55c5be8236794e23ce8b00162917b5d3dbe83b7e
hiram
  Fri Jan 16 16:37:31 2026 -0800
now checking for lift over existing and providing a download link refs #31811

diff --git src/hg/js/liftRequest.js src/hg/js/liftRequest.js
index 50a8f6e8fae..9152c7bb50e 100644
--- src/hg/js/liftRequest.js
+++ src/hg/js/liftRequest.js
@@ -1,93 +1,159 @@
 var assembly1Value = "";
 var assembly2Value = "";
+var genome1 = "";
+var genome2 = "";
+
+// 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;
+    }
+//    alert(liftPath);
+    liftPath += "/liftOver/" + asm1 + "To";
+    liftPath += asm2.charAt(0).toUpperCase() + asm2.slice(1);
+    liftPath += ".over.chain.gz";
+    return(liftPath);
+}
+
+function checkAssemblyCompatibility(asm1, asm2) {
+    // Your API call here
+    console.log("Checking compatibility for:", 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);
+//               console.log("liftPath: ", liftPath);
+               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;
+            }
+            console.log("itemsReturned: ", response.itemsReturned);
+            // Handle response
+        }
+    });
+}
+
+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));
+    console.log("asm1 genome:", item.genome);
+    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));
+    console.log("asm2 genome:", item.genome);
+    document.getElementById("liftExists").style.display = "none";
+    checkBothAssembliesSelected();
 }
 
 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;
     }
 
     // Build the API URL with query parameters
-    comment = comments.slice(0, 1000); // make sure that URL is not too long
+    var comment = comments.slice(0, 1000); // make sure that URL is not too long
     var apiUrl = "/cgi-bin/hubApi/liftRequest?" +
         "fromGenome=" + encodeURIComponent(assembly1Value) + ";" +
         "toGenome=" + encodeURIComponent(assembly2Value) + ";" +
         "email=" + encodeURIComponent(email) + ";" +
-        "comment=" + encodeURIComponent(comments);
+        "comment=" + encodeURIComponent(comment);
 
     $.ajax({
         url: apiUrl,
         type: "GET",
         success: function(response) {
             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, "https://hgwdev-demo-chmalee.gi.ucsc.edu/cgi-bin/hubApi/findGenome?browser=mustExist&q=");
+    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, "https://hgwdev-demo-chmalee.gi.ucsc.edu/cgi-bin/hubApi/findGenome?browser=mustExist&q=");
+    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);
     });
 });