Fixed some aesthetic issues on the main page and removed references to TemplatePage

7 files changed, 39 insertions, 62 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index ade2d242..aa37c29e 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -45,7 +45,6 @@ from utility.THCell import THCell
 from utility.TDCell import TDCell
 from base.trait import GeneralTrait
 from base import data_set
-from base.templatePage import templatePage
 from utility import webqtlUtil, helper_functions, corr_result_helpers
 from dbFunction import webqtlDatabaseFunction
 import utility.webqtlUtil #this is for parallel computing only.
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index d734117e..e1df5b24 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -48,7 +48,6 @@ from utility.THCell import THCell
 from utility.TDCell import TDCell
 from base.trait import GeneralTrait
 from base import data_set
-from base.templatePage import templatePage
 from utility import webqtlUtil, helper_functions, corr_result_helpers
 from dbFunction import webqtlDatabaseFunction
 import utility.webqtlUtil #this is for parallel computing only.
diff --git a/wqflask/wqflask/dataSharing/SharingInfoPage.py b/wqflask/wqflask/dataSharing/SharingInfoPage.py
index 7ad44440..c32eec50 100755
--- a/wqflask/wqflask/dataSharing/SharingInfoPage.py
+++ b/wqflask/wqflask/dataSharing/SharingInfoPage.py
@@ -32,7 +32,6 @@ import urlparse
 
 import flask
 
-from base.templatePage import templatePage
 from base import webqtlConfig
 from dbFunction import webqtlDatabaseFunction
 import SharingBody
@@ -42,10 +41,9 @@ import SharingInfo
 #########################################
 #      Sharing Info Page
 #########################################
-class SharingInfoPage(templatePage):
+class SharingInfoPage():
 
     def __init__(self, fd):
-        templatePage.__init__(self, fd)
         self.redirect_url = None   # Set if you want a redirect
         print("fd is:", pf(fd.__dict__))
         # Todo: Need a [0] in line below????d
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 11fd2644..929f5abb 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -19,7 +19,6 @@ from utility import webqtlUtil, Plot, Bunch, helper_functions
 from base.trait import GeneralTrait
 from base import data_set
 from dbFunction import webqtlDatabaseFunction
-from base.templatePage import templatePage
 from basicStatistics import BasicStatisticsFunctions
 
 from pprint import pformat as pf
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/docs.css b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
index b95c44ed..2d6a713c 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/docs.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
@@ -25,25 +25,28 @@ h3 code {
 
 /* Tweak navbar brand link to be super sleek
 -------------------------------------------------- */
-
+/*
 body > .navbar {
   font-size: 12px;
   font-weight: bold;
 }
+*/
 
 /* Change the docs' brand */
-body > .navbar .brand {
-  padding-right: 0;
-  padding-left: 0;
+
+body > .navbar .navbar-brand {
+  padding-right: 20px;
+  padding-left: 20px;
   margin-left: 20px;
   float: left;
   font-weight: bold;
-  color: #336699;
+  color: #ffffff;
   text-shadow: 0 1px 0 rgba(255,255,255,.1), 0 0 30px rgba(255,255,255,.125);
   -webkit-transition: all .2s linear;
      -moz-transition: all .2s linear;
           transition: all .2s linear;
 }
+
 body > .navbar .brand:hover {
   text-decoration: none;
   text-shadow: 0 1px 0 rgba(255,255,255,.1), 0 0 30px rgba(255,255,255,.4);
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 3d4e6d28..462a59a2 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -74,6 +74,13 @@
                             <a href="/">Search</a>
                         </li>
                         <li class="">
+                            <a href="/collections/list">Collections
+                                {% if g.user_session.user_ob %}
+                                <span class="badge badge-info">{{ g.user_session.user_ob.display_num_collections() }}</span>
+                                {% endif %}
+                            </a>
+                        </li>
+                        <li class="">
                             <a href="/help">Help</a>
                         </li>
                         <li class="">
@@ -92,14 +99,6 @@
                             <a href="/environments">Environments</a>
                         </li>
                         <li class="">
-                            <a href="/collections/list">Collections
-                                {% if g.user_session.user_ob %}
-                                <span class="badge badge-info">{{ g.user_session.user_ob.display_num_collections() }}</span>
-                                {% endif %}
-                            </a>
-                        </li>
-
-                        <li class="">
                             {% if g.user_session.logged_in %}
                             <a id="login_out" title="Signed in as {{ g.user_session.user_ob.name_and_org }}." href="/n/logout">Sign out</a>
                             {% else %}
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 538a6799..ba017bfb 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -29,19 +29,19 @@
 
                                 <div class="form-group">
                                     <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
-                                    <div class="col-xs-10 controls">
+                                    <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
                                         <div class="col-xs-8">
                                           <select name="species" id="species" class="form-control selectpicker span3" style="width: 280px !important;"></select>
                                         </div>
                                         <div class="col-xs-4">
-                                          <input id="make_default" class="btn btn-default form-control" value="Make Default">
+                                          <input id="make_default" class="btn btn-primary form-control" value="Make Default">
                                         </div>
                                     </div>
                                 </div>
 
                                 <div class="form-group">
                                     <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
-                                    <div class="col-xs-4 controls input-append">
+                                    <div class="col-xs-10 controls input-append">
                                         <div class="col-xs-8">
                                           <select name="group" id="group" class="form-control selectpicker span3" style="width: 280px !important;"></select>
                                           <i class="icon-question-sign"></i>
@@ -51,7 +51,7 @@
 
                                 <div class="form-group">
                                     <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
-                                    <div class="col-xs-4 controls">
+                                    <div class="col-xs-10 controls">
                                         <div class="col-xs-8">
                                           <select name="type" id="type" class="form-control selectpicker span3" style="width: 280px !important;"></select>
                                         </div>
@@ -60,7 +60,7 @@
 
                                 <div class="form-group">
                                     <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
-                                    <div class="col-xs-4 controls input-append">
+                                    <div class="col-xs-10 controls input-append">
                                         <div class="col-xs-8">
                                           <select name="dataset" id="dataset" class="form-control selectpicker span5" style="width: 450px !important;"></select>
                                           <i class="icon-question-sign"></i>
@@ -86,15 +86,15 @@
 
                                 <!--  GET ANY HELP   -->
                                 <div class="form-group">
-                                    <label for="tfor" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+                                    <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
                                     <div class="col-xs-10 controls">
-                                        <div class="col-xs-10">
-                                          <p>Enter terms, genes, ID numbers in the
-                                             <b>Search</b> field<br>
-                                             Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
-                                             synap*)<br>
-                                             Use <b>quotes</b> for terms such as <i>"tyrosine
-                                             kinase"</i></p>
+                                        <div class="col-xs-2 controls" style="width: 100px !important;">
+                                            <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
+                                        </div>                                    
+                                        <div class="col-xs-9 controls">
+                                            Enter terms, genes, ID numbers in the <b>Search</b> field
+                                            Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*)
+                                            Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>
                                         </div>
                                     </div>
                                 </div>
@@ -103,10 +103,6 @@
                                 <!--  SEARCH, MAKE DEFAULT -->
 
                                 <div class="form-group">
-
-                                    <div class="col-xs-3 controls" style="width: 100px !important;">
-                                        <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
-                                    </div>
                                 </div>
 
                                 <input type="hidden" name="FormID" value="searchResult" class="form-control">
@@ -159,7 +155,7 @@
                       </ul>
                 </section>
             </div>
-            <div style="padding-left:120px" class="col-xs-6" style="width: 600px !important;">
+            <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
                 <!--
                 <section id="tour-info">
                     <div class="page-header">
@@ -207,32 +203,16 @@
 
                         <li>GeneNetwork Source Code at <a href="https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
                     </ul>
-                    <h3>Mirror and development sites</h3>
-                    <ul>
-                        <li><a href="http://www.genenetwork.org/" target="_blank">
-                        Main GN site</a> at UTHSC</li>
-
-                        <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
-                        Australia</a> at the UWA</li>
+                    <h3>GN1 Mirror and development sites</h3>
 
-                        <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
-                        California</a> at UCLA</li>
-
-                        <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
-                        Germany</a> at the HZI</li>
-
-                        <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
-                        Netherlands</a> at the Hubrecht
-                        (development)</li>
-
-                        <li><a href="http://genenetwork.memphis.edu/" target="_blank">
-                        Memphis</a> at the U of M</li>
-
-                        <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
-                        Singapore</a> at the NUS</li>
-
-                        <li><a href="http://genenetwork.epfl.ch/" target="_blank">
-                        Switzerland</a> at the EPFL</li>
+                    <ul>
+                        <li><a href="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN1 site at UTHSC</a> (main site)</li>
+                        <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
+                        <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
+                        <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
+                        <li><a href="http://genenetwork.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
+                        <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
+                        <li><a href="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
                     </ul>
                 </section>