9f3887a28c44e1170456a5e782da504a49ac3b88
hiram
  Mon Aug 19 15:26:08 2024 -0700
rearrangements following input suggestions refs #32596

diff --git src/hg/js/assemblySearch.js src/hg/js/assemblySearch.js
index f8832b0..f555584 100644
--- src/hg/js/assemblySearch.js
+++ src/hg/js/assemblySearch.js
@@ -1,168 +1,179 @@
 document.addEventListener('DOMContentLoaded', function() {
     var searchForm = document.getElementById('searchForm');
     var searchInput = document.getElementById('searchBox');
     var clearButton = document.getElementById('clearSearch');
 
     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('limitResultCount');
-        var browserExist = document.querySelector('input[name="browserExist"]:checked').value;
+        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);
     });
 });
 
 // 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('searchString').innerHTML = "";
     document.getElementById('matchCounts').innerHTML = "0";
     document.getElementById('availableAssemblies').innerHTML = "0";
     document.getElementById('elapsedTime').innerHTML = "0";
 
     // Clear existing table content
     tableHeader.innerHTML = '';
     tableBody.innerHTML = '';
     metaData.innerHTML = '';
 
     // Extract the genomic entries and the extra info
     const genomicEntries = {};
     const extraInfo = {};
 
     for (const key in jsonData) {
         if (jsonData[key].scientificName) {
             genomicEntries[key] = jsonData[key];
         } else {
             extraInfo[key] = jsonData[key];
         }
     }
 
     // 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>count</th>';
-    headerRow += '<th>name</th>';
-    headerRow += '<th>scientificName</th>';
-    headerRow += '<th>commonName</th>';
+    headerRow += '<th>view/<br>request</th>';
+    headerRow += '<th>English common name</th>';
+    headerRow += '<th>scientific name</th>';
+    headerRow += '<th>assembly</th>';
     headerRow += '<th>clade</th>';
     headerRow += '<th>description</th>';
     headerRow += '</tr>';
     tableHeader.innerHTML = headerRow;
 
     var count = 0;
     for (const id in genomicEntries) {
         var dataRow = '<tr>';
-        dataRow += "<th>" + ++count + "</th>";
-        var urlReference = id;
+        var browserUrl = id;
+        var ncbiUrl = id;
         if (genomicEntries[id].browserExists) {
           if (id.startsWith("GC")) {
-            urlReference = "<a href='/h/" + id + "?position=lastDbPos' target=_blank>" + id + "</a>";
+            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 {
-            urlReference = "<a href='/cgi-bin/hgTracks?db=" + id + "' target=_blank>" + id + "</a>";
+            browserUrl = "<a href='/cgi-bin/hgTracks?db=" + id + "' target=_blank>view</a>";
           }
+          dataRow += "<th>" + browserUrl + "</th>";
+        } else {
+          dataRow += "<th>request</th>";
         }
-        dataRow += "<th>" + urlReference + "</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);
 
     document.getElementById('searchString').innerHTML = extraInfo['genomeSearch'];
     document.getElementById('matchCounts').innerHTML = extraInfo['totalMatchCount'].toLocaleString();
     document.getElementById('availableAssemblies').innerHTML = extraInfo['availableAssemblies'].toLocaleString();
     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();
 }	//	function populateTableAndInfo(jsonData)
 
 function enableButtons() {
     document.getElementById('submitButton').disabled = false;
     document.getElementById('clearSearch').disabled = false;
 }
 
 function disableButtons() {
     document.getElementById('submitButton').disabled = true;
     document.getElementById('clearSearch').disabled = true;
 }
 
 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") {
       const words = query.split(/\s+/);
       if (words.length > 1) {	// not needed on only one word
         var queryPlus = "";	// compose new query string
         words.forEach(word => {
           if (word.startsWith("+")) {
             queryPlus += " " + word;	// space separated 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 url = "/cgi-bin/hubApi/findGenome?genomeSearch=" + encodeURIComponent(queryString);
     url += ";browser=" + browserExist;
     url += ";maxItemsOutput=" + resultLimit;
 
     xhr.open('GET', 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('searchString').innerHTML = queryString;
             document.getElementById('matchCounts').innerHTML = "0";
             document.getElementById('availableAssemblies').innerHTML = "0";
             document.getElementById('elapsedTime').innerHTML = "0";
         }
     };
 
     xhr.onerror = function() {
         alert('console.log("Request failed")');
         console.log('Request failed');
     };
 
     xhr.send();
 }