25f258c7fdfbdf417a917fcd00fff78d698def9b
chmalee
  Fri Aug 30 12:01:24 2024 -0700
Big run through of changes to accomodate jquery 3.7.1 upgrade. Most of the changes are replacing the event methods with a change to .on(event, function(..)). A couple more changes are removing calls to jquery.type(). Also fixes various plugins and styles

diff --git src/hg/js/autocomplete.js src/hg/js/autocomplete.js
index d25fef5..1d60c19 100644
--- src/hg/js/autocomplete.js
+++ src/hg/js/autocomplete.js
@@ -1,202 +1,211 @@
 // support stuff for auto-complete using jQuery UI's autocomplete widget
 //
 // requires ajax.js
 // requires utils.js
 /* suggest (aka gene search)
    Requires three elements on page: positionDisplay (static display), positionInput (input textbox) and position (hidden).
 */
 /* jshint esnext: true */
 
 var hgTracks = hgTracks || {};
 
 var suggestBox = {
     ajaxGet: function ajaxGet(db) {
         // Returns autocomplete source function
         // db is the relevant assembly (e.g. "hg18")
         var cache = {}; // cache is is used as a hash to cache responses from the server.
         return function(request, callback) {
             var key = request.term;
             if (key.length < 2) {
                 // show the most recent searches
                 let searchStack = window.localStorage.getItem("searchStack");
                 if (key.length === 0 && searchStack) {
                     let searchObj = JSON.parse(searchStack);
                     let currDb = getDb();
                     if (currDb in searchObj) {
                         // sort the results list according to the stack order:
                         let entries = Object.entries(searchObj[currDb].results);
                         let stack = searchObj[currDb].stack;
                         let callbackData = [];
                         for (let s of stack) {
                             callbackData.push(searchObj[currDb].results[s]);
                         }
                         callback(callbackData);
                     }
                     return;
                 } else {
                     return;
                 }
             }
             if (!cache[key]) {
                 $.ajax({
                     url: "../cgi-bin/hgSuggest",
                     data: "db=" + db + "&prefix=" + encodeURIComponent(key),
                     // dataType: "json",  // XXXX this doesn't work under IE, so we retrieve as text and do an eval to force to an object.
                     trueSuccess: function(response, status) {
                         // We get a lot of duplicate requests (especially the first letters of words),
                         // so we keep a cache of the suggestions lists we've retreived.
                         cache[this.key] = response;
                         this.cont(JSON.parse(response));
                     },
                     success: catchErrorOrDispatch,
                     error: function(request, status, errorThrown) {
                         // tolerate errors (i.e. don't report them) to avoid spamming people on flaky network connections
                         // with tons of error messages (#8816).
                     },
                     key: key,
                     cont: callback
                 });
             } else {
                 callback(JSON.parse(cache[key]));
             }
             // warn(request.term);
         };
     },
 
     clearFindMatches: function() {
         // clear any hgFind.matches set by a previous user selection (e.g. when user directly edits the search box)
         if ($('#hgFindMatches').length) $('#hgFindMatches').remove();
     },
 
     updateFindMatches: function(val) {
         // highlight genes choosen from suggest list (#6330)
         if ($('#hgFindMatches').length) $('#hgFindMatches').val(val);
         else $('#positionInput').parents('form').append("<input type='hidden' id='hgFindMatches' name='hgFind.matches' " + "value='" + val + "'>");
     },
 
     initialized: false,
 
     lastMouseDown : null,
 
     init: function(db, assemblySupportsGeneSuggest, selectCallback, clickCallback) {
         // selectCallback(item): called when the user selects a new genomic position from the list
         // clickCallback(position): called when the user clicks on positionDisplay
         this.initialized = true;
         var lastSelected = null; // this is the last value entered by the user via a suggestion (used to distinguish manual entry in the same field)
         var $posInput = $('#positionInput');
         if ($posInput[0] !== document.activeElement) {
             // Reset value before adding watermark -- only if user is not already typing here
             $posInput.val("");
         }
         var waterMark = suggestBox.restoreWatermark(db, assemblySupportsGeneSuggest);
         if (assemblySupportsGeneSuggest) {
-            $('#positionInput').autocomplete({
+            $.widget("custom.autocompletePosInput",
+                $.ui.autocomplete,
+                {
+                _renderMenu: function(ul, items) {
+                    var that = this;
+                    jQuery.each(items, function(index, item) {
+                        that._renderItemData(ul, item);
+                    });
+                    if ($(this)[0].term === "") {
+                        ul.append("<div class='autoCompleteInfo' style='color:grey'>Showing 5 most recent searches. Enter 2 or more characters to start auto-complete search. Click the go button or press Enter to search across all tracks, hubs and our website. See 'examples' link above.</div>");
+                    } else {
+                        ul.append("<div class='autoCompleteInfo' style='color:grey'>Click the go button or press Enter to search across all tracks, hubs and our website. See 'examples' link above.</div>");
+                    }
+                },
+                _renderItem: function(ul, item) {
+                    // In order to use HTML markup in the autocomplete, one has to overwrite
+                    // autocomplete's _renderItem method using .html instead of .text.
+                    // http://forum.jquery.com/topic/using-html-in-autocomplete
+                    let clockIcon = '';
+                    if ($("#positionInput").val().length < 2) {
+                        clockIcon = '<svg xmlns="http://www.w3.org/2000/svg" height=".75em" width=".75em" viewBox="0 0 512 512"><!--!Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free Copyright 2024 Fonticons, Inc.--><path d="M75 75L41 41C25.9 25.9 0 36.6 0 57.9V168c0 13.3 10.7 24 24 24H134.1c21.4 0 32.1-25.9 17-41l-30.8-30.8C155 85.5 203 64 256 64c106 0 192 86 192 192s-86 192-192 192c-40.8 0-78.6-12.7-109.7-34.4c-14.5-10.1-34.4-6.6-44.6 7.9s-6.6 34.4 7.9 44.6C151.2 495 201.7 512 256 512c141.4 0 256-114.6 256-256S397.4 0 256 0C185.3 0 121.3 28.7 75 75zm181 53c-13.3 0-24 10.7-24 24V256c0 6.4 2.5 12.5 7 17l72 72c9.4 9.4 24.6 9.4 33.9 0s9.4-24.6 0-33.9l-65-65V152c0-13.3-10.7-24-24-24z"/></svg>&nbsp';
+                    }
+                    return $("<li></li>")
+                        .data("ui-autocomplete-item", item)
+                        .append($("<a></a>").html(clockIcon + item.label))
+                        .appendTo(ul);
+                }
+            });
+            $('#positionInput').autocompletePosInput({
                 delay: 500,
                 minLength: 0,
                 source: this.ajaxGet(db),
                 open: function(event, ui) {
                     var pos = $(this).offset().top + $(this).height();
                     if (!isNaN(pos)) {
                         var maxHeight = $(window).height() - pos - 30; // take off a little more because IE needs it
                         var auto = $('.ui-autocomplete');
                         var curHeight = $(auto).children().length * 21;
                         if (curHeight > maxHeight) $(auto).css({
                             maxHeight: maxHeight + 'px',
                             overflow: 'scroll',
                             zIndex: 12
                         });
                         else $(auto).css({
                             maxHeight: 'none',
                             overflow: 'hidden',
                             zIndex: 12
                         });
+                        // we need to remove the ui-menu-item class from the informational div
+                        // because it is not selectable/focuseable
+                        document.querySelectorAll('.autoCompleteInfo').forEach(function(i) {
+                            i.classList.remove("ui-menu-item");
+                        });
                     }
                 },
                 select: function(event, ui) {
                     lastSelected = ui.item.value;
                     suggestBox.updateFindMatches(ui.item.internalId);
                     addRecentSearch(db, ui.item.geneSymbol, ui.item);
                     selectCallback(ui.item);
                     // jQuery('body').css('cursor', 'wait');
                     // document.TrackHeaderForm.submit();
                 }
-            })
-            ._renderMenu = function(ul, items) {
-                var that = this;
-                jQuery.each(items, function(index, item) {
-                    that._renderItem(ul, item);
             });
-                if ($(this)[0].term === "") {
-                    ul.append("<div style='color:grey'>Showing 5 most recent searches. Enter 2 or more characters to start auto-complete search. Click the go button or press Enter to search across all tracks, hubs and our website. See 'examples' link above.</div>");
-                } else {
-                    ul.append("<div style='color:grey'>Click the go button or press Enter to search across all tracks, hubs and our website. See 'examples' link above.</div>");
-                }
-            };
-            $("#positionInput")._renderItem = function(ul, item) {
-                // In order to use HTML markup in the autocomplete, one has to overwrite
-                // autocomplete's _renderItem method using .html instead of .text.
-                // http://forum.jquery.com/topic/using-html-in-autocomplete
-                let clockIcon = '';
-                if ($("#positionInput").val().length < 2) {
-                    clockIcon = '<svg xmlns="http://www.w3.org/2000/svg" height=".75em" width=".75em" viewBox="0 0 512 512"><!--!Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free Copyright 2024 Fonticons, Inc.--><path d="M75 75L41 41C25.9 25.9 0 36.6 0 57.9V168c0 13.3 10.7 24 24 24H134.1c21.4 0 32.1-25.9 17-41l-30.8-30.8C155 85.5 203 64 256 64c106 0 192 86 192 192s-86 192-192 192c-40.8 0-78.6-12.7-109.7-34.4c-14.5-10.1-34.4-6.6-44.6 7.9s-6.6 34.4 7.9 44.6C151.2 495 201.7 512 256 512c141.4 0 256-114.6 256-256S397.4 0 256 0C185.3 0 121.3 28.7 75 75zm181 53c-13.3 0-24 10.7-24 24V256c0 6.4 2.5 12.5 7 17l72 72c9.4 9.4 24.6 9.4 33.9 0s9.4-24.6 0-33.9l-65-65V152c0-13.3-10.7-24-24-24z"/></svg>&nbsp';
-                }
-                return $("<li></li>")
-                    .data("item.autocomplete", item)
-                    .append($("<a></a>").html(clockIcon + item.label))
-                    .appendTo(ul);
-            };
         }
 
         // I want to set focus to the suggest element, but unforunately that prevents PgUp/PgDn from
         // working, which is a major annoyance.
-        $('#positionInput').focus(function() {$(this).autocomplete("search", "");});
-        $("#positionInput").change(function(event) {
+        $('#positionInput').on("focus", function() {$(this).autocompletePosInput("search", "");});
+        $("#positionInput").on("change", function(event) {
             if (!lastSelected || lastSelected !== $('#positionInput').val()) {
                 // This handles case where user typed or edited something rather than choosing from a suggest list;
                 // in this case, we only change the position hidden; we do NOT update the displayed coordinates.
                 var val = $('#positionInput').val();
                 // handles case where users zeroes out positionInput; in that case we revert to currently displayed position
                 if (!val || val.length === 0 || val === waterMark)
                     val = $('#positionDisplay').text();
                 else
                     val = val.replace(/\u2013|\u2014/g, "-");  // replace en-dash and em-dash with hyphen
                 $('#position').val(val);
                 suggestBox.clearFindMatches();
             }
         });
 
-        $("#positionDisplay").mousedown(function(event) {
+        $("#positionDisplay").on("mousedown", function(event) {
             // this let's the user click on the genomic position (e.g. if they want to edit it)
             lastMouseDown = event.offsetX;
         });
 
-        $("#positionDisplay").mouseup(function(event) {
+        $("#positionDisplay").on("mouseup", function(event) {
             if (event.offsetX !== lastMouseDown)
                 return; 
             // this let's the user click on the genomic position (e.g. if they want to edit it)
             clickCallback($(this).text());
             $('#positionInput').val($(this).text());
             suggestBox.clearFindMatches();
             if (hgTracks.windows)
                 {
                 genomePos.positionDisplayDialog();
                 }
         });
     },
 
     restoreWatermark: function(db, assemblySupportsGeneSuggest) {
         var waterMark;
         var $posInput = $('#positionInput');
         if (assemblySupportsGeneSuggest) {
                 waterMark = "gene, chromosome range, search terms, help pages, see examples";
         } else {
             waterMark = "chromosome range, search terms, help pages, see examples";
         }
             //$('input[name="hgt.positionInput"]').val("");
         $posInput.val("");
         $posInput.Watermark(waterMark, '#686868');
 
         return waterMark;
     }, 
 
 };