From 97b4a8324b93b07e7654de0e5bc7ed22cb806cdf Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Fri, 13 Dec 2024 16:22:17 -0500
Subject: [PATCH 01/10] List Manager: add filter by type

---
 js/source/legacy/CXGN/List.js |  57 +++++--
 mason/site/list.mas           | 285 ++++++++++++++++------------------
 2 files changed, 175 insertions(+), 167 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index ba864e01e5..55db3de07a 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -335,8 +335,10 @@ CXGN.List.prototype = {
         });
     },
 
-    renderLists: function(div) {
+    renderLists: function(div, { type, autocreated = true } = {}) {
         var lists = this.availableLists();
+        var types = this.allListTypes();
+
         var html = '';
         html = html + '<div class="well well-sm"><form class="form-horizontal"><div class="form-group form-group-sm"><label class="col-sm-3 control-label">Create New List: </label><div class="col-sm-9"><div class="input-group"><input id="add_list_input" type="text" class="form-control" placeholder="Create New List. Type New List Name Here" /><span class="input-group-btn"><button class="btn btn-primary btn-sm" type="button" id="add_list_button" value="new list">New List</button></span></div></div></div><div class="form-group form-group-sm"><label class="col-sm-3 control-label"></label><div class="col-sm-9">';
         html = html + '<input id="add_list_input_description" type="text" class="form-control" placeholder="Description For New List" /></div></div></form></div>';
@@ -346,25 +348,40 @@ CXGN.List.prototype = {
             jQuery('#'+div+'_div').html(html);
         }
 
-        html += '<div class="well well-sm"><table id="private_list_data_table" class="table table-hover table-condensed">';
+        // Add list type filter
+        html += "<div class='well'>";
+        html += "<div style='display: flex; flex-wrap: wrap; align-items: baseline; column-gap: 15px; margin-bottom: 15px'>";
+        html += "<p style='white-space: nowrap'><strong>Filter Lists by Type</strong>:</p>";
+        html += "<select id='render_lists_type' class='form-control' style='max-width: 200px'>";
+        html += "<option value=''>Any</option>";
+        for ( let i = 0; i < types.length; i++ ) {
+            let selected = type && type === types[i][1] ? 'selected' : '';
+            html += "<option value='" + types[i][1] + "' " + selected + ">"+types[i][1]+"</option>";
+        }
+        html += "</select>";
+        html += "</div>";
+
+        html += '<table id="private_list_data_table" class="table table-hover table-condensed">';
         html += '<thead><tr><th>List Name</th><th>Description</th><th>Date Created</th><th>Date Modified</th><th>Count</th><th>Type</th><th>Validate</th><th>View</th><th>Delete</th><th>Download</th><th>Share</th><th>Group</th></tr></thead><tbody>';
         for (var i = 0; i < lists.length; i++) {
-            html += '<tr><td><a href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><b>'+lists[i][1]+'</b></a></td>';
-            html += '<td>'+lists[i][2]+'</td>';
-            html += '<td>'+lists[i][7]+'</td>';
-            html += '<td>'+lists[i][8]+'</td>';
-            html += '<td>'+lists[i][3]+'</td>';
-            html += '<td>'+lists[i][5]+'</td>';
-            html += '<td><a onclick="javascript:validateList(\''+lists[i][0]+'\',\''+lists[i][5]+'\')"><span class="glyphicon glyphicon-ok"></span></a></td>';
-            html += '<td><a title="View" id="view_list_'+lists[i][1]+'" href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><span class="glyphicon glyphicon-th-list"></span></span></td>';
-            html += '<td><a title="Delete" id="delete_list_'+lists[i][1]+'" href="javascript:deleteList('+lists[i][0]+')"><span class="glyphicon glyphicon-remove"></span></a></td>';
-            html += '<td><a target="_blank" title="Download" id="download_list_'+lists[i][1]+'" href="/list/download?list_id='+lists[i][0]+'"><span class="glyphicon glyphicon-arrow-down"></span></a></td>';
-            if (lists[i][6] == 0){
-                html += '<td><a title="Make Public" id="share_list_'+lists[i][1]+'" href="javascript:togglePublicList('+lists[i][0]+')"><span class="glyphicon glyphicon-share-alt"></span></a></td>';
-            } else if (lists[i][6] == 1){
-                html += '<td><a title="Make Private" id="share_list_'+lists[i][1]+'" href="javascript:togglePublicList('+lists[i][0]+')"><span class="glyphicon glyphicon-ban-circle"></span></a></td>';
+            if ( !type || type === lists[i][5] ) {
+                html += '<tr><td><a href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><b>'+lists[i][1]+'</b></a></td>';
+                html += '<td>'+lists[i][2]+'</td>';
+                html += '<td>'+lists[i][7]+'</td>';
+                html += '<td>'+lists[i][8]+'</td>';
+                html += '<td>'+lists[i][3]+'</td>';
+                html += '<td>'+lists[i][5]+'</td>';
+                html += '<td><a onclick="javascript:validateList(\''+lists[i][0]+'\',\''+lists[i][5]+'\')"><span class="glyphicon glyphicon-ok"></span></a></td>';
+                html += '<td><a title="View" id="view_list_'+lists[i][1]+'" href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><span class="glyphicon glyphicon-th-list"></span></span></td>';
+                html += '<td><a title="Delete" id="delete_list_'+lists[i][1]+'" href="javascript:deleteList('+lists[i][0]+')"><span class="glyphicon glyphicon-remove"></span></a></td>';
+                html += '<td><a target="_blank" title="Download" id="download_list_'+lists[i][1]+'" href="/list/download?list_id='+lists[i][0]+'"><span class="glyphicon glyphicon-arrow-down"></span></a></td>';
+                if (lists[i][6] == 0){
+                    html += '<td><a title="Make Public" id="share_list_'+lists[i][1]+'" href="javascript:togglePublicList('+lists[i][0]+')"><span class="glyphicon glyphicon-share-alt"></span></a></td>';
+                } else if (lists[i][6] == 1){
+                    html += '<td><a title="Make Private" id="share_list_'+lists[i][1]+'" href="javascript:togglePublicList('+lists[i][0]+')"><span class="glyphicon glyphicon-ban-circle"></span></a></td>';
+                }
+                html += '<td><input type="checkbox" id="list_select_checkbox_'+lists[i][0]+'" name="list_select_checkbox" value="'+lists[i][0]+'"/></td></tr>';
             }
-            html += '<td><input type="checkbox" id="list_select_checkbox_'+lists[i][0]+'" name="list_select_checkbox" value="'+lists[i][0]+'"/></td></tr>';
         }
         html = html + '</tbody></table></div>';
         html += '<div id="list_group_select_action"></div>';
@@ -413,6 +430,12 @@ CXGN.List.prototype = {
             }
             jQuery("#list_group_select_action").html(list_group_select_action_html);
         });
+
+        jQuery("#render_lists_type").on("change", function() {
+            var type = $(this).val();
+            var lo = new CXGN.List();
+            lo.renderLists('list_dialog', { type });
+        });
     },
 
     renderPublicLists: function(div) {
diff --git a/mason/site/list.mas b/mason/site/list.mas
index ca16fe9b24..bdc389837a 100644
--- a/mason/site/list.mas
+++ b/mason/site/list.mas
@@ -10,8 +10,7 @@
       </div>
       <div class="modal-body">
         <div class="container-fluid">
-	  <div id="list_dialog_div">
-	  </div>
+          <div id="list_dialog_div"></div>
         </div>
       </div>
       <div class="modal-footer">
@@ -31,8 +30,7 @@
       </div>
       <div class="modal-body">
         <div class="container-fluid">
-	  <div id="public_list_dialog_div">
-	  </div>
+          <div id="public_list_dialog_div"></div>
         </div>
       </div>
       <div class="modal-footer">
@@ -51,8 +49,7 @@
       </div>
       <div class="modal-body">
         <div class="container-fluid">
-	  <div id="list_item_dialog_div">
-	  </div>
+          <div id="list_item_dialog_div"></div>
         </div>
       </div>
       <div class="modal-footer">
@@ -64,166 +61,154 @@
 
 
 <div class="modal fade" id="validate_accession_error_display" name="validate_accession_error_display" tabindex="-1" role="dialog" aria-labelledby="listValidationErrorDialog">
-    <div class="modal-dialog modal-lg" role="document">
-        <div class="modal-content">
-            <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-                <h4 class="modal-title" id="listValidationErrorDialog">List Validation Report: Failed</h4>
-            </div>
-            <div class="modal-body">
-              <div class="container-fluid">
-		<div id='validate_stock_missing_accessions_html' style='display:none'></div>
-	      </div>
-	      <div id='validate_stock_add_missing_accessions_for_list' style='display:none'></div>
-              <div class="well">
-		
-                <h3>Elements not found:</h3>
-
-		<div id="elements_not_found_stats"></div>
-
-		<table id="missing_accessions_table" style="margin:0pt">
-		</table><br />
-					
-                <div id="validate_stock_add_missing_accessions">
-                </div>
-
-		<div class='well well-sm'><h3>Optional: Add Missing Accessions to A List</h3>
-		  <div id='validate_stock_add_missing_accessions_for_list_div'></div>
-		  <div id='stocks_with_wrong_case'></div>
-		</div>
-		
-		<div id="validate_stock_missing_accessions"></div>
-		
-		<div id="adjust_case_div">
-		  <h3>Mismatched case</h3>
-		  <table id="wrong_case_table" style="margin:0pt">
-		  </table>
-		  <br />
-		  
-		</div>
-		
-		<div id="wrong_case_message_div"></div>
-		<br />
-		
-		<button class="btn btn-default" id="adjust_case_action_button" disabled>Adjust Case</button>
-		<br /><br />
-		<div>
-		  Click the Adjust Case button to align the case in the list with what is in the database.
-		</div>
-		
-		<h3>Multiple mismatched case</h3>
-		<div id="multiple_case_match_message_div">
-		  <br />
-		  Items listed here have mulitple case mismatches and must be fixed manually. If accessions need to be merged, contact the database directly.
-		</div>
-		
-		<table id="multiple_wrong_case_table" style="margin:0pt">
-		</table>
-		
-		<div id="multiple_case_match_div"><br /><br /></div>
-		
-		<h3>List elements matching a synonym</h3>
-		<div id="synonym_matches_div">
-		  
-		  <table id="element_matches_synonym"  style="margin:0pt">
-		  </table>
-		  <br />
-		  <button class="btn btn-default" id="replace_synonyms_with_uniquenames_button">Replace synonyms with corresponding DB name</button>
-		  
-		</div>
-		
-		<div id="synonym_message"></div>
-		<br />
-		
-		<h3>Multiple synonym matches</h3>
-		<div id="multiple_synonym_matches_div">
-		  <table id="element_matches_multiple_synonyms_table" style="margin:0pt">
-		  </table>
-		  
-		  Multiple synonym matches have to be resolved manually. Contact database administrators if necessary.
-		</div>
-              </div>
-            </div>
-	</div>
-	
-        <div class="modal-footer">
-          <button id="close_missing_accessions_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+  <div class="modal-dialog modal-lg" role="document">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h4 class="modal-title" id="listValidationErrorDialog">List Validation Report: Failed</h4>
+      </div>
+      <div class="modal-body">
+        <div class="container-fluid">
+          <div id='validate_stock_missing_accessions_html' style='display:none'></div>
         </div>
+        <div id='validate_stock_add_missing_accessions_for_list' style='display:none'></div>
+        <div class="well">
+          <h3>Elements not found:</h3>
+          <div id="elements_not_found_stats"></div>
+          <table id="missing_accessions_table" style="margin:0pt"></table>
+          <br />
+          <div id="validate_stock_add_missing_accessions"></div>
+
+          <div class='well well-sm'>
+            <h3>Optional: Add Missing Accessions to A List</h3>
+            <div id='validate_stock_add_missing_accessions_for_list_div'></div>
+            <div id='stocks_with_wrong_case'></div>
+          </div>
+
+          <div id="validate_stock_missing_accessions"></div>
+
+          <div id="adjust_case_div">
+            <h3>Mismatched case</h3>
+            <table id="wrong_case_table" style="margin:0pt"></table>
+            <br />
+          </div>
+
+          <div id="wrong_case_message_div"></div>
+          <br />
+
+          <button class="btn btn-default" id="adjust_case_action_button" disabled>Adjust Case</button>
+          <br /><br />
+          <div>
+            Click the Adjust Case button to align the case in the list with what is in the database.
+          </div>
+
+          <h3>Multiple mismatched case</h3>
+          <div id="multiple_case_match_message_div">
+            <br />
+            Items listed here have mulitple case mismatches and must be fixed manually. If accessions need to be merged, contact the database directly.
+          </div>
+
+          <table id="multiple_wrong_case_table" style="margin:0pt"></table>
+
+          <div id="multiple_case_match_div"><br /><br /></div>
+
+          <h3>List elements matching a synonym</h3>
+          <div id="synonym_matches_div">
+
+            <table id="element_matches_synonym"  style="margin:0pt"></table>
+            <br />
+            <button class="btn btn-default" id="replace_synonyms_with_uniquenames_button">Replace synonyms with corresponding DB name</button>
+
+          </div>
+
+          <div id="synonym_message"></div>
+          <br />
+
+          <h3>Multiple synonym matches</h3>
+          <div id="multiple_synonym_matches_div">
+            <table id="element_matches_multiple_synonyms_table" style="margin:0pt"></table>
+            Multiple synonym matches have to be resolved manually. Contact database administrators if necessary.
+          </div>
+        </div>
+      </div>
     </div>
+
+    <div class="modal-footer">
+      <button id="close_missing_accessions_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+    </div>
+  </div>
 </div>
 
 
 <div class="modal fade" id="fuzzy_search_result_display" name="fuzzy_search_result_display" tabindex="-1" role="dialog" aria-labelledby="fuzzySearchResultDialog">
-    <div class="modal-dialog modal-xl" role="document">
-        <div class="modal-content">
-            <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-                <h4 class="modal-title" id="fuzzySearchResultDialog">Fuzzy Search Results</h4>
-            </div>
-            <div class="modal-body">
-                <div class="container-fluid">
-                    <div id="fuzzy_search_result_display_html">
-                    </div>
-                </div>
-            </div>
-            <div class="modal-footer">
-                <button id="download_fuzzy_search_result" type="button" class="btn btn-primary" onclick="javascript:downloadFuzzyResponse()" >Download</button>
-                <button id="close_fuzzy_search_result_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
-            </div>
+  <div class="modal-dialog modal-xl" role="document">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h4 class="modal-title" id="fuzzySearchResultDialog">Fuzzy Search Results</h4>
+      </div>
+      <div class="modal-body">
+        <div class="container-fluid">
+          <div id="fuzzy_search_result_display_html"></div>
         </div>
+      </div>
+      <div class="modal-footer">
+        <button id="download_fuzzy_search_result" type="button" class="btn btn-primary" onclick="javascript:downloadFuzzyResponse()" >Download</button>
+        <button id="close_fuzzy_search_result_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+      </div>
     </div>
+  </div>
 </div>
 
 <div class="modal fade" id="synonym_search_result_display" name="synonym_search_result_display" tabindex="-1" role="dialog" aria-labelledby="synonymSearchResultDialog">
-    <div class="modal-dialog modal-lg" role="document">
-        <div class="modal-content">
-            <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-                <h4 class="modal-title" id="synonymSearchResultDialog">Synonym Search Results</h4>
-            </div>
-            <div class="modal-body">
-                <div class="container-fluid">
-                    <div id="synonym_search_result_display_html">
-                    </div>
-                </div>
-            </div>
-            <div class="modal-footer">
-              <form id="new-list-from-unames" class="form-inline" style="float:left">
-                <label>Create a New List from Unique Names:</label>
-                <input name="name" type="text" class="form-control" placeholder="List Name...">
-                <button class="btn btn-primary" type="submit">Save</button>
-              </form>
-              <form class="form-inline" style="float:right">
-                <button id="close_fuzzy_search_result_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
-              </form>
-            </div>
+  <div class="modal-dialog modal-lg" role="document">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h4 class="modal-title" id="synonymSearchResultDialog">Synonym Search Results</h4>
+      </div>
+      <div class="modal-body">
+        <div class="container-fluid">
+          <div id="synonym_search_result_display_html"></div>
         </div>
+      </div>
+      <div class="modal-footer">
+        <form id="new-list-from-unames" class="form-inline" style="float:left">
+          <label>Create a New List from Unique Names:</label>
+          <input name="name" type="text" class="form-control" placeholder="List Name...">
+          <button class="btn btn-primary" type="submit">Save</button>
+        </form>
+        <form class="form-inline" style="float:right">
+          <button id="close_fuzzy_search_result_dialog" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+        </form>
+      </div>
     </div>
+  </div>
 </div>
 
 <div class="modal fade" id="availible_seedlots_modal" name="availible_seedlots_modal" tabindex="-1" role="dialog" aria-labelledby="availible_seedlots_modal">
-    <div class="modal-dialog modal-xl" role="document">
-        <div class="modal-content">
-            <div class="modal-header">
-                <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-                <h4>Available Seedlots</h4>
-            </div>
-            <div class="modal-body">
-                <div class="container-fluid">
-                    <& /tools/available_seedlots.mas &>
-                </div>
-            </div>
-            <div class="modal-footer">
-              <form id="new-list-from-seedlots" class="form-inline" style="float:left">
-                <label>Create a New List from Selected Seedlots:</label>
-                <input name="name" type="text" class="form-control" placeholder="List Name...">
-                <button class="btn btn-primary" type="submit">Save</button>
-              </form>
-              <form class="form-inline" style="float:right">
-                <a href="/breeders/seedlots/" class="btn btn-primary">Manage Seedlots</a>
-                <button id="close_availible_seedlots_modal" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
-              </form>
-            </div>
+  <div class="modal-dialog modal-xl" role="document">
+    <div class="modal-content">
+      <div class="modal-header">
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h4>Available Seedlots</h4>
+      </div>
+      <div class="modal-body">
+        <div class="container-fluid">
+          <& /tools/available_seedlots.mas &>
         </div>
+      </div>
+      <div class="modal-footer">
+        <form id="new-list-from-seedlots" class="form-inline" style="float:left">
+          <label>Create a New List from Selected Seedlots:</label>
+          <input name="name" type="text" class="form-control" placeholder="List Name...">
+          <button class="btn btn-primary" type="submit">Save</button>
+        </form>
+        <form class="form-inline" style="float:right">
+          <a href="/breeders/seedlots/" class="btn btn-primary">Manage Seedlots</a>
+          <button id="close_availible_seedlots_modal" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+        </form>
+      </div>
     </div>
+  </div>
 </div>

From 890b20920ed268d1ac38793b996662a81a1f16e7 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Mon, 16 Dec 2024 09:12:13 -0500
Subject: [PATCH 02/10] List Manager: add filter for autocreated lists

---
 js/source/legacy/CXGN/List.js | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index 55db3de07a..70b9d82eaa 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -54,6 +54,8 @@ CXGN.List = function () {
 
 
 
+// User preference for displaying autocreated lists
+const default_render_lists_autocreated = localStorage.getItem("render_lists_autocreated") === 'true';
 
 
 CXGN.List.prototype = {
@@ -335,7 +337,7 @@ CXGN.List.prototype = {
         });
     },
 
-    renderLists: function(div, { type, autocreated = true } = {}) {
+    renderLists: function(div, { type, autocreated = default_render_lists_autocreated } = {}) {
         var lists = this.availableLists();
         var types = this.allListTypes();
 
@@ -351,20 +353,30 @@ CXGN.List.prototype = {
         // Add list type filter
         html += "<div class='well'>";
         html += "<div style='display: flex; flex-wrap: wrap; align-items: baseline; column-gap: 15px; margin-bottom: 15px'>";
+
+        // Filter by List Type
         html += "<p style='white-space: nowrap'><strong>Filter Lists by Type</strong>:</p>";
-        html += "<select id='render_lists_type' class='form-control' style='max-width: 200px'>";
+        html += "<select id='render_lists_type' class='render_lists_filter form-control' style='max-width: 200px'>";
         html += "<option value=''>Any</option>";
         for ( let i = 0; i < types.length; i++ ) {
             let selected = type && type === types[i][1] ? 'selected' : '';
             html += "<option value='" + types[i][1] + "' " + selected + ">"+types[i][1]+"</option>";
         }
         html += "</select>";
+
+        html += "<div style='width: 30px'></div>";
+
+        // Autocreated filter
+        html += "<p style='white-space: nowrap'><strong>Include Autocreated Lists</strong>:</p>";
+        let checked = autocreated ? 'checked' : ''
+        html += "<input id='render_lists_autocreated' class='render_lists_filter' type='checkbox' " + checked + " />";
+
         html += "</div>";
 
         html += '<table id="private_list_data_table" class="table table-hover table-condensed">';
         html += '<thead><tr><th>List Name</th><th>Description</th><th>Date Created</th><th>Date Modified</th><th>Count</th><th>Type</th><th>Validate</th><th>View</th><th>Delete</th><th>Download</th><th>Share</th><th>Group</th></tr></thead><tbody>';
         for (var i = 0; i < lists.length; i++) {
-            if ( !type || type === lists[i][5] ) {
+            if ( (!type || type === lists[i][5]) && (autocreated || !(lists[i][2] || '').startsWith("Autocreated")) ) {
                 html += '<tr><td><a href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><b>'+lists[i][1]+'</b></a></td>';
                 html += '<td>'+lists[i][2]+'</td>';
                 html += '<td>'+lists[i][7]+'</td>';
@@ -431,10 +443,12 @@ CXGN.List.prototype = {
             jQuery("#list_group_select_action").html(list_group_select_action_html);
         });
 
-        jQuery("#render_lists_type").on("change", function() {
-            var type = $(this).val();
+        jQuery(".render_lists_filter").on("change", function() {
+            var type = jQuery('#render_lists_type').val();
+            var autocreated = jQuery("#render_lists_autocreated").is(":checked");
+            localStorage?.setItem("render_lists_autocreated", autocreated);
             var lo = new CXGN.List();
-            lo.renderLists('list_dialog', { type });
+            lo.renderLists('list_dialog', { type, autocreated });
         });
     },
 

From 3f1b558e88060eeceee12c063e330c52df43d087 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Mon, 16 Dec 2024 16:22:19 -0500
Subject: [PATCH 03/10] List Manager: union and intersection list item
 combination

---
 js/source/legacy/CXGN/List.js | 103 +++++++++++++++++++++++++---------
 1 file changed, 78 insertions(+), 25 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index 70b9d82eaa..54a7315979 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -395,7 +395,9 @@ CXGN.List.prototype = {
                 html += '<td><input type="checkbox" id="list_select_checkbox_'+lists[i][0]+'" name="list_select_checkbox" value="'+lists[i][0]+'"/></td></tr>';
             }
         }
-        html = html + '</tbody></table></div>';
+        html += '</tbody></table>';
+        html += '<p style="color: #999; margin-top: 15px;">Select multiple lists by checking them in the <strong>Group</strong> column to delete them all, make them all public/private, or combine the list items into a new list.</p>';
+        html += '</div>';
         html += '<div id="list_group_select_action"></div>';
 
         jQuery('#'+div+'_div').html(html);
@@ -432,13 +434,32 @@ CXGN.List.prototype = {
                     selected.push(jQuery(this).attr('value'));
                 });
 
-                list_group_select_action_html = '<hr><div class="row well well-sm"><div class="col-sm-4">For Selected Lists:</div><div class="col-sm-8">';
-                if (total == 1) {
+                list_group_select_action_html = '<hr><div class="well well-sm" style="padding: 20px">';
+                if (total > 0) {
+                    list_group_select_action_html += '<div class="row">';
+                    list_group_select_action_html += '<div class="col-sm-4"><p><strong>Modify Selected Lists:</strong></p></div>';
+                    list_group_select_action_html += '<div class="col-sm-8">';
                     list_group_select_action_html += '<a id="delete_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:deleteSelectedListGroup(['+selected+'])">Delete</a>&nbsp;<a id="make_public_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePublicSelectedListGroup(['+selected+'])">Make Public</a>&nbsp;<a id="make_private_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePrivateSelectedListGroup(['+selected+'])">Make Private</a>';
-                } else if (total > 1) {
-                    list_group_select_action_html += '<a id="delete_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:deleteSelectedListGroup(['+selected+'])">Delete</a>&nbsp;<a id="make_public_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePublicSelectedListGroup(['+selected+'])">Make Public</a>&nbsp;<a id="make_private_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePrivateSelectedListGroup(['+selected+'])">Make Private</a><br/><br/><div class="input-group input-group-sm"><input type="text" class="form-control" id="new_combined_list_name" placeholder="New List Name"><span class="input-group-btn"><a id="combine_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:combineSelectedListGroup(['+selected+'])">Combine</a></span></div>';
+                    list_group_select_action_html += '</div>';  // end column
+                    list_group_select_action_html += '</div>';  // end row
+                }
+                if (total > 1) {
+                    var unionIcon = '<svg xmlns="http://www.w3.org/2000/svg" width="24px" height="24px" viewBox="0 0 256 256"><path fill="currentColor" d="M172.91 83.09a78 78 0 1 0-89.82 89.82a78 78 0 1 0 89.82-89.82M226 160a65 65 0 0 1-.62 8.9l-53.76-53.77A77.8 77.8 0 0 0 174 96v-.49A66.1 66.1 0 0 1 226 160M45.31 53.79l55.5 55.5a77.9 77.9 0 0 0-12 19L34 73.48a66 66 0 0 1 11.31-19.69m88.92 96l-28-28a66.5 66.5 0 0 1 15.52-15.52l28 28a66.5 66.5 0 0 1-15.52 15.48ZM162 96a65.6 65.6 0 0 1-6 27.49L132.51 100A65.6 65.6 0 0 1 160 94h1.95c.05.7.05 1.35.05 2m-52.71 4.81l-55.5-55.5A66 66 0 0 1 73.48 34l54.8 54.81a77.9 77.9 0 0 0-18.99 12M94 160a65.6 65.6 0 0 1 6-27.49L123.49 156A65.6 65.6 0 0 1 96 162c-.65 0-1.3 0-2-.05zm52.71-4.81l55.5 55.5A66 66 0 0 1 182.52 222l-54.8-54.81a77.9 77.9 0 0 0 18.99-12m8.48-8.48a77.9 77.9 0 0 0 12-19L222 182.52a66 66 0 0 1-11.35 19.69Zm5.3-64.7H160a77.8 77.8 0 0 0-19.13 2.38L87.1 30.62A65 65 0 0 1 96 30a66.1 66.1 0 0 1 64.49 52ZM30 96a65 65 0 0 1 .62-8.9l53.76 53.77A77.8 77.8 0 0 0 82 160v.49A66.1 66.1 0 0 1 30 96m65.51 78H96a77.8 77.8 0 0 0 19.13-2.38l53.77 53.76a65 65 0 0 1-8.9.62a66.1 66.1 0 0 1-64.49-52"/></svg>';
+                    var intersectionIcon = '<svg xmlns="http://www.w3.org/2000/svg" width="24px" height="24px" viewBox="0 0 256 256"><path fill="currentColor" d="M174.63 81.37a80 80 0 1 0-93.26 93.26a80 80 0 1 0 93.26-93.26M100.69 136L120 155.31A63.5 63.5 0 0 1 96 160a63.5 63.5 0 0 1 4.69-24m33.75 11.13l-25.57-25.57a64.7 64.7 0 0 1 12.69-12.69l25.57 25.57a64.7 64.7 0 0 1-12.69 12.69M155.31 120L136 100.69A63.5 63.5 0 0 1 160 96a63.5 63.5 0 0 1-4.69 24M32 96a64 64 0 0 1 126-16a80.08 80.08 0 0 0-77.95 78A64.11 64.11 0 0 1 32 96m128 128a64.11 64.11 0 0 1-62-48a80.08 80.08 0 0 0 78-78a64 64 0 0 1-16 126"/></svg>';
+
+                    list_group_select_action_html += '<div class="row" style="margin-top: 15px">';
+                    list_group_select_action_html += '<div class="col-sm-4"><p><strong>Combine List Items From Selected Lists to a New List:</strong></p></div>';
+                    list_group_select_action_html += '<div class="col-sm-8">';
+                    list_group_select_action_html += '<div class="input-group input-group-sm">'
+                    list_group_select_action_html += '<input type="text" class="form-control" id="new_combined_list_name" placeholder="New List Name"><span class="input-group-btn">';
+                    list_group_select_action_html += '<button id="combine_selected_list_group" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'union\')">' + unionIcon + 'Union</button>';
+                    list_group_select_action_html += '<button id="combine_selected_list_group" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'intersection\')">' + intersectionIcon + 'Intersection</button>';
+                    list_group_select_action_html += '</input></span>';
+                    list_group_select_action_html += '</div>';  // End input group
+                    list_group_select_action_html += '</div>';  // end column
+                    list_group_select_action_html += '</div>';  // end row
                 }
-                list_group_select_action_html += '</div></div>';
+                list_group_select_action_html += '</div>'; // End well
             }
             jQuery("#list_group_select_action").html(list_group_select_action_html);
         });
@@ -1755,36 +1776,68 @@ function makePrivateSelectedListGroup(list_ids) {
     }
 }
 
-function combineSelectedListGroup(list_ids) {
+/**
+ * Combine the items from the selected lists and create a new list
+ * The items can be combined either using a union method or intersection method
+ * @param {Array[Integer]} list_ids Array of List IDs of Lists to combine
+ * @param {String} type Method of combining lists (either 'union' or 'intersection', union is default)
+ */
+function combineSelectedListGroup(list_ids, type = 'union') {
     var arrayLength = list_ids.length;
     var list_name = jQuery('#new_combined_list_name').val();
-    if (confirm('Combine selected lists into a new list called '+list_name+'?')) {
-        var arrayItems = [];
+    if ( !list_name || list_name === '' ) return alert("You must enter a new list name first");
+
+    if ( confirm('Combine selected lists into a new list called '+list_name+'?') ) {
         var lo = new CXGN.List();
-        var first_list_type = lo.getListType(list_ids[0]);
-        var same_list_types = true;
-        for (var i=0; i<arrayLength; i++) {
+
+        // Check if the selected lists are the same list type
+        var list_types = [];
+        for ( var i=0; i<arrayLength; i++ ) {
             var list_type = lo.getListType(list_ids[i]);
-            if (list_type != first_list_type) {
-                same_list_types = false;
-                if (!confirm('Are you sure you want to combine these list types: '+first_list_type+' and '+list_type)) {
-                    return;
-                }
-            }
+            if ( !list_types.includes(list_type) ) list_types.push(list_type);
         }
+        if ( list_types.length > 1 && !confirm('Are you sure you want to combine these list types: ' + list_types.join(', ')) ) return;
+
+        // Create new list
         var new_list_id = lo.newList(list_name);
-        if (same_list_types == true) {
-            lo.setListType(new_list_id, first_list_type);
+        if ( list_types.length === 1 ) {
+            lo.setListType(new_list_id, list_types[0]);
         }
-        for (var i=0; i<arrayLength; i++) {
-            list = lo.getListData(list_ids[i]);
-            var numElements = list.elements.length;
-            for (var j=0; j<numElements; j++) {
-                arrayItems.push(list.elements[j][1]);
+
+        // Combine list items
+        var arrayItems = [];
+
+        // INTERSECTION
+        if ( type === 'intersection' ) {
+            var allListItems = [];
+            for ( var i=0; i<arrayLength; i++ ) {
+                list = lo.getListData(list_ids[i]);
+                var listItems = [];
+                for ( var j=0; j<list.elements.length; j++ ) {
+                    listItems.push(list.elements[j][1]);
+                }
+                allListItems.push(listItems);
             }
+            arrayItems = allListItems.reduce((result, array) => result.filter(value => array.includes(value)));
         }
+
+        // UNION
+        else {
+            for ( var i=0; i<arrayLength; i++ ) {
+                list = lo.getListData(list_ids[i]);
+                for ( var j=0; j<list.elements.length; j++ ) {
+                    arrayItems.push(list.elements[j][1]);
+                }
+            }
+        }
+
+        // Get unique set of items
+        arrayItems = [...new Set(arrayItems)];
+
+        // Add combined items to new list
         lo.addBulk(new_list_id, arrayItems);
         lo.renderLists('list_dialog');
+        alert("Added " + arrayItems.length + " items to the new List " + list_name);
     }
 }
 

From e3b313aa4080671b3bf21640a4cfe1d40414280f Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Wed, 18 Dec 2024 14:47:35 -0500
Subject: [PATCH 04/10] List Manager: retain page and sort order when
 refreshing the table

---
 js/source/legacy/CXGN/List.js | 34 ++++++++++++++++++++--------------
 1 file changed, 20 insertions(+), 14 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index 54a7315979..f9392e95f7 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -54,8 +54,9 @@ CXGN.List = function () {
 
 
 
-// User preference for displaying autocreated lists
-const default_render_lists_autocreated = localStorage.getItem("render_lists_autocreated") === 'true';
+// Keep track of the rendered lists page number and sort column between refreshes
+var render_lists_page = 0;  // first page
+var render_lists_order = [[0, "asc"]];  // sort by list name, ascending
 
 
 CXGN.List.prototype = {
@@ -337,7 +338,9 @@ CXGN.List.prototype = {
         });
     },
 
-    renderLists: function(div, { type, autocreated = default_render_lists_autocreated } = {}) {
+    renderLists: function(div) {
+        var type = jQuery('#render_lists_type').val();
+        var autocreated = jQuery("#render_lists_autocreated").is(":checked");
         var lists = this.availableLists();
         var types = this.allListTypes();
 
@@ -377,12 +380,13 @@ CXGN.List.prototype = {
         html += '<thead><tr><th>List Name</th><th>Description</th><th>Date Created</th><th>Date Modified</th><th>Count</th><th>Type</th><th>Validate</th><th>View</th><th>Delete</th><th>Download</th><th>Share</th><th>Group</th></tr></thead><tbody>';
         for (var i = 0; i < lists.length; i++) {
             if ( (!type || type === lists[i][5]) && (autocreated || !(lists[i][2] || '').startsWith("Autocreated")) ) {
+                console.log(lists[i][2]);
                 html += '<tr><td><a href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><b>'+lists[i][1]+'</b></a></td>';
-                html += '<td>'+lists[i][2]+'</td>';
-                html += '<td>'+lists[i][7]+'</td>';
-                html += '<td>'+lists[i][8]+'</td>';
-                html += '<td>'+lists[i][3]+'</td>';
-                html += '<td>'+lists[i][5]+'</td>';
+                html += '<td>'+(lists[i][2] ? lists[i][2] : '')+'</td>';
+                html += '<td>'+(lists[i][7] ? new Date(lists[i][7]).toLocaleString() : '')+'</td>';
+                html += '<td>'+(lists[i][8] ? new Date(lists[i][8]).toLocaleString() : '')+'</td>';
+                html += '<td>'+(lists[i][3] ? lists[i][3] : '0')+'</td>';
+                html += '<td>'+(lists[i][5] ? lists[i][5] : '&lt;NOT SET&gt;')+'</td>';
                 html += '<td><a onclick="javascript:validateList(\''+lists[i][0]+'\',\''+lists[i][5]+'\')"><span class="glyphicon glyphicon-ok"></span></a></td>';
                 html += '<td><a title="View" id="view_list_'+lists[i][1]+'" href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><span class="glyphicon glyphicon-th-list"></span></span></td>';
                 html += '<td><a title="Delete" id="delete_list_'+lists[i][1]+'" href="javascript:deleteList('+lists[i][0]+')"><span class="glyphicon glyphicon-remove"></span></a></td>';
@@ -402,10 +406,14 @@ CXGN.List.prototype = {
 
         jQuery('#'+div+'_div').html(html);
 
-        jQuery('#private_list_data_table').DataTable({
+        var table = jQuery('#private_list_data_table').DataTable({
             "destroy": true,
-            "columnDefs": [   { "orderable": false, "targets": [4,5,6,7,8] }  ]
+            "columnDefs": [{ "orderable": false, "targets": [6,7,8,9,10,11] }],
+            "order": render_lists_order
         });
+        table.page(render_lists_page).draw('page');
+        table.on('order', () => render_lists_order = table.order());
+        table.on('page', () => render_lists_page = table.page.info().page);
 
         jQuery('#add_list_button').click(function() {
             var lo = new CXGN.List();
@@ -465,11 +473,9 @@ CXGN.List.prototype = {
         });
 
         jQuery(".render_lists_filter").on("change", function() {
-            var type = jQuery('#render_lists_type').val();
-            var autocreated = jQuery("#render_lists_autocreated").is(":checked");
-            localStorage?.setItem("render_lists_autocreated", autocreated);
+            render_lists_page = 0;
             var lo = new CXGN.List();
-            lo.renderLists('list_dialog', { type, autocreated });
+            lo.renderLists('list_dialog');
         });
     },
 

From 5d4c448e997a154cbecd8aeab29ecefe9efe50f4 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Wed, 18 Dec 2024 15:33:24 -0500
Subject: [PATCH 05/10] List Manager: fix bug selected lists after page size
 has changed

---
 js/source/legacy/CXGN/List.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index f9392e95f7..bc4f8e5d74 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -383,8 +383,8 @@ CXGN.List.prototype = {
                 console.log(lists[i][2]);
                 html += '<tr><td><a href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><b>'+lists[i][1]+'</b></a></td>';
                 html += '<td>'+(lists[i][2] ? lists[i][2] : '')+'</td>';
-                html += '<td>'+(lists[i][7] ? new Date(lists[i][7]).toLocaleString() : '')+'</td>';
-                html += '<td>'+(lists[i][8] ? new Date(lists[i][8]).toLocaleString() : '')+'</td>';
+                html += '<td>'+(lists[i][7] ? new Date(lists[i][7]).toLocaleDateString() : '')+'</td>';
+                html += '<td>'+(lists[i][8] ? new Date(lists[i][8]).toLocaleDateString() : '')+'</td>';
                 html += '<td>'+(lists[i][3] ? lists[i][3] : '0')+'</td>';
                 html += '<td>'+(lists[i][5] ? lists[i][5] : '&lt;NOT SET&gt;')+'</td>';
                 html += '<td><a onclick="javascript:validateList(\''+lists[i][0]+'\',\''+lists[i][5]+'\')"><span class="glyphicon glyphicon-ok"></span></a></td>';
@@ -431,7 +431,7 @@ CXGN.List.prototype = {
             lo.renderPublicLists('public_list_dialog_div');
         });
 
-        jQuery("input[name='list_select_checkbox']").click(function() {
+        jQuery('body').on("click", "input[name='list_select_checkbox']", function() {
             var total=jQuery("input[name='list_select_checkbox']:checked").length;
             var list_group_select_action_html='';
             if (total == 0) {

From 5bd1bed4a1a54fb4e053e0672836a4bffc36d5d7 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Wed, 18 Dec 2024 15:42:02 -0500
Subject: [PATCH 06/10] Remove debugging output

---
 js/source/legacy/CXGN/List.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index bc4f8e5d74..3ae654d3d2 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -380,7 +380,6 @@ CXGN.List.prototype = {
         html += '<thead><tr><th>List Name</th><th>Description</th><th>Date Created</th><th>Date Modified</th><th>Count</th><th>Type</th><th>Validate</th><th>View</th><th>Delete</th><th>Download</th><th>Share</th><th>Group</th></tr></thead><tbody>';
         for (var i = 0; i < lists.length; i++) {
             if ( (!type || type === lists[i][5]) && (autocreated || !(lists[i][2] || '').startsWith("Autocreated")) ) {
-                console.log(lists[i][2]);
                 html += '<tr><td><a href="javascript:showListItems(\'list_item_dialog\','+lists[i][0]+')"><b>'+lists[i][1]+'</b></a></td>';
                 html += '<td>'+(lists[i][2] ? lists[i][2] : '')+'</td>';
                 html += '<td>'+(lists[i][7] ? new Date(lists[i][7]).toLocaleDateString() : '')+'</td>';

From e6a47a49e6c7709b706a585f4a815c3ff21a3446 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Thu, 19 Dec 2024 10:20:14 -0500
Subject: [PATCH 07/10] List Manager: fix combine list button IDs

---
 js/source/legacy/CXGN/List.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index 3ae654d3d2..e56573f537 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -459,8 +459,8 @@ CXGN.List.prototype = {
                     list_group_select_action_html += '<div class="col-sm-8">';
                     list_group_select_action_html += '<div class="input-group input-group-sm">'
                     list_group_select_action_html += '<input type="text" class="form-control" id="new_combined_list_name" placeholder="New List Name"><span class="input-group-btn">';
-                    list_group_select_action_html += '<button id="combine_selected_list_group" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'union\')">' + unionIcon + 'Union</button>';
-                    list_group_select_action_html += '<button id="combine_selected_list_group" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'intersection\')">' + intersectionIcon + 'Intersection</button>';
+                    list_group_select_action_html += '<button id="combine_selected_list_group_union" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'union\')">' + unionIcon + 'Union</button>';
+                    list_group_select_action_html += '<button id="combine_selected_list_group_intersection" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'intersection\')">' + intersectionIcon + 'Intersection</button>';
                     list_group_select_action_html += '</input></span>';
                     list_group_select_action_html += '</div>';  // End input group
                     list_group_select_action_html += '</div>';  // end column

From bb9c92b417c895d225a092bd92f1a8f0ff1aa81a Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Thu, 19 Dec 2024 10:24:37 -0500
Subject: [PATCH 08/10] Tests: fix list group tests, combine union and
 intersection

---
 t/selenium2/01_list/list_groups.t | 57 +++++++++++++++++++++++++++----
 1 file changed, 50 insertions(+), 7 deletions(-)

diff --git a/t/selenium2/01_list/list_groups.t b/t/selenium2/01_list/list_groups.t
index c2fe9d3b30..a5c72d5c79 100644
--- a/t/selenium2/01_list/list_groups.t
+++ b/t/selenium2/01_list/list_groups.t
@@ -62,17 +62,19 @@ $d->while_logged_in_as("submitter", sub {
 
     sleep(1);
 
-    $d->find_element_ok("list_select_checkbox_808", "id", "checkbox select list")->click();
+    ## Combine two lists using union
+
+    $d->find_element_ok("list_select_checkbox_808", "id", "checkbox select list 808")->click();
 
     sleep(1);
 
-    $d->find_element_ok("list_select_checkbox_810", "id", "checkbox select list")->click();
+    $d->find_element_ok("list_select_checkbox_810", "id", "checkbox select list 810")->click();
 
     sleep(1);
 
-    $d->find_element_ok("new_combined_list_name", "id", "combine selected list group")->send_keys("combined_list");
+    $d->find_element_ok("new_combined_list_name", "id", "name selected list group - union")->send_keys("combined_list_union");
 
-    $d->find_element_ok("combine_selected_list_group", "id", "combine selected list group")->click();
+    $d->find_element_ok("combine_selected_list_group_union", "id", "combine selected list group - union")->click();
 
     sleep(1);
 
@@ -80,15 +82,56 @@ $d->while_logged_in_as("submitter", sub {
 
     sleep(1);
 
-    $d->find_element_ok("view_list_combined_list", "id", "check view combined list");
+    ok($d->driver->get_alert_text() =~ m/Added 4 items to the new List combined_list_union/i, 'created selected list group - union');
+    $d->accept_alert_ok();
 
     sleep(1);
 
-    $d->find_element_ok("list_select_checkbox_808", "id", "checkbox select list")->click();
+    $d->find_element_ok("view_list_combined_list_union", "id", "check view combined list - union");
 
     sleep(1);
 
-    $d->find_element_ok("list_select_checkbox_810", "id", "checkbox select list")->click();
+    ## Combine two lists using intersection
+
+    $d->find_element_ok("list_select_checkbox_808", "id", "checkbox select list 808")->click();
+
+    sleep(1);
+
+    $d->find_element_ok("list_select_checkbox_4", "id", "checkbox select list 4")->click();
+
+    sleep(1);
+
+    $d->find_element_ok("new_combined_list_name", "id", "name selected list group - intersection")->send_keys("combined_list_intersection");
+
+    $d->find_element_ok("combine_selected_list_group_intersection", "id", "combine selected list group - intersection")->click();
+
+    sleep(1);
+
+    $d->accept_alert_ok();
+
+    sleep(1);
+
+    # Accept alert about mismatched list types (one list doesn't have it's type set)
+    $d->accept_alert_ok();
+
+    sleep(1);
+
+    ok($d->driver->get_alert_text() =~ m/Added 2 items to the new List combined_list_intersection/i, 'created selected list group - intersection');
+    $d->accept_alert_ok();
+
+    sleep(1);
+
+    $d->find_element_ok("view_list_combined_list_intersection", "id", "check view combined list - intersection");
+
+    sleep(1);
+
+    ## Delete list group
+
+    $d->find_element_ok("list_select_checkbox_808", "id", "checkbox select list 808")->click();
+
+    sleep(1);
+
+    $d->find_element_ok("list_select_checkbox_810", "id", "checkbox select list 810")->click();
 
     sleep(1);
 

From 6c7a8e7e798abd798ce15e114e51c914677a58dc Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Wed, 8 Jan 2025 15:19:51 -0500
Subject: [PATCH 09/10] List Manager: Move multi-list functions to table header

---
 js/source/legacy/CXGN/List.js | 90 +++++++++++++++++++++--------------
 1 file changed, 53 insertions(+), 37 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index e56573f537..97c0820173 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -353,11 +353,17 @@ CXGN.List.prototype = {
             jQuery('#'+div+'_div').html(html);
         }
 
-        // Add list type filter
+        // List Table Container
         html += "<div class='well'>";
-        html += "<div style='display: flex; flex-wrap: wrap; align-items: baseline; column-gap: 15px; margin-bottom: 15px'>";
+
+        // Table Header
+        html += "<div style='display: flex; flex-wrap: wrap; column-gap: 30px; justify-content: space-between; margin-bottom: 15px'>";
+
+        // Filter Container
+        html += "<div style='display: flex; flex-direction: column; row-gap: 15px'>"
 
         // Filter by List Type
+        html += "<div style='display: flex; align-items: baseline; column-gap: 15px;'>"
         html += "<p style='white-space: nowrap'><strong>Filter Lists by Type</strong>:</p>";
         html += "<select id='render_lists_type' class='render_lists_filter form-control' style='max-width: 200px'>";
         html += "<option value=''>Any</option>";
@@ -366,16 +372,25 @@ CXGN.List.prototype = {
             html += "<option value='" + types[i][1] + "' " + selected + ">"+types[i][1]+"</option>";
         }
         html += "</select>";
-
-        html += "<div style='width: 30px'></div>";
+        html += "</div>";
 
         // Autocreated filter
+        html += "<div style='display: flex; align-items: baseline; column-gap: 15px;'>";
         html += "<p style='white-space: nowrap'><strong>Include Autocreated Lists</strong>:</p>";
         let checked = autocreated ? 'checked' : ''
         html += "<input id='render_lists_autocreated' class='render_lists_filter' type='checkbox' " + checked + " />";
+        html += "</div>";
+
+        // End Filter Container
+        html += "</div>";
 
+        // Multiple List Container
+        html += "<div id='list_group_select_action' style='flex-grow: 1; width: min-content; min-width: 500px;'></div>";
+
+        // End Header
         html += "</div>";
 
+        // List Table
         html += '<table id="private_list_data_table" class="table table-hover table-condensed">';
         html += '<thead><tr><th>List Name</th><th>Description</th><th>Date Created</th><th>Date Modified</th><th>Count</th><th>Type</th><th>Validate</th><th>View</th><th>Delete</th><th>Download</th><th>Share</th><th>Group</th></tr></thead><tbody>';
         for (var i = 0; i < lists.length; i++) {
@@ -399,9 +414,7 @@ CXGN.List.prototype = {
             }
         }
         html += '</tbody></table>';
-        html += '<p style="color: #999; margin-top: 15px;">Select multiple lists by checking them in the <strong>Group</strong> column to delete them all, make them all public/private, or combine the list items into a new list.</p>';
         html += '</div>';
-        html += '<div id="list_group_select_action"></div>';
 
         jQuery('#'+div+'_div').html(html);
 
@@ -430,46 +443,49 @@ CXGN.List.prototype = {
             lo.renderPublicLists('public_list_dialog_div');
         });
 
-        jQuery('body').on("click", "input[name='list_select_checkbox']", function() {
+        function render_selected_lists_container() {
             var total=jQuery("input[name='list_select_checkbox']:checked").length;
             var list_group_select_action_html='';
-            if (total == 0) {
-                list_group_select_action_html += '';
-            } else {
+            if (total > 1) {
                 var selected = [];
                 jQuery("input[name='list_select_checkbox']:checked").each(function() {
                     selected.push(jQuery(this).attr('value'));
                 });
 
-                list_group_select_action_html = '<hr><div class="well well-sm" style="padding: 20px">';
-                if (total > 0) {
-                    list_group_select_action_html += '<div class="row">';
-                    list_group_select_action_html += '<div class="col-sm-4"><p><strong>Modify Selected Lists:</strong></p></div>';
-                    list_group_select_action_html += '<div class="col-sm-8">';
-                    list_group_select_action_html += '<a id="delete_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:deleteSelectedListGroup(['+selected+'])">Delete</a>&nbsp;<a id="make_public_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePublicSelectedListGroup(['+selected+'])">Make Public</a>&nbsp;<a id="make_private_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePrivateSelectedListGroup(['+selected+'])">Make Private</a>';
-                    list_group_select_action_html += '</div>';  // end column
-                    list_group_select_action_html += '</div>';  // end row
-                }
-                if (total > 1) {
-                    var unionIcon = '<svg xmlns="http://www.w3.org/2000/svg" width="24px" height="24px" viewBox="0 0 256 256"><path fill="currentColor" d="M172.91 83.09a78 78 0 1 0-89.82 89.82a78 78 0 1 0 89.82-89.82M226 160a65 65 0 0 1-.62 8.9l-53.76-53.77A77.8 77.8 0 0 0 174 96v-.49A66.1 66.1 0 0 1 226 160M45.31 53.79l55.5 55.5a77.9 77.9 0 0 0-12 19L34 73.48a66 66 0 0 1 11.31-19.69m88.92 96l-28-28a66.5 66.5 0 0 1 15.52-15.52l28 28a66.5 66.5 0 0 1-15.52 15.48ZM162 96a65.6 65.6 0 0 1-6 27.49L132.51 100A65.6 65.6 0 0 1 160 94h1.95c.05.7.05 1.35.05 2m-52.71 4.81l-55.5-55.5A66 66 0 0 1 73.48 34l54.8 54.81a77.9 77.9 0 0 0-18.99 12M94 160a65.6 65.6 0 0 1 6-27.49L123.49 156A65.6 65.6 0 0 1 96 162c-.65 0-1.3 0-2-.05zm52.71-4.81l55.5 55.5A66 66 0 0 1 182.52 222l-54.8-54.81a77.9 77.9 0 0 0 18.99-12m8.48-8.48a77.9 77.9 0 0 0 12-19L222 182.52a66 66 0 0 1-11.35 19.69Zm5.3-64.7H160a77.8 77.8 0 0 0-19.13 2.38L87.1 30.62A65 65 0 0 1 96 30a66.1 66.1 0 0 1 64.49 52ZM30 96a65 65 0 0 1 .62-8.9l53.76 53.77A77.8 77.8 0 0 0 82 160v.49A66.1 66.1 0 0 1 30 96m65.51 78H96a77.8 77.8 0 0 0 19.13-2.38l53.77 53.76a65 65 0 0 1-8.9.62a66.1 66.1 0 0 1-64.49-52"/></svg>';
-                    var intersectionIcon = '<svg xmlns="http://www.w3.org/2000/svg" width="24px" height="24px" viewBox="0 0 256 256"><path fill="currentColor" d="M174.63 81.37a80 80 0 1 0-93.26 93.26a80 80 0 1 0 93.26-93.26M100.69 136L120 155.31A63.5 63.5 0 0 1 96 160a63.5 63.5 0 0 1 4.69-24m33.75 11.13l-25.57-25.57a64.7 64.7 0 0 1 12.69-12.69l25.57 25.57a64.7 64.7 0 0 1-12.69 12.69M155.31 120L136 100.69A63.5 63.5 0 0 1 160 96a63.5 63.5 0 0 1-4.69 24M32 96a64 64 0 0 1 126-16a80.08 80.08 0 0 0-77.95 78A64.11 64.11 0 0 1 32 96m128 128a64.11 64.11 0 0 1-62-48a80.08 80.08 0 0 0 78-78a64 64 0 0 1-16 126"/></svg>';
-
-                    list_group_select_action_html += '<div class="row" style="margin-top: 15px">';
-                    list_group_select_action_html += '<div class="col-sm-4"><p><strong>Combine List Items From Selected Lists to a New List:</strong></p></div>';
-                    list_group_select_action_html += '<div class="col-sm-8">';
-                    list_group_select_action_html += '<div class="input-group input-group-sm">'
-                    list_group_select_action_html += '<input type="text" class="form-control" id="new_combined_list_name" placeholder="New List Name"><span class="input-group-btn">';
-                    list_group_select_action_html += '<button id="combine_selected_list_group_union" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'union\')">' + unionIcon + 'Union</button>';
-                    list_group_select_action_html += '<button id="combine_selected_list_group_intersection" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'intersection\')">' + intersectionIcon + 'Intersection</button>';
-                    list_group_select_action_html += '</input></span>';
-                    list_group_select_action_html += '</div>';  // End input group
-                    list_group_select_action_html += '</div>';  // end column
-                    list_group_select_action_html += '</div>';  // end row
-                }
-                list_group_select_action_html += '</div>'; // End well
+                // Delete / Public / Private Functions
+                list_group_select_action_html += '<div class="row">';
+                list_group_select_action_html += '<div class="col-sm-4"><p><strong>Modify Selected Lists:</strong></p></div>';
+                list_group_select_action_html += '<div class="col-sm-8">';
+                list_group_select_action_html += '<a id="delete_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:deleteSelectedListGroup(['+selected+'])">Delete</a>&nbsp;<a id="make_public_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePublicSelectedListGroup(['+selected+'])">Make Public</a>&nbsp;<a id="make_private_selected_list_group" class="btn btn-primary btn-sm" style="color:white" href="javascript:makePrivateSelectedListGroup(['+selected+'])">Make Private</a>';
+                list_group_select_action_html += '</div>';  // end column
+                list_group_select_action_html += '</div>';  // end row
+
+                // Union / Intersection Icons
+                var unionIcon = '<svg xmlns="http://www.w3.org/2000/svg" width="24px" height="24px" viewBox="0 0 256 256"><path fill="currentColor" d="M172.91 83.09a78 78 0 1 0-89.82 89.82a78 78 0 1 0 89.82-89.82M226 160a65 65 0 0 1-.62 8.9l-53.76-53.77A77.8 77.8 0 0 0 174 96v-.49A66.1 66.1 0 0 1 226 160M45.31 53.79l55.5 55.5a77.9 77.9 0 0 0-12 19L34 73.48a66 66 0 0 1 11.31-19.69m88.92 96l-28-28a66.5 66.5 0 0 1 15.52-15.52l28 28a66.5 66.5 0 0 1-15.52 15.48ZM162 96a65.6 65.6 0 0 1-6 27.49L132.51 100A65.6 65.6 0 0 1 160 94h1.95c.05.7.05 1.35.05 2m-52.71 4.81l-55.5-55.5A66 66 0 0 1 73.48 34l54.8 54.81a77.9 77.9 0 0 0-18.99 12M94 160a65.6 65.6 0 0 1 6-27.49L123.49 156A65.6 65.6 0 0 1 96 162c-.65 0-1.3 0-2-.05zm52.71-4.81l55.5 55.5A66 66 0 0 1 182.52 222l-54.8-54.81a77.9 77.9 0 0 0 18.99-12m8.48-8.48a77.9 77.9 0 0 0 12-19L222 182.52a66 66 0 0 1-11.35 19.69Zm5.3-64.7H160a77.8 77.8 0 0 0-19.13 2.38L87.1 30.62A65 65 0 0 1 96 30a66.1 66.1 0 0 1 64.49 52ZM30 96a65 65 0 0 1 .62-8.9l53.76 53.77A77.8 77.8 0 0 0 82 160v.49A66.1 66.1 0 0 1 30 96m65.51 78H96a77.8 77.8 0 0 0 19.13-2.38l53.77 53.76a65 65 0 0 1-8.9.62a66.1 66.1 0 0 1-64.49-52"/></svg>';
+                var intersectionIcon = '<svg xmlns="http://www.w3.org/2000/svg" width="24px" height="24px" viewBox="0 0 256 256"><path fill="currentColor" d="M174.63 81.37a80 80 0 1 0-93.26 93.26a80 80 0 1 0 93.26-93.26M100.69 136L120 155.31A63.5 63.5 0 0 1 96 160a63.5 63.5 0 0 1 4.69-24m33.75 11.13l-25.57-25.57a64.7 64.7 0 0 1 12.69-12.69l25.57 25.57a64.7 64.7 0 0 1-12.69 12.69M155.31 120L136 100.69A63.5 63.5 0 0 1 160 96a63.5 63.5 0 0 1-4.69 24M32 96a64 64 0 0 1 126-16a80.08 80.08 0 0 0-77.95 78A64.11 64.11 0 0 1 32 96m128 128a64.11 64.11 0 0 1-62-48a80.08 80.08 0 0 0 78-78a64 64 0 0 1-16 126"/></svg>';
+
+                // Union / Intersection Functions
+                list_group_select_action_html += '<div class="row" style="margin-top: 15px">';
+                list_group_select_action_html += '<div class="col-sm-4"><p><strong>Combine List Items From Selected Lists to a New List:</strong></p></div>';
+                list_group_select_action_html += '<div class="col-sm-8">';
+                list_group_select_action_html += '<div class="input-group input-group-sm">'
+                list_group_select_action_html += '<input type="text" class="form-control" id="new_combined_list_name" placeholder="New List Name"><span class="input-group-btn">';
+                list_group_select_action_html += '<button id="combine_selected_list_group_union" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'union\')">' + unionIcon + 'Union</button>';
+                list_group_select_action_html += '<button id="combine_selected_list_group_intersection" class="btn btn-primary btn-sm" style="color:white; display: inline-flex; align-items: center; gap: 5px;" onclick="javascript:combineSelectedListGroup(['+selected+'], \'intersection\')">' + intersectionIcon + 'Intersection</button>';
+                list_group_select_action_html += '</input></span>';
+                list_group_select_action_html += '</div>';  // End input group
+                list_group_select_action_html += '</div>';  // end column
+                list_group_select_action_html += '</div>';  // end row
+            }
+            else {
+                list_group_select_action_html += '<div style="width: 100%; text-align: right">';
+                list_group_select_action_html += '<p><em>Select 2 or more lists in the <strong>Group</strong> column to modify or combine them</em></p>';
+                list_group_select_action_html += '</div>';
             }
             jQuery("#list_group_select_action").html(list_group_select_action_html);
-        });
+        }
+        jQuery('body').on("click", "input[name='list_select_checkbox']", render_selected_lists_container);
+        render_selected_lists_container();
 
         jQuery(".render_lists_filter").on("change", function() {
             render_lists_page = 0;

From 5bcec4c6ced224f845551657fd52f183fad171fa Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Thu, 9 Jan 2025 08:43:34 -0500
Subject: [PATCH 10/10] List Manager: return error message when combining lists
 with no common items

---
 js/source/legacy/CXGN/List.js | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index 97c0820173..decb5000f1 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -1819,12 +1819,6 @@ function combineSelectedListGroup(list_ids, type = 'union') {
         }
         if ( list_types.length > 1 && !confirm('Are you sure you want to combine these list types: ' + list_types.join(', ')) ) return;
 
-        // Create new list
-        var new_list_id = lo.newList(list_name);
-        if ( list_types.length === 1 ) {
-            lo.setListType(new_list_id, list_types[0]);
-        }
-
         // Combine list items
         var arrayItems = [];
 
@@ -1854,8 +1848,15 @@ function combineSelectedListGroup(list_ids, type = 'union') {
 
         // Get unique set of items
         arrayItems = [...new Set(arrayItems)];
+        if ( !arrayItems || arrayItems.length === 0 ) {
+            return alert("The selected lists don't have any list items in common.  New list not created.");
+        }
 
         // Add combined items to new list
+        var new_list_id = lo.newList(list_name);
+        if ( list_types.length === 1 ) {
+            lo.setListType(new_list_id, list_types[0]);
+        }
         lo.addBulk(new_list_id, arrayItems);
         lo.renderLists('list_dialog');
         alert("Added " + arrayItems.length + " items to the new List " + list_name);