54ea59ee208f0e498cfeb3d6ca7f1478fca8d5a4
hiram
  Wed Sep 11 13:31:29 2024 -0700
adding documention for all pop up informations boxes refs #32596

diff --git src/hg/js/assemblySearch.js src/hg/js/assemblySearch.js
index 88c3cf6..035d175 100644
--- src/hg/js/assemblySearch.js
+++ src/hg/js/assemblySearch.js
@@ -248,38 +248,38 @@
           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"><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>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</span></div></th>';
-  headerRow += '<th><div class="tooltip">Scientific name&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptext">scientific name</span></div></th>';
+  headerRow += '<th><div class="tooltip">Scientific name&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptext">Binomial scientific name</span></div></th>';
   headerRow += '<th><div class="tooltip">NCBI Assembly&nbsp;&#9432;<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&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 GenArk system.</span></div></th>';
-  headerRow += '<th><div class="tooltip">Description&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptextright">other meta data for this assembly.</span></div></th>';
-  headerRow += '<th><div class="tooltip">Status&nbsp;&#9432;<span onclick="event.stopPropagation()" class="tooltiptextright">various other status</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 advanced search options";
     stateObject.advancedSearchVisible = true;
   } else {
     searchOptions.style.display = "none";
     advancedSearchButton.textContent = "Show advanced search options";
@@ -413,38 +413,38 @@
             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>" + genomicEntries[id].priority + " ";
         var hardSpace = "&nbsp;";
-        if (genomicEntries[id].refSeqCategory) {
-           status += " " + genomicEntries[id].refSeqCategory;
-           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);