Made a bunch of cosmetic changes to various pages and fixed a couple searches

11 files changed, 130 insertions, 126 deletions

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 8bd5919b..d734117e 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -193,7 +193,7 @@ class CorrelationMatrix(object):
         m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
         eigen = base.eigen(m)
         print("eigen:", eigen)
-        #pca = stats.princomp(m, cor = "TRUE")
+        pca = stats.princomp(m, cor = "TRUE")
         print("pca:", pca)
 
         return pca
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index f9082495..fd7bd916 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -96,7 +96,7 @@ class QuickMrnaAssaySearch(DoSearch):
 
 
 class MrnaAssaySearch(DoSearch):
-    """A search within an mRNA expression dataset"""
+    """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites"""
 
     DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch"
 
@@ -358,7 +358,7 @@ class RifSearch(MrnaAssaySearch):
     def run(self):
         where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and
             MATCH (GeneRIF_BASIC.comment)
-            AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term)
+            AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term[0])
 
         from_clause = ", GeneRIF_BASIC "
         query = self.compile_final_query(from_clause, where_clause)
@@ -375,8 +375,8 @@ class WikiSearch(MrnaAssaySearch):
             and GeneRIF.versionId=0 and GeneRIF.display>0
             and (GeneRIF.comment REGEXP '%s' or GeneRIF.initial = '%s')
                 """ % (self.dataset.type,
-                       "[[:<:]]"+self.search_term[0]+"[[:>:]]",
-                       self.search_term[0])
+                       "[[:<:]]"+str(self.search_term[0])+"[[:>:]]",
+                       str(self.search_term[0]))
 
         from_clause = ", GeneRIF "
         query = self.compile_final_query(from_clause, where_clause)
@@ -390,7 +390,7 @@ class GoSearch(MrnaAssaySearch):
 
     def run(self):
         field = 'GOterm.acc'
-        go_id = 'GO:' + ('0000000'+self.search_term)[-7:]
+        go_id = 'GO:' + ('0000000'+self.search_term[0])[-7:]
 
         statements = ("""%s.symbol=GOgene_product.symbol and
            GOassociation.gene_product_id=GOgene_product.id and
@@ -651,8 +651,9 @@ class PositionSearch(DoSearch):
                                                               self.dataset.type,
                                                               max(self.mb_min, self.mb_max))
 
-    def real_run(self):
+    def run(self):
 
+        self.setup()
         self.query = self.compile_final_query(where_clause = self.where_clause)
 
         return self.execute(self.query)
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
index 0bf1f944..3dc73a7a 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
@@ -1038,7 +1038,7 @@ h2,
 .h2,
 h3,
 .h3 {
-  margin-top: 20px;
+  margin-top: 10px;
   margin-bottom: 10px;
 }
 h1 small,
@@ -1080,27 +1080,27 @@ h6 .small,
 }
 h1,
 .h1 {
-  font-size: 36px;
+  font-size: 30px;
 }
 h2,
 .h2 {
-  font-size: 30px;
+  font-size: 24px;
 }
 h3,
 .h3 {
-  font-size: 24px;
+  font-size: 18px;
 }
 h4,
 .h4 {
-  font-size: 18px;
+  font-size: 14px;
 }
 h5,
 .h5 {
-  font-size: 14px;
+  font-size: 12px;
 }
 h6,
 .h6 {
-  font-size: 12px;
+  font-size: 10px;
 }
 p {
   margin: 0 0 10px;
@@ -2884,7 +2884,7 @@ fieldset[disabled] .btn-default.active {
 }
 .btn-primary {
   color: #fff;
-  background-color: #428bca;
+  background-color: #369;
   border-color: #357ebd;
 }
 .btn-primary:hover,
@@ -3872,7 +3872,7 @@ select[multiple].input-group-sm > .input-group-btn > .btn {
 }
 .navbar {
   position: relative;
-  min-height: 50px;
+  min-height: 30px;
   border: 1px solid transparent;
 }
 /*
@@ -3987,10 +3987,10 @@ select[multiple].input-group-sm > .input-group-btn > .btn {
 }
 .navbar-brand {
   float: left;
-  height: 50px;
-  padding: 15px 15px;
-  font-size: 18px;
-  line-height: 20px;
+  height: 30px;
+  padding: 6px 15px;
+  font-size: 15px;
+  line-height: 18px;
 }
 .navbar-brand:hover,
 .navbar-brand:focus {
@@ -4738,8 +4738,8 @@ a.thumbnail.active {
   color: #333;
 }
 .alert {
-  padding: 15px;
-  margin-bottom: 20px;
+  padding: 10px;
+  margin-bottom: 5px;
   border: 1px solid transparent;
   border-radius: 4px;
 }
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/docs.css b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
index ea4d6994..b95c44ed 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/docs.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
@@ -27,7 +27,7 @@ h3 code {
 -------------------------------------------------- */
 
 body > .navbar {
-  font-size: 14px;
+  font-size: 12px;
   font-weight: bold;
 }
 
@@ -98,16 +98,16 @@ hr.soften {
 
 }
 .jumbotron h1 {
-  font-size: 80px;
+  font-size: 60px;
   font-weight: bold;
   letter-spacing: -1px;
   line-height: 1;
 }
 .jumbotron p {
-  font-size: 20px;
+  font-size: 15px;
   font-weight: 300;
-  line-height: 30px;
-  margin-bottom: 30px;
+  line-height: 20px;
+  margin-bottom: 10px;
 }
 
 /* Link styles (used on .masthead-links as well) */
@@ -230,10 +230,10 @@ hr.soften {
   border-bottom: 1px solid #ddd;
 }
 .subhead h1 {
-  font-size: 40px;
+  font-size: 30px;
 }
 .subhead p {
-  margin-bottom: 20px;
+  margin-bottom: 10px;
 }
 .subhead .navbar {
   display: none;
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
index c3a11092..076b6dae 100644
--- a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
@@ -13,7 +13,7 @@ body {
 
 /* Finesse the page header spacing */
 .page-header {
-  margin-bottom: 30px;
+  margin-bottom: 10px;
 }
 .page-header .lead {
   margin-bottom: 10px;
@@ -68,7 +68,7 @@ body {
   float: left;
 }
 .navbar-nav > li > a {
-  padding: 15px;
+  padding: 5px;
 }
 
 /* Redeclare since we override the float above */
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 240481cc..3d4e6d28 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -42,7 +42,6 @@
 {% macro flash_me() -%}
     {% with messages = get_flashed_messages(with_categories=true) %}
         {% if messages %}
-        <br />
         <div class="container">
             {% for category, message in messages %}
                 <div class="alert {{ category }}">{{ message }}</div>
@@ -72,7 +71,7 @@
                 <div>
                     <ul class="nav navbar-nav">
                         <li class="">
-                            <a href="/">Home</a>
+                            <a href="/">Search</a>
                         </li>
                         <li class="">
                             <a href="/help">Help</a>
@@ -143,7 +142,6 @@
             <a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
             <a href="http://www.python.org/">python</a> and good intentions.
         </p>
-        <p>Special thanks to CYP1A2 and AHR.</p>
         <br />
         <p>GeneNetwork is supported by:</p>
         <UL>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 237a0d4e..3d777866 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -1,5 +1,10 @@
 {% extends "base.html" %}
 {% block title %}View Collection{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+{% endblock %}
 {% block content %}
 <!-- Start of body -->
     {% if uc %}
@@ -10,13 +15,7 @@
             'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }}
     {% endif %}
     <div class="container">
-        <div class="page-header">
-            <h1>Your Collection</h1>
-            {% if uc %}
-            <h2>{{ uc.name }}</h2>
-            {% endif %}
-
-            <div class="form-group">
+        <div>
             {% if uc %}
             <form action="/collections/delete" method="post">
                 {% if uc %}
@@ -51,40 +50,18 @@
                     <input type="submit" class="btn btn-primary" value="Heatmap" />
                 </div>
             </form>
-            </div>
-
-            <!--
-            <form action="/corr_matrix" method="post">
-                {% if uc %}
-                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-                {% endif %}
-                <input type="hidden" name="trait_list" id="trait_list" value= "
-                {% for this_trait in trait_obs %}
-                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
-                {% endfor %}" >
-                <input type="submit"
-                       class="btn btn-small"
-                       value="Correlation Matrix" />
-            </form>
-            <form action="/heatmap" method="post">
-                {% if uc %}
-                <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
-                {% endif %}
-                <input type="hidden" name="trait_list" id="trait_list" value= "
-                {% for this_trait in trait_obs %}
-                    {{ this_trait.name }}:{{ this_trait.dataset.name }},
-                {% endfor %}" >
-                <input type="submit"
-                       class="btn btn-small"
-                       value="Heatmap" />
-            </form>
-            -->
         </div>
 
-
-
-        <div class="bs-docs-example">
-        <table class="table table-hover" id='trait_table'>
+        <div>
+            <br />
+            <br />
+            <br />
+            <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
+            <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
+            <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
+            <br />
+            <br />
+        <table class="table table-hover table-striped" id='trait_table'>
             <thead>
                 <tr>
                     <th></th>
@@ -126,15 +103,7 @@
             </tbody>
 
         </table>
-
         <br />
-
-        <button class="btn" id="select_all"><i class="icon-ok"></i> Select All</button>
-        <button class="btn" id="deselect_all"><i class="icon-remove"></i> Deselect All</button>
-        <button class="btn" id="invert"><i class="icon-resize-vertical"></i> Invert</button>
-        <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Add Record to Other Collection</button>
-        <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
-        <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
         </div>
     </div>
 
@@ -144,4 +113,48 @@
 
 {% block js %}
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+    <script language="javascript" type="text/javascript">
+        $(document).ready( function () {
+            console.time("Creating table");
+            $('#trait_table').dataTable( {
+                "aoColumns": [
+                    { "bSortable": false },
+                    { "sType": "natural" },
+                    { "sType": "natural",
+                      "sWidth": "35%"  },
+                    { "sType": "natural",
+                      "sWidth": "15%"  },
+                    { "sType": "cust-txt" },
+                    { "sType": "natural",
+                      "sWidth": "10%"  },
+                    { "sType": "natural",
+                      "sWidth": "15%"  },
+                    { "sType": "cust-txt" }
+                ],
+                "columns": [
+                    { "width": "50%" },
+                    null,
+                    null,
+                    null,
+                    null,
+                    null
+                ],
+                "sDom": "ftir",
+                "iDisplayLength": -1,
+                "autoWidth": true,
+                "bLengthChange": true,
+                "bDeferRender": true,
+                "bSortClasses": false
+            } );
+            console.timeEnd("Creating table");
+        });
+        
+    </script>
+
+
 {% endblock %}
+
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 1caca702..adc004a5 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -16,7 +16,7 @@
         
         {{ flash_me() }}
         
-        <div class="row" style="width: 1200px !important;">
+        <div class="row" style="width: 1400px !important;">
 
             <div class="col-xs-5 col-xs-5">
                 <section id="search">
@@ -72,15 +72,20 @@
                                 </div>
 
                                 <!--  GET ANY HELP   -->
+                                <div class="form-group">
+                                    <label for="tfor" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+                                    <div class="col-xs-10 controls">
+                                        <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>
+                                </div>
 
-                                <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>
 
-                                <!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
+                                <!--  SEARCH, MAKE DEFAULT -->
 
                                 <div class="form-group">
 
@@ -90,9 +95,6 @@
                                     <div class="col-xs-4 controls" style="width: 150px !important;">
                                         <input id="make_default" type="submit" class="btn btn-default form-control" value="Make Default">
                                     </div>
-                                    <div class="col-xs-5 controls" style="width: 200px !important;">
-                                        <input type="submit" class="btn btn-default form-control" value="Advanced Search">
-                                    </div>
                                 </div>
 
                                 <input type="hidden" name="FormID" value="searchResult" class="form-control">
@@ -113,12 +115,16 @@
                     <p>To try them out copy these examples into the search field:</p>
 
                       <ul>
-                        <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
+                        <!--<li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
                         chromosome 1 between 25 and 30 Mb.</li>
 
                         <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
                         highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
-                        linkage between 23 and 46.</li>
+                        linkage between 23 and 46.</li>-->
+
+                        <li><b>MEAN=(15 16)</b> finds highly expressed genes (15 to 16 log2 units).</li>
+
+                        <li><b>LRS=(23 46)</b> finds genes with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a> linkage between 23 and 46.</li>
 
                         <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
                         GeneRIF</a> links.</li>
@@ -127,7 +133,7 @@
                         GeneWiki</a> for genes that you or other users have annotated
                         with the word <i>nicotine</i>.</li>
 
-                        <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
+                        <!--<li><b>GO:0045202</b> searches for synapse-associated genes listed in the
                         <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
                             Gene Ontology</a>.</li>
 
@@ -139,9 +145,10 @@
                         <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
                         finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
                         trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
-                        scores between 9 and 999.</li>
+                        scores between 9 and 999.</li>-->
                       </ul>
                 </section>
+                <!--
                 <section id="tour-info">
                     <div class="page-header">
                         <h1>Tour and more info</h1>
@@ -167,6 +174,7 @@
                       and advice on their use and citation.</p>
 
                 </section>
+                -->
 
                 <section id="websites">
                     <div class="page-header">
@@ -214,17 +222,6 @@
                         <li><a href="http://genenetwork.epfl.ch/" target="_blank">
                         Switzerland</a> at the EPFL</li>
                     </ul>
-                    <h3>History and archive</h3>
-
-                    <p>The
-                    <a href="http://artemis.uthsc.edu" target="_blank">
-                        time machine</a>
-                    has earlier versions that correspond to specific publication dates.
-                    </p>
-
-                    <h3>The next generation</h3>
-                       <p>Try the <a href="http://alexandria.uthsc.edu/" target="_blank">
-                      development</a> site to explore experimental data and features.</p>
                 </section>
 
                 <!--<section id="getting-started">
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 61df445c..ecf8278c 100755
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -13,7 +13,7 @@
             <h4>Don't have an account?</h4>
 
 
-            <a href="/n/register" class="btn btn-info modalize">Create a new account</a>
+            <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
 
 
             <hr />
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 5e63a237..055ab979 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -14,9 +14,15 @@
 
         <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
 
-        <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a></p>
+        <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a>
+           to find all records that match
+                {% for word in search_terms %}
+                    <strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}
+                {% endfor %}.
+
+        </p>
 
-        <p>To find all records that match:</p>
+        <!--
         <ul>
             {% if search_terms %}
             <li>
@@ -26,9 +32,9 @@
             </li>
             {% endif %}
         </ul>
+        -->
 
-        <p>To study a record, click on its ID below.<br />
-        Check records below and click Add button to add to selection.</p>
+        <p>To study a record, click on its ID below. Check records below and click Add button to add to selection.</p>
 
         <div>
             <br />
@@ -174,7 +180,7 @@
                     null,
                     null
                 ],
-                "sDom": "ftir",
+                "sDom": "tir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bLengthChange": true,
@@ -205,7 +211,7 @@
                     null,
                     null
                 ],
-                "sDom": "ftir",
+                "sDom": "tir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bLengthChange": true,
diff --git a/wqflask/wqflask/templates/whats_new.html b/wqflask/wqflask/templates/whats_new.html
index dca9e7b3..753c0d7d 100755
--- a/wqflask/wqflask/templates/whats_new.html
+++ b/wqflask/wqflask/templates/whats_new.html
@@ -3,25 +3,14 @@
 {% block content %}
 <!-- Start of body -->
 
-	<TR>
-		<TD bgColor=#eeeeee class="solidBorder">
-            <Table width= "100%" cellSpacing=0 cellPadding=5><TR>
                 <!-- Body Start from Here -->
-                <TD valign="top" height="200" width="100%" bgcolor="#eeeeee">
-
-                <P class="title">Latest Updates and News from Genenetwork  <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P>
-
-
+                <P class="title">Latest Updates and News from Genenetwork </P>
                 {% for news_item in news_items %}
                     <h4>{{ news_item.title }} ({{ news_item.date }})</h4>
                     {{ news_item.details | safe }}
                     <br /><br />
                 {% endfor %}
 
-            <p />
-
-		</TD>
-	</TR>