55372fae7778bb8a83ddceb3e3f942b45e9000ce
hiram
  Wed Aug 21 09:23:10 2024 -0700
remove debug alerts refs #32596

diff --git src/hg/js/assemblySearch.js src/hg/js/assemblySearch.js
index 55a1ba9..fb444a1 100644
--- src/hg/js/assemblySearch.js
+++ src/hg/js/assemblySearch.js
@@ -1,446 +1,444 @@
 // global variables:
 
 var measureTiming = false;
 var urlParams;
 var searchFor = "";
 var maxItemsOutput = 500;
 var asmIdText = null;
 var betterCommonName = null;
 var comment = null;
 var requestSubmitButton = null;
 
 // 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 queryString = window.location.search.replaceAll(";", "&");
     urlParams = new URLSearchParams(queryString);
     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;
        }
     }
 
     var searchForm = document.getElementById('searchForm');
     var searchInput = document.getElementById('searchBox');
     var clearButton = document.getElementById('clearSearch');
     asmIdText = document.getElementById("formAsmId");
     betterCommonName = document.getElementById("betterCommonName");
     comment = document.getElementById("comment");
     requestSubmitButton = document.getElementById("submitButton");
 
     document.getElementById("modalFeedback").addEventListener("submit", checkForm, false);
     modalInit();
 
     clearButton.addEventListener('click', function() {
         searchInput.value = ''; // Clear the search input field
     });
 
     searchForm.addEventListener('submit', function(event) {
         event.preventDefault(); // Prevent form submission
 
         var searchTerm = document.getElementById('searchBox').value;
         var resultCountLimit = document.getElementById('maxItemsOutput');
         var browserExist = "mustExist";
         var mustExist = document.getElementById('mustExist').checked;
         var notExist = document.getElementById('notExist').checked;
         if (mustExist && notExist) {
            browserExist = "mayExist";
         } else if (notExist) {
            browserExist = "notExist";
         }
         var wordMatch = document.querySelector('input[name="wordMatch"]:checked').value;
         makeRequest(searchTerm, browserExist, resultCountLimit.value, wordMatch);
     });
 
     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('searchFor')) {
        searchFor = urlParams.get('searchFor');
        if (searchFor.length > 0) {
           searchInput.value = searchFor;
           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>';
   headerRow += '<th><div class=tooltip>view/<br>request &#9432;<span onclick="event.stopPropagation()" class="tooltiptext"><em>"view"</em> opens the genome browser for an existing assembly, <em>"request"</em> opens an assembly request form.</span></div></th>';
   headerRow += '<th><div class="tooltip">English common name &#9432;<span onclick="event.stopPropagation()" class="tooltiptext">English common name</span></div></th>';
   headerRow += '<th><div class="tooltip">scientific name (count) &#9432;<span onclick="event.stopPropagation()" class="tooltiptext">binomial scientific name</span></div></th>';
   headerRow += '<th><div class="tooltip">NCBI Assembly &#9432;<span onclick="event.stopPropagation()" class="tooltiptext">Links to NCBI resource record.</span></div></th>';
   headerRow += '<th><div class="tooltip"><em>genark</em> clade &#9432;<span onclick="event.stopPropagation()" class="tooltiptextright">clade specification as found in the GenArk system.</span></div></th>';
   headerRow += '<th><div class="tooltip">description &#9432;<span onclick="event.stopPropagation()" class="tooltiptextright">other meta data for this assembly.</span></div></th>';
   headerRow += '</tr>';
   tableHead.innerHTML = headerRow;
 }
 
 // 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) {
         var dataRow = '<tr>';
         var browserUrl = id;
         var ncbiUrl = id;
         if (genomicEntries[id].browserExists) {
           if (id.startsWith("GC")) {
             browserUrl = "<a href='/h/" + id + "?position=lastDbPos' target=_blank>view</a>";
             ncbiUrl = "<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>";
           }
           dataRow += "<th>" + browserUrl + "</th>";
         } else {
           dataRow += "<th><button type=button' onclick='asmOpenModal(this)' name=" + id + "'>request</button></th>";
         }
         dataRow += "<td>" + genomicEntries[id].scientificName + "</td>";
         dataRow += "<td>" + genomicEntries[id].commonName + "</td>";
         dataRow += "<th>" + ncbiUrl + "</th>";
         dataRow += "<td>" + genomicEntries[id].clade + "</td>";
         dataRow += "<td>" + genomicEntries[id].description + "</td>";
         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.genomeSearch + "'</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";
     }
 }	//	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;
-alert("request url: '" + url + "'");
 // 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)
 
 
 function checkForm(e) {
-alert("checkForm");
   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;
   }
   if(form.email.value === "") {
     alert("Please enter a valid Email address");
     form.email.focus();
     if (e.preventDefault) {
       e.preventDefault();
     } else {
       e.returnValue = false;
     }
     return;
   }
 // 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;
     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 makeRequest(query, browserExist, resultLimit, wordMatch) {
     // Disable the submit button
     disableButtons();
     var queryString = query;
     // for allWords, place + sign in front of each word if not already there
     if (wordMatch === "allWords") {
       var words = query.split(/\s+/);
       if (words.length > 1) {	// not needed on only one word
         var queryPlus = "";	// compose new query string
         words.forEach(function(word) {
           if (word.startsWith("+")) {
             queryPlus += " " + word; // space separates each word
           } else {
             queryPlus += " +" + word;
           }
         });
       queryString = queryPlus.trimStart();	// remove first space character
       }
     }
 
     // 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 url = "/findGenome?genomeSearch=" + encodeURIComponent(queryString);
     url += ";browser=" + browserExist;
     url += ";maxItemsOutput=" + resultLimit;
 
     var apiUrl = "<a href='" + urlPrefix + url + "' target=_blank>" + url + "</a>";
     document.getElementById("recentAjax").innerHTML = apiUrl;
 
     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";
             enableButtons();
             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";
             enableButtons();
 	    var tableBody = document.getElementById('tableBody');
             var metaData = document.getElementById('metaData');
             tableBody.innerHTML = '';
             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();
 }