679ee3ed1c4d6f8ff2e2d4fdd7d72b83117c7c49
hiram
  Sun Jan 18 22:12:13 2026 -0800
provide links to browsers as well as lift over chain.gz files refs #31811

diff --git src/hg/js/liftRequest.js src/hg/js/liftRequest.js
index de14abd2141..4ed186feff4 100644
--- src/hg/js/liftRequest.js
+++ src/hg/js/liftRequest.js
@@ -1,190 +1,208 @@
 var assembly1Value = "";
 var assembly2Value = "";
 var genome1 = "";
 var genome2 = "";
 
 /* check if a file exists at the specified URL */
 function fileExists(url, callback) {
     $.ajax({
         type: 'HEAD',
         url: url,
         success: function() {
             callback(true);  // file exists
         },
         error: function() {
             callback(false); // file doesn't exist or not accessible
         }
     });
 }
 
 // Convert GCA_029289425.2 into the path: GCA/028/289/425/GCA_029289425.2
 function gcPath(identifier) {
     var parts = identifier.split('_');
     var prefix = parts[0];
     var numeric = parts[1].split('.')[0];
     var groups = numeric.match(/.{1,3}/g);
     return prefix + "/" + groups.join("/") + "/" + identifier;
 }
 
 function liftOverPath(asm1, asm2) {
     var liftPath = "";
     if (/^GC[AF]_/.test(asm1)) {
         liftPath = "https://hgdownload.soe.ucsc.edu/hubs/";
         liftPath += gcPath(asm1);
     } else {
         liftPath = "https://hgdownload.soe.ucsc.edu/goldenPath/";
         liftPath += asm1;
     }
     liftPath += "/liftOver/" + asm1 + "To";
     liftPath += asm2.charAt(0).toUpperCase() + asm2.slice(1);
     liftPath += ".over.chain.gz";
     return(liftPath);
 }
 
 function checkAssemblyCompatibility(asm1, asm2) {
     $.ajax({
         url: "/cgi-bin/hubApi/liftOver/listExisting?fromGenome=" + encodeURIComponent(asm1) +
              ";" + "toGenome=" + encodeURIComponent(asm2),
         success: function(response) {
             console.log(JSON.stringify(response, null, 2));
             if (response.itemsReturned === 1) {
-               var liftPath = liftOverPath(asm1, asm2);
-               fileExists(liftPath, function(exists) {
+               var liftPath1 = liftOverPath(asm1, asm2);
+               var liftPath2 = liftOverPath(asm2, asm1);
+               var browser1 = "/cgi-bin/hgTracks?db=" + asm1;
+               var browser2 = "/cgi-bin/hgTracks?db=" + asm2
+               fileExists(liftPath1, function(exists) {
                    if (exists) {
+                   document.getElementById("genome1Link").href = browser1;
+                   document.getElementById("genome1Link").textContent = assembly1Value;
+
+                   document.getElementById("genome1LiftOver").href = liftPath1;
+                   document.getElementById("genome1LiftOver").textContent = asm1 + " to " + asm2;
+
+                   // Make visible
+                  document.getElementById("liftExists").style.display = "block";
+                   }
+               });
+               fileExists(liftPath2, function(exists) {
+                   if (exists) {
+                   document.getElementById("genome2Link").href = browser2;
+                   document.getElementById("genome2Link").textContent = assembly2Value;
+
+                   document.getElementById("genome2LiftOver").href = liftPath2;
+                   document.getElementById("genome2LiftOver").textContent = asm2 + " to " + asm1;
+                   // Make visible
                   document.getElementById("liftExists").style.display = "block";
-                   var liftMessage = 'An alignment already exists between these assemblies.<br>' +
-              '<a href="' + liftPath + '" download>Click here to download the chain file</a>';
-                   document.getElementById("liftPath").innerHTML = liftMessage;
                    }
                });
             }
         }
     });
 }
 
 function checkBothAssembliesSelected() {
     if (genome1 && genome2) { // Both assemblies are now selected
         checkAssemblyCompatibility(genome1, genome2);
     }
 }
 
 function assembly1Select(selectEle, item) {
     selectEle.innerHTML = item.label;
     assembly1Value = item.value || item.label;
     genome1 = item.genome;
 //    console.log("asm1:", JSON.stringify(item, null, 2));
     document.getElementById("liftExists").style.display = "none";
     checkBothAssembliesSelected();
 }
 
 function assembly2Select(selectEle, item) {
     selectEle.innerHTML = item.label;
     assembly2Value = item.value || item.label;
     genome2 = item.genome;
 //    console.log("asm2:", JSON.stringify(item, null, 2));
     document.getElementById("liftExists").style.display = "none";
     checkBothAssembliesSelected();
 }
 
 function validateEmail(checkEmail) {
     // Require at least one dot in domain
     var validEmail = /^[a-zA-Z0-9.!#$%&'*+/=?^_`{|}~-]+@[a-zA-Z0-9-]+(?:\.[a-zA-Z0-9-]+)+$/;
 
     if (!validEmail.test(checkEmail)) {
         alert("You have entered an invalid email address !");
         return false;
     }
     return true;
 }
 
 function submitForm() {
     var email = document.getElementById("emailInput").value;
     var comments = document.getElementById("commentsInput").value;
 
     // Hide any previous error message
     document.getElementById("errorMessage").style.display = "none";
 
     if (!assembly1Value) {
         alert("Please select Assembly 1");
         return;
     }
     if (!assembly2Value) {
         alert("Please select Assembly 2");
         return;
     }
     if (!email) {
         alert("Please enter an email address");
         return;
     }
     if (! validateEmail(email)) {
         return;
     }
 
     // Build the API URL with query parameters
     var comment = comments.slice(0, 1000); // make sure that URL is not too long
     comment += ", from: " + assembly1Value + ", to: " + assembly2Value;
     var apiUrl = "/cgi-bin/hubApi/liftRequest?" +
         "fromGenome=" + encodeURIComponent(genome1) + ";" +
         "toGenome=" + encodeURIComponent(genome2) + ";" +
         "email=" + encodeURIComponent(email) + ";" +
         "comment=" + encodeURIComponent(comment);
 
     $.ajax({
         url: apiUrl,
         type: "GET",
         success: function(response) {
             console.log(JSON.stringify(response));
             localStorage.setItem('liftRequestEmail', email);
             document.getElementById("formContainer").style.display = "none";
             document.getElementById("successMessage").style.display = "block";
         },
         error: function(xhr, status, error) {
             var errorMsg = "Error submitting request";
             if (xhr.responseJSON && xhr.responseJSON.error) {
                 errorMsg = xhr.responseJSON.error;
             } else if (xhr.responseText) {
                 try {
                     var parsed = JSON.parse(xhr.responseText);
                     if (parsed.error) {
                         errorMsg = parsed.error;
                     }
                 } catch (e) {
                     errorMsg = error || status || "Unknown error occurred";
                 }
             } else if (error) {
                 errorMsg = error;
             }
             document.getElementById("errorText").textContent = errorMsg;
             document.getElementById("errorMessage").style.display = "block";
         }
     });
 }
 
 document.addEventListener("DOMContentLoaded", () => {
     // Assembly 1 autocomplete
     let selectEle1 = document.getElementById("genomeLabel1");
     let boundSelect1 = assembly1Select.bind(null, selectEle1);
     initSpeciesAutoCompleteDropdown('genomeSearch1', boundSelect1, "/cgi-bin/hubApi/findGenome?browser=mustExist;q=");
 
     let btn1 = document.getElementById("genomeSearchButton1");
     btn1.addEventListener("click", () => {
         let val = document.getElementById("genomeSearch1").value;
         $("[id='genomeSearch1']").autocompleteCat("search", val);
     });
 
     // Assembly 2 autocomplete
     let selectEle2 = document.getElementById("genomeLabel2");
     let boundSelect2 = assembly2Select.bind(null, selectEle2);
     initSpeciesAutoCompleteDropdown('genomeSearch2', boundSelect2, "/cgi-bin/hubApi/findGenome?browser=mustExist;q=");
 
     let btn2 = document.getElementById("genomeSearchButton2");
     btn2.addEventListener("click", () => {
         let val = document.getElementById("genomeSearch2").value;
         $("[id='genomeSearch2']").autocompleteCat("search", val);
     });
     // restore saved email if it exists
     var savedEmail = localStorage.getItem('liftRequestEmail');
     if (savedEmail) {
         document.getElementById("emailInput").value = savedEmail;
     }
 });