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

10 files changed, 79 insertions, 15 deletions

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..dfac58d3 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,13 @@ def check_packaged_js_files(args_obj, parser):
         "/js/nvd3/nv.d3.min.css",
         "/js/qtip2/jquery.qtip.min.js",
         "/js/js_alt/md5.min.js",
+        "/js/purescript-genome-browser/js/purescript-genetics-browser.js",
+        "/js/purescript-genome-browser/css/purescript-genetics-browser.css",
+        "/js/cytoscape/cytoscape.min.js",
+        "/js/cytoscape-panzoom/cytoscape-panzoom.js",
+        "/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
+        "/js/cytoscape-qtip/cytoscape-qtip.js",
+        "/css/d3-tip/d3-tip.css",
     ]
 
     print("Checking links")
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index f791457f..b27a6b06 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% block title %}Comparison Bar Chart{% endblock %}
 {% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 {% block content %} <!-- Start of body -->
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 4e150618..96ad9c35 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -4,7 +4,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
 {% endblock %}
 {% block content %}
 
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index e374eb4e..f90ee20c 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" />
-    <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='cytoscape-panzoom/cytoscape.js-panzoom.css') }}">
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}">
     <style>
         /* The Cytoscape Web container must have its dimensions set. */
@@ -67,10 +67,10 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='qtip2/jquery.qtip.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="/js/cytoscape/cytoscape.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-panzoom/cytoscape-panzoom.js') }}"></script>
     <!-- should be using cytoscape-popper for tips, see docs -->
-    <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-qtip/cytoscape-qtip.js') }}"></script>
 
     <!--
          Loads flash - who wants that?
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index 497838dd..b16de42e 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% block title %}Heatmap{% endblock %}
 {% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 {% block content %} <!-- Start of body -->
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 1130bcce..70df1dde 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -4,7 +4,7 @@
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
-    <link rel="stylesheet" type="text/css" href="/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='purescript-genome-browser/css/purescript-genetics-browser.css') }}" />
 
     <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
 
@@ -359,7 +359,7 @@
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='purescript-genome-browser/js/purescript-genetics-browser.js') }}"></script>
 
     <script>
         js_data = {{ js_data | safe }}
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index be3d0402..3c2ec601 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" />
-    <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='cytoscape-panzoom/cytoscape.js-panzoom.css') }}">
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}">
     <style>
         /* The Cytoscape Web container must have its dimensions set. */
@@ -144,10 +144,10 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='qtip2/jquery.qtip.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
 
-    <script language="javascript" type="text/javascript" src="/js/cytoscape/cytoscape.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-panzoom/cytoscape-panzoom.js') }}"></script>
     <!-- should be using cytoscape-popper for tips, see docs -->
-    <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-qtip/cytoscape-qtip.js') }}"></script>
 
     <!--
         Loads flash - who wants that?
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index f1646af7..d64bb4b4 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -4,7 +4,7 @@
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='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" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..07efbe62 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -5,7 +5,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
@@ -221,6 +221,33 @@
                   primary_table.search($(this).val()).draw();
                 } );
 
+                $('.toggle-vis').on('click', function (e) {
+                    e.preventDefault();
+
+                    function toggle_column(column) {
+                        //ZS: Toggle column visibility
+                        column.visible( ! column.visible() );
+                        if (column.visible()){
+                            $(this).removeClass("active");
+                        } else {
+                            $(this).addClass("active");
+                        }
+                    }
+
+                    // Get the column API object
+                    var target_cols = $(this).attr('data-column').split(",")
+                    for (let i = 0; i < target_cols.length; i++){
+                        console.log("THE COL:", target_cols[i])
+                        var column = primary_table.column( target_cols[i] );
+                        toggle_column(column);
+
+                        {% if sample_groups|length != 1 %}
+                        var column2 = other_table.column( target_cols[i] );
+                        toggle_column(column2);
+                        {% endif %}
+                    }
+                } );
+
                 {% if sample_groups|length != 1 %}
                 $('#other_searchbox').on( 'keyup', function () {
                   other_table.search($(this).val()).draw();
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 2e730248..4ad11a5e 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,6 +1,36 @@
 <div>
     {% for sample_type in sample_groups %}
       <div class="sample-table-container">
+        {% if loop.index == 1 %}
+        <b>Show/Hide Columns:</b>
+        <br>
+        <button class="toggle-vis" data-column="1">ID</button>
+        <button class="toggle-vis" data-column="2">Sample</button>
+        <button class="toggle-vis" data-column="3">Value</button>
+        {% if sample_groups[0].se_exists %}
+        <button class="toggle-vis" data-column="4,5">SE</button>
+        {% if has_num_cases %}
+        <button class="toggle-vis" data-column="6">N</button>
+        {% set attr_start_pos = 7 %}
+        {% else %}
+        {% set attr_start_pos = 6 %}
+        {% endif %}
+        {% else %}
+        {% if has_num_cases %}
+        <button class="toggle-vis" data-column="4">N</button>
+        {% set attr_start_pos = 5 %}
+        {% else %}
+        {% set attr_start_pos = 4 %}
+        {% endif %}
+        {% endif %}
+        {% if sample_groups[0].attributes %}
+        {% for attribute in sample_groups[0].attributes %}
+        <button class="toggle-vis" data-column="{{ loop.index + attr_start_pos - 1 }}">{{ sample_groups[0].attributes[attribute].name }}</button>
+        {% endfor %}
+        {% endif %}
+        <br>
+        <br>
+        {% endif %}
         <div class="sample-table-search-container">
           <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control sample-table-search" placeholder="Search This Table For ...">
         </div>