minor template fixes

2 files changed, 99 insertions, 165 deletions

diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html
index b9fe1656..caaf6300 100644
--- a/wqflask/wqflask/templates/ctl_setup.html
+++ b/wqflask/wqflask/templates/ctl_setup.html
@@ -1,86 +1,69 @@
 {% extends "base.html" %}
 {% block title %}CTL analysis{% endblock %}
-
-{% block content %} <!-- Start of body -->
+{% block content %}
+<!-- Start of body -->
 <div class="container">
-  {% if request.form['trait_list'].split(",")|length < 2 %}
-  <div class="alert alert-danger" role="alert">
-    <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
-    <span class="sr-only">Error:</span>
-    <h2>Too few traits as input</h2>
-    Please make sure you select enough traits to perform CTL. Your collection needs to contain at least 2 different traits. You provided {{request.form['trait_list'].split(',')|length}} traits as input.
-  </div>
-  {% else %}
-  <h1>CTL analysis</h1>
-  CTL analysis is published as open source software, if you are using this method in your publications, please cite:<br><br>
-  Arends D, Li Y, Brockmann GA, Jansen RC, Williams RW, Prins P<br>
-  Correlation trait locus (CTL) mapping: Phenotype network inference subject to genotype.<br>
-  The Journal of Open Source Software (2016)<br>
-  Published in <a href="http://joss.theoj.org/papers/10.21105/joss.00087"><img src="http://joss.theoj.org/papers/10.21105/joss.00087/status.svg"></a>
-  <br><br>
-
-    <form class="col-md-8" action="/ctl_results" method="post" class="form-horizontal" id="ctl_form">
-
-
-      <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
-
-      <div class="form-group row">
-      <label for="Strategy" class="col-md-3 col-form-label col-form-label-sm">Strategy</label>
-      <div class="col-md-9">
-        <select  class="form-control col-md-9" name="strategy" id="strategy">
-          <option value="Exact">Exact</option>
-          <option value="Full">Full</option>
-          <option value="Pairwise">Pairwise</option>
-        </select>
-      </div>
+    {% if request.form['trait_list'].split(",")|length < 2 %} <div class="alert alert-danger" role="alert">
+        <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
+        <span class="sr-only">Error:</span>
+        <h2>Too few traits as input</h2>
+        Please make sure you select enough traits to perform CTL. Your collection needs to contain at least 2 different traits. You provided {{request.form['trait_list'].split(',')|length}} traits as input.
+</div>
+{% else %}
+<h1>CTL analysis</h1>
+CTL analysis is published as open source software, if you are using this method in your publications, please cite:<br><br>
+Arends D, Li Y, Brockmann GA, Jansen RC, Williams RW, Prins P<br>
+Correlation trait locus (CTL) mapping: Phenotype network inference subject to genotype.<br>
+The Journal of Open Source Software (2016)<br>
+Published in <a href="http://joss.theoj.org/papers/10.21105/joss.00087"><img src="http://joss.theoj.org/papers/10.21105/joss.00087/status.svg"></a>
+<br><br>
+<form class="col-md-8" action="/ctl_results" method="post" class="form-horizontal" id="ctl_form">
+    <input type="hidden" name="trait_list" id="trait_list" value="{{request.form['trait_list']}}">
+    <div class="form-group row">
+        <label for="Strategy" class="col-md-3 col-form-label col-form-label-sm">Strategy</label>
+        <div class="col-md-9">
+            <select class="form-control col-md-9" name="strategy" id="strategy">
+                <option value="Exact">Exact</option>
+                <option value="Full">Full</option>
+                <option value="Pairwise">Pairwise</option>
+            </select>
+        </div>
     </div>
-
-
-        <div class="form-group row">
-          <label for="corType" class="col-md-3 col-form-label col-form-label-sm">Types of correlation coefficients:</label>
-          <div class="col-md-9">
+    <div class="form-group row">
+        <label for="corType" class="col-md-3 col-form-label col-form-label-sm">Types of correlation coefficients:</label>
+        <div class="col-md-9">
             <select class="form-control  col-md-9" name="parametric" id="parametric">
-            <option value="False">spearman</option>
-            <option value="True">pearson</option>
-          </select>
-          </div>
-
+                <option value="False">spearman</option>
+                <option value="True">pearson</option>
+            </select>
         </div>
-
-
-            <div class="form-group row">
-      <label for="Permutations" class="col-md-3 col-form-label col-form-label-sm">Number of permutation <span style="color:red;">(Used when strategy is Full or Pairwise)</span></label>
-      <div class="col-md-9">
-        <select class="form-control" name="nperm" id="nperm">
-          <option value="100">100</option>
-          <option value="1000" selected="selected">1000</option>
-          <option value="10000">10000</option>
-        </select>
-      </div>
     </div>
-
-
     <div class="form-group row">
-      <label for="Significance" class="col-md-3 col-form-label col-form-label-sm"> Significance level</label>
-      <div class="col-md-9">
-        <select  class="form-control" name="significance" id="significance">
-          <option value="0.1">0.1</option>
-          <option value="0.05" selected="selected">0.05</option>
-          <option value="0.001">0.001</option>
-        </select>
-      </div>
-      
+        <label for="Permutations" class="col-md-3 col-form-label col-form-label-sm">Number of permutation <span style="color:red;">(Used when strategy is Full or Pairwise)</span></label>
+        <div class="col-md-9">
+            <select class="form-control" name="nperm" id="nperm">
+                <option value="100">100</option>
+                <option value="1000" selected="selected">1000</option>
+                <option value="10000">10000</option>
+            </select>
+        </div>
     </div>
-
-        <div class="form-group">
-            <div class="text-center">
-                <input type="submit" class="btn btn-primary" value="Run CTL using these settings" />
-            </div>
+    <div class="form-group row">
+        <label for="Significance" class="col-md-3 col-form-label col-form-label-sm"> Significance level</label>
+        <div class="col-md-9">
+            <select class="form-control" name="significance" id="significance">
+                <option value="0.1">0.1</option>
+                <option value="0.05" selected="selected">0.05</option>
+                <option value="0.001">0.001</option>
+            </select>
+        </div>
+    </div>
+    <div class="form-group">
+        <div class="text-center">
+            <input type="submit" class="btn btn-primary" value="Run CTL using these settings" />
         </div>
-
-
-
-    </form>
+    </div>
+</form>
 {% endif %}
 </div>
-{% endblock %}
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/gn3_ctl_results.html b/wqflask/wqflask/templates/gn3_ctl_results.html
index 08944b0f..ca45fe76 100644
--- a/wqflask/wqflask/templates/gn3_ctl_results.html
+++ b/wqflask/wqflask/templates/gn3_ctl_results.html
@@ -1,119 +1,72 @@
 {% extends "base.html" %}
 {% block title %}Ctl results{% endblock %}
 {% block content %}
-
 <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
-
 <link REL="stylesheet" TYPE="text/css" href="{{ url_for('css', filename='bootstrap/css/bootstrap.css') }}" />
 <link rel="stylesheet" href="https://cdn.datatables.net/1.11.3/css/jquery.dataTables.min.css">
-
 <style type="text/css">
-    
-
 .carousel-control-next,
-.carousel-control-prev /*, .carousel-indicators */ {
+.carousel-control-prev
+
+/*, .carousel-indicators */
+    {
     filter: invert(100%);
 }
-
-
 </style>
 <div style="margin-top:10px">
     <div>
-
         <div style="text-align: center;">
-        <h3>CTL/QTL Plots for Individual Traits</h3>
-         <h4> {{ctl_plots|length}} phenotypes as input</h4>
-            
+            <h3>CTL/QTL Plots for Individual Traits</h3>
+            <h4> {{ctl_plots|length}} phenotypes as input</h4>
+        </div>
+        <div id="carouselExampleControls" class="carousel slide" data-interval="false">
+            <div class="carousel-inner">
+                {% for ctl_plot in ctl_plots %}
+                <div class="item{% if loop.index == 1 %} active{% endif %}">
+                    <img style="width:1000px;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ ctl_plot | safe }}" alt="First slide">
+                </div>
+                {% endfor %}
+                <a class="carousel-control-prev" href="#carouselExampleControls" role="button" data-slide="prev">
+                    <span class="carousel-control-prev-icon" aria-hidden="true"></span>
+                    <span class="sr-only">Previous</span>
+                </a>
+                <a class="carousel-control-next" href="#carouselExampleControls" role="button" data-slide="next">
+                    <span class="carousel-control-next-icon" aria-hidden="true"></span>
+                    <span class="sr-only">Next</span>
+                </a>
+            </div>
         </div>
-
-
-    <div id="carouselExampleControls" class="carousel slide"  data-interval="false">
-  <div class="carousel-inner">
-
-    {% for ctl_plot in ctl_plots %}
-
-
-    <div class="item{% if loop.index == 1 %} active{% endif %}">
-      <img style="width:1000px;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ ctl_plot | safe }}" alt="First slide">
-    </div>
-
-    {% endfor %}
-
-      <a class="carousel-control-prev" href="#carouselExampleControls" role="button" data-slide="prev">
-    <span class="carousel-control-prev-icon" aria-hidden="true"></span>
-    <span class="sr-only">Previous</span>
-  </a>
-  <a class="carousel-control-next" href="#carouselExampleControls" role="button" data-slide="next">
-    <span class="carousel-control-next-icon" aria-hidden="true"></span>
-    <span class="sr-only">Next</span>
-  </a>
-
-  </div>
-
-</div>
-
-
     </div>
-
-        <div >
-
+    <div>
         <div style="text-align:center;">
-        <h2 >Ctl line plot</h2>
-         <h4>Plot the CTL for genome-wide CTL on all traits (the output of CTLscan).</h4>
-            
+            <h2>Ctl line plot</h2>
+            <h4>Plot the CTL for genome-wide CTL on all traits (the output of CTLscan).</h4>
         </div>
-
-        <div class="row">   
-               <div class="col-8">
-                   
-         
-                    <img style="width:100%;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ image_data | safe }}">
-
-
-                </div>
-
-
-
-                    <div class= "col-4">
-                        
-                        <ol style="height: 100%;display:flex;flex-direction: column;align-items: center;justify-content: center;">
-
-                            {% for trait in  phenotypes %}
-
-
-                            {% set trait_data = trait.split(':') %}
-                            
-
-                            <li><a href="/show_trait?trait_id={{trait_data[0]}}&dataset={{trait_data[1]}}">{{trait_data[0]}}</a></li>
-
-
-                            {% endfor %}
-                        </ol>
-                    </div>
-            
+        <div class="row">
+            <div class="col-8">
+                <img style="width:100%;height: 600px;" class="center-block" src="data:image/jpeg;base64,{{ image_data | safe }}">
+            </div>
+            <div class="col-4">
+                <ol style="height: 100%;display:flex;flex-direction: column;align-items: center;justify-content: center;">
+                    {% for trait in phenotypes %}
+                    {% set trait_data = trait.split(':') %}
+                    <li><a href="/show_trait?trait_id={{trait_data[0]}}&dataset={{trait_data[1]}}">{{trait_data[0]}}</a></li>
+                    {% endfor %}
+                </ol>
+            </div>
         </div>
-
     </div>
     <h2 style="text-align:center">Significant CTL </h2>
     <table id="significance" width="80vw"></table>
-
     <div style="text-align: center;margin-top: 20px;">
         <h3 style="text-align:center;">Network figure</h3>
-
-        <div  style="margin-top: 20px;">
-
-<p>Use tools like cytoscape to visualize the network</p>
-
-<a href="/ctl_network_files/{{network_file_name}}/sif" class="btn btn-secondary btn-lg mx-2">Download Sif file</a>
-
-<a href="/ctl_network_files/{{network_file_name}}/nodes" class="btn btn-secondary btn-lg mx-2">Download Node file</a>
+        <div style="margin-top: 20px;">
+            <p>Use tools like cytoscape to visualize the network</p>
+            <a href="/ctl_network_files/{{network_file_name}}/sif" class="btn btn-secondary btn-lg mx-2">Download Sif file</a>
+            <a href="/ctl_network_files/{{network_file_name}}/nodes" class="btn btn-secondary btn-lg mx-2">Download Node file</a>
         </div>
     </div>
-
-
-
 </div>
-
 <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
 <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
@@ -121,8 +74,6 @@
 <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
 <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
 <script type="text/javascript">
-
-
 let { data_set_rows, col_names } = {{ significance_data | safe }}