From 0dfdbcbb83ffe9b349c870d02a5812bcb296a74b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 4 Dec 2020 14:57:02 -0600
Subject: Added option to toggle columns on show_trait page, including case
 attribute columns

---
 wqflask/wqflask/templates/show_trait.html          | 27 +++++++++++++++++++
 .../wqflask/templates/show_trait_edit_data.html    | 30 ++++++++++++++++++++++
 2 files changed, 57 insertions(+)

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..3923ad2f 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -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>
-- 
cgit v1.2.3


From 18d01454548f7fb30f6fc24d9d8fb38840e76901 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 12:18:26 +0300
Subject: replace datatatable/jquery.js in templates

---
 wqflask/wqflask/templates/admin/create_group.html      | 4 +++-
 wqflask/wqflask/templates/admin/search_for_groups.html | 4 +++-
 wqflask/wqflask/templates/ctl_results.html             | 4 +++-
 wqflask/wqflask/templates/network_graph.html           | 4 +++-
 wqflask/wqflask/templates/pair_scan_results.html       | 4 +++-
 5 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
index 5a6929fb..4ab70007 100644
--- a/wqflask/wqflask/templates/admin/create_group.html
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -80,7 +80,9 @@
 {% endblock %}
 
 {% block js %}
-    <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='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html
index f304a172..1df4d0a2 100644
--- a/wqflask/wqflask/templates/admin/search_for_groups.html
+++ b/wqflask/wqflask/templates/admin/search_for_groups.html
@@ -63,7 +63,9 @@
 {% endblock %}
 
 {% block js %}
-    <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='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
 
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index e374eb4e..7ce67d0e 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -64,7 +64,9 @@
         gn2_url = "{{ gn2_url | safe }}"
     </script>
 
-    <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='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='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>
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index be3d0402..33f0365b 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -140,7 +140,9 @@
         gn2_url       = "{{ gn2_url | safe }}"
     </script>
 
-    <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='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='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>
 
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index f1646af7..14a62e0d 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -64,7 +64,9 @@
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
-    <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='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
     <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/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
-- 
cgit v1.2.3


From 51b70d89d5b085b9f81e5da2b695873ca53e54f9 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 12:31:24 +0300
Subject: replace jszip lib in templates

---
 wqflask/wqflask/templates/collections/list.html   | 2 +-
 wqflask/wqflask/templates/collections/view.html   | 2 +-
 wqflask/wqflask/templates/correlation_page.html   | 2 +-
 wqflask/wqflask/templates/gsearch_gene.html       | 2 +-
 wqflask/wqflask/templates/gsearch_pheno.html      | 2 +-
 wqflask/wqflask/templates/search_result_page.html | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 9e0c0f07..b04672ec 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -69,7 +69,7 @@
     <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <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="/static/new/js_external/jszip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.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="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
     <script>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index ccec495b..afc47bc2 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -162,7 +162,7 @@
 {% endblock %}
 
 {% block js %}
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <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/plugins/sorting/natural.js') }}"></script>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 06ee9056..01789d67 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -171,7 +171,7 @@
     <script type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
 
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index d5bc4141..6fd0abe8 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -48,7 +48,7 @@
 {% block js %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <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="/static/new/js_external/jszip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.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="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index ccd4a9d9..0dc6fe5f 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -48,7 +48,7 @@
 {% block js %}
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <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="/static/new/js_external/jszip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.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="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 87c97c50..1a2d2112 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -183,7 +183,7 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
 
     <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="/static/new/js_external/jszip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.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="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
-- 
cgit v1.2.3


From 1c202735fc279f42e70d2cdef6ee8b9214ca0f44 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 12:41:44 +0300
Subject: replace colorbox jquery.colorbox  in templates

---
 wqflask/wqflask/templates/base.html | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index faa59deb..5c8343d1 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -254,7 +254,9 @@
     <script type="text/javascript" src="/static/new/js_external/json2.js"></script>
     <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.9.1/jquery-ui.min.js" type="text/javascript"></script>
 
-    <script language="javascript" type="text/javascript" src="/static/packages/colorbox/jquery.colorbox.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
     <!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
 
     <script type="text/javascript" src="/static/new/js_external/parsley.min.js"></script>
-- 
cgit v1.2.3


From 5fc3f0647beafc1290ede2f5242275c2f0e54ed9 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 12:57:10 +0300
Subject: replace jscolor lib in templates

---
 wqflask/wqflask/templates/corr_scatterplot.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 1133fcd2..145cfcf7 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -349,7 +349,7 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.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="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/jscolor.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jscolor/jscolor.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
-- 
cgit v1.2.3


From e96b568adbb0e3ac2c3e0b1ab72d0bfd354db6a7 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:00:42 +0300
Subject: replace cytoscape js in templates

---
 wqflask/wqflask/templates/ctl_results.html   | 2 +-
 wqflask/wqflask/templates/network_graph.html | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index e374eb4e..20935612 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -67,7 +67,7 @@
     <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="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/js/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>
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index be3d0402..017298b9 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -144,7 +144,7 @@
     <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="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/js/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>
-- 
cgit v1.2.3


From 8666d17de2a0b9e20be82f115df9af8d5693dbae Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:02:30 +0300
Subject: replace cytoscape-panzoom js in templates

---
 wqflask/wqflask/templates/ctl_results.html   | 2 +-
 wqflask/wqflask/templates/network_graph.html | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 20935612..28d462ee 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -68,7 +68,7 @@
     <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="{{ url_for('js', filename='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-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>
 
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 017298b9..1c0eabee 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -145,7 +145,7 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.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="/js/cytoscape-panzoom/cytoscape-panzoom.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>
 
-- 
cgit v1.2.3


From 5ae193d969c0e21bdd02de577d00f8c8b8ba8148 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:04:30 +0300
Subject: replace cytoscape panzoom css in templates

---
 wqflask/wqflask/templates/ctl_results.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 28d462ee..17390d96 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. */
-- 
cgit v1.2.3


From 2554b98807701d5026dc365b301da62617e88b69 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:06:42 +0300
Subject: replace ctyoscape-qtip js in templates

---
 wqflask/wqflask/templates/ctl_results.html   | 2 +-
 wqflask/wqflask/templates/network_graph.html | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 17390d96..f90ee20c 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -70,7 +70,7 @@
     <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/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 1c0eabee..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. */
@@ -147,7 +147,7 @@
     <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?
-- 
cgit v1.2.3


From db8e71d7146cb9859aaac4a38beb729b019c37f8 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:13:46 +0300
Subject: replace nouislider js in templates

---
 wqflask/wqflask/templates/show_trait.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..469ba1af 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -148,7 +148,7 @@
     <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 type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='nouislider/nouislider.js') }}"></script>
 
     <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
     <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
-- 
cgit v1.2.3


From 423b0ce832e7fd5ce52a9383491756e66835f62a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:15:55 +0300
Subject: replace nouislider  css in templates

---
 wqflask/wqflask/templates/show_trait.html | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 469ba1af..07fb1209 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -7,8 +7,7 @@
     <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='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" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='nouislider/nouislider.min.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 
 {% endblock %}
-- 
cgit v1.2.3


From fabd1049a3d79833ee204e3bf6791526a8770b54 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:35:18 +0300
Subject: replace ckeditor in templates

---
 wqflask/wqflask/templates/docedit.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/docedit.html b/wqflask/wqflask/templates/docedit.html
index b87c5b41..50bb96c0 100644
--- a/wqflask/wqflask/templates/docedit.html
+++ b/wqflask/wqflask/templates/docedit.html
@@ -16,7 +16,7 @@
 			{{content|safe}}
         </textarea>
         <button class="submit_changes" style="margin-top: 20px;">Submit Changes</button>
-        <script src="/static/packages/ckeditor/ckeditor.js"></script>
+        <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='ckeditor/ckeditor.js') }}"></script>
         <script type="text/javascript">
             CKEDITOR.replace('ckcontent',	{
                 height: '650px',
-- 
cgit v1.2.3


From 050b5c2cfe21753c07fef818f5b6fbf22a42a3e2 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:38:56 +0300
Subject: replace purescript_genome_browser in templates

---
 wqflask/wqflask/templates/mapping_results.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 9542c29d..7332f450 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -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 }}
-- 
cgit v1.2.3


From 1878e066c2c4b4d2a2369aeedd23f12dbfe83524 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:43:01 +0300
Subject: replace purescript-genome-browser css in templates

---
 wqflask/wqflask/templates/mapping_results.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 7332f450..4c7452fe 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" />
 
-- 
cgit v1.2.3


From 506ef2eb500660ca7b16fcc99801b3c7e7a0f309 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 17:27:30 +0300
Subject: replace datatable-scroller in templates

---
 wqflask/wqflask/templates/show_trait.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..25aa6230 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -147,7 +147,7 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.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 type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
+   <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/scroller.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
 
     <script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
-- 
cgit v1.2.3


From 1bb40a56dd5a0a3d526284385835fb51c290c394 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 17:38:37 +0300
Subject: add replace colorbox css

---
 wqflask/wqflask/static/new/css/colorbox.css | 238 ++++++++++++++++++++++++++++
 wqflask/wqflask/templates/base.html         |   2 +-
 2 files changed, 239 insertions(+), 1 deletion(-)
 create mode 100644 wqflask/wqflask/static/new/css/colorbox.css

diff --git a/wqflask/wqflask/static/new/css/colorbox.css b/wqflask/wqflask/static/new/css/colorbox.css
new file mode 100644
index 00000000..8b9fb388
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/colorbox.css
@@ -0,0 +1,238 @@
+/*
+    Colorbox Core Style:
+    The following CSS is consistent between example themes and should not be altered.
+*/
+#colorbox,
+#cboxOverlay,
+#cboxWrapper {
+    position: absolute;
+    top: 0;
+    left: 0;
+    z-index: 9999;
+    overflow: hidden;
+}
+
+#cboxOverlay {
+    position: fixed;
+    width: 100%;
+    height: 100%;
+}
+
+#cboxMiddleLeft,
+#cboxBottomLeft {
+    clear: left;
+}
+
+#cboxContent {
+    position: relative;
+}
+
+#cboxLoadedContent {
+    overflow: auto;
+    -webkit-overflow-scrolling: touch;
+}
+
+#cboxTitle {
+    margin: 0;
+}
+
+#cboxLoadingOverlay,
+#cboxLoadingGraphic {
+    position: absolute;
+    top: 0;
+    left: 0;
+    width: 100%;
+    height: 100%;
+}
+
+#cboxPrevious,
+#cboxNext,
+#cboxClose,
+#cboxSlideshow {
+    cursor: pointer;
+}
+
+.cboxPhoto {
+    float: left;
+    margin: auto;
+    border: 0;
+    display: block;
+    max-width: none;
+    -ms-interpolation-mode: bicubic;
+}
+
+.cboxIframe {
+    width: 100%;
+    height: 100%;
+    display: block;
+    border: 0;
+}
+
+#colorbox,
+#cboxContent,
+#cboxLoadedContent {
+    box-sizing: content-box;
+    -moz-box-sizing: content-box;
+    -webkit-box-sizing: content-box;
+}
+
+/* 
+    User Style:
+    Change the following styles to modify the appearance of Colorbox.  They are
+    ordered & tabbed in a way that represents the nesting of the generated HTML.
+*/
+#cboxOverlay {
+    background: #fff;
+}
+
+#colorbox {
+    outline: 0;
+}
+
+#cboxTopLeft {
+    width: 25px;
+    height: 25px;
+    background: url(images/border1.png) no-repeat 0 0;
+}
+
+#cboxTopCenter {
+    height: 25px;
+    background: url(images/border1.png) repeat-x 0 -50px;
+}
+
+#cboxTopRight {
+    width: 25px;
+    height: 25px;
+    background: url(images/border1.png) no-repeat -25px 0;
+}
+
+#cboxBottomLeft {
+    width: 25px;
+    height: 25px;
+    background: url(images/border1.png) no-repeat 0 -25px;
+}
+
+#cboxBottomCenter {
+    height: 25px;
+    background: url(images/border1.png) repeat-x 0 -75px;
+}
+
+#cboxBottomRight {
+    width: 25px;
+    height: 25px;
+    background: url(images/border1.png) no-repeat -25px -25px;
+}
+
+#cboxMiddleLeft {
+    width: 25px;
+    background: url(images/border2.png) repeat-y 0 0;
+}
+
+#cboxMiddleRight {
+    width: 25px;
+    background: url(images/border2.png) repeat-y -25px 0;
+}
+
+#cboxContent {
+    background: #fff;
+    overflow: hidden;
+}
+
+.cboxIframe {
+    background: #fff;
+}
+
+#cboxError {
+    padding: 50px;
+    border: 1px solid #ccc;
+}
+
+#cboxLoadedContent {
+    margin-bottom: 20px;
+}
+
+#cboxTitle {
+    position: absolute;
+    bottom: 0px;
+    left: 0;
+    text-align: center;
+    width: 100%;
+    color: #999;
+}
+
+#cboxCurrent {
+    position: absolute;
+    bottom: 0px;
+    left: 100px;
+    color: #999;
+}
+
+#cboxLoadingOverlay {
+    background: #fff url(images/loading.gif) no-repeat 5px 5px;
+}
+
+/* these elements are buttons, and may need to have additional styles reset to avoid unwanted base styles */
+#cboxPrevious,
+#cboxNext,
+#cboxSlideshow,
+#cboxClose {
+    border: 0;
+    padding: 0;
+    margin: 0;
+    overflow: visible;
+    width: auto;
+    background: none;
+}
+
+/* avoid outlines on :active (mouseclick), but preserve outlines on :focus (tabbed navigating) */
+#cboxPrevious:active,
+#cboxNext:active,
+#cboxSlideshow:active,
+#cboxClose:active {
+    outline: 0;
+}
+
+#cboxSlideshow {
+    position: absolute;
+    bottom: 0px;
+    right: 42px;
+    color: #444;
+}
+
+#cboxPrevious {
+    position: absolute;
+    bottom: 0px;
+    left: 0;
+    color: #444;
+}
+
+#cboxNext {
+    position: absolute;
+    bottom: 0px;
+    left: 63px;
+    color: #444;
+}
+
+#cboxClose {
+    position: absolute;
+    bottom: 0;
+    right: 0;
+    display: block;
+    color: #444;
+}
+
+/*
+  The following fixes a problem where IE7 and IE8 replace a PNG's alpha transparency with a black fill
+  when an alpha filter (opacity change) is set on the element or ancestor element.  This style is not applied to or needed in IE9.
+  See: http://jacklmoore.com/notes/ie-transparency-problems/
+*/
+.cboxIE #cboxTopLeft,
+.cboxIE #cboxTopCenter,
+.cboxIE #cboxTopRight,
+.cboxIE #cboxBottomLeft,
+.cboxIE #cboxBottomCenter,
+.cboxIE #cboxBottomRight,
+.cboxIE #cboxMiddleLeft,
+.cboxIE #cboxMiddleRight {
+    filter: progid:DXImageTransform.Microsoft.gradient(startColorstr=#00FFFFFF, endColorstr=#00FFFFFF);
+}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 5c8343d1..b0d22277 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -17,7 +17,7 @@
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" />
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css"  />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/colorbox.css"  />
     <!--<link rel="stylesheet" type="text/css" href="/static/new/css/main.css"  />-->
     <link rel="stylesheet" type="text/css" href="/static/new/css/parsley.css"  />
 
-- 
cgit v1.2.3


From 16c1566041d4f871d2b4904392260261a7ee99f3 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 17:47:38 +0300
Subject: add buttons.datatables css

---
 wqflask/wqflask/templates/admin/group_manager.html        | 2 +-
 wqflask/wqflask/templates/admin/manage_user.html          | 2 +-
 wqflask/wqflask/templates/admin/set_group_privileges.html | 2 +-
 wqflask/wqflask/templates/admin/view_group.html           | 2 +-
 wqflask/wqflask/templates/set_group_privileges.html       | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index c8ed6851..c0b99e75 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -2,7 +2,7 @@
 {% block title %}Group Manager{% endblock %}
 {% block 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/DataTables/extensions/buttons.dataTables.css">
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
diff --git a/wqflask/wqflask/templates/admin/manage_user.html b/wqflask/wqflask/templates/admin/manage_user.html
index 7afe075f..3ef90b90 100644
--- a/wqflask/wqflask/templates/admin/manage_user.html
+++ b/wqflask/wqflask/templates/admin/manage_user.html
@@ -2,7 +2,7 @@
 {% block title %}View and Edit Group{% endblock %}
 {% block 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/DataTables/extensions/buttons.dataTables.css">
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
diff --git a/wqflask/wqflask/templates/admin/set_group_privileges.html b/wqflask/wqflask/templates/admin/set_group_privileges.html
index bc52788f..04842453 100644
--- a/wqflask/wqflask/templates/admin/set_group_privileges.html
+++ b/wqflask/wqflask/templates/admin/set_group_privileges.html
@@ -2,7 +2,7 @@
 {% block title %}Set Group Privileges{% endblock %}
 {% block 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/DataTables/extensions/buttons.dataTables.css">
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html
index 9e3cce7b..26692fe8 100644
--- a/wqflask/wqflask/templates/admin/view_group.html
+++ b/wqflask/wqflask/templates/admin/view_group.html
@@ -2,7 +2,7 @@
 {% block title %}View and Edit Group{% endblock %}
 {% block 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/DataTables/extensions/buttons.dataTables.css">
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
diff --git a/wqflask/wqflask/templates/set_group_privileges.html b/wqflask/wqflask/templates/set_group_privileges.html
index 98b0cc12..a0a53292 100644
--- a/wqflask/wqflask/templates/set_group_privileges.html
+++ b/wqflask/wqflask/templates/set_group_privileges.html
@@ -2,7 +2,7 @@
 {% block title %}Set Group Privileges{% endblock %}
 {% block 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/DataTables/extensions/buttons.dataTables.css">
+     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
-- 
cgit v1.2.3


From 8bf342d5d02b4023814a79605c3f5f23a7ea67a0 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 22:08:41 +0300
Subject: add
 cytocape.min.js,cytoscape-panzoom.js,cytoscape.js-panzoom.css,cytoscape-qtip.js
 to mechanical rob

---
 test/requests/link_checker.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..5bc30798 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,11 @@ 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/cytoscape/cytoscape.min.js",
+        "/js/cytoscape-panzoom/cytoscape-panzoom.js",
+        "/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
+        "/js/cytoscape-qtip/cytoscape-qtip.js",
+
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From d0a3db3851bc2895a8775b1dc7c01a92f9c8c85c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 7 Dec 2020 14:22:54 -0600
Subject: Changed the logic in create_trait so that permissions should always
 be set, and added an assert that 'name' is passed instead of using if/else,
 since it should always be passed

---
 wqflask/base/trait.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index ec8c40a0..50bd8874 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -25,19 +25,19 @@ def create_trait(**kw):
     assert bool(kw.get('dataset')) != bool(
         kw.get('dataset_name')), "Needs dataset ob. or name"
 
-    if kw.get('name'):
-        if kw.get('dataset_name'):
-            if kw.get('dataset_name') != "Temp":
-                dataset = create_dataset(kw.get('dataset_name'))
-        else:
-            dataset = kw.get('dataset')
+    assert bool(kw.get('name')), "Needs trait name"
 
+    if kw.get('dataset_name'):
         if kw.get('dataset_name') != "Temp":
-            if dataset.type == 'Publish':
-                permissions = check_resource_availability(
-                    dataset, kw.get('name'))
-            else:
-                permissions = check_resource_availability(dataset)
+            dataset = create_dataset(kw.get('dataset_name'))
+    else:
+        dataset = kw.get('dataset')
+
+    if dataset.type == 'Publish':
+        permissions = check_resource_availability(
+            dataset, kw.get('name'))
+    else:
+        permissions = check_resource_availability(dataset)
 
     if "view" in permissions['data']:
         the_trait = GeneralTrait(**kw)
-- 
cgit v1.2.3


From bf08713e14dad10f7af6637e8cd4e52025e33e3e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 7 Dec 2020 14:23:52 -0600
Subject: Fixed issue where the correlation scatterplot link wasn't being
 displayed after the recent correlation table changes

Fixed issue where the Sample p(r/rho) sort wasn't sorting using scientific notation, which resulted in the initial sort being bad
---
 wqflask/wqflask/templates/correlation_page.html | 39 +++++++++++++++++++------
 1 file changed, 30 insertions(+), 9 deletions(-)

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 06ee9056..68566ee5 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -345,8 +345,15 @@
                       'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
                       'type': "natural-minus-na",
                       'width': "40px",
-                      'data': "sample_r",
-                      'orderSequence': [ "desc", "asc"]
+                      'data': null,
+                      'orderSequence': [ "desc", "asc"],
+                      'render': function(data, type, row, meta) {
+                        if (data.sample_r != "N/A") {
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                        } else {
+                          return data.sample_r
+                        }
+                      }
                     },
                     {
                       'title': "N",
@@ -357,7 +364,7 @@
                     },
                     {
                       'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
-                      'type': "natural-minus-na",
+                      'type': "scientific",
                       'width': "65px",
                       'data': "sample_p",
                       'orderSequence': [ "desc", "asc"]
@@ -459,8 +466,15 @@
                       'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
                       'type': "natural-minus-na",
                       'width': "40px",
-                      'data': "sample_r",
-                      'orderSequence': [ "desc", "asc"]
+                      'data': null,
+                      'orderSequence': [ "desc", "asc"],
+                      'render': function(data, type, row, meta) {
+                        if (data.sample_r != "N/A") {
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                        } else {
+                          return data.sample_r
+                        }
+                      }
                     },
                     {
                       'title': "N",
@@ -471,7 +485,7 @@
                     },
                     {
                       'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
-                      'type': "natural-minus-na",
+                      'type': "scientific",
                       'width': "65px",
                       'data': "sample_p",
                       'orderSequence': [ "desc", "asc"]
@@ -506,8 +520,15 @@
                       'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
                       'type': "natural-minus-na",
                       'width': "40px",
-                      'data': "sample_r",
-                      'orderSequence': [ "desc", "asc"]
+                      'data': null,
+                      'orderSequence': [ "desc", "asc"],
+                      'render': function(data, type, row, meta) {
+                        if (data.sample_r != "N/A") {
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+                        } else {
+                          return data.sample_r
+                        }
+                      }
                     },
                     {
                       'title': "N",
@@ -518,7 +539,7 @@
                     },
                     {
                       'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
-                      'type': "natural-minus-na",
+                      'type': "scientific",
                       'width': "65px",
                       'data': "sample_p",
                       'orderSequence': [ "desc", "asc"]
-- 
cgit v1.2.3


From b3b2a6a6792896c59b8dbbd3bbe1bf8c650b223e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 12:56:22 +0300
Subject: add ckeditor to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..5888146d 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,7 @@ 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/ckeditor/ckeditor.js",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 971cf481a125a7da763a818a06dea946b6e5e81f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 12:59:01 +0300
Subject: add purescript-genetics-browser.js to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..ed28aaf0 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,7 @@ 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",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 1995fbcf19645feaa1aabbab921e90c6877b4c4d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 12:59:51 +0300
Subject: add purescript-genetics-browser.css

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index ed28aaf0..f19ee155 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -117,6 +117,7 @@ def check_packaged_js_files(args_obj, parser):
         "/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",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 233ad63b9cdd6d80895bf551a4ec11d6649728ea Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 13:02:32 +0300
Subject: add nouislider.min.css to mechanical-rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..8c73d20a 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,7 @@ 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",
+        "/css/nouislider/nouislider.min.css",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 2f8ba729e65960478b09f5ad64699831004310f8 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 13:03:44 +0300
Subject: add nouislider.js to mechanical-rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 8c73d20a..81bf4792 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -117,6 +117,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/qtip2/jquery.qtip.min.js",
         "/js/js_alt/md5.min.js",
         "/css/nouislider/nouislider.min.css",
+        "/js/nouislider/nouislider.js",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 7122dcbd014e463e7b90b74d8c40f520b1064710 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 13:43:03 +0300
Subject: add jscolor to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..7ee0dfb2 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,7 @@ 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/jscolor/jscolor.js",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From ece54a359552c55c359115d2a7c4949bafda874d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 13:48:08 +0300
Subject: scroller.dataTables.min.js to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..2716434a 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -103,6 +103,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/DataTablesExtensions/colResize/dataTables.colResize.js",
         "/js/DataTablesExtensions/colReorder/js/dataTables.colReorder.js",
         "/js/DataTablesExtensions/buttons/js/buttons.colVis.min.js",
+        "/js/DataTablesExtensions/scroller/js/scroller.dataTables.min.js",
         "/js/DataTables/js/jquery.dataTables.js",
         "/css/DataTablesExtensions/scroller/css/scroller.dataTables.min.css",
         # Datatables plugins:
-- 
cgit v1.2.3


From bc66593b6ac99e74b0949e23fe6a6f3fc2c9cae5 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 13:55:18 +0300
Subject: add datatablejquery to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 2716434a..069dc025 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -117,6 +117,7 @@ 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/DataTables/js/jquery.js",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 20e4b1e2599dc641aa9d3a08b8686a3953bd1165 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 13:57:38 +0300
Subject: add jquery.datatables css to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 069dc025..2cde3252 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -118,6 +118,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/qtip2/jquery.qtip.min.js",
         "/js/js_alt/md5.min.js",
         "/js/DataTables/js/jquery.js",
+        "/css/DataTables/css/jquery.dataTables.css",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From dd69862d269c4adbba0e524965c2b967bfc243fe Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 14:03:56 +0300
Subject: add jquery.colorbox-min.js to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..3cc3fc9d 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,7 @@ 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/colorbox/jquery.colorbox-min.js",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From cec8e3078784abf0224b23592d56745a09d7060f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 14:17:57 +0300
Subject: add jszip to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..dd0bbb65 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,7 @@ 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/jszip/jszip.min.js",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 713e1798256c01ab8b29f2f6209987091d8b08bf Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 16:15:59 +0300
Subject: remove duplicate lib in templates/base.html

---
 wqflask/wqflask/templates/base.html | 2 --
 1 file changed, 2 deletions(-)

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index b0d22277..95a2c39e 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -255,8 +255,6 @@
     <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.9.1/jquery-ui.min.js" type="text/javascript"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
-<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
-<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
     <!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
 
     <script type="text/javascript" src="/static/new/js_external/parsley.min.js"></script>
-- 
cgit v1.2.3


From 6de952648e36e7382ca692066aadbc48d613fb3c Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 16:40:20 +0300
Subject: remove duplicate libs

---
 wqflask/wqflask/templates/admin/create_group.html      | 2 --
 wqflask/wqflask/templates/admin/search_for_groups.html | 2 --
 wqflask/wqflask/templates/ctl_results.html             | 4 +---
 wqflask/wqflask/templates/network_graph.html           | 5 +----
 wqflask/wqflask/templates/pair_scan_results.html       | 2 --
 5 files changed, 2 insertions(+), 13 deletions(-)

diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
index 4ab70007..38ae834c 100644
--- a/wqflask/wqflask/templates/admin/create_group.html
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -81,8 +81,6 @@
 
 {% block js %}
      <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html
index 1df4d0a2..0e1ec720 100644
--- a/wqflask/wqflask/templates/admin/search_for_groups.html
+++ b/wqflask/wqflask/templates/admin/search_for_groups.html
@@ -64,8 +64,6 @@
 
 {% block js %}
      <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
 
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 7ce67d0e..5b8a4cc2 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -64,9 +64,7 @@
         gn2_url = "{{ gn2_url | safe }}"
     </script>
 
-     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='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>
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 33f0365b..06937293 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -139,10 +139,7 @@
         elements_list = {{ elements | safe }}
         gn2_url       = "{{ gn2_url | safe }}"
     </script>
-
-     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='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>
 
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index 14a62e0d..a706403b 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -65,8 +65,6 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
      <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
     <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/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
-- 
cgit v1.2.3


From f09b3780ca8845a887db0c75564c76bd9a38bb64 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 15:02:42 +0300
Subject: replace d3-tip css in templates

---
 wqflask/wqflask/templates/comparison_bar_chart.html | 2 +-
 wqflask/wqflask/templates/correlation_matrix.html   | 2 +-
 wqflask/wqflask/templates/heatmap.html              | 2 +-
 wqflask/wqflask/templates/pair_scan_results.html    | 2 +-
 wqflask/wqflask/templates/show_trait.html           | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

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/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/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 3923ad2f..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" />
-- 
cgit v1.2.3


From 97eecd445a1f006400ba162a848353ca5435148a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 15:03:12 +0300
Subject: add d3-tip.css to mechanical rob

---
 test/requests/link_checker.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 6ac26ba7..3e83991a 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -116,6 +116,7 @@ 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",
+        "/css/d3-tip/d3-tip.css",
     ]
 
     print("Checking links")
-- 
cgit v1.2.3


From 61b0f112e75c22ff34aebcfa3f9361f575133b60 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 8 Dec 2020 13:19:50 -0600
Subject: Show the total number of markers in the mapping results table instead
 of just the trimmed number

---
 wqflask/wqflask/marker_regression/run_mapping.py | 8 ++++++--
 wqflask/wqflask/templates/mapping_results.html   | 5 ++++-
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index c474e0e0..891fcc66 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -426,6 +426,8 @@ class RunMapping(object):
                               marker['display_pos'] = "N/A"
                           self.qtl_results.append(marker)
 
+              total_markers = len(self.qtl_results)
+
               with Bench("Exporting Results"):
                   export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
 
@@ -489,13 +491,15 @@ class RunMapping(object):
                       perm_results = self.perm_output,
                       significant = significant_for_browser,
                       browser_files = browser_files,
-                      selected_chr = this_chr
+                      selected_chr = this_chr,
+                      total_markers = total_markers
                   )
               else:
                 self.js_data = dict(
                     chr_lengths = chr_lengths,
                     browser_files = browser_files,
-                    selected_chr = this_chr
+                    selected_chr = this_chr,
+                    total_markers = total_markers
                 )
 
     def run_rqtl_plink(self):
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 9542c29d..1130bcce 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -388,8 +388,11 @@
                     "targets": 0,
                     "orderable": false
                 } ],
+                "language": {
+                  "info": "Showing1 from _START_ to _END_ of " + js_data.total_markers + " records",
+                },
                 "order": [[1, "asc" ]],
-                "sDom": "RZtir",
+                "sDom": "iRZtir",
                 "iDisplayLength": -1,
                 "autoWidth": false,
                 "deferRender": true,
-- 
cgit v1.2.3


From 03c2ec3eddfaf5279a008b7408c8dc2ccfd57d47 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 8 Dec 2020 13:31:57 -0600
Subject: Added hover text for BNW buttons

---
 wqflask/wqflask/templates/collections/view.html   | 2 +-
 wqflask/wqflask/templates/correlation_page.html   | 2 +-
 wqflask/wqflask/templates/search_result_page.html | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index ccec495b..50e1a792 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -44,7 +44,7 @@
               GeneWeaver
             </button>
 
-            <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+            <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" >
               BNW
            </button>
 
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 68566ee5..3cca7495 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -49,7 +49,7 @@
               GeneWeaver
             </button>
 
-            <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+            <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" >
               BNW
            </button>
 
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 87c97c50..6be60f64 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -92,7 +92,7 @@
                   GeneWeaver
                 </button>
 
-                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+                <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" >
                   BNW
                </button>
 
-- 
cgit v1.2.3