8295800d611b301861e0b6e8597e856ae96abf78
chmalee
Mon Nov 24 16:19:31 2025 -0800
successful HGVS searches get saved into the 'recent searches' dropdown on hgTracks. the position box tries to suggest hgvs when the search term is longer than 8 characters, otherwise we assume it's a gene, refs #35984
diff --git src/hg/js/autocomplete.js src/hg/js/autocomplete.js
index bca7a215600..f5da6076455 100644
--- src/hg/js/autocomplete.js
+++ src/hg/js/autocomplete.js
@@ -1,213 +1,237 @@
// 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]) {
+ if (key.length < 8) {
+ // probably a gene name
$.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 {
+ // probably an hgvs term?
+ $.ajax({
+ url: "../cgi-bin/hgSuggest",
+ data: "db=" + db + "&prefix=" + encodeURIComponent(key) + "&type=hgvs",
+ // dataType: "json", // XXXX this doesn't work under IE, so we retrieve as text and do an eval to force to an object.
+ trueSuccess: function(response, status) {
+ // We get a lot of duplicate requests (especially the first letters of words),
+ // so we keep a cache of the suggestions lists we've retreived.
+ cache[this.key] = response;
+ this.cont(JSON.parse(response));
+ },
+ success: catchErrorOrDispatch,
+ error: function(request, status, errorThrown) {
+ // tolerate errors (i.e. don't report them) to avoid spamming people on flaky network connections
+ // with tons of error messages (#8816).
+ },
+ key: key,
+ cont: callback
+ });
+ }
} else {
callback(JSON.parse(cache[key]));
}
// warn(request.term);
};
},
clearFindMatches: function() {
// clear any hgFind.matches set by a previous user selection (e.g. when user directly edits the search box)
if ($('#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("");
},
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) {
$.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("
Showing 5 most recent searches. Enter 2 or more characters to start auto-complete search.
");
} else {
ul.append("
Click 'Search' or press Enter to search all tracks, hubs and our web pages. See 'examples' link.
");
}
},
_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 = ' ';
}
return $("")
.data("ui-autocomplete-item", item)
.append($("").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);
+ let key = typeof(ui.item.geneSymbol) !== 'undefined' ? ui.item.geneSymbol : ui.item.value;
+ addRecentSearch(db, key, ui.item);
selectCallback(ui.item);
// jQuery('body').css('cursor', 'wait');
// document.TrackHeaderForm.submit();
}
});
}
// I want to set focus to the suggest element, but unforunately that prevents PgUp/PgDn from
// working, which is a major annoyance.
if (typeof $(this).autocompletePosInput !== 'undefined') {
$('#positionInput').on("focus", function() {$(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").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;
});
$("#positionDisplay").on("mouseup", function(event) {
if (event.offsetX !== lastMouseDown)
return;
// this let's the user click on the genomic position (e.g. if they want to edit it)
clickCallback($(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;
},
};