From a57241a160757ac737658b33ea7cc8ad670a0e61 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 3 Dec 2020 00:01:52 +0300
Subject: add hide  empty column in table script

---
 .../static/new/javascript/auto_hide_column.js      | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 wqflask/wqflask/static/new/javascript/auto_hide_column.js

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
new file mode 100644
index 00000000..652b2ad7
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -0,0 +1,22 @@
+
+$(function (){
+$("table th").each(function(index,col_th){
+	var filter_counter = 0;
+	// map each column to row ie  column i to ith element
+	var column_tds = $(this).closest('table').find('tr td:nth-child(' + (index + 1) + ')')
+	column_tds.each(function(j,col_td){
+		if(this.innerHTML==''||this.innerHTML=="N/A"){
+			filter_counter+=1;
+		}
+		else{
+			// break
+			return false;
+		}
+	})
+	if (filter_counter == ($('table tr').length - 1)){
+		$(this).hide();
+        column_tds.hide();
+
+	}
+})
+})
\ No newline at end of file
-- 
cgit v1.2.3


From 8746f2e93fe889ac0ba9e801b3684764fffa2945 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 3 Dec 2020 00:04:52 +0300
Subject: add table row index

---
 wqflask/wqflask/static/new/javascript/auto_hide_column.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
index 652b2ad7..73b639dc 100644
--- a/wqflask/wqflask/static/new/javascript/auto_hide_column.js
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -1,10 +1,10 @@
 
 $(function (){
-$("table th").each(function(index,col_th){
+$("table th").each(function(th_index,col_th){
 	var filter_counter = 0;
 	// map each column to row ie  column i to ith element
 	var column_tds = $(this).closest('table').find('tr td:nth-child(' + (index + 1) + ')')
-	column_tds.each(function(j,col_td){
+	column_tds.each(function(td_index,col_td){
 		if(this.innerHTML==''||this.innerHTML=="N/A"){
 			filter_counter+=1;
 		}
-- 
cgit v1.2.3


From f199a59587bad2b20c4122562eb707931b045669 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 3 Dec 2020 00:47:54 +0300
Subject: add support for multiple tables

---
 .../static/new/javascript/auto_hide_column.js      | 37 +++++++++++-----------
 1 file changed, 18 insertions(+), 19 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
index 73b639dc..14348ccd 100644
--- a/wqflask/wqflask/static/new/javascript/auto_hide_column.js
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -1,22 +1,21 @@
+$(function(){
+	$("table").each(function(table){
+		$(this).find("th").each(function(col_index,col_th){
+			var filter_counter=0
+			var col_td=$(this).closest('table').find('tr td:nth-child(' + (col_index + 1) + ')')
+			col_td.each(function(td_index,col_td){
+				if(this.innerHTML==""||this.innerHTML=="N/A"){
+					filter_counter+=1
+				}
+				else{
+					return false
+				}
+			})
+			if (filter_counter==$(this).closest("table").find("tr").length-1){
+					$(this).hide();
+                   col_td.hide();
 
-$(function (){
-$("table th").each(function(th_index,col_th){
-	var filter_counter = 0;
-	// map each column to row ie  column i to ith element
-	var column_tds = $(this).closest('table').find('tr td:nth-child(' + (index + 1) + ')')
-	column_tds.each(function(td_index,col_td){
-		if(this.innerHTML==''||this.innerHTML=="N/A"){
-			filter_counter+=1;
-		}
-		else{
-			// break
-			return false;
-		}
+			}
+		})
 	})
-	if (filter_counter == ($('table tr').length - 1)){
-		$(this).hide();
-        column_tds.hide();
-
-	}
 })
-})
\ No newline at end of file
-- 
cgit v1.2.3


From 953727abb0b2c9075b486e3adfb13f029ebb00b1 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 3 Dec 2020 18:46:37 +0300
Subject: add datatable filter for empty  columns

---
 .../static/new/javascript/auto_hide_column.js      | 47 +++++++++++++---------
 1 file changed, 27 insertions(+), 20 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
index 14348ccd..94bb8a90 100644
--- a/wqflask/wqflask/static/new/javascript/auto_hide_column.js
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -1,21 +1,28 @@
-$(function(){
-	$("table").each(function(table){
-		$(this).find("th").each(function(col_index,col_th){
-			var filter_counter=0
-			var col_td=$(this).closest('table').find('tr td:nth-child(' + (col_index + 1) + ')')
-			col_td.each(function(td_index,col_td){
-				if(this.innerHTML==""||this.innerHTML=="N/A"){
-					filter_counter+=1
-				}
-				else{
-					return false
-				}
-			})
-			if (filter_counter==$(this).closest("table").find("tr").length-1){
-					$(this).hide();
-                   col_td.hide();
+function filterDatable(datatable){
+        let visitedColumns=[]
+        let columnCount=datatable.columns().header().length;
+        let numberOfRows=datatable.data().length;
+        for (let i=0;i<numberOfRows;i++){
+            if (visitedColumns.length==columnCount){
+                break;
+            }
+            let rowObj=datatable.rows(i).data()
+            rowObj.data().each(function(rowData,v){
+                if (visitedColumns.length==columnCount){
+                    return false;
+                }
+                for (let j=0;j<rowData.length;j++){
+                    if (j in visitedColumns||visitedColumns.length==columnCount){
+                        break;
+                    }
+                    if (rowData[j]!="N/A" && rowData[j]!=""){
 
-			}
-		})
-	})
-})
+                        visitedColumns.push(j)
+                    }
+                }
+            })
+        }
+        emptyColumns=Array.from(Array(columnCount).keys()).filter((item)=>visitedColumns.indexOf(item)<0);
+        return datatable.columns(emptyColumns).visible(false);
+
+}
-- 
cgit v1.2.3


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(+)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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 0319428bc26ba7d956dc7564ad69feeae7c9ef90 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 12:23:01 +0300
Subject: replace js_alt/timeago in templates

---
 wqflask/wqflask/templates/admin/ind_user_manager.html    | 2 +-
 wqflask/wqflask/templates/collections/list.html          | 2 +-
 wqflask/wqflask/templates/collections/not_logged_in.html | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/admin/ind_user_manager.html b/wqflask/wqflask/templates/admin/ind_user_manager.html
index e859b442..b821e5d5 100644
--- a/wqflask/wqflask/templates/admin/ind_user_manager.html
+++ b/wqflask/wqflask/templates/admin/ind_user_manager.html
@@ -103,7 +103,7 @@
 
 {% block js %}
 
-    <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.js') }}"></script>
     <script>
         $('body').timeago();
     </script>
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 9e0c0f07..280ca6cc 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -66,7 +66,7 @@
 {% endblock %}
 
 {% block js %}
-    <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.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>
diff --git a/wqflask/wqflask/templates/collections/not_logged_in.html b/wqflask/wqflask/templates/collections/not_logged_in.html
index a4c8747e..49b0e07d 100644
--- a/wqflask/wqflask/templates/collections/not_logged_in.html
+++ b/wqflask/wqflask/templates/collections/not_logged_in.html
@@ -5,7 +5,7 @@
     {{ header("Not logged in") }}
 
 
-    <div id "collections_holder" class="container">
+    <div id="collections_holder" class="container">
         <div class="page-header">
             <h1>Please log in in order to use this feature.</h1>
         </div>
@@ -16,7 +16,7 @@
 {% endblock %}
 
 {% block js %}
-    <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.js') }}"></script>
     <script>
         $('body').timeago();
     </script>
-- 
cgit v1.2.3


From f9fd76752944e9952a48fd2fa3718db5b11fc40e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 12:25:35 +0300
Subject: replace js_alt/parsley in templates

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

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index faa59deb..51a21324 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -257,7 +257,9 @@
     <script language="javascript" type="text/javascript" src="/static/packages/colorbox/jquery.colorbox.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>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
+<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
 
     {% block js %}
     {% endblock %}
-- 
cgit v1.2.3


From 4f55eeda63106694f8fad1355b7ecef2baad257e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 12:27:26 +0300
Subject: replace jstat in templates

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

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..918894f5 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -133,7 +133,7 @@
     <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
-    <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='js_alt/jstat.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
     <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
     <script type="text/javascript" src="/static/new/javascript/colorbrewer.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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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 2f5b606af6dd1deb381e0acc0ef6605d6849fa63 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:21:32 +0300
Subject: replace underscore js in templates

---
 wqflask/wqflask/templates/admin/create_group.html   | 2 +-
 wqflask/wqflask/templates/comparison_bar_chart.html | 2 +-
 wqflask/wqflask/templates/correlation_matrix.html   | 2 +-
 wqflask/wqflask/templates/correlation_page.html     | 2 +-
 wqflask/wqflask/templates/heatmap.html              | 2 +-
 wqflask/wqflask/templates/pair_scan_results.html    | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
index 5a6929fb..cb255ea9 100644
--- a/wqflask/wqflask/templates/admin/create_group.html
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -82,7 +82,7 @@
 {% block js %}
     <script language="javascript" type="text/javascript" src="/static/new/packages/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>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
 
     <script type="text/javascript" charset="utf-8">
     </script>
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index f791457f..6f5527db 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -31,7 +31,7 @@
     <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='d3-tip/d3-tip.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.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='js_alt/underscore.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/comparison_bar_chart.js"></script>
 
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 4e150618..4b449927 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -133,7 +133,7 @@
 
     <script type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.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='js_alt/underscore.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='chroma/chroma.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 06ee9056..46257833 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -172,7 +172,7 @@
     <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="/static/packages/underscore/underscore-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='DataTables/js/jquery.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index 497838dd..4fa562cc 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -39,6 +39,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/curvechart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/iplotMScanone_noeff.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='js_alt/underscore.min.js') }}"></script>
 
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index f1646af7..684a331e 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -69,6 +69,6 @@
     <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>
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.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='js_alt/underscore.min.js') }}"></script>
 
 {% endblock %}
\ No newline at end of file
-- 
cgit v1.2.3


From f337f93af938612eb4e5ca95d97a6b339f9c8a0d Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:23:40 +0300
Subject: replace underscore-string in templates

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

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..98b71a8b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -131,7 +131,7 @@
 
     <script type="text/javascript" src="https://d3js.org/d3.v3.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
     <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
-- 
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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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 ecd85a3d6656cbae8dddd59d2ceed3186d157e8f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 7 Dec 2020 13:51:00 +0300
Subject: replace datatable/images in css

---
 wqflask/wqflask/static/new/css/marker_regression.css | 4 ++--
 wqflask/wqflask/static/new/css/show_trait.css        | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index e0a5ceea..9f56b63d 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -48,10 +48,10 @@ table.dataTable thead th{
 }
 
 table.dataTable thead .sorting_asc {
-  background-image: url("../packages/DataTables/images/sort_asc_disabled.png");
+  background-image: url("/js/DataTables/images/sort_asc_disabled.png");
 }
 table.dataTable thead .sorting_desc {
-  background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
+  background-image: url("/js/DataTables/images/sort_desc_disabled.png");
 }
 
 table.dataTable thead th {
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 39c6ba53..27404801 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -25,10 +25,10 @@ table.dataTable thead th, table.dataTable tfoot th{
 }
 
 table.dataTable thead .sorting_asc {
-  background-image: url("../packages/DataTables/images/sort_asc_disabled.png");
+  background-image: url("/js/DataTables/images/sort_asc_disabled.png");
 }
 table.dataTable thead .sorting_desc {
-  background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
+  background-image: url("/js/DataTables/images/sort_desc_disabled.png");
 }
 
 table.dataTable thead th, table.dataTable tfoot {
-- 
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(-)

(limited to 'wqflask')

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

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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 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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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 977e0068b4038e65c0a03c80c304adac9951507c Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 01:46:27 +0300
Subject: replace return with filter for conditional queries for correlations

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

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 4f25e90a..6026e0a1 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -38,7 +38,7 @@
           </div>
 
           <div class="form-group">
-              <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
+              <label for="corr_return_results" class="col-xs-2 control-label">Filter</label>
               <div class="col-xs-4 controls">
                   <select name="corr_return_results" class="form-control">
                       {% for return_result in corr_tools.return_results_menu %}
-- 
cgit v1.2.3


From 6b9627b7b3559a64c5523bad8b5b376ae786a69b Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 04:40:52 +0300
Subject: refactor filter datatable function

---
 .../static/new/javascript/auto_hide_column.js      | 43 ++++++++++------------
 1 file changed, 19 insertions(+), 24 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
index 94bb8a90..f879e0d1 100644
--- a/wqflask/wqflask/static/new/javascript/auto_hide_column.js
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -1,28 +1,23 @@
-function filterDatable(datatable){
-        let visitedColumns=[]
-        let columnCount=datatable.columns().header().length;
-        let numberOfRows=datatable.data().length;
-        for (let i=0;i<numberOfRows;i++){
-            if (visitedColumns.length==columnCount){
+function filterDatatable(datatable){
+    let visitedFoundColumns=[]
+    let columnCount=datatable.columns().header().length;
+    let numberOfRows=datatable.data().length;
+    for (let i=0;i<numberOfRows;i++){
+        if (visitedFoundColumns.length==columnCount){
+            break;
+        }
+        let rowObj=datatable.rows(i).data()[0]
+        for(let col=0;col<rowObj.length;col++){
+            if (visitedFoundColumns.length==columnCount){
                 break;
             }
-            let rowObj=datatable.rows(i).data()
-            rowObj.data().each(function(rowData,v){
-                if (visitedColumns.length==columnCount){
-                    return false;
-                }
-                for (let j=0;j<rowData.length;j++){
-                    if (j in visitedColumns||visitedColumns.length==columnCount){
-                        break;
-                    }
-                    if (rowData[j]!="N/A" && rowData[j]!=""){
-
-                        visitedColumns.push(j)
-                    }
-                }
-            })
+            if (visitedFoundColumns.includes(col) || rowObj[col]=="N/A"||rowObj[col]==""){
+                continue;
+            }
+            visitedFoundColumns.push(col)
         }
-        emptyColumns=Array.from(Array(columnCount).keys()).filter((item)=>visitedColumns.indexOf(item)<0);
-        return datatable.columns(emptyColumns).visible(false);
+    }
+    emptyColumns=Array.from(Array(columnCount).keys()).filter((item)=>visitedFoundColumns.indexOf(item)<0);
+    return datatable.columns(emptyColumns).visible(false);
 
-}
+}
\ No newline at end of file
-- 
cgit v1.2.3


From 3a4357113cf52ef71a686736d30dad0291f33e33 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 04:50:26 +0300
Subject: replace item with column

---
 wqflask/wqflask/static/new/javascript/auto_hide_column.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
index f879e0d1..2fc89786 100644
--- a/wqflask/wqflask/static/new/javascript/auto_hide_column.js
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -17,7 +17,7 @@ function filterDatatable(datatable){
             visitedFoundColumns.push(col)
         }
     }
-    emptyColumns=Array.from(Array(columnCount).keys()).filter((item)=>visitedFoundColumns.indexOf(item)<0);
+    emptyColumns=Array.from(Array(columnCount).keys()).filter((column)=>visitedFoundColumns.indexOf(column)<0);
     return datatable.columns(emptyColumns).visible(false);
 
 }
\ No newline at end of file
-- 
cgit v1.2.3


From 8e92e8b01779c97b58becf997604269bd6bb5bb7 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 13:16:01 +0300
Subject: replace plotly js in templates

---
 wqflask/wqflask/templates/comparison_bar_chart.html | 2 +-
 wqflask/wqflask/templates/corr_scatterplot.html     | 2 +-
 wqflask/wqflask/templates/mapping_results.html      | 2 +-
 wqflask/wqflask/templates/show_trait.html           | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index f791457f..9ea43097 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -32,7 +32,7 @@
     <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/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/comparison_bar_chart.js"></script>
 
 {% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 1133fcd2..41354cf5 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -354,6 +354,6 @@
     <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>
     <!--<script language="javascript" type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>-->
-    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 9542c29d..268144ec 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -350,7 +350,7 @@
     <script type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
-    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
     {% if manhattan_plot == True and selectedChr == -1 %}
     <script type="text/javascript" src="/static/new/js_external/jscolor.js"></script>
     {% endif %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7b74a3f6..18325abc 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -135,7 +135,7 @@
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
     <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
 
     <script type="text/javascript" src="/static/new/javascript/stats.js"></script>
-- 
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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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 d03d66a15f0f400006ed61712f7e4ac82f041d33 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 18:24:33 +0300
Subject: remove duplicates in base.html

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

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 51a21324..4a6023b3 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -258,8 +258,7 @@
     <!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
-<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
-<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
+
 
     {% block js %}
     {% endblock %}
-- 
cgit v1.2.3


From eb5853e2327e399bd012c2ac085754cbb3db0bfb Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 8 Dec 2020 19:23:17 +0300
Subject: use Limit to for correlation

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

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 6026e0a1..ba72ff27 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -38,7 +38,7 @@
           </div>
 
           <div class="form-group">
-              <label for="corr_return_results" class="col-xs-2 control-label">Filter</label>
+              <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label>
               <div class="col-xs-4 controls">
                   <select name="corr_return_results" class="form-control">
                       {% for return_result in corr_tools.return_results_menu %}
-- 
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(-)

(limited to 'wqflask')

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(-)

(limited to 'wqflask')

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


From 28223e97e3e24c0ac759d7523d701b875cd6df7b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 8 Dec 2020 17:04:41 -0600
Subject: Added method as a parameter for the correlation scatterplot so that
 it will default to the Spearman tab when the link is from a Spearman
 correlation

---
 wqflask/wqflask/correlation/corr_scatter_plot.py  | 2 ++
 wqflask/wqflask/templates/corr_scatterplot.html   | 8 ++++----
 wqflask/wqflask/templates/correlation_matrix.html | 3 ++-
 3 files changed, 8 insertions(+), 5 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 6ab8c3d8..c87776bb 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -29,6 +29,8 @@ class CorrScatterPlot(object):
         self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
         #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3)
 
+        self.method = params['method']
+
         primary_samples = self.dataset_1.group.samplelist
         if self.dataset_1.group.parlist != None:
             primary_samples += self.dataset_1.group.parlist
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 1133fcd2..cd1998fa 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -118,17 +118,17 @@
   {% endif %}
 
   <ul class="nav nav-tabs">
-    <li class="active">
+    <li {% if method == 'pearson' %}class="active"{% endif %}>
       <a href="#tp1" data-toggle="tab">Pearson</a>
     </li>
-    <li>
+    <li {% if method == 'spearman' %}class="active"{% endif %}>
       <a href="#tp2" data-toggle="tab">Spearman Rank</a>
     </li>
   </ul>
 
   <div class="tab-content" style="min-width: 800px;">
 
-    <div class="tab-pane active" id="tp1">
+    <div class="tab-pane {% if method == 'pearson' %}active{% endif %}" id="tp1">
       <br>
       <div id="scatterplot2"></div>
       <br>
@@ -243,7 +243,7 @@
       </div>
     </div>
 
-    <div class="tab-pane" id="tp2">
+    <div class="tab-pane {% if method == 'spearman' %}active{% endif %}" id="tp2">
       <br>
       <div id="srscatterplot2"></div>
       <br>
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 96ad9c35..fb0380c9 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -32,6 +32,7 @@
       {% endfor %}
     </tr>
     {% for trait in traits %}
+    {% set outer_loop = loop.index %}
     <tr>
       <td align="center"><input type="checkbox" class="checkbox" style="margin-left: 3px; margin-right: 1px;"></td>
       <td align="right" style="padding-right: 4px;" >
@@ -54,7 +55,7 @@
       {% if result[1] == 0 %}
       <td nowrap="ON" align="middle" bgcolor="#eeeeee" style="padding: 3px; line-height: 1.1;">N/A</td>
       {% else %}
-      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?method={% if loop.index > outer_loop %}spearman{% else %}pearson{% endif %}&dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
       {% endif %}
       {% endif %}
       {% endfor %}
-- 
cgit v1.2.3


From 77bf00aa228a0be2cc4ad083c9f0e3d98e1fd126 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 8 Dec 2020 17:05:49 -0600
Subject: Added method to the links to the scatterplot in the correlation paage

---
 wqflask/wqflask/templates/correlation_page.html | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 3cca7495..ee6c3aae 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -349,7 +349,7 @@
                       '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>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&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
                         }
@@ -470,7 +470,7 @@
                       '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>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&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
                         }
@@ -524,7 +524,7 @@
                       '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>"
+                          return "<a target\"_blank\" href=\"corr_scatter_plot?method={% if corr_method == 'spearman' %}spearman{% else %}pearson{% endif %}&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
                         }
-- 
cgit v1.2.3


From 4e3537b9e7525ea7a886cd12205bc40a53c5046a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 9 Dec 2020 17:32:11 +0300
Subject: add changes to auto_hide_column

---
 .../static/new/javascript/auto_hide_column.js      | 36 ++++++++++------------
 1 file changed, 17 insertions(+), 19 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
index 2fc89786..1a4dc039 100644
--- a/wqflask/wqflask/static/new/javascript/auto_hide_column.js
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -1,23 +1,21 @@
-function filterDatatable(datatable){
-    let visitedFoundColumns=[]
-    let columnCount=datatable.columns().header().length;
-    let numberOfRows=datatable.data().length;
-    for (let i=0;i<numberOfRows;i++){
-        if (visitedFoundColumns.length==columnCount){
-            break;
-        }
-        let rowObj=datatable.rows(i).data()[0]
-        for(let col=0;col<rowObj.length;col++){
-            if (visitedFoundColumns.length==columnCount){
-                break;
+    function filterDatatable(datatable){
+        let invalidColumns=[]
+        let columnCount=datatable.columns().header().length;
+        let numberOfRows=datatable.rows().count();
+        for (let col=0; col<columnCount; col++){
+            colObj = datatable.column(col).nodes().to$();
+            allNAs = true;
+            for (let i=0;i<numberOfRows;i++){
+                cellContent = colObj[i].childNodes[0].data
+                if (cellContent != "N/A" && cellContent != ""){
+                    allNAs = false;
+                    break;
+                }
             }
-            if (visitedFoundColumns.includes(col) || rowObj[col]=="N/A"||rowObj[col]==""){
-                continue;
+            if (allNAs){
+                invalidColumns.push(col)
             }
-            visitedFoundColumns.push(col)
         }
-    }
-    emptyColumns=Array.from(Array(columnCount).keys()).filter((column)=>visitedFoundColumns.indexOf(column)<0);
-    return datatable.columns(emptyColumns).visible(false);
+        return datatable.columns(invalidColumns).visible(false);
 
-}
\ No newline at end of file
+    }
\ No newline at end of file
-- 
cgit v1.2.3


From cdba483dfae360b99a77551b82d27f2d5b6c7b08 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 9 Dec 2020 15:16:56 -0600
Subject: Fixed mistake in string formatting the bootstrap option for qtlreaper
 mapping

---
 wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 505ae295..b2eb58ae 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -33,7 +33,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
                 )
 
             opt_list.append("-b")
-            opt_list.append(f"--n_bootstrap{str(num_bootstrap)}")
+            opt_list.append(f"--n_bootstrap {str(num_bootstrap)}")
             opt_list.append(f"--bootstrap_output{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
         if num_perm > 0:
             permu_filename =("{this_dataset.group.name}_PERM_" + 
-- 
cgit v1.2.3


From 66ea1d85feb8cb17a5e8ef9429b7f5353243d634 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 9 Dec 2020 15:19:01 -0600
Subject: Fixed another string formatting mistake with setting the bootstrap
 output file

---
 wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index b2eb58ae..8341ee55 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -34,7 +34,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
 
             opt_list.append("-b")
             opt_list.append(f"--n_bootstrap {str(num_bootstrap)}")
-            opt_list.append(f"--bootstrap_output{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
+            opt_list.append(f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
         if num_perm > 0:
             permu_filename =("{this_dataset.group.name}_PERM_" + 
             ''.join(random.choice(string.ascii_uppercase + 
-- 
cgit v1.2.3


From 0253f1f483ecdcf4cceb65f55efee739a58d0e4e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 10 Dec 2020 12:29:04 -0600
Subject: Replaced the Scroller import with the CDN one until we figure out why
 the new import doesn't work

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

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index b02f8140..c95a0522 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -146,7 +146,7 @@
     <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 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="https://cdn.datatables.net/scroller/2.0.3/js/dataTables.scroller.min.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 05f8cf8e500a79eecb51db07e6dc5dd96131925e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 10 Dec 2020 15:22:29 -0600
Subject: Added an export for the Correlation Matrix

---
 .../wqflask/correlation_matrix/show_corr_matrix.py | 43 +++++++++++++++++++---
 wqflask/wqflask/templates/correlation_matrix.html  | 17 ++++++++-
 wqflask/wqflask/views.py                           | 11 ++++++
 3 files changed, 64 insertions(+), 7 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0269ce68..a77877d2 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -20,24 +20,23 @@
 
 import datetime
 import math
+import random
+import string
+
 import numpy as np
 import scipy
 import rpy2.robjects as robjects
-import utility.webqtlUtil  # this is for parallel computing only.
-import utility.logger
+from rpy2.robjects.packages import importr
 
 from base import data_set
+from base.webqtlConfig import GENERATED_TEXT_DIR
 from functools import reduce
 from functools import cmp_to_key
-from rpy2.robjects.packages import importr
-
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import corr_result_helpers
 from utility.redis_tools import get_redis_conn
 
-logger = utility.logger.getLogger(__name__)
-
 Redis = get_redis_conn()
 THIRTY_DAYS = 60 * 60 * 24 * 30
 
@@ -135,6 +134,8 @@ class CorrelationMatrix(object):
             self.corr_results.append(corr_result_row)
             self.pca_corr_results.append(pca_corr_result_row)
 
+        self.export_filename, self.export_filepath = export_corr_matrix(self.corr_results)
+
         self.trait_data_array = []
         for trait_db in self.trait_list:
             this_trait = trait_db[0]
@@ -232,6 +233,36 @@ class CorrelationMatrix(object):
             loadings_array.append(loadings_row)
         return loadings_array
 
+def export_corr_matrix(corr_results):
+    corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+    matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename)
+    with open(matrix_export_path, "w+") as output_file:
+        output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
+        output_file.write("\n")
+        output_file.write("Correlation ")
+        for i, item in enumerate(corr_results[0]):
+            output_file.write("Trait" + str(i + 1) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
+        output_file.write("\n")
+        for i, row in enumerate(corr_results):
+            output_file.write("Trait" + str(i + 1) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
+            for item in row:
+                output_file.write(str(item[1]) + "\t")
+            output_file.write("\n")
+
+        output_file.write("\n")
+        output_file.write("\n")
+        output_file.write("N ")
+        for i, item in enumerate(corr_results[0]):
+            output_file.write("Trait" + str(i) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
+        output_file.write("\n")
+        for i, row in enumerate(corr_results):
+            output_file.write("Trait" + str(i) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
+            for item in row:
+                output_file.write(str(item[2]) + "\t")
+            output_file.write("\n")
+
+    return corr_matrix_filename, matrix_export_path
+
 def zScore(trait_data_array):
     NN = len(trait_data_array[0])
     if NN < 10:
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 96ad9c35..78d7e9aa 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -1,10 +1,11 @@
 {% extends "base.html" %}
+{% block title %}Correlation Matrix{% 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/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="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
 {% endblock %}
 {% block content %}
 
@@ -63,6 +64,12 @@
   </tbody>
 </table>
 <br>
+<form method="post" target="_blank" action="/export_corr_matrix" id="matrix_export_form">
+  <input type="hidden" name="export_filepath" value="{{ export_filepath }}">
+  <input type="hidden" name="export_filename" value="{{ export_filename }}">
+  <button class="btn btn-default" id="export">Download <span class="glyphicon glyphicon-download"></span></button>
+</form>
+<br>
 {% if pca_works == "True" %}
 <h2>PCA Traits</h2>
 <div style="margin-bottom: 20px; overflow:hidden;">
@@ -172,6 +179,14 @@
         "paging": false,
         "orderClasses": true
       } );
+
+      export_corr_matrix = function() {
+            $('#matrix_export_form').attr('action', '/export_corr_matrix');
+            return $('#matrix_export_form').submit();
+      }
+
+      $('#export').click(export_corr_matrix);
+
     </script>
 
 {% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3557a62a..25563e86 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -799,6 +799,17 @@ def export_mapping_results():
 
     return response
 
+@app.route("/export_corr_matrix", methods = ('POST',))
+def export_corr_matrix():
+    file_path = request.form.get("export_filepath")
+    file_name = request.form.get("export_filename")
+    results_csv = open(file_path, "r").read()
+    response = Response(results_csv,
+                        mimetype='text/csv',
+                        headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"})
+
+    return response
+
 @app.route("/export", methods = ('POST',))
 def export():
     logger.info("request.form:", request.form)
-- 
cgit v1.2.3


From d1ef84a3ba6312a53076d40ee899933172866477 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 14 Dec 2020 12:42:58 -0600
Subject: Added a template for the tool bottons on the search result,
 correlation, and collection pages (since the buttons are the same and it's
 redundant currently)

---
 wqflask/wqflask/templates/collections/view.html   | 36 +---------------------
 wqflask/wqflask/templates/correlation_page.html   | 36 +---------------------
 wqflask/wqflask/templates/search_result_page.html | 37 +----------------------
 wqflask/wqflask/templates/tool_buttons.html       | 35 +++++++++++++++++++++
 4 files changed, 38 insertions(+), 106 deletions(-)
 create mode 100644 wqflask/wqflask/templates/tool_buttons.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 99a6f2de..66945ed7 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -28,41 +28,7 @@
                 {{ this_trait.name }}:{{ this_trait.dataset.name }}:{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }},
             {% endfor %}" >
 
-            <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
-                Correlations
-            </button>
-
-            <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
-                Networks
-            </button>
-
-            <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
-              WebGestalt
-            </button>
-
-            <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
-              GeneWeaver
-            </button>
-
-            <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>
-
-            <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
-                WGCNA
-            </button>
-
-            <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
-                CTL Maps
-            </button>
-
-            <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
-                MultiMap
-            </button>
-
-            <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
-                Comparison Bar Chart
-            </button>
+            {% include 'tool_buttons.html' %}
 
           </form>
         </div>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 7acccc25..49b2bf26 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -33,41 +33,7 @@
                 {{ this_trait.name }}:{{ this_trait.dataset }},
             {% endfor %}" >
 
-            <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
-                Correlations
-            </button>
-
-            <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
-                Networks
-            </button>
-
-            <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
-              WebGestalt
-            </button>
-
-            <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
-              GeneWeaver
-            </button>
-
-            <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>
-
-            <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
-                WGCNA
-            </button>
-
-            <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
-                CTL Maps
-            </button>
-
-            <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
-                MultiMap
-            </button>
-
-            <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
-                Comparison Bar Chart
-            </button>
+            {% include 'tool_buttons.html' %}
 
           </form>
         </div>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 3be2e395..92f14ade 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -75,42 +75,7 @@
                 {{ this_trait.name }}:{{ this_trait.dataset }},
             {% endfor %}" >
 
-
-                <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
-                    Correlations
-                </button>
-
-                <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
-                    Networks
-                </button>
-
-                <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
-                  WebGestalt
-                </button>
-
-                <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
-                  GeneWeaver
-                </button>
-
-                <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>
-
-                <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
-                    WGCNA
-                </button>
-
-                <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
-                    CTL Maps
-                </button>
-
-                <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
-                    MultiMap
-                </button>
-
-                <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
-                    Comparison Bar Chart
-                </button>
+            {% include 'tool_buttons.html' %}
 
           </form>
         </div>
diff --git a/wqflask/wqflask/templates/tool_buttons.html b/wqflask/wqflask/templates/tool_buttons.html
new file mode 100644
index 00000000..5b2dbf3d
--- /dev/null
+++ b/wqflask/wqflask/templates/tool_buttons.html
@@ -0,0 +1,35 @@
+<button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
+    Correlations
+</button>
+
+<button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" >
+    Networks
+</button>
+
+<button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" >
+  WebGestalt
+</button>
+
+<button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" >
+  GeneWeaver
+</button>
+
+<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>
+
+<button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" >
+    WGCNA
+</button>
+
+<button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" >
+    CTL Maps
+</button>
+
+<button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" >
+    MultiMap
+</button>
+
+<button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
+    Comparison Bar Chart
+</button>
\ No newline at end of file
-- 
cgit v1.2.3


From 67ec0db7ef88a4ce49f6f6161bea978674f7123a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 15 Dec 2020 14:52:39 +0300
Subject: Replace twitter-post-fetcher (#526)

* replace twitter fetcher in templates

* add twitter post fetcher to mechanical rob

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>---
 test/requests/link_checker.py                  | 1 +
 wqflask/wqflask/templates/index_page_orig.html | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 0a371bb8..64707514 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -137,6 +137,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
         "/js/cytoscape-qtip/cytoscape-qtip.js",
         "/css/d3-tip/d3-tip.css",
+        "/js/javascript-twitter-post-fetcher/js/twitterFetcher_min.js",
         "/js/DataTables/images/sort_asc_disabled.png",
         "/js/DataTables/images/sort_desc_disabled.png",
     ]
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 13ca52df..7efbdccf 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -326,7 +326,7 @@
         }
     </script>
 
-    <script type="text/javascript" src="/twitter/js/twitterFetcher_min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='javascript-twitter-post-fetcher/js/twitterFetcher_min.js') }}"></script>
 
     <script type="text/javascript">
       var configProfile = {
-- 
cgit v1.2.3


From 93ba2a098a349977a8d54a75f7c871205ee2ddb1 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Tue, 15 Dec 2020 14:55:03 +0300
Subject: Replace typeahead lib (#527)

* replace typeahead js in templates

* add typeahead.bundle.js to mechanical rob

* remove duplicate libs in snp_browser.html

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>---
 test/requests/link_checker.py              | 1 +
 wqflask/wqflask/templates/snp_browser.html | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 64707514..a22c2b54 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/typeahead/typeahead.bundle.js",
         "/js/underscore-string/underscore.string.min.js",
         "/js/js_alt/jstat.min.js",
         "/js/js_alt/parsley.min.js",
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index fb564b28..a96b8e3b 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -217,7 +217,7 @@
 {% block js %}
   <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>
-  <script language="javascript" type="text/javascript" src="/static/new/js_external/typeahead.bundle.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='typeahead/typeahead.bundle.js') }}"></script>
 
   <script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script>
 
-- 
cgit v1.2.3


From f8fc508f86ba015097a027055c429e61d310523f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 11:21:32 -0600
Subject: Removed Index and Record from hideable columns in search result and
 correlation pages

---
 wqflask/wqflask/templates/correlation_page.html   | 2 --
 wqflask/wqflask/templates/search_result_page.html | 2 --
 2 files changed, 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 49b2bf26..82caee21 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -86,8 +86,6 @@
         <div class="show-hide-container" style="float: left; clear: left;">
           <b>Show/Hide Columns:</b>
           <br>
-          <button class="toggle-vis" data-column="1">Index</button>
-          <button class="toggle-vis" data-column="2">Record</button>
           {% if target_dataset.type == 'ProbeSet' %}
           <button class="toggle-vis" data-column="3">Symbol</button>
           <button class="toggle-vis" data-column="4">Description</button>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 92f14ade..adc2f140 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -106,8 +106,6 @@
           <div class="show-hide-container">
             <b>Show/Hide Columns:</b>
             <br>
-            <button class="toggle-vis" data-column="1">Index</button>
-            <button class="toggle-vis" data-column="2">Record</button>
             {% if dataset.type == 'ProbeSet' %}
             <button class="toggle-vis" data-column="3">Symbol</button>
             <button class="toggle-vis" data-column="4">Description</button>
-- 
cgit v1.2.3


From 49a5d53533477250a1add2ba866d42e86dfd12b3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 11:29:47 -0600
Subject: Changed High P to Peak LOD and changed the width of the column some

---
 wqflask/wqflask/templates/correlation_page.html   |  8 ++++----
 wqflask/wqflask/templates/search_result_page.html | 12 ++++++------
 2 files changed, 10 insertions(+), 10 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 82caee21..db04a530 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -91,7 +91,7 @@
           <button class="toggle-vis" data-column="4">Description</button>
           <button class="toggle-vis" data-column="5">Location</button>
           <button class="toggle-vis" data-column="6">Mean</button>
-          <button class="toggle-vis" data-column="7">High P</button>
+          <button class="toggle-vis" data-column="7">Peak LOD</button>
           <button class="toggle-vis" data-column="8">Peak Location</button>
           <button class="toggle-vis" data-column="9">Effect Size</button>
           {% elif target_dataset.type == 'Publish' %}
@@ -102,7 +102,7 @@
           <button class="toggle-vis" data-column="7">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button>
           <button class="toggle-vis" data-column="8">N</button>
           <button class="toggle-vis" data-column="9">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button>
-          <button class="toggle-vis" data-column="10">High P</button>
+          <button class="toggle-vis" data-column="10">Peak LOD</button>
           <button class="toggle-vis" data-column="11">Peak Location</button>
           <button class="toggle-vis" data-column="12">Effect Size</button>
           {% else %}
@@ -355,7 +355,7 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "High P<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+                      'title': "Peak LOD<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "60px",
@@ -455,7 +455,7 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "High P<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+                      'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "60px",
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index adc2f140..4a3080a3 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -111,7 +111,7 @@
             <button class="toggle-vis" data-column="4">Description</button>
             <button class="toggle-vis" data-column="5">Location</button>
             <button class="toggle-vis" data-column="6">Mean</button>
-            <button class="toggle-vis" data-column="7">High P</button>
+            <button class="toggle-vis" data-column="7">Peak LOD</button>
             <button class="toggle-vis" data-column="8">Peak Location</button>
             <button class="toggle-vis" data-column="9">Effect Size</button>
             {% elif dataset.type == 'Publish' %}
@@ -119,7 +119,7 @@
             <button class="toggle-vis" data-column="4">Mean</button>
             <button class="toggle-vis" data-column="5">Authors</button>
             <button class="toggle-vis" data-column="6">Year</button>
-            <button class="toggle-vis" data-column="7">High P</button>
+            <button class="toggle-vis" data-column="7">Peak LOD</button>
             <button class="toggle-vis" data-column="8">Peak Location</button>
             <button class="toggle-vis" data-column="9">Effect Size</button>
             {% endif %}
@@ -277,10 +277,10 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+                      'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
-                      'width': "65px",
+                      'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
@@ -346,10 +346,10 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+                      'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
-                      'width': "80px",
+                      'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-- 
cgit v1.2.3


From 5a2284984e75a4a25debdfcbdc8c2951a799c4cb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 11:52:58 -0600
Subject: Changed LRS to LOD score for correlation page table

---
 wqflask/wqflask/correlation/show_corr_results.py  | 13 ++++++++-----
 wqflask/wqflask/templates/correlation_page.html   |  6 +++---
 wqflask/wqflask/templates/search_result_page.html |  4 ++--
 3 files changed, 13 insertions(+), 10 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 0c1cea0e..8536ce51 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -493,14 +493,15 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
             results_dict['description'] = "N/A"
             results_dict['location'] = trait.location_repr
             results_dict['mean'] = "N/A"
-            results_dict['lrs_score'] = "N/A"
             results_dict['additive'] = "N/A"
             if bool(trait.description_display):
                 results_dict['description'] = trait.description_display
             if bool(trait.mean):
                 results_dict['mean'] = f"{float(trait.mean):.3f}"
-            if trait.LRS_score_repr != "N/A":
-                results_dict['lrs_score'] = f"{float(trait.LRS_score_repr):.1f}"
+            try:
+                trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}"
+            except:
+                trait_dict['lod_score'] = "N/A"
             results_dict['lrs_location'] = trait.LRS_location_repr
             if bool(trait.additive):
                 results_dict['additive'] = f"{float(trait.additive):.3f}"
@@ -544,8 +545,10 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
                 else:
                     results_dict['pubmed_link'] = trait.pubmed_link
                     results_dict['pubmed_text'] = trait.pubmed_text
-
-            results_dict['lrs_score'] = trait.LRS_score_repr
+            try:
+                trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}"
+            except:
+                trait_dict['lod_score'] = "N/A"
             results_dict['lrs_location'] = trait.LRS_location_repr
             if bool(trait.additive):
                 results_dict['additive'] = f"{float(trait.additive):.3f}"
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index db04a530..a9a3a2ca 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -355,9 +355,9 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Peak LOD<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+                      'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
                       'type': "natural-minus-na",
-                      'data': "lrs_score",
+                      'data': "lod_score",
                       'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
@@ -457,7 +457,7 @@
                     {
                       'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
                       'type': "natural-minus-na",
-                      'data': "lrs_score",
+                      'data': "lod_score",
                       'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 4a3080a3..f2334512 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -279,7 +279,7 @@
                     {
                       'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
                       'type': "natural-minus-na",
-                      'data': "lrs_score",
+                      'data': "lod_score",
                       'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
@@ -348,7 +348,7 @@
                     {
                       'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
                       'type': "natural-minus-na",
-                      'data': "lrs_score",
+                      'data': "lod_score",
                       'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
-- 
cgit v1.2.3


From 2f84b17bbd632fd7591c2b8c51bb071e6e16d92d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 11:53:40 -0600
Subject: Changed string formatting to use preferable Python 3 syntax and
 converted LRS scores to LOD scores for the search results page

---
 wqflask/wqflask/search_results.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index ce836ce2..0d0894a4 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -126,11 +126,14 @@ views.py).
                     trait_dict['mean'] = "N/A"
                     trait_dict['additive'] = "N/A"
                     if this_trait.mean != "" and this_trait.mean != None:
-                        trait_dict['mean'] = '%.3f' % this_trait.mean
-                    trait_dict['lrs_score'] = this_trait.LRS_score_repr
+                        trait_dict['mean'] = f"{this_trait.mean:.3f}"
+                    try:
+                        trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}"
+                    except:
+                        trait_dict['lod_score'] = "N/A"
                     trait_dict['lrs_location'] = this_trait.LRS_location_repr
                     if this_trait.additive != "":
-                        trait_dict['additive'] = '%.3f' % this_trait.additive
+                        trait_dict['additive'] = f"{this_trait.additive:.3f}"
                 elif this_trait.dataset.type == "Geno":
                     trait_dict['location'] = this_trait.location_repr
                 elif this_trait.dataset.type == "Publish":
@@ -143,12 +146,15 @@ views.py).
                     trait_dict['pubmed_text'] = this_trait.pubmed_text
                     trait_dict['mean'] = "N/A"
                     if this_trait.mean != "" and this_trait.mean != None:
-                        trait_dict['mean'] = '%.3f' % this_trait.mean
-                    trait_dict['lrs_score'] = this_trait.LRS_score_repr
+                        trait_dict['mean'] = f"{this_trait.mean:.3f}"
+                    try:
+                        trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}"
+                    except:
+                        trait_dict['lod_score'] = "N/A"
                     trait_dict['lrs_location'] = this_trait.LRS_location_repr
                     trait_dict['additive'] = "N/A"
                     if this_trait.additive != "":
-                        trait_dict['additive'] = '%.3f' % this_trait.additive
+                        trait_dict['additive'] = f"{this_trait.additive:.3f}"
                 # Convert any bytes in dict to a normal utf-8 string
                 for key in trait_dict.keys():
                     if isinstance(trait_dict[key], bytes):
-- 
cgit v1.2.3


From fde06d3a6b0ea22224f17e179c7ea226e658d02e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 13:50:04 -0600
Subject: Changed the Hide No Value function to use DataTables API

---
 .../wqflask/static/new/javascript/show_trait.js    | 33 ++++++++++++++++++----
 .../templates/show_trait_transform_and_filter.html |  2 +-
 2 files changed, 28 insertions(+), 7 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 87c35984..e8768325 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -731,14 +731,35 @@ filter_by_value = function() {
   }
 };
 
+hide_no_value_filter = function( settings, data, dataIndex ) {
+  this_value = table_api.column(3).nodes().to$()[dataIndex].childNodes[0].value;
+  if (this_value == "x"){
+    return false
+  } else {
+    return true
+  }
+}
+
 hide_no_value = function() {
-  return $('.value_se').each((function(_this) {
-    return function(_index, element) {
-      if ($(element).find('.trait-value-input').val() === 'x') {
-        return $(element).hide();
+
+  tables = ['samples_primary', 'samples_other'];
+  filter_active = $(this).data("active");
+  for (_i = 0, _len = tables.length; _i < _len; _i++) {
+    table = tables[_i];
+    if ($('#' + table).length) {
+      table_api = $('#' + table).DataTable();
+      if (filter_active == "true"){
+        table_api.draw();
+        $(this).data("active", "false");
+      } else {
+        $.fn.dataTable.ext.search.push(hide_no_value_filter);
+        table_api.search();
+        table_api.draw();
+        $.fn.dataTable.ext.search.splice($.fn.dataTable.ext.search.indexOf(hide_no_value_filter, 1));
+        $(this).data("active", "true");
       }
-    };
-  })(this));
+    }
+  }
 };
 $('#hide_no_value').click(hide_no_value);
 
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index d7eac378..b70ca590 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -80,7 +80,7 @@
       <input type="button" id="filter_by_value" class="btn btn-danger" value="Filter">
     </div>
     <div>
-      <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
+      <input data-active="false" type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
       <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
       <input type="button" class="btn btn-success reset" value="Reset">
       <span class="input-append">
-- 
cgit v1.2.3


From 9a6195abd1867e602234f182d73029e700612bd4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 13:55:24 -0600
Subject: Fixed Reset button to also reset hidden rows + changed Hide No Value
 button to change its text when active

---
 wqflask/wqflask/static/new/javascript/show_trait.js | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index e8768325..5dc9e456 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -741,7 +741,6 @@ hide_no_value_filter = function( settings, data, dataIndex ) {
 }
 
 hide_no_value = function() {
-
   tables = ['samples_primary', 'samples_other'];
   filter_active = $(this).data("active");
   for (_i = 0, _len = tables.length; _i < _len; _i++) {
@@ -749,9 +748,11 @@ hide_no_value = function() {
     if ($('#' + table).length) {
       table_api = $('#' + table).DataTable();
       if (filter_active == "true"){
+        $(this).val("Hide No Value")
         table_api.draw();
         $(this).data("active", "false");
       } else {
+        $(this).val("Show No Value")
         $.fn.dataTable.ext.search.push(hide_no_value_filter);
         table_api.search();
         table_api.draw();
@@ -775,6 +776,7 @@ $('#block_outliers').click(block_outliers);
 reset_samples_table = function() {
   $('input[name="transform"]').val("");
   $('span[name="transform_text"]').text("")
+  $('#hide_no_value').val("Hide No Value")
   tables = ['samples_primary', 'samples_other'];
   for (_i = 0, _len = tables.length; _i < _len; _i++) {
     table = tables[_i];
@@ -792,6 +794,7 @@ reset_samples_table = function() {
           this_node.value = this_node.attributes["data-value"].value;
         }
       }
+      table_api.draw();
     }
   }
 };
-- 
cgit v1.2.3


From 66f7e4977f751e3b533ee8fcdbba3547b9e0eace Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 14:00:06 -0600
Subject: Fixed mistake with the way lod score was being set for correlation
 results

---
 wqflask/wqflask/correlation/show_corr_results.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 8536ce51..7d3b9b9f 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -499,9 +499,9 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
             if bool(trait.mean):
                 results_dict['mean'] = f"{float(trait.mean):.3f}"
             try:
-                trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}"
+                results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
             except:
-                trait_dict['lod_score'] = "N/A"
+                results_dict['lod_score'] = "N/A"
             results_dict['lrs_location'] = trait.LRS_location_repr
             if bool(trait.additive):
                 results_dict['additive'] = f"{float(trait.additive):.3f}"
@@ -546,9 +546,9 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
                     results_dict['pubmed_link'] = trait.pubmed_link
                     results_dict['pubmed_text'] = trait.pubmed_text
             try:
-                trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}"
+                results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
             except:
-                trait_dict['lod_score'] = "N/A"
+                results_dict['lod_score'] = "N/A"
             results_dict['lrs_location'] = trait.LRS_location_repr
             if bool(trait.additive):
                 results_dict['additive'] = f"{float(trait.additive):.3f}"
-- 
cgit v1.2.3


From e744352ec32809f791754fe7828c7e81813b24c7 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Dec 2020 14:57:37 +0300
Subject: Replace jquery libs(jquery cookie,jquery ui,jquery js) (#512)

* replace jquery-ui in templates

* replace jquery-cookie library in templates

* replace jquery.min.js in templates

* add jquery-ui to mechanical rob

* add  jquery-cookie to mechanical rob

* add jquery min  js to mechanical rob

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>---
 test/requests/link_checker.py          | 3 +++
 wqflask/wqflask/templates/base.html    | 6 +++---
 wqflask/wqflask/templates/loading.html | 2 +-
 3 files changed, 7 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index a22c2b54..eb27d9fe 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -117,6 +117,9 @@ 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/jquery-ui/jquery-ui.min.js",
+        "/js/jquery-cookie/jquery.cookie.js",
+        "/js/jquery/jquery.min.js",
         "/js/typeahead/typeahead.bundle.js",
         "/js/underscore-string/underscore.string.min.js",
         "/js/js_alt/jstat.min.js",
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index bb618294..e368a4be 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -238,7 +238,7 @@
       <!--</div>-->
     </div>
 
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
+    <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
     <script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
     <script>
             //http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
@@ -250,9 +250,9 @@
               }
             })
     </script>
-    <script src="/static/new/js_external/jquery.cookie.js"></script>
+    <script src="{{ url_for('js', filename='jquery-cookie/jquery.cookie.js') }}" type="text/javascript"></script>
     <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 src="{{ url_for('js', filename='jquery-ui/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 type="text/javascript" src="/static/new/javascript/login.js"></script>-->
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 9b335dfe..94e17724 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -38,7 +38,7 @@
     </div>
   </div>
 </form>
-<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
+<script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
 <script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
 <script  type="text/javascript">
 
-- 
cgit v1.2.3


From 3a4fb64d27e59f38042ef51b79aedbd1d9163b9e Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Dec 2020 15:02:55 +0300
Subject: Replace shapiro wilk lib (#528)

* replace shapiro-wilk in templates

* add shapiro-wilk.js to mechanical rob---
 test/requests/link_checker.py             | 1 +
 wqflask/wqflask/templates/show_trait.html | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask')

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index eb27d9fe..f73ec185 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -144,6 +144,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/javascript-twitter-post-fetcher/js/twitterFetcher_min.js",
         "/js/DataTables/images/sort_asc_disabled.png",
         "/js/DataTables/images/sort_desc_disabled.png",
+        "/js/shapiro-wilk/shapiro-wilk.js",
     ]
 
     print("Checking links")
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 32cf3c0a..c881eb76 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -133,7 +133,7 @@
     <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='js_alt/jstat.min.js') }}"></script>
-    <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
+    <script type="text/javascript" src="{{ url_for('js', filename='shapiro-wilk/shapiro-wilk.js') }}"></script>
     <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
 
-- 
cgit v1.2.3


From 218a2aa198cb70761ddd20c94169941f3ea86188 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 16 Dec 2020 15:03:15 +0300
Subject: Replace zxcvbn async (#524)

* replace axcbn-async in templates

* add zxcvbn-async.min.js in mechanical rob

Co-authored-by: BonfaceKilz <bonfacemunyoki@gmail.com>---
 test/requests/link_checker.py                                         | 1 +
 wqflask/wqflask/templates/new_security/forgot_password_step2.html     | 2 +-
 wqflask/wqflask/templates/new_security/password_reset.html            | 2 +-
 wqflask/wqflask/templates/new_security/register_user.html             | 2 +-
 wqflask/wqflask/templates/new_security/registered.html                | 2 +-
 wqflask/wqflask/templates/new_security/thank_you.html                 | 2 +-
 wqflask/wqflask/templates/new_security/verification_still_needed.html | 2 +-
 7 files changed, 7 insertions(+), 6 deletions(-)

(limited to 'wqflask')

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index f73ec185..bc3b5861 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -141,6 +141,7 @@ def check_packaged_js_files(args_obj, parser):
         "/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
         "/js/cytoscape-qtip/cytoscape-qtip.js",
         "/css/d3-tip/d3-tip.css",
+        "/js/zxcvbn-async/zxcvbn-async.min.js",
         "/js/javascript-twitter-post-fetcher/js/twitterFetcher_min.js",
         "/js/DataTables/images/sort_asc_disabled.png",
         "/js/DataTables/images/sort_desc_disabled.png",
diff --git a/wqflask/wqflask/templates/new_security/forgot_password_step2.html b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
index 473fa377..5dc424e5 100644
--- a/wqflask/wqflask/templates/new_security/forgot_password_step2.html
+++ b/wqflask/wqflask/templates/new_security/forgot_password_step2.html
@@ -21,6 +21,6 @@
 
 {% block js %}
     {% include "new_security/_scripts.html" %}
-    <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/password_reset.html b/wqflask/wqflask/templates/new_security/password_reset.html
index 7110dc79..4e3ea59f 100644
--- a/wqflask/wqflask/templates/new_security/password_reset.html
+++ b/wqflask/wqflask/templates/new_security/password_reset.html
@@ -74,6 +74,6 @@
 {% block js %}
 
     {% include "new_security/_scripts.html" %}
-    <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/register_user.html b/wqflask/wqflask/templates/new_security/register_user.html
index 325d8aa5..2506f4ee 100644
--- a/wqflask/wqflask/templates/new_security/register_user.html
+++ b/wqflask/wqflask/templates/new_security/register_user.html
@@ -101,6 +101,6 @@
 {% block js %}
 
     {% include "new_security/_scripts.html" %}
-    <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/registered.html b/wqflask/wqflask/templates/new_security/registered.html
index e71d5598..eaed3ed0 100644
--- a/wqflask/wqflask/templates/new_security/registered.html
+++ b/wqflask/wqflask/templates/new_security/registered.html
@@ -20,6 +20,6 @@
 {% block js %}
 
     {% include "new_security/_scripts.html" %}
-    <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/thank_you.html b/wqflask/wqflask/templates/new_security/thank_you.html
index 459bd66a..f492fb51 100644
--- a/wqflask/wqflask/templates/new_security/thank_you.html
+++ b/wqflask/wqflask/templates/new_security/thank_you.html
@@ -19,6 +19,6 @@
 
 {% block js %}
     {% include "new_security/_scripts.html" %}
-    <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/verification_still_needed.html b/wqflask/wqflask/templates/new_security/verification_still_needed.html
index 3aa24e37..91768eb9 100644
--- a/wqflask/wqflask/templates/new_security/verification_still_needed.html
+++ b/wqflask/wqflask/templates/new_security/verification_still_needed.html
@@ -22,6 +22,6 @@
 
 {% block js %}
     {% include "new_security/_scripts.html" %}
-    <script type="text/javascript" src="/static/new/js_external/zxcvbn/zxcvbn-async.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='zxcvbn-async/zxcvbn-async.min.js') }}"></script>
     <script type="text/javascript" src="/static/new/javascript/password_strength.js"></script>
 {% endblock %}
-- 
cgit v1.2.3