7e0265c006a53ca478096ed136cc07712fb593e1
hiram
  Fri Jan 30 16:52:23 2026 -0800
beware, returned json data can now include a key "liftable" and it can have the value "null" refs #36232

diff --git src/hg/js/assemblySearch.js src/hg/js/assemblySearch.js
index 506928cdedc..7475b09f83e 100644
--- src/hg/js/assemblySearch.js
+++ src/hg/js/assemblySearch.js
@@ -1,866 +1,866 @@
 // global variables:
 
 /* jshint esnext: true */
 
 var debug = false;
 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;
        } 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&nbsp;&#9432;<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&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptext">English common name.  This field may also include a unique identifier and the year the assembly was released.</span></div></th>';
   headerRow += '<th><div class="tooltip">Scientific name&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptext">The Scientific name is the standardized, Latin-based designation used in biological taxonomy to formally classify and identify a species.  Obtained from NCBI taxonomy.</span></div></th>';
   headerRow += '<th><div class="tooltip">NCBI Assembly&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptext">The GC accession number for the assembly, if available, links to the corresponding NCBI resource record or UCSC download options for local UCSC assemblies.</span></div></th>';
   headerRow += '<th><div class="tooltip">Year&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptextright">Year assembly was released.</span></div></th>';
   headerRow += '<th><div class="tooltip"><em>GenArk</em> clade&nbsp;&#9432;<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&nbsp;&#9432;<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&nbsp;&#9432;<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) {
+        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 = '<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 breakSpace = "";	// first one does not need the break
         if (genomicEntries[id].versionStatus) {
            status += breakSpace + genomicEntries[id].versionStatus;
            breakSpace = "<br>";	// subsequent words will have the break
         }
         if (genomicEntries[id].refSeqCategory) {
            status += breakSpace + genomicEntries[id].refSeqCategory;
            breakSpace = "<br>";	// subsequent words will have the break
         }
         if (genomicEntries[id].assemblyLevel) {
            status += breakSpace + genomicEntries[id].assemblyLevel;
         }
         status += "</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>Query: </em><b>'" + extraInfo.q.trim() + "'</b>, ";
     if ( itemCount === totalMatchCount ) {
       resultCounts += "<em>Matches </em><b>" + itemCount.toLocaleString() + "</b> <em>assemblies, </em>";
     } else {
       resultCounts += "<em>Matches </em><b>" + totalMatchCount.toLocaleString() + "</b> <em>assemblies, </em> ";
       resultCounts += "<em>limited display here of </em><b>" + itemCount.toLocaleString() + "</b> <em>matching assemblies, </em> ";
     }
     resultCounts += "<em>from a total of </em><b>" + availableAssemblies.toLocaleString() + "</b>.";
     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("'","&rsquo;");
 //    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").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();
 }