e4c2e7d703179df583c9749af4f03f5eefe36d49 hiram Sat Nov 16 16:23:30 2024 -0800 can safely limit all incoming strings to a safe length before passing on refs #32596 diff --git src/hg/js/assemblySearch.js src/hg/js/assemblySearch.js index f2ce780..95f885d 100644 --- src/hg/js/assemblySearch.js +++ src/hg/js/assemblySearch.js @@ -1,862 +1,868 @@ // global variables: /* jshint esnext: true */ var debug = true; var measureTiming = true; 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; } else { // any other string turns it on debug = true; } } // add extra element to the help text bullet list for API example if (debug) { var searchTipList = document.getElementById("searchTipList"); // Create a new list item var li = document.createElement("li"); li.innerHTML = "example API call: <span id=\"recentAjax\">n/a</span>"; // 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 = '<tr><td style="text-align:center;" colspan=8><b>(empty table)</b></td></tr>'; 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 = '<tr>'; let circleQuestion = '<svg width="24" height="24"> <circle cx="12" cy="12" r="10" fill="#4444ff" /> <text x="50%" y="50%" text-anchor="middle" fill="white" font-size="13px" font-family="Verdana" dy=".3em">?</text>?</svg>'; headerRow += '<th><div class=tooltip>view/<br>request ⓘ<span onclick="event.stopPropagation()" class="tooltiptext"><b>view</b> opens the genome browser for an existing assembly, <b>request</b> opens an assembly request form.</span></div></th>'; headerRow += '<th><div class="tooltip">English common name ⓘ<span onclick="event.stopPropagation()" class="tooltiptext">English common name</span></div></th>'; headerRow += '<th><div class="tooltip">Scientific name ⓘ<span onclick="event.stopPropagation()" class="tooltiptext">Binomial scientific name</span></div></th>'; headerRow += '<th><div class="tooltip">NCBI Assembly ⓘ<span onclick="event.stopPropagation()" class="tooltiptext">Links to NCBI resource record<br>or UCSC downloads for local UCSC assemblies</span></div></th>'; headerRow += '<th><div class="tooltip">Year ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">Year assembly was released.</span></div></th>'; headerRow += '<th><div class="tooltip"><em>GenArk</em> clade ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">Clade specification as found in the <a href="https://hgdownload.soe.ucsc.edu/hubs/index.html" target=_blank>GenArk</a> system, this is not a strict taxonomy category, merely a division of assemblies into several categories.</span></div></th>'; headerRow += '<th><div class="tooltip">Description ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">Description may include other names, the <b>taxId</b>, year of assembly release and assembly center.</span></div></th>'; headerRow += '<th><div class="tooltip">Status ⓘ<span onclick="event.stopPropagation()" class="tooltiptextright">When specified, status will show the <b>Assembly status</b> the <b>RefSeq category</b> and the <b>Assembly level</b>.</span></div></th>'; headerRow += '</tr>'; 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 += "<span class='highlight'>" + subWord + "</span>"; } 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 += "<span class='highlight'>" + subWord + "</span>"; } 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].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 = '<tr>'; var browserUrl = id; var asmInfoUrl = id; if (genomicEntries[id].browserExists) { if (id.startsWith("GC")) { browserUrl = "<a href='/h/" + id + "?position=lastDbPos' target=_blank>view</a>"; asmInfoUrl = "<a href='https://www.ncbi.nlm.nih.gov/assembly/" + id + "' target=_blank>" + id + "</a>"; } else { browserUrl = "<a href='/cgi-bin/hgTracks?db=" + id + "' target=_blank>view</a>"; asmInfoUrl = "<a href='https://hgdownload.soe.ucsc.edu/goldenPath/" + id + "/bigZips/' target=_blank>" + id + "</a>"; } dataRow += "<th>" + browserUrl + "</th>"; } else { dataRow += "<th><button type=button' onclick='asmOpenModal(this)' name=" + id + ">request</button></th>"; } dataRow += "<td>" + genomicEntries[id].commonName + "</td>"; dataRow += "<td>" + genomicEntries[id].scientificName + "</td>"; dataRow += "<th>" + asmInfoUrl + "</th>"; dataRow += "<td>" + genomicEntries[id].year + "</td>"; dataRow += "<td>" + genomicEntries[id].clade + "</td>"; dataRow += "<td>" + genomicEntries[id].description + "</td>"; var status = "<td>"; var hardSpace = " "; if (genomicEntries[id].versionStatus) { status += " " + genomicEntries[id].versionStatus; hardSpace = ""; } if (genomicEntries[id].refSeqCategory) { status += " " + genomicEntries[id].refSeqCategory; hardSpace = ""; } if (genomicEntries[id].assemblyLevel) { status += " " + genomicEntries[id].assemblyLevel; hardSpace = ""; } status += "</td>"; // status += hardSpace + "</td>"; dataRow += status; dataRow += '</tr>'; 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 = "<em>results for search string: </em><b>'" + extraInfo.q.trim() + "'</b>, "; if ( itemCount === totalMatchCount ) { resultCounts += "<em>showing </em><b>" + itemCount.toLocaleString() + "</b> <em>match results</em>, "; } else { resultCounts += "<em>showing </em><b>" + itemCount.toLocaleString() + "</b> <em>match results</em> "; resultCounts += "<em>from </em><b>" + totalMatchCount.toLocaleString() + "</b> <em>total matches,</em> "; } resultCounts += "<em>out of </em><b>" + availableAssemblies.toLocaleString() + "</b> <em>total number of assemblies</em>"; document.getElementById('resultCounts').innerHTML = resultCounts; if (measureTiming) { var etMs = extraInfo.elapsedTimeMs; var elapsedTime = "<b>" + etMs.toLocaleString() + "</b> <em>milliseconds</em>"; if ( etMs > 1000 ) { var etSec = etMs/1000; elapsedTime = "<b>" + etSec.toFixed(2) + "</b> <em>seconds</em>"; } 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 urlComponents = encodeURIComponent(name) + "&email=" + encodeURIComponent(email) + "&asmId=" + encodeURIComponent(asmId) + "&betterName=" + encodeURIComponent(betterName) + "&comment=" + encodeURIComponent(comment); var url = "/cgi-bin/asr?name=" + urlComponents; // information about escaping characters: // https://stackoverflow.com/questions/10772066/escaping-special-character-in-a-url/10772079 // encodeURI() will not encode: ~!@#$&*()=:/,;?+' // encodeURIComponent() will not encode: ~!*()' // var encoded = encodeURIComponent(url); // encoded = encoded.replace("'","’"); // var encoded = encodeURI(cleaner); var xmlhttp = new XMLHttpRequest(); xmlhttp.onreadystatechange = function() { if (4 === this.readyState && 200 === this.status) { requestSubmitButton.value = "request completed"; } else { if (4 === this.readyState && 404 === this.status) { failedRequest(url); } } }; xmlhttp.open("GET", url, true); xmlhttp.send(); } // sendRequest: function(name, email. asmId) // 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(); document.execCommand('copy'); document.body.removeChild(textArea); buttonEl.innerHTML = 'Copied'; ev.preventDefault(); } // 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").textContent = descr; + 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) historyUrl += ";debug=1"; if (measureTiming) historyUrl += ";measureTiming=1"; var url = "/findGenome" + historyUrl; if (debug) { var apiUrl = "<a href='" + urlPrefix + url + "' target=_blank>" + url + "</a>"; 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.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 = "<tr><td style='text-align:center;' colspan=8><b>no results found for query: <em>'" + queryString + "'</em></b></td></tr>"; var metaData = document.getElementById('metaData'); metaData.innerHTML = ''; // metaData.innerHTML = "<b>no results found for query: '" + queryString + "'</b>"; document.getElementById('resultCounts').innerHTML = ""; document.getElementById('elapsedTime').innerHTML = "0"; } }; xhr.onerror = function() { alert('console.log("Request failed")'); console.log('Request failed'); }; xhr.send(); }