From 3c46a58f50f339ec56027db6d2108de5b21d63ac Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 Apr 2017 16:52:47 +0000
Subject: Fixed issue with correlation result trait links if target dataset is
 different from base dataset

Improved collection list and view table appearances

Added question mark image for glossary entries in table headers

Fixed issue where extra decimal place sometimes appeared in bar chart Y axis tick values
---
 wqflask/runserver.py                               |   3 ++
 .../wqflask/static/new/images/question_mark.jpg    | Bin 0 -> 47158 bytes
 wqflask/wqflask/static/new/javascript/bar_chart.js |  11 ++++++
 wqflask/wqflask/templates/collections/list.html    |   9 ++++-
 wqflask/wqflask/templates/collections/view.html    |   8 -----
 wqflask/wqflask/templates/correlation_page.html    |   2 +-
 wqflask/wqflask/templates/search_result_page.html  |  39 +++++++++++----------
 7 files changed, 43 insertions(+), 29 deletions(-)
 create mode 100644 wqflask/wqflask/static/new/images/question_mark.jpg

diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index a6ae28af..50805643 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -11,6 +11,9 @@ import logging
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
+import signal
+signal.signal(signal.SIGPIPE, signal.SIG_DFL)
+
 BLUE  = '\033[94m'
 GREEN = '\033[92m'
 BOLD  = '\033[1m'
diff --git a/wqflask/wqflask/static/new/images/question_mark.jpg b/wqflask/wqflask/static/new/images/question_mark.jpg
new file mode 100644
index 00000000..82df7e81
Binary files /dev/null and b/wqflask/wqflask/static/new/images/question_mark.jpg differ
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js
index 7ec35148..d8540580 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.js
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.js
@@ -253,6 +253,17 @@
             })())
           ]);
           console.log("values: ", values);
+
+          decimal_exists = "False";
+          for(i=0; i < values.length; i++){
+              if (values[i]['y'] % 1 != 0){
+                  decimal_exists = "True";
+                  break;
+              }
+          }
+          if (decimal_exists == "False"){
+              _this.chart.yAxis.tickFormat(d3.format('d'))
+          }
           d3.select("#bar_chart_container svg").datum([
             {
               values: values
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 5a30c98c..b1284895 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -51,7 +51,7 @@
             <tbody>
             {% for uc in collections %}
                 <tr class="collection_line">
-                    <td style="padding-right: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
+                    <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
                     <td align="right">{{ loop.index }}
                     {% if g.user_session.user_ob %}
                     <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
@@ -89,6 +89,13 @@
     {% endif %}
     <script>
             $('#trait_table').dataTable( {
+                "drawCallback": function( settings ) {
+                     $('#trait_table tr').click(function(event) {
+                         if (event.target.type !== 'checkbox') {
+                             $(':checkbox', this).trigger('click');
+                         }
+                     });
+                },
                 "columns": [
                     { "type": "natural", "width": "3%" },
                     { "type": "natural", "width": "8%" },
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 094bc273..cae03b4a 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -181,14 +181,6 @@
                     {
                         extend: 'columnsToggle',
                         columns: ':not(:first-child)',
-                        columnText: function ( dt, idx, title ) {
-                            console.log("TITLE:", title)
-                            if (title == "Additive Effect  ?"){
-                                return "Additive Effect"
-                            } else {
-                                return title;
-                            }
-                        },
                         postfixButtons: [ 'colvisRestore' ]
                     }
                 ],
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 3bde7dc7..f5fe2120 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -104,7 +104,7 @@
                         <td>
                             <a href="{{ url_for('show_trait_page',
                                     trait_id = trait.name,
-                                    dataset = dataset.name
+                                    dataset = trait.dataset.name
                                     )}}">
                                 {{ trait.name }}
                             </a>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index d4ec18e3..93e24cc7 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -77,16 +77,16 @@
           {% endif %}
 -->
 
-          <div id="table_container" style="width: {% if dataset.type == 'ProbeSet' %}1300{% elif dataset.type == 'Publish' %}1200{% elif dataset.type == 'Geno' %}500{% endif %}px;">
+          <div id="table_container" style="width: {% if dataset.type == 'ProbeSet' %}1300{% elif dataset.type == 'Publish' %}1300{% elif dataset.type == 'Geno' %}400{% endif %}px;">
             <table class="display dataTable nowrap" id='trait_table' style="float: left;">
                 <thead>
                     <tr>
                         <th></th>
                     {% for header in header_fields %}
                         {% if header == 'Max LRS' %}
-                        <th data-export="Max LRS">Max LRS</th>
+                        <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                         {% elif header == 'Additive Effect' %}
-                        <th data-export="Additive Effect">Additive <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                         {% else %}
                         <th data-export="{{header}}">{{header}}</th>
                         {% endif %}
@@ -99,9 +99,9 @@
                         <th></th>
                     {% for header in header_fields %}
                         {% if header == 'Max LRS' %}
-                        <th data-export="Max LRS">Max LRS</th>
+                        <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                         {% elif header == 'Additive Effect' %}
-                        <th data-export="Additive Effect">Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                         {% else %}
                         <th data-export="{{header}}">{{header}}</th>
                         {% endif %}
@@ -252,6 +252,7 @@
                      $('.trait_checkbox:checkbox').on("change", change_buttons);
                 },
                 "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(0).attr('style', 'padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;');
                     $('td', row).eq(1).attr('align', 'right');
                     $('td', row).eq(1).attr('data-export', index+1);
                     $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text());
@@ -281,12 +282,12 @@
                     { "type": "natural", "width": "2%" },
                     { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "6%" },
+                    { "type": "natural" },
                     { "type": "natural", "width": "30%" },
-                    { "type": "natural", "width": "25%" },
                     { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "6%" },
                     { "type": "natural", "width": "10%" },
-                    { "type": "natural", "width": "9%" }
+                    { "type": "natural", "width": "8%" }
                 ],
                 "columnDefs": [ {
                     "targets": 0,
@@ -295,8 +296,7 @@
                 "order": [[1, "asc" ]],
                 buttons: [
                     {
-                        extend: 'colvis',
-                        text: 'Show or Hide Columns',
+                        extend: 'columnsToggle',
                         columns: ':not(:first-child)',
                         postfixButtons: [ 'colvisRestore' ]
                     }
@@ -306,10 +306,10 @@
                 "autoWidth": false,
                 "deferRender": true,
                 "bSortClasses": false,
-                "scrollY": "600px",
-                "scrollCollapse": true,
-                "scroller": true,
-                "paging": false
+                "scrollCollapse": false,
+                "scroller": false,
+                "paging": false,
+                "orderClasses": true
             } );
             {% elif dataset.type == 'Geno' %}
             $('#trait_table').DataTable( {
@@ -322,6 +322,7 @@
                      $('.trait_checkbox:checkbox').on("change", change_buttons);
                 },
                 "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(0).attr('style', 'padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;');
                     $('td', row).eq(1).attr('align', 'right');
                     $('td', row).eq(1).attr('data-export', index+1);
                     $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text());
@@ -329,10 +330,10 @@
                 },
                 "data": json_trait_list,
                 "columns": [
-                    { "type": "natural", "width": "8%" },
+                    { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "12%" },
-                    { "type": "natural", "width": "40%" },
-                    { "type": "natural", "width": "40%"}
+                    { "type": "natural" },
+                    { "type": "natural", "width": "30%"}
                 ],
                 "columnDefs": [ {
                     "targets": 0,
@@ -341,8 +342,7 @@
                 "order": [[1, "asc" ]],
                 buttons: [
                     {
-                        extend: 'colvis',
-                        text: 'Show or Hide Columns',
+                        extend: 'columnsToggle',
                         columns: ':not(:first-child)',
                         postfixButtons: [ 'colvisRestore' ]
                     }
@@ -355,7 +355,8 @@
                 "scrollY": "600px",
                 "scrollCollapse": true,
                 "scroller": true,
-                "paging": false
+                "paging": false,
+                "orderClasses": true
             } );
             {% endif %}
 
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