Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into HEAD

15 files changed, 47 insertions, 43 deletions

diff --git a/doc/API_readme.md b/doc/API_readme.md
index 652376a0..be6668dc 100644
--- a/doc/API_readme.md
+++ b/doc/API_readme.md
@@ -6,17 +6,17 @@
 
 To get a list of species with data available in GN (and their associated names and ids):
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/species
+curl http://genenetwork.org/api/v_pre1/species
 [ { "FullName": "Mus musculus", "Id": 1, "Name": "mouse", "TaxonomyId": 10090 }, ... { "FullName": "Populus trichocarpa", "Id": 10, "Name": "poplar", "TaxonomyId": 3689 } ]
 ```
 
 Or to get a single species info:
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/species/mouse
+curl http://genenetwork.org/api/v_pre1/species/mouse
 ``` 
 OR 
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json
+curl http://genenetwork.org/api/v_pre1/species/mouse.json
 ```
 
 *For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later*
@@ -26,33 +26,33 @@ curl http://gn2.genenetwork.org/api/v_pre1/species/mouse.json
 This query can optionally filter by species:
 
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/groups (for all species)
+curl http://genenetwork.org/api/v_pre1/groups (for all species)
 ```
 OR
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets)
+curl http://genenetwork.org/api/v_pre1/groups/mouse (for just mouse groups/RISets)
 [ { "DisplayName": "BXD", "FullName": "BXD RI Family", "GeneticType": "riset", "Id": 1, "MappingMethodId": "1", "Name": "BXD", "SpeciesId": 1, "public": 2 }, ... { "DisplayName": "AIL LGSM F34 and F39-43 (GBS)", "FullName": "AIL LGSM F34 and F39-43 (GBS)", "GeneticType": "intercross", "Id": 72, "MappingMethodId": "2", "Name": "AIL-LGSM-F34-F39-43-GBS", "SpeciesId": 1, "public": 2 } ]
 ```
 
 ## Fetch Genotypes for Group/RISet ##
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/genotypes/bimbam/BXD
-curl http://gn2.genenetwork.org/api/v_pre1/genotypes/BXD.bimbam
+curl http://genenetwork.org/api/v_pre1/genotypes/bimbam/BXD
+curl http://genenetwork.org/api/v_pre1/genotypes/BXD.bimbam
 ```
 Returns a group's genotypes in one of several formats - bimbam, rqtl2, or geno (a format used by qtlreaper which is just a CSV file consisting of marker positions and genotypes)
 
 Rqtl2 genotype queries can also include the dataset name and will return a zip of the genotypes, phenotypes, and gene map (marker names/positions). For example:
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip
+curl http://genenetwork.org/api/v_pre1/genotypes/rqtl2/BXD/HC_M2_0606_P.zip
 ```
 
 ## Fetch Datasets ##
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/datasets/bxd
+curl http://genenetwork.org/api/v_pre1/datasets/bxd
 ```
 OR
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd
+curl http://genenetwork.org/api/v_pre1/datasets/mouse/bxd
 [ { "AvgID": 1, "CreateTime": "Fri, 01 Aug 2003 00:00:00 GMT", "DataScale": "log2", "FullName": "UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, CD Cohorts (Mar 2017) log2", "Id": 1, "Long_Abbreviation": "BXDMicroArray_ProbeSet_August03", "ProbeFreezeId": 3, "ShortName": "Brain U74Av2 08/03 MAS5", "Short_Abbreviation": "Br_U_0803_M", "confidentiality": 0, "public": 0 }, ... { "AvgID": 3, "CreateTime": "Tue, 14 Aug 2018 00:00:00 GMT", "DataScale": "log2", "FullName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Id": 859, "Long_Abbreviation": "EPFLMouseLiverCDRMAApr18", "ProbeFreezeId": 181, "ShortName": "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA", "Short_Abbreviation": "EPFLMouseLiverCDRMA0818", "confidentiality": 0, "public": 1 } ]
 ```
 (I added the option to specify species just in case we end up with the same group name across multiple species at some point, though it's currently unnecessary)
@@ -61,11 +61,11 @@ curl http://gn2.genenetwork.org/api/v_pre1/datasets/mouse/bxd
 ### For mRNA Assay/"ProbeSet" ###
 
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P
+curl http://genenetwork.org/api/v_pre1/dataset/HC_M2_0606_P
 ```
 OR
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
+curl http://genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
 { "confidential": 0, "data_scale": "log2", "dataset_type": "mRNA expression", "full_name": "Hippocampus Consortium M430v2 (Jun06) PDNN", "id": 112, "name": "HC_M2_0606_P", "public": 2, "short_name": "Hippocampus M430v2 BXD 06/06 PDNN", "tissue": "Hippocampus mRNA", "tissue_id": 9 }
 ```
 (This also has the option to specify group/riset)
@@ -73,26 +73,26 @@ curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/HC_M2_0606_P```
 ### For "Phenotypes" (basically non-mRNA Expression; stuff like weight, sex, etc) ###
 For these traits, the query fetches publication info and takes the group and phenotype 'ID' as input. For example:
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/dataset/bxd/10001
+curl http://genenetwork.org/api/v_pre1/dataset/bxd/10001
 { "dataset_type": "phenotype", "description": "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]", "id": 10001, "name": "CBLWT2", "pubmed_id": 11438585, "title": "Genetic control of the mouse cerebellum: identification of quantitative trait loci modulating size and architecture", "year": "2001" }
 ```
 
 ## Fetch Sample Data for Dataset ##
 ``` 
-curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv
+curl http://genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv
 ```
 
 Returns a CSV file with sample/strain names as the columns and trait IDs as rows
 
 ## Fetch Sample Data for Single Trait ##
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at
+curl http://genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at
 [ { "data_id": 23415463, "sample_name": "129S1/SvImJ", "sample_name_2": "129S1/SvImJ", "se": 0.123, "value": 8.201 }, { "data_id": 23415463, "sample_name": "A/J", "sample_name_2": "A/J", "se": 0.046, "value": 8.413 }, { "data_id": 23415463, "sample_name": "AKR/J", "sample_name_2": "AKR/J", "se": 0.134, "value": 8.856 }, ... ]
 ```
 
 ## Fetch Trait List for Dataset ##
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json
+curl http://genenetwork.org/api/v_pre1/traits/HXBBXHPublish.json
 [ { "Additive": 0.0499967532467532, "Id": 10001, "LRS": 16.2831307029479, "Locus": "rs106114574", "PhenotypeId": 1449, "PublicationId": 319, "Sequence": 1 }, ... ]
 ```
 
@@ -101,7 +101,7 @@ Both JSON and CSV formats can be specified, with JSON as default. There is also
 ## Fetch Trait Info (Name, Description, Location, etc) ##
 ### For mRNA Expression/"ProbeSet" ###
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at
+curl http://genenetwork.org/api/v_pre1/trait/HC_M2_0606_P/1436869_at
 { "additive": -0.214087568058076, "alias": "HHG1; HLP3; HPE3; SMMCI; Dsh; Hhg1", "chr": "5", "description": "sonic hedgehog (hedgehog)", "id": 99602, "locus": "rs8253327", "lrs": 12.7711275309832, "mb": 28.457155, "mean": 9.27909090909091, "name": "1436869_at", "p_value": 0.306, "se": null, "symbol": "Shh" }
 ```
 
@@ -110,7 +110,7 @@ For phenotypes this just gets the  max LRS, its location, and additive effect (a
 
 Since each group/riset only has one phenotype "dataset", this query takes either the group/riset name or the group/riset name + "Publish" (for example "BXDPublish", which is the dataset name in the DB) as input
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/trait/BXD/10001
+curl http://genenetwork.org/api/v_pre1/trait/BXD/10001
 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 }
 ```
 
@@ -130,7 +130,7 @@ Each method's query takes the following parameters respectively (more will be ad
 
 Example query:
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true
+curl http://genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true
 ```
 
 ### R/qtl ###
@@ -146,7 +146,7 @@ curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&
 
 Example query:
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100
+curl http://genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100
 ```
 
 Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case)
@@ -164,6 +164,6 @@ This query currently takes the following parameters (though more will be added):
 
 Example query:
 ```
-curl http://gn2.genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100
+curl http://genenetwork.org/api/v_pre1/correlation?trait_id=1427571_at&db=HC_M2_0606_P&target_db=BXDPublish&type=sample&return_count=100
 [ { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20511 }, { "#_strains": 6, "p_value": 0.004804664723032055, "sample_r": -0.942857142857143, "trait": 20724 }, { "#_strains": 12, "p_value": 1.8288943424888848e-05, "sample_r": -0.9233615170820528, "trait": 13536 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": 0.8928571428571429, "trait": 10157 }, { "#_strains": 7, "p_value": 0.006807187408935392, "sample_r": -0.8928571428571429, "trait": 20392 }, ... ]
 ```
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index fae62875..8652e6b7 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -56,7 +56,7 @@ from pprint import pformat as pf
 from db.gn_server import menu_main
 from db.call import fetchall,fetchone,fetch1
 
-from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists
+from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
 from utility.logger import getLogger
 logger = getLogger(__name__ )
 
@@ -94,7 +94,7 @@ Publish or ProbeSet. E.g.
         """
         self.datasets = {}
         if rebuild: #ZS: May make this the only option
-            data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content)
+            data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content)
             #data = gen_menu.gen_dropdown_json()
         else:
             file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 5525472e..e454c593 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -14,6 +14,7 @@ from base.data_set import create_dataset
 from db import webqtlDatabaseFunction
 from utility import webqtlUtil
 from utility import hmac
+from utility.tools import GN2_BASE_URL
 
 from wqflask import app
 
@@ -135,9 +136,9 @@ class GeneralTrait(object):
 
         alias = 'Not available'
         if self.symbol:
-            human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper())
-            mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize())
-            other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower())
+            human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+            mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+            other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
 
             if human_response and mouse_response and other_response:
                 alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 0fbedccb..9354ece6 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -234,6 +234,8 @@ def show_settings():
 GN_VERSION         = get_setting('GN_VERSION')
 HOME               = get_setting('HOME')
 WEBSERVER_MODE     = get_setting('WEBSERVER_MODE')
+GN2_BASE_URL       = get_setting('GN2_BASE_URL')
+GN2_BRANCH_URL     = get_setting('GN2_BRANCH_URL')
 GN_SERVER_URL      = get_setting('GN_SERVER_URL')
 SERVER_PORT        = get_setting_int('SERVER_PORT')
 SQL_URI            = get_setting('SQL_URI')
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 6fda02fd..4415b86a 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -20,7 +20,7 @@ from base import data_set
 from base import trait as TRAIT
 
 from utility import helper_functions
-from utility.tools import locate
+from utility.tools import locate, GN2_BRANCH_URL
 
 from rpy2.robjects.packages import importr
 
@@ -56,6 +56,8 @@ class CTL(object):
         self.edges_list = []
         logger.info("Obtained pointers to CTL functions")
 
+        self.gn2_url = GN2_BRANCH_URL
+
     def addNode(self, gt):
         node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name),
                                 'sid' : str(gt.name), 
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 05caa100..b0ca5ced 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -13,6 +13,7 @@ import sys
 # sys.path.append("..") Never in a running webserver
 
 from db import webqtlDatabaseFunction
+from utility.tools import GN2_BASE_URL
 
 import logging
 from utility.logger import getLogger
@@ -919,7 +920,7 @@ def get_aliases(symbol, species):
         return []
 
     filtered_aliases = []
-    response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + symbol_string)
+    response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string)
     if response:
         alias_list = json.loads(response.content)
 
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index a332db46..152e4168 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -47,6 +47,7 @@ from utility.TDCell import TDCell
 from base.trait import GeneralTrait
 from base import data_set
 from utility import webqtlUtil, helper_functions, corr_result_helpers
+from utility.tools import GN2_BRANCH_URL
 from db import webqtlDatabaseFunction
 import utility.webqtlUtil #this is for parallel computing only.
 from wqflask.correlation import correlation_functions
@@ -195,6 +196,7 @@ class NetworkGraph(object):
             self.nodes_list.append(node_dict)
 
         self.elements = json.dumps(self.nodes_list + self.edges_list)
+        self.gn2_url = GN2_BRANCH_URL
 
         groups = []
         for sample in self.all_sample_list:
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 698389ab..8f702d58 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -28,6 +28,7 @@ from flask import render_template, Flask, g
 
 from utility import formatting
 from utility import hmac
+from utility.tools import GN2_BASE_URL
 from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 
 from utility.logger import getLogger
@@ -295,7 +296,7 @@ def get_aliases(symbol_list, species):
     symbols_string = ",".join(updated_symbols)
 
     filtered_aliases = []
-    response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases2/" + symbols_string)
+    response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string)
     if response:
         alias_lists = json.loads(response.content)
         seen = set()
diff --git a/wqflask/wqflask/static/new/javascript/ctl_graph.js b/wqflask/wqflask/static/new/javascript/ctl_graph.js
index 94bd7e9d..bd950592 100644
--- a/wqflask/wqflask/static/new/javascript/ctl_graph.js
+++ b/wqflask/wqflask/static/new/javascript/ctl_graph.js
@@ -82,18 +82,12 @@ window.onload=function() {
     function create_qtips(cy){
         cy.nodes().qtip({
                             content: function(){
-                                gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().sid + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>'
+                                gn_link = '<b>'+'<a href="' + gn2_url + '/show_trait?trait_id=' + this.data().sid + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>'
                                 ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>' 
                                 omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>' 
                                 qtip_content = gn_link + ncbi_link + omim_link
                                 return qtip_content
-                                //return '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id + '&dataset=' + this.data().dataset + '" >'+this.data().id +'<a>'+'</b>' 
                             },
-                            // content: {
-                                // title: '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.target() + '&dataset=' + this.dataset() + '" >'+this.target() +'<a>'+'</b>',
-                                // text: this.target,
-                                // button: true
-                            // },
                             position: {
                                 my: 'top center',
                                 at: 'bottom center'
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index fad600d2..794804f4 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -74,7 +74,6 @@ redo_dropdown = function(dropdown, items) {
     this_opt_group = null
     for (_i = 0, _len = group_family_list.length; _i < _len; _i++) {
       item = group_family_list[_i];
-      console.log("THE ITEM:", item)
       if (item[2] != "None" && current_family == ""){
         current_family = item[2]
         this_opt_group = $("<optgroup label=\"" + item[2] + "\">")
diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js
index 4d507a18..02c3b817 100644
--- a/wqflask/wqflask/static/new/javascript/network_graph.js
+++ b/wqflask/wqflask/static/new/javascript/network_graph.js
@@ -85,7 +85,7 @@ window.onload=function() {
         cy.nodes().qtip({
                             content: function(){
                                 qtip_content = ''
-                                gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id.split(":")[0] + '&dataset=' + this.data().id.split(":")[1] + '" >'+this.data().id +'</a>'+'</b><br>'
+                                gn_link = '<b>'+'<a href="' + gn2_url + '/show_trait?trait_id=' + this.data().id.split(":")[0] + '&dataset=' + this.data().id.split(":")[1] + '" >'+this.data().id +'</a>'+'</b><br>'
                                 qtip_content += gn_link
                                 if (typeof(this.data().geneid) !== 'undefined'){
                                     ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>'
@@ -115,7 +115,7 @@ window.onload=function() {
                                 correlation_line = '<b>Sample r: ' + this.data().correlation + '</b><br>'
                                 p_value_line = 'Sample p(r): ' + this.data().p_value + '<br>'
                                 overlap_line = 'Overlap: ' + this.data().overlap + '<br>'
-                                scatter_plot = '<a href="http://gn2-zach.genenetwork.org/corr_scatter_plot?dataset_1=' + this.data().source.split(":")[1] + '&dataset_2=' + this.data().target.split(":")[1] + '&trait_1=' + this.data().source.split(":")[0] + '&trait_2=' + this.data().target.split(":")[0] + '" >View Scatterplot</a>'
+                                scatter_plot = '<a href="' + gn2_url + '/corr_scatter_plot?dataset_1=' + this.data().source.split(":")[1] + '&dataset_2=' + this.data().target.split(":")[1] + '&trait_1=' + this.data().source.split(":")[0] + '&trait_2=' + this.data().target.split(":")[0] + '" >View Scatterplot</a>'
                                 return correlation_line + p_value_line + overlap_line + scatter_plot
                             },
                             position: {
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index d85075a9..0108d93a 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -61,6 +61,7 @@
 
     <script>
         elements_list = {{ elements | safe }}
+        gn2_url = "{{ gn2_url | safe }}"
     </script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 0116245d..f8720d39 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -219,9 +219,9 @@
                     <h3>GN1 Mirror and development sites</h3>
 
                     <ul>
-                        <li><a href="http://www.genenetwork.org/">Main GN1 site at UTHSC</a> (main site)</li>
+                        <li><a href="http://gn1.genenetwork.org/">Main GN1 site at UTHSC</a> (main site)</li>
                         <li><a href="http://genenetwork.helmholtz-hzi.de/">Germany at the HZI</a></li>
-                        <li><a href="http://gn2.genenetwork.org/">Memphis at the U of M</a></li>
+                        <li><a href="http://genenetwork.org/">Memphis at the U of M</a></li>
                     </ul>
                 </section>
 
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 963531cb..06b71f53 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -254,8 +254,8 @@
                     </div>
                     <h3>GeneNetwork v2:</h3>
                       <ul>
-                        <li><a href="http://gn2.genenetwork.org/">Main website</a> at UTHSC</li>
-                        <!--<li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>-->
+                        <li><a href="http://genenetwork.org/">Main website</a> at UTHSC</li>
+                        <!--<li><a href="http://test-genenetwork.org/">Testing website</a> at UTHSC</li>-->
                       </ul>
                     <h3>GeneNetwork v1:</h3>
                     <ul>
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 4492dd3f..25af7bb1 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -137,6 +137,7 @@
 
     <script>
         elements_list = {{ elements | safe }}
+        gn2_url       = "{{ gn2_url | safe }}"
     </script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>