562b1b24f9d7cf5157c799f733ba219e2e9f7da9
max
Wed Sep 9 09:06:30 2026 -0700
Assembly search page uses the shared copyToClipboard instead of its own copy
The page carried a copy of copyToClipboard marked "borrowed this code from
utils.js", and the two had already drifted apart: the fix that stops the button
claiming a copy that a browser refused went into one and not the other. The
page now loads utils.js, as nine other static pages already do, and its own
copy is gone. jquery is already loaded by the page header, so nothing else was
needed.
The page also declared a global named debug, which utils.js declares too. Both
start out false and the two uses in utils.js are in functions this page never
calls, so nothing was broken, but the page flag is now searchDebug. The debug
URL parameter and stateObject.debug keep their names.
refs #38294
diff --git src/hg/js/assemblySearch.js src/hg/js/assemblySearch.js
index 1f767e4dc78..f9cb67a62be 100644
--- src/hg/js/assemblySearch.js
+++ src/hg/js/assemblySearch.js
@@ -1,878 +1,825 @@
// global variables:
/* jshint esnext: true */
-var debug = false;
+var searchDebug = false; // not "debug": utils.js owns that global name
var measureTiming = false;
var urlParams;
var query = "";
var maxItemsOutput = 500;
var asmIdText = null;
// adjust default here and in assemblySearch.html
var browserExist = "mayExist";
var betterCommonName = null;
var comment = null;
var stateObject = {}; // maintain page state
var requestSubmitButton = null;
var completedAsmId = new Map(); // keep track of requests completed
// so they won't be repeated
var maxLength = 1024; // limit all incoming strings to this length
// This function is called on DOMContentLoaded as the initialization
// procedure for first time page draw
document.addEventListener('DOMContentLoaded', function() {
// allow semi colon separators as well as ampersand
var urlArgList = window.location.search.replaceAll(";", "&");
urlParams = new URLSearchParams(urlArgList);
if (urlParams.has('level')) {
let asmLevel = urlParams.get('level');
document.getElementById('asmLevelAny').checked = true; // default
// only one of these four cases will be true
if (asmLevel === "complete")
document.getElementById('asmLevelComplete').checked = true;
if (asmLevel === "chromosome")
document.getElementById('asmLevelChromosome').checked = true;
if (asmLevel === "scaffold")
document.getElementById('asmLevelScaffold').checked = true;
if (asmLevel === "contig")
document.getElementById('asmLevelContig').checked = true;
}
if (urlParams.has('status')) {
let asmStatus = urlParams.get('status');
document.getElementById('statusAny').checked = true; // default
// only one of these three cases will be true
if (asmStatus === "latest")
document.getElementById('statusLatest').checked = true;
if (asmStatus === "replaced")
document.getElementById('statusReplaced').checked = true;
if (asmStatus === "suppressed")
document.getElementById('statusSuppressed').checked = true;
}
if (urlParams.has('category')) {
let refSeqCategory = urlParams.get('category');
document.getElementById('refSeqAny').checked = true; // default
// only one of these etwo cases will be true
if (refSeqCategory === "reference")
document.getElementById('refSeqReference').checked = true;
if (refSeqCategory === "representative")
document.getElementById('refSeqRepresentative').checked = true;
}
// default starts as hidden
let copyIcon0 = document.getElementById('copyIcon0');
stateObject.copyIcon0 = copyIcon0.innerHTML;
document.getElementById('urlCopyLink').style.display = "none";
stateObject.advancedSearchVisible = false;
advancedSearchVisible(false);
if (urlParams.has('advancedSearch')) {
let advancedSearch = urlParams.get('advancedSearch');
advancedSearchVisible(advancedSearch);
stateObject.advancedSearchVisible = advancedSearch;
}
if (urlParams.has('measureTiming')) { // accepts no value or other string
var measureValue = urlParams.get('measureTiming');
if ("0" === measureValue | "off" === measureValue) {
measureTiming = false;
} else { // any other string turns it on
measureTiming = true;
}
}
if (urlParams.has('browser')) {
var browserValue = urlParams.get('browser');
if ("mayExist" === browserValue) {
browserExist = "mayExist";
document.getElementById('mustExist').checked = true;
document.getElementById('notExist').checked = true;
} else if ("mustExist" === browserValue) {
browserExist = "mustExist";
document.getElementById('mustExist').checked = true;
document.getElementById('notExist').checked = false;
} else if ("notExist" === browserValue) {
browserExist = "notExist";
document.getElementById('mustExist').checked = false;
document.getElementById('notExist').checked = true;
// } else {
// not going to worry about this here today, but there should be
// a non-obtrusive dialog pop-up message about illegal arguments
// alert("warning: illegal value for browser=... must be one of: mayExist, mustExist, notExist");
}
}
if (urlParams.has('debug')) { // accepts no value or other string
var debugValue = urlParams.get('debug');
if ("0" === debugValue | "off" === debugValue) {
- debug = false;
+ searchDebug = false;
} else { // any other string turns it on
- debug = true;
+ searchDebug = true;
}
}
// add extra element to the help text bullet list for API example
- if (debug) {
+ if (searchDebug) {
var searchTipList = document.getElementById("searchTipList");
// Create a new list item
var li = document.createElement("li");
li.innerHTML = "example API call: n/a";
// Append the new list item to the ordered list
searchTipList.appendChild(li);
}
var searchForm = document.getElementById('searchForm');
var advancedSearchButton = document.getElementById('advancedSearchButton');
var searchInput = document.getElementById('searchBox');
var clearButton = document.getElementById('clearSearch');
asmIdText = document.getElementById("formAsmId");
asmIdText.textContent = asmIdText.textContent.substring(0,maxLength);
betterCommonName = document.getElementById("betterCommonName");
betterCommonName.value = betterCommonName.value.substring(0,maxLength);
comment = document.getElementById("comment");
comment.value = comment.value.substring(0,maxLength);
requestSubmitButton = document.getElementById("submitButton");
document.getElementById("modalFeedback").addEventListener("submit", checkForm, false);
modalInit();
var tableBody = document.getElementById('tableBody');
tableBody.innerHTML = '
(empty table)
';
clearButton.addEventListener('click', function() {
searchInput.value = ''; // Clear the search input field
});
searchForm.addEventListener('submit', function(event) {
event.preventDefault(); // Prevent form submission
// the trim() removes stray white space before or after the string
var searchTerm = document.getElementById('searchBox').value.trim();
var resultCountLimit = document.getElementById('maxItemsOutput');
var mustExist = document.getElementById('mustExist').checked;
var notExist = document.getElementById('notExist').checked;
browserExist = "mustExist";
if (mustExist && notExist) {
browserExist = "mayExist";
} else if (notExist) {
browserExist = "notExist";
}
makeRequest(searchTerm, browserExist, resultCountLimit.value);
});
advancedSearchButton.addEventListener('click', function() {
document.getElementById('urlCopyLink').style.display = "none";
let searchOptions = document.getElementById("advancedSearchOptions");
// I don't know why it is false the first time ?
if (! searchOptions.style.display || searchOptions.style.display === "none") {
advancedSearchVisible(true);
} else {
advancedSearchVisible(false);
}
});
// restore history on back button
window.addEventListener('popstate', function(e) {
var state = event.state;
if (state) {
stateObject.queryString = state.queryString;
stateObject.advancedSearchVisible = state.advancedSearchVisible;
stateObject.maxItemsOutput = state.maxItemsOutput;
stateObject.browser = state.browser;
stateObject.debug = state.debug;
stateObject.measureTiming = state.measureTiming;
stateObject.wordMatch = state.wordMatch;
stateObject.asmStatus = state.asmStatus;
stateObject.refSeqCategory = state.refSeqCategory;
stateObject.asmLevel = state.asmLevel;
stateObject.jsonData = state.jsonData;
document.getElementById('mustExist').checked = false;
document.getElementById('notExist').checked = false;
if (stateObject.browser === "mustExist") {
document.getElementById('mustExist').checked = true;
}
if (stateObject.browser === "notExist") {
document.getElementById('notExist').checked = true;
}
if (stateObject.browser === "mayExist") {
document.getElementById('mustExist').checked = true;
document.getElementById('notExist').checked = true;
}
advancedSearchVisible(stateObject.advancedSearchVisible);
if (stateObject.wordMatch === "allWords") {
document.getElementById("allWords").checked = true;
} else {
document.getElementById("anyWord").checked = true;
}
// only one of these four cases will be true
if (stateObject.asmStatus === "statusAny")
document.getElementById('statusAny').checked = true;
if (stateObject.asmStatus === "latest")
document.getElementById('statusLatest').checked = true;
if (stateObject.asmStatus === "replaced")
document.getElementById('statusReplaced').checked = true;
if (stateObject.asmStatus === "suppressed")
document.getElementById('statusSuppressed').checked = true;
// only one of these three cases will be true
if (stateObject.refSeqCategory === "refSeqAny")
document.getElementById('refSeqAny').checked = true;
if (stateObject.refSeqCategory === "reference")
document.getElementById('refSeqReference').checked = true;
if (stateObject.refSeqCategory === "representative")
document.getElementById('refSeqRepresentative').checked = true;
// only one of these five cases will be true
if (stateObject.asmLevel === "asmLevelAny")
document.getElementById('asmLevelAny').checked = true;
if (stateObject.asmLevel === "complete")
document.getElementById('asmLevelComplete').checked = true;
if (stateObject.asmLevel === "chromosome")
document.getElementById('asmLevelChromosome').checked = true;
if (stateObject.asmLevel === "scaffold")
document.getElementById('asmLevelScaffold').checked = true;
if (stateObject.asmLevel === "contig")
document.getElementById('asmLevelContig').checked = true;
document.getElementById('searchBox').value = stateObject.queryString;
populateTableAndInfo(JSON.parse(stateObject.jsonData));
// alert("state: '" + JSON.stringify(stateObject) + "'");
}
});
var tableHeader = document.getElementById('tableHeader');
headerRefresh(tableHeader);
if (urlParams.has('maxItemsOutput')) {
maxItemsOutput = parseInt(urlParams.get('maxItemsOutput'), 10);
if (maxItemsOutput < 1) {
maxItemsOutput = 1;
} else if (maxItemsOutput > 1000) {
maxItemsOutput = 1000;
}
document.getElementById('maxItemsOutput').value = maxItemsOutput;
}
if (urlParams.has('q')) {
query = urlParams.get('q').trim();
if (query.length > 0) {
searchInput.value = query;
document.getElementById('submitSearch').click();
}
}
document.getElementById("measureTiming").style.display = "none";
});
// refresh the thead columns in the specified table
function headerRefresh(tableHead) {
// clear existing content
tableHead.innerHTML = '';
// re-populate header row - the sortable system added a class to
// the last sorted column, need to rebuild the headerRow to get the
// header back to pristine condition for the next sort
var headerRow = '
';
let circleQuestion = '';
headerRow += '
View/ request ⓘview opens the genome browser for an existing assembly, request opens an assembly request form.
';
headerRow += '
English common name ⓘEnglish common name. This field may also include a unique identifier and the year the assembly was released.
';
headerRow += '
Scientific name ⓘThe Scientific name is the standardized, Latin-based designation used in biological taxonomy to formally classify and identify a species. Obtained from NCBI taxonomy.
';
headerRow += '
NCBI Assembly ⓘThe GC accession number for the assembly, if available, links to the corresponding NCBI resource record or UCSC download options for local UCSC assemblies.
';
headerRow += '
Year ⓘYear assembly was released.
';
headerRow += '
GenArk clade ⓘClade specification as found in the GenArk system, this is not a strict taxonomy category, merely a division of assemblies into several categories.
';
headerRow += '
Description ⓘDescription may include other names, the taxId, year of assembly release and assembly center.
';
headerRow += '
Status ⓘWhen specified, status will show the Assembly status the RefSeq category and the Assembly level.
';
headerRow += '
';
tableHead.innerHTML = headerRow;
}
// call with visible true to make visible, false to hide
function advancedSearchVisible(visible) {
var advancedSearchButton = document.getElementById("advancedSearchButton");
var searchOptions = document.getElementById("advancedSearchOptions");
if (visible) {
searchOptions.style.display = "flex";
advancedSearchButton.textContent = "Hide search options";
stateObject.advancedSearchVisible = true;
} else {
searchOptions.style.display = "none";
advancedSearchButton.textContent = "Show search options";
stateObject.advancedSearchVisible = false;
}
}
// Function to highlight words in the result that match the words
// in the queryString. Work through each item of the rowData object,
// for each string, find out if it matches any of the words in the
// queryString. This is tricky, there are extra characters besides
// just [a-zA-Z] that are getting in the way of these matches, where
// the MySQL could match, for example: checking:
// 'HG02257' =? '(HG02257.pat'
// 'HG02257' =? 'HG02257.alt.pat.f1_v2'
// doesn't match here, but MySQL match did
function highlightMatch(queryString, rowData) {
// fixup the queryString words to get rid of the special characters
var words = queryString.split(/\s+/);
var wholeWord = []; // going to be words that match completely
var prefix = []; // going to be words that match prefix
for (let word of words) {
var noPrefix = word.replace(/^[-+]/, ''); // remove + - beginning
if (noPrefix.endsWith("*")) {
let subPrefix = noPrefix.replace(/\*$/, '').match(/(\w+)/g);
if (subPrefix.length > 1) {
let i = 0;
for ( ; i < subPrefix.length - 1; i++) {
wholeWord.push(subPrefix[i]);
}
prefix.push(subPrefix[i].replace(/\*$/, ''));
} else {
prefix.push(noPrefix.replace(/\*$/, ''));
}
} else {
wholeWord.push(noPrefix);
}
}
if (wholeWord.length > 0) {
for (let word of wholeWord) {
for (let key in rowData) {
if (rowData.hasOwnProperty(key)) {
if (typeof rowData[key] === 'string') {
let wholeSubs = word.match(/(\w+)/g);
if (wholeSubs && wholeSubs.length > 0) {
for (let whole of wholeSubs) {
let newString = "";
let value = rowData[key];
let subWords = value.match(/(\w+)|(\W+)/g);
for (let subWord of subWords) {
if ( whole.toLowerCase() === subWord.toLowerCase() ) {
newString += "" + subWord + "";
} else {
newString += subWord;
}
}
newString = newString.trim();
if (newString !== rowData[key])
rowData[key] = newString;
} // for (let whole of wholeSubs)
} // if (wholeSubs.length > 0)
} // if (typeof rowData[key] === 'string')
} // if (rowData.hasOwnProperty(key))
} // for (let key in rowData)
} // for (let word of wholeWord)
} // if (wholeWord.length > 0)
if (prefix.length > 0) {
for (let word of prefix) {
for (let key in rowData) {
if (rowData.hasOwnProperty(key)) {
if (typeof rowData[key] === 'string') {
let value = rowData[key];
let subWords = value.match(/(\w+)|(\W+)/g);
let newString = "";
for (let subWord of subWords) {
if ( subWord.toLowerCase().startsWith(word.toLowerCase())) {
newString += "" + subWord + "";
} else {
newString += subWord;
}
}
newString = newString.trim();
if (newString !== rowData[key])
rowData[key] = newString;
}
}
}
}
}
}
// Function to generate the table and extra information
function populateTableAndInfo(jsonData) {
var tableHeader = document.getElementById('tableHeader');
var tableBody = document.getElementById('tableBody');
var metaData = document.getElementById('metaData');
document.getElementById('resultCounts').innerHTML = "";
document.getElementById('elapsedTime').innerHTML = "0";
// Clear existing table content
tableHeader.innerHTML = '';
tableBody.innerHTML = '';
metaData.innerHTML = '';
// Extract the genomic entries and the extra info
var genomicEntries = {};
var extraInfo = {};
for (var key in jsonData) {
if (jsonData[key] && jsonData[key].scientificName) {
genomicEntries[key] = jsonData[key];
} else {
extraInfo[key] = jsonData[key];
}
}
headerRefresh(tableHeader);
var count = 0;
for (var id in genomicEntries) {
highlightMatch(extraInfo.q.trim(), genomicEntries[id]);
var dataRow = '
';
var browserUrl = id;
var asmInfoUrl = id;
if (genomicEntries[id].browserExists) {
if (id.startsWith("GC")) {
browserUrl = "view";
asmInfoUrl = "" + id + "";
} else {
browserUrl = "view";
asmInfoUrl = "" + id + "";
}
dataRow += "
" + browserUrl + "
";
} else {
dataRow += "
";
}
dataRow += "
" + genomicEntries[id].commonName + "
";
dataRow += "
" + genomicEntries[id].scientificName + "
";
dataRow += "
" + asmInfoUrl + "
";
dataRow += "
" + genomicEntries[id].year + "
";
dataRow += "
" + genomicEntries[id].clade + "
";
dataRow += "
" + genomicEntries[id].description + "
";
var status = "
";
var breakSpace = ""; // first one does not need the break
if (genomicEntries[id].versionStatus) {
status += breakSpace + genomicEntries[id].versionStatus;
breakSpace = " "; // subsequent words will have the break
}
if (genomicEntries[id].refSeqCategory) {
status += breakSpace + genomicEntries[id].refSeqCategory;
breakSpace = " "; // subsequent words will have the break
}
if (genomicEntries[id].assemblyLevel) {
status += breakSpace + genomicEntries[id].assemblyLevel;
}
status += "
";
dataRow += status;
dataRow += '
';
tableBody.innerHTML += dataRow;
}
var dataTable = document.getElementById('dataTable');
sorttable.makeSortable(dataTable);
var itemCount = parseInt(extraInfo.itemCount, 10);
var totalMatchCount = parseInt(extraInfo.totalMatchCount, 10);
var availableAssemblies = parseInt(extraInfo.availableAssemblies, 10);
var resultCounts = "Query: '" + extraInfo.q.trim() + "', ";
if ( itemCount === totalMatchCount ) {
resultCounts += "Matches " + itemCount.toLocaleString() + "assemblies, ";
} else {
resultCounts += "Matches " + totalMatchCount.toLocaleString() + "assemblies, ";
resultCounts += "limited display here of " + itemCount.toLocaleString() + "matching assemblies, ";
}
resultCounts += "from a total of " + availableAssemblies.toLocaleString() + ".";
document.getElementById('resultCounts').innerHTML = resultCounts;
if (measureTiming) {
var etMs = extraInfo.elapsedTimeMs;
var elapsedTime = "" + etMs.toLocaleString() + "milliseconds";
if ( etMs > 1000 ) {
var etSec = etMs/1000;
elapsedTime = "" + etSec.toFixed(2) + "seconds";
}
document.getElementById('elapsedTime').innerHTML = elapsedTime.toLocaleString();
document.getElementById("measureTiming").style.display = "inline";
} else {
document.getElementById("measureTiming").style.display = "none";
}
document.getElementById('urlCopyLink').style.display = "inline";
} // function populateTableAndInfo(jsonData)
function enableButtons() {
document.getElementById('submitSearch').disabled = false;
document.getElementById('clearSearch').disabled = false;
}
function disableButtons() {
document.getElementById('submitSearch').disabled = true;
document.getElementById('clearSearch').disabled = true;
}
function parentTable(e) {
while (e) {
e = e.parentNode;
if (e.tagName.toLowerCase() === 'table') {
return e;
}
}
return undefined;
}
function whichRow(e) {
while (e) {
if (e.rowIndex) {
return e.rowIndex;
}
e = e.parentNode;
}
return undefined;
}
function closeModal(e)
{
document.getElementById("modalWrapper").className = "";
if (e.preventDefault) {
e.preventDefault();
} else {
e.returnValue = false;
}
}
function clickHandler(e) {
if(!e.target) e.target = e.srcElement;
if(e.target.tagName === "DIV") {
if(e.target.id != "modalWindow") closeModal(e);
}
}
function keyHandler(e) {
if(e.keyCode === 27) closeModal(e);
}
function modalInit() {
if(document.addEventListener) {
document.getElementById("modalClose").addEventListener("click", closeModal, false);
document.addEventListener("click", clickHandler, false);
document.addEventListener("keydown", keyHandler, false);
} else {
document.getElementById("modalClose").attachEvent("onclick", closeModal);
document.attachEvent("onclick", clickHandler);
document.attachEvent("onkeydown", keyHandler);
}
}
function failedRequest(url) {
requestSubmitButton.value = "request failed";
requestSubmitButton.disabled = true;
// garStatus.innerHTML = "FAILED: '" + url + "'";
}
function sendRequest(name, email, asmId, betterName, comment) {
var url = "/cgi-bin/hubApi/assemblyRequest?" +
"asmId=" + encodeURIComponent(asmId) + ";" +
"name=" + encodeURIComponent(name) + ";" +
"email=" + encodeURIComponent(email) + ";" +
"betterName=" + encodeURIComponent(betterName) + ";" +
"comment=" + encodeURIComponent(comment);
var xmlhttp = new XMLHttpRequest();
xmlhttp.onreadystatechange = function() {
if (4 === this.readyState && 200 === this.status) {
requestSubmitButton.value = "request completed";
} else if (4 === this.readyState && this.status >= 400) {
failedRequest(url);
}
};
xmlhttp.open("GET", url, true);
xmlhttp.send();
} // sendRequest: function(name, email, asmId, betterName, comment)
-// borrowed this code from utils.js
-function copyToClipboard(ev) {
- /* copy a piece of text to clipboard. event.target is some DIV or SVG that is an icon.
- * The attribute data-target of this element is the ID of the element that contains the text to copy.
- * The text is either in the attribute data-copy or the innerText.
- * see C function printCopyToClipboardButton(iconId, targetId);
- * */
-
- ev.preventDefault();
-
- var buttonEl = ev.target.closest("button"); // user can click SVG or BUTTON element
-
- var targetId = buttonEl.getAttribute("data-target");
- if (targetId===null)
- targetId = ev.target.parentNode.getAttribute("data-target");
- var textEl = document.getElementById(targetId);
- var text = textEl.getAttribute("data-copy");
- if (text===null)
- text = textEl.innerText;
-
- var textArea = document.createElement("textarea");
- textArea.value = text;
- // Avoid scrolling to bottom
- textArea.style.top = "0";
- textArea.style.left = "0";
- textArea.style.position = "fixed";
- document.body.appendChild(textArea);
- textArea.focus();
- textArea.select();
- var ok = false;
- try {
- ok = document.execCommand('copy');
- } catch (e) {
- ok = false;
- }
- document.body.removeChild(textArea);
- if (ok) {
- /* Say "Copied", then put the button's own label back after three seconds so it is clear
- * that the button can be used again. This page does not load utils.js, so it cannot call
- * copyButtonSaysCopied() there; keep the two in step. */
- if (buttonEl.copyButtonLabel === undefined)
- buttonEl.copyButtonLabel = buttonEl.innerHTML;
- if (buttonEl.copyButtonTimer)
- clearTimeout(buttonEl.copyButtonTimer);
- buttonEl.innerHTML = 'Copied';
- buttonEl.copyButtonTimer = setTimeout(function() {
- buttonEl.innerHTML = buttonEl.copyButtonLabel;
- buttonEl.copyButtonTimer = null;
- }, 3000);
- }
- return ok;
-}
-
// do not allow both checkboxes to go off
function atLeastOneCheckBoxOn(e) {
var mustExist = document.getElementById('mustExist').checked;
var notExist = document.getElementById('notExist').checked;
if (! mustExist && ! notExist ) { // turn on the other one when both off
if (e.name === "mustExist") {
document.getElementById('notExist').checked = true;
} else {
document.getElementById('mustExist').checked = true;
}
}
}
function checkForm(e) {
if (requestSubmitButton.value === "request completed") {
if (e.preventDefault) {
e.preventDefault();
} else {
e.returnValue = false;
}
closeModal(e);
return;
}
var form = (e.target) ? e.target : e.srcElement;
if(form.name.value === "") {
alert("Please enter your Name");
form.name.focus();
if (e.preventDefault) {
e.preventDefault();
} else {
e.returnValue = false;
}
return;
}
form.name.value = form.name.value.substring(0,maxLength);
if(form.email.value === "") {
alert("Please enter a valid Email address");
form.email.focus();
if (e.preventDefault) {
e.preventDefault();
} else {
e.returnValue = false;
}
return;
}
form.email.value = form.email.value.substring(0,maxLength);
// validation regex from:
// https://www.w3resource.com/javascript/form/email-validation.php
// another example from
// https://www.simplilearn.com/tutorials/javascript-tutorial/email-validation-in-javascript
// var validRegex = /^[a-zA-Z0-9.!#$%&'*+/=?^_`{|}~-]+@[a-zA-Z0-9-]+(?:\.[a-zA-Z0-9-]+)*$/;
// another example from
// https://ui.dev/validate-email-address-javascript/
// return /\S+@\S+\.\S+/.test(email)
// return /^[^\s@]+@[^\s@]+\.[^\s@]+$/.test(email)
// var re = /^[^\s@]+@[^\s@]+$/;
// if (re.test(email)) { OK }
// var validEmail = /^\w+([\.-]?\w+)*@\w+([\.-]?\w+)*(\.\w{2,3})+$/;
var validEmail = /^[a-zA-Z0-9.!#$%&'*+/=?^_`{|}~-]+@[a-zA-Z0-9-]+(?:\.[a-zA-Z0-9-]+)*$/;
if(! validEmail.test(form.email.value)) {
alert("You have entered an invalid email address!");
form.email.focus();
if (e.preventDefault) {
e.preventDefault();
} else {
e.returnValue = false;
}
return;
}
sendRequest(form.name.value, form.email.value, asmIdText.textContent, betterCommonName.value, comment.value);
if (e.preventDefault) {
e.preventDefault();
} else {
e.returnValue = false;
}
} // checkForm: function(e)
function asmOpenModal(e) {
if (e.name) {
var modalWindow = document.getElementById("modalWindow");
var pTable = parentTable(e);
var thisRow = whichRow(e);
var colGroup = document.getElementById('colDefinitions');
var comName = "n/a";
var sciName = "n/a";
var descr = "n/a";
var i = 0;
for (i = 0; i < colGroup.children.length; i++) {
if (colGroup.children[i].id === "comName") {
comName = pTable.rows[thisRow].cells[i].innerText;
} else if (colGroup.children[i].id === "sciName") {
sciName = pTable.rows[thisRow].cells[i].innerText;
} else if (colGroup.children[i].id === "description") {
descr = pTable.rows[thisRow].cells[i].innerText;
}
}
document.getElementById("commonName").textContent = comName;
document.getElementById("formSciName").textContent = sciName;
document.getElementById("formAsmId").textContent = e.name;
document.getElementById("comment").value = descr;
if (completedAsmId.has(e.name)) {
requestSubmitButton.value = "request completed";
requestSubmitButton.disabled = false;
document.getElementById("modalWrapper").className = "overlay";
return;
} else {
completedAsmId.set(e.name, true);
requestSubmitButton.value = "Submit request";
}
document.getElementById("modalWrapper").className = "overlay";
requestSubmitButton.disabled = false;
var overflow = modalWindow.offsetHeight - document.documentElement.clientHeight;
if (overflow > 0) {
modalWindow.style.maxHeight = (parseInt(window.getComputedStyle(modalWindow).height) - overflow) + "px";
}
modalWindow.style.marginTop = (-modalWindow.offsetHeight)/2 + "px";
modalWindow.style.marginLeft = (-modalWindow.offsetWidth)/2 + "px";
}
if (e.preventDefault) {
e.preventDefault();
} else {
e.returnValue = false;
}
}
function optionsChange(e) {
// options are changing, share URL is no longer viable, eliminate it
document.getElementById('copyIcon0').innerHTML = stateObject.copyIcon0;
document.getElementById('urlCopyLink').style.display = "none";
}
function makeRequest(query, browserExist, resultLimit) {
// Disable the submit button
disableButtons();
var wordMatch = document.querySelector('input[name="wordMatch"]:checked').value;
var asmStatus = document.querySelector('input[name="asmStatus"]:checked').value;
var refSeqCategory = document.querySelector('input[name="refSeqCategory"]:checked').value;
var asmLevel = document.querySelector('input[name="asmLevel"]:checked').value;
// start with what the user requested:
var queryString = query;
// for allWords, place + sign in front of each word if not already there
if (wordMatch === "allWords") {
var words = queryString.split(/\s+/);
if (words.length > 1) { // not needed on only one word
var queryPlus = ""; // compose new query string
let inQuote = false;
words.forEach(function(word) {
if (word.match(/^[-+]?"/)) {
if (/^[-+]/.test(word))
queryPlus += " " + word; // do not add + to - or + already there
else
queryPlus += " +" + word;
inQuote = true;
} else if (inQuote) {
queryPlus += " " + word; // space separates each word
if (word.endsWith('"'))
inQuote = false;
} else if (/^[-+]/.test(word)) {
queryPlus += " " + word; // do not add + to - or + already there
} else {
queryPlus += " +" + word;
}
});
queryString = queryPlus.trim();
}
}
// remove stray white space from beginning or end
queryString = queryString.trim();
// Show the wait spinner
document.querySelector(".submitContainer").classList.add("loading");
document.getElementById("loadingSpinner").style.display = "block";
var xhr = new XMLHttpRequest();
var urlPrefix = "/cgi-bin/hubApi";
var historyUrl = "?q=" + encodeURIComponent(queryString);
historyUrl += ";browser=" + browserExist;
historyUrl += ";maxItemsOutput=" + resultLimit;
if (asmStatus !== "statusAny") // default is any assembly status
historyUrl += ";status=" + asmStatus; // something specific is being requested
if (refSeqCategory !== "refSeqAny") // default is any RefSeq category
historyUrl += ";category=" + refSeqCategory; // something specific
if (asmLevel !== "asmLevelAny") // default is any level of assembly
historyUrl += ";level=" + asmLevel; // something specific
- if (debug)
+ if (searchDebug)
historyUrl += ";debug=1";
if (measureTiming)
historyUrl += ";measureTiming=1";
var url = "/findGenome" + historyUrl;
- if (debug) {
+ if (searchDebug) {
var apiUrl = "" + url + "";
document.getElementById("recentAjax").innerHTML = apiUrl;
}
stateObject.queryString = queryString;
var searchOptions = document.getElementById("advancedSearchOptions");
if (searchOptions.style.display === "flex") {
stateObject.advancedSearchVisible = true;
historyUrl += ";advancedSearch=true";
} else {
stateObject.advancedSearchVisible = false;
}
stateObject.maxItemsOutput = maxItemsOutput;
stateObject.browser = browserExist;
- stateObject.debug = debug;
+ stateObject.debug = searchDebug;
stateObject.measureTiming = measureTiming;
stateObject.wordMatch = wordMatch;
stateObject.asmStatus = asmStatus;
stateObject.refSeqCategory = refSeqCategory;
stateObject.asmLevel = asmLevel;
let urlText0 = document.getElementById('urlText0');
let hostName = window.location.hostname;
urlText0.innerHTML = "https://" + hostName + "/assemblySearch.html" + historyUrl;
xhr.open('GET', urlPrefix + url, true);
xhr.onload = function() {
if (xhr.status === 200) {
// Hide the wait spinner once the AJAX request is complete
document.querySelector(".submitContainer").classList.remove("loading");
document.getElementById("loadingSpinner").style.display = "none";
document.getElementById('copyIcon0').innerHTML = stateObject.copyIcon0;
enableButtons();
stateObject.jsonData = xhr.responseText;
history.pushState(stateObject, '', historyUrl);
var data = JSON.parse(xhr.responseText);
populateTableAndInfo(data);
} else {
// Hide the wait spinner once the AJAX request is complete
document.querySelector(".submitContainer").classList.remove("loading");
document.getElementById("loadingSpinner").style.display = "none";
document.getElementById('copyIcon0').innerHTML = stateObject.copyIcon0;
document.getElementById('urlCopyLink').style.display = "none";
enableButtons();
var tableBody = document.getElementById('tableBody');
tableBody.innerHTML = "
no results found for query: '" + queryString + "'
";
var metaData = document.getElementById('metaData');
metaData.innerHTML = '';
// metaData.innerHTML = "no results found for query: '" + queryString + "'";
document.getElementById('resultCounts').innerHTML = "";
document.getElementById('elapsedTime').innerHTML = "0";
}
};
xhr.onerror = function() {
alert('console.log("Request failed")');
console.log('Request failed');
};
xhr.send();
}