF2 Liver (2005) mlratio"
+               ],
+               [
+                  "193",
+                  "UCLA_CTB6B6CTF2_LIVER_FEMALE",
+                  "UCLA CTB6B6CTF2 Liver Female mlratio"
+               ],
+               [
+                  "192",
+                  "UCLA_CTB6B6CTF2_LIVER_MALE",
+                  "UCLA CTB6B6CTF2 Liver Male mlratio"
                ]
             ],
             "Muscle mRNA": [
@@ -2848,6 +2897,16 @@
                   "173",
                   "UCLA_CTB6B6CTF2_MUSCLE_2005",
                   "UCLA CTB6/B6CTF2 Muscle (2005) mlratio"
+               ],
+               [
+                  "195",
+                  "UCLA_CTB6B6CTF2_MUSCLE_FEMALE",
+                  "UCLA CTB6B6CTF2 Muscle Female mlratio"
+               ],
+               [
+                  "194",
+                  "UCLA_CTB6B6CTF2_MUSCLE_MALE",
+                  "UCLA CTB6B6CTF2 Muscle Male mlratio"
                ]
             ],
             "Phenotypes": [
@@ -2942,6 +3001,11 @@
             ],
             "Hippocampus mRNA": [
                [
+                  "212",
+                  "Illum_LXS_Hipp_RSE_1008",
+                  "Hippocampus Illumina RSE (Oct08) RankInv beta"
+               ],
+               [
                   "214",
                   "Illum_LXS_Hipp_NOE_1008",
                   "Hippocampus Illumina NOE (Oct08) RankInv beta"
@@ -2962,11 +3026,6 @@
                   "Hippocampus Illumina NON (Oct08) RankInv beta"
                ],
                [
-                  "212",
-                  "Illum_LXS_Hipp_RSE_1008",
-                  "Hippocampus Illumina RSE (Oct08) RankInv beta"
-               ],
-               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3130,16 +3189,32 @@
          "Scripps-2013": {}
       },
       "rat": {
-         "HSNIH": {
+         "HSNIH-Palmer": {
             "Phenotypes": [
                [
-                  "619",
-                  "HSNIHPublish",
-                  "HSNIH Published Phenotypes"
+                  "None",
+                  "HSNIH-PalmerPublish",
+                  "HSNIH-Palmer Published Phenotypes"
+               ]
+            ]
+         },
+         "HSNIH-RGSMC": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "HSNIH-RGSMCPublish",
+                  "HSNIH-RGSMC Published Phenotypes"
                ]
             ]
          },
          "HXBBXH": {
+            "Adipose mRNA": [
+               [
+                  "799",
+                  "FGUCAS_BAdip0516",
+                  "FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2 **"
+               ]
+            ],
             "Adrenal Gland mRNA": [
                [
                   "220",
@@ -3460,8 +3535,12 @@
       ],
       "rat": [
          [
-            "HSNIH",
-            "NIH Heterogeneous Stock"
+            "HSNIH-Palmer",
+            "NIH Heterogeneous Stock (Palmer)"
+         ],
+         [
+            "HSNIH-RGSMC",
+            "NIH Heterogeneous Stock (RGSMC 2013)"
          ],
          [
             "HXBBXH",
@@ -4351,6 +4430,10 @@
                "Adipose mRNA"
             ],
             [
+               "Adipose Proteome",
+               "Adipose Proteome"
+            ],
+            [
                "Adrenal Gland mRNA",
                "Adrenal Gland mRNA"
             ],
@@ -4465,6 +4548,10 @@
             [
                "T Cell (regulatory) mRNA",
                "T Cell (regulatory) mRNA"
+            ],
+            [
+               "Ventral Tegmental Area mRNA",
+               "Ventral Tegmental Area mRNA"
             ]
          ],
          "BXH": [
@@ -4656,7 +4743,13 @@
          "Scripps-2013": []
       },
       "rat": {
-         "HSNIH": [
+         "HSNIH-Palmer": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ]
+         ],
+         "HSNIH-RGSMC": [
             [
                "Phenotypes",
                "Phenotypes"
@@ -4672,6 +4765,10 @@
                "Genotypes"
             ],
             [
+               "Adipose mRNA",
+               "Adipose mRNA"
+            ],
+            [
                "Adrenal Gland mRNA",
                "Adrenal Gland mRNA"
             ],