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

14 files changed, 26 insertions, 22 deletions

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>