From 9bffb453218182c6dc00ffc624c958193eb0f798 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 3 May 2023 18:05:21 +0200
Subject: [PATCH 01/61] refactor pca pops select menu

---
 js/source/legacy/solGS/pca.js | 60 ++++++++++++++++++++++++++---------
 1 file changed, 45 insertions(+), 15 deletions(-)

diff --git a/js/source/legacy/solGS/pca.js b/js/source/legacy/solGS/pca.js
index 8dfa773ac2..a06d2b3b94 100644
--- a/js/source/legacy/solGS/pca.js
+++ b/js/source/legacy/solGS/pca.js
@@ -8,6 +8,12 @@
 var solGS = solGS || function solGS() {};
 
 solGS.pca = {
+  canvas: "#pca_canvas",
+  pcaPlotDivPrefix: "#pca_plot",
+  pcaMsgDiv: "#pca_message",
+  pcaPopsDiv: "#pca_pops_list",
+  pcaPopsSelectMenuId: "#pca_pops_list_select",
+
   getPcaArgs: function () {
     var page = location.pathname;
     var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("pca_div");
@@ -134,7 +140,7 @@ solGS.pca = {
     }
   },
 
-  loadPcaPops: function (selectId, selectName, dataStr) {
+  displayPcaPop: function (selectId, selectName, dataStr) {
     if (selectId.length === 0) {
       alert("The list is empty. Please select a list with content.");
     } else {
@@ -157,6 +163,32 @@ solGS.pca = {
     }
   },
 
+  populatePcaPopsMenu: function () {
+    var list = new CXGN.List();
+    var lists = list.getLists(["accessions", "plots", "trials"]);
+    var pcaPrivatePops = list.convertArrayToJson(lists.private_lists);
+
+    var menuId = this.pcaPopsSelectMenuId;
+    var menu = new OptionsMenu(menuId);
+    pcaPrivatePops = pcaPrivatePops.flat();
+    var menuElem = menu.addOptions(pcaPrivatePops);
+    
+    if (lists.public_lists[0]) {
+      var pcaPublicLists = list.convertArrayToJson(lists.public_lists);
+      menu.addOptionsSeparator("public lists");
+      menuElem = menu.addOptions(pcaPublicLists);
+    }
+
+    var datasetPops = solGS.dataset.getDatasetPops(["accessions", "trials"]);
+    if (datasetPops) {
+      menu.addOptionsSeparator("datasets");
+      menuElem = menu.addOptions(datasetPops);
+    }
+
+    var pcaPopsDiv = this.pcaPopsDiv;
+    jQuery(pcaPopsDiv).append(menuElem).show();
+  },
+
   selectRow: function (selectId, selectName, dataStr) {
     var pcaPopId = `${dataStr}_${selectId}`;
     var listId;
@@ -933,11 +965,8 @@ jQuery(document).ready(function () {
   var url = location.pathname;
 
   if (url.match(/pca\/analysis/)) {
-    solGS.selectMenu.populateMenu(
-      "pca_pops",
-      ["accessions", "plots", "trials"],
-      ["accessions", "trials"]
-    );
+    solGS.pca.populatePcaPopsMenu();
+
     var pcaArgs = solGS.pca.getPcaArgsFromUrl();
     var pcaPopId = pcaArgs.pca_pop_id;
     if (pcaPopId) {
@@ -976,21 +1005,22 @@ jQuery(document).ready(function () {
     jQuery("#pca_data_type_select").html('<option selected="genotype">Genotype</option>');
   }
 
+  var pcaPopsDiv = solGS.pca.pcaPopsSelectMenuId;
+
   if (url.match(/pca\/analysis/)) {
     jQuery("<option>", {
       value: "",
       selected: true,
-    }).prependTo("#pca_pops_list_select");
+    }).prependTo(pcaPopsDiv);
+
+    var pcaPopsDiv = solGS.pca.pcaPopsSelectMenuId;
+    jQuery(pcaPopsDiv).change(function () {
+      console.log(`this.pcaPopsSelectMenuId changed: ${pcaPopsDiv}`);
+      var selectedPop = jQuery("option:selected", this).data("pop");
 
-    jQuery("#pca_pops_list_select").change(function () {
-      var selectedPop = solGS.selectMenu.getSelectedPop("pca_pops");
-      if (selectedPop.selected_id) {
+      if (selectedPop.id) {
         jQuery("#pca_pop_go_btn").click(function () {
-          solGS.pca.loadPcaPops(
-            selectedPop.selected_id,
-            selectedPop.selected_name,
-            selectedPop.data_str
-          );
+          solGS.pca.displayPcaPop(selectedPop.id, selectedPop.name, selectedPop.data_str);
         });
       }
     });

From 69de6d7f35096ad3d53bf9240b1612778d293543 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Thu, 4 May 2023 09:22:39 +0200
Subject: [PATCH 02/61] refactor lists creation code for reusability

---
 js/source/legacy/CXGN/List.js | 57 ++++++++++++++++++++++++++++++-----
 1 file changed, 50 insertions(+), 7 deletions(-)

diff --git a/js/source/legacy/CXGN/List.js b/js/source/legacy/CXGN/List.js
index eb6631d952..cff1464a45 100644
--- a/js/source/legacy/CXGN/List.js
+++ b/js/source/legacy/CXGN/List.js
@@ -672,16 +672,15 @@ CXGN.List.prototype = {
         return addeditems;
     },
 
-    /* listSelect: Creates an html select with lists of requested types.
+
+    /* getLists: Creates a js object with private and public  lists of the requested list types.
 
        Parameters:
-         div_name: The div_name where the select should appear
-         types: a list of list types that should be listed in the menu
-         add_empty_element: text. if present, add an empty element with the
-           provided text as description
+        types: a list of list types e.g. ['accessions', 'trials']
+      Returns:
+       a js object with 'private_lists' and public_lists, each with arrays of the requested list types
     */
-
-    listSelect: function(div_name, types, empty_element, refresh, hide_public_lists) {
+    getLists: function(types) {
         var lists = new Array();
         var public_lists = new Array();
 
@@ -706,6 +705,50 @@ CXGN.List.prototype = {
             public_lists = this.publicLists();
         }
 
+        return {
+            'private_lists': lists,
+            'public_lists': public_lists
+        }
+    },
+
+    /*
+    converts an array of list data arrays into an array of list data objects (named values)
+    */
+    convertArrayToJson: function (listsArray) {
+
+        var jsonArray = [];
+        if (listsArray) {
+            listsArray.forEach(function (array) {
+
+                var listObj = {
+                    id: array[0],
+                    name: array[1],
+                    type:array[5],
+                    count: array[3]
+                }
+
+                jsonArray.push(listObj);
+            });
+        }
+
+        return jsonArray;
+    },
+
+    /* listSelect: Creates an html select with lists of requested types.
+
+       Parameters:
+         div_name: The div_name where the select should appear
+         types: a list of list types that should be listed in the menu
+         add_empty_element: text. if present, add an empty element with the
+           provided text as description
+    */
+
+    listSelect: function(div_name, types, empty_element, refresh, hide_public_lists) {
+    
+        var allLists = this.getLists(types);
+        var lists = allLists.private_lists;
+        var public_lists = allLists.public_lists;
+
         var html = '<select class="form-control input-sm" id="'+div_name+'_list_select" name="'+div_name+'_list_select" >';
         if (empty_element) {
             html += '<option value="" >'+empty_element+'</option>\n';

From a5377fc589326f9449136148252dc87bfbe1f64a Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Tue, 9 May 2023 10:14:52 +0200
Subject: [PATCH 03/61] use ajax promises

---
 js/source/legacy/solGS/pca.js | 434 ++++++++++++++++++++--------------
 t/selenium2/solgs/pca.t       |  20 +-
 2 files changed, 262 insertions(+), 192 deletions(-)

diff --git a/js/source/legacy/solGS/pca.js b/js/source/legacy/solGS/pca.js
index a06d2b3b94..e4bb1dfc74 100644
--- a/js/source/legacy/solGS/pca.js
+++ b/js/source/legacy/solGS/pca.js
@@ -11,8 +11,8 @@ solGS.pca = {
   canvas: "#pca_canvas",
   pcaPlotDivPrefix: "#pca_plot",
   pcaMsgDiv: "#pca_message",
-  pcaPopsDiv: "#pca_pops_list",
-  pcaPopsSelectMenuId: "#pca_pops_list_select",
+  pcaPopsDiv: "#pca_pops_select_div",
+  pcaPopsSelectMenuId: "#pca_pops_select",
 
   getPcaArgs: function () {
     var page = location.pathname;
@@ -122,7 +122,7 @@ solGS.pca = {
 
       var reg = /\d+-+\d+/;
       if (pcaPopId.match(reg)) {
-        var ids = pcaPopd.split("-");
+        var ids = pcaPopId.split("-");
         args["training_pop_id"] = ids[0];
         args["selection_pop_id"] = ids[1];
       }
@@ -140,8 +140,8 @@ solGS.pca = {
     }
   },
 
-  displayPcaPop: function (selectId, selectName, dataStr) {
-    if (selectId.length === 0) {
+  displaySelectedPcaPop: function (selectedPop) {
+    if (selectedPop.length === 0) {
       alert("The list is empty. Please select a list with content.");
     } else {
       var pcaTable = jQuery("#pca_pops_table").doesExist();
@@ -151,9 +151,8 @@ solGS.pca = {
         jQuery("#pca_pops_selected").append(pcaTable).show();
       }
 
-      var addRow = this.selectRow(selectId, selectName, dataStr);
-      var pcaPopId = `${dataStr}_${selectId}`;
-      console.log(`row ${addRow}`);
+      var addRow = this.selectRow(selectedPop);
+      var pcaPopId = `${selectedPop.data_str}_${selectedPop.id}`;
       var tdId = "#pca_" + pcaPopId;
       var addedRow = jQuery(tdId).doesExist();
 
@@ -164,40 +163,28 @@ solGS.pca = {
   },
 
   populatePcaPopsMenu: function () {
-    var list = new CXGN.List();
-    var lists = list.getLists(["accessions", "plots", "trials"]);
-    var pcaPrivatePops = list.convertArrayToJson(lists.private_lists);
-
+    var listTypes = ["accessions", "plots", "trials"];
+    var datasetTypes = ["accessions", "trials"];
     var menuId = this.pcaPopsSelectMenuId;
     var menu = new OptionsMenu(menuId);
-    pcaPrivatePops = pcaPrivatePops.flat();
-    var menuElem = menu.addOptions(pcaPrivatePops);
-    
-    if (lists.public_lists[0]) {
-      var pcaPublicLists = list.convertArrayToJson(lists.public_lists);
-      menu.addOptionsSeparator("public lists");
-      menuElem = menu.addOptions(pcaPublicLists);
-    }
-
-    var datasetPops = solGS.dataset.getDatasetPops(["accessions", "trials"]);
-    if (datasetPops) {
-      menu.addOptionsSeparator("datasets");
-      menuElem = menu.addOptions(datasetPops);
-    }
-
+    var selectMenu = menu.getSelectMenuByTypes(listTypes, datasetTypes);
     var pcaPopsDiv = this.pcaPopsDiv;
-    jQuery(pcaPopsDiv).append(menuElem).show();
+    jQuery(pcaPopsDiv).append(selectMenu).show();
   },
 
-  selectRow: function (selectId, selectName, dataStr) {
-    var pcaPopId = `${dataStr}_${selectId}`;
+  selectRow: function (selectedPop) {
+    var selectedId = selectedPop.id;
+    var selectedName = selectedPop.name;
+    var dataStr = selectedPop.data_str;
+
+    var pcaPopId = `${dataStr}_${selectedId}`;
     var listId;
     var datasetId;
 
     if (dataStr.match(/dataset/)) {
-      datasetId = selectId;
+      datasetId = selectedId;
     } else if (dataStr.match(/list/)) {
-      listId = selectId;
+      listId = selectedId;
     }
     var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("pca_div");
     var pcaArgs = {
@@ -205,21 +192,15 @@ solGS.pca = {
       data_structure: dataStr,
       dataset_id: datasetId,
       list_id: listId,
-      pca_pop_name: selectName,
+      pca_pop_name: selectedName,
       genotyping_protocol_id: protocolId,
       analysis_type: "pca analysis",
     };
 
-    pcaArgs = JSON.stringify(pcaArgs);
     var runPcaId = this.getRunPcaId(pcaPopId);
-    var onClickVal =
-      '<button type="button" id="' +
-      runPcaId +
-      '" class="btn btn-success"  data-selected-pop=\'' +
-      pcaArgs +
-      "' onclick=\"solGS.pca.checkCachedPca('" +
-      pcaPopId +
-      "')\">Run PCA</button>";
+
+    pcaArgs = JSON.stringify(pcaArgs);
+    var onClickVal = `<button type="button" id=${runPcaId} class="btn btn-success" data-selected-pop='${pcaArgs}'>Run PCA</button>`;
 
     var dataType = ["Genotype", "Phenotype"];
     var dataTypeOpts = this.createDataTypeSelect(dataType, pcaPopId);
@@ -229,7 +210,7 @@ solGS.pca = {
       pcaPopId +
       '">' +
       "<td>" +
-      selectName +
+      selectedName +
       "</td>" +
       "<td>" +
       dataStr +
@@ -247,10 +228,10 @@ solGS.pca = {
     return addRow;
   },
 
-  getSelectedPopPcaArgs: function (pcaPopId) {
+  getSelectedPopPcaArgs: function (runPcaElemId) {
     var pcaArgs;
 
-    var runPcaElemId = this.getRunPcaId(pcaPopId);
+    // var runPcaElemId = this.getRunPcaId(pcaPopId);
     var selectedPopDiv = document.getElementById(runPcaElemId);
     if (selectedPopDiv) {
       var selectedPopData = selectedPopDiv.dataset;
@@ -271,21 +252,18 @@ solGS.pca = {
   },
 
   checkCachedPca: function (pcaArgs) {
-    if (location.pathname.match(/pca\/analysis/)) {
-      pcaArgs = this.getSelectedPopPcaArgs(pcaArgs);
-    }
-
-    if (pcaArgs.analysis_page.match(/\pca\/analysis/)) {
+    if (document.URL.match(/pca\/analysis/)) {
       var message = this.validatePcaParams(pcaArgs);
 
       if (message) {
-        jQuery("#pca_message").prependTo(jQuery("#pca_canvas")).html(message).show().fadeOut(9400);
+        jQuery(this.pcaMsgDiv).prependTo(jQuery(this.canvas)).html(message).show().fadeOut(9400);
       }
 
       var page = pcaArgs.analysis_page;
     }
     pcaArgs = JSON.stringify(pcaArgs);
-    jQuery.ajax({
+
+    var checkCache = jQuery.ajax({
       type: "POST",
       dataType: "json",
       data: {
@@ -293,72 +271,59 @@ solGS.pca = {
         arguments: pcaArgs,
       },
       url: "/solgs/check/cached/result/",
-      // });
-
-      success: function (res) {
-        pcaArgs = JSON.parse(pcaArgs);
-        if (res.scores) {
-          var plotData = solGS.pca.structurePlotData(res);
-          var downloadLinks = solGS.pca.pcaDownloadLinks(res);
-          solGS.pca.plotPca(plotData, downloadLinks);
-        } else {
-          solGS.pca.optJobSubmission(page, pcaArgs);
-        }
-      },
-      error: function () {
-        alert("Error occured checking for cached output.");
-      },
     });
-  },
-
-  optJobSubmission: function (page, args) {
-    var title =
-      "<p>This analysis may take a long time. " +
-      "Do you want to submit the analysis and get an email when it completes?</p>";
-
-    var jobSubmit = '<div id= "pca_submit">' + title + "</div>";
-
-    jQuery(jobSubmit).appendTo("body");
-
-    jQuery("#pca_submit").dialog({
-      height: 200,
-      width: 400,
-      modal: true,
-      title: "pca job submission",
-      buttons: {
-        OK: {
-          text: "Yes",
-          class: "btn btn-success",
-          id: "queue_job",
-          click: function () {
-            jQuery(this).dialog("close");
-            solGS.submitJob.checkUserLogin(page, args);
-          },
-        },
-
-        No: {
-          text: "No, I will wait till it completes.",
-          class: "btn btn-warning",
-          id: "no_queue",
-          click: function () {
-            jQuery(this).dialog("close");
 
-            solGS.pca.runPcaAnalysis(args);
-          },
-        },
-
-        Cancel: {
-          text: "Cancel",
-          class: "btn btn-info",
-          id: "cancel_queue_info",
-          click: function () {
-            jQuery(this).dialog("close");
-          },
-        },
-      },
-    });
+    return checkCache;
   },
 
+  // optJobSubmission: function (page, args) {
+  //   var title =
+  //     "<p>This analysis may take a long time. " +
+  //     "Do you want to submit the analysis and get an email when it completes?</p>";
+
+  //   var jobSubmit = '<div id= "pca_submit">' + title + "</div>";
+
+  //   jQuery(jobSubmit).appendTo("body");
+
+  //   jQuery("#pca_submit").dialog({
+  //     height: 200,
+  //     width: 400,
+  //     modal: true,
+  //     title: "pca job submission",
+  //     buttons: {
+  //       OK: {
+  //         text: "Yes",
+  //         class: "btn btn-success",
+  //         id: "queue_job",
+  //         //   click: function () {
+  //         //     jQuery(this).dialog("close");
+  //         //     solGS.submitJob.checkUserLogin(page, args);
+  //         //   },
+  //       },
+
+  //       No: {
+  //         text: "No, I will wait till it completes.",
+  //         class: "btn btn-warning",
+  //         id: "no_queue",
+  //         // click: function () {
+  //         //   jQuery(this).dialog("close");
+
+  //         //   solGS.pca.runPcaAnalysis(args);
+  //         // },
+  //       },
+
+  //       Cancel: {
+  //         text: "Cancel",
+  //         class: "btn btn-info",
+  //         id: "cancel_queue_info",
+  //         click: function () {
+  //           jQuery(this).dialog("close");
+  //         },
+  //       },
+  //     },
+  //   });
+  // },
+
   pcaDataTypeSelectId: function (pcaPopId) {
     if (location.pathname.match(/pca\/analysis/) && pcaPopId) {
       return `pca_data_type_select_${pcaPopId}`;
@@ -380,63 +345,18 @@ solGS.pca = {
   },
 
   runPcaAnalysis: function (pcaArgs) {
-    jQuery("#pca_canvas .multi-spinner-container").prependTo("#pca_canvas");
-    jQuery("#pca_canvas .multi-spinner-container").show();
-    jQuery("#pca_message").prependTo(jQuery("#pca_canvas"));
-    jQuery("#pca_message").html("Running PCA... please wait...it may take minutes.");
-
-    var runPcaId = this.getRunPcaId(pcaArgs.pca_pop_id);
-    jQuery("#" + runPcaId).hide();
     pcaArgs = JSON.stringify(pcaArgs);
 
-    jQuery.ajax({
+    var pcaAnalysis = jQuery.ajax({
       type: "POST",
       dataType: "json",
       data: {
         arguments: pcaArgs,
       },
       url: "/run/pca/analysis",
-
-      success: function (res) {
-        jQuery("#pca_canvas .multi-spinner-container").hide();
-        if (res.scores) {
-          var listId = res.list_id;
-          var listName;
-
-          if (listId != undefined) {
-            var list = new CXGN.List();
-            listName = list.listNameById(listId);
-          }
-
-          var plotData = {
-            scores: res.scores,
-            variances: res.variances,
-            loadings: res.loadings,
-            pca_pop_id: res.pca_pop_id,
-            list_id: listId,
-            list_name: listName,
-            trials_names: res.trials_names,
-            output_link: res.output_link,
-            data_type: res.data_type,
-          };
-
-          var downloadLinks = solGS.pca.pcaDownloadLinks(res);
-          solGS.pca.plotPca(plotData, downloadLinks);
-
-          jQuery("#pca_message").empty();
-          jQuery(runPcaId).show();
-        } else {
-          jQuery("#pca_canvas .multi-spinner-container").hide();
-          jQuery("#pca_message").html("Error occured running the PCA.");
-          jQuery(runPcaId).show();
-        }
-      },
-      error: function (res) {
-        jQuery("#pca_canvas .multi-spinner-container").hide();
-        jQuery("#pca_message").html("Error occured running the PCA.");
-        jQuery(runPcaId).show();
-      },
     });
+
+    return pcaAnalysis;
   },
 
   validatePcaParams: function (valArgs) {
@@ -510,7 +430,7 @@ solGS.pca = {
       jQuery("#list_id").remove();
     }
 
-    jQuery("#pca_canvas").append('<input type="hidden" id="list_id" value=' + listId + "></input>");
+    jQuery(this.canvas).append('<input type="hidden" id="list_id" value=' + listId + "></input>");
   },
 
   getListId: function () {
@@ -562,7 +482,7 @@ solGS.pca = {
     var listId = res.list_id;
     var listName;
 
-    if (listId != undefined) {
+    if (listId) {
       var list = new CXGN.List();
       listName = list.listNameById(listId);
     }
@@ -613,6 +533,26 @@ solGS.pca = {
     return url;
   },
 
+  cleanUpOnSuccess: function (pcaPopId) {
+
+    jQuery(this.pcaMsgDiv).empty();
+    jQuery(`${this.canvas} .multi-spinner-container`).hide();
+    jQuery(`#${this.getRunPcaId(pcaPopId)}`).show();
+
+  },
+
+  feedBackOnFailure: function (pcaPopId, msg) {
+    jQuery(`${this.canvas} .multi-spinner-container`).hide();
+
+    jQuery(this.pcaMsgDiv)
+      .html(msg)
+      .fadeOut(8400);
+
+      jQuery(`#${this.getRunPcaId(pcaPopId)}`).show();
+
+  },
+
+
   plotPca: function (plotData, downloadLinks) {
     var scores = plotData.scores;
     var variances = plotData.variances;
@@ -652,7 +592,7 @@ solGS.pca = {
     var totalH = height + pad.top + pad.bottom + 100;
     var totalW = width + pad.left + pad.right + 400;
 
-    var pcaCanvasDivId = "#pca_canvas";
+    var pcaCanvasDivId = this.canvas;
     var pcaPlotDivId = plotData.pca_pop_id.replace(/-/g, "_");
     pcaPlotDivId = "pca_plot_" + pcaPlotDivId;
 
@@ -963,6 +903,7 @@ solGS.pca = {
 
 jQuery(document).ready(function () {
   var url = location.pathname;
+  var canvas = solGS.pca.canvas;
 
   if (url.match(/pca\/analysis/)) {
     solGS.pca.populatePcaPopsMenu();
@@ -974,24 +915,18 @@ jQuery(document).ready(function () {
         pcaArgs["pca_pop_id"] = pcaArgs.data_structure + "_" + pcaPopId;
       }
       pcaArgs["analysis_page"] = url;
-      solGS.pca.checkCachedPca(pcaArgs);
+
+      solGS.pca.checkCachedPca(pcaArgs).done(function (res) {
+        if (res.scores) {
+          var plotData = solGS.pca.structurePlotData(res);
+          var downloadLinks = solGS.pca.pcaDownloadLinks(res);
+          solGS.pca.plotPca(plotData, downloadLinks);
+        }
+      });
     }
   }
 
-  jQuery("#run_pca").click(function () {
-    var pcaArgs = solGS.pca.getPcaArgs();
-    var pcaPopId = pcaArgs.pca_pop_id;
-    var runPcaId = solGS.pca.getRunPcaId(pcaPopId);
-
-    jQuery("#" + runPcaId).hide();
-
-    var pcaUrl = solGS.pca.generatePcaUrl(pcaPopId);
-    pcaArgs["analysis_page"] = pcaUrl;
-
-    solGS.pca.checkCachedPca(pcaArgs);
-  });
-
-  jQuery("#pca_canvas").on("click", "a", function (e) {
+  jQuery(canvas).on("click", "a", function (e) {
     var buttonId = e.target.id;
     var pcaPlotId = buttonId.replace(/download_/, "");
     saveSvgAsPng(document.getElementById("#" + pcaPlotId), pcaPlotId + ".png", { scale: 2 });
@@ -1015,18 +950,153 @@ jQuery(document).ready(function () {
 
     var pcaPopsDiv = solGS.pca.pcaPopsSelectMenuId;
     jQuery(pcaPopsDiv).change(function () {
-      console.log(`this.pcaPopsSelectMenuId changed: ${pcaPopsDiv}`);
       var selectedPop = jQuery("option:selected", this).data("pop");
 
       if (selectedPop.id) {
         jQuery("#pca_pop_go_btn").click(function () {
-          solGS.pca.displayPcaPop(selectedPop.id, selectedPop.name, selectedPop.data_str);
+          if (!selectedPop.data_str) {
+            selectedPop.data_str = "list";
+          }
+          solGS.pca.displaySelectedPcaPop(selectedPop);
         });
       }
     });
   }
 });
 
+jQuery(document).ready(function () {
+  jQuery("#pca_div").on("click", function (e) {
+    var runPcaBtnId = e.target.id;
+    if (runPcaBtnId.match(/run_pca/)) {
+      var pcaArgs = solGS.pca.getPcaArgs();
+      var pcaPopId = pcaArgs.pca_pop_id;
+      if (!pcaPopId) {
+        pcaArgs = solGS.pca.getSelectedPopPcaArgs(runPcaBtnId);
+      }
+      pcaPopId = pcaArgs.pca_pop_id;
+      var canvas = solGS.pca.canvas;
+      // var pcaPlotDivId = solGS.pca.pcaPlotDivPrefix;
+      var pcaMsgDiv = solGS.pca.pcaMsgDiv;
+      runPcaBtnId = `#${runPcaBtnId}`;
+      var pcaUrl = solGS.pca.generatePcaUrl(pcaPopId);
+      pcaArgs["analysis_page"] = pcaUrl;
+
+      jQuery(runPcaBtnId).hide();
+      jQuery(`${canvas} .multi-spinner-container`).show();
+      jQuery(pcaMsgDiv).html("Running pca... please wait...").show();
+
+      solGS.pca
+        .checkCachedPca(pcaArgs)
+        .done(function (res) {
+          if (res.scores) {
+            var plotData = solGS.pca.structurePlotData(res);
+            var downloadLinks = solGS.pca.pcaDownloadLinks(res);
+            solGS.pca.plotPca(plotData, downloadLinks);
+
+             solGS.pca.cleanUpOnSuccess(pcaPopId);
+          } else {
+            var page = location.pathname;
+            var pcaUrl = solGS.pca.generatePcaUrl(pcaArgs.pca_pop_id);
+            pcaArgs["analysis_page"] = pcaUrl;
+
+            var title =
+              "<p>This analysis may take a long time. " +
+              "Do you want to submit the analysis and get an email when it completes?</p>";
+
+            var jobSubmit = '<div id= "pca_submit">' + title + "</div>";
+
+            jQuery(jobSubmit).appendTo("body");
+
+            jQuery("#pca_submit").dialog({
+              height: 200,
+              width: 400,
+              modal: true,
+              title: "pca job submission",
+              buttons: {
+                OK: {
+                  text: "Yes",
+                  class: "btn btn-success",
+                  id: "queue_job",
+                  click: function () {
+                    jQuery(this).dialog("close");
+                    solGS.submitJob.checkUserLogin(pcaUrl, pcaArgs);
+                  },
+                },
+
+                No: {
+                  text: "No, I will wait till it completes.",
+                  class: "btn btn-warning",
+                  id: "no_queue",
+                  click: function () {
+                    jQuery(this).dialog("close");
+
+                    solGS.pca
+                      .runPcaAnalysis(pcaArgs)
+                      .done(function (res) {
+                        if (res.scores) {
+                          var downloadLinks = solGS.pca.pcaDownloadLinks(res);
+                          var plotData = solGS.pca.structurePlotData(res);
+                          solGS.pca.plotPca(plotData, downloadLinks);
+
+                          solGS.pca.cleanUpOnSuccess(pcaPopId);
+                        } else {
+                          var msg = "There is no PCA output for this dataset.";
+                          solGS.pca.feedBackOnFailure(pcaPopId, msg);
+                        }
+                      })
+                      .fail(function (res) {
+                        var msg = "Error occured running the PCA.";
+                        solGS.pca.feedBackOnFailure(pcaPopId, msg);
+                      });
+                  },
+                },
+
+                Cancel: {
+                  text: "Cancel",
+                  class: "btn btn-info",
+                  id: "cancel_queue_info",
+                  click: function () {
+                    jQuery(this).dialog("close");
+                  },
+                },
+              },
+            });
+            jQuery(jobSubmit).show();
+
+            jQuery("#queue_job").on("click", function (e) {
+              solGS.submitJob.checkUserLogin(page, args);
+            });
+
+            jQuery("#queue_no").on("click", function (e) {
+              solGS.pca
+                .runPcaAnalysis(pcaArgs)
+                .done(function (res) {
+                  if (res.scores) {
+                    var plotData = solGS.pca.structurePlotData(res);
+                    var downloadLinks = solGS.pca.pcaDownloadLinks(res);
+                    solGS.pca.plotPca(plotData, downloadLinks);
+
+                   solGS.pca.cleanUpOnSuccess(pcaPopId);
+                  } else {
+                    var msg = "There is no PCA output for this dataset.";
+                    solGS.pca.feedBackOnFailurepcaPopId, (msg);
+                  }
+                })
+                .fail(function (res) {
+                  var msg = "Error occured running the PCA.";
+                        solGS.pca.feedBackOnFailure(pcaPopId,msg);
+                });
+            });
+          }
+        })
+        .fail(function () {
+          var msg = "Error occured checking for cached output.";
+          solGS.pca.feedBackOnFailure(pcaPopId,msg);
+        });
+    }
+  });
+});
+
 jQuery.fn.doesExist = function () {
   return jQuery(this).length > 0;
 };
diff --git a/t/selenium2/solgs/pca.t b/t/selenium2/solgs/pca.t
index c8e3e84e71..f0c1e3d2df 100644
--- a/t/selenium2/solgs/pca.t
+++ b/t/selenium2/solgs/pca.t
@@ -56,7 +56,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->get_ok('/pca/analysis', 'pca home page');
     sleep(5);
 
-    $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -75,7 +75,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->find_element_ok('Go back', 'partial_link_text', 'go back to pca pg')->click();
     sleep(3);
 
-   $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
+   $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -90,7 +90,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-   $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
+   $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -106,7 +106,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="'. $plots_list_name . '"]', 'xpath', 'plots list')->click();
+    $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="'. $plots_list_name . '"]', 'xpath', 'plots list')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -122,7 +122,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select clones list')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -138,7 +138,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-   $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
+   $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -156,7 +156,7 @@ $d->while_logged_in_as("submitter", sub {
 
     `rm -r $cache_dir`;
 
-    $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'accessions dataset')->click();
+    $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'accessions dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(20);
@@ -172,7 +172,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $plots_dt_name . '"]', 'xpath', 'plots dataset')->click();
+    $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $plots_dt_name . '"]', 'xpath', 'plots dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(20);
@@ -189,7 +189,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
 
 
-    $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'trials dataset')->click();
+    $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'trials dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(20);
@@ -205,7 +205,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="pca_pops_list_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'trials dataset')->click();
+    $d->find_element_ok('//select[@id="pca_pops_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'trials dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(20);

From 48fbf49f5216b63760c111bfbbcbf4edf83e09ae Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Tue, 9 May 2023 10:18:43 +0200
Subject: [PATCH 04/61] fix typo

---
 js/source/legacy/solGS/pca.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/source/legacy/solGS/pca.js b/js/source/legacy/solGS/pca.js
index e4bb1dfc74..a880c9316f 100644
--- a/js/source/legacy/solGS/pca.js
+++ b/js/source/legacy/solGS/pca.js
@@ -1079,7 +1079,7 @@ jQuery(document).ready(function () {
                    solGS.pca.cleanUpOnSuccess(pcaPopId);
                   } else {
                     var msg = "There is no PCA output for this dataset.";
-                    solGS.pca.feedBackOnFailurepcaPopId, (msg);
+                    solGS.pca.feedBackOnFailure(pcaPopId, msg);
                   }
                 })
                 .fail(function (res) {

From 59a212e8105e2d4c15add8cf8b10126035ba0453 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Tue, 9 May 2023 11:08:58 +0200
Subject: [PATCH 05/61] add more methods

---
 js/source/legacy/solGS/OptionsMenu.js | 73 ++++++++++++++++++++-------
 1 file changed, 55 insertions(+), 18 deletions(-)

diff --git a/js/source/legacy/solGS/OptionsMenu.js b/js/source/legacy/solGS/OptionsMenu.js
index 5f07dc6c23..4448ca39fe 100644
--- a/js/source/legacy/solGS/OptionsMenu.js
+++ b/js/source/legacy/solGS/OptionsMenu.js
@@ -1,48 +1,85 @@
 /*
-creates and populates select populations menu for analysis tools.
+creates and populates select menu with lists and datasets for analysis tools.
 */
 
 class OptionsMenu {
-  constructor(elemId, elemClass, label) {
-    elemId = elemId.replace(/#/, "");
-    this.elemId = elemId;
-    this.elemClass = elemClass || "form-control";
+  constructor(menuId, menuClass, label) {
+    menuId = menuId.replace(/#/, "");
+    menuClass = menuClass.replace(/\./, "");
+
+    this.menuId = menuId;
+    this.menuClass = menuClass || "form-control";
     this.label = label || "Select a population";
+    this.menu;
   }
 
   createOptionsMenu() {
     var menu = document.createElement("select");
-    menu.id = this.elemId;
-    menu.className = this.elemClass;
+    menu.id = this.menuId;
+    menu.className = this.menuClass;
 
     var option = document.createElement("option");
     option.selected = this.label;
-    option.value = this.label;
+    option.value = "";
     option.innerHTML = this.label;
+    // option.disabled = true;
 
     menu.appendChild(option);
 
+    this.menu = menu;
     return menu;
   }
 
   addOptions(data) {
-    var menu = this.createOptionsMenu();
+    var menu = this.menu;
+    if (!menu) {
+      menu = this.createOptionsMenu();
+    }
 
-    // var ids = [];
     data.forEach(function (dt) {
-      // if (!ids.includes(dt.id)) {
-        var option = document.createElement("option");
+      var option = document.createElement("option");
 
-        option.value = dt.id;
-        option.dataset.pop = JSON.stringify(dt);
-        option.innerHTML = dt.name;
+      option.value = dt.id;
+      option.dataset.pop = JSON.stringify(dt);
+      option.innerHTML = dt.name;
 
-        menu.appendChild(option);
+      menu.appendChild(option);
 
-        // ids.push(dt.id);
-      // }
     });
 
     return menu;
   }
+
+  addOptionsSeparator (text) {
+    var option = document.createElement("option");
+    option.innerHTML = `-------- ${text.toUpperCase()} --------`;
+    option.disabled = true;
+
+    this.menu.appendChild(option);
+  }
+
+  getSelectMenuByTypes (listTypes, datasetTypes) {
+    var list = new CXGN.List();
+    var lists = list.getLists(listTypes);
+    var privateLists = list.convertArrayToJson(lists.private_lists);
+
+    privateLists = privateLists.flat();
+    var selectMenu = this.addOptions(privateLists);
+
+    if (lists.public_lists[0]) {
+      var publicLists = list.convertArrayToJson(lists.public_lists);
+      this.addOptionsSeparator("public lists");
+      selectMenu = this.addOptions(publicLists);
+    }
+
+    var datasetPops = solGS.dataset.getDatasetPops(datasetTypes);
+    if (datasetPops) {
+      this.addOptionsSeparator("datasets");
+      selectMenu = this.addOptions(datasetPops);
+    }
+
+    return selectMenu;
+   
+  }
+
 }

From 73adfc8cd888397d5abe66945b92002591203cfc Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Tue, 9 May 2023 14:24:53 +0200
Subject: [PATCH 06/61] update select element id

---
 t/selenium2/solgs/hcluster.t | 96 ++++++++++++++++++------------------
 t/selenium2/solgs/kcluster.t | 96 ++++++++++++++++++------------------
 2 files changed, 96 insertions(+), 96 deletions(-)

diff --git a/t/selenium2/solgs/hcluster.t b/t/selenium2/solgs/hcluster.t
index 3e127ac771..7839add0cd 100644
--- a/t/selenium2/solgs/hcluster.t
+++ b/t/selenium2/solgs/hcluster.t
@@ -366,9 +366,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -398,9 +398,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -434,9 +434,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -455,9 +455,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial tr pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial tr pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -476,9 +476,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial tr pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial tr pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -497,9 +497,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial tr pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial tr pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -531,9 +531,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="139-DMCP-3-FRW-5"]', 'xpath', 'select sel index pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]', 'xpath', 'select sel index pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -554,9 +554,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -575,9 +575,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -604,9 +604,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -631,9 +631,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -650,9 +650,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -677,9 +677,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -710,9 +710,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="139-DMCP-3-FRW-5"]', 'xpath', 'select sel index pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]', 'xpath', 'select sel index pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -751,9 +751,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="139-DMCP-3-FRW-5"]', 'xpath', 'select sel index pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]', 'xpath', 'select sel index pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -777,9 +777,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -968,9 +968,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="Training population 2804608595"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
    $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -989,9 +989,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="Training population 2804608595"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -1010,9 +1010,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'click cluster pops')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'click cluster pops')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="Training population 2804608595"]', 'xpath', 'select tr pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]', 'xpath', 'select tr pop')->click();
     sleep(5);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -1045,9 +1045,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'click cluster pops')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'click cluster pops')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="2804608595-DMCP-3-FRW-5"]', 'xpath', 'si')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="2804608595-DMCP-3-FRW-5"]', 'xpath', 'si')->click();
     sleep(5);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -1080,9 +1080,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -1114,9 +1114,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -1135,9 +1135,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
@@ -1156,9 +1156,9 @@ $d->while_logged_in_as("submitter", sub {
     my $clustering = $d->find_element('Clustering', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $clustering);
     sleep(5);
-    $d->find_element_ok('cluster_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('cluster_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial sel pop')->click();
     sleep(3);
     $d->find_element_ok('//*[starts-with(@id, "cluster_type_select")]', 'xpath', 'select hierarchical')->send_keys('Hierarchical');
     sleep(2);
diff --git a/t/selenium2/solgs/kcluster.t b/t/selenium2/solgs/kcluster.t
index ca31348803..421a5d5549 100644
--- a/t/selenium2/solgs/kcluster.t
+++ b/t/selenium2/solgs/kcluster.t
@@ -743,11 +743,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(2);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-            '//select[@id="cluster_select_pops"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select accessions list sel pop'
@@ -809,11 +809,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(2);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(2);
         $d->find_element_ok(
-            '//select[@id="cluster_select_pops"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select accessions dataset sel pop'
@@ -884,11 +884,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-            '//select[@id="cluster_select_pops"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select accessions dataset sel pop'
@@ -929,11 +929,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial tr pop'
         )->click();
@@ -970,11 +970,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial tr pop'
         )->click();
@@ -1013,11 +1013,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial tr pop'
         )->click();
@@ -1075,11 +1075,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="139-DMCP-3-FRW-5"]',
+'//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]',
             'xpath', 'select sel index pop'
         )->click();
         sleep(3);
@@ -1122,11 +1122,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -1169,11 +1169,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -1217,11 +1217,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -1268,11 +1268,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -1309,11 +1309,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -1358,11 +1358,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -1419,11 +1419,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="139-DMCP-3-FRW-5"]',
+'//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]',
             'xpath', 'select sel index pop'
         )->click();
         sleep(3);
@@ -1492,11 +1492,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="139-DMCP-3-FRW-5"]',
+'//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]',
             'xpath', 'select sel index pop'
         )->click();
         sleep(3);
@@ -1543,11 +1543,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -1862,11 +1862,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="Training population 2804608595"]',
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
             'xpath',
             'select list sel pop'
         )->click();
@@ -1903,11 +1903,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="Training population 2804608595"]',
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
             'xpath',
             'select list sel pop'
         )->click();
@@ -1942,11 +1942,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'click cluster pops' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'click cluster pops' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="Training population 2804608595"]',
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
             'xpath',
             'select tr pop'
         )->click();
@@ -2009,11 +2009,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'click cluster pops' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'click cluster pops' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="2804608595-DMCP-3-FRW-5"]',
+'//select[@id="cluster_pops_select"]/option[text()="2804608595-DMCP-3-FRW-5"]',
             'xpath', 'si'
         )->click();
         sleep(5);
@@ -2079,11 +2079,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id',
+        $d->find_element_ok( 'cluster_pops_select', 'id',
             'select dataset type sl pop - GEBV' )->click();
         sleep(3);
         $d->find_element_ok(
-            '//select[@id="cluster_select_pops"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2150,11 +2150,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id',
+        $d->find_element_ok( 'cluster_pops_select', 'id',
             'select list type sl pop -- GEBV' )->click();
         sleep(3);
         $d->find_element_ok(
-            '//select[@id="cluster_select_pops"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
@@ -2195,11 +2195,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();
@@ -2239,11 +2239,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $clustering );
         sleep(5);
-        $d->find_element_ok( 'cluster_select_pops', 'id',
+        $d->find_element_ok( 'cluster_pops_select', 'id',
             'select trial sl pop -- GEBV' )->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="cluster_select_pops"]/option[text()="trial2 NaCRRI"]',
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
             'xpath',
             'select trial sel pop'
         )->click();

From 940d4466d68fe0bffba941d94f1fe8dcf3456468 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 09:18:28 +0200
Subject: [PATCH 07/61] added a function for getting a list of datasets

---
 js/source/legacy/solGS/Dataset.js | 665 ++++++++++++++----------------
 1 file changed, 314 insertions(+), 351 deletions(-)

diff --git a/js/source/legacy/solGS/Dataset.js b/js/source/legacy/solGS/Dataset.js
index 121fc41420..46f3f2ca56 100644
--- a/js/source/legacy/solGS/Dataset.js
+++ b/js/source/legacy/solGS/Dataset.js
@@ -4,357 +4,320 @@
  *
  */
 
-
 var solGS = solGS || function solGS() {};
 
 solGS.dataset = {
-
-	getDataset: function(id) {
-
-		var dataset = new CXGN.Dataset();
-		var allDatasets = dataset.getDatasets();
-		var data = {};
-
-		for (var i = 0; i < allDatasets.length; i++) {
-			if (allDatasets[i][0] == id) {
-				data.name = allDatasets[i][1];
-				data.id = id;
-			}
-		}
-
-		return data;
-
-	},
-
-
-	getDatasetsMenu: function(dType) {
-		if (!Array.isArray(dType)) {
-			dType = [dType];
-		}
-		var dataset = new CXGN.Dataset();
-		var allDatasets = dataset.getDatasets();
-
-		var sp = ' ----------- ';
-		var dMenu = '<option disabled>' + sp + 'DATASETS' + sp + '</option>';
-
-		var dsIds = [];
-
-		for (var i = 0; i < allDatasets.length; i++) {
-			var id = allDatasets[i][0];
-			var name = allDatasets[i][1];
-			var d = dataset.getDataset(id);
-
-			for (var j = 0; j < dType.length; j++) {
-				if (d.categories[dType[j]] && d.categories[dType[j]].length) {
-
-					if (!dsIds.includes(id)) {
-
-						if (document.URL.match(/solgs\/search/)) {
-							var accessions = d.categories['accessions'];
-							if (accessions == null) {
-								accessions = '';
-							}
-
-							if (accessions.length < 1) {
-								dsIds.push(id);
-								dMenu += '<option name="dataset" value=' + id + '>' + name + '</option>';
-							} else {
-								console.log('NOT ADDING ' + name)
-							}
-						} else {
-							dsIds.push(id);
-							dMenu += '<option name="dataset" value=' + id + '>' + name + '</option>';
-						}
-					}
-				}
-			}
-		}
-
-		return dMenu;
-	},
-
-
-	datasetTrainingPop: function(datasetId) {
-
-		var dataset = new CXGN.Dataset();
-		var d = dataset.getDataset(datasetId);
-		var plots = d.categories['plots'];
-
-		if (plots == '') {
-			plots = null;
-		}
-
-		if (d.categories['trials'] &&
-			plots == null) {
-
-			this.datasetTrialsTrainingPop(datasetId);
-
-		} else if (d.categories['trials'] &&
-			d.categories['plots']) {
-
-			this.datasetPlotsTrainingPop(datasetId);
-		}
-
-	},
-
-
-	datasetTrialsTrainingPop: function(datasetId) {
-		jQuery.ajax({
-			type: 'POST',
-			dataType: "json",
-			url: '/solgs/get/dataset/trials',
-			data: {
-				'dataset_id': datasetId
-			},
-			success: function(res) {
-
-				var trialsIds = res.trials_ids;
-				var comboPopsId = res.combo_pops_id;
-				var genoProId = res.genotyping_protocol_id;
-
-				if (trialsIds) {
-					var args = {
-						'combo_pops_id': [comboPopsId],
-						'combo_pops_list': trialsIds,
-						'genotyping_protocol_id': genoProId,
-					};
-
-					var singleArgs = {
-						'trial_id': trialsIds[0],
-						'genotyping_protocol_id': genoProId,
-					};
-
-					if (trialsIds.length > 1) {
-						console.log('geno pro id ' + genoProId)
-						solGS.combinedTrials.downloadCombinedTrialsTrainingPopData(args);
-					} else {
-						console.log('geno pro id ' + genoProId)
-						solGS.combinedTrials.downloadSingleTrialTrainingPopData(singleArgs);
-					}
-				} else {
-					Alert('No trials ids were found for this dataset')
-				}
-			},
-			error: function(res) {
-				Alert('Error Occurred fetching trials ids in the dataset. ' + res.responseText)
-			}
-		});
-
-	},
-
-
-	datasetPlotsTrainingPop: function(datasetId, datasetName) {
-		this.queueDatasetPlotsTrainingPop(datasetId, datasetName);
-	},
-
-
-	queueDatasetPlotsTrainingPop: function(datasetId, datasetName) {
-
-		var args = this.createDatasetTrainingReqArgs(datasetId, datasetName);
-		var modelId = args.training_pop_id;
-
-		var hostName = window.location.protocol + '//' + window.location.host;
-		var page = hostName + '/solgs/population/' + modelId;
-
-		solGS.waitPage(page, args);
-
-	},
-
-	createDatasetTrainingReqArgs: function(datasetId, datasetName) {
-
-		var dataset = new CXGN.Dataset();
-		var d = dataset.getDataset(datasetId);
-
-		var protocolId = d.categories['genotyping_protocols'] ?
-			d.categories['genotyping_protocols'][0] :
-			null;
-
-
-		if (!protocolId) {
-			protocolId = jQuery('#genotyping_protocol_id').val();
-		}
-
-		var popId = 'dataset_' + datasetId;
-		var popType = 'dataset_training';
-
-		var args = {
-			'dataset_name': datasetName,
-			'dataset_id': datasetId,
-			'analysis_type': 'training_dataset',
-			'data_set_type': 'single_population',
-			'training_pop_id': popId,
-			'population_type': popType,
-			'genotyping_protocol_id': protocolId
-		};
-
-		return args;
-
-
-	},
-
-	createDatasetSelectionArgs: function(datasetId, datasetName) {
-
-		var trainingPopDetails = solGS.getPopulationDetails();
-		var selectionPopId = 'dataset_' + datasetId;
-
-		var trainingTraitsIds = solGS.getTrainingTraitsIds();
-
-		var dataset = new CXGN.Dataset();
-		var d = dataset.getDataset(datasetId);
-
-		var protocolId;
-		if (d.categories['genotyping_protocols']) {
-			protocolId = d.categories['genotyping_protocols'][0];
-		} else {
-			protocolId = jQuery('#genotyping_protocol_id').val();
-		}
-
-		var args = {
-			'dataset_id': datasetId,
-			'dataset_name': datasetName,
-			'training_pop_id': trainingPopDetails.training_pop_id,
-			'selection_pop_id': selectionPopId,
-			'training_traits_ids': trainingTraitsIds,
-			'data_set_type': trainingPopDetails.data_set_type,
-			'genotyping_protocol_id': protocolId
-		};
-
-		return args;
-	},
-
-	checkPredictedDatasetSelection: function(datasetId, datasetName) {
-
-		var args = this.createDatasetSelectionArgs(datasetId, datasetName);
-
-		var trainingPopGenoPro = jQuery('#genotyping_protocol_id').val();
-		var selectionPopGenoPro = args.genotyping_protocol_id;
-
-		if (trainingPopGenoPro != selectionPopGenoPro) {
-
-			var msg = 'This dataset of selection candidates has a ' +
-				'different genotyping protocol from the training ' +
-				'population. Please use a dataset with ' +
-				'a matching genotyping protocol.';
-
-			solGS.alertMessage(msg);
-		} else {
-			args = JSON.stringify(args);
-
-			jQuery.ajax({
-				type: 'POST',
-				dataType: 'json',
-				data: {
-					'arguments': args
-				},
-				url: '/solgs/check/predicted/dataset/selection',
-				success: function(response) {
-					args = JSON.parse(args);
-
-					if (response.output) {
-						solGS.dataset.displayPredictedDatasetTypeSelectionPops(args, response.output);
-
-						if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
-							solGS.sIndex.populateSindexMenu();
-							solGS.correlation.populateGenCorrMenu();
-							solGS.geneticGain.ggSelectionPopulations();
-							solGS.cluster.listClusterPopulations();
-						}
-					} else {
-						solGS.dataset.queueDatasetSelectionPredictionJob(datasetId);
-					}
-				}
-			});
-		}
-
-	},
-
-	queueDatasetSelectionPredictionJob: function(datasetId) {
-
-		var args = this.createDatasetSelectionArgs(datasetId);
-		var modelId = args.training_pop_id;
-		var selectionPopId = args.selection_pop_id;
-
-		var hostName = window.location.protocol + '//' + window.location.host;
-		var page = hostName + '/solgs/selection/' + selectionPopId + '/model/' + modelId;
-
-		solGS.waitPage(page, args);
-
-	},
-
-
-	displayPredictedDatasetTypeSelectionPops: function(args, output) {
-
-		var datasetName = args.dataset_name;
-		var datasetId = args.dataset_id;
-
-		var traitId = args.trait_id;
-		var selectionPopId = args.selection_pop_id;
-		var trainingPopId = args.training_pop_id;
-
-		var url = '/solgs/selection/' + selectionPopId + '/model/' + trainingPopId;
-		var datasetIdArg = '\'' + datasetId + '\'';
-		var listSource = '\'from_db\'';
-		var popIdName = {
-			'id': 'dataset_' + datasetId,
-			'name': datasetName,
-			'pop_type': 'dataset_selection'
-		};
-		popIdName = JSON.stringify(popIdName);
-		var hiddenInput = '<input type="hidden" value=\'' + popIdName + '\'/>';
-
-		var predictedListTypeSelectionPops = jQuery("#list_type_selection_pops_table").doesExist();
-
-		if (predictedListTypeSelectionPops == false) {
-
-			var predictedListTypeSelectionTable = '<table id="list_type_selection_pops_table" class="table"><thead><tr>' +
-				'<th>List-based selection population</th>' +
-				'<th>View GEBVs</th>' +
-				'</tr></thead><tbody>' +
-				'<tr id="list_prediction_output_' + datasetId + '">' +
-				'<td>' +
-				'<b>' + datasetName + '</b>' +
-				'</td>' +
-				'<td><data>' + hiddenInput + '</data>' +
-				output +
-				'</td></tr></tbody></table>';
-
-			jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
-
-		} else {
-			var datasetIdArg = '\'' + datasetId + '\'';
-			var datasetSource = '\'from_db\'';
-
-			var popIdName = {
-				id: 'dataset_' + datasetId,
-				name: datasetName,
-				pop_type: 'dataset_selection'
-			};
-			popIdName = JSON.stringify(popIdName);
-			var hiddenInput = '<input type="hidden" value=\'' + popIdName + '\'/>';
-
-			var addRow = '<tr id="list_prediction_output_' + datasetId + '"><td>' +
-				'<b>' + datasetName +
-				'</td>' +
-				'<td> <data>' + hiddenInput + '</data>' +
-				output +
-				'</td></tr>';
-
-			var trId = '#list_prediction_output_' + datasetId;
-			var samePop = jQuery(trId).doesExist();
-
-			if (samePop == false) {
-				jQuery("#list_type_selection_pops_table tr:last").after(addRow);
-
-			} else {
-				jQuery(trId).remove();
-				jQuery("#list_type_selection_pops_table").append(addRow).show();
-			}
-
-		}
-
-	},
-
-
-	/////
-}
-/////
\ No newline at end of file
+  getDataset: function (id) {
+    var dataset = new CXGN.Dataset();
+    var allDatasets = dataset.getDatasets();
+    var data = {};
+
+    for (var i = 0; i < allDatasets.length; i++) {
+      if (allDatasets[i][0] == id) {
+        data.name = allDatasets[i][1];
+        data.id = id;
+      }
+    }
+
+    return data;
+  },
+
+  getDatasetPops: function (dType) {
+    if (!Array.isArray(dType)) {
+      dType = [dType];
+    }
+    var dataset = new CXGN.Dataset();
+    var allDatasets = dataset.getDatasets();
+
+    var dsIds = [];
+    var datasetPops = [];
+    for (var i = 0; i < allDatasets.length; i++) {
+      var id = allDatasets[i][0];
+      var name = allDatasets[i][1];
+      var d = dataset.getDataset(id);
+
+      for (var j = 0; j < dType.length; j++) {
+        if (d.categories[dType[j]] && d.categories[dType[j]].length) {
+          if (!dsIds.includes(id)) {
+            var dsObj = {
+              id: id,
+              name: name,
+              type: dType[j],
+              data_str: "dataset",
+            };
+            datasetPops.push(dsObj);
+            dsIds.push(id);
+          }
+        }
+      }
+    }
+
+    return datasetPops;
+  },
+
+  datasetTrainingPop: function (datasetId) {
+    var dataset = new CXGN.Dataset();
+    var d = dataset.getDataset(datasetId);
+    var plots = d.categories["plots"];
+
+    if (plots == "") {
+      plots = null;
+    }
+
+    if (d.categories["trials"] && plots == null) {
+      this.datasetTrialsTrainingPop(datasetId);
+    } else if (d.categories["trials"] && d.categories["plots"]) {
+      this.datasetPlotsTrainingPop(datasetId);
+    }
+  },
+
+  datasetTrialsTrainingPop: function (datasetId) {
+    jQuery.ajax({
+      type: "POST",
+      dataType: "json",
+      url: "/solgs/get/dataset/trials",
+      data: {
+        dataset_id: datasetId,
+      },
+      success: function (res) {
+        var trialsIds = res.trials_ids;
+        var comboPopsId = res.combo_pops_id;
+        var genoProId = res.genotyping_protocol_id;
+
+        if (trialsIds) {
+          var args = {
+            combo_pops_id: [comboPopsId],
+            combo_pops_list: trialsIds,
+            genotyping_protocol_id: genoProId,
+          };
+
+          var singleArgs = {
+            trial_id: trialsIds[0],
+            genotyping_protocol_id: genoProId,
+          };
+
+          if (trialsIds.length > 1) {
+            console.log("geno pro id " + genoProId);
+            solGS.combinedTrials.downloadCombinedTrialsTrainingPopData(args);
+          } else {
+            console.log("geno pro id " + genoProId);
+            solGS.combinedTrials.downloadSingleTrialTrainingPopData(singleArgs);
+          }
+        } else {
+          Alert("No trials ids were found for this dataset");
+        }
+      },
+      error: function (res) {
+        Alert("Error Occurred fetching trials ids in the dataset. " + res.responseText);
+      },
+    });
+  },
+
+  datasetPlotsTrainingPop: function (datasetId, datasetName) {
+    this.queueDatasetPlotsTrainingPop(datasetId, datasetName);
+  },
+
+  queueDatasetPlotsTrainingPop: function (datasetId, datasetName) {
+    var args = this.createDatasetTrainingReqArgs(datasetId, datasetName);
+    var modelId = args.training_pop_id;
+
+    var hostName = window.location.protocol + "//" + window.location.host;
+    var page = hostName + "/solgs/population/" + modelId;
+
+    solGS.waitPage(page, args);
+  },
+
+  createDatasetTrainingReqArgs: function (datasetId, datasetName) {
+    var dataset = new CXGN.Dataset();
+    var d = dataset.getDataset(datasetId);
+
+    var protocolId = d.categories["genotyping_protocols"]
+      ? d.categories["genotyping_protocols"][0]
+      : null;
+
+    if (!protocolId) {
+      protocolId = jQuery("#genotyping_protocol_id").val();
+    }
+
+    var popId = "dataset_" + datasetId;
+    var popType = "dataset_training";
+
+    var args = {
+      dataset_name: datasetName,
+      dataset_id: datasetId,
+      analysis_type: "training_dataset",
+      data_set_type: "single_population",
+      training_pop_id: popId,
+      population_type: popType,
+      genotyping_protocol_id: protocolId,
+    };
+
+    return args;
+  },
+
+  createDatasetSelectionArgs: function (datasetId, datasetName) {
+    var trainingPopDetails = solGS.getPopulationDetails();
+    var selectionPopId = "dataset_" + datasetId;
+
+    var trainingTraitsIds = solGS.getTrainingTraitsIds();
+
+    var dataset = new CXGN.Dataset();
+    var d = dataset.getDataset(datasetId);
+
+    var protocolId;
+    if (d.categories["genotyping_protocols"]) {
+      protocolId = d.categories["genotyping_protocols"][0];
+    } else {
+      protocolId = jQuery("#genotyping_protocol_id").val();
+    }
+
+    var args = {
+      dataset_id: datasetId,
+      dataset_name: datasetName,
+      training_pop_id: trainingPopDetails.training_pop_id,
+      selection_pop_id: selectionPopId,
+      training_traits_ids: trainingTraitsIds,
+      data_set_type: trainingPopDetails.data_set_type,
+      genotyping_protocol_id: protocolId,
+    };
+
+    return args;
+  },
+
+  checkPredictedDatasetSelection: function (datasetId, datasetName) {
+    var args = this.createDatasetSelectionArgs(datasetId, datasetName);
+
+    var trainingPopGenoPro = jQuery("#genotyping_protocol_id").val();
+    var selectionPopGenoPro = args.genotyping_protocol_id;
+
+    if (trainingPopGenoPro != selectionPopGenoPro) {
+      var msg =
+        "This dataset of selection candidates has a " +
+        "different genotyping protocol from the training " +
+        "population. Please use a dataset with " +
+        "a matching genotyping protocol.";
+
+      solGS.alertMessage(msg);
+    } else {
+      args = JSON.stringify(args);
+
+      jQuery.ajax({
+        type: "POST",
+        dataType: "json",
+        data: {
+          arguments: args,
+        },
+        url: "/solgs/check/predicted/dataset/selection",
+        success: function (response) {
+          args = JSON.parse(args);
+
+          if (response.output) {
+            solGS.dataset.displayPredictedDatasetTypeSelectionPops(args, response.output);
+
+            if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
+              solGS.sIndex.populateSindexMenu();
+              solGS.correlation.populateGenCorrMenu();
+              solGS.geneticGain.ggSelectionPopulations();
+              solGS.cluster.listClusterPopulations();
+            }
+          } else {
+            solGS.dataset.queueDatasetSelectionPredictionJob(datasetId);
+          }
+        },
+      });
+    }
+  },
+
+  queueDatasetSelectionPredictionJob: function (datasetId) {
+    var args = this.createDatasetSelectionArgs(datasetId);
+    var modelId = args.training_pop_id;
+    var selectionPopId = args.selection_pop_id;
+
+    var hostName = window.location.protocol + "//" + window.location.host;
+    var page = hostName + "/solgs/selection/" + selectionPopId + "/model/" + modelId;
+
+    solGS.waitPage(page, args);
+  },
+
+  displayPredictedDatasetTypeSelectionPops: function (args, output) {
+    var datasetName = args.dataset_name;
+    var datasetId = args.dataset_id;
+
+    var traitId = args.trait_id;
+    var selectionPopId = args.selection_pop_id;
+    var trainingPopId = args.training_pop_id;
+
+    var url = "/solgs/selection/" + selectionPopId + "/model/" + trainingPopId;
+    var datasetIdArg = "'" + datasetId + "'";
+    var listSource = "'from_db'";
+    var popIdName = {
+      id: "dataset_" + datasetId,
+      name: datasetName,
+      pop_type: "dataset_selection",
+    };
+    popIdName = JSON.stringify(popIdName);
+    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+
+    var predictedListTypeSelectionPops = jQuery("#list_type_selection_pops_table").doesExist();
+
+    if (predictedListTypeSelectionPops == false) {
+      var predictedListTypeSelectionTable =
+        '<table id="list_type_selection_pops_table" class="table"><thead><tr>' +
+        "<th>List-based selection population</th>" +
+        "<th>View GEBVs</th>" +
+        "</tr></thead><tbody>" +
+        '<tr id="list_prediction_output_' +
+        datasetId +
+        '">' +
+        "<td>" +
+        "<b>" +
+        datasetName +
+        "</b>" +
+        "</td>" +
+        "<td><data>" +
+        hiddenInput +
+        "</data>" +
+        output +
+        "</td></tr></tbody></table>";
+
+      jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
+    } else {
+      var datasetIdArg = "'" + datasetId + "'";
+      var datasetSource = "'from_db'";
+
+      var popIdName = {
+        id: "dataset_" + datasetId,
+        name: datasetName,
+        pop_type: "dataset_selection",
+      };
+      popIdName = JSON.stringify(popIdName);
+      var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+
+      var addRow =
+        '<tr id="list_prediction_output_' +
+        datasetId +
+        '"><td>' +
+        "<b>" +
+        datasetName +
+        "</td>" +
+        "<td> <data>" +
+        hiddenInput +
+        "</data>" +
+        output +
+        "</td></tr>";
+
+      var trId = "#list_prediction_output_" + datasetId;
+      var samePop = jQuery(trId).doesExist();
+
+      if (samePop == false) {
+        jQuery("#list_type_selection_pops_table tr:last").after(addRow);
+      } else {
+        jQuery(trId).remove();
+        jQuery("#list_type_selection_pops_table").append(addRow).show();
+      }
+    }
+  },
+
+  /////
+};
+/////

From a9bcb902492255ed912cae7d58aceb758c014ffe Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 09:23:54 +0200
Subject: [PATCH 08/61] change func names, parameters...

---
 js/source/legacy/solGS/correlation.js | 72 ++++++++++++++++-----------
 1 file changed, 43 insertions(+), 29 deletions(-)

diff --git a/js/source/legacy/solGS/correlation.js b/js/source/legacy/solGS/correlation.js
index 67bb13da45..ceca4b27b4 100644
--- a/js/source/legacy/solGS/correlation.js
+++ b/js/source/legacy/solGS/correlation.js
@@ -12,8 +12,8 @@ solGS.correlation = {
   canvas: "#corr_canvas",
   corrPlotDivPrefix: "#corr_plot",
   corrMsgDiv: "#corr_message",
-  corrPopsSelectMenuId: "#corr_select_pops",
-  corrPopsDiv: "#corr_select_a_pop_div",
+  corrPopsSelectMenuId: "#corr_pops_select",
+  corrPopsDiv: "#corr_pops_select_div",
 
   getPhenoCorrArgs: function () {
     var corrPopId = jQuery("#corr_pop_id").val();
@@ -47,9 +47,9 @@ solGS.correlation = {
     return args;
   },
 
-  loadCorrelationPopsList: function (selectId, selectName, dataStr) {
-    var corrPopId = this.getCorrPopId(selectId, dataStr);
-    if (selectId.length === 0) {
+  displaySelectedCorrPop: function (selectedPop) {
+    var corrPopId = this.getCorrPopId(selectedPop.id, selectedPop.data_str);
+    if (selectedPop.length === 0) {
       alert("The list is empty. Please select a list with content.");
     } else {
       var tableId = "corr_pops_list_table";
@@ -59,7 +59,7 @@ solGS.correlation = {
         jQuery("#corr_pops_selected").append(corrTable).show();
       }
 
-      var addRow = this.selectRow(selectId, selectName, dataStr);
+      var addRow = this.selectRow(selectedPop);
       var tdId = "#corr_" + corrPopId;
       var addedRow = jQuery(tdId).doesExist();
 
@@ -101,8 +101,12 @@ solGS.correlation = {
     return table;
   },
 
-  selectRow: function (selectId, selectName, dataStr) {
-    var corrPopId = this.getCorrPopId(selectId, dataStr);
+  selectRow: function (selectedPop) {
+    var selectedId = selectedPop.id;
+    var selectedName = selectedPop.name;
+    var dataStr = selectedPop.data_str;
+
+    var corrPopId = this.getCorrPopId(selectedId, dataStr);
 
     // var dataTypeOpts = this.getDataTypeOpts({
     // 	'select_id': selectId,
@@ -115,9 +119,9 @@ solGS.correlation = {
     var datasetId;
 
     if (dataStr.match(/dataset/)) {
-      datasetId = selectId;
+      datasetId = selectedId;
     } else if (dataStr.match(/list/)) {
-      listId = selectId;
+      listId = selectedId;
     }
 
     var runCorrBtnId = this.getRunCorrBtnId(corrPopId);
@@ -128,7 +132,7 @@ solGS.correlation = {
       data_structure: dataStr,
       dataset_id: datasetId,
       list_id: listId,
-      corre_pop_name: selectName,
+      corre_pop_name: selectedName,
       data_type: "phenotype",
       correlation_type: "phenotypic",
       canvas: corrDivs.canvas,
@@ -147,7 +151,7 @@ solGS.correlation = {
       corrPopId +
       '">' +
       "<td>" +
-      selectName +
+      selectedName +
       "</td>" +
       "<td>" +
       dataStr +
@@ -340,6 +344,17 @@ solGS.correlation = {
     return { canvas: canvas, corr_msg_div: corrMsgDiv, corr_plot_div: corrPlotDiv };
   },
 
+  populateCorrPopsMenu: function () {
+    var listTypes = ["plots", "trials"];
+    var datasetTypes = ["accessions", "plots", "trials"];
+    var menuId = this.corrPopsSelectMenuId;
+    var menu = new OptionsMenu(menuId);
+    var selectMenu = menu.getSelectMenuByTypes(listTypes, datasetTypes);
+
+    var corrPopsDiv = this.corrPopsDiv;
+    jQuery(corrPopsDiv).append(selectMenu).show();
+  },
+
   ///////
 };
 ////////
@@ -486,12 +501,6 @@ jQuery(document).ready(function () {
         jQuery(corrMsgDiv).html("Error occured running correlation analysis.").fadeOut(8400);
       });
   });
-
-  var url = location.pathname;
-
-  if (url.match(/correlation\/analysis/)) {
-    solGS.selectMenu.populateMenu("corr_pops", ["plots", "trials"], ["plots", "trials"]);
-  }
 });
 
 jQuery(document).ready(function () {
@@ -510,23 +519,28 @@ jQuery(document).ready(function () {
 });
 
 jQuery(document).ready(function () {
-  jQuery("#corr_pops_list_select").change(function () {
-    var selectedPop = solGS.selectMenu.getSelectedPop("corr_pops");
-console.log(`selectedPop ${JSON.stringify(selectedPop)}`)
-    if (selectedPop.selected_id) {
-      jQuery("#corr_pop_go_btn").click(function () {
-console.log(`click corr_pop_go_btn selectedPop ${JSON.stringify(selectedPop)}`)
+  var corrPopsDiv = solGS.correlation.corrPopsDiv;
+  jQuery(corrPopsDiv).change(function () {
 
-        solGS.correlation.loadCorrelationPopsList(
-          selectedPop.selected_id,
-          selectedPop.selected_name,
-          selectedPop.data_str
-        );
+    var selectedPop = jQuery("option:selected", this).data("pop");
+    if (selectedPop.id) {
+      jQuery("#corr_pop_go_btn").click(function () {
+        if (!selectedPop.data_str) {
+          selectedPop.data_str = "list";
+        }
+        solGS.correlation.displaySelectedCorrPop(selectedPop);
       });
     }
   });
 });
 
+jQuery(document).ready(function () {
+  var url = location.pathname;
+  if (url.match(/correlation\/analysis/)) {
+    solGS.correlation.populateCorrPopsMenu();
+  }
+});
+
 jQuery(document).ready(function () {
   jQuery("#corr_canvas").on("click", "a", function (e) {
     var buttonId = e.target.id;

From f610f3add930dedfed80d4f2ed32b8808b8d7a06 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 09:24:47 +0200
Subject: [PATCH 09/61] update div id

---
 mason/solgs/tools/cluster/gebvs_cluster.mas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mason/solgs/tools/cluster/gebvs_cluster.mas b/mason/solgs/tools/cluster/gebvs_cluster.mas
index 028a89f4c1..fade2879c0 100644
--- a/mason/solgs/tools/cluster/gebvs_cluster.mas
+++ b/mason/solgs/tools/cluster/gebvs_cluster.mas
@@ -24,7 +24,7 @@ $pop_type
 
 <div class="row">
   <div class="form-group col-sm-3"
-       id="cluster_select_a_pop_div"
+       id="cluster_pops_select_div"
        style="margin-right:25px">
   </div>
 

From 6ebaa8d4805ac0efb6b537b28bc1ee31f79fd5ec Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 09:27:57 +0200
Subject: [PATCH 10/61] refactor select menu population..

---
 js/source/legacy/solGS/cluster.js | 64 ++++++++++++++++++++-----------
 1 file changed, 41 insertions(+), 23 deletions(-)

diff --git a/js/source/legacy/solGS/cluster.js b/js/source/legacy/solGS/cluster.js
index 34c633ace2..6d6b6691e1 100644
--- a/js/source/legacy/solGS/cluster.js
+++ b/js/source/legacy/solGS/cluster.js
@@ -10,8 +10,8 @@ solGS.cluster = {
   canvas: "#cluster_canvas",
   clusterPlotDivPrefix: "#cluster_plot",
   clusterMsgDiv: "#cluster_message",
-  clusterPopsDiv: "#cluster_select_a_pop_div",
-  clusterPopsSelectMenuId: "#cluster_select_pops",
+  clusterPopsDiv: "#cluster_pops_select_div",
+  clusterPopsSelectMenuId: "#cluster_pops_select",
 
   getClusterArgsFromUrl: function () {
     var page = location.pathname;
@@ -92,7 +92,7 @@ solGS.cluster = {
     }
   },
 
-  loadClusterGenotypesList: function (selectId, selectName, dataStr) {
+  displaySelectedClusterPop: function (selectId, selectName, dataStr) {
     var clusterPopId = this.getClusterPopId(selectId, dataStr);
     if (selectId.length === 0) {
       alert("The list is empty. Please select a list with content.");
@@ -263,7 +263,6 @@ solGS.cluster = {
     });
 
     dataTypeOpts = this.createDataTypeSelect(dataTypeOpts, clusterPopId);
-
     var kNumId = this.clusterKnumSelectId(clusterPopId);
     var runClusterId = this.clusterRunClusterId(clusterPopId);
 
@@ -787,13 +786,13 @@ solGS.cluster = {
       elbowLink = '<a href="' + elbowPlotFile + '" download=' + elbowFileName + '">Elbow plot</a>';
 
       if (kclusterMeansFile) {
-      var kclusterMeansFileName = kclusterMeansFile.split("/").pop();
-      kclusterMeansLink =
-        '<a href="' +
-        kclusterMeansFile +
-        '" download=' +
-        kclusterMeansFileName +
-        '">Cluster means</a>';
+        var kclusterMeansFileName = kclusterMeansFile.split("/").pop();
+        kclusterMeansLink =
+          '<a href="' +
+          kclusterMeansFile +
+          '" download=' +
+          kclusterMeansFileName +
+          '">Cluster means</a>';
       }
 
       var kclusterVariancesFileName = kclusterVariancesFile.split("/").pop();
@@ -822,11 +821,10 @@ solGS.cluster = {
 
     if (elbowPlotFile) {
       if (kclusterMeansLink) {
-        downloadLinks +=  " | " + kclusterMeansLink 
+        downloadLinks += " | " + kclusterMeansLink;
       }
 
-      downloadLinks +=
-        " | " + kclusterVariancesLink +  " | " + elbowLink;
+      downloadLinks += " | " + kclusterVariancesLink + " | " + elbowLink;
     }
 
     return downloadLinks;
@@ -913,6 +911,32 @@ solGS.cluster = {
     }
   },
 
+  populateClusterPopsMenu: function () {
+    var list = new CXGN.List();
+    var lists = list.getLists(["accessions", "plots", "trials"]);
+    var clusterPrivatePops = list.convertArrayToJson(lists.private_lists);
+
+    var menuId = this.clusterPopsSelectMenuId;
+    var menu = new OptionsMenu(menuId);
+    clusterPrivatePops = clusterPrivatePops.flat();
+    var menuElem = menu.addOptions(clusterPrivatePops);
+
+    if (lists.public_lists[0]) {
+      var clusterPublicLists = list.convertArrayToJson(lists.public_lists);
+      menu.addOptionsSeparator("public lists");
+      menuElem = menu.addOptions(clusterPublicLists);
+    }
+
+    var datasetPops = solGS.dataset.getDatasetPops(["accessions", "trials"]);
+    if (datasetPops) {
+      menu.addOptionsSeparator("datasets");
+      menuElem = menu.addOptions(datasetPops);
+    }
+
+    var clusterPopsDiv = this.clusterPopsDiv;
+    jQuery(clusterPopsDiv).append(menuElem).show();
+  },
+
   listClusterPopulations: function () {
     var modelData = solGS.sIndex.getTrainingPopulationData();
 
@@ -924,7 +948,6 @@ solGS.cluster = {
         clusterPops.push(trialSelPopsList);
       }
     }
-
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
       var listTypeSelPops = solGS.sIndex.getListTypeSelPopulations();
@@ -957,11 +980,7 @@ jQuery(document).ready(function () {
   var url = location.pathname;
 
   if (url.match(/cluster\/analysis/)) {
-    solGS.selectMenu.populateMenu(
-      "cluster_pops",
-      ["accessions", "plots", "trials"],
-      ["accessions", "trials"]
-    );
+    solGS.cluster.populateClusterPopsMenu();
 
     var clusterArgs = solGS.cluster.getClusterArgsFromUrl();
     var clusterPopId = clusterArgs.cluster_pop_id;
@@ -1006,7 +1025,7 @@ jQuery(document).ready(function () {
     var selectedPop = solGS.selectMenu.getSelectedPop("cluster_pops");
     if (selectedPop.selected_id) {
       jQuery("#cluster_pop_go_btn").click(function () {
-        solGS.cluster.loadClusterGenotypesList(
+        solGS.cluster.displaySelectedClusterPop(
           selectedPop.selected_id,
           selectedPop.selected_name,
           selectedPop.data_str
@@ -1085,7 +1104,7 @@ jQuery(document).ready(function () {
     jQuery(document).ready(checkClusterPop);
 
     function checkClusterPop() {
-      if (jQuery("#cluster_div #cluster_select_a_pop_div").is(":visible")) {
+      if (jQuery("#cluster_div #cluster_pops_select_div").is(":visible")) {
         jQuery("#cluster_div #cluster_options #cluster_data_type_opts").html(dataTypeOpts);
         jQuery("#cluster_div #cluster_options #cluster_type_opts").html(clusterTypeOpts);
         jQuery("#cluster_div #cluster_options").show();
@@ -1110,7 +1129,6 @@ jQuery(document).ready(function () {
   var clusterPopsDiv = solGS.cluster.clusterPopsDiv;
 
   jQuery(clusterPopsDiv).change(function () {
-
     var selectedPop = jQuery("option:selected", this).data("pop");
 
     var selectedPopId = selectedPop.id;

From 9b7e9f45e79994be62eddf939c7887d8a1f6a35e Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 10:49:47 +0200
Subject: [PATCH 11/61] convert the lib into object literal, implement
 OptionsMenu.js

---
 .../solGS/listTypeTrainingPopulation.js       | 144 +++++++++++-------
 1 file changed, 89 insertions(+), 55 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index b78ae7b96a..95e2365488 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -1,50 +1,23 @@
 
 /**
 
-For training population made from list of plots and trial.
+For training populations  from list of plots and trials.
 
 Isaak Y Tecle 
 iyt2@cornell.edu
 */
 
-JSAN.use("CXGN.List");
+// JSAN.use("CXGN.List");
 JSAN.use("jquery.blockUI");
 
+var solGS = solGS || function solGS() {};
 
-jQuery(document).ready( function() {
-    solGS.selectMenu.populateMenu("list_type_training_pops", ['plots', 'trials'],  ['plots', 'trials'] );
-          
-});
-
-
-jQuery(document).ready( function() {  
-    jQuery("#list_type_training_pops_list_select").change(function() { 
-        var selectedPop = solGS.selectMenu.getSelectedPop('list_type_training_pops');
-
-        if (selectedPop.selected_id) {  	
-            jQuery("#list_type_training_pop_go_btn").click(function() {
-
-                if (typeof selectedPop.data_str === 'undefined' || !selectedPop.data_str.match(/dataset/i)) {
-                    var listDetail = getListTypeTrainingPopDetail(selectedPop.selected_id);
-
-                    if (listDetail.type.match(/plots/)) {
-                        askTrainingJobQueueing(selectedPop.selected_id);
-                    } else {
-                        var trialsList = listDetail.list;
-                        var trialsNames = listDetail.list_elements_names;
-
-                        loadTrialListTypeTrainingPop(trialsNames);		    
-                    }
-                    } else {
-                        solGS.dataset.datasetTrainingPop(selectedPop.selected_id, selectedPop.selected_name);
-                    }
-                });
-        }	   
-    });       
-});
+solGS.listTypeTrainingPopulation = {
 
+ trainingPopsDiv: "#list_type_training_pops_select_div",
+ trainingPopsSelectMenuId: "#list_type_training_pops_select",
 
-function getTrainingListElementsNames (list) {
+getTrainingListElementsNames: function (list) {
    
     var names = [];
     for (var i = 0; i < list.length; i++) {
@@ -53,10 +26,36 @@ function getTrainingListElementsNames (list) {
 
     return names;
 
-}
+},
 
+populateTrainingPopsMenu: function  () {
+    var list = new CXGN.List();
+    var lists = list.getLists([ "plots", "trials"]);
+    var trainingPrivatePops = list.convertArrayToJson(lists.private_lists);
+
+    var menuId = this.trainingPopsSelectMenuId;
+    var menu = new OptionsMenu(menuId);
+    trainingPrivatePops = trainingPrivatePops.flat();
+    var menuElem = menu.addOptions(trainingPrivatePops);
+
+    if (lists.public_lists[0]) {
+      var trainingPublicLists = list.convertArrayToJson(lists.public_lists);
+      menu.addOptionsSeparator("public lists");
+      menuElem = menu.addOptions(trainingPublicLists);
+    }
+
+    var datasetPops = solGS.dataset.getDatasetPops(["accessions","plots", "trials"]);
+    if (datasetPops) {
+      menu.addOptionsSeparator("datasets");
+      menuElem = menu.addOptions(datasetPops);
+    }
 
-function getTrainingListElementsIds (list) {
+    var trainingPopsDiv = this.trainingPopsDiv;
+    jQuery(trainingPopsDiv).append(menuElem).show();
+  },
+
+
+getTrainingListElementsIds: function (list) {
    
     var ids = [];
     for (var i = 0; i < list.length; i++) {
@@ -65,10 +64,10 @@ function getTrainingListElementsIds (list) {
 
     return ids;
 
-}
+},
 
 
-function getListTypeTrainingPopDetail(listId) {   
+getListTypeTrainingPopDetail: function(listId) {   
     
     var list = new CXGN.List();
     
@@ -82,8 +81,8 @@ function getListTypeTrainingPopDetail(listId) {
 	listName      = list.listNameById(listId);
 	listElements  = listData.elements;
 
-	listElementsNames = getTrainingListElementsNames(listElements);
-	listElementsIds   = getTrainingListElementsIds(listElements);
+	listElementsNames = this.getTrainingListElementsNames(listElements);
+	listElementsIds   = this.getTrainingListElementsIds(listElements);
     }
   
     return {'name'          : listName,	    
@@ -93,10 +92,10 @@ function getListTypeTrainingPopDetail(listId) {
 	    'list_elements_ids' : listElementsIds,
            };
     
-}
+},
 
 
-function loadTrialListTypeTrainingPop (trialsNames) {
+loadTrialListTypeTrainingPop: function (trialsNames) {
    
     jQuery.ajax({
         type: 'POST',
@@ -111,11 +110,11 @@ function loadTrialListTypeTrainingPop (trialsNames) {
         }                       
     });
 
-}
+},
 
-function askTrainingJobQueueing (listId) {
+askTrainingJobQueueing: function (listId) {
  
-    var args = createTrainingReqArgs(listId);
+    var args = this.createTrainingReqArgs(listId);
     var modelId = args.training_pop_id;
     var protocolId = args.genotyping_protocol_id;
     
@@ -128,12 +127,12 @@ function askTrainingJobQueueing (listId) {
     
     solGS.waitPage(page, args);
 
-}
+},
 
 
-function createTrainingReqArgs (listId) {
+createTrainingReqArgs: function (listId) {
 
-    var genoList  = getListTypeTrainingPopDetail(listId);
+    var genoList  = this.getListTypeTrainingPopDetail(listId);
     var listName  = genoList.name;
     var list      = genoList.list;
     var popId     = getModelId(listId);
@@ -152,12 +151,12 @@ function createTrainingReqArgs (listId) {
 
     return args;
 
-}
+},
 
 
-function loadPlotListTypeTrainingPop(listId) {     
+loadPlotListTypeTrainingPop: function(listId) {     
   
-    var args  = createTrainingReqArgs(listId);
+    var args  = this.createTrainingReqArgs(listId);
     var popId = args.training_pop_id;
 
     if (window.Prototype) {
@@ -196,7 +195,11 @@ function loadPlotListTypeTrainingPop(listId) {
             }            
         });        
     }
-}
+},
+
+};
+
+
 
 
 jQuery.fn.doesExist = function(){
@@ -206,8 +209,8 @@ jQuery.fn.doesExist = function(){
 
 
 function getUserUploadedRefPop (listId) {
-   
-    var genoList       = getListTypeTrainingPopDetail(listId);
+ 
+    var genoList       = this.getListTypeTrainingPopDetail(listId);
     var listName       = genoList.name;
     var list           = genoList.list;
     var modelId        = getModelId(listId);
@@ -241,7 +244,7 @@ function getUserUploadedRefPop (listId) {
 
 function loadPopulationPage (url, listId, listSource) {   
     
-    var genoList       = getListTypeTrainingPopDetail(listId);
+    var genoList       = this.getListTypeTrainingPopDetail(listId);
     var listName       = genoList.name;
     var modelId        = getModelId(listId);
      
@@ -284,3 +287,34 @@ function getModelId (listId) {
 
 }
 
+jQuery(document).ready( function() {
+    solGS.listTypeTrainingPopulation.populateTrainingPopsMenu();
+          
+});
+
+
+jQuery(document).ready( function() {  
+    jQuery("#list_type_training_pops_select").change(function() { 
+        var selectedPop = jQuery("option:selected", this).data("pop");
+        if (selectedPop.id) {  	
+            jQuery("#list_type_training_pop_go_btn").click(function() {
+
+                if (typeof selectedPop.data_str === 'undefined' || !selectedPop.data_str.match(/dataset/i)) {
+                    var listDetail = solGS.listTypeTrainingPopulation.getListTypeTrainingPopDetail(selectedPop.id);
+
+                    if (listDetail.type.match(/plots/)) {
+                        solGS.listTypeTrainingPopulation.askTrainingJobQueueing(selectedPop.id);
+                    } else {
+                        var trialsList = listDetail.list;
+                        var trialsNames = listDetail.list_elements_names;
+
+                        solGS.listTypeTrainingPopulation.loadTrialListTypeTrainingPop(trialsNames);		    
+                    }
+                    } else {
+                        solGS.dataset.datasetTrainingPop(selectedPop.id, selectedPop.name);
+                    }
+                });
+        }	   
+    });       
+});
+

From f5a2cc202975867ce680cd4fa39c1f096fadc359 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 10:50:56 +0200
Subject: [PATCH 12/61] convert the lib into object literal, implement
 OptionsMenu.js

---
 .../solGS/listTypeTrainingPopulation.js       | 438 +++++++++---------
 1 file changed, 211 insertions(+), 227 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index 95e2365488..b85ce90643 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -1,4 +1,3 @@
-
 /**
 
 For training populations  from list of plots and trials.
@@ -13,24 +12,21 @@ JSAN.use("jquery.blockUI");
 var solGS = solGS || function solGS() {};
 
 solGS.listTypeTrainingPopulation = {
+  trainingPopsDiv: "#list_type_training_pops_select_div",
+  trainingPopsSelectMenuId: "#list_type_training_pops_select",
 
- trainingPopsDiv: "#list_type_training_pops_select_div",
- trainingPopsSelectMenuId: "#list_type_training_pops_select",
-
-getTrainingListElementsNames: function (list) {
-   
+  getTrainingListElementsNames: function (list) {
     var names = [];
     for (var i = 0; i < list.length; i++) {
-	names.push(list[i][1]);
+      names.push(list[i][1]);
     }
 
     return names;
+  },
 
-},
-
-populateTrainingPopsMenu: function  () {
+  populateTrainingPopsMenu: function () {
     var list = new CXGN.List();
-    var lists = list.getLists([ "plots", "trials"]);
+    var lists = list.getLists(["plots", "trials"]);
     var trainingPrivatePops = list.convertArrayToJson(lists.private_lists);
 
     var menuId = this.trainingPopsSelectMenuId;
@@ -44,7 +40,7 @@ populateTrainingPopsMenu: function  () {
       menuElem = menu.addOptions(trainingPublicLists);
     }
 
-    var datasetPops = solGS.dataset.getDatasetPops(["accessions","plots", "trials"]);
+    var datasetPops = solGS.dataset.getDatasetPops(["accessions", "plots", "trials"]);
     if (datasetPops) {
       menu.addOptionsSeparator("datasets");
       menuElem = menu.addOptions(datasetPops);
@@ -54,267 +50,255 @@ populateTrainingPopsMenu: function  () {
     jQuery(trainingPopsDiv).append(menuElem).show();
   },
 
-
-getTrainingListElementsIds: function (list) {
-   
+  getTrainingListElementsIds: function (list) {
     var ids = [];
     for (var i = 0; i < list.length; i++) {
-	ids.push(list[i][0]);
+      ids.push(list[i][0]);
     }
 
     return ids;
+  },
 
-},
-
-
-getListTypeTrainingPopDetail: function(listId) {   
-    
+  getListTypeTrainingPopDetail: function (listId) {
     var list = new CXGN.List();
-    
+
     var listData;
     var listType;
     var listName;
 
     if (listId) {
-        listData      = list.getListData(listId);
-	listType      = list.getListType(listId);
-	listName      = list.listNameById(listId);
-	listElements  = listData.elements;
+      listData = list.getListData(listId);
+      listType = list.getListType(listId);
+      listName = list.listNameById(listId);
+      listElements = listData.elements;
 
-	listElementsNames = this.getTrainingListElementsNames(listElements);
-	listElementsIds   = this.getTrainingListElementsIds(listElements);
+      listElementsNames = this.getTrainingListElementsNames(listElements);
+      listElementsIds = this.getTrainingListElementsIds(listElements);
     }
-  
-    return {'name'          : listName,	    
-	    'type'          : listType,
-	    'list_id'       : listId,
-	    'list_elements_names' : listElementsNames,
-	    'list_elements_ids' : listElementsIds,
-           };
-    
-},
-
-
-loadTrialListTypeTrainingPop: function (trialsNames) {
-   
+
+    return {
+      name: listName,
+      type: listType,
+      list_id: listId,
+      list_elements_names: listElementsNames,
+      list_elements_ids: listElementsIds,
+    };
+  },
+
+  loadTrialListTypeTrainingPop: function (trialsNames) {
     jQuery.ajax({
-        type: 'POST',
-        url: '/solgs/get/trial/id/',
-        dataType: 'json',
-        data: { 'trials_names': trialsNames},
-        success: function (res) {
-            solGS.combinedTrials.getCombinedPopsId(res.trials_ids);
-        },
-        error: function(response) {
-            alert('Error occured querying for trials ids');
-        }                       
+      type: "POST",
+      url: "/solgs/get/trial/id/",
+      dataType: "json",
+      data: { trials_names: trialsNames },
+      success: function (res) {
+        solGS.combinedTrials.getCombinedPopsId(res.trials_ids);
+      },
+      error: function (response) {
+        alert("Error occured querying for trials ids");
+      },
     });
+  },
 
-},
-
-askTrainingJobQueueing: function (listId) {
- 
+  askTrainingJobQueueing: function (listId) {
     var args = this.createTrainingReqArgs(listId);
     var modelId = args.training_pop_id;
     var protocolId = args.genotyping_protocol_id;
-    
-    var hostName = window.location.protocol + '//' + window.location.host;    
-    var page     = hostName + '/solgs/population/' + modelId;
+
+    var hostName = window.location.protocol + "//" + window.location.host;
+    var page = hostName + "/solgs/population/" + modelId;
 
     if (protocolId) {
-	page = page + '/gp/' + protocolId;
+      page = page + "/gp/" + protocolId;
     }
-    
-    solGS.waitPage(page, args);
-
-},
-
 
-createTrainingReqArgs: function (listId) {
+    solGS.waitPage(page, args);
+  },
 
-    var genoList  = this.getListTypeTrainingPopDetail(listId);
-    var listName  = genoList.name;
-    var list      = genoList.list;
-    var popId     = getModelId(listId);
-    var protocolId = jQuery('#genotyping_protocol_id').val();
-    var popType = 'list_reference';
+  createTrainingReqArgs: function (listId) {
+    var genoList = this.getListTypeTrainingPopDetail(listId);
+    var listName = genoList.name;
+    var list = genoList.list;
+    var popId = getModelId(listId);
+    var protocolId = jQuery("#genotyping_protocol_id").val();
+    var popType = "list_reference";
 
     var args = {
-	'list_name'       : listName,
-	'list_id'         : listId,
-	'analysis_type'   : 'training_dataset',
-	'data_set_type'   : 'single_population',
-        'training_pop_id' : popId,
-	'population_type' : popType,
-	'genotyping_protocol_id': protocolId
-    };  
+      list_name: listName,
+      list_id: listId,
+      analysis_type: "training_dataset",
+      data_set_type: "single_population",
+      training_pop_id: popId,
+      population_type: popType,
+      genotyping_protocol_id: protocolId,
+    };
 
     return args;
+  },
 
-},
-
-
-loadPlotListTypeTrainingPop: function(listId) {     
-  
-    var args  = this.createTrainingReqArgs(listId);
+  loadPlotListTypeTrainingPop: function (listId) {
+    var args = this.createTrainingReqArgs(listId);
     var popId = args.training_pop_id;
 
     if (window.Prototype) {
-	delete Array.prototype.toJSON;
+      delete Array.prototype.toJSON;
     }
-    
+
     args = JSON.stringify(args);
 
-    if ( args.list.length === 0) {       
-        alert('The list is empty. Please select a list with content.' );
-    }
-    else {  
-        jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-        jQuery.blockUI({message: 'Please wait..'});
-       
-        jQuery.ajax({
-            type: 'POST',
-            dataType: 'json',
-            data: {'arguments': args},
-            url: '/solgs/load/plots/list/training',                   
-            success: function(response) {
-                   
-                if (response.status == 'success') {
-    
-                    window.location = '/solgs/population/' + popId;                       
-		    jQuery.unblockUI();                        
-                      
-                } else {                                    
-                    alert("Error occured while querying for the training data.");
-                    jQuery.unblockUI();   
-                }                     
-            },
-            error: function(res) {
-                alert("Error occured while querying for the training data.");
-                jQuery.unblockUI();   
-            }            
-        });        
+    if (args.list.length === 0) {
+      alert("The list is empty. Please select a list with content.");
+    } else {
+      jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
+      jQuery.blockUI({ message: "Please wait.." });
+
+      jQuery.ajax({
+        type: "POST",
+        dataType: "json",
+        data: { arguments: args },
+        url: "/solgs/load/plots/list/training",
+        success: function (response) {
+          if (response.status == "success") {
+            window.location = "/solgs/population/" + popId;
+            jQuery.unblockUI();
+          } else {
+            alert("Error occured while querying for the training data.");
+            jQuery.unblockUI();
+          }
+        },
+        error: function (res) {
+          alert("Error occured while querying for the training data.");
+          jQuery.unblockUI();
+        },
+      });
     }
-},
-
+  },
 };
 
+jQuery.fn.doesExist = function () {
+  return jQuery(this).length > 0;
+};
 
-
-
-jQuery.fn.doesExist = function(){
-        return jQuery(this).length > 0;
- };
-
-
-
-function getUserUploadedRefPop (listId) {
- 
-    var genoList       = this.getListTypeTrainingPopDetail(listId);
-    var listName       = genoList.name;
-    var list           = genoList.list;
-    var modelId        = getModelId(listId);
-  
-    var url         =   '\'/solgs/population/'+ modelId + '\'';
-    var listIdArg   = '\'' + listId +'\'';
-    var listSource  = '\'from_db\'';
-    var popIdName   = {id : modelId, name: listName,};
-    popIdName       = JSON.stringify(popIdName);
-    var hiddenInput =  '<input type="hidden" value=\'' + popIdName + '\'/>';
-
-    var listSelPop ='<table id="list_reference_pops_table" style="width:100%; text-align:left"><tr>'
-                                + '<th>List-based training population</th>'
-                                + '<th>Models</th>'
-                                +'</tr>'
-                                + '<tr>'
-                                + '<td>'
-                                + '<a href="/solgs/population/' + modelId + '\" onclick="javascript:loadPopulationPage(' + url + ',' 
-                                + listIdArg + ',' + listSource + ')">' + '<data>'+ hiddenInput + '</data>'
-                                + listName + '</a>'
-                                + '</td>'
-                                + '<td id="list_reference_page_' + modelId +  '">'
-                                + '<a href="/solgs/population/' + modelId + '\" onclick="javascript:loadPopulationPage(' + url + ',' 
-                                + listIdArg + ',' + listSource + ')">' 
-                                + '[ Build model ]'+ '</a>'
-                                + '</td></tr></table>';
-
-    return listSelPop;
+function getUserUploadedRefPop(listId) {
+  var genoList = this.getListTypeTrainingPopDetail(listId);
+  var listName = genoList.name;
+  var list = genoList.list;
+  var modelId = getModelId(listId);
+
+  var url = "'/solgs/population/" + modelId + "'";
+  var listIdArg = "'" + listId + "'";
+  var listSource = "'from_db'";
+  var popIdName = { id: modelId, name: listName };
+  popIdName = JSON.stringify(popIdName);
+  var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+
+  var listSelPop =
+    '<table id="list_reference_pops_table" style="width:100%; text-align:left"><tr>' +
+    "<th>List-based training population</th>" +
+    "<th>Models</th>" +
+    "</tr>" +
+    "<tr>" +
+    "<td>" +
+    '<a href="/solgs/population/' +
+    modelId +
+    '" onclick="javascript:loadPopulationPage(' +
+    url +
+    "," +
+    listIdArg +
+    "," +
+    listSource +
+    ')">' +
+    "<data>" +
+    hiddenInput +
+    "</data>" +
+    listName +
+    "</a>" +
+    "</td>" +
+    '<td id="list_reference_page_' +
+    modelId +
+    '">' +
+    '<a href="/solgs/population/' +
+    modelId +
+    '" onclick="javascript:loadPopulationPage(' +
+    url +
+    "," +
+    listIdArg +
+    "," +
+    listSource +
+    ')">' +
+    "[ Build model ]" +
+    "</a>" +
+    "</td></tr></table>";
+
+  return listSelPop;
 }
 
-
-function loadPopulationPage (url, listId, listSource) {   
-    
-    var genoList       = this.getListTypeTrainingPopDetail(listId);
-    var listName       = genoList.name;
-    var modelId        = getModelId(listId);
-     
-    jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-    jQuery.blockUI({message: 'Please wait..'});
-   
-    jQuery.ajax({
-            type: 'POST',
-                url: url,
-                dataType: 'json',
-                data: {
-                       'list_reference': 1, 
-                       'model_id': modelId, 
-                       'list_source': listSource,
-                       'list_name'  : listName,
-                      },
-                success: function (response) {
-               
-                if (response.status == 'success') {                                 
-                    jQuery.unblockUI();                 
-                }
-                else {                
-                    alert('Fail: Error occured calculating GEBVs for the list of selection genotypes.');
-                    jQuery.unblockUI();
-                }
-            },
-                error: function(response) {
-                alert('error: ' + res.responseText);
-
-            }                       
-        });
-    
+function loadPopulationPage(url, listId, listSource) {
+  var genoList = this.getListTypeTrainingPopDetail(listId);
+  var listName = genoList.name;
+  var modelId = getModelId(listId);
+
+  jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
+  jQuery.blockUI({ message: "Please wait.." });
+
+  jQuery.ajax({
+    type: "POST",
+    url: url,
+    dataType: "json",
+    data: {
+      list_reference: 1,
+      model_id: modelId,
+      list_source: listSource,
+      list_name: listName,
+    },
+    success: function (response) {
+      if (response.status == "success") {
+        jQuery.unblockUI();
+      } else {
+        alert("Fail: Error occured calculating GEBVs for the list of selection genotypes.");
+        jQuery.unblockUI();
+      }
+    },
+    error: function (response) {
+      alert("error: " + res.responseText);
+    },
+  });
 }
 
-
-function getModelId (listId) {
-  
-    var modelId = 'list_' + listId; 
-    return modelId;
-
+function getModelId(listId) {
+  var modelId = "list_" + listId;
+  return modelId;
 }
 
-jQuery(document).ready( function() {
-    solGS.listTypeTrainingPopulation.populateTrainingPopsMenu();
-          
+jQuery(document).ready(function () {
+  solGS.listTypeTrainingPopulation.populateTrainingPopsMenu();
 });
 
-
-jQuery(document).ready( function() {  
-    jQuery("#list_type_training_pops_select").change(function() { 
-        var selectedPop = jQuery("option:selected", this).data("pop");
-        if (selectedPop.id) {  	
-            jQuery("#list_type_training_pop_go_btn").click(function() {
-
-                if (typeof selectedPop.data_str === 'undefined' || !selectedPop.data_str.match(/dataset/i)) {
-                    var listDetail = solGS.listTypeTrainingPopulation.getListTypeTrainingPopDetail(selectedPop.id);
-
-                    if (listDetail.type.match(/plots/)) {
-                        solGS.listTypeTrainingPopulation.askTrainingJobQueueing(selectedPop.id);
-                    } else {
-                        var trialsList = listDetail.list;
-                        var trialsNames = listDetail.list_elements_names;
-
-                        solGS.listTypeTrainingPopulation.loadTrialListTypeTrainingPop(trialsNames);		    
-                    }
-                    } else {
-                        solGS.dataset.datasetTrainingPop(selectedPop.id, selectedPop.name);
-                    }
-                });
-        }	   
-    });       
+jQuery(document).ready(function () {
+  jQuery("#list_type_training_pops_select").change(function () {
+    var selectedPop = jQuery("option:selected", this).data("pop");
+    if (selectedPop.id) {
+      jQuery("#list_type_training_pop_go_btn").click(function () {
+        if (
+          typeof selectedPop.data_str === "undefined" ||
+          !selectedPop.data_str.match(/dataset/i)
+        ) {
+          var listDetail = solGS.listTypeTrainingPopulation.getListTypeTrainingPopDetail(
+            selectedPop.id
+          );
+
+          if (listDetail.type.match(/plots/)) {
+            solGS.listTypeTrainingPopulation.askTrainingJobQueueing(selectedPop.id);
+          } else {
+            var trialsList = listDetail.list;
+            var trialsNames = listDetail.list_elements_names;
+
+            solGS.listTypeTrainingPopulation.loadTrialListTypeTrainingPop(trialsNames);
+          }
+        } else {
+          solGS.dataset.datasetTrainingPop(selectedPop.id, selectedPop.name);
+        }
+      });
+    }
+  });
 });
-

From c9e4dad64f05825d61383c9003ad09bbf0eaee7d Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 11:37:59 +0200
Subject: [PATCH 13/61] convert into object literal, implement OptionMenu..

---
 .../solGS/listTypeSelectionPopulation.js      | 687 +++++++++---------
 1 file changed, 349 insertions(+), 338 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index 6c91394178..e8c01c4a3f 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -1,5 +1,3 @@
-
-
 /**
 selection population upload from lists
 and files. Run prediction model on list selection population
@@ -9,440 +7,453 @@ Isaak Y Tecle
 iyt2@cornell.edu
 */
 
-JSAN.use("CXGN.List");
 JSAN.use("jquery.blockUI");
 
+var solGS = solGS || function solGS() {};
 
-jQuery(document).ready( function() {
-    solGS.selectMenu.populateMenu("list_type_selection_pops", ["accessions"], ['accessions', 'trials'] );
-          
-});
-
-
-jQuery(document).ready( function() {
-    jQuery("#list_type_selection_pops_list_select").change(function() {
-
-        var selectedPop = solGS.selectMenu.getSelectedPop('list_type_selection_pops');
-        if (selectedPop.selected_id) {
-
-	        jQuery(" #list_type_selection_pop_go_btn").click(function() {
-
-                if (typeof selectedPop.data_str === 'undefined' || !selectedPop.data_str.match(/dataset/i)) {
-                    var listDetail = getListTypeSelectionPopDetail(selectedPop.selected_id);
-
-                    if (listDetail.type.match(/accessions/)) {
-                        checkPredictedListSelection(selectedPop.selected_id);
-                    } else {
-                        //TO-DO
-                        //	var trialsList = listDetail.list;
-                        //	var trialsNames = listDetail.elementsNames;
-
-                        //	loadTrialListTypeSelectionPop(trialsNames);
-                    }
-                } else {
-                    solGS.dataset.checkPredictedDatasetSelection(selectedPop.selected_id, selectedPop.selected_name)
-                }
-            });
-        }
-    });
-});
-
-
-function checkPredictedListSelection (listId) {
+solGS.listTypeSelectionPopulation = {
+  selectionPopsDiv: "#list_type_selection_pops_select_div",
+  selectionPopsSelectMenuId: "#list_type_selection_pops_select",
 
-    var args =  createSelectionReqArgs(listId);
+  checkPredictedListSelection: function (listId) {
+    var args = this.createSelectionReqArgs(listId);
     args = JSON.stringify(args);
 
     jQuery.ajax({
-	type: 'POST',
-	dataType: 'json',
-	data: {'arguments': args},
-	url: '/solgs/check/predicted/list/selection',
-	success: function(response) {
-
-	    args = JSON.parse(args);
-
-	    if (response.output) {
-		displayPredictedListTypeSelectionPops(args, response.output);
-
-		if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
-		    solGS.sIndex.populateSindexMenu();
-		    solGS.correlation.populateGenCorrMenu();
-		    solGS.geneticGain.ggSelectionPopulations();
-		    solGS.cluster.listClusterPopulations();
-		}
-	    } else {
-		askSelectionJobQueueing(listId);
-	    }
-	}
+      type: "POST",
+      dataType: "json",
+      data: { arguments: args },
+      url: "/solgs/check/predicted/list/selection",
+      success: function (response) {
+        args = JSON.parse(args);
+
+        if (response.output) {
+          solGS.listTypeSelectionPopulation.displayPredictedListTypeSelectionPops(
+            args,
+            response.output
+          );
+
+          if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
+            solGS.sIndex.populateSindexMenu();
+            solGS.correlation.populateGenCorrMenu();
+            solGS.geneticGain.ggSelectionPopulations();
+            solGS.cluster.listClusterPopulations();
+          }
+        } else {
+          solGS.listTypeSelectionPopulation.askSelectionJobQueueing(listId);
+        }
+      },
     });
+  },
 
-}
-
-
-function getSelectionListElementsNames (list) {
-
+  getSelectionListElementsNames: function (list) {
     var names = [];
     for (var i = 0; i < list.length; i++) {
-	names.push(list[i][1]);
+      names.push(list[i][1]);
     }
 
     return names;
+  },
 
-}
-
+  getListTypeSelectionPopDetail: function (listId) {
+    if (typeof listId == "number") {
+      var list = new CXGN.List();
 
-function getListTypeSelectionPopDetail(listId) {
+      var listData;
+      var listType;
+      var listName;
 
-    if (typeof(listId) == 'number') {
-	var list = new CXGN.List();
+      if (listId) {
+        listData = list.getListData(listId);
+        listType = list.getListType(listId);
+        listName = list.listNameById(listId);
+        elemCount = listData.elements;
+      }
 
-	var listData;
-	var listType;
-	var listName;
-
-	if (listId) {
-            listData      = list.getListData(listId);
-	    listType      = list.getListType(listId);
-	    listName      = list.listNameById(listId);
-	    elemCount     = listData.elements;
-	}
-
-	return {'name'          : listName,
-		'list_id'       : listId,
-		'type'          : listType,
-		'elements_count' : elemCount
-               };
+      return { name: listName, list_id: listId, type: listType, elements_count: elemCount };
     }
-}
-
+  },
 
-function askSelectionJobQueueing (listId) {
-
-    var args = createSelectionReqArgs(listId);
+  askSelectionJobQueueing: function (listId) {
+    var args = this.createSelectionReqArgs(listId);
     var modelId = args.training_pop_id;
     var selectionPopId = args.selection_pop_id;
     var protocolId = args.genotyping_protocol_id;
 
-    var hostName = window.location.protocol + '//' + window.location.host;
-    var page     = hostName + '/solgs/selection/' + selectionPopId + '/model/' + modelId;
+    var hostName = window.location.protocol + "//" + window.location.host;
+    var page = hostName + "/solgs/selection/" + selectionPopId + "/model/" + modelId;
 
     solGS.waitPage(page, args);
-
-}
-
-
-function createSelectionReqArgs (listId) {
-
-    if (typeof(listId) == 'number') {
-	var genoList  = getListTypeSelectionPopDetail(listId);
-	var listName  = genoList.name;
-	var list      = genoList.list;
-	var modelId   = getModelId();
-	var traitId   = getTraitId();
-
-	var dataSetType = trainingDataSetType();
-
-	var popType = 'list_prediction';
-
-	var selectionPopId = 'list_' + listId;
-	var protocolId = jQuery('#genotyping_protocol_id').val();
-
-	var trainingTraitsIds = solGS.getTrainingTraitsIds();
-
-	var args = {
-	    'list_name'        : listName,
-	    'list_id'          : listId,
-	    'analysis_type'    : 'selection_prediction',
-	    'data_set_type'    : dataSetType,
-	    'training_pop_id'  : modelId,
-	    'selection_pop_id' : selectionPopId,
-	    'population_type'  : popType,
-	    'training_traits_ids' : trainingTraitsIds,
-	    'genotyping_protocol_id': protocolId
-	};
-
-	return args;
+  },
+
+  createSelectionReqArgs: function (listId) {
+    if (typeof listId == "number") {
+      var genoList = this.getListTypeSelectionPopDetail(listId);
+      var listName = genoList.name;
+      var list = genoList.list;
+      var modelId = this.getModelId();
+      var traitId = this.getTraitId();
+
+      var dataSetType = this.trainingDataSetType();
+
+      var popType = "list_prediction";
+
+      var selectionPopId = "list_" + listId;
+      var protocolId = jQuery("#genotyping_protocol_id").val();
+
+      var trainingTraitsIds = solGS.getTrainingTraitsIds();
+
+      var args = {
+        list_name: listName,
+        list_id: listId,
+        analysis_type: "selection_prediction",
+        data_set_type: dataSetType,
+        training_pop_id: modelId,
+        selection_pop_id: selectionPopId,
+        population_type: popType,
+        training_traits_ids: trainingTraitsIds,
+        genotyping_protocol_id: protocolId,
+      };
+
+      return args;
     }
+  },
 
-}
-
-
-function getGenotypesList(listId) {
-
+  getGenotypesList: function (listId) {
     var list = new CXGN.List();
     var genotypesList;
 
-    if (! listId == "") {
-        genotypesList = list.getListData(listId);
+    if (!listId == "") {
+      genotypesList = list.getListData(listId);
     }
 
     var listName = list.listNameById(listId);
     var listType = list.getListType(listId);
 
-    return {'name'      : listName,
-            'listId'      : listId,
-            'list_type' : listType,
-           };
-
-}
+    return { name: listName, listId: listId, list_type: listType };
+  },
 
-
-function loadGenotypesListTypeSelectionPop(args) {
-
-    var listDetail = getListTypeSelectionPopDetail(args.list_id);
+  loadGenotypesListTypeSelectionPop: function (args) {
+    var listDetail = this.getListTypeSelectionPopDetail(args.list_id);
 
     if (window.Prototype) {
-	delete Array.prototype.toJSON;
+      delete Array.prototype.toJSON;
     }
 
     args = JSON.stringify(args);
-    var len   = listDetail.elements_count;
+    var len = listDetail.elements_count;
 
     if (len === 0) {
-        alert('The list is empty. Please select a list with content.' );
-    }
-    else {
-	jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-	jQuery.blockUI({message: 'Please wait..'});
-
-        jQuery.ajax({
-            type: 'POST',
-            dataType: 'json',
-            data: {'arguments': args},
-            url: '/solgs/load/genotypes/list/selection',
-            success: function(response) {
-
-                if (response.status == 'success') {
-		    args = JSON.parse(args);
-		    var modelId  = args.training_pop_id;
-		    var traitId  = args.trait_id;
-		    var selPopId = args.selection_pop_id;
-		    var listId   = args.list_id
-
-		    if (window.location.href.match(/solgs\/trait\//)) {
-			window.location = "/solgs/selection/" + selPopId + '/model/' + modelId + '/trait/' + traitId;
-			jQuery.unblockUI();
-		    } else if (window.location.href.match(/solgs\/model\/combined\/populations\//)) {
-			window.location = "/solgs/selection/" + selPopId + '/model/combined/' + modelId + '/trait/' + traitId;
-			jQuery.unblockUI();
-		    } else {
-			displayPredictedListTypeSelectionPops(args, response.output);
-			solGS.sIndex.populateSindexMenu();
-			solGS.correlation.populateGenCorrMenu();
-			jQuery.unblockUI();
-		    }
-
-                } else {
-                    alert("fail: Error occured while querying for the genotype data of the accessions.");
-                    jQuery.unblockUI();
-                }
-            },
-            error: function(res) {
-                alert("Error occured while querying for the genotype data of the accessions.");
-                jQuery.unblockUI();
+      alert("The list is empty. Please select a list with content.");
+    } else {
+      jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
+      jQuery.blockUI({ message: "Please wait.." });
+
+      jQuery.ajax({
+        type: "POST",
+        dataType: "json",
+        data: { arguments: args },
+        url: "/solgs/load/genotypes/list/selection",
+        success: function (response) {
+          if (response.status == "success") {
+            args = JSON.parse(args);
+            var modelId = args.training_pop_id;
+            var traitId = args.trait_id;
+            var selPopId = args.selection_pop_id;
+            var listId = args.list_id;
+
+            if (window.location.href.match(/solgs\/trait\//)) {
+              window.location =
+                "/solgs/selection/" + selPopId + "/model/" + modelId + "/trait/" + traitId;
+              jQuery.unblockUI();
+            } else if (window.location.href.match(/solgs\/model\/combined\/populations\//)) {
+              window.location =
+                "/solgs/selection/" + selPopId + "/model/combined/" + modelId + "/trait/" + traitId;
+              jQuery.unblockUI();
+            } else {
+              displayPredictedListTypeSelectionPops(args, response.output);
+              solGS.sIndex.populateSindexMenu();
+              solGS.correlation.populateGenCorrMenu();
+              jQuery.unblockUI();
             }
-        });
+          } else {
+            alert("fail: Error occured while querying for the genotype data of the accessions.");
+            jQuery.unblockUI();
+          }
+        },
+        error: function (res) {
+          alert("Error occured while querying for the genotype data of the accessions.");
+          jQuery.unblockUI();
+        },
+      });
     }
-}
-
-
+  },
 
-function predictGenotypesListSelectionPop (args) {
-
-    var modelId  = args.training_pop_id;
-    var traitId  = args.trait_id;
+  predictGenotypesListSelectionPop: function (args) {
+    var modelId = args.training_pop_id;
+    var traitId = args.trait_id;
     var selPopId = args.selection_pop_id;
 
-    var url = '/solgs/selection/' + selPopId + '/model/' + modelId;
+    var url = "/solgs/selection/" + selPopId + "/model/" + modelId;
 
     jQuery.ajax({
-	dataType: 'json',
-	type    : 'POST',
- 	data    : {'trait_id': traitId, 'list_source': 'from_db', 'list_prediction': 1},
-	url     : url,
-	success : function (res) {
-	    if (res.status == 'success') {
-		window.location = "/solgs/selection/" + selPopId + '/model/' + modelId + '/trait/' + traitId;
-	    } else {
-		window.location = window.location.href;
-	    }
-	}
+      dataType: "json",
+      type: "POST",
+      data: { trait_id: traitId, list_source: "from_db", list_prediction: 1 },
+      url: url,
+      success: function (res) {
+        if (res.status == "success") {
+          window.location =
+            "/solgs/selection/" + selPopId + "/model/" + modelId + "/trait/" + traitId;
+        } else {
+          window.location = window.location.href;
+        }
+      },
     });
 
     jQuery.unblockUI();
-}
-
-
-jQuery.fn.doesExist = function(){
-        return jQuery(this).length > 0;
- };
-
-
-function getModelId () {
+  },
 
+  getModelId: function () {
     var modelId;
     var modelIdExists = jQuery("#model_id").doesExist();
     var comboPopsIdExists = jQuery("#combo_pops_id").doesExist();
     var popIdExists = jQuery("#population_id").doesExist();
 
     if (jQuery("#model_id").val()) {
-        modelId = jQuery("#model_id").val();
-    }
-    else if (jQuery("#population_id").val()) {
-	modelId = jQuery("#population_id").val();
-    }
-    else if (jQuery("#combo_pops_id").val() ) {
-        modelId = jQuery("#combo_pops_id").val();
+      modelId = jQuery("#model_id").val();
+    } else if (jQuery("#population_id").val()) {
+      modelId = jQuery("#population_id").val();
+    } else if (jQuery("#combo_pops_id").val()) {
+      modelId = jQuery("#combo_pops_id").val();
     }
 
     return modelId;
-}
-
-
-function trainingDataSetType () {
+  },
 
+  trainingDataSetType: function () {
     var dataSetType;
     var referer = document.URL;
 
-    if ( referer.match(/\/combined\//) ) {
-        dataSetType = 'combined_populations';
+    if (referer.match(/\/combined\//)) {
+      dataSetType = "combined_populations";
     } else {
-        dataSetType = 'single_population';
+      dataSetType = "single_population";
     }
 
     return dataSetType;
-}
-
-
-function getTraitId () {
+  },
 
+  getTraitId: function () {
     var traitId;
     var traitIdExists = jQuery("#trait_id").doesExist();
 
-    if ( traitIdExists == true ) {
-        traitId = jQuery("#trait_id").val();
+    if (traitIdExists == true) {
+      traitId = jQuery("#trait_id").val();
     }
 
     return traitId;
-}
-
+  },
 
-function displayPredictedListTypeSelectionPops(args, output) {
-
-    var listName       = args.list_name;
-    var listId         = args.list_id;
-    var traitId        = args.trait_id;
+  displayPredictedListTypeSelectionPops: function (args, output) {
+    var listName = args.list_name;
+    var listId = args.list_id;
+    var traitId = args.trait_id;
     var selectionPopId = args.selection_pop_id;
-    var trainingPopId  = args.training_pop_id;
+    var trainingPopId = args.training_pop_id;
 
-    var url =   '/solgs/selection/'+ selectionPopId + '/model/'+ trainingPopId;
-    var listIdArg   = '\'' + listId +'\'';
-    var listSource  = '\'from_db\'';
-    var popIdName   = {'id' : 'list_' + listId, 'name' : listName, 'pop_type': 'list_selection'};
-    popIdName       = JSON.stringify(popIdName);
-    var hiddenInput =  '<input type="hidden" value=\'' + popIdName + '\'/>';
+    var url = "/solgs/selection/" + selectionPopId + "/model/" + trainingPopId;
+    var listIdArg = "'" + listId + "'";
+    var listSource = "'from_db'";
+    var popIdName = { id: "list_" + listId, name: listName, pop_type: "list_selection" };
+    popIdName = JSON.stringify(popIdName);
+    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
 
     var predictedListTypeSelectionPops = jQuery("#list_type_selection_pops_table").doesExist();
 
-    if ( predictedListTypeSelectionPops == false) {
-
-	var predictedListTypeSelectionTable ='<table id="list_type_selection_pops_table" class="table"><thead><tr>'
-            + '<th>List-based selection population</th>'
-            + '<th>View GEBVs</th>'
-            + '</tr></thead><tbody>'
-            + '<tr id="list_prediction_output_' + listId +  '">'
-            + '<td>'
-            + '<b>' + listName + '</b>'
-            + '</td>'
-            + '<td><data>'+ hiddenInput + '</data>'
-            + output
-            + '</td></tr></tbody></table>';
-
-	jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
-
+    if (predictedListTypeSelectionPops == false) {
+      var predictedListTypeSelectionTable =
+        '<table id="list_type_selection_pops_table" class="table"><thead><tr>' +
+        "<th>List-based selection population</th>" +
+        "<th>View GEBVs</th>" +
+        "</tr></thead><tbody>" +
+        '<tr id="list_prediction_output_' +
+        listId +
+        '">' +
+        "<td>" +
+        "<b>" +
+        listName +
+        "</b>" +
+        "</td>" +
+        "<td><data>" +
+        hiddenInput +
+        "</data>" +
+        output +
+        "</td></tr></tbody></table>";
+
+      jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
     } else {
-        var listIdArg = '\'' + listId +'\'';
-        var listSource = '\'from_db\'';
-
-        var popIdName   = {id : 'list_' + listId, name: listName, pop_type: 'list_selection'};
-        popIdName       = JSON.stringify(popIdName);
-        var hiddenInput =  '<input type="hidden" value=\'' + popIdName + '\'/>';
-
-        var addRow = '<tr id="list_prediction_output_' + listId +  '"><td>'
-	    + '<b>' + listName
-            + '</td>'
-            + '<td> <data>'+ hiddenInput + '</data>'
-            + output
-            + '</td></tr>';
-
-	var trId = '#list_prediction_output_' + listId;
-        var samePop = jQuery(trId).doesExist();
-
-        if (samePop == false) {
-            jQuery("#list_type_selection_pops_table tr:last").after(addRow);
-
-        } else {
-	    jQuery(trId).remove();
-	    jQuery("#list_type_selection_pops_table").append(addRow).show();
-	}
-
+      var listIdArg = "'" + listId + "'";
+      var listSource = "'from_db'";
+
+      var popIdName = { id: "list_" + listId, name: listName, pop_type: "list_selection" };
+      popIdName = JSON.stringify(popIdName);
+      var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+
+      var addRow =
+        '<tr id="list_prediction_output_' +
+        listId +
+        '"><td>' +
+        "<b>" +
+        listName +
+        "</td>" +
+        "<td> <data>" +
+        hiddenInput +
+        "</data>" +
+        output +
+        "</td></tr>";
+
+      var trId = "#list_prediction_output_" + listId;
+      var samePop = jQuery(trId).doesExist();
+
+      if (samePop == false) {
+        jQuery("#list_type_selection_pops_table tr:last").after(addRow);
+      } else {
+        jQuery(trId).remove();
+        jQuery("#list_type_selection_pops_table").append(addRow).show();
+      }
     }
+  },
 
-}
+  populateSelectionPopsMenu: function () {
+    var list = new CXGN.List();
+    var lists = list.getLists(["accessions", "trials"]);
+    var selectionPrivatePops = list.convertArrayToJson(lists.private_lists);
+
+    var menuId = this.selectionPopsSelectMenuId;
+    var menu = new OptionsMenu(menuId);
+    selectionPrivatePops = selectionPrivatePops.flat();
+    var menuElem = menu.addOptions(selectionPrivatePops);
+
+    if (lists.public_lists[0]) {
+      var selectionPublicLists = list.convertArrayToJson(lists.public_lists);
+      menu.addOptionsSeparator("public lists");
+      menuElem = menu.addOptions(selectionPublicLists);
+    }
 
+    var datasetPops = solGS.dataset.getDatasetPops(["accessions", "trials"]);
+    if (datasetPops) {
+      menu.addOptionsSeparator("datasets");
+      menuElem = menu.addOptions(datasetPops);
+    }
 
-function loadPredictionOutput (url, listId, listSource) {
+    var selectionPopsDiv = this.selectionPopsDiv;
+    jQuery(selectionPopsDiv).append(menuElem).show();
+  },
+
+  getListTypeSelPopulations: function () {
+    var listTypeSelPopsDiv = document.getElementById("list_type_selection_pops_selected");
+    var listTypeSelPopsTable = listTypeSelPopsDiv.getElementsByTagName("table");
+    var listTypeSelPopsRows = listTypeSelPopsTable[0].rows;
+
+    var popsList = [];
+    for (var i = 1; i < listTypeSelPopsRows.length; i++) {
+      var row = listTypeSelPopsRows[i];
+      var popRow = row.innerHTML;
+
+      var predict = popRow.match(/predict/gi);
+      if (!predict) {
+        var selPopsInput = row.getElementsByTagName("input")[0];
+        var sIndexPopData = selPopsInput.value;
+        popsList.push(JSON.parse(sIndexPopData));
+      }
+    }
+    return popsList;
+  },
 
-    var traitId = getTraitId();
-    var modelId = getModelId();
+  loadPredictionOutput: function (url, listId, listSource) {
+    var traitId = this.getTraitId();
+    var modelId = this.getModelId();
 
     jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-    jQuery.blockUI({message: 'Please wait..'});
+    jQuery.blockUI({ message: "Please wait.." });
 
     jQuery.ajax({
-        type: 'POST',
-        url: url,
-        dataType: 'json',
-        data: {
-            'list_prediction': 1,
-            'trait_id': traitId,
-            'model_id': modelId,
-            'prediction_id': listId,
-            'list_source': listSource,
-        },
-
-        success: function (response) {
-
-            if (response.status == 'success') {
-
-                var tdId = '#list_prediction_output_' + listId;
-                jQuery(tdId).html(response.output);
+      type: "POST",
+      url: url,
+      dataType: "json",
+      data: {
+        list_prediction: 1,
+        trait_id: traitId,
+        model_id: modelId,
+        prediction_id: listId,
+        list_source: listSource,
+      },
+
+      success: function (response) {
+        if (response.status == "success") {
+          var tdId = "#list_prediction_output_" + listId;
+          jQuery(tdId).html(response.output);
+
+          var page = document.URL;
+
+          if (page.match("/traits/all/population/") != null) {
+            solGS.sIndex.populateSindexMenu();
+            solGS.correlation.populateGenCorrMenu();
+          }
+
+          jQuery.unblockUI();
+        } else {
+          if (response.status == "failed") {
+            alert("Error occured while uploading the list of selection genotypes.");
+          } else {
+            alert(response.status);
+          }
 
-                var page = document.URL;
+          jQuery.unblockUI();
+        }
+      },
 
-                if (page.match('/traits/all/population/') != null) {
-                    solGS.sIndex.populateSindexMenu();
-                    solGS.correlation.populateGenCorrMenu();
-                }
+      error: function (response) {
+        alert("error: " + res.responseText);
+      },
+    });
+  },
+};
 
-                jQuery.unblockUI();
-            }
-            else {
-                if(response.status == 'failed') {
-                    alert("Error occured while uploading the list of selection genotypes.");
-                } else {
-                    alert(response.status);
-                }
-
-                jQuery.unblockUI();
-            }
-        },
+jQuery.fn.doesExist = function () {
+  return jQuery(this).length > 0;
+};
 
-        error: function(response) {
-            alert('error: ' + res.responseText);
+jQuery(document).ready(function () {
+  solGS.listTypeSelectionPopulation.populateSelectionPopsMenu();
+});
 
+jQuery(document).ready(function () {
+  jQuery("#list_type_selection_pops_select").change(function () {
+    var selectedPop = jQuery("option:selected", this).data("pop");
+    if (selectedPop.id) {
+      jQuery(" #list_type_selection_pop_go_btn").click(function () {
+        if (
+          typeof selectedPop.data_str === "undefined" ||
+          !selectedPop.data_str.match(/dataset/i)
+        ) {
+          var listDetail = solGS.listTypeSelectionPopulation.getListTypeSelectionPopDetail(
+            selectedPop.id
+          );
+
+          if (listDetail.type.match(/accessions/)) {
+            solGS.listTypeSelectionPopulation.checkPredictedListSelection(selectedPop.id);
+          } else {
+            //TO-DO
+            //	var trialsList = listDetail.list;
+            //	var trialsNames = listDetail.elementsNames;
+            //	loadTrialListTypeSelectionPop(trialsNames);
+          }
+        } else {
+          solGS.dataset.checkPredictedDatasetSelection(selectedPop.id, selectedPop.name);
         }
-    });
-
-}
+      });
+    }
+  });
+});

From c863a72fe8a17090385c934617d3da085060e769 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 10 May 2023 11:52:37 +0200
Subject: [PATCH 14/61] convert into object literal

---
 .../legacy/solGS/selectionPopulations.js      | 336 +++++++++---------
 1 file changed, 167 insertions(+), 169 deletions(-)

diff --git a/js/source/legacy/solGS/selectionPopulations.js b/js/source/legacy/solGS/selectionPopulations.js
index fc42147fcd..e7472c596e 100644
--- a/js/source/legacy/solGS/selectionPopulations.js
+++ b/js/source/legacy/solGS/selectionPopulations.js
@@ -1,216 +1,214 @@
 /**
-* search and display selection populations
-* relevant to a training population.
-* Isaak Y Tecle <iyt2@cornell.edu>
-*
-*/
+ * search and display selection populations
+ * relevant to a training population.
+ * Isaak Y Tecle <iyt2@cornell.edu>
+ *
+ */
 
+var solGS = solGS || function solGS() {};
 
-
-function checkSelectionPopulations () {
-
-	var args = solGS.getModelArgs();
-	args = JSON.stringify(args);
+solGS.selectionPopulation = {
+  checkSelectionPopulations: function () {
+    var args = solGS.getModelArgs();
+    args = JSON.stringify(args);
 
     jQuery.ajax({
-        type: 'POST',
-		data: {'arguments': args},
-        dataType: 'json',
-        url: '/solgs/check/selection/populations/',
-        success: function(response) {
-            if (response.data) {
-			jQuery("#selection_populations").show();
-			jQuery("#search_all_selection_pops").show();
-
-			displaySelectionPopulations(response.data);
-            } else {
-				jQuery("#search_all_selection_pops").show();
-            }
-		}
+      type: "POST",
+      data: { arguments: args },
+      dataType: "json",
+      url: "/solgs/check/selection/populations/",
+      success: function (response) {
+        if (response.data) {
+          jQuery("#selection_populations").show();
+          jQuery("#search_all_selection_pops").show();
+
+          solGS.selectionPopulation.displaySelectionPopulations(response.data);
+        } else {
+          jQuery("#search_all_selection_pops").show();
+        }
+      },
     });
+  },
 
-}
-
-function checkSelectionPopulationRelevance (popName) {
-	var modelVars= solGS.getModelArgs();
-	modelVars['selection_pop_name'] = popName;
+  checkSelectionPopulationRelevance: function (popName) {
+    var modelVars = solGS.getModelArgs();
+    modelVars["selection_pop_name"] = popName;
 
     jQuery("#selection_pops_message")
-	.html("Checking if the model can be used on " + popName + "...please wait...")
-	.show();
+      .html("Checking if the model can be used on " + popName + "...please wait...")
+      .show();
 
-	var popData = JSON.stringify(modelVars);
+    var popData = JSON.stringify(modelVars);
     jQuery.ajax({
-        type: 'POST',
-        dataType: 'json',
-		data: {arguments: popData},
-        url: '/solgs/check/selection/population/relevance/',
-        success: function(res) {
-
-	     if (res.selection_pop_id) {
-		
-		if (res.selection_pop_id != res.training_pop_id ) {
-
-		    if (res.similarity >= 0.5 ) {
-
-			jQuery("#selection_pops_message ").hide();
-			jQuery("#selection_populations").show();
-
-			var selPopExists = jQuery('#selection_pops_list:contains(' + popName + ')').length;
-			if (!selPopExists) {
-			    displaySelectionPopulations(res.selection_pop_data);
-			}
-
-		    } else {
-
-			jQuery("#selection_pops_message")
-			.html(popName +" is genotyped by a marker set different  "
-			      + "from the one used for the training population. "
-			      + "Therefore you can not predict its GEBVs using this model.")
-			.show();
-		    }
-		} else {
-		    jQuery("#selection_pops_message")
-			.html(popName +" is the same population as the "
-			      + "the training population. "
-			      + "Please select a different selection population.")
-			.show()
-			.fadeOut(5000);
-		}
-	    } else {
-
-		jQuery("#selection_pops_message")
-		    .html(popName + " does not exist in the database.")
-		    .show()
-			.fadeOut(5000);
-	    }
-	},
-	error: function (res) {
-
-	    jQuery("#selection_pops_message")
-		    .html("Error occured processing the query.")
-		    .show()
-			.fadeOut(5000);
-	}
+      type: "POST",
+      dataType: "json",
+      data: { arguments: popData },
+      url: "/solgs/check/selection/population/relevance/",
+      success: function (res) {
+        if (res.selection_pop_id) {
+          if (res.selection_pop_id != res.training_pop_id) {
+            if (res.similarity >= 0.5) {
+              jQuery("#selection_pops_message ").hide();
+              jQuery("#selection_populations").show();
+
+              var selPopExists = jQuery("#selection_pops_list:contains(" + popName + ")").length;
+              if (!selPopExists) {
+                solGS.selectionPopulation.displaySelectionPopulations(res.selection_pop_data);
+              }
+            } else {
+              jQuery("#selection_pops_message")
+                .html(
+                  popName +
+                    " is genotyped by a marker set different  " +
+                    "from the one used for the training population. " +
+                    "Therefore you can not predict its GEBVs using this model."
+                )
+                .show();
+            }
+          } else {
+            jQuery("#selection_pops_message")
+              .html(
+                popName +
+                  " is the same population as the " +
+                  "the training population. " +
+                  "Please select a different selection population."
+              )
+              .show()
+              .fadeOut(5000);
+          }
+        } else {
+          jQuery("#selection_pops_message")
+            .html(popName + " does not exist in the database.")
+            .show()
+            .fadeOut(5000);
+        }
+      },
+      error: function (res) {
+        jQuery("#selection_pops_message")
+          .html("Error occured processing the query.")
+          .show()
+          .fadeOut(5000);
+      },
     });
+  },
 
-}
-
-function searchSelectionPopulations () {
+  searchSelectionPopulations: function () {
     var args = solGS.getModelArgs();
 
     jQuery.ajax({
-        type: 'POST',
-        dataType: 'json',
-		data: args ,
-        url: '/solgs/search/selection/populations/' + popId,
-        success: function(res) {
-
-	    if (res.data) {
-
-		jQuery('#selection_populations').show();
-		displaySelectionPopulations(res.data);
-		jQuery('#search_all_selection_pops').hide();
-		jQuery('#selection_pops_message').hide();
-            } else {
-
-				var msg =  '<p>There are no relevant selection populations in the database.'
-		                     + 'If you have or want to make your own set of selection candidates'
-		                     + 'use the form below.</p>';
-
-				jQuery('#selection_pops_message')
-					.html(msg)
-					.show()
-					.fadeOut(5000);
-	      }
-	}
+      type: "POST",
+      dataType: "json",
+      data: args,
+      url: "/solgs/search/selection/populations/" + popId,
+      success: function (res) {
+        if (res.data) {
+          jQuery("#selection_populations").show();
+          solGS.selectionPopulation.displaySelectionPopulations(res.data);
+          jQuery("#search_all_selection_pops").hide();
+          jQuery("#selection_pops_message").hide();
+        } else {
+          var msg =
+            "<p>There are no relevant selection populations in the database." +
+            "If you have or want to make your own set of selection candidates" +
+            "use the form below.</p>";
+
+          jQuery("#selection_pops_message").html(msg).show().fadeOut(5000);
+        }
+      },
     });
-}
+  },
 
+  getPredictedTrialTypeSelectionPops: function () {
+    var selPopsTable = jQuery("#selection_pops_list").html();
+    var selPopsRows;
 
-function displaySelectionPopulations (data) {
+    if (selPopsTable !== null) {
+      selPopsRows = jQuery("#selection_pops_list").find("tbody > tr");
+    }
 
-    var tableRow = jQuery('#selection_pops_list tr').length;
+    var popsList = [];
+
+    for (var i = 0; i < selPopsRows.length; i++) {
+      var row = selPopsRows[i];
+      var popRow = row.innerHTML;
+      var predict = popRow.match(/predict/gi);
+      if (!predict) {
+        var selPopsInput = row.getElementsByTagName("input")[0];
+        var sIndexPopData = selPopsInput.value;
+        popsList.push(JSON.parse(sIndexPopData));
+      }
+    }
 
-    if (tableRow === 1) {
+    return popsList;
+  },
 
-	jQuery('#selection_pops_list').dataTable({
-	    'searching' : false,
-	    'ordering'  : false,
-	    'processing': true,
-	    'paging': false,
-	    'info': false,
-	    "data": data
-	});
+  displaySelectionPopulations: function (data) {
+    var tableRow = jQuery("#selection_pops_list tr").length;
 
+    if (tableRow === 1) {
+      jQuery("#selection_pops_list").dataTable({
+        searching: false,
+        ordering: false,
+        processing: true,
+        paging: false,
+        info: false,
+        data: data,
+      });
     } else {
-
-	jQuery('#selection_pops_list').dataTable().fnAddData(data);
+      jQuery("#selection_pops_list").dataTable().fnAddData(data);
     }
-}
-
-function getPopulationId () {
+  },
 
+  getPopulationId: function () {
     var populationId = jQuery("#population_id").val();
 
     if (!populationId) {
-        populationId = jQuery("#model_id").val();
+      populationId = jQuery("#model_id").val();
     }
 
     if (!populationId) {
-        populationId = jQuery("#combo_pops_id").val();
+      populationId = jQuery("#combo_pops_id").val();
     }
 
     return populationId;
+  },
+};
 
-}
-
-jQuery(document).ready( function () {
-    checkSelectionPopulations();
-
+jQuery(document).ready(function () {
+  solGS.selectionPopulation.checkSelectionPopulations();
 });
 
-jQuery(document).ready( function() {
-
-    jQuery("#search_all_selection_pops").click(function() {
-
-	searchSelectionPopulations();
-	jQuery("#selection_pops_message")
-	    .html("<br/><br/>Searching for all selection populations relevant to this model...please wait...");
-    });
-
+jQuery(document).ready(function () {
+  jQuery("#search_all_selection_pops").click(function () {
+    solGS.selectionPopulation.searchSelectionPopulations();
+    jQuery("#selection_pops_message").html(
+      "<br/><br/>Searching for all selection populations relevant to this model...please wait..."
+    );
+  });
 });
 
-jQuery(document).ready( function () {
-
-    jQuery('#population_search_entry').keyup(function(e){
+jQuery(document).ready(function () {
+  jQuery("#population_search_entry").keyup(function (e) {
+    jQuery("#population_search_entry").css("border", "solid #96d3ec");
 
-	jQuery("#population_search_entry")
-		.css('border', 'solid #96d3ec');
+    jQuery("#form-feedback-search-trials").empty();
 
-	jQuery("#form-feedback-search-trials")
-	    .empty();
-
-	if(e.keycode == 13) {
-     	    jQuery('#search_selection_pop').click();
-    	}
-    });
-
-    jQuery('#search_selection_pop').on('click', function () {
-
-	jQuery("#selection_pops_message").hide();
+    if (e.keycode == 13) {
+      jQuery("#search_selection_pop").click();
+    }
+  });
 
-	var entry = jQuery('#population_search_entry').val();
+  jQuery("#search_selection_pop").on("click", function () {
+    jQuery("#selection_pops_message").hide();
 
-	if (entry) {
-	    checkSelectionPopulationRelevance(entry);
-	}  else {
-	    jQuery("#population_search_entry")
-		.css('border', 'solid #FF0000');
+    var entry = jQuery("#population_search_entry").val();
 
-	    jQuery("#form-feedback-search-trials")
-		.text('Please enter trial name.');
-	}
-    });
+    if (entry) {
+      solGS.selectionPopulation.checkSelectionPopulationRelevance(entry);
+    } else {
+      jQuery("#population_search_entry").css("border", "solid #FF0000");
 
+      jQuery("#form-feedback-search-trials").text("Please enter trial name.");
+    }
+  });
 });

From 0f3f8c755d57aee0207f9b948ba7a5951091d659 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Thu, 11 May 2023 09:16:20 +0200
Subject: [PATCH 15/61] stringify req data

---
 js/source/legacy/solGS/selectionPopulations.js | 3 ++-
 lib/SGN/Controller/solGS/Search.pm             | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/js/source/legacy/solGS/selectionPopulations.js b/js/source/legacy/solGS/selectionPopulations.js
index e7472c596e..74e06b88c0 100644
--- a/js/source/legacy/solGS/selectionPopulations.js
+++ b/js/source/legacy/solGS/selectionPopulations.js
@@ -95,10 +95,11 @@ solGS.selectionPopulation = {
   searchSelectionPopulations: function () {
     var args = solGS.getModelArgs();
 
+    args = JSON.stringify(args);
     jQuery.ajax({
       type: "POST",
       dataType: "json",
-      data: args,
+      data: {'arguments': args},
       url: "/solgs/search/selection/populations/" + popId,
       success: function (res) {
         if (res.data) {
diff --git a/lib/SGN/Controller/solGS/Search.pm b/lib/SGN/Controller/solGS/Search.pm
index 28f2db6ce4..350443d04d 100644
--- a/lib/SGN/Controller/solGS/Search.pm
+++ b/lib/SGN/Controller/solGS/Search.pm
@@ -335,7 +335,8 @@ sub check_training_population : Path('/solgs/check/training/population/')
 sub search_selection_pops : Path('/solgs/search/selection/populations/') {
     my ( $self, $c, $tr_pop_id ) = @_;
 
-    $c->stash->{training_pop_id} = $tr_pop_id;
+    $c->controller('solGS::Utils')
+      ->stash_json_args( $c, $c->req->param('arguments') );
 
     $self->search_all_relevant_selection_pops( $c, $tr_pop_id );
     my $selection_pops_list = $c->stash->{all_relevant_selection_pops};

From 6843eacc7a2384ce072d67bd5472cc272526fcc9 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Thu, 11 May 2023 09:21:43 +0200
Subject: [PATCH 16/61] move selection populations related func to more
 relevant libs

---
 js/source/entries/heritability.js             |  2 +-
 js/source/legacy/heritability/heritability.js |  2 +-
 .../legacy/qualityControl/qualityControl.js   |  2 +-
 js/source/legacy/solGS/cluster.js             |  4 +-
 js/source/legacy/solGS/correlation.js         |  4 +-
 js/source/legacy/solGS/geneticGain.js         |  4 +-
 js/source/legacy/solGS/selectionIndex.js      | 48 +------------------
 7 files changed, 11 insertions(+), 55 deletions(-)

diff --git a/js/source/entries/heritability.js b/js/source/entries/heritability.js
index a9a31ecc6e..af934e31dc 100644
--- a/js/source/entries/heritability.js
+++ b/js/source/entries/heritability.js
@@ -86,7 +86,7 @@ function listGenCorPopulations ()  {
     var listTypeSelPops = jQuery("#list_type_selection_pops_table").length;
    
     if (listTypeSelPops) {
-        var selPopsList = solGS.sIndex.getListTypeSelPopulations();
+        var selPopsList = solGS.listTypeSelPopulations.getListTypeSelPops();
 
         if (selPopsList) {
             jQuery("#h2_select_a_population_div ul").append(selPopsList);  
diff --git a/js/source/legacy/heritability/heritability.js b/js/source/legacy/heritability/heritability.js
index 31de465afd..b0615252cb 100644
--- a/js/source/legacy/heritability/heritability.js
+++ b/js/source/legacy/heritability/heritability.js
@@ -91,7 +91,7 @@ function listGenCorPopulations ()  {
     var listTypeSelPops = jQuery("#list_type_selection_pops_table").length;
    
     if (listTypeSelPops) {
-        var selPopsList = solGS.sIndex.getListTypeSelPopulations();
+        var selPopsList = solGS.listTypeSelPopulations.getListTypeSelPops();
 
         if (selPopsList) {
             jQuery("#h2_select_a_population_div ul").append(selPopsList);  
diff --git a/js/source/legacy/qualityControl/qualityControl.js b/js/source/legacy/qualityControl/qualityControl.js
index ac91fca354..a3bd579125 100644
--- a/js/source/legacy/qualityControl/qualityControl.js
+++ b/js/source/legacy/qualityControl/qualityControl.js
@@ -91,7 +91,7 @@ function listGenCorPopulations ()  {
     var listTypeSelPops = jQuery("#list_type_selection_pops_table").length;
    
     if (listTypeSelPops) {
-        var selPopsList = solGS.sIndex.getListTypeSelPopulations();
+        var selPopsList = solGS.listTypeSelPopulations.getListTypeSelPops();
 
         if (selPopsList) {
             jQuery("#qc_select_a_population_div ul").append(selPopsList);  
diff --git a/js/source/legacy/solGS/cluster.js b/js/source/legacy/solGS/cluster.js
index 6d6b6691e1..5f4fe916b7 100644
--- a/js/source/legacy/solGS/cluster.js
+++ b/js/source/legacy/solGS/cluster.js
@@ -943,14 +943,14 @@ solGS.cluster = {
     var clusterPops = [modelData];
 
     if (modelData.id.match(/list/) == null) {
-      var trialSelPopsList = solGS.sIndex.getPredictedTrialTypeSelectionPops();
+      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
       if (trialSelPopsList) {
         clusterPops.push(trialSelPopsList);
       }
     }
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.sIndex.getListTypeSelPopulations();
+      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
       if (listTypeSelPops) {
         clusterPops.push(listTypeSelPops);
       }
diff --git a/js/source/legacy/solGS/correlation.js b/js/source/legacy/solGS/correlation.js
index ceca4b27b4..4bcd982f5b 100644
--- a/js/source/legacy/solGS/correlation.js
+++ b/js/source/legacy/solGS/correlation.js
@@ -203,7 +203,7 @@ solGS.correlation = {
     var corrPops = [modelData];
 
     if (modelData.id.match(/list/) == null) {
-      var trialSelPopsList = solGS.sIndex.getPredictedTrialTypeSelectionPops();
+      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
       if (trialSelPopsList) {
         corrPops.push(trialSelPopsList);
       }
@@ -211,7 +211,7 @@ solGS.correlation = {
 
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.sIndex.getListTypeSelPopulations();
+      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
       if (listTypeSelPops) {
         corrPops.push(listTypeSelPops);
       }
diff --git a/js/source/legacy/solGS/geneticGain.js b/js/source/legacy/solGS/geneticGain.js
index 9564dac62e..6cc5a91097 100644
--- a/js/source/legacy/solGS/geneticGain.js
+++ b/js/source/legacy/solGS/geneticGain.js
@@ -218,7 +218,7 @@ solGS.geneticGain = {
 
     var ggPops = [];
     if (ggArgs.training_pop_id.match(/list/) == null) {
-      var trialSelPopsList = solGS.sIndex.getPredictedTrialTypeSelectionPops();
+      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
       if (trialSelPopsList) {
         ggPops.push(trialSelPopsList);
       }
@@ -226,7 +226,7 @@ solGS.geneticGain = {
 
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.sIndex.getListTypeSelPopulations();
+      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
       if (listTypeSelPops) {
         ggPops.push(listTypeSelPops);
       }
diff --git a/js/source/legacy/solGS/selectionIndex.js b/js/source/legacy/solGS/selectionIndex.js
index f544a7db59..c81f930757 100644
--- a/js/source/legacy/solGS/selectionIndex.js
+++ b/js/source/legacy/solGS/selectionIndex.js
@@ -21,7 +21,7 @@ solGS.sIndex = {
     var sIndexPops = [modelData];
 
     if (modelData.id.match(/list/) == null) {
-      var trialSelPopsList = solGS.sIndex.getPredictedTrialTypeSelectionPops();
+      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
       if (trialSelPopsList) {
         sIndexPops.push(trialSelPopsList);
       }
@@ -29,7 +29,7 @@ solGS.sIndex = {
 
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.sIndex.getListTypeSelPopulations();
+      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
       if (listTypeSelPops) {
         sIndexPops.push(listTypeSelPops);
       }
@@ -67,30 +67,6 @@ solGS.sIndex = {
     solGS.sIndex.indexed.push(siId);
   },
 
-  getPredictedTrialTypeSelectionPops: function () {
-    var selPopsTable = jQuery("#selection_pops_list").html();
-    var selPopsRows;
-
-    if (selPopsTable !== null) {
-      selPopsRows = jQuery("#selection_pops_list").find("tbody > tr");
-    }
-
-    var popsList = [];
-
-    for (var i = 0; i < selPopsRows.length; i++) {
-      var row = selPopsRows[i];
-      var popRow = row.innerHTML;
-      var predict = popRow.match(/predict/gi);
-      if (!predict) {
-        var selPopsInput = row.getElementsByTagName("input")[0];
-        var sIndexPopData = selPopsInput.value;
-        popsList.push(JSON.parse(sIndexPopData));
-      }
-    }
-
-    return popsList;
-  },
-
   displaySindexForm: function (modelId, selectedPopId) {
     if (modelId === selectedPopId) {
       selectedPopId = undefined;
@@ -416,26 +392,6 @@ solGS.sIndex = {
     };
   },
 
-  getListTypeSelPopulations: function () {
-    var listTypeSelPopsDiv = document.getElementById("list_type_selection_pops_selected");
-    var listTypeSelPopsTable = listTypeSelPopsDiv.getElementsByTagName("table");
-    var listTypeSelPopsRows = listTypeSelPopsTable[0].rows;
-
-    var popsList = [];
-    for (var i = 1; i < listTypeSelPopsRows.length; i++) {
-      var row = listTypeSelPopsRows[i];
-      var popRow = row.innerHTML;
-
-      var predict = popRow.match(/predict/gi);
-      if (!predict) {
-        var selPopsInput = row.getElementsByTagName("input")[0];
-        var sIndexPopData = selPopsInput.value;
-        popsList.push(JSON.parse(sIndexPopData));
-      }
-    }
-    return popsList;
-  },
-
   getTrainingPopulationData: function () {
     var modelId = jQuery("#si_canvas #model_id").val();
     var modelName = jQuery("#si_canvas #model_name").val();

From 69c4c5d3ee517fb9ae7983ea8874d345dd11fd2a Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Thu, 11 May 2023 14:26:22 +0200
Subject: [PATCH 17/61] refactor to separate object creation and implementation

---
 .../legacy/solGS/selectionPopulations.js      | 264 ++++++++++--------
 1 file changed, 146 insertions(+), 118 deletions(-)

diff --git a/js/source/legacy/solGS/selectionPopulations.js b/js/source/legacy/solGS/selectionPopulations.js
index 74e06b88c0..8ba911f443 100644
--- a/js/source/legacy/solGS/selectionPopulations.js
+++ b/js/source/legacy/solGS/selectionPopulations.js
@@ -8,123 +8,65 @@
 var solGS = solGS || function solGS() {};
 
 solGS.selectionPopulation = {
+  msgDiv: "#selection_pops_message",
+  resultSelDiv: "#selection_pops_result",
+  selPopsDiv: "#selection_pops_div",
+  searchBtn: "#search_selection_pop",
+  searchBox: "#population_search_entry",
+  selPopsTable: "#selection_pops_table",
+  searchAllSelPops: "#search_all_selection_pops",
+  searchFormFeedBack: "#form-feedback-search-trials",
+
   checkSelectionPopulations: function () {
     var args = solGS.getModelArgs();
     args = JSON.stringify(args);
 
-    jQuery.ajax({
+    var checkPop = jQuery.ajax({
       type: "POST",
       data: { arguments: args },
       dataType: "json",
       url: "/solgs/check/selection/populations/",
-      success: function (response) {
-        if (response.data) {
-          jQuery("#selection_populations").show();
-          jQuery("#search_all_selection_pops").show();
-
-          solGS.selectionPopulation.displaySelectionPopulations(response.data);
-        } else {
-          jQuery("#search_all_selection_pops").show();
-        }
-      },
     });
+
+    return checkPop;
   },
 
   checkSelectionPopulationRelevance: function (popName) {
     var modelVars = solGS.getModelArgs();
     modelVars["selection_pop_name"] = popName;
 
-    jQuery("#selection_pops_message")
-      .html("Checking if the model can be used on " + popName + "...please wait...")
-      .show();
-
     var popData = JSON.stringify(modelVars);
-    jQuery.ajax({
+    var checkRelevance = jQuery.ajax({
       type: "POST",
       dataType: "json",
       data: { arguments: popData },
       url: "/solgs/check/selection/population/relevance/",
-      success: function (res) {
-        if (res.selection_pop_id) {
-          if (res.selection_pop_id != res.training_pop_id) {
-            if (res.similarity >= 0.5) {
-              jQuery("#selection_pops_message ").hide();
-              jQuery("#selection_populations").show();
-
-              var selPopExists = jQuery("#selection_pops_list:contains(" + popName + ")").length;
-              if (!selPopExists) {
-                solGS.selectionPopulation.displaySelectionPopulations(res.selection_pop_data);
-              }
-            } else {
-              jQuery("#selection_pops_message")
-                .html(
-                  popName +
-                    " is genotyped by a marker set different  " +
-                    "from the one used for the training population. " +
-                    "Therefore you can not predict its GEBVs using this model."
-                )
-                .show();
-            }
-          } else {
-            jQuery("#selection_pops_message")
-              .html(
-                popName +
-                  " is the same population as the " +
-                  "the training population. " +
-                  "Please select a different selection population."
-              )
-              .show()
-              .fadeOut(5000);
-          }
-        } else {
-          jQuery("#selection_pops_message")
-            .html(popName + " does not exist in the database.")
-            .show()
-            .fadeOut(5000);
-        }
-      },
-      error: function (res) {
-        jQuery("#selection_pops_message")
-          .html("Error occured processing the query.")
-          .show()
-          .fadeOut(5000);
-      },
     });
+
+    return checkRelevance;
   },
 
   searchSelectionPopulations: function () {
     var args = solGS.getModelArgs();
+    var popId = args.training_pop_id;
 
     args = JSON.stringify(args);
-    jQuery.ajax({
+    var searchPops = jQuery.ajax({
       type: "POST",
       dataType: "json",
-      data: {'arguments': args},
+      data: { arguments: args },
       url: "/solgs/search/selection/populations/" + popId,
-      success: function (res) {
-        if (res.data) {
-          jQuery("#selection_populations").show();
-          solGS.selectionPopulation.displaySelectionPopulations(res.data);
-          jQuery("#search_all_selection_pops").hide();
-          jQuery("#selection_pops_message").hide();
-        } else {
-          var msg =
-            "<p>There are no relevant selection populations in the database." +
-            "If you have or want to make your own set of selection candidates" +
-            "use the form below.</p>";
-
-          jQuery("#selection_pops_message").html(msg).show().fadeOut(5000);
-        }
-      },
     });
+
+    return searchPops;
   },
 
   getPredictedTrialTypeSelectionPops: function () {
-    var selPopsTable = jQuery("#selection_pops_list").html();
+    var selPopsTable = jQuery(this.selPopsTable).html();
     var selPopsRows;
 
     if (selPopsTable !== null) {
-      selPopsRows = jQuery("#selection_pops_list").find("tbody > tr");
+      selPopsRows = jQuery(this.selPopsTable).find("tbody > tr");
     }
 
     var popsList = [];
@@ -143,11 +85,15 @@ solGS.selectionPopulation = {
     return popsList;
   },
 
+  feedbackOnFail: function (msg) {
+    jQuery(this.msgDiv).html(msg).show().fadeOut(8000);
+  },
+
   displaySelectionPopulations: function (data) {
-    var tableRow = jQuery("#selection_pops_list tr").length;
+    var tableRow = jQuery(`${this.selPopsTable} tr`).length;
 
     if (tableRow === 1) {
-      jQuery("#selection_pops_list").dataTable({
+      jQuery(this.selPopsTable).dataTable({
         searching: false,
         ordering: false,
         processing: true,
@@ -156,60 +102,142 @@ solGS.selectionPopulation = {
         data: data,
       });
     } else {
-      jQuery("#selection_pops_list").dataTable().fnAddData(data);
+      jQuery(this.selPopsTable).dataTable().fnAddData(data);
     }
   },
+};
 
-  getPopulationId: function () {
-    var populationId = jQuery("#population_id").val();
-
-    if (!populationId) {
-      populationId = jQuery("#model_id").val();
-    }
+jQuery(document).ready(function () {
+  var resultSelDiv = solGS.selectionPopulation.resultSelDiv;
+  var msgDiv = solGS.selectionPopulation.msgDiv;
+  var searchAllSelPops = solGS.selectionPopulation.searchAllSelPops;
+  var searchBox = solGS.selectionPopulation.searchBox;
+  var selPopsTable = solGS.selectionPopulation.selPopsTable;
+  var selPopsDiv = solGS.selectionPopulation.selPopsDiv;
+  var searchBtn = solGS.selectionPopulation.searchBtn;
+  var searchFormFeedBack = solGS.selectionPopulation.searchFormFeedBack;
+
+  // jQuery(searchBtn).hide();
+
+  solGS.selectionPopulation
+    .checkSelectionPopulations()
+    .done(function (res) {
+      if (res.data) {
+        jQuery(resultSelDiv).show();
+
+        solGS.selectionPopulation.displaySelectionPopulations(res.data);
+      } else {
+        var msg = "No result found.";
+        solGS.selectionPopulation.feedbackOnFail(msg);
+      }
 
-    if (!populationId) {
-      populationId = jQuery("#combo_pops_id").val();
-    }
+      // jQuery(searchBtn).show();
+    })
+    .fail(function () {
+      var msg = "Errro occured querying for selection populations";
+      solGS.selectionPopulation.feedbackOnFail(msg);
+      // jQuery(searchBtn).show();
+    });
 
-    return populationId;
-  },
-};
+  jQuery(searchAllSelPops).click(function () {
+    var msg =
+      "<br/><br/>Searching for all selection populations relevant to this model...please wait...";
+    jQuery(msgDiv).html(msg).show();
 
-jQuery(document).ready(function () {
-  solGS.selectionPopulation.checkSelectionPopulations();
-});
+    solGS.selectionPopulation
+      .searchSelectionPopulations()
+      .done(function (res) {
+        if (res.data) {
+          jQuery(resultSelDiv).show();
+          solGS.selectionPopulation.displaySelectionPopulations(res.data);
+          jQuery(searchAllSelPops).hide();
+          jQuery(this.msgDiv).hide();
+        } else {
+          var msg =
+            "<p>There are no relevant selection populations in the database." +
+            "If you have or want to make your own set of selection candidates" +
+            "use the form below.</p>";
 
-jQuery(document).ready(function () {
-  jQuery("#search_all_selection_pops").click(function () {
-    solGS.selectionPopulation.searchSelectionPopulations();
-    jQuery("#selection_pops_message").html(
-      "<br/><br/>Searching for all selection populations relevant to this model...please wait..."
-    );
+          jQuery(this.msgDiv).html(msg).show().fadeOut(8000);
+        }
+      })
+      .fail(function () {
+        var msg = "Error occured searching for the selection populations.";
+        jQuery(this.msgDiv).html(msg).show().fadeOut(8000);
+      });
   });
-});
 
-jQuery(document).ready(function () {
-  jQuery("#population_search_entry").keyup(function (e) {
-    jQuery("#population_search_entry").css("border", "solid #96d3ec");
+  jQuery(searchBox).keyup(function (e) {
+    jQuery(searchBox).css("border", "solid #96d3ec");
 
-    jQuery("#form-feedback-search-trials").empty();
+    jQuery(searchFormFeedBack).empty();
 
     if (e.keycode == 13) {
-      jQuery("#search_selection_pop").click();
+      jQuery(searchBtn).click();
     }
   });
 
-  jQuery("#search_selection_pop").on("click", function () {
-    jQuery("#selection_pops_message").hide();
-
-    var entry = jQuery("#population_search_entry").val();
+  jQuery(searchBtn).on("click", function () {
+    jQuery(searchBtn).hide();
+
+    var popName = jQuery(searchBox).val();
+    if (popName) {
+      var selPopExists = jQuery(`${selPopsTable}:contains(${popName})`).length;
+
+      if (selPopExists) {
+        jQuery(searchBtn).show();
+        var msg = `${popName} is already in the search result table`;
+        solGS.selectionPopulation.feedbackOnFail(msg);
+      } else {
+        jQuery(msgDiv)
+          .html(`Checking if the model can be used on ${popName} ...please wait...`)
+          .show();
+        jQuery(`${selPopsDiv} .multi-spinner-container`).show();
+
+        solGS.selectionPopulation
+          .checkSelectionPopulationRelevance(popName)
+          .done(function (res) {
+            if (res.selection_pop_id) {
+              if (res.selection_pop_id != res.training_pop_id) {
+                if (res.similarity >= 0.5) {
+                  jQuery(msgDiv).hide();
+                  jQuery(resultSelDiv).show();
+
+                  var selPopExists = jQuery(`${selPopsTable}:contains(${popName})`).length;
+                  if (!selPopExists) {
+                    solGS.selectionPopulation.displaySelectionPopulations(res.selection_pop_data);
+                  }
+                } else {
+                  var msg = `${popName} is genotyped by a marker set different  
+                  from the one used for the training population. Therefore you can not predict its GEBVs using this model.`;
+
+                  solGS.selectionPopulation.feedbackOnFail(msg);
+                }
+              } else {
+                var msg = `${popName} is the same population as the the training population. Please select a different selection population.`;
+
+                solGS.selectionPopulation.feedbackOnFail(msg);
+              }
+            } else {
+              var msg = `${popName} does not exist in the database.`;
+              solGS.selectionPopulation.feedbackOnFail(msg);
+            }
 
-    if (entry) {
-      solGS.selectionPopulation.checkSelectionPopulationRelevance(entry);
+            jQuery(searchBtn).show();
+            jQuery(`${selPopsDiv} .multi-spinner-container`).hide();
+          })
+          .fail(function () {
+            var msg = "Error occured processing the query.";
+            solGS.selectionPopulation.feedbackOnFail(msg);
+            jQuery(searchBtn).show();
+            jQuery(`${selPopsDiv} .multi-spinner-container`).hide();
+          });
+      }
     } else {
-      jQuery("#population_search_entry").css("border", "solid #FF0000");
+      jQuery(searchBox).css("border", "solid #FF0000");
 
-      jQuery("#form-feedback-search-trials").text("Please enter trial name.");
+      jQuery(searchFormFeedBack).text("Please enter trial name.");
+      jQuery(searchBtn).show();
     }
   });
 });

From 52e2268093e65eb84c82098f1a95297ac113ccc5 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 12 May 2023 16:42:45 +0200
Subject: [PATCH 18/61] update selection_pops_table id

---
 t/selenium2/solgs/combine_trials.t         | 6 +++---
 t/selenium2/solgs/correlation.t            | 4 ++--
 t/selenium2/solgs/hcluster.t               | 4 ++--
 t/selenium2/solgs/kcluster.t               | 4 ++--
 t/selenium2/solgs/list_type_training_pop.t | 6 +++---
 t/selenium2/solgs/pca.t                    | 4 ++--
 t/selenium2/solgs/selection_index.t        | 4 ++--
 t/selenium2/solgs/solgs.t                  | 6 +++---
 8 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/t/selenium2/solgs/combine_trials.t b/t/selenium2/solgs/combine_trials.t
index 39ddbfc9b6..768f314b43 100644
--- a/t/selenium2/solgs/combine_trials.t
+++ b/t/selenium2/solgs/combine_trials.t
@@ -186,7 +186,7 @@ $d->while_logged_in_as("submitter", sub {
 	sleep(5);
 	$d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
 	sleep(100);
-	$d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+	$d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
 	sleep(5);
 	$d->find_element_ok('queue_job', 'id', 'job queueing')->click();
 	sleep(2);
@@ -335,7 +335,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(20);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
@@ -351,7 +351,7 @@ $d->while_logged_in_as("submitter", sub {
 	#$d->get_ok('/solgs/models/combined/trials/2804608595/traits/1971973596/gp/1');
 
 	sleep(5);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "FRW")]', 'xpath', 'go back')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "FRW")]', 'xpath', 'go back')->click();
     sleep(5);
 	$d->driver->go_back();
 	sleep(3);
diff --git a/t/selenium2/solgs/correlation.t b/t/selenium2/solgs/correlation.t
index 3382897277..6ec359c384 100644
--- a/t/selenium2/solgs/correlation.t
+++ b/t/selenium2/solgs/correlation.t
@@ -177,7 +177,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(3);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
@@ -335,7 +335,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(30);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
diff --git a/t/selenium2/solgs/hcluster.t b/t/selenium2/solgs/hcluster.t
index 7839add0cd..3a9ccd58bf 100644
--- a/t/selenium2/solgs/hcluster.t
+++ b/t/selenium2/solgs/hcluster.t
@@ -297,7 +297,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(30);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
@@ -913,7 +913,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(20);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
diff --git a/t/selenium2/solgs/kcluster.t b/t/selenium2/solgs/kcluster.t
index 421a5d5549..25556ee556 100644
--- a/t/selenium2/solgs/kcluster.t
+++ b/t/selenium2/solgs/kcluster.t
@@ -625,7 +625,7 @@ $d->while_logged_in_as(
             'search for selection pop' )->click();
         sleep(30);
         $d->find_element_ok(
-'//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]',
+'//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]',
             'xpath',
             'click training pop'
         )->click();
@@ -1771,7 +1771,7 @@ $d->while_logged_in_as(
             'search for selection pop' )->click();
         sleep(20);
         $d->find_element_ok(
-'//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]',
+'//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]',
             'xpath',
             'click training pop'
         )->click();
diff --git a/t/selenium2/solgs/list_type_training_pop.t b/t/selenium2/solgs/list_type_training_pop.t
index ae74f4aaad..a623f8a54b 100644
--- a/t/selenium2/solgs/list_type_training_pop.t
+++ b/t/selenium2/solgs/list_type_training_pop.t
@@ -109,7 +109,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(3);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(130);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
@@ -236,7 +236,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(15);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
@@ -248,7 +248,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(150);
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "FRW")]', 'xpath', 'go back')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "FRW")]', 'xpath', 'go back')->click();
     sleep(5);
 
     $d->driver->go_back();
diff --git a/t/selenium2/solgs/pca.t b/t/selenium2/solgs/pca.t
index f0c1e3d2df..525587d54c 100644
--- a/t/selenium2/solgs/pca.t
+++ b/t/selenium2/solgs/pca.t
@@ -349,7 +349,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(10);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(3);
@@ -498,7 +498,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(20);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click sel pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click sel pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(4);
diff --git a/t/selenium2/solgs/selection_index.t b/t/selenium2/solgs/selection_index.t
index c2cf463437..21a812a2c7 100644
--- a/t/selenium2/solgs/selection_index.t
+++ b/t/selenium2/solgs/selection_index.t
@@ -115,7 +115,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
@@ -264,7 +264,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(20);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
diff --git a/t/selenium2/solgs/solgs.t b/t/selenium2/solgs/solgs.t
index 6cee0869d9..eed0829b42 100644
--- a/t/selenium2/solgs/solgs.t
+++ b/t/selenium2/solgs/solgs.t
@@ -158,7 +158,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(30);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
@@ -325,7 +325,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('search_selection_pop', 'id', 'search for selection pop')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click training pop')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
@@ -337,7 +337,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(250);
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="selection_pops_list"]//*[contains(text(), "FRW")]', 'xpath', 'go back')->click();
+    $d->find_element_ok('//table[@id="selection_pops_table"]//*[contains(text(), "FRW")]', 'xpath', 'go back')->click();
     sleep(5);
 
     $d->driver->go_back();

From 00b94e1ffd729b557fa1939b885b512aa332dce7 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 15 May 2023 09:40:22 +0200
Subject: [PATCH 19/61] update div elm id

---
 mason/solgs/tools/select_menu.mas | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/mason/solgs/tools/select_menu.mas b/mason/solgs/tools/select_menu.mas
index 768767e8a6..b64a27b3a5 100644
--- a/mason/solgs/tools/select_menu.mas
+++ b/mason/solgs/tools/select_menu.mas
@@ -24,13 +24,13 @@ my $analysis_abbr = $analysis_type =~ /correlation/ ? 'corr' : $analysis_type;
 </%perl>
 
 <& /util/import_css.mas, paths => ['/static/css/solgs/solgs.css'] &>
-<& /util/import_javascript.mas, classes => [ "solGS.Dataset", "CXGN.List", "solGS.selectMenu"] &>
+<& /util/import_javascript.mas, classes => [ "solGS.Dataset", "CXGN.List", "solGS.OptionsMenu"] &>
 
-<div id="select_menu">
+<div id="select_menu" style="padding-top: 20px;">
   <div class="select_menu_block" id="<% $analysis_type %>_pops_label">
     <label for="<% $analysis_abbr %>_pops_label">Select a <% $label %> population</label>
   </div>
-  <div class="select_menu_block" id="<% $analysis_abbr %>_pops_list"></div>
+  <div class="select_menu_block" id="<% $analysis_abbr %>_pops_select_div"></div>
   <div class="select_menu_block go_btn" id="<% $analysis_abbr %>_pop_go_btn">
     <input type="button" value="View" />
   </div>

From 3794c0445c5d27fcc09030059883dc986d416422 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 15 May 2023 09:42:32 +0200
Subject: [PATCH 20/61] update div ids

---
 mason/solgs/search/selection_populations.mas | 23 ++++++++++----------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/mason/solgs/search/selection_populations.mas b/mason/solgs/search/selection_populations.mas
index e209cc01d4..ec9152b6e9 100644
--- a/mason/solgs/search/selection_populations.mas
+++ b/mason/solgs/search/selection_populations.mas
@@ -1,6 +1,7 @@
 <%doc>
 
-displays list of prediction populations and their GS output.
+displays selection populations one can apply the model on.  If predicted output exists for a
+selection population, a link to the output is displayed.
 
 </%doc>
 
@@ -41,7 +42,8 @@ if ($c->req->path =~ /solgs\/traits\/all\/population/) {
     title       => $title,
 &>
 
-  <div  class="form-inline">
+  <div  id="selection_pops_div">
+    <div id="search_div" class="form-inline">
     <input  type="text"
 	    class="form-control"
 	    placeholder="search for a selection population"
@@ -52,31 +54,28 @@ if ($c->req->path =~ /solgs\/traits\/all\/population/) {
 	    id="search_selection_pop">
       <span class="glyphicon glyphicon-search"></span>
     </button>
-<div style="color:red" id="form-feedback-search-trials"> </div>
-  <!-- <button id="search_all_selection_pops" style="position:absolute;right:20px;display:none;" class="btn btn-success" type="submit">  -->
-  <!--     <span value="Search for all relevant selection populations">Search for all relevant selection populations</span>  -->
-  <!--   </button> -->
+    <div  id="form-feedback-search-trials" style="color:red"> </div>
   </div>
 
 
   <div id="selection_pops_message"  class="message"></div>
-
-  <div id="selection_populations" style="display:none;">
-    <table class="table" id="selection_pops_list" style="text-align:left;">
+  <& /solgs/spinner/spinner.mas &>
+  
+  <div id="selection_pops_result" style="padding: 20px 0px 20px 0px;display:none;">
+    <table class="table" id="selection_pops_table" style="text-align:left;">
       <thead>
 	<tr>
 	  <th>Selection population</th>
 	  <th>Description</th>
 	  <th>Year</th>
-      <th>More details</th>
+    <th>More details</th>
 	  <th>View GEBVs</th>
 	</tr>
       </thead>
   </table>
   </div>
 
-  <br />
-
   <& /solgs/search/list_type_selection_population.mas &>
 
 </&>
+</div>
\ No newline at end of file

From d9a59be0be5e412ab26ef90b0a329f0652c261b7 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 15 May 2023 09:44:19 +0200
Subject: [PATCH 21/61] add condition for replace

---
 js/source/legacy/solGS/OptionsMenu.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/js/source/legacy/solGS/OptionsMenu.js b/js/source/legacy/solGS/OptionsMenu.js
index 4448ca39fe..14578314a1 100644
--- a/js/source/legacy/solGS/OptionsMenu.js
+++ b/js/source/legacy/solGS/OptionsMenu.js
@@ -5,11 +5,13 @@ creates and populates select menu with lists and datasets for analysis tools.
 class OptionsMenu {
   constructor(menuId, menuClass, label) {
     menuId = menuId.replace(/#/, "");
+    if(menuClass) {
     menuClass = menuClass.replace(/\./, "");
+    }
 
     this.menuId = menuId;
     this.menuClass = menuClass || "form-control";
-    this.label = label || "Select a population";
+    this.label = label || ''; // || "Select a population";
     this.menu;
   }
 

From b95c762b8f0892592fd3517891ae249710371f4b Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 15 May 2023 09:45:43 +0200
Subject: [PATCH 22/61] update getdatasets method name

---
 js/source/legacy/solGS/selectMenu.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/source/legacy/solGS/selectMenu.js b/js/source/legacy/solGS/selectMenu.js
index f8e29cfb55..14448fa33e 100644
--- a/js/source/legacy/solGS/selectMenu.js
+++ b/js/source/legacy/solGS/selectMenu.js
@@ -32,7 +32,7 @@ solGS.selectMenu = {
         
         var list = new CXGN.List();
         var listMenu = list.listSelect(div, listTypes);
-        var dMenu = solGS.dataset.getDatasetsMenu(dsTypes);
+        var dMenu = solGS.dataset.getDatasetPops(dsTypes);
 
         if (listMenu.match(/option/) != null) {
             var divListId = this.divListId(div);

From bc6a4286374556ef9f7910520abe84c6f1e995b2 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 17 May 2023 09:04:34 +0200
Subject: [PATCH 23/61] add comment about trials search filtering

---
 lib/SGN/Controller/solGS/AJAX/solGS.pm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/SGN/Controller/solGS/AJAX/solGS.pm b/lib/SGN/Controller/solGS/AJAX/solGS.pm
index f8b45fe3b7..9d8a5278f7 100644
--- a/lib/SGN/Controller/solGS/AJAX/solGS.pm
+++ b/lib/SGN/Controller/solGS/AJAX/solGS.pm
@@ -62,6 +62,8 @@ sub solgs_population_search_autocomplete_GET :Args() {
         
         if ($page_type =~ /training_model/) 
         {
+            #filter out trials of analysis_type (with stored analyzed results) from search
+            #result of trials relevant to selection prediction. 
             if (!$is_computation)
             {
                 push @response_list, $row->name;
@@ -69,6 +71,8 @@ sub solgs_population_search_autocomplete_GET :Args() {
         }  
     else
 	{  
+        #filter out trials of analysis_type (with stored analyzed results) and with out phenotype data from search
+        #result of trials relevant to training populations. 
         my $has_phenotype = $c->controller('solGS::Search')->model($c)->has_phenotype($pop_id);            
         if ($has_phenotype && !$is_computation)
         {

From 11c9c4c83803d2f13b2cee71c248961d54e8782b Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 17 May 2023 09:23:01 +0200
Subject: [PATCH 24/61] rename OptionsMenu class to SelectMenu

---
 js/source/legacy/solGS/OptionsMenu.js         |  87 ------------
 js/source/legacy/solGS/anova.js               |   2 +-
 js/source/legacy/solGS/cluster.js             |   4 +-
 js/source/legacy/solGS/correlation.js         |   4 +-
 js/source/legacy/solGS/geneticGain.js         |   2 +-
 .../solGS/listTypeSelectionPopulation.js      |   2 +-
 .../solGS/listTypeTrainingPopulation.js       |   2 +-
 js/source/legacy/solGS/pca.js                 |   2 +-
 js/source/legacy/solGS/selectMenu.js          | 127 ++++++++++--------
 js/source/legacy/solGS/selectMenu_backup.js   |  76 +++++++++++
 js/source/legacy/solGS/selectionIndex.js      |   2 +-
 mason/solgs/population/models/detail.mas      |   2 +-
 mason/solgs/tools/anova/analysis.mas          |   2 +-
 mason/solgs/tools/select_menu.mas             |   2 +-
 14 files changed, 158 insertions(+), 158 deletions(-)
 delete mode 100644 js/source/legacy/solGS/OptionsMenu.js
 create mode 100644 js/source/legacy/solGS/selectMenu_backup.js

diff --git a/js/source/legacy/solGS/OptionsMenu.js b/js/source/legacy/solGS/OptionsMenu.js
deleted file mode 100644
index 14578314a1..0000000000
--- a/js/source/legacy/solGS/OptionsMenu.js
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
-creates and populates select menu with lists and datasets for analysis tools.
-*/
-
-class OptionsMenu {
-  constructor(menuId, menuClass, label) {
-    menuId = menuId.replace(/#/, "");
-    if(menuClass) {
-    menuClass = menuClass.replace(/\./, "");
-    }
-
-    this.menuId = menuId;
-    this.menuClass = menuClass || "form-control";
-    this.label = label || ''; // || "Select a population";
-    this.menu;
-  }
-
-  createOptionsMenu() {
-    var menu = document.createElement("select");
-    menu.id = this.menuId;
-    menu.className = this.menuClass;
-
-    var option = document.createElement("option");
-    option.selected = this.label;
-    option.value = "";
-    option.innerHTML = this.label;
-    // option.disabled = true;
-
-    menu.appendChild(option);
-
-    this.menu = menu;
-    return menu;
-  }
-
-  addOptions(data) {
-    var menu = this.menu;
-    if (!menu) {
-      menu = this.createOptionsMenu();
-    }
-
-    data.forEach(function (dt) {
-      var option = document.createElement("option");
-
-      option.value = dt.id;
-      option.dataset.pop = JSON.stringify(dt);
-      option.innerHTML = dt.name;
-
-      menu.appendChild(option);
-
-    });
-
-    return menu;
-  }
-
-  addOptionsSeparator (text) {
-    var option = document.createElement("option");
-    option.innerHTML = `-------- ${text.toUpperCase()} --------`;
-    option.disabled = true;
-
-    this.menu.appendChild(option);
-  }
-
-  getSelectMenuByTypes (listTypes, datasetTypes) {
-    var list = new CXGN.List();
-    var lists = list.getLists(listTypes);
-    var privateLists = list.convertArrayToJson(lists.private_lists);
-
-    privateLists = privateLists.flat();
-    var selectMenu = this.addOptions(privateLists);
-
-    if (lists.public_lists[0]) {
-      var publicLists = list.convertArrayToJson(lists.public_lists);
-      this.addOptionsSeparator("public lists");
-      selectMenu = this.addOptions(publicLists);
-    }
-
-    var datasetPops = solGS.dataset.getDatasetPops(datasetTypes);
-    if (datasetPops) {
-      this.addOptionsSeparator("datasets");
-      selectMenu = this.addOptions(datasetPops);
-    }
-
-    return selectMenu;
-   
-  }
-
-}
diff --git a/js/source/legacy/solGS/anova.js b/js/source/legacy/solGS/anova.js
index 40cfaa7f8b..d6f78f7933 100644
--- a/js/source/legacy/solGS/anova.js
+++ b/js/source/legacy/solGS/anova.js
@@ -108,7 +108,7 @@ solGS.anova = {
     var menuId = this.anovaTraitsSelectMenuId;
     var optionsLabel = "Select a trait";
     var menuClass = "form-control";
-    var menu = new OptionsMenu(menuId, menuClass, optionsLabel);
+    var menu = new SelectMenu(menuId, menuClass, optionsLabel);
     traits = traits.flat();
     var menuElem = menu.addOptions(traits);
 
diff --git a/js/source/legacy/solGS/cluster.js b/js/source/legacy/solGS/cluster.js
index 5f4fe916b7..a460d6b075 100644
--- a/js/source/legacy/solGS/cluster.js
+++ b/js/source/legacy/solGS/cluster.js
@@ -917,7 +917,7 @@ solGS.cluster = {
     var clusterPrivatePops = list.convertArrayToJson(lists.private_lists);
 
     var menuId = this.clusterPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     clusterPrivatePops = clusterPrivatePops.flat();
     var menuElem = menu.addOptions(clusterPrivatePops);
 
@@ -963,7 +963,7 @@ solGS.cluster = {
     }
 
     var menuId = this.clusterPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     clusterPops = clusterPops.flat();
     var menuElem = menu.addOptions(clusterPops);
 
diff --git a/js/source/legacy/solGS/correlation.js b/js/source/legacy/solGS/correlation.js
index 4bcd982f5b..a8274e9e77 100644
--- a/js/source/legacy/solGS/correlation.js
+++ b/js/source/legacy/solGS/correlation.js
@@ -218,7 +218,7 @@ solGS.correlation = {
     }
 
     var menuId = this.corrPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     corrPops = corrPops.flat();
     var menuElem = menu.addOptions(corrPops);
     var corrPopDiv = this.corrPopsDiv;
@@ -348,7 +348,7 @@ solGS.correlation = {
     var listTypes = ["plots", "trials"];
     var datasetTypes = ["accessions", "plots", "trials"];
     var menuId = this.corrPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     var selectMenu = menu.getSelectMenuByTypes(listTypes, datasetTypes);
 
     var corrPopsDiv = this.corrPopsDiv;
diff --git a/js/source/legacy/solGS/geneticGain.js b/js/source/legacy/solGS/geneticGain.js
index 6cc5a91097..9e04da0a6b 100644
--- a/js/source/legacy/solGS/geneticGain.js
+++ b/js/source/legacy/solGS/geneticGain.js
@@ -233,7 +233,7 @@ solGS.geneticGain = {
     }
 
     var menuId = this.ggPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     ggPops = ggPops.flat();
 
     var menuElem = menu.addOptions(ggPops);
diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index e8c01c4a3f..cf7aba3e5b 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -331,7 +331,7 @@ solGS.listTypeSelectionPopulation = {
     var selectionPrivatePops = list.convertArrayToJson(lists.private_lists);
 
     var menuId = this.selectionPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     selectionPrivatePops = selectionPrivatePops.flat();
     var menuElem = menu.addOptions(selectionPrivatePops);
 
diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index b85ce90643..70967c6301 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -30,7 +30,7 @@ solGS.listTypeTrainingPopulation = {
     var trainingPrivatePops = list.convertArrayToJson(lists.private_lists);
 
     var menuId = this.trainingPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     trainingPrivatePops = trainingPrivatePops.flat();
     var menuElem = menu.addOptions(trainingPrivatePops);
 
diff --git a/js/source/legacy/solGS/pca.js b/js/source/legacy/solGS/pca.js
index a880c9316f..ffe2927d01 100644
--- a/js/source/legacy/solGS/pca.js
+++ b/js/source/legacy/solGS/pca.js
@@ -166,7 +166,7 @@ solGS.pca = {
     var listTypes = ["accessions", "plots", "trials"];
     var datasetTypes = ["accessions", "trials"];
     var menuId = this.pcaPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     var selectMenu = menu.getSelectMenuByTypes(listTypes, datasetTypes);
     var pcaPopsDiv = this.pcaPopsDiv;
     jQuery(pcaPopsDiv).append(selectMenu).show();
diff --git a/js/source/legacy/solGS/selectMenu.js b/js/source/legacy/solGS/selectMenu.js
index 14448fa33e..72e46aad50 100644
--- a/js/source/legacy/solGS/selectMenu.js
+++ b/js/source/legacy/solGS/selectMenu.js
@@ -1,76 +1,87 @@
-/* 
-A library with methods for adding populations select menu and 
-getting selected population id. 
+/*
+creates and populates select menu with lists and datasets for analysis tools.
 */
 
-var solGS = solGS || function solGS () {};
-
-solGS.selectMenu = {
-
-    divPrefix: function(div) {
-
-    if (!div.match(/pops/)) {
-        div = `${div}_pops`;
+class SelectMenu {
+  constructor(menuId, menuClass, label) {
+    menuId = menuId.replace(/#/, "");
+    if(menuClass) {
+    menuClass = menuClass.replace(/\./, "");
     }
 
-    console.log(`selectMenu div ${div}`)
-    return div;
-
-    },
+    this.menuId = menuId;
+    this.menuClass = menuClass || "form-control";
+    this.label = label || ''; // || "Select a population";
+    this.menu;
+  }
+
+  createSelectMenu() {
+    var menu = document.createElement("select");
+    menu.id = this.menuId;
+    menu.className = this.menuClass;
+
+    var option = document.createElement("option");
+    option.selected = this.label;
+    option.value = "";
+    option.innerHTML = this.label;
+    // option.disabled = true;
+
+    menu.appendChild(option);
+
+    this.menu = menu;
+    return menu;
+  }
+
+  addOptions(data) {
+    var menu = this.menu;
+    if (!menu) {
+      menu = this.createSelectMenu();
+    }
 
-    divListId: function(div) {
-        div = this.divPrefix(div)
-        return `#${div}_list`;
-    },
+    data.forEach(function (dt) {
+      var option = document.createElement("option");
 
-    divListSelectId: function(div) {
-        return this.divListId(div) + '_select';
-    },
+      option.value = dt.id;
+      option.dataset.pop = JSON.stringify(dt);
+      option.innerHTML = dt.name;
 
-    populateMenu: function(div, listTypes, dsTypes) {
-        div = this.divPrefix(div);
-        
-        var list = new CXGN.List();
-        var listMenu = list.listSelect(div, listTypes);
-        var dMenu = solGS.dataset.getDatasetPops(dsTypes);
+      menu.appendChild(option);
 
-        if (listMenu.match(/option/) != null) {
-            var divListId = this.divListId(div);
-            var divListSelectId = this.divListSelectId(div);
+    });
 
-            jQuery( divListId).append(listMenu);
-            jQuery(divListSelectId).append(dMenu);
+    return menu;
+  }
 
-            jQuery("<option>", {
-            value: '',
-            selected: true
-            }).prependTo(divListSelectId);
+  addOptionsSeparator (text) {
+    var option = document.createElement("option");
+    option.innerHTML = `-------- ${text.toUpperCase()} --------`;
+    option.disabled = true;
 
-        } else {
-            jQuery(divListId).append("<select><option>no lists found - Log in</option></select>");
-        }
-    },
+    this.menu.appendChild(option);
+  }
 
-    getSelectedPop: function(div) {
-        
-        var divId = this.divListSelectId(div);
+  getSelectMenuByTypes (listTypes, datasetTypes) {
+    var list = new CXGN.List();
+    var lists = list.getLists(listTypes);
+    var privateLists = list.convertArrayToJson(lists.private_lists);
 
-        var selectedId = jQuery(divId).find("option:selected").val();
-        selectedId = parseInt(selectedId);
-        var selectedName = jQuery(divId).find("option:selected").text();
-        var dataStr = jQuery(divId).find("option:selected").attr('name');
+    privateLists = privateLists.flat();
+    var selectMenu = this.addOptions(privateLists);
 
-        if (!dataStr) {
-            dataStr = 'list';
-        }
-        
-        return {'selected_id': selectedId,
-        'selected_name': selectedName,
-        'data_str': dataStr
-    };
+    if (lists.public_lists[0]) {
+      var publicLists = list.convertArrayToJson(lists.public_lists);
+      this.addOptionsSeparator("public lists");
+      selectMenu = this.addOptions(publicLists);
+    }
 
-    },
+    var datasetPops = solGS.dataset.getDatasetPops(datasetTypes);
+    if (datasetPops) {
+      this.addOptionsSeparator("datasets");
+      selectMenu = this.addOptions(datasetPops);
+    }
 
+    return selectMenu;
+   
+  }
 
 }
-		
diff --git a/js/source/legacy/solGS/selectMenu_backup.js b/js/source/legacy/solGS/selectMenu_backup.js
new file mode 100644
index 0000000000..14448fa33e
--- /dev/null
+++ b/js/source/legacy/solGS/selectMenu_backup.js
@@ -0,0 +1,76 @@
+/* 
+A library with methods for adding populations select menu and 
+getting selected population id. 
+*/
+
+var solGS = solGS || function solGS () {};
+
+solGS.selectMenu = {
+
+    divPrefix: function(div) {
+
+    if (!div.match(/pops/)) {
+        div = `${div}_pops`;
+    }
+
+    console.log(`selectMenu div ${div}`)
+    return div;
+
+    },
+
+    divListId: function(div) {
+        div = this.divPrefix(div)
+        return `#${div}_list`;
+    },
+
+    divListSelectId: function(div) {
+        return this.divListId(div) + '_select';
+    },
+
+    populateMenu: function(div, listTypes, dsTypes) {
+        div = this.divPrefix(div);
+        
+        var list = new CXGN.List();
+        var listMenu = list.listSelect(div, listTypes);
+        var dMenu = solGS.dataset.getDatasetPops(dsTypes);
+
+        if (listMenu.match(/option/) != null) {
+            var divListId = this.divListId(div);
+            var divListSelectId = this.divListSelectId(div);
+
+            jQuery( divListId).append(listMenu);
+            jQuery(divListSelectId).append(dMenu);
+
+            jQuery("<option>", {
+            value: '',
+            selected: true
+            }).prependTo(divListSelectId);
+
+        } else {
+            jQuery(divListId).append("<select><option>no lists found - Log in</option></select>");
+        }
+    },
+
+    getSelectedPop: function(div) {
+        
+        var divId = this.divListSelectId(div);
+
+        var selectedId = jQuery(divId).find("option:selected").val();
+        selectedId = parseInt(selectedId);
+        var selectedName = jQuery(divId).find("option:selected").text();
+        var dataStr = jQuery(divId).find("option:selected").attr('name');
+
+        if (!dataStr) {
+            dataStr = 'list';
+        }
+        
+        return {'selected_id': selectedId,
+        'selected_name': selectedName,
+        'data_str': dataStr
+    };
+
+    },
+
+
+}
+		
diff --git a/js/source/legacy/solGS/selectionIndex.js b/js/source/legacy/solGS/selectionIndex.js
index c81f930757..6cd347914d 100644
--- a/js/source/legacy/solGS/selectionIndex.js
+++ b/js/source/legacy/solGS/selectionIndex.js
@@ -36,7 +36,7 @@ solGS.sIndex = {
     }
 
     var menuId = this.siPopsSelectMenuId;
-    var menu = new OptionsMenu(menuId);
+    var menu = new SelectMenu(menuId);
     sIndexPops = sIndexPops.flat();
     var menuElem = menu.addOptions(sIndexPops);
     var siPopsDiv = this.siPopsDiv;
diff --git a/mason/solgs/population/models/detail.mas b/mason/solgs/population/models/detail.mas
index 90b40da7b9..1c1df9165e 100644
--- a/mason/solgs/population/models/detail.mas
+++ b/mason/solgs/population/models/detail.mas
@@ -51,7 +51,7 @@ $selection_traits_ids = join(',', @$selection_pop_analyzed_traits_ids);
 <& /util/import_css.mas, paths => ['/static/css/solgs/solgs.css'] &>
 
 <& /util/import_javascript.mas, classes => ["solGS.listTypeSelectionPopulation",
-"solGS.genotypingProtocol", "save-svg-as-png.saveSvgAsPng", "solGS.OptionsMenu"] &>
+"solGS.genotypingProtocol", "save-svg-as-png.saveSvgAsPng", "solGS.selectMenu"] &>
 
 <& /page/page_title.mas,
    title => "Prediction models from $training_pop_name"
diff --git a/mason/solgs/tools/anova/analysis.mas b/mason/solgs/tools/anova/analysis.mas
index a14b5ec6d5..f5351e0e06 100644
--- a/mason/solgs/tools/anova/analysis.mas
+++ b/mason/solgs/tools/anova/analysis.mas
@@ -21,7 +21,7 @@ $training_pop_id   => undef,
 
 <& /util/import_css.mas, paths => ['/static/css/solgs/anova.css'] &>
 
-<& /util/import_javascript.mas, classes => ["solGS.anova", "solGS.OptionsMenu"] &>
+<& /util/import_javascript.mas, classes => ["solGS.anova", "solGS.selectMenu"] &>
 
 
 <&| /page/info_section.mas,
diff --git a/mason/solgs/tools/select_menu.mas b/mason/solgs/tools/select_menu.mas
index b64a27b3a5..b9bebfb5a7 100644
--- a/mason/solgs/tools/select_menu.mas
+++ b/mason/solgs/tools/select_menu.mas
@@ -24,7 +24,7 @@ my $analysis_abbr = $analysis_type =~ /correlation/ ? 'corr' : $analysis_type;
 </%perl>
 
 <& /util/import_css.mas, paths => ['/static/css/solgs/solgs.css'] &>
-<& /util/import_javascript.mas, classes => [ "solGS.Dataset", "CXGN.List", "solGS.OptionsMenu"] &>
+<& /util/import_javascript.mas, classes => [ "solGS.Dataset", "CXGN.List", "solGS.selectMenu"] &>
 
 <div id="select_menu" style="padding-top: 20px;">
   <div class="select_menu_block" id="<% $analysis_type %>_pops_label">

From 00fe279cf9f30eb278d718035dc1d5f66aee5e81 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 19 May 2023 11:15:42 +0200
Subject: [PATCH 25/61] separate si object creation from implementation

---
 js/source/legacy/solGS/selectionIndex.js | 345 +++++++++++------------
 1 file changed, 170 insertions(+), 175 deletions(-)

diff --git a/js/source/legacy/solGS/selectionIndex.js b/js/source/legacy/solGS/selectionIndex.js
index 6cd347914d..1271f34332 100644
--- a/js/source/legacy/solGS/selectionIndex.js
+++ b/js/source/legacy/solGS/selectionIndex.js
@@ -4,7 +4,6 @@
  *
  */
 
-// JSAN.use('jquery.blockUI');
 
 var solGS = solGS || function solGS() {};
 
@@ -12,16 +11,17 @@ solGS.sIndex = {
   canvas: "#si_canvas",
   siPlotDivPrefix: "#si_plot",
   siMsgDiv: "#si_message",
-  siPopsDiv: "#si_select_a_pop_div",
+  siPopsDiv: "#si_select_pops_div",
   siPopsSelectMenuId: "#si_select_pops",
+  siFormId: "#si_form",
 
   populateSindexMenu: function () {
     var modelData = this.getTrainingPopulationData();
 
     var sIndexPops = [modelData];
 
-    if (modelData.id.match(/list/) == null) {
-      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
+    if (!modelData.id.match(/list/)) {
+      var trialSelPopsList = solGS.selectionPopulation.getPredictedTrialTypeSelectionPops();
       if (trialSelPopsList) {
         sIndexPops.push(trialSelPopsList);
       }
@@ -40,7 +40,6 @@ solGS.sIndex = {
     sIndexPops = sIndexPops.flat();
     var menuElem = menu.addOptions(sIndexPops);
     var siPopsDiv = this.siPopsDiv;
-
     jQuery(siPopsDiv).empty().append(menuElem).show();
   },
 
@@ -67,50 +66,24 @@ solGS.sIndex = {
     solGS.sIndex.indexed.push(siId);
   },
 
-  displaySindexForm: function (modelId, selectedPopId) {
-    if (modelId === selectedPopId) {
-      selectedPopId = undefined;
-    }
-
-    var protocolId = jQuery("#genotyping_protocol_id").val();
-    var trainingTraitsIds = jQuery("#training_traits_ids").val();
-    var traitsCode = jQuery("#training_traits_code").val();
-    if (trainingTraitsIds) {
-      trainingTraitsIds = trainingTraitsIds.split(",");
+  displaySindexForm: function (modelId, siPopId) {
+    if (modelId === siPopId) {
+      siPopId = undefined;
     }
 
-    var args = {
-      selection_pop_id: selectedPopId,
-      training_pop_id: modelId,
-      training_traits_ids: trainingTraitsIds,
-      training_traits_code: traitsCode,
-      genotyping_protocol_id: protocolId,
-    };
+    var args = solGS.getModelArgs();
+    args.selection_pop_id = siPopId;
 
     args = JSON.stringify(args);
 
-    jQuery.ajax({
+    var siForm = jQuery.ajax({
       type: "POST",
       dataType: "json",
       url: "/solgs/selection/index/form",
       data: { arguments: args },
-      success: function (res) {
-        if (res.status == "success") {
-          var table;
-          var traits = res.traits;
-
-          if (traits.length > 1) {
-            table = solGS.sIndex.selectionIndexForm(traits);
-          } else {
-            var msg = "There is only one trait with valid GEBV predictions.";
-            jQuery("#si_select_a_pop_div").empty();
-            jQuery("#si_select_a_pop_div_text").empty().append(msg);
-          }
-
-          jQuery("#si_canvas #selection_index_form").empty().append(table);
-        }
-      },
     });
+
+    return siForm;
   },
 
   selectionIndexForm: function (predictedTraits) {
@@ -148,124 +121,25 @@ solGS.sIndex = {
     return trait;
   },
 
-  calcSelectionIndex: function (params, legend, trainingPopId, selectionPopId) {
-    if (params) {
-      var canvas = this.canvas;
-      var siMsgDiv = this.siMsgDiv;
+  calcSelectionIndex: function (params, legend, trainingPopId, siPopId) {
+    var siArgs = solGS.getModelArgs();
 
-      jQuery(`${canvas} .multi-spinner-container`).show();
-      var msg = "Calculating selection index...please wait...";
-      jQuery(siMsgDiv).html(msg).show();
+    if (trainingPopId != siPopId) {
+      siArgs["selection_pop_id"] = siPopId;
+    }
 
-      var trainingTraitsIds = jQuery("#training_traits_ids").val();
-      if (trainingTraitsIds) {
-        trainingTraitsIds = trainingTraitsIds.split(",");
-      }
-      var protocolId = jQuery("#genotyping_protocol_id").val();
-      var traitsCode = jQuery("#training_traits_code").val();
+    siArgs["rel_wts"] = params;
 
-      if (trainingPopId == selectionPopId) {
-        selectionPopId = "";
-      }
+    siArgs = JSON.stringify(siArgs);
 
-      var siArgs = {
-        training_pop_id: trainingPopId,
-        selection_pop_id: selectionPopId,
-        rel_wts: params,
-        training_traits_ids: trainingTraitsIds,
-        training_traits_code: traitsCode,
-        genotyping_protocol_id: protocolId,
-      };
-
-      siArgs = JSON.stringify(siArgs);
-
-      jQuery.ajax({
-        type: "POST",
-        dataType: "json",
-        data: { arguments: siArgs },
-        url: "/solgs/calculate/selection/index/",
-        success: function (res) {
-          if (res.status == "success") {
-            var sindexFile = res.sindex_file;
-            var gebvsSindexFile = res.gebvs_sindex_file;
-
-            var fileNameSindex = sindexFile.split("/").pop();
-            var fileNameGebvsSindex = gebvsSindexFile.split("/").pop();
-            var sindexLink = `<a href="${sindexFile}" download="${fileNameSindex}">Indices</a>`;
-            var gebvsSindexLink = `<a href="${gebvsSindexFile}" download="${fileNameGebvsSindex}">Weighted GEBVs+indices</a>`;
-
-            var sIndexName = res.sindex_name;
-
-            let caption = `<br/><strong>Index Name:</strong> ${sIndexName} <strong>Download:</strong> ${sindexLink} |  ${gebvsSindexLink} ${legend}`;
-            let histo = {
-              canvas: canvas,
-              plot_id: `#${sIndexName}`,
-              named_values: res.indices,
-              caption: caption,
-            };
-
-            solGS.histogram.plotHistogram(histo);
-
-            var popType = jQuery("#si_selected_pop_type").val();
-            var popId = jQuery("#si_selected_pop_id").val();
-            jQuery(siMsgDiv).hide();
-
-            var genArgs = solGS.correlation.getGeneticCorrArgs(
-              popId,
-              popType,
-              res.index_file,
-              sIndexName
-            );
-            // var canvas = genArgs.canvas;
-            var corrPlotDivId = genArgs.corr_plot_div;
-            // var corrMsgDiv = genArgs.corr_msg_div;
-            jQuery(`${canvas} .multi-spinner-container`).show();
-            jQuery(siMsgDiv).html("Running correlation... please wait...").show();
-
-            solGS.correlation
-              .runGeneticCorrelation(genArgs)
-              .done(function (res) {
-                if (res.status.match(/success/)) {
-                  genArgs["corr_table_file"] = res.corre_table_file;
-                  var corrDownload = solGS.correlation.createCorrDownloadLink(genArgs);
-
-                  solGS.heatmap.plot(res.data, canvas, corrPlotDivId, corrDownload);
-                  var popName = jQuery("#si_selected_pop_name").val();
-                  var legendValues = solGS.sIndex.legendParams();
-
-                  var popDiv = popName.replace(/\s+/g, "");
-                  var relWtsId = legendValues.params.replace(/[{",}:\s+<b/>]/gi, "");
-
-                  var corLegDiv = `<div id="si_correlation_${popDiv}_${relWtsId}">`;
-
-                  var corLegDivVal = jQuery(corLegDiv).html(legendValues.legend);
-
-                  jQuery(canvas).append(corLegDivVal).show();
-                  jQuery(`${canvas} .multi-spinner-container`).hide();
-                  jQuery(siMsgDiv).empty();
-                }
-              })
-              .fail(function (res) {
-                jQuery(siMsgDiv).html("Error occured running correlation analysis.").fadeOut(8400);
-              });
-
-            jQuery("#si_canvas #selected_pop").val("");
-
-            var sIndexed = {
-              sindex_id: popId,
-              sindex_name: sIndexName,
-            };
-
-            solGS.sIndex.saveIndexedPops(sIndexed);
-            solGS.cluster.listClusterPopulations();
-          }
-        },
-        error: function (res) {
-          var msg = "error occured calculating selection index.";
-          jQuery(siMsgDiv).html(msg).show();
-        },
-      });
-    }
+    var calcSindex = jQuery.ajax({
+      type: "POST",
+      dataType: "json",
+      data: { arguments: siArgs },
+      url: "/solgs/calculate/selection/index/",
+    });
+
+    return calcSindex;
   },
 
   validateRelativeWts: function (nm, val) {
@@ -318,13 +192,13 @@ solGS.sIndex = {
   },
 
   legendParams: function () {
-    var selectedPopName = jQuery("#si_canvas #si_selected_pop_name").val();
+    var siPopName = jQuery("#si_canvas #si_selected_pop_name").val();
 
-    if (!selectedPopName) {
-      selectedPopName = jQuery("#si_canvas #default_si_selected_pop_name").val();
+    if (!siPopName) {
+      siPopName = jQuery("#si_canvas #default_si_selected_pop_name").val();
     }
 
-    var rel_form = document.getElementById("selection_index_form");
+    var rel_form = document.getElementById("si_form");
     var all = rel_form.getElementsByTagName("input");
 
     var params = {};
@@ -372,10 +246,10 @@ solGS.sIndex = {
       }
     }
     var legend;
-    if (selectedPopName) {
-      var popName = "<strong>Population name:</strong> " + selectedPopName;
+    if (siPopName) {
+      var popName = "<strong>Population name:</strong> " + siPopName;
 
-      var divId = selectedPopName.replace(/\s/g, "");
+      var divId = siPopName.replace(/\s/g, "");
       var relWtsId = trRelWts.replace(/[:\s+relative<>b/weigths]/gi, "");
       legend =
         `<div id="si_legend_${divId}_${relWtsId}">` +
@@ -393,12 +267,11 @@ solGS.sIndex = {
   },
 
   getTrainingPopulationData: function () {
-    var modelId = jQuery("#si_canvas #model_id").val();
-    var modelName = jQuery("#si_canvas #model_name").val();
+    var modelArgs = solGS.getModelArgs();
 
     return {
-      id: modelId,
-      name: modelName,
+      id: modelArgs.training_pop_id,
+      name: modelArgs.training_pop_name,
       pop_type: "training",
     };
   },
@@ -407,13 +280,41 @@ solGS.sIndex = {
 };
 ////
 
-solGS.sIndex.indexed = [];
+
 
 jQuery(document).ready(function () {
+  solGS.sIndex.indexed = [];
+
   setTimeout(function () {
     solGS.sIndex.populateSindexMenu();
     var modelId = jQuery("#training_pop_id").val();
-    solGS.sIndex.displaySindexForm(modelId, modelId);
+    var canvas = solGS.sIndex.canvas;
+    var siPopsDiv = solGS.sIndex.siPopsDiv;
+    var siMsgDiv = solGS.sIndex.siMsgDiv;
+    var siFormId = solGS.sIndex.siFormId;
+
+    solGS.sIndex
+      .displaySindexForm(modelId, modelId)
+      .done(function (res) {
+        if (res.status == "success") {
+          var table;
+          var traits = res.traits;
+
+          if (traits.length > 1) {
+            table = solGS.sIndex.selectionIndexForm(traits);
+          } else {
+            var msg = "There is only one trait with valid GEBV predictions.";
+            jQuery(siPopsDiv).empty();
+            jQuery(siMsgDiv).empty().append(msg);
+          }
+
+          jQuery(`${canvas} ${siFormId}`).empty().append(table);
+        }
+      })
+      .fail(function () {
+        var msg = "Error occured creating the selection index form.";
+        jQuery(siMsgDiv).empty().append(msg);
+      });
   }, 5000);
 });
 
@@ -422,22 +323,116 @@ jQuery(document).ready(function () {
   jQuery(siPopsDiv).change(function () {
     var selectedPop = jQuery("option:selected", this).data("pop");
 
-    var selectedPopId = selectedPop.id;
-    var selectedPopName = selectedPop.name;
+    var siPopId = selectedPop.id;
+    var siPopName = selectedPop.name;
     var selectedPopType = selectedPop.pop_type;
-    console.log(`sindex selectedPop ${(selectedPopId, selectedPopName, selectedPopType)}`);
-    jQuery("#si_selected_pop_name").val(selectedPopName);
-    jQuery("#si_selected_pop_id").val(selectedPopId);
+    jQuery("#si_selected_pop_name").val(siPopName);
+    jQuery("#si_selected_pop_id").val(siPopId);
     jQuery("#si_selected_pop_type").val(selectedPopType);
   });
 });
 
 jQuery(document).on("click", "#calculate_si", function () {
-  var modelId = jQuery("#training_pop_id").val();
-  var selectionPopId = jQuery("#si_canvas #si_selected_pop_id").val();
-  var popType = jQuery("#si_canvas #si_selected_pop_type").val();
+  var canvas = solGS.sIndex.canvas;
+  var siMsgDiv = solGS.sIndex.siMsgDiv;
 
-  solGS.sIndex.selectionIndex(modelId, selectionPopId);
+  jQuery(`${canvas} .multi-spinner-container`).show();
+  var msg = "Calculating selection index...please wait...";
+  jQuery(siMsgDiv).html(msg).show();
+
+  var modelId = jQuery("#training_pop_id").val();
+  var siPopId = jQuery(`${canvas} #si_selected_pop_id`).val();
+  var popType = jQuery(`${canvas} #si_selected_pop_type`).val();
+
+  solGS.sIndex.selectionIndex(modelId, siPopId);
+  var legendValues = solGS.sIndex.legendParams();
+
+  var legend = legendValues.legend;
+  var params = legendValues.params;
+  var validate = legendValues.validate;
+  if (params && validate) {
+    solGS.sIndex
+      .calcSelectionIndex(params, legend, modelId, siPopId)
+      .done(function (res) {
+        if (res.status == "success") {
+          var sindexFile = res.sindex_file;
+          var gebvsSindexFile = res.gebvs_sindex_file;
+
+          var fileNameSindex = sindexFile.split("/").pop();
+          var fileNameGebvsSindex = gebvsSindexFile.split("/").pop();
+          var sindexLink = `<a href="${sindexFile}" download="${fileNameSindex}">Indices</a>`;
+          var gebvsSindexLink = `<a href="${gebvsSindexFile}" download="${fileNameGebvsSindex}">Weighted GEBVs+indices</a>`;
+
+          var sIndexName = res.sindex_name;
+
+          let caption = `<br/><strong>Index Name:</strong> ${sIndexName} <strong>Download:</strong> ${sindexLink} |  ${gebvsSindexLink} ${legend}`;
+          let histo = {
+            canvas: canvas,
+            plot_id: `#${sIndexName}`,
+            named_values: res.indices,
+            caption: caption,
+          };
+
+          solGS.histogram.plotHistogram(histo);
+
+          
+          jQuery(siMsgDiv).hide();
+
+          var genArgs = solGS.correlation.getGeneticCorrArgs(
+            siPopId,
+            popType,
+            res.index_file,
+            sIndexName
+          );
+      
+          var corrPlotDivId = genArgs.corr_plot_div;
+         
+          jQuery(`${canvas} .multi-spinner-container`).show();
+          jQuery(siMsgDiv).html("Running correlation... please wait...").show();
+
+          solGS.correlation
+            .runGeneticCorrelation(genArgs)
+            .done(function (res) {
+              if (res.status.match(/success/)) {
+                genArgs["corr_table_file"] = res.corre_table_file;
+                var corrDownload = solGS.correlation.createCorrDownloadLink(genArgs);
+
+                solGS.heatmap.plot(res.data, canvas, corrPlotDivId, corrDownload);
+                var popName = jQuery("#si_selected_pop_name").val();
+                var legendValues = solGS.sIndex.legendParams();
+
+                var popDiv = popName.replace(/\s+/g, "");
+                var relWtsId = legendValues.params.replace(/[{",}:\s+<b/>]/gi, "");
+
+                var corLegDiv = `<div id="si_correlation_${popDiv}_${relWtsId}">`;
+
+                var corLegDivVal = jQuery(corLegDiv).html(legendValues.legend);
+
+                jQuery(canvas).append(corLegDivVal).show();
+                jQuery(`${canvas} .multi-spinner-container`).hide();
+                jQuery(siMsgDiv).empty();
+              }
+            })
+            .fail(function (res) {
+              jQuery(siMsgDiv).html("Error occured running correlation analysis.").fadeOut(8400);
+            });
+
+          jQuery("#si_canvas #selected_pop").val("");
+
+          var sIndexed = {
+            sindex_id: siPopId,
+            sindex_name: sIndexName,
+          };
+
+          solGS.sIndex.saveIndexedPops(sIndexed);
+          solGS.cluster.listClusterPopulations();
+        }
+      })
+      .fail(function () {
+        var msg = "error occured calculating selection index.";
+        jQuery(siMsgDiv).html(msg).show();
+      });
+  }
 });
 
 jQuery(document).ready(function () {

From 95f7045a93e4c19b3412be942879ae70b3c7f6f4 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 19 May 2023 15:17:44 +0200
Subject: [PATCH 26/61] use getModelArgs func

---
 js/source/legacy/solGS/correlation.js | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/js/source/legacy/solGS/correlation.js b/js/source/legacy/solGS/correlation.js
index a8274e9e77..092807008b 100644
--- a/js/source/legacy/solGS/correlation.js
+++ b/js/source/legacy/solGS/correlation.js
@@ -198,12 +198,17 @@ solGS.correlation = {
   },
 
   populateGenCorrMenu: function () {
-    var modelData = solGS.sIndex.getTrainingPopulationData();
-
+    var modelData = solGS.getModelArgs();
+    modelData = {
+      id: modelData.training_pop_id,
+      name: modelData.training_pop_name,
+      pop_type: 'training'
+    }
     var corrPops = [modelData];
 
-    if (modelData.id.match(/list/) == null) {
-      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
+    if (!modelData.id.match(/list/)) {
+      var trialSelPopsList = solGS.selectionPopulation.getPredictedTrialTypeSelectionPops();
+
       if (trialSelPopsList) {
         corrPops.push(trialSelPopsList);
       }

From 2a017acaecca06358a115cd780276378cbf52180 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 19 May 2023 15:18:42 +0200
Subject: [PATCH 27/61] fix selectionPopulation obj name

---
 js/source/legacy/solGS/cluster.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/source/legacy/solGS/cluster.js b/js/source/legacy/solGS/cluster.js
index a460d6b075..7fa625b819 100644
--- a/js/source/legacy/solGS/cluster.js
+++ b/js/source/legacy/solGS/cluster.js
@@ -943,7 +943,7 @@ solGS.cluster = {
     var clusterPops = [modelData];
 
     if (modelData.id.match(/list/) == null) {
-      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
+      var trialSelPopsList = solGS.selectionPopulation.getPredictedTrialTypeSelectionPops();
       if (trialSelPopsList) {
         clusterPops.push(trialSelPopsList);
       }

From c530c5344bf1f81c7837efcf52e7560768436245 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 19 May 2023 15:20:07 +0200
Subject: [PATCH 28/61] add training_traits_code prop to modelArgs

---
 js/source/legacy/solGS/solGS.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/js/source/legacy/solGS/solGS.js b/js/source/legacy/solGS/solGS.js
index 843de747c4..ffd18e6f45 100644
--- a/js/source/legacy/solGS/solGS.js
+++ b/js/source/legacy/solGS/solGS.js
@@ -781,10 +781,12 @@ solGS.getTraitDetails = function (traitId) {
 
 solGS.getTrainingTraitsIds = function () {
   var trainingTraitsIds = jQuery("#training_traits_ids").val();
+  var trainingTraitsCode = jQuery("#training_traits_code").val();
   var traitId = jQuery("#trait_id").val();
 
   if (trainingTraitsIds) {
     trainingTraitsIds = trainingTraitsIds.split(",");
+
   } else if (traitId) {
     trainingTraitsIds = [traitId];
   }
@@ -796,6 +798,7 @@ solGS.getModelArgs = function () {
   var args = this.getTrainingPopArgs();
   var trainingTraitsIds = this.getTrainingTraitsIds();
   if (trainingTraitsIds) {
+    args["training_traits_code"] = jQuery("#training_traits_code").val();
     args["training_traits_ids"] = trainingTraitsIds;
   }
 

From 8cbceb6896c4d6ff044a9c1f9331abf933449a98 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 19 May 2023 15:22:13 +0200
Subject: [PATCH 29/61] tweak var naming

---
 js/source/legacy/solGS/selectionPopulations.js | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/js/source/legacy/solGS/selectionPopulations.js b/js/source/legacy/solGS/selectionPopulations.js
index 8ba911f443..e050256a2d 100644
--- a/js/source/legacy/solGS/selectionPopulations.js
+++ b/js/source/legacy/solGS/selectionPopulations.js
@@ -64,9 +64,9 @@ solGS.selectionPopulation = {
   getPredictedTrialTypeSelectionPops: function () {
     var selPopsTable = jQuery(this.selPopsTable).html();
     var selPopsRows;
-
     if (selPopsTable !== null) {
       selPopsRows = jQuery(this.selPopsTable).find("tbody > tr");
+
     }
 
     var popsList = [];
@@ -77,8 +77,9 @@ solGS.selectionPopulation = {
       var predict = popRow.match(/predict/gi);
       if (!predict) {
         var selPopsInput = row.getElementsByTagName("input")[0];
-        var sIndexPopData = selPopsInput.value;
-        popsList.push(JSON.parse(sIndexPopData));
+        var selPopData = selPopsInput.value;
+
+        popsList.push(JSON.parse(selPopData));
       }
     }
 

From 7d441036b0d93e3ba560ad34020df12c51435d91 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 22 May 2023 14:18:05 +0200
Subject: [PATCH 30/61] update html elements ids

---
 js/source/legacy/solGS/geneticGain.js                     | 4 ++--
 mason/solgs/tools/correlation/genetic_correlation.mas     | 2 +-
 .../tools/genetic_gain/multi_traits_genetic_gain.mas      | 2 +-
 mason/solgs/tools/selection_index/selection_index.mas     | 8 ++++----
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/js/source/legacy/solGS/geneticGain.js b/js/source/legacy/solGS/geneticGain.js
index 9e04da0a6b..fbc0c8519c 100644
--- a/js/source/legacy/solGS/geneticGain.js
+++ b/js/source/legacy/solGS/geneticGain.js
@@ -14,7 +14,7 @@ solGS.geneticGain = {
   canvas: "#gg_canvas",
   ggPlotDivPrefix: "#gg_plot",
   ggMsgDiv: "#gg_message",
-  ggPopsDiv: "#gg_select_a_pop_div",
+  ggPopsDiv: "#gg_pops_select_div",
   ggPopsSelectMenuId: "#gg_select_pops",
 
   gebvsComparison: function () {
@@ -218,7 +218,7 @@ solGS.geneticGain = {
 
     var ggPops = [];
     if (ggArgs.training_pop_id.match(/list/) == null) {
-      var trialSelPopsList = solGS.selectionPopulations.getPredictedTrialTypeSelectionPops();
+      var trialSelPopsList = solGS.selectionPopulation.getPredictedTrialTypeSelectionPops();
       if (trialSelPopsList) {
         ggPops.push(trialSelPopsList);
       }
diff --git a/mason/solgs/tools/correlation/genetic_correlation.mas b/mason/solgs/tools/correlation/genetic_correlation.mas
index 683ca0d4ed..fca1360e8c 100644
--- a/mason/solgs/tools/correlation/genetic_correlation.mas
+++ b/mason/solgs/tools/correlation/genetic_correlation.mas
@@ -56,7 +56,7 @@ $training_pop_name
 
 
     <div class="row">
-      <div class="form-group col-sm-3" id="corr_select_a_pop_div" style="margin-right:35px"></div>
+      <div class="form-group col-sm-3" id="corr_pops_select_div" style="margin-right:35px"></div>
       <input class="button" type="submit" value="Run correlation" id="run_genetic_correlation" />
     </div>
     <div id="corr_canvas">
diff --git a/mason/solgs/tools/genetic_gain/multi_traits_genetic_gain.mas b/mason/solgs/tools/genetic_gain/multi_traits_genetic_gain.mas
index 12c66a081f..0f981be9b5 100644
--- a/mason/solgs/tools/genetic_gain/multi_traits_genetic_gain.mas
+++ b/mason/solgs/tools/genetic_gain/multi_traits_genetic_gain.mas
@@ -22,7 +22,7 @@ $training_traits_ids
 
 
 <div class="row">  
-  <div class="form-group col-sm-3" id="gg_select_a_pop_div" style="margin-right:35px"></div>
+  <div class="form-group col-sm-3" id="gg_pops_select_div" style="margin-right:35px"></div>
   <input id="check_genetic_gain" class="button" type="submit" value="Check Genetic Gain" />
 </div>
 
diff --git a/mason/solgs/tools/selection_index/selection_index.mas b/mason/solgs/tools/selection_index/selection_index.mas
index 36cfe3ac3d..1a8bb34881 100644
--- a/mason/solgs/tools/selection_index/selection_index.mas
+++ b/mason/solgs/tools/selection_index/selection_index.mas
@@ -43,14 +43,14 @@ $training_pop_name
   <div id="si_canvas">
 
     <div class="row">
-      <div class="form-group col-sm-3" id="si_select_a_pop_div" style="margin-right:35px"></div>
+      <div class="form-group col-sm-3" id="si_select_pops_div" style="margin-right:35px"></div>
       <div id="si_help"><p> And assign relative weights to traits.<i style="color:#5cb85c;" class="fa fa-question-circle" id="si_tooltip" title="<% $si_tooltip %>"> </i></p></div>
     </div>
 
    
     <div id="si_selected_pop_div" style="display:none">
-      <input type="hidden" id="model_id" value="<% $training_pop_id %>" />
-      <input type="hidden" id="model_name" value="<% $training_pop_name %>" />
+      <input type="hidden" id="training_pop_id" value="<% $training_pop_id %>" />
+      <input type="hidden" id="training_pop_name" value="<% $training_pop_name %>" />
       <input type="hidden" id="si_default_selected_pop_name" value="<% $training_pop_name %>"/>
       <input type="hidden" id="si_default_selected_pop_type" value="<% $pop_type %>"/>
       <input type="hidden" id="si_default_selected_pop_id" value="<% $training_pop_id %>"/>
@@ -59,7 +59,7 @@ $training_pop_name
       <input type="hidden" id="si_selected_pop_type" value="" />
     </div>
 
-    <div id="selection_index_form"> </div>
+    <div id="si_form"> </div>
 
     <& /solgs/spinner/spinner.mas &>
     <div id="si_message"  class="message"> </div>

From 042c4d0c758488a96f01a67a55fca2008179c0f4 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 31 May 2023 14:33:53 +0200
Subject: [PATCH 31/61] all clustering types tests

---
 t/selenium2/solgs/cluster.t | 3251 +++++++++++++++++++++++++++++++++++
 1 file changed, 3251 insertions(+)
 create mode 100644 t/selenium2/solgs/cluster.t

diff --git a/t/selenium2/solgs/cluster.t b/t/selenium2/solgs/cluster.t
new file mode 100644
index 0000000000..baaffebf5a
--- /dev/null
+++ b/t/selenium2/solgs/cluster.t
@@ -0,0 +1,3251 @@
+
+use strict;
+
+use lib 't/lib';
+
+use File::Spec::Functions qw / catfile catdir/;
+use Test::More;
+use SGN::Test::WWW::WebDriver;
+use SGN::Test::Fixture;
+use SGN::Test::solGSData;
+
+my $d = SGN::Test::WWW::WebDriver->new();
+my $f = SGN::Test::Fixture->new();
+
+my $solgs_data = SGN::Test::solGSData->new(
+    {
+        'fixture'                => $f,
+        'accessions_list_subset' => 60,
+        'plots_list_subset'      => 60
+    }
+);
+
+my $cache_dir    = $solgs_data->site_cluster_shared_dir();
+my $protocol_dir = $solgs_data->default_protocol_dir();
+my $cluster_dir  = catdir( $protocol_dir, 'cluster' );
+my $log_dir      = catdir( $protocol_dir, 'log' );
+
+my $accessions_list = $solgs_data->load_accessions_list();
+
+# my $accessions_list = $solgs_data->get_list_details('accessions');
+my $accessions_list_name = $accessions_list->{list_name};
+my $accessions_list_id   = 'list_' . $accessions_list->{list_id};
+print STDERR
+  "\naccessions list: $accessions_list_name -- $accessions_list_id\n";
+my $plots_list = $solgs_data->load_plots_list();
+
+# my $plots_list =  $solgs_data->get_list_details('plots');
+my $plots_list_name = $plots_list->{list_name};
+my $plots_list_id   = 'list_' . $plots_list->{list_id};
+
+print STDERR "\nadding trials list\n";
+my $trials_list = $solgs_data->load_trials_list();
+
+# my $trials_list =  $solgs_data->get_list_details('trials');
+my $trials_list_name = $trials_list->{list_name};
+my $trials_list_id   = 'list_' . $trials_list->{list_id};
+print STDERR "\nadding trials dataset\n";
+
+# my $trials_dt =  $solgs_data->get_dataset_details('trials');
+my $trials_dt      = $solgs_data->load_trials_dataset();
+my $trials_dt_name = $trials_dt->{dataset_name};
+my $trials_dt_id   = 'dataset_' . $trials_dt->{dataset_id};
+print STDERR "\nadding accessions dataset\n";
+
+# my $accessions_dt =  $solgs_data->get_dataset_details('accessions');
+my $accessions_dt      = $solgs_data->load_accessions_dataset();
+my $accessions_dt_name = $accessions_dt->{dataset_name};
+my $accessions_dt_id   = 'dataset_' . $accessions_dt->{dataset_id};
+
+print STDERR "\nadding plots dataset\n";
+
+# my $plots_dt =  $solgs_data->get_dataset_details('plots');
+my $plots_dt      = $solgs_data->load_plots_dataset();
+my $plots_dt_name = $plots_dt->{dataset_name};
+my $plots_dt_id   = 'dataset_' . $plots_dt->{dataset_id};
+
+#$accessions_dt_name = '' . $accessions_dt_name . '';
+print STDERR "\ntrials dt: $trials_dt_name -- $trials_dt_id\n";
+print STDERR "\naccessions dt: $accessions_dt_name -- $accessions_dt_id\n";
+print STDERR "\nplots dt: $plots_dt_name -- $plots_dt_id\n";
+
+print STDERR "\ntrials list: $trials_list_name -- $trials_list_id\n";
+print STDERR
+  "\naccessions list: $accessions_list_name -- $accessions_list_id\n";
+print STDERR "\nplots list: $plots_list_name -- $plots_list_id\n";
+
+`rm -r $cache_dir`;
+
+# `rm -r /tmp/localhost/GBSApeKIgenotypingv4/log/`;
+
+$d->while_logged_in_as(
+    "submitter",
+    sub {
+
+        $d->get_ok( '/cluster/analysis', 'cluster home page' );
+        sleep(5);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'select clones list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run clones list (genotype) clustering'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(60);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -10);",
+            $sel_pops );
+        sleep(60);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-'
+              . $accessions_list_id
+              . '-genotype-k-4-gp-1"]',
+            'xpath',
+            'check k-means plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'select clones list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(5);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(40);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, 500);",
+            $sel_pops );
+        sleep(40);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-'
+              . $accessions_list_id
+              . '-genotype-gp-1"]',
+            'xpath',
+            'check hierarchical plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $plots_list_name . '"]',
+            'xpath',
+            'select plots list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run plots list (phenotype) clustering'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(60);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -10);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-' . $plots_list_id . '-phenotype-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $plots_list_name . '"]',
+            'xpath',
+            'select plots list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(40);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, 500);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-' . $plots_list_id . '-phenotype"]',
+            'xpath', 'check hierarchical plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_list_name . '"]',
+            'xpath',
+            'select trials list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run trials list (genotype) clustering'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -10);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-'
+              . $trials_list_id
+              . '-genotype-k-4-gp-1"]',
+            'xpath',
+            'check k-means plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_list_name . '"]',
+            'xpath',
+            'select trials list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run trials list (phenotype) clustering'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(100);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -10);",
+            $sel_pops );
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-' . $trials_list_id . '-phenotype-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_list_name . '"]',
+            'xpath',
+            'select trials list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, 600);",
+            $sel_pops );
+
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-'
+              . $trials_list_id
+              . '-genotype-gp-1"]',
+            'xpath',
+            'check hierarchical plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        `rm -r /tmp/localhost`;
+        sleep(5);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_list_name . '"]',
+            'xpath',
+            'select trials list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'queue_job', 'id', 'job queueing' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'trials list pheno analysis name' )
+          ->send_keys('trials list clustering');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+
+        $d->driver->go_back();
+        sleep(5);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_list_name . '"]',
+            'xpath',
+            'select trials list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(5);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, 500);",
+            $sel_pops );
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-' . $trials_list_id . '-phenotype"]',
+            'xpath',
+            'check heirarchical plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_dt_name . '"]',
+            'xpath',
+            'select trials dataset'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, 500);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-' . $trials_dt_id . '-phenotype"]',
+            'xpath', 'check hierarchical plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_list_name . '"]',
+            'xpath',
+            'select trials list'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run trials list (pheno) cluster'
+        )->click();
+        sleep(5);
+
+        # $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
+        # sleep(60);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -10);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-' . $trials_list_id . '-phenotype-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_dt_name . '"]',
+            'xpath',
+            'select trials dataset'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run trials dataset (genotype) cluster'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, 500);",
+            $sel_pops );
+        sleep(2);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-' . $trials_dt_id . '-genotype-k-4-gp-1"]',
+            'xpath',
+            'plot displayed'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_list_select"]/option[text()="'
+              . $trials_dt_name . '"]',
+            'xpath',
+            'select trials dataset'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath', 'go btn' )
+          ->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run trials dataset (phenotype) cluster'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(80);
+
+        my $sel_pops = $d->find_element( '//*[contains(text(), "Select a")]',
+            'xpath', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, 500);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-' . $trials_dt_id . '-phenotype-k-4"]',
+            'xpath', 'check kmeans plot' )->click();
+        sleep(5);
+
+        `rm -r /tmp/localhost`;
+        sleep(5);
+
+        $d->get_ok( '/breeders/trial/139', 'trial detail home page' );
+        sleep(5);
+
+        my $analysis_tools = $d->find_element(
+            'Analysis Tools',
+            'partial_link_text',
+            'toogle analysis tools'
+        );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-50);",
+            $analysis_tools );
+        sleep(5);
+        $d->find_element_ok(
+            'Analysis Tools',
+            'partial_link_text',
+            'toogle analysis tools'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'Clustering', 'partial_link_text',
+            'expand cluster sec' )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run phenotype cluster'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(60);
+        $d->find_element_ok( '//img[@id="k-means-plot-139-phenotype-k-4"]',
+            'xpath', 'plot displayed' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(5);
+
+        my $analysis_tools = $d->find_element(
+            'Analysis Tools',
+            'partial_link_text',
+            'toogle analysis tools'
+        );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-50);",
+            $analysis_tools );
+        sleep(5);
+        $d->find_element_ok(
+            'Analysis Tools',
+            'partial_link_text',
+            'toogle analysis tools'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'Clustering', 'partial_link_text',
+            'expand cluster sec' )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok( '//img[@id="hierarchical-plot-139-phenotype"]',
+            'xpath', 'plot displayed' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(5);
+
+        my $analysis_tools =
+          $d->find_element( 'cluster_canvas', 'id', 'toogle analysis tools' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-50);",
+            $analysis_tools );
+        sleep(5);
+        $d->find_element_ok(
+            'Analysis Tools',
+            'partial_link_text',
+            'toogle analysis tools'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'Clustering', 'partial_link_text',
+            'expand cluster sec' )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok( '//img[@id="hierarchical-plot-139-genotype-gp-1"]',
+            'xpath', 'check hierarchical plot' )->click();
+        sleep(2);
+
+        $d->driver->refresh();
+        sleep(5);
+
+        my $analysis_tools =
+          $d->find_element( 'cluster_canvas', 'id', 'toogle analysis tools' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-50);",
+            $analysis_tools );
+        sleep(5);
+        $d->find_element_ok(
+            'Analysis Tools',
+            'partial_link_text',
+            'toogle analysis tools'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'Clustering', 'partial_link_text',
+            'expand cluster sec' )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(1);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(1);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run genotype cluster'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(80);
+        $d->find_element_ok( '//img[@id="k-means-plot-139-genotype-k-4-gp-1"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(2);
+
+        ############## solGS #####################
+        `rm -r $cache_dir`;
+
+        $d->get_ok( '/solgs', 'solgs homepage' );
+        sleep(4);
+
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->send_keys('Kasese solgs trial');
+        sleep(5);
+        $d->find_element_ok( 'search_training_pop', 'id',
+            'search for training pop' )->click();
+        sleep(5);
+        $d->find_element_ok( 'Kasese', 'partial_link_text',
+            'create training pop' )->click();
+        sleep(5);
+        $d->find_element_ok( 'queue_job', 'id', 'submit job tr pop' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id', 'training data job name' )
+          ->send_keys('Test Kasese Tr pop');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(80);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(3);
+
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->send_keys('Kasese solgs trial');
+        sleep(5);
+        $d->find_element_ok( 'search_training_pop', 'id',
+            'search for training pop' )->click();
+        sleep(5);
+        $d->find_element_ok( 'Kasese', 'partial_link_text',
+            'create training pop' )->click();
+        sleep(15);
+
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[1]/td/input',
+            'xpath', 'select 1st trait' )->click();
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[2]/td/input',
+            'xpath', 'select 2nd trait' )->click();
+        $d->find_element_ok( 'runGS', 'id', 'build multi models' )->click();
+        sleep(3);
+        $d->find_element_ok( 'queue_job', 'id', 'multi models job queueing' )
+          ->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id', 'job name' )
+          ->send_keys('Test DMCP-FRW modeling  Kasese');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(5);
+
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[1]/td/input',
+            'xpath', 'select 1st trait' )->click();
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[2]/td/input',
+            'xpath', 'select 2nd trait' )->click();
+        $d->find_element_ok( 'runGS', 'id', 'build multi models' )->click();
+        sleep(10);
+
+#         # #
+# ##############################################################
+# # $d->get_ok('solgs/traits/all/population/139/traits/1971973596/gp/1', 'models page');
+# #
+# # sleep(15);
+# #####################################################################
+
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->send_keys('trial2 NaCRRI');
+        sleep(2);
+        $d->find_element_ok( 'search_selection_pop', 'id',
+            'search for selection pop' )->click();
+        sleep(30);
+        $d->find_element_ok(
+'//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]',
+            'xpath',
+            'click training pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'queue_job', 'id', 'no job queueing' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'multi trials sel job name' )
+          ->send_keys('Test DMCP-FRW selection pred nacrri');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(15);
+
+        $d->find_element_ok(
+'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'accessions list sl pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath',
+            'select list sel pop' )->click();
+        sleep(5);
+        $d->find_element_ok(
+'//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]',
+            'xpath',
+            'click list sel pred'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'queue_job', 'id', 'no job queueing' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id', 'list sel job name' )
+          ->send_keys('clones list dmc-frw sel pred');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(250);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(15);
+
+        $d->find_element_ok(
+'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'accession select list sl pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath',
+            'select dataset sel pop' )->click();
+        sleep(5);
+        $d->find_element_ok(
+'//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]',
+            'xpath',
+            'list sel pred'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'queue_job', 'id', 'no job queueing' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id', 'dataset sel job name' )
+          ->send_keys('dataset clones sel pred');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(5);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -200);",
+            $sel_pops );
+
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(5);
+        my $list = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'select list sel pop'
+        );
+        $list->click();
+        sleep(5);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -100);",
+            $sel_pops );
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(2);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'select accessions list sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(80);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-'
+              . $accessions_list_id
+              . '-traits-1971973596-gebv-k-4"]',
+            'xpath',
+            'check k-means plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
+            $sel_pops );
+        sleep(2);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(2);
+        my $dataset = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        );
+        $dataset->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(5);
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(2);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select accessions dataset sel pop'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(80);
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-'
+              . $accessions_dt_id
+              . '-traits-1971973596-genotype-k-4-gp-1"]',
+            'xpath',
+            'check k-means plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(5);
+        my $dataset = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select accessions dataset sel pop'
+        );
+        $dataset->click();
+        sleep(5);
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(15);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select accessions dataset sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(60);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-'
+              . $accessions_dt_id
+              . '-traits-1971973596-gebv-k-4"]',
+            'xpath',
+            'check k-means plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(5);
+        my $dataset = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        );
+        $dataset->click();
+        sleep(5);
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(15);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-139-'
+              . $accessions_dt_id
+              . '-traits-1971973596-gebv"]',
+            'xpath',
+            'check hierarchical plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(5);
+
+        my $dataset = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        );
+        $dataset->click();
+        sleep(5);
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'GO select dataset sel popp'
+        )->click();
+        sleep(15);
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(180);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-139-'
+              . $accessions_dt_id
+              . '-traits-1971973596-genotype-gp-1"]',
+            'xpath',
+            'check hierarchical plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//select[@id="cluster_data_type_select"]/option[text()="Phenotype"]',
+            'xpath', 'select ghenotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(80);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-traits-1971973596-phenotype-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(80);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-traits-1971973596-genotype-k-4-gp-1"]',
+            'xpath', 'check k-means plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(40);
+        $d->find_element_ok(
+'//img[@id="hierarchical-plot-139-traits-1971973596-genotype-gp-1"]',
+            'xpath', 'check hierarchical plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(60);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-traits-1971973596-gebv-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-139-traits-1971973596-gebv"]',
+            'xpath', 'check hierarchical plot' )->click();
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $cor = $d->find_element( 'Genetic correlation',
+            'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $cor );
+        sleep(5);
+        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial type tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'DMCP', 'id', 'rel wt 1st' )->send_keys(3);
+        sleep(5);
+        $d->find_element_ok( 'FRW', 'id', 'rel wt 2st' )->send_keys(5);
+        sleep(5);
+        $d->find_element_ok( 'calculate_si', 'id', 'calc selection index' )
+          ->click();
+        sleep(60);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]',
+            'xpath', 'select sel index pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "selection_proportion_input")]',
+            'xpath', 'fill in sel prop' )->send_keys('15');
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        sleep(1);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(60);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-139-139-DMCP-3-FRW-5-genotype-k-4-gp-1-sp-15"]',
+            'xpath', 'plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $cor = $d->find_element( 'Genetic correlation',
+            'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $cor );
+        sleep(5);
+        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial type tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'DMCP', 'id', 'rel wt 1st' )->send_keys(3);
+        sleep(5);
+        $d->find_element_ok( 'FRW', 'id', 'rel wt 2st' )->send_keys(5);
+        sleep(5);
+        $d->find_element_ok( 'calculate_si', 'id', 'calc selection index' )
+          ->click();
+        sleep(130);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]',
+            'xpath', 'select sel index pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "selection_proportion_input")]',
+            'xpath', 'fill in sel prop' )->send_keys('15');
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(40);
+        $d->find_element_ok(
+'//img[@id="hierarchical-plot-139-139-DMCP-3-FRW-5-genotype-gp-1-sp-15"]',
+            'xpath', 'plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run trial2 NaCRRI  geno cluster'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id',
+            'no job queueing -- trial2 NaCRRI  geno cluster' )->click();
+        sleep(200);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-139-141-traits-1971973596-genotype-k-4-gp-1"]',
+            'xpath', 'check trial2 NaCRRI  geno k-means plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+'//img[@id="hierarchical-plot-139-141-traits-1971973596-genotype-gp-1"]',
+            'xpath', 'check hierarchical plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(80);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-141-traits-1971973596-gebv-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="GEBV"]',
+            'xpath',
+            'select gebv'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(40);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-139-141-traits-1971973596-gebv"]',
+            'xpath', 'check hierarchical plot' )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        `rm -r $cluster_dir`;
+        sleep(3);
+        `rm -r $log_dir`;
+        sleep(5);
+
+# # $d->get_ok('solgs/traits/all/population/139/traits/1971973596/gp/1', 'models page');
+# # sleep(15);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'queue_job', 'id',
+            'queueing trial2 NaCRRI  geno km clustering' )->click();
+        sleep(3);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'analysis name -Nacrri sel pop geno clustering' )
+          ->send_keys('Nacrri sel pop geno clustering');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(20);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-139-141-traits-1971973596-genotype-k-4-gp-1"]',
+            'xpath', 'check k-means plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'queue_job', 'id',
+            'queueing trial2 NaCRRI  gebv cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'analysis name -Nacrri sel pop gebv clustering' )
+          ->send_keys('Nacrri sel pop gebv clustering');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(10);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-141-traits-1971973596-gebv-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $cor = $d->find_element( 'Genetic correlation',
+            'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $cor );
+        sleep(5);
+        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial type tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'DMCP', 'id', 'rel wt 1st' )->send_keys(3);
+        sleep(5);
+        $d->find_element_ok( 'FRW', 'id', 'rel wt 2st' )->send_keys(5);
+        sleep(5);
+        $d->find_element_ok( 'calculate_si', 'id', 'calc selection index' )
+          ->click();
+        sleep(60);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]',
+            'xpath', 'select sel index pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "selection_proportion_input")]',
+            'xpath', 'fill in sel prop' )->send_keys('15');
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'queue_job', 'id', 'no job queueing' )->click();
+        sleep(3);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'analysis name -Nacrri sel pop sindex clustering' )
+          ->send_keys('Nacrri sel pop sindex clustering');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(140);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(3);
+
+        my $cor = $d->find_element( 'Genetic correlation',
+            'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $cor );
+        sleep(5);
+        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+            'xpath',
+            'select trial type tr pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'DMCP', 'id', 'rel wt 1st' )->send_keys(3);
+        sleep(5);
+        $d->find_element_ok( 'FRW', 'id', 'rel wt 2st' )->send_keys(5);
+        sleep(5);
+        $d->find_element_ok( 'calculate_si', 'id', 'calc selection index' )
+          ->click();
+        sleep(60);
+        #
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="139-DMCP-3-FRW-5"]',
+            'xpath', 'select sel index pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "selection_proportion_input")]',
+            'xpath', 'fill in sel prop' )->send_keys('15');
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(140);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-139-139-DMCP-3-FRW-5-genotype-k-4-gp-1-sp-15"]',
+            'xpath', 'plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+#########################
+        `rm -r $cluster_dir`;
+        sleep(3);
+        `rm -r $log_dir`;
+        sleep(5);
+########################################
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id',
+            'wait to finish clustering trial2 NaCRRI genotype' )->click();
+        sleep(200);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-139-141-traits-1971973596-genotype-k-4-gp-1"]',
+            'xpath', 'check k-means plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+# #    #  #######    #
+# #    #  $d->get_ok('/solgs/trait/70666/population/139/gp/1', 'open model page');
+# #    #  sleep(5);
+# #    #
+
+        my $clustering =
+          $d->find_element( 'Models summary', 'partial_link_text',
+            'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok(
+            '//table[@id="model_summary"]//*[contains(text(), "FRW")]',
+            'xpath', 'click training pop' )->click();
+        sleep(5);
+        ######
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id',
+            'wait to finish clustering in single trial model page' )->click();
+        sleep(200);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-139-70666-genotype-k-4-gp-1"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-139-70666-genotype-gp-1"]',
+            'xpath', 'check hierarchical plot' )->click();
+        sleep(5);
+
+# #    #  #$d->get_ok('/solgs/model/combined/populations/2804608595/trait/70741/gp/1', 'open combined trials model page');
+# #    # # sleep(2);
+# #    #
+
+        $d->get_ok( '/solgs', 'solgs home page' );
+        sleep(2);
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->send_keys('Kasese solgs trial');
+        sleep(2);
+        $d->find_element_ok( 'search_training_pop', 'id',
+            'search for training pop' )->click();
+        sleep(1);
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->clear();
+        sleep(2);
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->send_keys('trial2 nacrri');
+        sleep(5);
+        $d->find_element_ok( 'search_training_pop', 'id',
+            'search for training pop' )->click();
+        sleep(1);
+
+        $d->find_element_ok(
+            '//table[@id="searched_trials_table"]//input[@value="139"]',
+            'xpath', 'select trial kasese' )->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//table[@id="searched_trials_table"]//input[@value="141"]',
+            'xpath', 'select trial nacrri' )->click();
+        sleep(2);
+        $d->find_element_ok( 'done_selecting', 'id', 'done selecting' )
+          ->click();
+        sleep(2);
+        $d->find_element_ok( 'combine_trait_trials', 'id', 'combine trials' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok( 'queue_job', 'id', 'submit job tr pop' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id', 'job queueing' )
+          ->send_keys('combined trials');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(10);
+
+#         ####################
+# #  #$d->get('/solgs/populations/combined/2804608595/gp/1', 'combo trials tr pop page');
+# #    #  #sleep(5);
+# #    #
+#         ##################
+        $d->get_ok( '/solgs', 'solgs homepage' );
+        sleep(2);
+
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->send_keys('Kasese solgs trial');
+        sleep(2);
+        $d->find_element_ok( 'search_training_pop', 'id',
+            'search for training pop' )->click();
+        sleep(1);
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->clear();
+        sleep(2);
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'population search form' )->send_keys('trial2 nacrri');
+        sleep(5);
+        $d->find_element_ok( 'search_training_pop', 'id',
+            'search for training pop' )->click();
+        sleep(3);
+
+        $d->find_element_ok(
+            '//table[@id="searched_trials_table"]//input[@value="139"]',
+            'xpath', 'select trial kasese' )->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//table[@id="searched_trials_table"]//input[@value="141"]',
+            'xpath', 'select trial nacrri' )->click();
+        sleep(2);
+        $d->find_element_ok( 'done_selecting', 'id', 'done selecting' )
+          ->click();
+        sleep(2);
+        $d->find_element_ok( 'combine_trait_trials', 'id', 'combine trials' )
+          ->click();
+        sleep(15);
+
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[1]/td/input',
+            'xpath', 'select 1st trait' )->click();
+        sleep(1);
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[2]/td/input',
+            'xpath', 'select 2nd trait' )->click();
+        sleep(1);
+        $d->find_element_ok( 'runGS', 'id',
+            'run combined trials build multi models' )->click();
+        sleep(10);
+        $d->find_element_ok( 'queue_job', 'id', 'combined trials job queueing' )
+          ->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'combined trials multi models job name' )
+          ->send_keys('Test DMCP-FRW modeling combo trials');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(200);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(15);
+
+# # ###########################
+# # # $d->get('/solgs/populations/combined/2804608595/gp/1', 'combo trials tr pop page');
+# #  # sleep(5);
+# #   ############################
+
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[1]/td/input',
+            'xpath', 'select 1st trait' )->click();
+        sleep(1);
+        $d->find_element_ok(
+            '//table[@id="population_traits_list"]/tbody/tr[2]/td/input',
+            'xpath', 'select 2nd trait' )->click();
+        sleep(1);
+        $d->find_element_ok( 'runGS', 'id',
+            ' go to combined trials multi models page' )->click();
+        sleep(10);
+
+        $d->find_element_ok( 'population_search_entry', 'id',
+            'combo trials models sel population search form' )
+          ->send_keys('trial2 NaCRRI');
+        sleep(5);
+        $d->find_element_ok( 'search_selection_pop', 'id',
+            'search for selection pop' )->click();
+        sleep(20);
+        $d->find_element_ok(
+'//table[@id="selection_pops_table"]//*[contains(text(), "Predict")]',
+            'xpath',
+            'click training pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'queue_job', 'id',
+            'trial sel pop prediction job queueing' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'sel pop prediction analysis name' )
+          ->send_keys('combo DMCP-FRW selection pred nacrri');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(250);
+        $d->find_element_ok( 'Go back', 'partial_link_text',
+            'go back to combo trials multi models pg' )->click();
+        sleep(15);
+
+        $d->find_element_ok(
+'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'list sl pop'
+        )->click();
+        sleep(10);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath',
+            'select list sel pop' )->click();
+        sleep(5);
+        $d->find_element_ok(
+'//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]',
+            'xpath',
+            'click list sel pred'
+        )->click();
+        sleep(20);
+        $d->find_element_ok( 'queue_job', 'id',
+            'list type sel pop prediction job queueing' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'list type  sel pop prediction analysis name' )
+          ->send_keys('combo clones list dmc-frw sel pred');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(250);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(5);
+
+        $d->find_element_ok(
+'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select list sl pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//input[@value="View"]', 'xpath',
+            'select dataset sel pop' )->click();
+        sleep(5);
+        $d->find_element_ok(
+'//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]',
+            'xpath',
+            'click accessions dataset sel pred'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'queue_job', 'id',
+            'dataset sel pop prediction job queueing' )->click();
+        sleep(2);
+        $d->find_element_ok( 'analysis_name', 'id',
+            'dataset sel pop prediction analysis name' )
+          ->send_keys('combo dataset clones sel pred');
+        sleep(2);
+        $d->find_element_ok( 'user_email', 'id', 'user email' )
+          ->send_keys('email@email.com');
+        sleep(2);
+        $d->find_element_ok( 'submit_job', 'id', 'submit' )->click();
+        sleep(250);
+        $d->find_element_ok( 'Go back', 'partial_link_text', 'go back' )
+          ->click();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-2804608595-traits-1971973596-phenotype-k-4"]',
+            'xpath', 'check k-means plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Phenotype"]',
+            'xpath',
+            'select phenotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+'//img[@id="hierarchical-plot-2804608595-traits-1971973596-phenotype"]',
+            'xpath', 'check hierarchical plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select phenotype' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing -- GEBV' )
+          ->click();
+        sleep(200);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-2804608595-traits-1971973596-gebv-k-4"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select phenotype' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-2804608595-traits-1971973596-gebv"]',
+            'xpath', 'check hierarchical plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'click cluster pops' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
+            'xpath',
+            'select tr pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing-- Genotype' )
+          ->click();
+        sleep(200);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-2804608595-traits-1971973596-genotype-k-4-gp-1"]',
+            'xpath', 'plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'click cluster pops' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="Training population 2804608595"]',
+            'xpath',
+            'select tr pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+'//img[@id="hierarchical-plot-2804608595-traits-1971973596-genotype-gp-1"]',
+            'xpath', 'plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $cor = $d->find_element( 'Genetic correlation',
+            'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $cor );
+        sleep(5);
+        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="si_select_pops"]/option[text()="Training population 2804608595"]',
+            'xpath',
+            'select combo pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'DMCP', 'id', 'rel wt 1st' )->send_keys(3);
+        sleep(5);
+        $d->find_element_ok( 'FRW', 'id', 'rel wt 2st' )->send_keys(5);
+        sleep(5);
+        $d->find_element_ok( 'calculate_si', 'id', 'calc selection index' )
+          ->click();
+        sleep(50);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'click cluster pops' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="2804608595-DMCP-3-FRW-5"]',
+            'xpath', 'si'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//select[@id="cluster_data_type_select"]/option[text()="Genotype"]',
+            'xpath', 'genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "selection_proportion_input")]',
+            'xpath', 'fill in sel prop' )->send_keys('15');
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(140);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-2804608595-2804608595-DMCP-3-FRW-5-genotype-k-4-gp-1-sp-15"]',
+            'xpath', 'plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(5);
+
+# #$d->get_ok('/solgs/models/combined/trials/2804608595/traits/1971973596/gp/1', 'combined trials models summary page');
+        ## sleep(5);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(5);
+        my $dataset = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        );
+        $dataset->click();
+        sleep(5);
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(15);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id',
+            'select dataset type sl pop - GEBV' )->click();
+        sleep(3);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run GEBV cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-2804608595-'
+              . $accessions_dt_id
+              . '-traits-1971973596-gebv-k-4"]',
+            'xpath',
+            'check k-means plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(5);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
+            $sel_pops );
+        sleep(5);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(5);
+        my $dataset = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        );
+        $dataset->click();
+        sleep(5);
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(15);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_dt_name . '"]',
+            'xpath',
+            'select dataset sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-2804608595-'
+              . $accessions_dt_id
+              . '-traits-1971973596-gebv"]',
+            'xpath',
+            'check hierarchical plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(5);
+
+        my $sel_pops =
+          $d->find_element( 'Predict', 'partial_link_text', 'scroll up' );
+        my $elem = $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0, -200);",
+            $sel_pops );
+
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list type sel pop'
+        )->click();
+        sleep(5);
+        $d->find_element_ok( 'list_type_selection_pops_list_select',
+            'id', 'select clones list menu' )->click();
+        sleep(5);
+        my $list = $d->find_element_ok(
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'select list sel pop'
+        );
+        $list->click();
+        sleep(5);
+        $d->find_element_ok(
+            '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(15);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id',
+            'select list type sl pop -- GEBV' )->click();
+        sleep(3);
+        $d->find_element_ok(
+            '//select[@id="cluster_pops_select"]/option[text()="'
+              . $accessions_list_name . '"]',
+            'xpath',
+            'select list sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(180);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-2804608595-'
+              . $accessions_list_id
+              . '-traits-1971973596-gebv-k-4"]',
+            'xpath',
+            'check k-means plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-2804608595-141-traits-1971973596-genotype-k-4-gp-1"]',
+            'xpath', 'check k-means plot'
+        )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id', 'select list sl pop' )
+          ->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(40);
+        $d->find_element_ok(
+'//img[@id="hierarchical-plot-2804608595-141-traits-1971973596-gebv"]',
+            'xpath', 'check hierarchical plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        # #
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok( 'cluster_pops_select', 'id',
+            'select trial sl pop -- GEBV' )->click();
+        sleep(3);
+        $d->find_element_ok(
+'//select[@id="cluster_pops_select"]/option[text()="trial2 NaCRRI"]',
+            'xpath',
+            'select trial sel pop'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+            '//select[@id="cluster_data_type_select"]/option[text()="GEBV"]',
+            'xpath', 'select gebv' )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(140);
+        $d->find_element_ok(
+'//img[@id="k-means-plot-2804608595-141-traits-1971973596-gebv-k-4"]',
+            'xpath', 'check k-means plot'
+        )->click();
+        sleep(3);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Models summary', 'partial_link_text',
+            'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
+            $clustering );
+        sleep(5);
+        $d->find_element_ok(
+            '//table[@id="model_summary"]//*[contains(text(), "DMCP")]',
+            'xpath', 'go to  training model pg' )->click();
+        sleep(5);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select k-means' )->send_keys('K-means');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'clear k number' )->clear();
+        $d->find_element_ok( '//*[starts-with(@id, "k_number_input")]',
+            'xpath', 'select k number' )->send_keys(4);
+        sleep(2);
+        $d->find_element_ok(
+            '//*[starts-with(@id, "run_cluster")]',
+            'xpath',
+            'run genotype cluster'
+        )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(200);
+        $d->find_element_ok(
+            '//img[@id="k-means-plot-2804608595-70741-genotype-k-4-gp-1"]',
+            'xpath', 'check k-means plot' )->click();
+        sleep(5);
+
+        $d->driver->refresh();
+        sleep(3);
+
+        my $clustering =
+          $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
+        $d->driver->execute_script(
+            "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);",
+            $clustering );
+        sleep(5);
+
+        $d->find_element_ok( '//*[starts-with(@id, "cluster_type_select")]',
+            'xpath', 'select hierarchical' )->send_keys('Hierarchical');
+        sleep(2);
+        $d->find_element_ok(
+'//*[starts-with(@id, "cluster_data_type_select")]/option[text()="Genotype"]',
+            'xpath',
+            'select genotype'
+        )->click();
+        sleep(2);
+        $d->find_element_ok( '//*[starts-with(@id, "run_cluster")]',
+            'xpath', 'run cluster' )->click();
+        sleep(3);
+        $d->find_element_ok( 'no_queue', 'id', 'no job queueing' )->click();
+        sleep(130);
+        $d->find_element_ok(
+            '//img[@id="hierarchical-plot-2804608595-70741-genotype-gp-1"]',
+            'xpath', 'check hierarchical plot' )->click();
+        sleep(5);
+
+        foreach
+          my $list_id ( $trials_list_id, $accessions_list_id, $plots_list_id )
+        {
+            $list_id =~ s/\w+_//g;
+            $solgs_data->delete_list($list_id);
+        }
+
+        foreach
+          my $dataset_id ( $trials_dt_id, $accessions_dt_id, $plots_dt_id )
+        {
+            $dataset_id =~ s/\w+_//g;
+            $solgs_data->delete_dataset($dataset_id);
+        }
+
+    }
+);
+
+done_testing();

From 9b24699a44549a023208a36a00695e2994bbfebe Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Tue, 6 Jun 2023 14:42:17 +0200
Subject: [PATCH 32/61] refactor ajax calls

---
 .../solGS/listTypeTrainingPopulation.js       | 244 +++++++++---------
 1 file changed, 126 insertions(+), 118 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index 70967c6301..4dc947843b 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -86,18 +86,14 @@ solGS.listTypeTrainingPopulation = {
   },
 
   loadTrialListTypeTrainingPop: function (trialsNames) {
-    jQuery.ajax({
+    var trialsList = jQuery.ajax({
       type: "POST",
       url: "/solgs/get/trial/id/",
       dataType: "json",
       data: { trials_names: trialsNames },
-      success: function (res) {
-        solGS.combinedTrials.getCombinedPopsId(res.trials_ids);
-      },
-      error: function (response) {
-        alert("Error occured querying for trials ids");
-      },
     });
+
+    return trialsList;
   },
 
   askTrainingJobQueueing: function (listId) {
@@ -119,9 +115,9 @@ solGS.listTypeTrainingPopulation = {
     var genoList = this.getListTypeTrainingPopDetail(listId);
     var listName = genoList.name;
     var list = genoList.list;
-    var popId = getModelId(listId);
+    var popId = this.getModelId(listId);
     var protocolId = jQuery("#genotyping_protocol_id").val();
-    var popType = "list_reference";
+    var popType = "list_training";
 
     var args = {
       list_name: listName,
@@ -149,29 +145,125 @@ solGS.listTypeTrainingPopulation = {
     if (args.list.length === 0) {
       alert("The list is empty. Please select a list with content.");
     } else {
-      jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-      jQuery.blockUI({ message: "Please wait.." });
+      // jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
+      // jQuery.blockUI({ message: "Please wait.." });
 
-      jQuery.ajax({
+      var plotsList = jQuery.ajax({
         type: "POST",
         dataType: "json",
         data: { arguments: args },
         url: "/solgs/load/plots/list/training",
-        success: function (response) {
-          if (response.status == "success") {
-            window.location = "/solgs/population/" + popId;
-            jQuery.unblockUI();
-          } else {
-            alert("Error occured while querying for the training data.");
-            jQuery.unblockUI();
-          }
-        },
-        error: function (res) {
-          alert("Error occured while querying for the training data.");
-          jQuery.unblockUI();
-        },
       });
+
+      return plotsList;
     }
+
+    //       success: function (response) {
+    //         if (response.status == "success") {
+    //           window.location = "/solgs/population/" + popId;
+    //           jQuery.unblockUI();
+    //         } else {
+    //           alert("Error occured while querying for the training data.");
+    //           jQuery.unblockUI();
+    //         }
+    //       },
+    //       error: function (res) {
+    //         alert("Error occured while querying for the training data.");
+    //         jQuery.unblockUI();
+    //       },
+    //     });
+    //   }
+  },
+
+  getModelId: function (listId) {
+    var modelId = "list_" + listId;
+    return modelId;
+  },
+
+  getUserUploadedRefPop: function (listId) {
+    var genoList = this.getListTypeTrainingPopDetail(listId);
+    var listName = genoList.name;
+    var list = genoList.list;
+    var modelId = this.getModelId(listId);
+
+    var url = "'/solgs/population/" + modelId + "'";
+    var listIdArg = "'" + listId + "'";
+    var listSource = "'from_db'";
+    var popIdName = { id: modelId, name: listName };
+    popIdName = JSON.stringify(popIdName);
+    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+
+    var listSelPop =
+      '<table id="list_reference_pops_table" style="width:100%; text-align:left"><tr>' +
+      "<th>List-based training population</th>" +
+      "<th>Models</th>" +
+      "</tr>" +
+      "<tr>" +
+      "<td>" +
+      '<a href="/solgs/population/' +
+      modelId +
+      '" onclick="javascript:loadPopulationPage(' +
+      url +
+      "," +
+      listIdArg +
+      "," +
+      listSource +
+      ')">' +
+      "<data>" +
+      hiddenInput +
+      "</data>" +
+      listName +
+      "</a>" +
+      "</td>" +
+      '<td id="list_reference_page_' +
+      modelId +
+      '">' +
+      '<a href="/solgs/population/' +
+      modelId +
+      '" onclick="javascript:loadPopulationPage(' +
+      url +
+      "," +
+      listIdArg +
+      "," +
+      listSource +
+      ')">' +
+      "[ Build model ]" +
+      "</a>" +
+      "</td></tr></table>";
+
+    return listSelPop;
+  },
+
+  loadPopulationPage: function (url, listId, listSource) {
+    var genoList = this.getListTypeTrainingPopDetail(listId);
+    var listName = genoList.name;
+    var modelId = this.getModelId(listId);
+
+    jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
+    jQuery.blockUI({ message: "Please wait.." });
+
+    jQuery.ajax({
+      type: "POST",
+      url: url,
+      dataType: "json",
+      data: {
+        list_reference: 1,
+        model_id: modelId,
+        list_source: listSource,
+        list_name: listName,
+      },
+      success: function (response) {
+        if (response.status == "success") {
+          jQuery.unblockUI();
+        } else {
+          alert("Fail: Error occured calculating GEBVs for the list of selection genotypes.");
+          jQuery.unblockUI();
+        }
+      },
+      error: function (response) {
+        alert("error: " + res.responseText);
+      },
+    });
   },
 };
 
@@ -179,97 +271,6 @@ jQuery.fn.doesExist = function () {
   return jQuery(this).length > 0;
 };
 
-function getUserUploadedRefPop(listId) {
-  var genoList = this.getListTypeTrainingPopDetail(listId);
-  var listName = genoList.name;
-  var list = genoList.list;
-  var modelId = getModelId(listId);
-
-  var url = "'/solgs/population/" + modelId + "'";
-  var listIdArg = "'" + listId + "'";
-  var listSource = "'from_db'";
-  var popIdName = { id: modelId, name: listName };
-  popIdName = JSON.stringify(popIdName);
-  var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
-
-  var listSelPop =
-    '<table id="list_reference_pops_table" style="width:100%; text-align:left"><tr>' +
-    "<th>List-based training population</th>" +
-    "<th>Models</th>" +
-    "</tr>" +
-    "<tr>" +
-    "<td>" +
-    '<a href="/solgs/population/' +
-    modelId +
-    '" onclick="javascript:loadPopulationPage(' +
-    url +
-    "," +
-    listIdArg +
-    "," +
-    listSource +
-    ')">' +
-    "<data>" +
-    hiddenInput +
-    "</data>" +
-    listName +
-    "</a>" +
-    "</td>" +
-    '<td id="list_reference_page_' +
-    modelId +
-    '">' +
-    '<a href="/solgs/population/' +
-    modelId +
-    '" onclick="javascript:loadPopulationPage(' +
-    url +
-    "," +
-    listIdArg +
-    "," +
-    listSource +
-    ')">' +
-    "[ Build model ]" +
-    "</a>" +
-    "</td></tr></table>";
-
-  return listSelPop;
-}
-
-function loadPopulationPage(url, listId, listSource) {
-  var genoList = this.getListTypeTrainingPopDetail(listId);
-  var listName = genoList.name;
-  var modelId = getModelId(listId);
-
-  jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-  jQuery.blockUI({ message: "Please wait.." });
-
-  jQuery.ajax({
-    type: "POST",
-    url: url,
-    dataType: "json",
-    data: {
-      list_reference: 1,
-      model_id: modelId,
-      list_source: listSource,
-      list_name: listName,
-    },
-    success: function (response) {
-      if (response.status == "success") {
-        jQuery.unblockUI();
-      } else {
-        alert("Fail: Error occured calculating GEBVs for the list of selection genotypes.");
-        jQuery.unblockUI();
-      }
-    },
-    error: function (response) {
-      alert("error: " + res.responseText);
-    },
-  });
-}
-
-function getModelId(listId) {
-  var modelId = "list_" + listId;
-  return modelId;
-}
-
 jQuery(document).ready(function () {
   solGS.listTypeTrainingPopulation.populateTrainingPopsMenu();
 });
@@ -290,10 +291,17 @@ jQuery(document).ready(function () {
           if (listDetail.type.match(/plots/)) {
             solGS.listTypeTrainingPopulation.askTrainingJobQueueing(selectedPop.id);
           } else {
-            var trialsList = listDetail.list;
+            // var trialsList = listDetail.list;
             var trialsNames = listDetail.list_elements_names;
 
-            solGS.listTypeTrainingPopulation.loadTrialListTypeTrainingPop(trialsNames);
+            solGS.listTypeTrainingPopulation
+              .loadTrialListTypeTrainingPop(trialsNames)
+              .done(function (res) {
+                solGS.combinedTrials.getCombinedPopsId(res.trials_ids);
+              })
+              .fail(function (res) {
+                alert("Error occured querying for trials ids");
+              });
           }
         } else {
           solGS.dataset.datasetTrainingPop(selectedPop.id, selectedPop.name);

From dcd356ed377a600cc1acbd5ba3b382fa5b2f3be3 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 7 Jun 2023 14:34:00 +0200
Subject: [PATCH 33/61] simplify and cleanup

---
 .../solGS/listTypeSelectionPopulation.js      | 291 +++---------------
 1 file changed, 48 insertions(+), 243 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index cf7aba3e5b..fce4355b2f 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -7,7 +7,7 @@ Isaak Y Tecle
 iyt2@cornell.edu
 */
 
-JSAN.use("jquery.blockUI");
+// JSAN.use("jquery.blockUI");
 
 var solGS = solGS || function solGS() {};
 
@@ -19,31 +19,14 @@ solGS.listTypeSelectionPopulation = {
     var args = this.createSelectionReqArgs(listId);
     args = JSON.stringify(args);
 
-    jQuery.ajax({
+    var checkPredicted = jQuery.ajax({
       type: "POST",
       dataType: "json",
       data: { arguments: args },
       url: "/solgs/check/predicted/list/selection",
-      success: function (response) {
-        args = JSON.parse(args);
-
-        if (response.output) {
-          solGS.listTypeSelectionPopulation.displayPredictedListTypeSelectionPops(
-            args,
-            response.output
-          );
-
-          if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
-            solGS.sIndex.populateSindexMenu();
-            solGS.correlation.populateGenCorrMenu();
-            solGS.geneticGain.ggSelectionPopulations();
-            solGS.cluster.listClusterPopulations();
-          }
-        } else {
-          solGS.listTypeSelectionPopulation.askSelectionJobQueueing(listId);
-        }
-      },
     });
+
+    return checkPredicted;
   },
 
   getSelectionListElementsNames: function (list) {
@@ -81,7 +64,8 @@ solGS.listTypeSelectionPopulation = {
     var protocolId = args.genotyping_protocol_id;
 
     var hostName = window.location.protocol + "//" + window.location.host;
-    var page = hostName + "/solgs/selection/" + selectionPopId + "/model/" + modelId;
+    var page =
+      hostName + "/solgs/selection/" + selectionPopId + "/model/" + modelId + "/gp/" + protocolId;
 
     solGS.waitPage(page, args);
   },
@@ -90,17 +74,14 @@ solGS.listTypeSelectionPopulation = {
     if (typeof listId == "number") {
       var genoList = this.getListTypeSelectionPopDetail(listId);
       var listName = genoList.name;
-      var list = genoList.list;
-      var modelId = this.getModelId();
-      var traitId = this.getTraitId();
-
-      var dataSetType = this.trainingDataSetType();
 
-      var popType = "list_prediction";
+      var modelArgs = solGS.getModelArgs();
+      var modelId = modelArgs.training_pop_id;
+      var dataSetType = modelArgs.data_set_type;
+      var popType = "list_selection";
 
       var selectionPopId = "list_" + listId;
-      var protocolId = jQuery("#genotyping_protocol_id").val();
-
+      var protocolId = modelArgs.genotyping_protocol_id;
       var trainingTraitsIds = solGS.getTrainingTraitsIds();
 
       var args = {
@@ -119,167 +100,25 @@ solGS.listTypeSelectionPopulation = {
     }
   },
 
-  getGenotypesList: function (listId) {
-    var list = new CXGN.List();
-    var genotypesList;
-
-    if (!listId == "") {
-      genotypesList = list.getListData(listId);
-    }
-
-    var listName = list.listNameById(listId);
-    var listType = list.getListType(listId);
-
-    return { name: listName, listId: listId, list_type: listType };
-  },
-
-  loadGenotypesListTypeSelectionPop: function (args) {
-    var listDetail = this.getListTypeSelectionPopDetail(args.list_id);
-
-    if (window.Prototype) {
-      delete Array.prototype.toJSON;
-    }
-
-    args = JSON.stringify(args);
-    var len = listDetail.elements_count;
-
-    if (len === 0) {
-      alert("The list is empty. Please select a list with content.");
-    } else {
-      jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-      jQuery.blockUI({ message: "Please wait.." });
-
-      jQuery.ajax({
-        type: "POST",
-        dataType: "json",
-        data: { arguments: args },
-        url: "/solgs/load/genotypes/list/selection",
-        success: function (response) {
-          if (response.status == "success") {
-            args = JSON.parse(args);
-            var modelId = args.training_pop_id;
-            var traitId = args.trait_id;
-            var selPopId = args.selection_pop_id;
-            var listId = args.list_id;
-
-            if (window.location.href.match(/solgs\/trait\//)) {
-              window.location =
-                "/solgs/selection/" + selPopId + "/model/" + modelId + "/trait/" + traitId;
-              jQuery.unblockUI();
-            } else if (window.location.href.match(/solgs\/model\/combined\/populations\//)) {
-              window.location =
-                "/solgs/selection/" + selPopId + "/model/combined/" + modelId + "/trait/" + traitId;
-              jQuery.unblockUI();
-            } else {
-              displayPredictedListTypeSelectionPops(args, response.output);
-              solGS.sIndex.populateSindexMenu();
-              solGS.correlation.populateGenCorrMenu();
-              jQuery.unblockUI();
-            }
-          } else {
-            alert("fail: Error occured while querying for the genotype data of the accessions.");
-            jQuery.unblockUI();
-          }
-        },
-        error: function (res) {
-          alert("Error occured while querying for the genotype data of the accessions.");
-          jQuery.unblockUI();
-        },
-      });
-    }
-  },
-
-  predictGenotypesListSelectionPop: function (args) {
-    var modelId = args.training_pop_id;
-    var traitId = args.trait_id;
-    var selPopId = args.selection_pop_id;
-
-    var url = "/solgs/selection/" + selPopId + "/model/" + modelId;
-
-    jQuery.ajax({
-      dataType: "json",
-      type: "POST",
-      data: { trait_id: traitId, list_source: "from_db", list_prediction: 1 },
-      url: url,
-      success: function (res) {
-        if (res.status == "success") {
-          window.location =
-            "/solgs/selection/" + selPopId + "/model/" + modelId + "/trait/" + traitId;
-        } else {
-          window.location = window.location.href;
-        }
-      },
-    });
-
-    jQuery.unblockUI();
-  },
-
-  getModelId: function () {
-    var modelId;
-    var modelIdExists = jQuery("#model_id").doesExist();
-    var comboPopsIdExists = jQuery("#combo_pops_id").doesExist();
-    var popIdExists = jQuery("#population_id").doesExist();
-
-    if (jQuery("#model_id").val()) {
-      modelId = jQuery("#model_id").val();
-    } else if (jQuery("#population_id").val()) {
-      modelId = jQuery("#population_id").val();
-    } else if (jQuery("#combo_pops_id").val()) {
-      modelId = jQuery("#combo_pops_id").val();
-    }
-
-    return modelId;
-  },
-
-  trainingDataSetType: function () {
-    var dataSetType;
-    var referer = document.URL;
-
-    if (referer.match(/\/combined\//)) {
-      dataSetType = "combined_populations";
-    } else {
-      dataSetType = "single_population";
-    }
-
-    return dataSetType;
-  },
-
-  getTraitId: function () {
-    var traitId;
-    var traitIdExists = jQuery("#trait_id").doesExist();
-
-    if (traitIdExists == true) {
-      traitId = jQuery("#trait_id").val();
-    }
-
-    return traitId;
-  },
-
   displayPredictedListTypeSelectionPops: function (args, output) {
     var listName = args.list_name;
     var listId = args.list_id;
-    var traitId = args.trait_id;
-    var selectionPopId = args.selection_pop_id;
-    var trainingPopId = args.training_pop_id;
 
-    var url = "/solgs/selection/" + selectionPopId + "/model/" + trainingPopId;
-    var listIdArg = "'" + listId + "'";
-    var listSource = "'from_db'";
     var popIdName = { id: "list_" + listId, name: listName, pop_type: "list_selection" };
     popIdName = JSON.stringify(popIdName);
     var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
 
-    var predictedListTypeSelectionPops = jQuery("#list_type_selection_pops_table").doesExist();
+    var tableId = "list_type_selection_pops_table";
+    var trId = "list_selection_" + listId;
+    var predictedListTypeSelectionPops = jQuery(`#${tableId}`).doesExist();
 
     if (predictedListTypeSelectionPops == false) {
       var predictedListTypeSelectionTable =
-        '<table id="list_type_selection_pops_table" class="table"><thead><tr>' +
+        `<table id="${tableId}" class="table"><thead><tr>` +
         "<th>List-based selection population</th>" +
         "<th>View GEBVs</th>" +
         "</tr></thead><tbody>" +
-        '<tr id="list_prediction_output_' +
-        listId +
-        '">' +
+        `<tr id="${trId}">` +
         "<td>" +
         "<b>" +
         listName +
@@ -293,17 +132,9 @@ solGS.listTypeSelectionPopulation = {
 
       jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
     } else {
-      var listIdArg = "'" + listId + "'";
-      var listSource = "'from_db'";
-
-      var popIdName = { id: "list_" + listId, name: listName, pop_type: "list_selection" };
-      popIdName = JSON.stringify(popIdName);
-      var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
-
       var addRow =
-        '<tr id="list_prediction_output_' +
-        listId +
-        '"><td>' +
+        `<tr id="${trId}">` +
+        "<td>" +
         "<b>" +
         listName +
         "</td>" +
@@ -313,14 +144,13 @@ solGS.listTypeSelectionPopulation = {
         output +
         "</td></tr>";
 
-      var trId = "#list_prediction_output_" + listId;
-      var samePop = jQuery(trId).doesExist();
+      var samePop = jQuery(`#${trId}`).doesExist();
 
       if (samePop == false) {
-        jQuery("#list_type_selection_pops_table tr:last").after(addRow);
+        jQuery(`#${tableId} tr:last`).after(addRow);
       } else {
-        jQuery(trId).remove();
-        jQuery("#list_type_selection_pops_table").append(addRow).show();
+        jQuery(`#${trId}`).remove();
+        jQuery(`#${tableId}`).append(addRow).show();
       }
     }
   },
@@ -370,55 +200,6 @@ solGS.listTypeSelectionPopulation = {
     }
     return popsList;
   },
-
-  loadPredictionOutput: function (url, listId, listSource) {
-    var traitId = this.getTraitId();
-    var modelId = this.getModelId();
-
-    jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-    jQuery.blockUI({ message: "Please wait.." });
-
-    jQuery.ajax({
-      type: "POST",
-      url: url,
-      dataType: "json",
-      data: {
-        list_prediction: 1,
-        trait_id: traitId,
-        model_id: modelId,
-        prediction_id: listId,
-        list_source: listSource,
-      },
-
-      success: function (response) {
-        if (response.status == "success") {
-          var tdId = "#list_prediction_output_" + listId;
-          jQuery(tdId).html(response.output);
-
-          var page = document.URL;
-
-          if (page.match("/traits/all/population/") != null) {
-            solGS.sIndex.populateSindexMenu();
-            solGS.correlation.populateGenCorrMenu();
-          }
-
-          jQuery.unblockUI();
-        } else {
-          if (response.status == "failed") {
-            alert("Error occured while uploading the list of selection genotypes.");
-          } else {
-            alert(response.status);
-          }
-
-          jQuery.unblockUI();
-        }
-      },
-
-      error: function (response) {
-        alert("error: " + res.responseText);
-      },
-    });
-  },
 };
 
 jQuery.fn.doesExist = function () {
@@ -430,7 +211,8 @@ jQuery(document).ready(function () {
 });
 
 jQuery(document).ready(function () {
-  jQuery("#list_type_selection_pops_select").change(function () {
+  var menuId = solGS.listTypeSelectionPopulation.selectionPopsSelectMenuId;
+  jQuery(`${menuId}`).change(function () {
     var selectedPop = jQuery("option:selected", this).data("pop");
     if (selectedPop.id) {
       jQuery(" #list_type_selection_pop_go_btn").click(function () {
@@ -443,7 +225,30 @@ jQuery(document).ready(function () {
           );
 
           if (listDetail.type.match(/accessions/)) {
-            solGS.listTypeSelectionPopulation.checkPredictedListSelection(selectedPop.id);
+            solGS.listTypeSelectionPopulation
+              .checkPredictedListSelection(selectedPop.id)
+              .done(function (res) {
+                var args = solGS.listTypeSelectionPopulation.createSelectionReqArgs(selectedPop.id);
+
+                if (res.output) {
+                  solGS.listTypeSelectionPopulation.displayPredictedListTypeSelectionPops(
+                    args,
+                    res.output
+                  );
+
+                  if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
+                    solGS.sIndex.populateSindexMenu();
+                    solGS.correlation.populateGenCorrMenu();
+                    solGS.geneticGain.ggSelectionPopulations();
+                    solGS.cluster.listClusterPopulations();
+                  }
+                } else {
+                  solGS.listTypeSelectionPopulation.askSelectionJobQueueing(listId);
+                }
+              })
+              .fail(function () {
+                alert("Error occured checking if the selection population has predicted output.");
+              });
           } else {
             //TO-DO
             //	var trialsList = listDetail.list;

From 5a5164ac1f721e430e1bf38cf458b606e9e65e5d Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Thu, 8 Jun 2023 14:45:32 +0200
Subject: [PATCH 34/61] clean up

---
 .../solGS/listTypeTrainingPopulation.js       |  2 +-
 lib/SGN/Controller/solGS/List.pm              | 43 ++-----------------
 2 files changed, 5 insertions(+), 40 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index 4dc947843b..aa91a95ece 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -1,6 +1,6 @@
 /**
 
-For training populations  from list of plots and trials.
+For training populations options from list of plots and trials and datasets.
 
 Isaak Y Tecle 
 iyt2@cornell.edu
diff --git a/lib/SGN/Controller/solGS/List.pm b/lib/SGN/Controller/solGS/List.pm
index c92a9b94b2..69ef30e28d 100644
--- a/lib/SGN/Controller/solGS/List.pm
+++ b/lib/SGN/Controller/solGS/List.pm
@@ -57,14 +57,15 @@ sub generate_check_value : Path('/solgs/generate/checkvalue') Args(0) {
 
 }
 
-sub check_predicted_list_selection :Path('/solgs/check/predicted/list/selection') Args(0) {
+sub check_predicted_list_selection :
+  Path('/solgs/check/predicted/list/selection') Args(0) {
     my ( $self, $c ) = @_;
 
     my $args = $c->req->param('arguments');
     $c->controller('solGS::Utils')->stash_json_args( $c, $args );
 
-    my $training_pop_id = $c->stash->{training_pop_id}; 
-    my $selection_pop_id = $c->stash->{selection_pop_id};    
+    my $training_pop_id  = $c->stash->{training_pop_id};
+    my $selection_pop_id = $c->stash->{selection_pop_id};
 
     $c->controller('solGS::Download')
       ->selection_prediction_download_urls( $c, $training_pop_id,
@@ -79,42 +80,6 @@ sub check_predicted_list_selection :Path('/solgs/check/predicted/list/selection'
 
 }
 
-sub load_list_selection_pop : Path('/solgs/load/genotypes/list/selection') Args(0) {
-    my ( $self, $c ) = @_;
-
-    my $args = $c->req->param('arguments');
-    $c->controller('solGS::Utils')->stash_json_args( $c, $args );
-
-    my $training_pop_id = $c->stash->{training_pop_id};   
-    my $selection_pop_id = $c->stash->{selection_pop_id};    
-    my $protocol_id = $c->stash->{genotyping_protocol_id};
-
-    $self->get_genotypes_list_details($c);
-
-    my $genotypes_list = $c->stash->{genotypes_list};
-    my $genotypes_ids  = $c->stash->{genotypes_ids};
-
-    $self->genotypes_list_genotype_file( $c, $selection_pop_id, $protocol_id );
-    my $genotype_file = $c->stash->{genotypes_list_genotype_file};
-
-    $self->create_list_population_metadata_file( $c, $selection_pop_id );
-
-    my $ret->{status} = 'failed';
-
-    if ( -s $genotype_file ) {
-        $self->predict_list_selection_gebvs($c);
-
-        $ret->{status} = $c->stash->{status};
-        $ret->{output} = $c->stash->{selection_prediction_download};
-    }
-
-    $ret = to_json($ret);
-
-    $c->res->content_type('application/json');
-    $c->res->body($ret);
-
-}
-
 sub get_trial_id : Path('/solgs/get/trial/id') Args(0) {
     my ( $self, $c ) = @_;
 

From 992c974abb7ae9593c0d4b2d57b0a4cfa709832d Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 9 Jun 2023 15:45:25 +0200
Subject: [PATCH 35/61] draft solGSList class

---
 js/source/legacy/solGS/List.js | 50 ++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 js/source/legacy/solGS/List.js

diff --git a/js/source/legacy/solGS/List.js b/js/source/legacy/solGS/List.js
new file mode 100644
index 0000000000..7422aafbe1
--- /dev/null
+++ b/js/source/legacy/solGS/List.js
@@ -0,0 +1,50 @@
+/**
+
+A list object template with methods for getting details about the list.
+Isaak Y Tecle 
+iyt2@cornell.edu
+*/
+
+class solGSList {
+
+    constructor(listId) {
+        this.listId = listId;
+        this.listObj = new CXGN.List();
+
+    }
+
+    getListDetail() {  
+    
+        return {
+          name: this.listObj.listNameById(this.listId),
+          type: this.listObj.getListType(this.listId),
+          list_id: this.listId,
+        };
+    }
+
+    getListElementsIds() {
+        var listData = this.listObj.getListData(this.listId);
+        var listElems = listData.elements;
+        var ids = [];
+        for (var i = 0; i < listElems.length; i++) {
+          ids.push(listElems[i][0]);
+        }
+    
+        return ids;
+      }
+
+      getListElementsNames () {
+        var listData = this.listObj.getListData(this.listId);
+        var listElems = listData.elements;
+        var names = [];
+        for (var i = 0; i < listElems.length; i++) {
+          names.push(listElems[i][1]);
+        }
+    
+        return names;
+      }
+     
+};
+
+
+  

From 0de50ac91634adf5faebb86cbfa253560282df01 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 9 Jun 2023 15:48:29 +0200
Subject: [PATCH 36/61] replace redundunt code with solGSList object

---
 js/source/legacy/solGS/List.js                |  69 +++++----
 .../solGS/listTypeSelectionPopulation.js      |  36 +----
 .../solGS/listTypeTrainingPopulation.js       | 131 ++++++++++--------
 .../search/list_type_training_population.mas  |   2 +-
 4 files changed, 109 insertions(+), 129 deletions(-)

diff --git a/js/source/legacy/solGS/List.js b/js/source/legacy/solGS/List.js
index 7422aafbe1..431f68ffc4 100644
--- a/js/source/legacy/solGS/List.js
+++ b/js/source/legacy/solGS/List.js
@@ -6,45 +6,38 @@ iyt2@cornell.edu
 */
 
 class solGSList {
-
-    constructor(listId) {
-        this.listId = listId;
-        this.listObj = new CXGN.List();
-
-    }
-
-    getListDetail() {  
-    
-        return {
-          name: this.listObj.listNameById(this.listId),
-          type: this.listObj.getListType(this.listId),
-          list_id: this.listId,
-        };
+  constructor(listId) {
+    this.listId = listId;
+    this.listObj = new CXGN.List();
+  }
+
+  getListDetail() {
+    return {
+      name: this.listObj.listNameById(this.listId),
+      type: this.listObj.getListType(this.listId),
+      list_id: this.listId,
+    };
+  }
+
+  getListElementsIds() {
+    var listData = this.listObj.getListData(this.listId);
+    var listElems = listData.elements;
+    var ids = [];
+    for (var i = 0; i < listElems.length; i++) {
+      ids.push(listElems[i][0]);
     }
 
-    getListElementsIds() {
-        var listData = this.listObj.getListData(this.listId);
-        var listElems = listData.elements;
-        var ids = [];
-        for (var i = 0; i < listElems.length; i++) {
-          ids.push(listElems[i][0]);
-        }
-    
-        return ids;
-      }
-
-      getListElementsNames () {
-        var listData = this.listObj.getListData(this.listId);
-        var listElems = listData.elements;
-        var names = [];
-        for (var i = 0; i < listElems.length; i++) {
-          names.push(listElems[i][1]);
-        }
-    
-        return names;
-      }
-     
-};
+    return ids;
+  }
 
+  getListElementsNames() {
+    var listData = this.listObj.getListData(this.listId);
+    var listElems = listData.elements;
+    var names = [];
+    for (var i = 0; i < listElems.length; i++) {
+      names.push(listElems[i][1]);
+    }
 
-  
+    return names;
+  }
+}
diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index fce4355b2f..021eb38d4f 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -29,33 +29,6 @@ solGS.listTypeSelectionPopulation = {
     return checkPredicted;
   },
 
-  getSelectionListElementsNames: function (list) {
-    var names = [];
-    for (var i = 0; i < list.length; i++) {
-      names.push(list[i][1]);
-    }
-
-    return names;
-  },
-
-  getListTypeSelectionPopDetail: function (listId) {
-    if (typeof listId == "number") {
-      var list = new CXGN.List();
-
-      var listData;
-      var listType;
-      var listName;
-
-      if (listId) {
-        listData = list.getListData(listId);
-        listType = list.getListType(listId);
-        listName = list.listNameById(listId);
-        elemCount = listData.elements;
-      }
-
-      return { name: listName, list_id: listId, type: listType, elements_count: elemCount };
-    }
-  },
 
   askSelectionJobQueueing: function (listId) {
     var args = this.createSelectionReqArgs(listId);
@@ -72,8 +45,9 @@ solGS.listTypeSelectionPopulation = {
 
   createSelectionReqArgs: function (listId) {
     if (typeof listId == "number") {
-      var genoList = this.getListTypeSelectionPopDetail(listId);
-      var listName = genoList.name;
+      const listObj = new solGSList(listId);
+      var listDetail = listObj.getListDetail();
+      var listName = listDetail.name;
 
       var modelArgs = solGS.getModelArgs();
       var modelId = modelArgs.training_pop_id;
@@ -223,7 +197,9 @@ jQuery(document).ready(function () {
           var listDetail = solGS.listTypeSelectionPopulation.getListTypeSelectionPopDetail(
             selectedPop.id
           );
-
+          const listObj = new solGSList(selectedPop.id);
+          var listDetail = listObj.getListDetail();
+    
           if (listDetail.type.match(/accessions/)) {
             solGS.listTypeSelectionPopulation
               .checkPredictedListSelection(selectedPop.id)
diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index aa91a95ece..7ac5bdaf41 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -6,24 +6,12 @@ Isaak Y Tecle
 iyt2@cornell.edu
 */
 
-// JSAN.use("CXGN.List");
-JSAN.use("jquery.blockUI");
-
 var solGS = solGS || function solGS() {};
 
 solGS.listTypeTrainingPopulation = {
   trainingPopsDiv: "#list_type_training_pops_select_div",
   trainingPopsSelectMenuId: "#list_type_training_pops_select",
 
-  getTrainingListElementsNames: function (list) {
-    var names = [];
-    for (var i = 0; i < list.length; i++) {
-      names.push(list[i][1]);
-    }
-
-    return names;
-  },
-
   populateTrainingPopsMenu: function () {
     var list = new CXGN.List();
     var lists = list.getLists(["plots", "trials"]);
@@ -50,40 +38,6 @@ solGS.listTypeTrainingPopulation = {
     jQuery(trainingPopsDiv).append(menuElem).show();
   },
 
-  getTrainingListElementsIds: function (list) {
-    var ids = [];
-    for (var i = 0; i < list.length; i++) {
-      ids.push(list[i][0]);
-    }
-
-    return ids;
-  },
-
-  getListTypeTrainingPopDetail: function (listId) {
-    var list = new CXGN.List();
-
-    var listData;
-    var listType;
-    var listName;
-
-    if (listId) {
-      listData = list.getListData(listId);
-      listType = list.getListType(listId);
-      listName = list.listNameById(listId);
-      listElements = listData.elements;
-
-      listElementsNames = this.getTrainingListElementsNames(listElements);
-      listElementsIds = this.getTrainingListElementsIds(listElements);
-    }
-
-    return {
-      name: listName,
-      type: listType,
-      list_id: listId,
-      list_elements_names: listElementsNames,
-      list_elements_ids: listElementsIds,
-    };
-  },
 
   loadTrialListTypeTrainingPop: function (trialsNames) {
     var trialsList = jQuery.ajax({
@@ -112,9 +66,10 @@ solGS.listTypeTrainingPopulation = {
   },
 
   createTrainingReqArgs: function (listId) {
-    var genoList = this.getListTypeTrainingPopDetail(listId);
-    var listName = genoList.name;
-    var list = genoList.list;
+    const listObj = new solGSList(listId);
+    var listDetail = listObj.getListDetail();
+    var listName = listDetail.name;
+
     var popId = this.getModelId(listId);
     var protocolId = jQuery("#genotyping_protocol_id").val();
     var popType = "list_training";
@@ -134,7 +89,6 @@ solGS.listTypeTrainingPopulation = {
 
   loadPlotListTypeTrainingPop: function (listId) {
     var args = this.createTrainingReqArgs(listId);
-    var popId = args.training_pop_id;
 
     if (window.Prototype) {
       delete Array.prototype.toJSON;
@@ -181,9 +135,9 @@ solGS.listTypeTrainingPopulation = {
   },
 
   getUserUploadedRefPop: function (listId) {
-    var genoList = this.getListTypeTrainingPopDetail(listId);
-    var listName = genoList.name;
-    var list = genoList.list;
+    const listObj = new solGSList(listId);
+    var listDetail = listObj.getListDetail();
+    var listName = listDetail.name;
     var modelId = this.getModelId(listId);
 
     var url = "'/solgs/population/" + modelId + "'";
@@ -234,9 +188,68 @@ solGS.listTypeTrainingPopulation = {
     return listSelPop;
   },
 
+  displayListTypeTrainingPops: function (listId) {
+    const listObj = new solGSList(listId);
+    var listDetail = listObj.getListDetail();
+    var listName = listDetail.name;
+    var modelId = this.getModelId(listId);
+
+
+    var popIdName = { id: modelId, name: listName, pop_type: "list_training" };
+    popIdName = JSON.stringify(popIdName);
+    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+
+    var tableId = "list_type_training_pops_table";
+    var trId = "list_training_" + listId;
+    var listTypeSelectionPops = jQuery(`#${tableId}`).doesExist();
+
+    if (listTypeSelectionPops == false) {
+      var listTypeTrainingTable =
+        `<table id="${tableId}" class="table"><thead><tr>` +
+        "<th>List-based tranining population</th>" +
+        "<th>View Population</th>" +
+        "</tr></thead><tbody>" +
+        `<tr id="${trId}">` +
+        "<td>" +
+        "<b>" +
+        listName +
+        "</b>" +
+        "</td>" +
+        "<td><data>" +
+        hiddenInput +
+        "</data>" +
+        output +
+        "</td></tr></tbody></table>";
+
+      jQuery("#list_type_training_pops_selected").append(listTypeTrainingTable).show();
+    } else {
+      var addRow =
+        `<tr id="${trId}">` +
+        "<td>" +
+        "<b>" +
+        listName +
+        "</td>" +
+        "<td> <data>" +
+        hiddenInput +
+        "</data>" +
+        output +
+        "</td></tr>";
+
+      var samePop = jQuery(`#${trId}`).doesExist();
+
+      if (samePop == false) {
+        jQuery(`#${tableId} tr:last`).after(addRow);
+      } else {
+        jQuery(`#${trId}`).remove();
+        jQuery(`#${tableId}`).append(addRow).show();
+      }
+    }
+  },
+
   loadPopulationPage: function (url, listId, listSource) {
-    var genoList = this.getListTypeTrainingPopDetail(listId);
-    var listName = genoList.name;
+    const listObj = new solGSList(listId);
+    var listDetail = listObj.getListDetail();
+    var listName = listDetail.name;
     var modelId = this.getModelId(listId);
 
     jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
@@ -284,15 +297,13 @@ jQuery(document).ready(function () {
           typeof selectedPop.data_str === "undefined" ||
           !selectedPop.data_str.match(/dataset/i)
         ) {
-          var listDetail = solGS.listTypeTrainingPopulation.getListTypeTrainingPopDetail(
-            selectedPop.id
-          );
+          const list = new solGSList(selectedPop.id);
+          var listDetail = list.getListDetail();
 
           if (listDetail.type.match(/plots/)) {
             solGS.listTypeTrainingPopulation.askTrainingJobQueueing(selectedPop.id);
           } else {
-            // var trialsList = listDetail.list;
-            var trialsNames = listDetail.list_elements_names;
+            var trialsNames = list.getListElementsNames();
 
             solGS.listTypeTrainingPopulation
               .loadTrialListTypeTrainingPop(trialsNames)
diff --git a/mason/solgs/search/list_type_training_population.mas b/mason/solgs/search/list_type_training_population.mas
index 54d7862797..f0a1d75ed3 100644
--- a/mason/solgs/search/list_type_training_population.mas
+++ b/mason/solgs/search/list_type_training_population.mas
@@ -20,7 +20,7 @@ my $referer = $c->req->path;
 my $search_params = '?dsp=genotyping_protocols,trials|plots,traits,accessions&dsr=/' . $referer;
 </%perl>
 
-<& /util/import_javascript.mas, classes => ["solGS.listTypeTrainingPopulation"] &>
+<& /util/import_javascript.mas, classes => ["CXGN.List", "solGS.List", "solGS.listTypeTrainingPopulation"] &>
 
 <&| /page/info_section.mas, 
     collapsible => 1, 

From 2af275bfdac374f40fdf2ddc14ce6821c2d7f4d3 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 12 Jun 2023 12:03:40 +0200
Subject: [PATCH 37/61] load List.js lib

---
 mason/solgs/search/list_type_selection_population.mas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mason/solgs/search/list_type_selection_population.mas b/mason/solgs/search/list_type_selection_population.mas
index 437e0dff30..51e76c259f 100644
--- a/mason/solgs/search/list_type_selection_population.mas
+++ b/mason/solgs/search/list_type_selection_population.mas
@@ -21,7 +21,7 @@ my $referer = $c->req->path;
 my $search_params = '?dsp=genotyping_protocols,trials|accessions&dsr=/' . $referer;
 </%perl>
 
-<& /util/import_javascript.mas, classes => ["solGS.listTypeSelectionPopulation"] &>
+<& /util/import_javascript.mas, classes => ["solGS.List", "solGS.listTypeSelectionPopulation"] &>
 
 <& /solgs/tools/select_menu.mas,
 analysis_type => 'list_type_selection',

From 22534d6f4e8740a2dfd2e4f0d3052d0f4d971229 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 12 Jun 2023 12:04:12 +0200
Subject: [PATCH 38/61] clean up

---
 js/source/legacy/solGS/listTypeSelectionPopulation.js | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index 021eb38d4f..1a5978c6c6 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -194,9 +194,7 @@ jQuery(document).ready(function () {
           typeof selectedPop.data_str === "undefined" ||
           !selectedPop.data_str.match(/dataset/i)
         ) {
-          var listDetail = solGS.listTypeSelectionPopulation.getListTypeSelectionPopDetail(
-            selectedPop.id
-          );
+
           const listObj = new solGSList(selectedPop.id);
           var listDetail = listObj.getListDetail();
     

From 01e7a05a6e75a7e05e0d82a5c3c979dbb3b207ff Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 12 Jun 2023 15:01:50 +0200
Subject: [PATCH 39/61] refactor redundant code

---
 js/source/legacy/solGS/Dataset.js             | 86 ++-----------------
 .../solGS/listTypeSelectionPopulation.js      | 41 +++------
 2 files changed, 20 insertions(+), 107 deletions(-)

diff --git a/js/source/legacy/solGS/Dataset.js b/js/source/legacy/solGS/Dataset.js
index 46f3f2ca56..428dae677e 100644
--- a/js/source/legacy/solGS/Dataset.js
+++ b/js/source/legacy/solGS/Dataset.js
@@ -176,7 +176,9 @@ solGS.dataset = {
       dataset_name: datasetName,
       training_pop_id: trainingPopDetails.training_pop_id,
       selection_pop_id: selectionPopId,
+      selection_pop_name: datasetName,
       training_traits_ids: trainingTraitsIds,
+      population_type: 'dataset_selection',
       data_set_type: trainingPopDetails.data_set_type,
       genotyping_protocol_id: protocolId,
     };
@@ -212,7 +214,10 @@ solGS.dataset = {
           args = JSON.parse(args);
 
           if (response.output) {
-            solGS.dataset.displayPredictedDatasetTypeSelectionPops(args, response.output);
+            solGS.listTypeSelectionPopulation.displayPredictedListTypeSelectionPops(
+              args,
+              response.output
+            );
 
             if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
               solGS.sIndex.populateSindexMenu();
@@ -239,85 +244,6 @@ solGS.dataset = {
     solGS.waitPage(page, args);
   },
 
-  displayPredictedDatasetTypeSelectionPops: function (args, output) {
-    var datasetName = args.dataset_name;
-    var datasetId = args.dataset_id;
-
-    var traitId = args.trait_id;
-    var selectionPopId = args.selection_pop_id;
-    var trainingPopId = args.training_pop_id;
-
-    var url = "/solgs/selection/" + selectionPopId + "/model/" + trainingPopId;
-    var datasetIdArg = "'" + datasetId + "'";
-    var listSource = "'from_db'";
-    var popIdName = {
-      id: "dataset_" + datasetId,
-      name: datasetName,
-      pop_type: "dataset_selection",
-    };
-    popIdName = JSON.stringify(popIdName);
-    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
-
-    var predictedListTypeSelectionPops = jQuery("#list_type_selection_pops_table").doesExist();
-
-    if (predictedListTypeSelectionPops == false) {
-      var predictedListTypeSelectionTable =
-        '<table id="list_type_selection_pops_table" class="table"><thead><tr>' +
-        "<th>List-based selection population</th>" +
-        "<th>View GEBVs</th>" +
-        "</tr></thead><tbody>" +
-        '<tr id="list_prediction_output_' +
-        datasetId +
-        '">' +
-        "<td>" +
-        "<b>" +
-        datasetName +
-        "</b>" +
-        "</td>" +
-        "<td><data>" +
-        hiddenInput +
-        "</data>" +
-        output +
-        "</td></tr></tbody></table>";
-
-      jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
-    } else {
-      var datasetIdArg = "'" + datasetId + "'";
-      var datasetSource = "'from_db'";
-
-      var popIdName = {
-        id: "dataset_" + datasetId,
-        name: datasetName,
-        pop_type: "dataset_selection",
-      };
-      popIdName = JSON.stringify(popIdName);
-      var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
-
-      var addRow =
-        '<tr id="list_prediction_output_' +
-        datasetId +
-        '"><td>' +
-        "<b>" +
-        datasetName +
-        "</td>" +
-        "<td> <data>" +
-        hiddenInput +
-        "</data>" +
-        output +
-        "</td></tr>";
-
-      var trId = "#list_prediction_output_" + datasetId;
-      var samePop = jQuery(trId).doesExist();
-
-      if (samePop == false) {
-        jQuery("#list_type_selection_pops_table tr:last").after(addRow);
-      } else {
-        jQuery(trId).remove();
-        jQuery("#list_type_selection_pops_table").append(addRow).show();
-      }
-    }
-  },
-
   /////
 };
 /////
diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index 1a5978c6c6..10048675ca 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -65,6 +65,7 @@ solGS.listTypeSelectionPopulation = {
         data_set_type: dataSetType,
         training_pop_id: modelId,
         selection_pop_id: selectionPopId,
+        selection_pop_name: listName,
         population_type: popType,
         training_traits_ids: trainingTraitsIds,
         genotyping_protocol_id: protocolId,
@@ -75,15 +76,14 @@ solGS.listTypeSelectionPopulation = {
   },
 
   displayPredictedListTypeSelectionPops: function (args, output) {
-    var listName = args.list_name;
-    var listId = args.list_id;
+    var selPopName = args.selection_pop_name;
+    var selPopId = args.selection_pop_id;
 
-    var popIdName = { id: "list_" + listId, name: listName, pop_type: "list_selection" };
-    popIdName = JSON.stringify(popIdName);
-    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+    var popDetail = {id: selPopId, name: selPopName, pop_type: args.population_type};
+    popDetail= JSON.stringify(popDetail);
 
     var tableId = "list_type_selection_pops_table";
-    var trId = "list_selection_" + listId;
+    var trId = `${args.population_type}_${selPopId}`;
     var predictedListTypeSelectionPops = jQuery(`#${tableId}`).doesExist();
 
     if (predictedListTypeSelectionPops == false) {
@@ -92,31 +92,18 @@ solGS.listTypeSelectionPopulation = {
         "<th>List-based selection population</th>" +
         "<th>View GEBVs</th>" +
         "</tr></thead><tbody>" +
-        `<tr id="${trId}">` +
-        "<td>" +
-        "<b>" +
-        listName +
-        "</b>" +
-        "</td>" +
-        "<td><data>" +
-        hiddenInput +
-        "</data>" +
-        output +
-        "</td></tr></tbody></table>";
+        `<tr id='${trId}' data-list-selection-pop='${popDetail}'>` +
+        `<td><b>${selPopName}</b></td>` +
+        `<td>${output}</td>` +
+        "</tr></tbody></table>";
 
       jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
     } else {
       var addRow =
-        `<tr id="${trId}">` +
-        "<td>" +
-        "<b>" +
-        listName +
-        "</td>" +
-        "<td> <data>" +
-        hiddenInput +
-        "</data>" +
-        output +
-        "</td></tr>";
+        `<tr id='${trId}' data-list-selection-pop='${popDetail}'>` +
+        `<td><b> ${selPopName}</b></td>`  +
+        `<td>${output}</td>` +
+        "</tr>";
 
       var samePop = jQuery(`#${trId}`).doesExist();
 

From 3e209868d5a15a790df71c6b65adb79f21e624b0 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Tue, 13 Jun 2023 14:28:53 +0200
Subject: [PATCH 40/61] refactor and display selected list/dataset before
 querying for training
 datajs/source/legacy/solGS/listTypeTrainingPopulation.js

---
 .../solGS/listTypeTrainingPopulation.js       | 270 +++++-------------
 1 file changed, 74 insertions(+), 196 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index 7ac5bdaf41..4cc46d29b5 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -38,7 +38,6 @@ solGS.listTypeTrainingPopulation = {
     jQuery(trainingPopsDiv).append(menuElem).show();
   },
 
-
   loadTrialListTypeTrainingPop: function (trialsNames) {
     var trialsList = jQuery.ajax({
       type: "POST",
@@ -56,12 +55,12 @@ solGS.listTypeTrainingPopulation = {
     var protocolId = args.genotyping_protocol_id;
 
     var hostName = window.location.protocol + "//" + window.location.host;
+
     var page = hostName + "/solgs/population/" + modelId;
 
     if (protocolId) {
       page = page + "/gp/" + protocolId;
     }
-
     solGS.waitPage(page, args);
   },
 
@@ -71,7 +70,7 @@ solGS.listTypeTrainingPopulation = {
     var listName = listDetail.name;
 
     var popId = this.getModelId(listId);
-    var protocolId = jQuery("#genotyping_protocol_id").val();
+    var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId();
     var popType = "list_training";
 
     var args = {
@@ -80,6 +79,7 @@ solGS.listTypeTrainingPopulation = {
       analysis_type: "training_dataset",
       data_set_type: "single_population",
       training_pop_id: popId,
+      training_pop_name: listName,
       population_type: popType,
       genotyping_protocol_id: protocolId,
     };
@@ -87,196 +87,47 @@ solGS.listTypeTrainingPopulation = {
     return args;
   },
 
-  loadPlotListTypeTrainingPop: function (listId) {
-    var args = this.createTrainingReqArgs(listId);
-
-    if (window.Prototype) {
-      delete Array.prototype.toJSON;
-    }
-
-    args = JSON.stringify(args);
-
-    if (args.list.length === 0) {
-      alert("The list is empty. Please select a list with content.");
-    } else {
-      // jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-      // jQuery.blockUI({ message: "Please wait.." });
-
-      var plotsList = jQuery.ajax({
-        type: "POST",
-        dataType: "json",
-        data: { arguments: args },
-        url: "/solgs/load/plots/list/training",
-      });
-
-      return plotsList;
-    }
-
-    //       success: function (response) {
-    //         if (response.status == "success") {
-    //           window.location = "/solgs/population/" + popId;
-    //           jQuery.unblockUI();
-    //         } else {
-    //           alert("Error occured while querying for the training data.");
-    //           jQuery.unblockUI();
-    //         }
-    //       },
-    //       error: function (res) {
-    //         alert("Error occured while querying for the training data.");
-    //         jQuery.unblockUI();
-    //       },
-    //     });
-    //   }
-  },
-
   getModelId: function (listId) {
     var modelId = "list_" + listId;
     return modelId;
   },
 
-  getUserUploadedRefPop: function (listId) {
-    const listObj = new solGSList(listId);
-    var listDetail = listObj.getListDetail();
-    var listName = listDetail.name;
-    var modelId = this.getModelId(listId);
-
-    var url = "'/solgs/population/" + modelId + "'";
-    var listIdArg = "'" + listId + "'";
-    var listSource = "'from_db'";
-    var popIdName = { id: modelId, name: listName };
-    popIdName = JSON.stringify(popIdName);
-    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
-
-    var listSelPop =
-      '<table id="list_reference_pops_table" style="width:100%; text-align:left"><tr>' +
-      "<th>List-based training population</th>" +
-      "<th>Models</th>" +
-      "</tr>" +
-      "<tr>" +
-      "<td>" +
-      '<a href="/solgs/population/' +
-      modelId +
-      '" onclick="javascript:loadPopulationPage(' +
-      url +
-      "," +
-      listIdArg +
-      "," +
-      listSource +
-      ')">' +
-      "<data>" +
-      hiddenInput +
-      "</data>" +
-      listName +
-      "</a>" +
-      "</td>" +
-      '<td id="list_reference_page_' +
-      modelId +
-      '">' +
-      '<a href="/solgs/population/' +
-      modelId +
-      '" onclick="javascript:loadPopulationPage(' +
-      url +
-      "," +
-      listIdArg +
-      "," +
-      listSource +
-      ')">' +
-      "[ Build model ]" +
-      "</a>" +
-      "</td></tr></table>";
-
-    return listSelPop;
-  },
-
-  displayListTypeTrainingPops: function (listId) {
-    const listObj = new solGSList(listId);
-    var listDetail = listObj.getListDetail();
-    var listName = listDetail.name;
-    var modelId = this.getModelId(listId);
-
+  displayListTypeTrainingPops: function (args) {
+    var trainingPopId = args.training_pop_id;
+    var trainingPopName = args.training_pop_name;
+    var popType = args.population_type;
+    var protocolId = args.genotyping_protocol_id;
 
-    var popIdName = { id: modelId, name: listName, pop_type: "list_training" };
-    popIdName = JSON.stringify(popIdName);
-    var hiddenInput = '<input type="hidden" value=\'' + popIdName + "'/>";
+    var popDetail = { id: trainingPopId, name: trainingPopName, pop_type: popType };
+    popDetail = JSON.stringify(popDetail);
 
     var tableId = "list_type_training_pops_table";
-    var trId = "list_training_" + listId;
-    var listTypeSelectionPops = jQuery(`#${tableId}`).doesExist();
+    var listTypeTrainingTable = jQuery(`#${tableId}`).doesExist();
 
-    if (listTypeSelectionPops == false) {
-      var listTypeTrainingTable =
+    if (listTypeTrainingTable == false) {
+      listTypeTrainingTable =
         `<table id="${tableId}" class="table"><thead><tr>` +
-        "<th>List-based tranining population</th>" +
-        "<th>View Population</th>" +
-        "</tr></thead><tbody>" +
-        `<tr id="${trId}">` +
-        "<td>" +
-        "<b>" +
-        listName +
-        "</b>" +
-        "</td>" +
-        "<td><data>" +
-        hiddenInput +
-        "</data>" +
-        output +
-        "</td></tr></tbody></table>";
+        "<th>List-based training population</th>" +
+        "<th>View GEBVs</th>" +
+        "</tr></thead><tbody>";
 
       jQuery("#list_type_training_pops_selected").append(listTypeTrainingTable).show();
-    } else {
-      var addRow =
-        `<tr id="${trId}">` +
-        "<td>" +
-        "<b>" +
-        listName +
-        "</td>" +
-        "<td> <data>" +
-        hiddenInput +
-        "</data>" +
-        output +
-        "</td></tr>";
-
-      var samePop = jQuery(`#${trId}`).doesExist();
-
-      if (samePop == false) {
-        jQuery(`#${tableId} tr:last`).after(addRow);
-      } else {
-        jQuery(`#${trId}`).remove();
-        jQuery(`#${tableId}`).append(addRow).show();
-      }
     }
-  },
 
-  loadPopulationPage: function (url, listId, listSource) {
-    const listObj = new solGSList(listId);
-    var listDetail = listObj.getListDetail();
-    var listName = listDetail.name;
-    var modelId = this.getModelId(listId);
+    var popPath = `/solgs/population/${trainingPopId}/gp/${protocolId}`;
+    var popLink = `<a href="${popPath}"  data-selected-pop='${popDetail}'>${trainingPopName}</a>`;
 
-    jQuery.blockUI.defaults.applyPlatformOpacityRules = false;
-    jQuery.blockUI({ message: "Please wait.." });
+    var trId = `${popType}_${trainingPopId}`;
+    var popDisplayed = jQuery(`#${trId}`).doesExist();
+    if (popDisplayed == false) {
+      var row =
+        `<tr id='${trId}' data-selected-pop='${popDetail}'>` +
+        `<td><b>${trainingPopName}</b></td>` +
+        `<td>${popLink}</td>` +
+        "</tr>";
 
-    jQuery.ajax({
-      type: "POST",
-      url: url,
-      dataType: "json",
-      data: {
-        list_reference: 1,
-        model_id: modelId,
-        list_source: listSource,
-        list_name: listName,
-      },
-      success: function (response) {
-        if (response.status == "success") {
-          jQuery.unblockUI();
-        } else {
-          alert("Fail: Error occured calculating GEBVs for the list of selection genotypes.");
-          jQuery.unblockUI();
-        }
-      },
-      error: function (response) {
-        alert("error: " + res.responseText);
-      },
-    });
+      jQuery(`#${tableId} tr:last`).after(row);
+    }
   },
 };
 
@@ -293,31 +144,58 @@ jQuery(document).ready(function () {
     var selectedPop = jQuery("option:selected", this).data("pop");
     if (selectedPop.id) {
       jQuery("#list_type_training_pop_go_btn").click(function () {
-        if (
-          typeof selectedPop.data_str === "undefined" ||
-          !selectedPop.data_str.match(/dataset/i)
-        ) {
+        if (typeof selectedPop.data_str === "undefined" || selectedPop.data_str.match(/list/i)) {
           const list = new solGSList(selectedPop.id);
           var listDetail = list.getListDetail();
-
-          if (listDetail.type.match(/plots/)) {
-            solGS.listTypeTrainingPopulation.askTrainingJobQueueing(selectedPop.id);
-          } else {
-            var trialsNames = list.getListElementsNames();
-
-            solGS.listTypeTrainingPopulation
-              .loadTrialListTypeTrainingPop(trialsNames)
-              .done(function (res) {
-                solGS.combinedTrials.getCombinedPopsId(res.trials_ids);
-              })
-              .fail(function (res) {
-                alert("Error occured querying for trials ids");
-              });
+          var args;
+          if (listDetail.type.match(/plots|trials/)) {
+            args = solGS.listTypeTrainingPopulation.createTrainingReqArgs(selectedPop.id);
+            solGS.listTypeTrainingPopulation.displayListTypeTrainingPops(args);
           }
         } else {
-          solGS.dataset.datasetTrainingPop(selectedPop.id, selectedPop.name);
+          args = solGS.dataset.createDatasetTrainingReqArgs(selectedPop.id, selectedPop.name);
         }
+        solGS.listTypeTrainingPopulation.displayListTypeTrainingPops(args);
       });
     }
   });
 });
+
+jQuery("#list_type_training_pops_table").ready(function () {
+  jQuery("body").on("click", "#list_type_training_pops_table tr a", function (row) {
+    row.preventDefault();
+
+    var selectedPop = row.target.dataset.selectedPop;
+
+    selectedPop = JSON.parse(selectedPop);
+
+    if (selectedPop.pop_type.match(/list/)) {
+      if (selectedPop.id.match(/list/)) {
+        var listId = selectedPop.id.replace(/list_/, "");
+      }
+
+      const list = new solGSList(listId);
+      var listDetail = list.getListDetail();
+      if (listDetail.type.match(/plots/)) {
+        solGS.listTypeTrainingPopulation.askTrainingJobQueueing(listId);
+      } else {
+        var trialsNames = list.getListElementsNames();
+
+        solGS.listTypeTrainingPopulation
+          .loadTrialListTypeTrainingPop(trialsNames)
+          .done(function (res) {
+            solGS.combinedTrials.getCombinedPopsId(res.trials_ids);
+          })
+          .fail(function (res) {
+            alert("Error occured querying for trials ids");
+          });
+      }
+    } else {
+      if (selectedPop.id.match(/dataset/)) {
+        var datasetId = selectedPop.id.replace(/dataset_/, "");
+      }
+
+      solGS.dataset.datasetTrainingPop(datasetId, selectedPop.name);
+    }
+  });
+});

From 34b2dafc7e768c63c2138f770093762e2aa648cc Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 14 Jun 2023 11:18:17 +0200
Subject: [PATCH 41/61] simplify list/dataset sel pops display

---
 .../solGS/listTypeSelectionPopulation.js      | 63 ++++++++-----------
 1 file changed, 26 insertions(+), 37 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index 10048675ca..0fdb1c5d96 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -1,7 +1,5 @@
 /**
-selection population upload from lists
-and files. Run prediction model on list selection population
-and display output.
+A search interface for list and dataset type selection populations
 
 Isaak Y Tecle
 iyt2@cornell.edu
@@ -29,7 +27,6 @@ solGS.listTypeSelectionPopulation = {
     return checkPredicted;
   },
 
-
   askSelectionJobQueueing: function (listId) {
     var args = this.createSelectionReqArgs(listId);
     var modelId = args.training_pop_id;
@@ -75,45 +72,38 @@ solGS.listTypeSelectionPopulation = {
     }
   },
 
-  displayPredictedListTypeSelectionPops: function (args, output) {
+  displayListTypeSelectionPops: function (args, output) {
     var selPopName = args.selection_pop_name;
     var selPopId = args.selection_pop_id;
 
-    var popDetail = {id: selPopId, name: selPopName, pop_type: args.population_type};
-    popDetail= JSON.stringify(popDetail);
+    var popDetail = { id: selPopId, name: selPopName, pop_type: args.population_type };
+    popDetail = JSON.stringify(popDetail);
 
     var tableId = "list_type_selection_pops_table";
-    var trId = `${args.population_type}_${selPopId}`;
-    var predictedListTypeSelectionPops = jQuery(`#${tableId}`).doesExist();
+    var listTypeSelectionTable = jQuery(`#${tableId}`).doesExist();
 
-    if (predictedListTypeSelectionPops == false) {
-      var predictedListTypeSelectionTable =
+    if (listTypeSelectionTable == false) {
+      listTypeSelectionTable =
         `<table id="${tableId}" class="table"><thead><tr>` +
-        "<th>List-based selection population</th>" +
+        "<th>List/datset type selection population</th>" +
         "<th>View GEBVs</th>" +
-        "</tr></thead><tbody>" +
-        `<tr id='${trId}' data-list-selection-pop='${popDetail}'>` +
-        `<td><b>${selPopName}</b></td>` +
-        `<td>${output}</td>` +
-        "</tr></tbody></table>";
+        "</tr></thead><tbody>";
+
+      jQuery("#list_type_selection_pops_selected").append(listTypeSelectionTable).show();
+    }
 
-      jQuery("#list_type_selection_pops_selected").append(predictedListTypeSelectionTable).show();
-    } else {
-      var addRow =
+    var trId = `${args.population_type}_${selPopId}`;
+    var popDisplayed = jQuery(`#${trId}`).doesExist();
+    if (popDisplayed == false) {
+      var row =
         `<tr id='${trId}' data-list-selection-pop='${popDetail}'>` +
-        `<td><b> ${selPopName}</b></td>`  +
+        `<td><b>${selPopName}</b></td>` +
         `<td>${output}</td>` +
         "</tr>";
 
-      var samePop = jQuery(`#${trId}`).doesExist();
-
-      if (samePop == false) {
-        jQuery(`#${tableId} tr:last`).after(addRow);
-      } else {
-        jQuery(`#${trId}`).remove();
-        jQuery(`#${tableId}`).append(addRow).show();
-      }
+      jQuery(`#${tableId} tr:last`).after(row);
     }
+
   },
 
   populateSelectionPopsMenu: function () {
@@ -175,16 +165,17 @@ jQuery(document).ready(function () {
   var menuId = solGS.listTypeSelectionPopulation.selectionPopsSelectMenuId;
   jQuery(`${menuId}`).change(function () {
     var selectedPop = jQuery("option:selected", this).data("pop");
+   
     if (selectedPop.id) {
       jQuery(" #list_type_selection_pop_go_btn").click(function () {
+
         if (
           typeof selectedPop.data_str === "undefined" ||
-          !selectedPop.data_str.match(/dataset/i)
+          selectedPop.data_str.match(/list/i)
         ) {
-
           const listObj = new solGSList(selectedPop.id);
           var listDetail = listObj.getListDetail();
-    
+
           if (listDetail.type.match(/accessions/)) {
             solGS.listTypeSelectionPopulation
               .checkPredictedListSelection(selectedPop.id)
@@ -192,10 +183,7 @@ jQuery(document).ready(function () {
                 var args = solGS.listTypeSelectionPopulation.createSelectionReqArgs(selectedPop.id);
 
                 if (res.output) {
-                  solGS.listTypeSelectionPopulation.displayPredictedListTypeSelectionPops(
-                    args,
-                    res.output
-                  );
+                  solGS.listTypeSelectionPopulation.displayListTypeSelectionPops(args, res.output);
 
                   if (document.URL.match(/solgs\/traits\/all\/|solgs\/models\/combined\//)) {
                     solGS.sIndex.populateSindexMenu();
@@ -204,7 +192,7 @@ jQuery(document).ready(function () {
                     solGS.cluster.listClusterPopulations();
                   }
                 } else {
-                  solGS.listTypeSelectionPopulation.askSelectionJobQueueing(listId);
+                  solGS.listTypeSelectionPopulation.askSelectionJobQueueing(selectedPop.id);
                 }
               })
               .fail(function () {
@@ -217,6 +205,7 @@ jQuery(document).ready(function () {
             //	loadTrialListTypeSelectionPop(trialsNames);
           }
         } else {
+        
           solGS.dataset.checkPredictedDatasetSelection(selectedPop.id, selectedPop.name);
         }
       });

From e69aa429f30a1515be5ce7981dc8872aa958964a Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 14 Jun 2023 11:20:17 +0200
Subject: [PATCH 42/61] update training pop req args and display func name

---
 js/source/legacy/solGS/Dataset.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/js/source/legacy/solGS/Dataset.js b/js/source/legacy/solGS/Dataset.js
index 428dae677e..a3d7c0c385 100644
--- a/js/source/legacy/solGS/Dataset.js
+++ b/js/source/legacy/solGS/Dataset.js
@@ -148,6 +148,7 @@ solGS.dataset = {
       analysis_type: "training_dataset",
       data_set_type: "single_population",
       training_pop_id: popId,
+      training_pop_name: datasetName,
       population_type: popType,
       genotyping_protocol_id: protocolId,
     };
@@ -178,7 +179,7 @@ solGS.dataset = {
       selection_pop_id: selectionPopId,
       selection_pop_name: datasetName,
       training_traits_ids: trainingTraitsIds,
-      population_type: 'dataset_selection',
+      population_type: "dataset_selection",
       data_set_type: trainingPopDetails.data_set_type,
       genotyping_protocol_id: protocolId,
     };
@@ -214,7 +215,7 @@ solGS.dataset = {
           args = JSON.parse(args);
 
           if (response.output) {
-            solGS.listTypeSelectionPopulation.displayPredictedListTypeSelectionPops(
+            solGS.listTypeSelectionPopulation.displayListTypeSelectionPops(
               args,
               response.output
             );

From d63cac4b3d3c7cfc1f848a8fdd7e6596d4cc9567 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 14 Jun 2023 11:21:57 +0200
Subject: [PATCH 43/61] use regex to remove text from ids

---
 .../solGS/listTypeTrainingPopulation.js       | 22 ++++++++-----------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/js/source/legacy/solGS/listTypeTrainingPopulation.js b/js/source/legacy/solGS/listTypeTrainingPopulation.js
index 4cc46d29b5..1050d6c4d4 100644
--- a/js/source/legacy/solGS/listTypeTrainingPopulation.js
+++ b/js/source/legacy/solGS/listTypeTrainingPopulation.js
@@ -107,8 +107,8 @@ solGS.listTypeTrainingPopulation = {
     if (listTypeTrainingTable == false) {
       listTypeTrainingTable =
         `<table id="${tableId}" class="table"><thead><tr>` +
-        "<th>List-based training population</th>" +
-        "<th>View GEBVs</th>" +
+        "<th>List/dataset type training population</th>" +
+        "<th>Detail page</th>" +
         "</tr></thead><tbody>";
 
       jQuery("#list_type_training_pops_selected").append(listTypeTrainingTable).show();
@@ -168,16 +168,16 @@ jQuery("#list_type_training_pops_table").ready(function () {
     var selectedPop = row.target.dataset.selectedPop;
 
     selectedPop = JSON.parse(selectedPop);
+    if (selectedPop.id.match(/\w+_/)) {
+      selectedPop.id = selectedPop.id.replace(/\w+_/, "");
+    }
 
     if (selectedPop.pop_type.match(/list/)) {
-      if (selectedPop.id.match(/list/)) {
-        var listId = selectedPop.id.replace(/list_/, "");
-      }
-
-      const list = new solGSList(listId);
+    
+      const list = new solGSList(selectedPop.id);
       var listDetail = list.getListDetail();
       if (listDetail.type.match(/plots/)) {
-        solGS.listTypeTrainingPopulation.askTrainingJobQueueing(listId);
+        solGS.listTypeTrainingPopulation.askTrainingJobQueueing(selectedPop.id);
       } else {
         var trialsNames = list.getListElementsNames();
 
@@ -191,11 +191,7 @@ jQuery("#list_type_training_pops_table").ready(function () {
           });
       }
     } else {
-      if (selectedPop.id.match(/dataset/)) {
-        var datasetId = selectedPop.id.replace(/dataset_/, "");
-      }
-
-      solGS.dataset.datasetTrainingPop(datasetId, selectedPop.name);
+      solGS.dataset.datasetTrainingPop(selectedPop.id, selectedPop.name);
     }
   });
 });

From 04ea58ca5bfb114fe90fb07945bb7dc2de099fea Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 14 Jun 2023 11:24:13 +0200
Subject: [PATCH 44/61] remove not used code..

---
 lib/SGN/Controller/solGS/List.pm | 38 --------------------------------
 1 file changed, 38 deletions(-)

diff --git a/lib/SGN/Controller/solGS/List.pm b/lib/SGN/Controller/solGS/List.pm
index 69ef30e28d..5621b04062 100644
--- a/lib/SGN/Controller/solGS/List.pm
+++ b/lib/SGN/Controller/solGS/List.pm
@@ -509,44 +509,6 @@ sub map_plots_genotypes {
 
 }
 
-sub load_plots_list_training : Path('/solgs/load/plots/list/training') Args(0) {
-    my ( $self, $c ) = @_;
-
-    my $args = $c->req->param('arguments');
-
-    my $json = JSON->new();
-    $args = $json->decode($args);
-
-    $c->stash->{list_name}              = $args->{list_name};
-    $c->stash->{list_id}                = $args->{list_id};
-    $c->stash->{model_id}               = $args->{training_pop_id};
-    $c->stash->{population_type}        = $args->{population_type};
-    $c->stash->{list_id}                = $args->{list_id};
-    $c->stash->{genotyping_protocol_id} = $args->{genotyping_protocol_id};
-
-    my $model_id = $c->stash->{model_id};
-
-    $self->plots_list_phenotype_file($c);
-    my $pheno_file = $c->stash->{plots_list_phenotype_file};
-
-    $self->genotypes_list_genotype_file( $c, $model_id );
-    my $geno_file = $c->stash->{genotypes_list_genotype_file};
-
-    $self->create_list_population_metadata_file( $c, $model_id );
-
-    my $ret->{status} = 'failed';
-
-    if ( -s $geno_file && -s $pheno_file ) {
-        $ret->{status} = 'success';
-    }
-
-    $ret = to_json($ret);
-
-    $c->res->content_type('application/json');
-    $c->res->body($ret);
-
-}
-
 sub transform_plots_genotypes_names {
     my ( $self, $c ) = @_;
 

From 136ba3d4071d91114b7fdda1498a537c72f21616 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Thu, 15 Jun 2023 15:43:39 +0200
Subject: [PATCH 45/61] update ids and pass tests

---
 t/selenium2/solgs/cluster.t                | 40 +++++++++++-----------
 t/selenium2/solgs/combine_trials.t         | 36 +++++++++----------
 t/selenium2/solgs/hcluster.t               | 28 +++++++--------
 t/selenium2/solgs/kcluster.t               | 28 +++++++--------
 t/selenium2/solgs/list_type_training_pop.t | 28 +++++++++------
 t/selenium2/solgs/solgs.t                  | 20 +++++------
 6 files changed, 93 insertions(+), 87 deletions(-)

diff --git a/t/selenium2/solgs/cluster.t b/t/selenium2/solgs/cluster.t
index baaffebf5a..8d72c008b1 100644
--- a/t/selenium2/solgs/cluster.t
+++ b/t/selenium2/solgs/cluster.t
@@ -926,7 +926,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'accessions list sl pop'
@@ -956,7 +956,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'accession select list sl pop'
@@ -997,11 +997,11 @@ $d->while_logged_in_as(
             'select list sel pop'
         )->click();
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
@@ -1072,11 +1072,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(2);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(2);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -1148,11 +1148,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select accessions dataset sel pop'
@@ -1217,11 +1217,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -1281,12 +1281,12 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
 
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2457,7 +2457,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'list sl pop'
@@ -2489,7 +2489,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select list sl pop'
@@ -2833,11 +2833,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2902,11 +2902,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2972,11 +2972,11 @@ $d->while_logged_in_as(
             'select list type sel pop'
         )->click();
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
diff --git a/t/selenium2/solgs/combine_trials.t b/t/selenium2/solgs/combine_trials.t
index 768f314b43..99e0dab715 100644
--- a/t/selenium2/solgs/combine_trials.t
+++ b/t/selenium2/solgs/combine_trials.t
@@ -219,9 +219,9 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
      sleep(10);
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
     $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click list sel pred')->click();
     sleep(5);
@@ -239,9 +239,9 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select list sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select list sl pop')->click();
     sleep(10);
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
     $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "DMCP")]', 'xpath', 'click list sel pred')->click();
     sleep(10);
@@ -261,11 +261,11 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'dataset')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'dataset')->click();
     sleep(10);
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'select dataset sel pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]/tbody/tr/td/a[contains(text(), "Predict")]', 'xpath', 'click list sel pred')->click();
+    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click list sel pred')->click();
     sleep(5);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
@@ -281,11 +281,11 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'select list sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'select list sl pop')->click();
      sleep(10);
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]/tbody/tr/td/a[contains(text(), "DMCP")]', 'xpath', 'click list sel pred')->click();
+    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "DMCP")]', 'xpath', 'click list sel pred')->click();
     sleep(10);
 
 #$d->get('/solgs/combined/model/2804608595/selection/dataset_5/trait/70741/gp/1', 'combo trials tr pop page');
@@ -356,9 +356,9 @@ $d->while_logged_in_as("submitter", sub {
 	$d->driver->go_back();
 	sleep(3);
 
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
     sleep(10);
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
     $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click list sel pred')->click();
     sleep(20);
@@ -372,9 +372,9 @@ $d->while_logged_in_as("submitter", sub {
     sleep(150);
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'list sl page')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'list sl page')->click();
     sleep(5);
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'select list sel pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
     $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "FRW")]', 'xpath', 'click list sel pred')->click();
     sleep(5);
@@ -382,9 +382,9 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->go_back();
     sleep(5);
 
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'select list sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'select list sl pop')->click();
      sleep(5);
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'select dataset sel pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
     $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click list sel pred')->click();
     sleep(5);
@@ -402,8 +402,8 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'select list sl pop')->click();
-    $d->find_element_ok('//input[@value="Go"]', 'xpath', 'dataset sel pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name. '"]', 'xpath', 'select list sl pop')->click();
+    $d->find_element_ok('//input[@value="View"]', 'xpath', 'dataset sel pop')->click();
     sleep(5);
     $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "FRW")]', 'xpath', 'dataset dmcp-frw pred')->click();
     sleep(10);
diff --git a/t/selenium2/solgs/hcluster.t b/t/selenium2/solgs/hcluster.t
index 3a9ccd58bf..cdbc12aa9c 100644
--- a/t/selenium2/solgs/hcluster.t
+++ b/t/selenium2/solgs/hcluster.t
@@ -310,7 +310,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(15);
 
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'accessions list sl pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'accessions list sl pop')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -328,7 +328,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(15);
 
 
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
@@ -352,9 +352,9 @@ $d->while_logged_in_as("submitter", sub {
 
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
-    $d->find_element_ok('list_type_selection_pops_list_select', 'id', 'select clones list menu')->click();
+    $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $list = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
+    my $list = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
     $list->click();
     sleep(5);
 
@@ -387,10 +387,10 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pops = $d->find_element('Predict', 'partial_link_text', 'scroll up');
     my $elem =$d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);", $sel_pops);
     sleep(5);
-    $d->find_element_ok('list_type_selection_pops_list_select', 'id', 'select clones list menu')->click();
+    $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
 
-    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
+    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
     $dataset->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'GO select dataset sel popp')->click();
@@ -423,9 +423,9 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pops = $d->find_element('Predict', 'partial_link_text', 'scroll up');
     my $elem =$d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);", $sel_pops);
     sleep(5);
-    $d->find_element_ok('list_type_selection_pops_list_select', 'id', 'select clones list menu')->click();
+    $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
+    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
     $dataset->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
@@ -926,7 +926,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(15);
 
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl pop')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -948,7 +948,7 @@ $d->while_logged_in_as("submitter", sub {
   #sleep(5);
 ########
 
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
@@ -1068,9 +1068,9 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pops = $d->find_element('Predict', 'partial_link_text', 'scroll up');
     my $elem =$d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);", $sel_pops);
     sleep(5);
-    $d->find_element_ok('list_type_selection_pops_list_select', 'id', 'select clones list menu')->click();
+    $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
+    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
     $dataset->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
@@ -1103,9 +1103,9 @@ $d->while_logged_in_as("submitter", sub {
 
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
-    $d->find_element_ok('list_type_selection_pops_list_select', 'id', 'select clones list menu')->click();
+    $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $list = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
+    my $list = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
     $list->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
diff --git a/t/selenium2/solgs/kcluster.t b/t/selenium2/solgs/kcluster.t
index 25556ee556..25910fdfa4 100644
--- a/t/selenium2/solgs/kcluster.t
+++ b/t/selenium2/solgs/kcluster.t
@@ -646,7 +646,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'accessions list sl pop'
@@ -676,7 +676,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'accession select list sl pop'
@@ -715,11 +715,11 @@ $d->while_logged_in_as(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
             'xpath', 'select list sel pop' )->click();
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
@@ -788,11 +788,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(2);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(2);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -862,11 +862,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select accessions dataset sel pop'
@@ -1793,7 +1793,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'list sl pop'
@@ -1825,7 +1825,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select list sl pop'
@@ -2057,11 +2057,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0, -600);",
             $sel_pops );
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2128,11 +2128,11 @@ $d->while_logged_in_as(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
             'xpath', 'select list type sel pop' )->click();
         sleep(5);
-        $d->find_element_ok( 'list_type_selection_pops_list_select',
+        $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_list_select"]/option[text()="'
+'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
diff --git a/t/selenium2/solgs/list_type_training_pop.t b/t/selenium2/solgs/list_type_training_pop.t
index a623f8a54b..7859771fa3 100644
--- a/t/selenium2/solgs/list_type_training_pop.t
+++ b/t/selenium2/solgs/list_type_training_pop.t
@@ -62,10 +62,14 @@ $d->while_logged_in_as("submitter", sub {
 
     $d->get_ok('/solgs', 'solgs home page');
     sleep(5);
- $d->find_element_ok('//select[@id="list_type_training_pops_list_select"]/option[text()="' . $plots_list_name . '"]', 'xpath', 'select list tr pop')->click();
+ $d->find_element_ok('//select[@id="list_type_training_pops_select"]/option[text()="' . $plots_list_name . '"]', 'xpath', 'select list tr pop')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
-    sleep(5);
+    sleep(3);
+    # $d->find_element_ok('//table[@id="list_type_training_pops_table"]//*a[contains(text()="' . $plots_list_name . '"]', 'xpath', 'click list sel pred')->click();
+    # sleep(3);
+    $d->find_element_ok( $plots_list_name , 'partial_link_text', 'list type training pop link')->click();
+    sleep(3);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
     $d->find_element_ok('analysis_name', 'id', 'no job queueing')->send_keys('plots list tr pop');
@@ -141,7 +145,7 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(10);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl pop')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -157,7 +161,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(150);
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sl pop')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -170,7 +174,7 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
@@ -190,7 +194,7 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -254,7 +258,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->go_back();
     sleep(6);
 
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl pop')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -270,7 +274,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(150);
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl page')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'list sl page')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -280,7 +284,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->go_back();
     sleep(5);
 
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dt sl pop')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dt sl pop')->click();
      sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
@@ -300,7 +304,7 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-     $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
+     $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
      sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'dataset sel pop')->click();
     sleep(5);
@@ -311,10 +315,12 @@ $d->while_logged_in_as("submitter", sub {
     $d->get('/solgs', 'solgs home page');
     sleep(4);
 
-    $d->find_element_ok('//select[@id="list_type_training_pops_list_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'trials list')->click();
+    $d->find_element_ok('//select[@id="list_type_training_pops_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'trials list')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(20);
+    $d->find_element_ok( $trials_list_name , 'partial_link_text', 'list type trials training pop link')->click();
+    sleep(3);
     $d->find_element_ok('queue_job', 'id', 'no job queueing')->click();
     sleep(2);
     $d->find_element_ok('analysis_name', 'id', 'no job queueing')->send_keys('trials list tr pop');
diff --git a/t/selenium2/solgs/solgs.t b/t/selenium2/solgs/solgs.t
index eed0829b42..44555cb8c0 100644
--- a/t/selenium2/solgs/solgs.t
+++ b/t/selenium2/solgs/solgs.t
@@ -198,7 +198,7 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
     sleep(15);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -218,7 +218,7 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(10);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]',  'xpath', 'select list sl pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]',  'xpath', 'select list sl pop')->click();
     sleep(15);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(15);
@@ -247,11 +247,11 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(12);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]/tbody/tr/td/a[contains(text(), "Predict")]', 'xpath', 'click list sel pred')->click();
+    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "Predict")]', 'xpath', 'click list sel pred')->click();
     sleep(2);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
@@ -267,11 +267,11 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
      sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
-    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]/tbody/tr/td/a[contains(text(), "DMCP")]', 'xpath', 'click list sel pred')->click();
+    $d->find_element_ok('//table[@id="list_type_selection_pops_table"]//*[contains(text(), "DMCP")]', 'xpath', 'click list sel pred')->click();
     sleep(10);
 
 	my $sel_pred = $d->find_element('Check Expected Genetic Gain', 'partial_link_text', 'scroll to GEBvs');
@@ -343,7 +343,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->go_back();
     sleep(6);
 
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]', 'xpath', 'select clones list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -359,7 +359,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(250);
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(2);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_list_name. '"]',  'xpath', 'list sl page')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name. '"]',  'xpath', 'list sl page')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select list sel pop')->click();
     sleep(5);
@@ -369,7 +369,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->go_back();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select list sl pop')->click();
      sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'select dataset sel pop')->click();
     sleep(5);
@@ -389,7 +389,7 @@ $d->while_logged_in_as("submitter", sub {
     my $sel_pred = $d->find_element('Predict', 'partial_link_text', 'scroll to selection pred');
     my $elem = $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-70);", $sel_pred);
     sleep(5);
-    $d->find_element_ok('//select[@id="list_type_selection_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
+    $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'dataset')->click();
      sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'dataset sel pop')->click();
     sleep(5);

From ab7a61ee825ad491108206c351104f787e19c4ba Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Thu, 15 Jun 2023 15:45:28 +0200
Subject: [PATCH 46/61] fix typo

---
 js/source/legacy/solGS/listTypeSelectionPopulation.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index 0fdb1c5d96..91ae6a7f06 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -85,7 +85,7 @@ solGS.listTypeSelectionPopulation = {
     if (listTypeSelectionTable == false) {
       listTypeSelectionTable =
         `<table id="${tableId}" class="table"><thead><tr>` +
-        "<th>List/datset type selection population</th>" +
+        "<th>List/dataset type selection population</th>" +
         "<th>View GEBVs</th>" +
         "</tr></thead><tbody>";
 

From e73e7380940f821eee9cd10c117f052b04a23f4c Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 16 Jun 2023 16:32:53 +0200
Subject: [PATCH 47/61] add to kinship response all output if cached

---
 lib/SGN/Controller/solGS/CachedResult.pm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/lib/SGN/Controller/solGS/CachedResult.pm b/lib/SGN/Controller/solGS/CachedResult.pm
index 1ad8a16196..ced15f801f 100644
--- a/lib/SGN/Controller/solGS/CachedResult.pm
+++ b/lib/SGN/Controller/solGS/CachedResult.pm
@@ -332,7 +332,7 @@ sub _check_combined_trials_model_selection_output {
 sub _check_kinship_output {
     my ( $self, $c, $kinship_pop_id, $protocol_id, $trait_id ) = @_;
 
-    $c->stash->{rest}{cached} =
+    $c->stash->{rest}=
       $self->check_kinship_output( $c, $kinship_pop_id, $protocol_id,
         $trait_id );
 }
@@ -531,10 +531,13 @@ sub check_kinship_output {
     my $files = $c->controller('solGS::Kinship')
       ->get_kinship_coef_files( $c, $pop_id, $protocol_id, $trait_id );
 
-    my $cached =
-      -s $files->{'json_file_adj'} && -s $files->{'matrix_file_adj'} ? 1 : 0;
+      if (-s $files->{'json_file_adj'} && -s $files->{'matrix_file_adj'}) {
 
-    return $cached;
+         my $res = $c->controller('solGS::Kinship')->structure_kinship_response($c);
+            return $res;
+      } else {
+        return {cached => 0};
+      }
 
 }
 

From 3a8ad9f7c23b3292925fa6512d7c240564790a1b Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Fri, 16 Jun 2023 16:34:28 +0200
Subject: [PATCH 48/61] abstract out response data structuring and apply
 formatting

---
 lib/SGN/Controller/solGS/Kinship.pm | 325 ++++++++++++++--------------
 1 file changed, 166 insertions(+), 159 deletions(-)

diff --git a/lib/SGN/Controller/solGS/Kinship.pm b/lib/SGN/Controller/solGS/Kinship.pm
index 7ca8cf9966..731561f8b0 100644
--- a/lib/SGN/Controller/solGS/Kinship.pm
+++ b/lib/SGN/Controller/solGS/Kinship.pm
@@ -1,6 +1,5 @@
 package SGN::Controller::solGS::Kinship;
 
-
 use Moose;
 use namespace::autoclean;
 
@@ -14,83 +13,69 @@ use File::Path qw / mkpath  /;
 use Scalar::Util qw /weaken reftype/;
 use Storable qw/ nstore retrieve /;
 
-
 BEGIN { extends 'Catalyst::Controller' }
 
-
 __PACKAGE__->config(
-    default   => 'application/json' => 'JSON',
-    map       => { 'application/json' => 'JSON'},
-    );
+    default => 'application/json' => 'JSON',
+    map     => { 'application/json' => 'JSON' },
+);
 
-
-sub kinship_analysis :Path('/kinship/analysis/') Args() {
-    my ($self, $c) = @_;
+sub kinship_analysis : Path('/kinship/analysis/') Args() {
+    my ( $self, $c ) = @_;
 
     $c->stash->{template} = '/solgs/tools/kinship/analysis.mas';
 
 }
 
-
-sub run_kinship_analysis :Path('/run/kinship/analysis') Args() {
-    my ($self, $c) = @_;
+sub run_kinship_analysis : Path('/run/kinship/analysis') Args() {
+    my ( $self, $c ) = @_;
 
     my $args = $c->req->param('arguments');
-    $c->controller('solGS::Utils')->stash_json_args($c, $args);
+    $c->controller('solGS::Utils')->stash_json_args( $c, $args );
 
     my $pop_id = $c->stash->{kinship_pop_id};
-    $self->stash_kinship_pop_id($c, $pop_id);
+    $self->stash_kinship_pop_id( $c, $pop_id );
     my $kinship_pop_id = $c->stash->{kinship_pop_id};
-    
+
     my $file_id = $c->controller('solGS::Files')->kinship_file_id($c);
     $c->stash->{file_id} = $file_id;
 
     my $trait_id = $c->stash->{trait_id};
-    if ($trait_id)
-    {
-	    $c->controller('solGS::Trait')->get_trait_details($c, $trait_id);
+    if ($trait_id) {
+        $c->controller('solGS::Trait')->get_trait_details( $c, $trait_id );
     }
 
     my $protocol_id = $c->stash->{genotyping_protocol_id};
 
-    my $kinship_files = $self->get_kinship_coef_files($c, $kinship_pop_id, $protocol_id, $trait_id);
-    my $json_file  = $kinship_files->{json_file_adj};
-
-    if (!-s $json_file)
-    {
-    if ($kinship_pop_id =~ /list/)
-    {
-	    $c->controller('solGS::List')->create_list_population_metadata_file($c, $file_id);
-	    $c->controller('solGS::List')->stash_list_metadata($c, $kinship_pop_id);
-    }
-
-    my $combo_pops_id = $c->stash->{combo_pops_id};
-    if ($c->stash->{combo_pops_id} )
-    {
-	    $c->controller('solGS::combinedTrials')->get_combined_pops_list($c, $c->stash->{combo_pops_id});
-	    $c->stash->{pops_ids_list} = $c->stash->{combined_pops_list};
-    }
-    
-    $self->run_kinship($c);
+    my $kinship_files =
+      $self->get_kinship_coef_files( $c, $kinship_pop_id, $protocol_id,
+        $trait_id );
+    my $json_file = $kinship_files->{json_file_adj};
+
+    if ( !-s $json_file ) {
+        if ( $kinship_pop_id =~ /list/ ) {
+            $c->controller('solGS::List')
+              ->create_list_population_metadata_file( $c, $file_id );
+            $c->controller('solGS::List')
+              ->stash_list_metadata( $c, $kinship_pop_id );
+        }
+
+        my $combo_pops_id = $c->stash->{combo_pops_id};
+        if ( $c->stash->{combo_pops_id} ) {
+            $c->controller('solGS::combinedTrials')
+              ->get_combined_pops_list( $c, $c->stash->{combo_pops_id} );
+            $c->stash->{pops_ids_list} = $c->stash->{combined_pops_list};
+        }
+
+        $self->run_kinship($c);
     }
 
     my $res = {};
-    if ($c->stash->{error})
-    {
-	$res->{result} = $c->stash->{error};
+    if ( $c->stash->{error} ) {
+        $res->{result} = $c->stash->{error};
     }
-    else
-    {
-        my $pop_name = $self->get_kinship_pop_name($c, $kinship_pop_id);
-
-        $res->{kinship_pop_name} = $pop_name;
-        $res->{kinship_file_id} = $file_id;
-        $res->{data} = read_file($json_file);
-
-        $self->prep_download_kinship_files($c);
-        $res->{kinship_table_file} = $c->stash->{download_kinship_table};
-        $res->{kinship_averages_file} = $c->stash->{download_kinship_averages};
-        $res->{inbreeding_file} = $c->stash->{download_inbreeding};
+    else {
+        $res = $self->structure_kinship_response($c);
     }
 
     $res = to_json($res);
@@ -98,77 +83,103 @@ sub run_kinship_analysis :Path('/run/kinship/analysis') Args() {
 
 }
 
+sub structure_kinship_response {
+    my ( $self, $c ) = @_;
+
+    my $kinship_pop_id = $c->stash->{kinship_pop_id};
+    my $pop_name       = $self->get_kinship_pop_name( $c, $kinship_pop_id );
+    my $protocol_id    = $c->stash->{genotyping_protocol_id};
+    my $trait_id = $c->stash->{trait_id};
+
+    my $file_id = $c->controller('solGS::Files')->kinship_file_id($c);
+    $c->stash->{file_id} = $file_id;
+
+    my $kinship_files =
+      $self->get_kinship_coef_files( $c, $kinship_pop_id, $protocol_id,
+        $trait_id );
+    my $json_file = $kinship_files->{json_file_adj};
+
+    my $res = {};
+
+    $res->{kinship_pop_name} = $pop_name;
+    $res->{kinship_file_id}  = $file_id;
+    $res->{data}             = read_file($json_file);
+
+    $self->prep_download_kinship_files($c);
+    $res->{kinship_table_file}    = $c->stash->{download_kinship_table};
+    $res->{kinship_averages_file} = $c->stash->{download_kinship_averages};
+    $res->{inbreeding_file}       = $c->stash->{download_inbreeding};
+
+    return $res;
+
+}
+
 sub get_kinship_pop_name {
-    my ($self, $c, $kinship_pop_id) = @_;
+    my ( $self, $c, $kinship_pop_id ) = @_;
 
-    my$pop_name;
-    if ($kinship_pop_id =~ /dataset/)
-    {
-	    $pop_name = $c->controller('solGS::Dataset')->get_dataset_name($c, $kinship_pop_id);
+    my $pop_name;
+    if ( $kinship_pop_id =~ /dataset/ ) {
+        $pop_name = $c->controller('solGS::Dataset')
+          ->get_dataset_name( $c, $kinship_pop_id );
     }
-    elsif ($kinship_pop_id =~ /list/)
-    {
-	    $c->controller('solGS::List')->stash_list_metadata($c, $kinship_pop_id);
-	    $pop_name = $c->stash->{list_name};
+    elsif ( $kinship_pop_id =~ /list/ ) {
+        $c->controller('solGS::List')
+          ->stash_list_metadata( $c, $kinship_pop_id );
+        $pop_name = $c->stash->{list_name};
     }
 
     return $pop_name;
 
 }
 
-
 sub stash_kinship_pop_id {
-    my ($self, $c, $pop_id) = @_;
+    my ( $self, $c, $pop_id ) = @_;
 
     $pop_id = $c->stash->{kinship_pop_id} if !$pop_id;
     my $data_str = $c->stash->{data_structure};
 
-    if ($data_str =~ /dataset|list/)
-    {
-        if ($pop_id !~ /dataset_|list_/) 
-        {
-	        $pop_id = $data_str . '_' . $pop_id;
-        } 
+    if ( $data_str =~ /dataset|list/ ) {
+        if ( $pop_id !~ /\w+_/ ) {
+            $pop_id = $data_str . '_' . $pop_id;
+        }
     }
 
     $c->stash->{kinship_pop_id} = $pop_id;
 }
 
-
 sub get_kinship_coef_files {
-    my ($self, $c, $pop_id, $protocol_id, $trait_id) = @_;
+    my ( $self, $c, $pop_id, $protocol_id, $trait_id ) = @_;
 
-    $c->stash->{pop_id} = $pop_id;
+    $c->stash->{pop_id}                 = $pop_id;
     $c->stash->{genotyping_protocol_id} = $protocol_id;
 
-    if ($trait_id)
-    {
-    	$c->controller('solGS::Trait')->get_trait_details($c, $trait_id);
+    if ($trait_id) {
+        $c->controller('solGS::Trait')->get_trait_details( $c, $trait_id );
     }
 
     $c->controller('solGS::Files')->relationship_matrix_adjusted_file($c);
-    my $json_file_adj = $c->stash->{relationship_matrix_adjusted_json_file};
+    my $json_file_adj   = $c->stash->{relationship_matrix_adjusted_json_file};
     my $matrix_file_adj = $c->stash->{relationship_matrix_adjusted_table_file};
 
     $c->controller('solGS::Files')->relationship_matrix_file($c);
     my $matrix_file_raw = $c->stash->{relationship_matrix_table_file};
-    my $json_file_raw = $c->stash->{relationship_matrix_json_file};
+    my $json_file_raw   = $c->stash->{relationship_matrix_json_file};
 
-    return {'json_file_raw' => $json_file_raw,
-	    'matrix_file_raw' => $matrix_file_raw,
-	    'json_file_adj' => $json_file_adj,
-	    'matrix_file_adj' => $matrix_file_adj,
+    return {
+        'json_file_raw'   => $json_file_raw,
+        'matrix_file_raw' => $matrix_file_raw,
+        'json_file_adj'   => $json_file_adj,
+        'matrix_file_adj' => $matrix_file_adj,
 
     };
 }
 
-
 sub kinship_output_files {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
-    my $pop_id = $c->stash->{kinship_pop_id};
+    my $pop_id      = $c->stash->{kinship_pop_id};
     my $protocol_id = $c->stash->{genotyping_protocol_id};
-    my $data_str = $c->stash->{data_structure};
+    my $data_str    = $c->stash->{data_structure};
 
     $c->stash->{pop_id} = $pop_id;
     $c->controller('solGS::Files')->inbreeding_coefficients_file($c);
@@ -177,53 +188,50 @@ sub kinship_output_files {
     $c->controller('solGS::Files')->average_kinship_file($c);
     my $ave_kinship_file = $c->stash->{average_kinship_file};
 
-    my $coef_files = $self->get_kinship_coef_files($c, $pop_id, $protocol_id);
+    my $coef_files = $self->get_kinship_coef_files( $c, $pop_id, $protocol_id );
 
-    my $file_list = join ("\t",
-                          $coef_files->{json_file_raw},
-			  $coef_files->{matrix_file_raw},
-			  $coef_files->{json_file_adj},
-			  $coef_files->{matrix_file_adj},
-			  $inbreeding_file,
-			  $ave_kinship_file
-	);
+    my $file_list = join( "\t",
+        $coef_files->{json_file_raw}, $coef_files->{matrix_file_raw},
+        $coef_files->{json_file_adj}, $coef_files->{matrix_file_adj},
+        $inbreeding_file,             $ave_kinship_file );
 
     my $tmp_dir = $c->stash->{kinship_temp_dir};
-    my $name = "kinship_output_files_${pop_id}";
-    my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
-    write_file($tempfile, $file_list);
+    my $name    = "kinship_output_files_${pop_id}";
+    my $tempfile =
+      $c->controller('solGS::Files')->create_tempfile( $tmp_dir, $name );
+    write_file( $tempfile, $file_list );
 
     $c->stash->{kinship_output_files} = $tempfile;
 
 }
 
-
 sub kinship_input_files {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
-    my $pop_id = $c->stash->{kinship_pop_id};
+    my $pop_id      = $c->stash->{kinship_pop_id};
     my $protocol_id = $c->stash->{genotyping_protocol_id};
-    my $data_str = $c->stash->{data_structure};
-
-    $c->controller('solGS::Files')->genotype_file_name($c, $pop_id, $protocol_id);
+    my $data_str    = $c->stash->{data_structure};
 
-    my $files = $c->stash->{genotype_files_list}
-	|| $c->stash->{genotype_file}
-	|| $c->stash->{genotype_file_name};
+    $c->controller('solGS::Files')
+      ->genotype_file_name( $c, $pop_id, $protocol_id );
 
+    my $files =
+         $c->stash->{genotype_files_list}
+      || $c->stash->{genotype_file}
+      || $c->stash->{genotype_file_name};
 
     my $tmp_dir = $c->stash->{kinship_temp_dir};
-    my $name = "kinship_input_files_${pop_id}";
-    my $tempfile =  $c->controller('solGS::Files')->create_tempfile($tmp_dir, $name);
-    write_file($tempfile, $files);
+    my $name    = "kinship_input_files_${pop_id}";
+    my $tempfile =
+      $c->controller('solGS::Files')->create_tempfile( $tmp_dir, $name );
+    write_file( $tempfile, $files );
 
     $c->stash->{kinship_input_files} = $tempfile;
 
 }
 
-
 sub run_kinship {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
     $self->kinship_query_jobs_file($c);
     $c->stash->{prerequisite_jobs} = $c->stash->{kinship_query_jobs_file};
@@ -235,26 +243,25 @@ sub run_kinship {
 
 }
 
-
 sub kinship_r_jobs_file {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
     $self->kinship_r_jobs($c);
     my $jobs = $c->stash->{kinship_r_jobs};
 
-    my $temp_dir = $c->stash->{kinship_temp_dir};
-    my $jobs_file =  $c->controller('solGS::Files')->create_tempfile($temp_dir, 'kinship-r-jobs-file');
+    my $temp_dir  = $c->stash->{kinship_temp_dir};
+    my $jobs_file = $c->controller('solGS::Files')
+      ->create_tempfile( $temp_dir, 'kinship-r-jobs-file' );
 
     nstore $jobs, $jobs_file
-	or croak "kinship r jobs : $! serializing kinship r jobs to $jobs_file";
+      or croak "kinship r jobs : $! serializing kinship r jobs to $jobs_file";
 
     $c->stash->{kinship_r_jobs_file} = $jobs_file;
 
 }
 
-
 sub kinship_r_jobs {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
     my $file_id = $c->stash->{kinship_pop_id};
 
@@ -272,91 +279,91 @@ sub kinship_r_jobs {
     $c->stash->{r_script}     = 'R/solGS/kinship.r';
 
     $c->controller('solGS::AsyncJob')->get_cluster_r_job_args($c);
-    my $jobs  = $c->stash->{cluster_r_job_args};
+    my $jobs = $c->stash->{cluster_r_job_args};
 
-    if (reftype $jobs ne 'ARRAY')
-    {
-	$jobs = [$jobs];
+    if ( reftype $jobs ne 'ARRAY' ) {
+        $jobs = [$jobs];
     }
 
     $c->stash->{kinship_r_jobs} = $jobs;
 
 }
 
-
 sub kinship_query_jobs_file {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
     $self->kinship_query_jobs($c);
     my $jobs = $c->stash->{kinship_query_jobs};
 
-    my $temp_dir = $c->stash->{kinship_temp_dir};
-    my $jobs_file =  $c->controller('solGS::Files')->create_tempfile($temp_dir, 'kinship-query-jobs-file');
+    my $temp_dir  = $c->stash->{kinship_temp_dir};
+    my $jobs_file = $c->controller('solGS::Files')
+      ->create_tempfile( $temp_dir, 'kinship-query-jobs-file' );
 
     nstore $jobs, $jobs_file
-	or croak "kinship query jobs : $! serializing kinship query jobs to $jobs_file";
+      or croak
+      "kinship query jobs : $! serializing kinship query jobs to $jobs_file";
 
     $c->stash->{kinship_query_jobs_file} = $jobs_file;
 
 }
 
-
 sub kinship_query_jobs {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
     my $kinship_pop_id = $c->stash->{kinship_pop_id};
-    my $protocol_id = $c->stash->{genotyping_protocol_id};
+    my $protocol_id    = $c->stash->{genotyping_protocol_id};
 
-    my $jobs = $c->controller('solGS::AsyncJob')->create_genotype_data_query_jobs($c, $kinship_pop_id, $protocol_id);
+    my $jobs = $c->controller('solGS::AsyncJob')
+      ->create_genotype_data_query_jobs( $c, $kinship_pop_id, $protocol_id );
 
-    if (reftype $jobs ne 'ARRAY')
-    {
-	$jobs = [$jobs];
+    if ( reftype $jobs ne 'ARRAY' ) {
+        $jobs = [$jobs];
     }
 
     $c->stash->{kinship_query_jobs} = $jobs;
 }
 
-
 sub prep_download_kinship_files {
-  my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
-  my $tmp_dir      = catfile($c->config->{tempfiles_subdir}, 'kinship');
-  my $base_tmp_dir = catfile($c->config->{basepath}, $tmp_dir);
+    my $tmp_dir      = catfile( $c->config->{tempfiles_subdir}, 'kinship' );
+    my $base_tmp_dir = catfile( $c->config->{basepath},         $tmp_dir );
 
-  mkpath ([$base_tmp_dir], 0, 0755);
+    mkpath( [$base_tmp_dir], 0, 0755 );
 
-  $c->controller('solGS::Files')->relationship_matrix_adjusted_file($c);
-  my $kinship_txt_file  = $c->stash->{relationship_matrix_adjusted_table_file};
+    $c->controller('solGS::Files')->relationship_matrix_adjusted_file($c);
+    my $kinship_txt_file = $c->stash->{relationship_matrix_adjusted_table_file};
 
-  $c->controller('solGS::Files')->inbreeding_coefficients_file($c);
-  my $inbreeding_file = $c->stash->{inbreeding_coefficients_file};
+    $c->controller('solGS::Files')->inbreeding_coefficients_file($c);
+    my $inbreeding_file = $c->stash->{inbreeding_coefficients_file};
 
-  $c->controller('solGS::Files')->average_kinship_file($c);
-  my $ave_kinship_file = $c->stash->{average_kinship_file};
+    $c->controller('solGS::Files')->average_kinship_file($c);
+    my $ave_kinship_file = $c->stash->{average_kinship_file};
 
-  $c->controller('solGS::Files')->copy_file($kinship_txt_file, $base_tmp_dir);
-  $c->controller('solGS::Files')->copy_file($inbreeding_file, $base_tmp_dir);
-  $c->controller('solGS::Files')->copy_file($ave_kinship_file, $base_tmp_dir);
+    $c->controller('solGS::Files')
+      ->copy_file( $kinship_txt_file, $base_tmp_dir );
+    $c->controller('solGS::Files')
+      ->copy_file( $inbreeding_file, $base_tmp_dir );
+    $c->controller('solGS::Files')
+      ->copy_file( $ave_kinship_file, $base_tmp_dir );
 
-  $kinship_txt_file = fileparse($kinship_txt_file);
-  $kinship_txt_file = catfile($tmp_dir, $kinship_txt_file);
+    $kinship_txt_file = fileparse($kinship_txt_file);
+    $kinship_txt_file = catfile( $tmp_dir, $kinship_txt_file );
 
-  $inbreeding_file = fileparse($inbreeding_file);
-  $inbreeding_file = catfile($tmp_dir, $inbreeding_file);
+    $inbreeding_file = fileparse($inbreeding_file);
+    $inbreeding_file = catfile( $tmp_dir, $inbreeding_file );
 
-  $ave_kinship_file = fileparse($ave_kinship_file);
-  $ave_kinship_file = catfile($tmp_dir, $ave_kinship_file);
+    $ave_kinship_file = fileparse($ave_kinship_file);
+    $ave_kinship_file = catfile( $tmp_dir, $ave_kinship_file );
 
-  $c->stash->{download_kinship_table} = $kinship_txt_file;
-  $c->stash->{download_kinship_averages} = $ave_kinship_file;
-  $c->stash->{download_inbreeding} = $inbreeding_file;
+    $c->stash->{download_kinship_table}    = $kinship_txt_file;
+    $c->stash->{download_kinship_averages} = $ave_kinship_file;
+    $c->stash->{download_inbreeding}       = $inbreeding_file;
 
 }
 
-
 sub begin : Private {
-    my ($self, $c) = @_;
+    my ( $self, $c ) = @_;
 
     $c->controller('solGS::Files')->get_solgs_dirs($c);
 

From e65bcb032f2848b49e0e6af272bbae2f94987a64 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 19 Jun 2023 16:22:04 +0200
Subject: [PATCH 49/61] update and pass

---
 t/selenium2/solgs/correlation.t     | 38 +++++++++++++-------------
 t/selenium2/solgs/kinship.t         | 42 ++++++++++++++---------------
 t/selenium2/solgs/selection_index.t | 16 +++++------
 3 files changed, 48 insertions(+), 48 deletions(-)

diff --git a/t/selenium2/solgs/correlation.t b/t/selenium2/solgs/correlation.t
index 6ec359c384..a22d5f3bb3 100644
--- a/t/selenium2/solgs/correlation.t
+++ b/t/selenium2/solgs/correlation.t
@@ -40,7 +40,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->get_ok('/correlation/analysis', 'correlation home page');
     sleep(5);
 
-    $d->find_element_ok('//select[@id="corr_pops_list_select"]/option[text()="'. $plots_list_name . '"]', 'xpath', 'plots list')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="'. $plots_list_name . '"]', 'xpath', 'plots list')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -56,7 +56,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="corr_pops_list_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
     sleep(10);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -72,7 +72,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="corr_pops_list_select"]/option[text()="' . $plots_dt_name . '"]', 'xpath', 'plots dataset')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="' . $plots_dt_name . '"]', 'xpath', 'plots dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(20);
@@ -90,7 +90,7 @@ $d->while_logged_in_as("submitter", sub {
 
     `rm -r $cache_dir`;
 
-    $d->find_element_ok('//select[@id="corr_pops_list_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'trials dataset')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'trials dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(20);
@@ -193,9 +193,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $cor);
     sleep(5);
-    $d->find_element_ok('corr_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('corr_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="corr_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('run_genetic_correlation', 'id',  'calc gen corr')->click();
     sleep(40);
@@ -207,9 +207,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $cor);
     sleep(5);
-    $d->find_element_ok('corr_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('corr_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="corr_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('run_genetic_correlation', 'id',  'calc gen corr')->click();
     sleep(40);
@@ -220,9 +220,9 @@ $d->while_logged_in_as("submitter", sub {
     my $si = $d->find_element('Calculate selection', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $si);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[contains(text(), "Kasese")]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[contains(text(), "Kasese")]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
@@ -268,10 +268,10 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('submit_job', 'id', 'submit')->click();
     sleep(200);
+
     $d->find_element_ok('Go back', 'partial_link_text', 'go back')->click();
     sleep(3);
 
-
     $d->find_element_ok('population_search_entry', 'id', 'population search form')->send_keys('Kasese solgs trial');
     sleep(2);
     $d->find_element_ok('search_training_pop', 'id', 'search for training pop')->click();
@@ -298,7 +298,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->find_element('Phenotypic correlation', 'partial_link_text', 'scroll to correlation')->click();
     sleep(1);
     $d->find_element_ok('run_pheno_correlation', 'id', 'run correlation')->click();
-    sleep(60);
+    sleep(100);
     $d->find_element_ok('//div[@id="corr_canvas"]//*[contains(text(), "DMCP")]', 'xpath', 'check corr plot');
     sleep(5);
     $d->find_element_ok('coefficients', 'partial_link_text',  'download corr coef table');
@@ -351,12 +351,12 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $cor);
     sleep(5);
-    $d->find_element_ok('corr_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('corr_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="corr_select_pops"]/option[text()="Training population 2804608595"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="Training population 2804608595"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('run_genetic_correlation', 'id',  'calc gen corr')->click();
-    sleep(70);
+    sleep(80);
     $d->find_element_ok('//div[@id="corr_canvas"]//*[contains(text(), "DMCP")]', 'xpath', 'check corr plot');
     sleep(5);
 
@@ -366,9 +366,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-200);", $cor);
     sleep(5);
-    $d->find_element_ok('corr_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('corr_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="corr_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="corr_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('run_genetic_correlation', 'id',  'calc gen corr')->click();
     sleep(70);
@@ -378,9 +378,9 @@ $d->while_logged_in_as("submitter", sub {
     my $si = $d->find_element('Calculate selection', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $si);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[contains(text(), "Training population")]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[contains(text(), "Training population")]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
diff --git a/t/selenium2/solgs/kinship.t b/t/selenium2/solgs/kinship.t
index a2dd2f59b7..0a6b94e940 100644
--- a/t/selenium2/solgs/kinship.t
+++ b/t/selenium2/solgs/kinship.t
@@ -63,11 +63,11 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->get_ok('/kinship/analysis', 'kinship home page');
     sleep(5);
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
     sleep(2);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
     sleep(40);
@@ -82,11 +82,11 @@ $d->while_logged_in_as("submitter", sub {
 
     $d->driver->refresh();
     sleep(3);
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
     sleep(2);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
     sleep(150);
@@ -104,11 +104,11 @@ $d->while_logged_in_as("submitter", sub {
     `rm -r $cache_dir`;
     sleep(3);
 
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
     sleep(2);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(2);
@@ -122,11 +122,11 @@ $d->while_logged_in_as("submitter", sub {
     sleep(10);
 
     # $d->get_ok('/kinship/analysis/list_17/gp/1', 'cluster home page');
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
     sleep(3);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     my $sel = $d->find_element('//div[@id="kinship_div"]//*[contains(text(), "Download")]', 'xpath', 'scroll up');
     my $elem =$d->driver->execute_script("arguments[0].scrollIntoView(true);window.scrollBy(0, 150);", $sel);
@@ -139,11 +139,11 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(5);
 
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select clones list')->click();
     sleep(4);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
     sleep(140);
@@ -153,11 +153,11 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(3);
 
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'select trials dataset')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'select trials dataset')->click();
     sleep(2);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
     sleep(160);
@@ -169,11 +169,11 @@ $d->while_logged_in_as("submitter", sub {
 
     `rm -r $cache_dir`;
     sleep(3);
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select clones list')->click();
     sleep(2);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(3);
     $d->find_element_ok('queue_job', 'id', 'job queueing')->click();
     sleep(3);
@@ -188,11 +188,11 @@ $d->while_logged_in_as("submitter", sub {
 
     # $d->get_ok('/kinship/analysis/dataset_4/gp/1', 'cluster home page');
     # sleep(20);
-    $d->find_element_ok('//select[@id="kinship_pops_list_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="kinship_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select clones list')->click();
     sleep(2);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(3);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(5);
     my $sel = $d->find_element('//div[@id="kinship_div"]//*[contains(text(), "Download")]', 'xpath', 'scroll up');
     my $elem =$d->driver->execute_script("arguments[0].scrollIntoView(true);window.scrollBy(0, 150);", $sel);
@@ -214,7 +214,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(2);
     $d->find_element_ok('Kinship', 'partial_link_text', 'expand kinship')->click();
     sleep(5);
-    $d->find_element_ok('run_kinship', 'id', 'select k number')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'select k number')->click();
     sleep(2);
     $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
     sleep(120);
@@ -281,7 +281,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('Kinship', 'partial_link_text', 'toogle kinship')->click();
     sleep(5);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
     sleep(120);
@@ -305,7 +305,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('Kinship', 'partial_link_text', 'toogle kinship')->click();
     sleep(5);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(120);
     my $sel = $d->find_element('//div[@id="kinship_div"]//*[contains(text(), "Download")]', 'xpath', 'scroll up');
     my $elem =$d->driver->execute_script("arguments[0].scrollIntoView(true);window.scrollBy(0, -100);", $sel);
@@ -400,7 +400,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('Kinship', 'partial_link_text', 'toogle kinship')->click();
     sleep(5);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(2);
     $d->find_element_ok('no_queue', 'id', 'no job queueing')->click();
     sleep(120);
@@ -422,7 +422,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('Kinship', 'partial_link_text', 'toogle kinship')->click();
     sleep(5);
-    $d->find_element_ok('run_kinship', 'id', 'run kinship')->click();
+    $d->find_element_ok('//*[starts-with(@id, "run_kinship")]', 'xpath', 'run kinship')->click();
     sleep(120);
     $d->find_element_ok('//*[contains(text(), "Diagonals")]', 'xpath', 'check output')->click();
     sleep(4);
diff --git a/t/selenium2/solgs/selection_index.t b/t/selenium2/solgs/selection_index.t
index 21a812a2c7..cd5c11065f 100644
--- a/t/selenium2/solgs/selection_index.t
+++ b/t/selenium2/solgs/selection_index.t
@@ -132,9 +132,9 @@ $d->while_logged_in_as("submitter", sub {
     my $si = $d->find_element('selection index', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $si);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
@@ -159,9 +159,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('selection index', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $cor);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(2);
     sleep(5);
@@ -280,9 +280,9 @@ $d->while_logged_in_as("submitter", sub {
     my $si = $d->find_element('selection index', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $si);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[contains(text(), "Training population 280")]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[contains(text(), "Training population 280")]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
@@ -305,9 +305,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('selection index', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $cor);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[text()="trial2 NaCRRI"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(2);
     sleep(5);

From 60131cd86d4e0c2e61a6761b8a2fb1fbbdb46ede Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 19 Jun 2023 16:23:08 +0200
Subject: [PATCH 50/61] apply formatting

---
 js/source/legacy/solGS/kinship.js | 894 ++++++++++++++++--------------
 1 file changed, 480 insertions(+), 414 deletions(-)

diff --git a/js/source/legacy/solGS/kinship.js b/js/source/legacy/solGS/kinship.js
index 017ed0e98d..d95ef1eca6 100644
--- a/js/source/legacy/solGS/kinship.js
+++ b/js/source/legacy/solGS/kinship.js
@@ -4,426 +4,492 @@
  *
  */
 
-
 var solGS = solGS || function solGS() {};
 
 solGS.kinship = {
-
-	getKinshipArgs: function() {
-
-		var page = location.pathname;
-		var kinshipPopId;
-		var kinshipUrlArgs;
-		var dataStr;
-		var trainingPopId;
-		var selectionPopId;
-
-		if (page.match(/solgs\/trait\/|solgs\/model\/combined\/trials\/|\/breeders\/trial\//)) {
-
-			trainingPopId = jQuery("#training_pop_id").val();
-			if (!trainingPopId) {
-				trainingPopId = jQuery("#trial_id").val();
-			}
-			kinshipPopId = trainingPopId;
-		} else if (page.match(/kinship\/analysis/)) {
-
-			kinshipUrlArgs = this.getKinshipArgsFromUrl();
-			kinshipPopId = kinshipUrlArgs.kinship_pop_id;
-			dataStr = kinshipUrlArgs.data_structure;
-			protocolId = kinshipUrlArgs.genotyping_protocol_id;
-
-		} else if (page.match(/\/selection\/|\/prediction\//)) {
-
-			selectionPopId = jQuery("#selection_pop_id").val();
-			kinshipPopId = selectionPopId;
-
-		} else if (page.match(/solgs\/traits\/all\/population\/|models\/combined\/trials\//)) {
-			trainingPopId = jQuery("#training_pop_id").val();
-			kinshipPopId = trainingPopId;
-			
-		}
-
-		if (page.match(/combined/)) {
-			var comboPopsId =  trainingPopId;
-		}
-
-		var protocolId = jQuery("#genotyping_protocol_id").val();
-		var traitId = jQuery("#trait_id").val();
-
-		return {
-			'kinship_pop_id': kinshipPopId,
-			'training_pop_id': trainingPopId,
-			'combo_pops_id': comboPopsId,
-			'selection_pop_id': selectionPopId,
-			'data_structure': dataStr,
-			'genotyping_protocol_id': protocolId,
-			'trait_id': traitId,
-			'analysis_type': 'kinship analysis'
-		};
-	},
-
-
-	getKinshipArgsFromUrl: function() {
-
-		var page = location.pathname;
-		if (page == '/kinship/analysis/') {
-			page = '/kinship/analysis';
-		}
-		var urlArgs = page.replace("/kinship/analysis", "")
-
-		if (urlArgs) {
-			var args = urlArgs.split(/\/+/);
-			var selectId = args[1];
-			var protocolId = args[3];
-
-			var dataStr;
-			var reg = /\d+/;
-			var popId = selectId.match(reg)[0];
-			if (selectId.match(/dataset/)) {
-				dataStr = 'dataset';
-			} else if (selectId.match(/list/)) {
-				dataStr = 'list';
-			}
-
-			var args = {
-				'kinship_pop_id': popId,
-				'data_structure': dataStr,
-				'genotyping_protocol_id': protocolId,
-			};
-
-			return args;
-		} else {
-			return {};
-		}
-
-	},
-
-
-	loadKinshipPops: function(selectId, selectName, dataStructure) {
-
-		if (selectId.length === 0) {
-			alert('The list is empty. Please select a list with content.');
-		} else {
-
-			var kinshipTable = jQuery("#kinship_pops_table").doesExist();
-
-			if (!kinshipTable) {
-				kinshipTable = this.createTable();
-				jQuery("#kinship_pops_selected").append(kinshipTable).show();
-			}
-
-			var onClickVal = '<button type="button" id="run_kinship" class="btn btn-success" onclick="solGS.kinship.runKinship(' +
-				selectId + ",'" + selectName + "'" + ",'" + dataStructure +
-				"'" + ')">Run Kinship</button>';
-
-
-			var dataType = ['Genotype'];
-			var dataTypeOpts = this.createDataTypeSelect(dataType);
-
-			var addRow = '<tr  name="' + dataStructure + '"' + ' id="' + selectId + '">' +
-				'<td>' + selectName + '</td>' +
-				'<td>' + dataStructure + '</td>' +
-				'<td>' + dataTypeOpts + '</td>' +
-				'<td id="list_kinship_page_' + selectId + '">' + onClickVal + '</td>' +
-				'<tr>';
-
-			var tdId = '#list_kinship_page_' + selectId;
-			var addedRow = jQuery(tdId).doesExist();
-
-			if (!addedRow) {
-				jQuery("#kinship_pops_table tr:last").after(addRow);
-			}
-		}
-
-	},
-
-	createTable: function() {
-		var kinshipTable = '<table id="kinship_pops_table" class="table table-striped"><tr>' +
-			'<th>Population</th>' +
-			'<th>Data structure type</th>' +
-			'<th>Data type</th>' +
-			'<th>Run Kinship</th>' +
-			'</tr>' +
-			'</td></tr></table>';
-
-		return kinshipTable;
-	},
-
-
-	createDataTypeSelect: function(opts) {
-		var dataTypeGroup = '<select class="form-control" id="kinship_data_type_select">';
-
-		for (var i = 0; i < opts.length; i++) {
-
-			dataTypeGroup += '<option value="' +
-				opts[i] + '">' +
-				opts[i] +
-				'</option>';
-		}
-		dataTypeGroup += '</select>';
-
-		return dataTypeGroup;
-	},
-
-
-	runKinship: function(selectId, selectName, dataStr) {
-
-		var kinshipArgs;
-	
-		var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId('kinship_div');
-		if (location.pathname.match(/kinship\/analysis/)) {
-
-		kinshipArgs = {
-			'kinship_pop_id': selectId,
-			'kinship_pop_name': selectName,
-			'data_structure': dataStr,
-			'genotyping_protocol_id': protocolId,
-			'analysis_type': 'kinship analysis'
-		};	
-		} else {
-			kinshipArgs = this.getKinshipArgs();
-			selectId = kinshipArgs.kinship_pop_id;
-		}
-
-	
-		var page;
-		if (dataStr) {
-			page = '/kinship/analysis/' + dataStr + '_' + selectId + '/gp/' + protocolId;
-		} else {
-			page = '/kinship/analysis/' + selectId + '/gp/' + protocolId;
-		}
-		
-		this.checkCachedKinship(page, kinshipArgs);
-
-	},
-
-	checkCachedKinship: function(page, args) {
-
-		args = JSON.stringify(args);
-
-		jQuery.ajax({
-			type: 'POST',
-			dataType: 'json',
-			data: {
-				'page': page,
-				'arguments': args
-			},
-			url: '/solgs/check/cached/result/',
-			success: function(response) {
-				args = JSON.parse(args);
-				if (response.cached) {
-					solGS.kinship.runKinshipAnalysis(page, args);
-				} else {
-					solGS.kinship.optJobSubmission(page, args);
-				}
-			},
-			error: function() {
-				alert('Error occured checking for cached output.')
-			}
-		});
-	},
-
-
-	optJobSubmission: function(page, args) {
-
-		var title = '<p>This analysis may take a long time. ' +
-			'Do you want to submit the analysis and get an email when it completes?</p>';
-
-		var jobSubmit = '<div id= "kinship_submit">' + title + '</div>';
-
-		jQuery(jobSubmit).appendTo('body');
-
-		jQuery('#kinship_submit')
-			.dialog({
-				height: 200,
-				width: 400,
-				modal: true,
-				title: "Kinship job submission",
-				buttons: {
-					OK: {
-						text: 'Yes',
-						class: 'btn btn-success',
-						id: 'queue_job',
-						click: function() {
-							jQuery(this).dialog("close");
-
-							solGS.submitJob.checkUserLogin(page, args);
-						},
-					},
-
-					No: {
-						text: 'No, I will wait till it completes.',
-						class: 'btn btn-warning',
-						id: 'no_queue',
-						click: function() {
-							jQuery(this).dialog("close");
-
-							solGS.kinship.runKinshipAnalysis(page, args);
-						},
-					},
-
-					Cancel: {
-						text: 'Cancel',
-						class: 'btn btn-info',
-						id: 'cancel_queue_info',
-						click: function() {
-							jQuery(this).dialog("close");
-						},
-					},
-				}
-			});
-
-	},
-
-	runKinshipAnalysis: function(page, args) {
-
-		var kinArgs = JSON.stringify(args)
-		jQuery("#run_kinship").hide();
-		jQuery("#kinship_message")
-			.text("Running kinship... please wait...it may take minutes.")
-			.show();
-
-		jQuery("#kinship_canvas .multi-spinner-container").show();
-
-		jQuery.ajax({
-			type: 'POST',
-			dataType: 'json',
-			data: {'arguments': kinArgs},
-			url: '/run/kinship/analysis/',
-			success: function(res) {
-				if (res.data) {
-						jQuery("#kinship_message")
-							.html("Generating heatmap... please wait...")
-							.show();
-	
-							var kinCanvas = "#kinship_canvas";
-							var kinPlotDivId = "#kinship_plot_" + res.kinship_file_id;
-							var links = solGS.kinship.addDowloandLinks(res);
-							solGS.heatmap.plot(res.data, kinCanvas, kinPlotDivId , links);
-	
-						jQuery("#kinship_canvas .multi-spinner-container").hide();
-						jQuery("#kinship_message").empty();
-	
-				} else {
-	
-						jQuery("#kinship_canvas .multi-spinner-container").hide();
-						jQuery("#kinship_message")
-							.css({
-								"padding-left": '0px'
-							})
-							.html("This population has no kinship output data.")
-							.fadeOut(8400);
-	
-						jQuery("#run_kinship").show();
-				} 
-			},
-			error: function(res) {
-				jQuery("#kinship_message")
-					.html('Error occured running the kinship.')
-					.show()
-					.fadeOut(8400);
-
-				jQuery("#kinship_canvas .multi-spinner-container").hide();
-			}
-		});
-	},
-
-
-	addDowloandLinks: function(res) {
-		console.log(`adddownloadlinks res: ${JSON.stringify(res)}`)
-		var popName = res.kinship_pop_name;
-		var kinFileId = res.kinship_file_id;
-		var kinshipFile = res.kinship_table_file;
-
-		var aveFile = res.kinship_averages_file;
-		var inbreedingFile = res.inbreeding_file;
-
-		var fileNameKinship = kinshipFile.split('/').pop();
-		var fileNameAve = aveFile.split('/').pop();
-		var fileNameInbreeding = inbreedingFile.split('/').pop();
-
-		kinshipFile = "<a href=\"" + kinshipFile +
-			"\" download=" + fileNameKinship + ">Kinship matrix</a>";
-
-		aveFile = "<a href=\"" + aveFile +
-			"\" download=" + fileNameAve + ">Average kinship</a>";
-
-		inbreedingFile = "<a href=\"" + inbreedingFile +
-			"\" download=" + fileNameInbreeding + ">Inbreeding coefficients</a>";
-
-			var kinDownloadBtn = "download_" + "kinship_plot_" + kinFileId;
-			var kinPlotLink = "<a href='#'  onclick='event.preventDefault();' id='" + kinDownloadBtn + "'> plot</a>";
-
-		var links = '<strong>Download:</strong> ';
-
-		if (popName) {
-			links = links + popName + ' ';
-		}
-
-		links = links + kinshipFile + ' | ' +
-			aveFile + ' | ' +
-			inbreedingFile + ' | ' + 
-			kinPlotLink;
-
-		return links;
-	},
-
-	///////
-}
-
-
-
-jQuery(document).ready(function() {
-
-	jQuery("#run_kinship").click(function() {
-		solGS.kinship.runKinship();
-	});
-
+  canvas: "#kinship_canvas",
+  kinshipPlotDivPrefix: "#kinship_plot",
+  kinshipMsgDiv: "#kinship_message",
+  kinshipPopsSelectMenuId: "#kinship_pops_select",
+  kinshipPopsDiv: "#kinship_pops_select_div",
+
+  getKinshipArgs: function () {
+    var page = location.pathname;
+    var kinshipPopId;
+    var kinshipUrlArgs;
+    var dataStr;
+    var trainingPopId;
+    var selectionPopId;
+
+    if (page.match(/solgs\/trait\/|solgs\/model\/combined\/trials\/|\/breeders\/trial\//)) {
+      trainingPopId = jQuery("#training_pop_id").val();
+      if (!trainingPopId) {
+        trainingPopId = jQuery("#trial_id").val();
+      }
+      kinshipPopId = trainingPopId;
+    } else if (page.match(/kinship\/analysis/)) {
+      kinshipUrlArgs = this.getKinshipArgsFromUrl();
+      kinshipPopId = kinshipUrlArgs.kinship_pop_id;
+      dataStr = kinshipUrlArgs.data_structure;
+      protocolId = kinshipUrlArgs.genotyping_protocol_id;
+    } else if (page.match(/\/selection\/|\/prediction\//)) {
+      selectionPopId = jQuery("#selection_pop_id").val();
+      kinshipPopId = selectionPopId;
+    } else if (page.match(/solgs\/traits\/all\/population\/|models\/combined\/trials\//)) {
+      trainingPopId = jQuery("#training_pop_id").val();
+      kinshipPopId = trainingPopId;
+    }
+
+    if (page.match(/combined/)) {
+      var comboPopsId = trainingPopId;
+    }
+
+    var protocolId = jQuery("#genotyping_protocol_id").val();
+    var traitId = jQuery("#trait_id").val();
+
+    return {
+      kinship_pop_id: kinshipPopId,
+      training_pop_id: trainingPopId,
+      combo_pops_id: comboPopsId,
+      selection_pop_id: selectionPopId,
+      data_structure: dataStr,
+      genotyping_protocol_id: protocolId,
+      trait_id: traitId,
+      analysis_type: "kinship analysis",
+    };
+  },
+
+  getKinshipArgsFromUrl: function () {
+    var page = location.pathname;
+    if (page == "/kinship/analysis/") {
+      page = "/kinship/analysis";
+    }
+    var urlArgs = page.replace("/kinship/analysis", "");
+
+    if (urlArgs) {
+      var args = urlArgs.split(/\/+/);
+      var selectId = args[1];
+      var protocolId = args[3];
+
+      var dataStr;
+      var reg = /\d+/;
+      var popId = selectId.match(reg)[0];
+      if (selectId.match(/dataset/)) {
+        dataStr = "dataset";
+      } else if (selectId.match(/list/)) {
+        dataStr = "list";
+      }
+
+      var args = {
+        kinship_pop_id: popId,
+        data_structure: dataStr,
+        genotyping_protocol_id: protocolId,
+      };
+
+      return args;
+    } else {
+      return {};
+    }
+  },
+
+  displaySelectedKinshipPop: function (selectedPop) {
+    if (selectedPop.length === 0) {
+      alert("The list is empty. Please select a list with content.");
+    } else {
+      var kinshipTable = jQuery("#kinship_pops_table").doesExist();
+
+      if (kinshipTable == false) {
+        kinshipTable = this.createTable();
+        jQuery("#kinship_pops_selected").append(kinshipTable).show();
+      }
+
+      var newRow = this.selectRow(selectedPop);
+      var kinshipPopId = `${selectedPop.data_str}_${selectedPop.id}`;
+      var tdId = this.getTableTdId(kinshipPopId);
+      var rowExists = jQuery(`#${tdId}`).doesExist();
+
+      if (!rowExists) {
+        jQuery("#kinship_pops_table tr:last").after(newRow);
+      }
+    }
+  },
+
+  getTableTdId: function (kinshipPopId) {
+    return `kinship_${kinshipPopId}`;
+  },
+
+  selectRow: function (selectedPop) {
+    var selectedId = selectedPop.id;
+    var selectedName = selectedPop.name;
+    var dataStr = selectedPop.data_str;
+
+    var kinshipPopId = `${dataStr}_${selectedId}`;
+
+    if (dataStr.match(/dataset/)) {
+      datasetId = selectedId;
+    } else if (dataStr.match(/list/)) {
+      listId = selectedId;
+    }
+
+    var kinshipArgs = {
+      kinship_pop_id: kinshipPopId,
+      kinship_pop_name: selectedName,
+      data_str: dataStr,
+      data_structure: dataStr,
+    };
+
+    var runKinshipBtnId = this.getRunKinshipBtnId(kinshipPopId);
+
+    kinshipArgs = JSON.stringify(kinshipArgs);
+    var runKinshipBtn =
+      `<button type="button" id=${runKinshipBtnId}` +
+      ` class="btn btn-success" data-selected-pop='${kinshipArgs}'>Run kinship</button>`;
+
+    var dataType = ["Genotype"];
+    var dataTypeOpts = this.createDataTypeSelect(dataType);
+
+    var tdId = this.getTableTdId(kinshipPopId);
+    var newRow =
+      `<tr  name="${kinshipPopId}" id="${kinshipPopId}">` +
+      ` <td>${selectedName}</td>` +
+      ` <td>${dataStr}</td>` +
+      ` <td>${dataTypeOpts}</td>` +
+      `<td id="${tdId}">` +
+      runKinshipBtn +
+      "</td>" +
+      "<tr>";
+
+    return newRow;
+  },
+
+  createTable: function () {
+    var kinshipTable =
+      '<table id="kinship_pops_table" class="table table-striped"><tr>' +
+      "<th>Population</th>" +
+      "<th>Data structure type</th>" +
+      "<th>Data type</th>" +
+      "<th>Run Kinship</th>" +
+      "</tr>" +
+      "</td></tr></table>";
+
+    return kinshipTable;
+  },
+
+  createDataTypeSelect: function (opts) {
+    var dataTypeGroup = '<select class="form-control" id="kinship_data_type_select">';
+
+    for (var i = 0; i < opts.length; i++) {
+      dataTypeGroup += '<option value="' + opts[i] + '">' + opts[i] + "</option>";
+    }
+    dataTypeGroup += "</select>";
+
+    return dataTypeGroup;
+  },
+
+  getSelectedPopKinshipArgs: function (runKinshipElemId) {
+    var kinshipArgs;
+
+    // var runKinshipElemId = this.getRunKinshipId(kinshipPopId);
+    var selectedPopDiv = document.getElementById(runKinshipElemId);
+    if (selectedPopDiv) {
+      var selectedPopData = selectedPopDiv.dataset;
+
+      var kinshipArgs = JSON.parse(selectedPopData.selectedPop);
+      var kinshipPopId = kinshipArgs.data_str + "_" + kinshipArgs.id;
+
+      var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("kinship_div");
+      var page = `/kinship/analysis/${kinshipPopId}/gp/${protocolId}`;
+
+      kinshipArgs["analysis_type"] = "kinship analysis";
+      kinshipArgs["genotyping_protocol_id"] = protocolId;
+      kinshipArgs["analysis_page"] = page;
+      kinshipArgs["data_structure"] = kinshipArgs.data_str;
+    }
+
+    return kinshipArgs;
+  },
+
+  checkCachedKinship: function (page, args) {
+    args = JSON.stringify(args);
+
+    var checkCached = jQuery.ajax({
+      type: "POST",
+      dataType: "json",
+      data: {
+        page: page,
+        arguments: args,
+      },
+      url: "/solgs/check/cached/result/",
+    });
+
+    return checkCached;
+  },
+
+  runKinshipAnalysis: function (args) {
+    var kinArgs = JSON.stringify(args);
+
+    var runKinship = jQuery.ajax({
+      type: "POST",
+      dataType: "json",
+      data: { arguments: kinArgs },
+      url: "/run/kinship/analysis/",
+    });
+
+    return runKinship;
+  },
+
+  addDowloandLinks: function (res) {
+    console.log(`adddownloadlinks res: ${JSON.stringify(res)}`);
+    var popName = res.kinship_pop_name;
+    var kinFileId = res.kinship_file_id;
+    var kinshipFile = res.kinship_table_file;
+
+    var aveFile = res.kinship_averages_file;
+    var inbreedingFile = res.inbreeding_file;
+
+    var fileNameKinship = kinshipFile.split("/").pop();
+    var fileNameAve = aveFile.split("/").pop();
+    var fileNameInbreeding = inbreedingFile.split("/").pop();
+
+    kinshipFile =
+      '<a href="' + kinshipFile + '" download=' + fileNameKinship + ">Kinship matrix</a>";
+
+    aveFile = '<a href="' + aveFile + '" download=' + fileNameAve + ">Average kinship</a>";
+
+    inbreedingFile =
+      '<a href="' +
+      inbreedingFile +
+      '" download=' +
+      fileNameInbreeding +
+      ">Inbreeding coefficients</a>";
+
+    var kinDownloadBtn = "download_" + "kinship_plot_" + kinFileId;
+    var kinPlotLink =
+      "<a href='#'  onclick='event.preventDefault();' id='" + kinDownloadBtn + "'> plot</a>";
+
+    var links = "<strong>Download:</strong> ";
+
+    if (popName) {
+      links = links + popName + " ";
+    }
+
+    links = links + kinshipFile + " | " + aveFile + " | " + inbreedingFile + " | " + kinPlotLink;
+
+    return links;
+  },
+
+  populateKinshipPopsMenu: function () {
+    var listTypes = ["accessions", "trials"];
+    var datasetTypes = ["accessions", "trials"];
+    var menuId = this.kinshipPopsSelectMenuId;
+    var menu = new SelectMenu(menuId);
+    var selectMenu = menu.getSelectMenuByTypes(listTypes, datasetTypes);
+
+    var kinshipPopsDiv = this.kinshipPopsDiv;
+    jQuery(kinshipPopsDiv).append(selectMenu).show();
+  },
+
+  getRunKinshipBtnId: function (rowId) {
+    if (location.pathname.match(/kinship\/analysis/) && rowId) {
+      return `run_kinship_${rowId}`;
+    } else {
+      return "run_kinship";
+    }
+  },
+
+  getKinshipPopId: function (selectId, dataStr) {
+    var kinshipPopId;
+    if (dataStr) {
+      kinshipPopId = `${dataStr}_${selectId}`;
+    } else {
+      kinshipPopId = selectId;
+    }
+
+    return kinshipPopId;
+  },
+
+  ///////
+};
+
+jQuery(document).ready(function () {
+  jQuery("#kinship_div").on("click", function (e) {
+    var runKinshipBtnId = e.target.id;
+    if (runKinshipBtnId.match(/run_kinship/)) {
+      var kinshipArgs = solGS.kinship.getKinshipArgs();
+      var kinshipPopId = kinshipArgs.kinship_pop_id;
+      if (!kinshipPopId) {
+        kinshipArgs = solGS.kinship.getSelectedPopKinshipArgs(runKinshipBtnId);
+      }
+      kinshipPopId = kinshipArgs.kinship_pop_id;
+      var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("kinship_div");
+
+      var canvas = solGS.kinship.canvas;
+      var kinshipPlotDivId = solGS.kinship.kinshipPlotDivPrefix;
+      var kinshipMsgDiv = solGS.kinship.kinshipMsgDiv;
+      runKinshipBtnId = `#${runKinshipBtnId}`;
+      var kinshipUrl = `/kinship/analysis/${kinshipPopId}/gp/${protocolId}`;
+      //    solGS.kinship.generateKinshipUrl(kinshipPopId);
+      kinshipArgs["analysis_page"] = kinshipUrl;
+
+      jQuery(runKinshipBtnId).hide();
+      jQuery(`${canvas} .multi-spinner-container`).show();
+
+      jQuery(runKinshipBtnId).hide();
+      jQuery(kinshipMsgDiv).text("Running kinship... please wait...it may take minutes.").show();
+
+      jQuery(`${canvas} .multi-spinner-container`).show();
+      solGS.kinship
+        .checkCachedKinship(kinshipUrl, kinshipArgs)
+        .done(function (res) {
+          if (res.data) {
+            jQuery(this.kinshipMsgDiv).html("Generating heatmap... please wait...").show();
+
+            kinshipPlotDivId = `${kinshipPlotDivId}_${res.kinship_file_id}`;
+
+            var links = solGS.kinship.addDowloandLinks(res);
+            solGS.heatmap.plot(res.data, canvas, kinshipPlotDivId, links);
+
+            jQuery(`${canvas} .multi-spinner-container`).hide();
+            jQuery(kinshipMsgDiv).empty();
+            jQuery(runKinshipBtnId).show();
+          } else {
+
+			jQuery(`${canvas} .multi-spinner-container`).hide();
+            jQuery(kinshipMsgDiv).empty();
+
+            var title =
+              "<p>This analysis may take a long time. " +
+              "Do you want to submit the analysis and get an email when it completes?</p>";
+
+            var jobSubmit = '<div id= "kinship_submit">' + title + "</div>";
+
+            jQuery(jobSubmit).appendTo("body");
+
+            jQuery("#kinship_submit").dialog({
+              height: 200,
+              width: 400,
+              modal: true,
+              title: "Kinship job submission",
+              buttons: {
+                OK: {
+                  text: "Yes",
+                  class: "btn btn-success",
+                  id: "queue_job",
+                  click: function () {
+                    jQuery(this).dialog("close");
+
+                    solGS.submitJob.checkUserLogin(kinshipUrl, kinshipArgs);
+                  },
+                },
+
+                No: {
+                  text: "No, I will wait till it completes.",
+                  class: "btn btn-warning",
+                  id: "no_queue",
+                  click: function () {
+                    jQuery(this).dialog("close");
+
+					jQuery(kinshipMsgDiv).text("Running kinship... please wait...it may take minutes.").show();
+					jQuery(`${canvas} .multi-spinner-container`).show();
+
+                    solGS.kinship
+                      .runKinshipAnalysis(kinshipArgs)
+                      .done(function (res) {
+                        if (res.data) {
+                          jQuery(kinshipMsgDiv)
+                            .html("Generating heatmap... please wait...")
+                            .show();
+
+                          kinshipPlotDivId = `${kinshipPlotDivId}_${res.kinship_file_id}`;
+
+                          var links = solGS.kinship.addDowloandLinks(res);
+                          solGS.heatmap.plot(res.data, canvas, kinshipPlotDivId, links);
+
+                          jQuery(`${canvas} .multi-spinner-container`).hide();
+                          jQuery(kinshipMsgDiv).empty();
+                          jQuery(runKinshipBtnId).show();
+                        } else {
+                          jQuery(`${canvas} .multi-spinner-container`).hide();
+                          jQuery(kinshipMsgDiv)
+                            .css({
+                              "padding-left": "0px",
+                            })
+                            .html("This population has no kinship output data.")
+                            .fadeOut(8400);
+
+                          jQuery(runKinshipBtnId).show();
+                        }
+                      })
+                      .fail(function () {
+                        jQuery(this.kinshipMsgDiv)
+                          .html("Error occured running the kinship.")
+                          .show()
+                          .fadeOut(8400);
+
+                        jQuery(`${canvas} .multi-spinner-container`).hide();
+                      });
+                  },
+                },
+
+                Cancel: {
+                  text: "Cancel",
+                  class: "btn btn-info",
+                  id: "cancel_queue_info",
+                  click: function () {
+                    jQuery(this).dialog("close");
+                  },
+                },
+              },
+            });
+          }
+        })
+        .fail(function () {
+          jQuery(kinshipMsgDiv).html("Error occured running the kinship.").show().fadeOut(8400);
+          jQuery(`${canvas} .multi-spinner-container`).hide();
+        });
+    }
+  });
 });
 
-jQuery(document).ready(function() {
-
-	var url = location.pathname;
-
-	if (url.match(/kinship\/analysis/)) {
-		solGS.selectMenu.populateMenu("kinship_pops", ['accessions', 'trials'], ['accessions', 'trials'])
-		var args = solGS.kinship.getKinshipArgsFromUrl();
-
-		if (args.kinship_pop_id) {
-
-			if (args.data_structure) {
-				args['kinship_pop_id'] = args.data_structure + '_' + args.kinship_pop_id;
-			}
-			
-			solGS.kinship.checkCachedKinship(url, args);
-		}
-	}
-
+jQuery(document).ready(function () {
+  var url = location.pathname;
+
+  if (url.match(/kinship\/analysis/)) {
+    solGS.kinship.populateKinshipPopsMenu();
+    var args = solGS.kinship.getKinshipArgsFromUrl();
+    if (args.kinship_pop_id) {
+      if (args.data_structure) {
+        args["kinship_pop_id"] = args.data_structure + "_" + args.kinship_pop_id;
+      }
+      solGS.kinship.checkCachedKinship(url, args);
+    }
+  }
 });
 
-jQuery(document).ready(function() {
-	jQuery("#kinship_canvas").on('click' , 'a', function(e) {
-		var buttonId = e.target.id;
-		var kinPlotId = buttonId.replace(/download_/, '');
-		console.log(`buttonID ${buttonId} -- kinplotId: ${kinPlotId}`)
-		saveSvgAsPng(document.getElementById("#" + kinPlotId),  kinPlotId + ".png", {scale: 1});	
-	});
+jQuery(document).ready(function () {
+  jQuery("#kinship_canvas").on("click", "a", function (e) {
+    var buttonId = e.target.id;
+    var kinPlotId = buttonId.replace(/download_/, "");
+    console.log(`buttonID ${buttonId} -- kinplotId: ${kinPlotId}`);
+    saveSvgAsPng(document.getElementById("#" + kinPlotId), kinPlotId + ".png", { scale: 1 });
+  });
 });
 
-jQuery(document).ready(function() {
-
-	var url = location.pathname;
-
-	if (url.match(/kinship\/analysis/)) {
-		jQuery("#kinship_pops_list_select").change(function() {
-			var selectedPop = solGS.selectMenu.getSelectedPop('kinship_pops');
-			if (selectedPop.selected_id) {
-				jQuery("#kinship_pop_go_btn").click(function() {
-					solGS.kinship.loadKinshipPops(selectedPop.selected_id, selectedPop.selected_name, selectedPop.data_str);
-				});
-			}
-		});
-	}
-
-
-});
\ No newline at end of file
+jQuery(document).ready(function () {
+  var url = location.pathname;
+
+  if (url.match(/kinship\/analysis/)) {
+    var kinshipPopsDiv = solGS.kinship.kinshipPopsSelectMenuId;
+    jQuery(kinshipPopsDiv).change(function () {
+      var selectedPop = jQuery("option:selected", this).data("pop");
+      if (selectedPop.id) {
+        jQuery("#kinship_pop_go_btn").click(function () {
+          if (!selectedPop.data_str) {
+            selectedPop.data_str = "list";
+          }
+          solGS.kinship.displaySelectedKinshipPop(selectedPop);
+        });
+      }
+    });
+  }
+});

From a3e5f6b0574f0ae013d44e5d575b7a0fffd99fdc Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 19 Jun 2023 16:24:10 +0200
Subject: [PATCH 51/61] change si selectmenu id name

---
 js/source/legacy/solGS/selectionIndex.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/source/legacy/solGS/selectionIndex.js b/js/source/legacy/solGS/selectionIndex.js
index 1271f34332..2a9a0d8f53 100644
--- a/js/source/legacy/solGS/selectionIndex.js
+++ b/js/source/legacy/solGS/selectionIndex.js
@@ -12,7 +12,7 @@ solGS.sIndex = {
   siPlotDivPrefix: "#si_plot",
   siMsgDiv: "#si_message",
   siPopsDiv: "#si_select_pops_div",
-  siPopsSelectMenuId: "#si_select_pops",
+  siPopsSelectMenuId: "#si_pops_select",
   siFormId: "#si_form",
 
   populateSindexMenu: function () {

From a2814706085863612b9a0c9142f9b230dadd1e3f Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 19 Jun 2023 16:25:20 +0200
Subject: [PATCH 52/61] apply formatting

---
 lib/SGN/Controller/solGS/CachedResult.pm | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/lib/SGN/Controller/solGS/CachedResult.pm b/lib/SGN/Controller/solGS/CachedResult.pm
index ced15f801f..19c430ce89 100644
--- a/lib/SGN/Controller/solGS/CachedResult.pm
+++ b/lib/SGN/Controller/solGS/CachedResult.pm
@@ -332,7 +332,7 @@ sub _check_combined_trials_model_selection_output {
 sub _check_kinship_output {
     my ( $self, $c, $kinship_pop_id, $protocol_id, $trait_id ) = @_;
 
-    $c->stash->{rest}=
+    $c->stash->{rest} =
       $self->check_kinship_output( $c, $kinship_pop_id, $protocol_id,
         $trait_id );
 }
@@ -404,7 +404,7 @@ sub check_cached_phenotype_data {
 sub check_single_trial_model_output {
     my ( $self, $c, $pop_id, $trait_id, $protocol_id ) = @_;
 
-    $c->stash->{trait_id} = $trait_id;
+    $c->stash->{trait_id}        = $trait_id;
     $c->stash->{training_pop_id} = $pop_id;
 
     $c->controller('solGS::Files')
@@ -453,8 +453,8 @@ sub check_combined_trials_model_all_traits_output {
 sub check_selection_pop_output {
     my ( $self, $c, $tr_pop_id, $sel_pop_id, $trait_id ) = @_;
 
-    $c->stash->{trait_id} = $trait_id;
-    $c->stash->{training_pop_id} = $tr_pop_id;
+    $c->stash->{trait_id}         = $trait_id;
+    $c->stash->{training_pop_id}  = $tr_pop_id;
     $c->stash->{selection_pop_id} = $sel_pop_id;
 
     $c->controller('solGS::Files')
@@ -531,13 +531,14 @@ sub check_kinship_output {
     my $files = $c->controller('solGS::Kinship')
       ->get_kinship_coef_files( $c, $pop_id, $protocol_id, $trait_id );
 
-      if (-s $files->{'json_file_adj'} && -s $files->{'matrix_file_adj'}) {
-
-         my $res = $c->controller('solGS::Kinship')->structure_kinship_response($c);
-            return $res;
-      } else {
-        return {cached => 0};
-      }
+    if ( -s $files->{'json_file_adj'} && -s $files->{'matrix_file_adj'} ) {
+        my $res =
+          $c->controller('solGS::Kinship')->structure_kinship_response($c);
+        return $res;
+    }
+    else {
+        return { cached => 0 };
+    }
 
 }
 

From 37a05a028c2a062d9a4b37498a484b718cbc1d18 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Mon, 19 Jun 2023 16:26:15 +0200
Subject: [PATCH 53/61] change div id name

---
 mason/solgs/tools/correlation/analysis.mas | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mason/solgs/tools/correlation/analysis.mas b/mason/solgs/tools/correlation/analysis.mas
index 573854da5a..ee1556da12 100644
--- a/mason/solgs/tools/correlation/analysis.mas
+++ b/mason/solgs/tools/correlation/analysis.mas
@@ -76,7 +76,7 @@ if ($url =~ /correlation\/analysis/) {
   title       => $title
   &>
 
-  <div id='correlation_div'>
+  <div id='corr_div'>
 
 % if ($url =~ /correlation\/analysis/) {
 

From fb1a158d933bb76b1a45571fba1e6b44d9ae75c3 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 21 Jun 2023 15:16:39 +0200
Subject: [PATCH 54/61] convert ajax req calls to promises

---
 js/source/legacy/solGS/cluster.js | 710 ++++++++++++++++++------------
 1 file changed, 438 insertions(+), 272 deletions(-)

diff --git a/js/source/legacy/solGS/cluster.js b/js/source/legacy/solGS/cluster.js
index 7fa625b819..13b3f1416e 100644
--- a/js/source/legacy/solGS/cluster.js
+++ b/js/source/legacy/solGS/cluster.js
@@ -82,7 +82,7 @@ solGS.cluster = {
 
       var reg = /\.+-\.+/;
       if (clusterPopId.match(reg)) {
-        var ids = clusterPopd.split("-");
+        var ids = clusterPopId.split("-");
         args["training_pop_id"] = ids[0];
         args["selection_pop_id"] = ids[1];
       }
@@ -92,39 +92,43 @@ solGS.cluster = {
     }
   },
 
-  displaySelectedClusterPop: function (selectId, selectName, dataStr) {
-    var clusterPopId = this.getClusterPopId(selectId, dataStr);
-    if (selectId.length === 0) {
+  displaySelectedClusterPop: function (selectedPop) {
+    var selectedId = selectedPop.id;
+    var selectedName = selectedPop.name;
+    var dataStr = selectedPop.data_str;
+    var clusterPopId = this.getClusterPopId(selectedId, dataStr);
+
+    if (selectedId.length === 0) {
       alert("The list is empty. Please select a list with content.");
     } else {
       var tableId = "cluster_pops_list_table";
       var clusterTable = jQuery("#" + tableId).doesExist();
-      if (clusterTable == false) {
+      if (!clusterTable) {
         clusterTable = this.getClusterPopsTable(tableId);
         jQuery("#cluster_pops_selected").append(clusterTable).show();
       }
 
-      var addRow = this.selectRow(selectId, selectName, dataStr);
-      var tdId = "#list_cluster_page_" + clusterPopId;
-      var addedRow = jQuery(tdId).doesExist();
+      var newRow = this.selectRow(selectedPop);
+      var tdId = "cluster_" + clusterPopId;
+      var rowExists = jQuery(`#${tdId}`).doesExist();
 
-      if (addedRow == false) {
-        jQuery("#" + tableId + " tr:last").after(addRow);
+      if (!rowExists) {
+        jQuery("#" + tableId + " tr:last").after(newRow);
       }
     }
   },
 
-  selectRowId: function (selectId) {
-    var rowId = "row_" + selectId;
+  selectRowId: function (selectedId) {
+    var rowId = "row_" + selectedId;
     return rowId;
   },
 
-  getClusterPopId: function (selectId, dataStr) {
+  getClusterPopId: function (selectedId, dataStr) {
     var clusterPopId;
     if (dataStr) {
-      clusterPopId = `${dataStr}_${selectId}`;
+      clusterPopId = `${dataStr}_${selectedId}`;
     } else {
-      clusterPopId = selectId;
+      clusterPopId = selectedId;
     }
 
     return clusterPopId;
@@ -198,20 +202,20 @@ solGS.cluster = {
   getDataTypeOpts: function (args) {
     if (args) {
       var dataStr = args.data_str;
-      var selectId = args.select_id;
-      var popType = args.pop_type;
+      var selectedId = args.id;
+      var popType = args.type;
     }
 
     var dataTypeOpts = [];
     var page = location.pathname;
 
-    if (selectId && isNaN(selectId)) {
-      selectId = selectId.replace(/\w+_/g, "");
+    if (selectedId && isNaN(selectedId)) {
+      selectedId = selectedId.replace(/\w+_/g, "");
     }
 
     if (page.match(/cluster\/analysis/)) {
       if (dataStr.match(/list/)) {
-        list = this.getListMetaData(selectId);
+        list = this.getListMetaData(selectedId);
 
         if (list.list_type.match(/accessions/)) {
           dataTypeOpts = ["Genotype"];
@@ -222,7 +226,7 @@ solGS.cluster = {
         }
       } else if (dataStr.match(/dataset/)) {
         var dataset = new CXGN.Dataset();
-        dt = dataset.getDataset(selectId);
+        dt = dataset.getDataset(selectedId);
 
         if (dt.categories["accessions"]) {
           dataTypeOpts = ["Genotype"];
@@ -253,63 +257,86 @@ solGS.cluster = {
     return dataTypeOpts;
   },
 
-  selectRow: function (selectId, selectName, dataStr) {
-    var clusterPopId = this.getClusterPopId(selectId, dataStr);
+  selectRow: function (selectedPop) {
+    let selectedId = selectedPop.id;
+    let selectedName = selectedPop.name;
+    let dataStr = selectedPop.data_str;
+
+    var clusterPopId = this.getClusterPopId(selectedId, dataStr);
     var clusterTypeOpts = this.createClusterTypeSelect(clusterPopId);
 
     var dataTypeOpts = this.getDataTypeOpts({
-      select_id: selectId,
+      id: selectedId,
+      name: selectedName,
       data_str: dataStr,
     });
 
     dataTypeOpts = this.createDataTypeSelect(dataTypeOpts, clusterPopId);
     var kNumId = this.clusterKnumSelectId(clusterPopId);
-    var runClusterId = this.clusterRunClusterId(clusterPopId);
+    var runClusterBtnId = this.clusterRunClusterId(clusterPopId);
 
     var kNum = '<input class="form-control" type="text" placeholder="3" id="' + kNumId + '"/>';
 
-    var onClickVal =
-      '<button type="button" id="' +
-      runClusterId +
-      '" class="btn btn-success" onclick="solGS.cluster.runCluster(' +
-      selectId +
-      ",'" +
-      selectName +
-      "'" +
-      ",'" +
-      dataStr +
-      "'" +
-      ')">Run Cluster</button>';
-
+    // var onClickVal =
+    //   '<button type="button" id="' +
+    //   runClusterId +
+    //   '" class="btn btn-success" onclick="solGS.cluster.runCluster(' +
+    //   selectedId +
+    //   ",'" +
+    //   selectedName +
+    //   "'" +
+    //   ",'" +
+    //   dataStr +
+    //   "'" +
+    //   ')">Run Cluster</button>';
+
+    var clusterArgs = JSON.stringify(selectedPop);
+    var runClusterBtn =
+      `<button type="button" id=${runClusterBtnId}` +
+      ` class="btn btn-success" data-selected-pop='${clusterArgs}'>Run cluster</button>`;
+
+    var tdId = `cluster_${clusterPopId}`;
     var row =
-      '<tr name="' +
-      dataStr +
-      '"' +
-      ' id="' +
-      clusterPopId +
-      '">' +
-      "<td>" +
-      selectName +
-      "</td>" +
-      "<td>" +
-      dataStr +
-      "</td>" +
-      "<td>" +
-      clusterTypeOpts +
-      "</td>" +
-      "<td>" +
-      dataTypeOpts +
-      "</td>" +
-      "<td>" +
-      kNum +
-      "</td>" +
-      '<td id="list_cluster_page_' +
-      clusterPopId +
-      '">' +
-      onClickVal +
+      `<tr  name="${clusterPopId}" id="${clusterPopId}">` +
+      ` <td>${selectedName}</td>` +
+      ` <td>${dataStr}</td>` +
+      ` <td>${clusterTypeOpts}</td>` +
+      ` <td>${dataTypeOpts}</td>` +
+      ` <td>${kNum}</td>` +
+      `<td id="${tdId}">` +
+      runClusterBtn +
       "</td>" +
       "<tr>";
 
+    // var row =
+    //   '<tr name="' +
+    //   dataStr +
+    //   '"' +
+    //   ' id="' +
+    //   clusterPopId +
+    //   '">' +
+    //   "<td>" +
+    //   selectedName +
+    //   "</td>" +
+    //   "<td>" +
+    //   dataStr +
+    //   "</td>" +
+    //   "<td>" +
+    //   clusterTypeOpts +
+    //   "</td>" +
+    //   "<td>" +
+    //   dataTypeOpts +
+    //   "</td>" +
+    //   "<td>" +
+    //   kNum +
+    //   "</td>" +
+    //   '<td id="cluster_' +
+    //   clusterPopId +
+    //   '">' +
+    //   onClickVal +
+    //   "</td>" +
+    //   "<tr>";
+
     return row;
   },
 
@@ -333,20 +360,21 @@ solGS.cluster = {
   },
 
   clusterResult: function (clusterArgs) {
+    var clusterPopId = clusterArgs.cluster_pop_id;
     var clusterType = clusterArgs.cluster_type;
     var kNumber = clusterArgs.k_number;
     var dataType = clusterArgs.data_type;
     var selectionProp = clusterArgs.selection_proportion;
-    var selectId = clusterArgs.select_id;
-    var selectName = clusterArgs.select_name;
+    var selectedId = clusterArgs.selected_id;
+    var selectedName = clusterArgs.selected_name;
     var dataStr = clusterArgs.data_structure;
 
     dataType = dataType.toLowerCase();
-    cluseterType = clusterType.toLowerCase();
+    clusterType = clusterType.toLowerCase();
     var protocolId = jQuery("#cluster_div #genotyping_protocol #genotyping_protocol_id").val();
 
     if (!protocolId) {
-      var protocolId = jQuery("#genotyping_protocol_id").val();
+      protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("cluster_div");
     }
 
     var trainingTraitsIds = jQuery("#training_traits_ids").val();
@@ -390,16 +418,16 @@ solGS.cluster = {
       popName = jQuery("#cluster_selected_pop_name").val();
     }
 
-    if (!selectName) {
-      selectName = popName;
+    if (!selectedName) {
+      selectedName = popName;
     }
 
-    if (!selectId) {
-      selectId = popId;
+    if (!selectedId) {
+      selectedId = popId;
     }
 
     var validateArgs = {
-      data_id: selectId,
+      data_id: selectedId,
       data_structure: dataStr,
       data_type: dataType,
       selection_proportion: selectionProp,
@@ -426,35 +454,38 @@ solGS.cluster = {
       var datasetId;
       var datasetName;
       var sIndexName;
-      var clusterPopId;
 
-      if (String(selectId).match(/list/)) {
+      if (String(selectedId).match(/list/)) {
         dataStr = "list";
-      } else if (String(selectId).match(/dataset/)) {
+      } else if (String(selectedId).match(/dataset/)) {
         dataStr = "dataset";
       }
 
       if (dataStr == "list") {
-        if (isNaN(selectId)) {
-          listId = selectId.replace("list_", "");
+        if (isNaN(selectedId)) {
+          listId = selectedId.replace("list_", "");
         } else {
-          listId = selectId;
+          listId = selectedId;
         }
       } else if (dataStr == "dataset") {
-        if (isNaN(selectId)) {
-          datasetId = selectId.replace("dataset_", "");
+        if (isNaN(selectedId)) {
+          datasetId = selectedId.replace("dataset_", "");
         } else {
-          datasetId = selectId;
+          datasetId = selectedId;
         }
 
-        datasetName = selectName;
+        datasetName = selectedName;
       }
 
-      if (dataStr.match(/list|dataset/) && !String(selectId).match(/list|dataset/)) {
-        clusterPopId = dataStr + "_" + selectId;
-      } else {
-        clusterPopId = popId;
-      }
+      // if (
+      //   // page.match(/cluster\/analysis/) &&
+      //   dataStr.match(/list|dataset/) &&
+      //   !String(selectedId).match(/list|dataset/)
+      // ) {
+      //   clusterPopId = dataStr + "_" + selectedId;
+      // } else {
+      //   clusterPopId = popId;
+      // }
       if (!clusterPopId) {
         if (url.match(/solgs\/trait\//)) {
           clusterPopId = popDetails.training_pop_id;
@@ -466,7 +497,7 @@ solGS.cluster = {
       }
 
       if (popType == "selection_index") {
-        sIndexName = selectName;
+        sIndexName = selectedName;
       }
 
       var traitsCode;
@@ -547,13 +578,14 @@ solGS.cluster = {
         k_number: kNumber,
         selection_proportion: selectionProp,
         sindex_name: sIndexName,
-        cluster_pop_name: selectName || "",
+        cluster_pop_name: selectedName || "",
         genotyping_protocol_id: protocolId,
         analysis_type: "cluster analysis",
         analysis_page: page,
       };
 
-      this.checkCachedCluster(page, clusterArgs);
+      return clusterArgs;
+      // this.checkCachedCluster(page, clusterArgs);
     }
   },
 
@@ -562,7 +594,7 @@ solGS.cluster = {
       args = JSON.stringify(args);
     }
 
-    jQuery.ajax({
+    var checkCached = jQuery.ajax({
       type: "POST",
       dataType: "json",
       data: {
@@ -570,72 +602,73 @@ solGS.cluster = {
         arguments: args,
       },
       url: "/solgs/check/cached/result/",
-      success: function (res) {
-        if (res.cached) {
-          solGS.cluster.runClusterAnalysis(args);
-        } else {
-          args = JSON.parse(args);
-          solGS.cluster.optJobSubmission(page, args);
-        }
-      },
-      error: function () {
-        alert("Error occured checking for cached output.");
-      },
     });
-  },
 
-  optJobSubmission: function (page, args) {
-    var title =
-      "<p>This analysis may take a long time. " +
-      "Do you want to submit the analysis and get an email when it completes?</p>";
-
-    var jobSubmit = '<div id= "cluster_submit">' + title + "</div>";
-
-    jQuery(jobSubmit).appendTo("body");
-
-    jQuery("#cluster_submit").dialog({
-      height: 200,
-      width: 400,
-      modal: true,
-      title: "cluster job submission",
-      buttons: {
-        OK: {
-          text: "Yes",
-          class: "btn btn-success",
-          id: "queue_job",
-          click: function () {
-            jQuery(this).dialog("close");
-            solGS.submitJob.checkUserLogin(page, args);
-          },
-        },
-
-        No: {
-          text: "No, I will wait till it completes.",
-          class: "btn btn-warning",
-          id: "no_queue",
-          click: function () {
-            jQuery(this).dialog("close");
-
-            solGS.cluster.runClusterAnalysis(args);
-          },
-        },
-
-        Cancel: {
-          text: "Cancel",
-          class: "btn btn-info",
-          id: "cancel_queue_info",
-          click: function () {
-            jQuery(this).dialog("close");
-          },
-        },
-      },
-    });
+    return checkCached;
+
+    //   success: function (res) {
+    //     if (res.cached) {
+    //       solGS.cluster.runClusterAnalysis(args);
+    //     } else {
+    //       args = JSON.parse(args);
+    //       solGS.cluster.optJobSubmission(page, args);
+    //     }
+    //   },
+    //   error: function () {
+    //     alert("Error occured checking for cached output.");
+    //   },
+    // });
   },
 
-  runClusterAnalysis: function (clusterArgs) {
-    var runClusterId;
+  // // optJobSubmission: function (page, args) {
+  // //   var title =
+  // //     "<p>This analysis may take a long time. " +
+  // //     "Do you want to submit the analysis and get an email when it completes?</p>";
+
+  // //   var jobSubmit = '<div id= "cluster_submit">' + title + "</div>";
+
+  // //   jQuery(jobSubmit).appendTo("body");
+
+  // //   jQuery("#cluster_submit").dialog({
+  // //     height: 200,
+  // //     width: 400,
+  // //     modal: true,
+  // //     title: "cluster job submission",
+  // //     buttons: {
+  // //       OK: {
+  // //         text: "Yes",
+  // //         class: "btn btn-success",
+  // //         id: "queue_job",
+  // //         click: function () {
+  // //           jQuery(this).dialog("close");
+  // //           solGS.submitJob.checkUserLogin(page, args);
+  // //         },
+  // //       },
+
+  // //       No: {
+  // //         text: "No, I will wait till it completes.",
+  // //         class: "btn btn-warning",
+  // //         id: "no_queue",
+  // //         click: function () {
+  // //           jQuery(this).dialog("close");
+
+  // //           solGS.cluster.runClusterAnalysis(args);
+  // //         },
+  // //       },
+
+  // //       Cancel: {
+  // //         text: "Cancel",
+  // //         class: "btn btn-info",
+  // //         id: "cancel_queue_info",
+  // //         click: function () {
+  // //           jQuery(this).dialog("close");
+  // //         },
+  // //       },
+  // //     },
+  // //   });
+  // },
 
-    var type = typeof clusterArgs;
+  runClusterAnalysis: function (clusterArgs) {
     var clusterPopId;
     if (typeof clusterArgs == "string") {
       clusterArgs = JSON.parse(clusterArgs);
@@ -652,50 +685,54 @@ solGS.cluster = {
       clusterArgs = JSON.stringify(clusterArgs);
     }
 
-    var canvas = this.canvas;
-    var clusterMsgDiv = this.clusterMsgDiv;
+    // var canvas = this.canvas;
+    // var clusterMsgDiv = this.clusterMsgDiv;
 
-    if (clusterArgs) {
-      jQuery(clusterMsgDiv)
-        .html(`Running ${clusterType} clustering... please wait...this may take minutes.`)
-        .show();
+    // // if (clusterArgs) {
+    // jQuery(clusterMsgDiv)
+    //   .html(`Running ${clusterType} clustering... please wait...this may take minutes.`)
+    //   .show();
 
-      jQuery(`${canvas} .multi-spinner-container`).show();
+    // jQuery(`${canvas} .multi-spinner-container`).show();
 
-      jQuery("#" + runClusterId).hide();
+    // jQuery("#" + runClusterId).hide();
 
-      jQuery.ajax({
-        type: "POST",
-        dataType: "json",
-        data: {
-          arguments: clusterArgs,
-        },
-        url: "/run/cluster/analysis",
-        success: function (res) {
-          if (res.result == "success") {
-            jQuery(`${canvas} .multi-spinner-container`).hide();
-
-            solGS.cluster.plotClusterOutput(res);
+    var runAnalysis = jQuery.ajax({
+      type: "POST",
+      dataType: "json",
+      data: {
+        arguments: clusterArgs,
+      },
+      url: "/run/cluster/analysis",
+    });
 
-            jQuery(clusterMsgDiv).empty();
-            jQuery("#" + runClusterId).show();
-          } else {
-            jQuery(clusterMsgDiv).html(
-              "Error occured running the clustering. Possibly the R script failed."
-            );
-            jQuery(`${canvas} .multi-spinner-container`).hide();
-            jQuery("#" + runClusterId).show();
-          }
-        },
-        error: function (res) {
-          jQuery(clusterMsgDiv).html("Error occured running the clustering");
-          jQuery(`${canvas} .multi-spinner-container`).hide();
-          jQuery("#" + runClusterId).show();
-        },
-      });
-    } else {
-      jQuery(clusterMsgDiv).html("Missing cluster parameters.").show().fadeOut(8400);
-    }
+    return runAnalysis;
+
+    //     success: function (res) {
+    //       if (res.result == "success") {
+    //         jQuery(`${canvas} .multi-spinner-container`).hide();
+
+    //         solGS.cluster.plotClusterOutput(res);
+
+    //         jQuery(clusterMsgDiv).empty();
+    //         jQuery("#" + runClusterId).show();
+    //       } else {
+    //         jQuery(clusterMsgDiv).html(
+    //           "Error occured running the clustering. Possibly the R script failed."
+    //         );
+    //         jQuery(`${canvas} .multi-spinner-container`).hide();
+    //         jQuery("#" + runClusterId).show();
+    //       }
+    //     },
+    //     error: function (res) {
+    //       jQuery(clusterMsgDiv).html("Error occured running the clustering");
+    //       jQuery(`${canvas} .multi-spinner-container`).hide();
+    //       jQuery("#" + runClusterId).show();
+    //     },
+    //   });
+    // } else {
+    //   jQuery(clusterMsgDiv).html("Missing cluster parameters.").show().fadeOut(8400);
+    // }
   },
 
   validateClusterParams: function (valArgs) {
@@ -847,16 +884,16 @@ solGS.cluster = {
     return clusterTable;
   },
 
-  runCluster: function (selectId, selectName, dataStr) {
-    var clusterPopId = this.getClusterPopId(selectId, dataStr);
+  runCluster: function (selectedId, selectedName, dataStr) {
+    var clusterPopId = this.getClusterPopId(selectedId, dataStr);
     var clusterOpts = solGS.cluster.clusteringOptions(clusterPopId);
     var clusterType = clusterOpts.cluster_type || "k-means";
     var kNumber = clusterOpts.k_number || 3;
     var dataType = clusterOpts.data_type || "genotype";
 
     var clusterArgs = {
-      select_id: selectId,
-      select_name: selectName,
+      selected_id: selectedId,
+      selected_name: selectedName,
       data_structure: dataStr,
       cluster_pop_id: clusterPopId,
       cluster_type: clusterType,
@@ -873,8 +910,8 @@ solGS.cluster = {
     var dataTypeId = this.clusterDataTypeSelectId(clusterPopId);
     var selectionPropId = this.clusterSelPropSelectId(clusterPopId);
 
-    var dataType = jQuery("#" + dataTypeId).val();
-    var clusterType = jQuery("#" + clusterTypeId).val();
+    var dataType = jQuery("#" + dataTypeId).val() || "genotype";
+    var clusterType = jQuery("#" + clusterTypeId).val() || "k-means";
     var kNumber = jQuery("#" + kNumId).val() || 3;
     var selectionProp = jQuery("#" + selectionPropId).val();
 
@@ -887,6 +924,10 @@ solGS.cluster = {
       selectionProp = selectionProp.replace(/\s+/g, "");
     }
 
+    // var clusterType = clusterOpts.cluster_type || "k-means";
+    // var kNumber = clusterOpts.k_number || 3;
+    // var dataType = clusterOpts.data_type || "genotype";
+
     return {
       data_type: dataType,
       cluster_type: clusterType,
@@ -937,6 +978,29 @@ solGS.cluster = {
     jQuery(clusterPopsDiv).append(menuElem).show();
   },
 
+  getSelectedPopClusterArgs: function (runClusterElemId) {
+    var clusterArgs;
+
+    // var runclusterElemId = this.getRunclusterId(clusterPopId);
+    var selectedPopDiv = document.getElementById(runClusterElemId);
+    if (selectedPopDiv) {
+      var selectedPopData = selectedPopDiv.dataset;
+
+      var clusterArgs = JSON.parse(selectedPopData.selectedPop);
+      var clusterPopId = clusterArgs.data_str + "_" + clusterArgs.id;
+
+      var protocolId = solGS.genotypingProtocol.getGenotypingProtocolId("cluster_div");
+      // var page = `/cluster/analysis/${clusterPopId}/gp/${protocolId}`;
+
+      clusterArgs["analysis_type"] = "cluster analysis";
+      clusterArgs["genotyping_protocol_id"] = protocolId;
+      clusterArgs["cluster_pop_id"] = clusterPopId;
+      clusterArgs["data_structure"] = clusterArgs.data_str;
+    }
+
+    return clusterArgs;
+  },
+
   listClusterPopulations: function () {
     var modelData = solGS.sIndex.getTrainingPopulationData();
 
@@ -950,7 +1014,7 @@ solGS.cluster = {
     }
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
+      var listTypeSelPops = solGS.listTypeSelectionPopulation.getListTypeSelPopulations();
       if (listTypeSelPops) {
         clusterPops.push(listTypeSelPops);
       }
@@ -981,11 +1045,24 @@ jQuery(document).ready(function () {
 
   if (url.match(/cluster\/analysis/)) {
     solGS.cluster.populateClusterPopsMenu();
+    var canvas = solGS.cluster.canvas;
+    var clusterMsgDiv = solGS.cluster.clusterMsgDiv;
 
     var clusterArgs = solGS.cluster.getClusterArgsFromUrl();
     var clusterPopId = clusterArgs.cluster_pop_id;
     if (clusterPopId) {
-      solGS.cluster.checkCachedCluster(url, clusterArgs);
+      jQuery(clusterMsgDiv).text("Running cluster... please wait...it may take minutes.").show();
+
+      jQuery(`${canvas} .multi-spinner-container`).show();
+
+      solGS.cluster.checkCachedCluster(url, clusterArgs).done(function (res) {
+        if (res.result == "success") {
+          solGS.cluster.plotClusterOutput(res);
+
+          jQuery(clusterMsgDiv).empty();
+          jQuery(`${canvas} .multi-spinner-container`).hide();
+        }
+      });
     }
   }
 });
@@ -1021,70 +1098,151 @@ jQuery(document).ready(function () {
 });
 
 jQuery(document).ready(function () {
-  jQuery("#cluster_pops_list_select").change(function () {
-    var selectedPop = solGS.selectMenu.getSelectedPop("cluster_pops");
-    if (selectedPop.selected_id) {
-      jQuery("#cluster_pop_go_btn").click(function () {
-        solGS.cluster.displaySelectedClusterPop(
-          selectedPop.selected_id,
-          selectedPop.selected_name,
-          selectedPop.data_str
-        );
-      });
-    }
-  });
-});
-
-jQuery(document).ready(function () {
-  jQuery("#run_cluster").click(function () {
-    var dataStr = jQuery("#data_structure").val();
-    var selectId;
-    var selectName;
-    if (dataStr == "dataset") {
-      selectId = jQuery("#dataset_id").val();
-    } else if (dataStr == "list") {
-      selectId = jQuery("#list_id").val();
-    }
+  jQuery("#cluster_div").on("click", function (e) {
+    var runClusterBtnId = e.target.id;
+    if (runClusterBtnId.match(/run_cluster/)) {
+      jQuery(clusterMsgDiv).text("Running cluster... please wait...it may take minutes.").show();
 
-    if (!dataStr) {
-      var popType = jQuery("#cluster_selected_pop_type").val();
+      jQuery(`${canvas} .multi-spinner-container`).show();
+      jQuery("#" + runClusterId).hide();
 
-      if (popType == "list") {
-        dataStr = "list";
-      } else if (popType == "dataset") {
-        dataStr = "dataset";
+      var canvas = solGS.cluster.canvas;
+      var clusterMsgDiv = solGS.cluster.clusterMsgDiv;
+      var runClusterId;
+
+      var page = location.pathname;
+      var selectedId, selectedName, dataStr;
+      if (page.match(/cluster\/analysis/)) {
+        var clusterArgs = solGS.cluster.getSelectedPopClusterArgs(runClusterBtnId);
+        selectedId = clusterArgs.id;
+        selectedName = clusterArgs.name;
+        dataStr = clusterArgs.data_str;
+      } else if (page.match(/breeders\/trial\//)) {
+        selectedId = jQuery("#trial_id").val();
+        selectedName = jQuery("#trial_name").val();
+      } else {
+        selectedId = jQuery("#cluster_selected_pop_id").val();
+        selectedName = jQuery("#cluster_selected_pop_name").val();
+        var popType = jQuery("#cluster_selected_pop_type").val();
+
+        if (popType) {
+          if (popType.match(/list/)) {
+            dataStr = "list";
+          } else if (popType.match(/dataset/)) {
+            dataStr = "dataset";
+          }
+        }
       }
-    }
 
-    if (selectId == undefined) {
-      selectId = jQuery("#cluster_selected_pop_id").val();
-    }
+      var clusterOptsId = "cluster_options";
+      var clusterPopId = solGS.cluster.getClusterPopId(selectedId, dataStr);
+      var clusterOpts = solGS.cluster.clusteringOptions(clusterPopId);
 
-    if (location.pathname.match(/breeders\/trial\//)) {
-      selectId = jQuery("#trial_id").val();
-      selectName = jQuery("#trial_name").val();
-    }
+      var clusterArgs = {
+        selected_id: selectedId,
+        selected_name: selectedName,
+        data_structure: dataStr,
+        cluster_pop_id: clusterPopId,
+        cluster_type: clusterOpts.cluster_type,
+        data_type: clusterOpts.data_type,
+        k_number: clusterOpts.k_number,
+        selection_proportion: clusterOpts.selection_proportion,
+      };
 
-    if (selectName == undefined) {
-      selectName = jQuery("#cluster_selected_pop_name").val();
-    }
+      clusterArgs = solGS.cluster.clusterResult(clusterArgs);
+      runClusterId = solGS.cluster.clusterRunClusterId(clusterPopId);
+      var page = clusterArgs.analysis_page;
 
-    var clusterOptsId = "cluster_options";
-    var clusterPopId = solGS.cluster.getClusterPopId(selectId, dataStr);
-    var clusterOpts = solGS.cluster.clusteringOptions(clusterPopId);
+      solGS.cluster
+        .checkCachedCluster(page, clusterArgs)
+        .done(function (res) {
+          if (res.result == "success") {
+            jQuery(`${canvas} .multi-spinner-container`).hide();
 
-    var clusterArgs = {
-      select_id: selectId,
-      select_name: selectName,
-      data_structure: dataStr,
-      cluster_pop_id: clusterPopId,
-      cluster_type: clusterOpts.cluster_type,
-      data_type: clusterOpts.data_type,
-      k_number: clusterOpts.k_number,
-      selection_proportion: clusterOpts.selection_proportion,
-    };
+            solGS.cluster.plotClusterOutput(res);
 
-    solGS.cluster.clusterResult(clusterArgs);
+            jQuery(clusterMsgDiv).empty();
+            jQuery("#" + runClusterId).show();
+          } else {
+            jQuery(`${canvas} .multi-spinner-container`).hide();
+            jQuery(clusterMsgDiv).empty();
+
+            var title =
+              "<p>This analysis may take a long time. " +
+              "Do you want to submit the analysis and get an email when it completes?</p>";
+
+            var jobSubmit = '<div id= "cluster_submit">' + title + "</div>";
+
+            jQuery(jobSubmit).appendTo("body");
+
+            jQuery("#cluster_submit").dialog({
+              height: 200,
+              width: 400,
+              modal: true,
+              title: "cluster job submission",
+              buttons: {
+                OK: {
+                  text: "Yes",
+                  class: "btn btn-success",
+                  id: "queue_job",
+                  click: function () {
+                    jQuery(this).dialog("close");
+                    solGS.submitJob.checkUserLogin(page, clusterArgs);
+                  },
+                },
+
+                No: {
+                  text: "No, I will wait till it completes.",
+                  class: "btn btn-warning",
+                  id: "no_queue",
+                  click: function () {
+                    jQuery(this).dialog("close");
+
+                    jQuery(clusterMsgDiv)
+                      .text("Running cluster... please wait...it may take minutes.")
+                      .show();
+                    jQuery(`${canvas} .multi-spinner-container`).show();
+
+                    solGS.cluster
+                      .runClusterAnalysis(clusterArgs)
+                      .done(function (res) {
+                        if (res.result == "success") {
+                          jQuery(`${canvas} .multi-spinner-container`).hide();
+
+                          solGS.cluster.plotClusterOutput(res);
+
+                          jQuery(clusterMsgDiv).empty();
+                          jQuery("#" + runClusterId).show();
+                        } else {
+                          jQuery(clusterMsgDiv).html(
+                            "Error occured running the clustering. Possibly the R script failed."
+                          );
+                          jQuery(`${canvas} .multi-spinner-container`).hide();
+                          jQuery("#" + runClusterId).show();
+                        }
+                      })
+                      .fail(function () {
+                        jQuery(clusterMsgDiv).html("Error occured running the clustering");
+                        jQuery(`${canvas} .multi-spinner-container`).hide();
+                        jQuery("#" + runClusterId).show();
+                      });
+                  },
+                },
+
+                Cancel: {
+                  text: "Cancel",
+                  class: "btn btn-info",
+                  id: "cancel_queue_info",
+                  click: function () {
+                    jQuery(this).dialog("close");
+                  },
+                },
+              },
+            });
+          }
+        })
+        .fail(function () {});
+    }
   });
 });
 
@@ -1128,31 +1286,39 @@ jQuery(document).ready(function () {
 jQuery(document).ready(function () {
   var clusterPopsDiv = solGS.cluster.clusterPopsDiv;
 
-  jQuery(clusterPopsDiv).change(function () {
+  jQuery(clusterPopsDiv).on("change", function () {
     var selectedPop = jQuery("option:selected", this).data("pop");
 
-    var selectedPopId = selectedPop.id;
-    var selectedPopName = selectedPop.name;
-    var selectedPopType = selectedPop.pop_type;
+    if (location.pathname.match(/cluster\/analysis/)) {
+      jQuery("#cluster_pop_go_btn").on("click", function () {
+        if (!selectedPop.data_str) {
+          selectedPop.data_str = "list";
+        }
 
-    var dataTypeId = solGS.cluster.clusterDataTypeSelectId(selectedPopId);
-    var dataType = jQuery("#" + dataTypeId).val();
+        solGS.cluster.displaySelectedClusterPop(selectedPop);
+      });
+    } else {
+      var selectedPopId = selectedPop.id;
+      var selectedPopName = selectedPop.name;
+      var selectedPopType = selectedPop.type || selectedPop.pop_type;
 
-    jQuery("#cluster_selected_pop_name").val(selectedPopName);
-    jQuery("#cluster_selected_pop_id").val(selectedPopId);
-    jQuery("#cluster_selected_pop_type").val(selectedPopType);
+      var dataTypeId = solGS.cluster.clusterDataTypeSelectId(selectedPopId);
+      var dataType = jQuery("#" + dataTypeId).val();
 
-    var dataTypeOpts = solGS.cluster.getDataTypeOpts({
-      pop_type: selectedPopType,
-    });
+      jQuery("#cluster_selected_pop_name").val(selectedPopName);
+      jQuery("#cluster_selected_pop_id").val(selectedPopId);
+      jQuery("#cluster_selected_pop_type").val(selectedPopType);
 
-    dataTypeOpts = solGS.cluster.createDataTypeSelect(dataTypeOpts, selectedPopId);
-    jQuery("#cluster_div #cluster_options #cluster_data_type_opts").html(dataTypeOpts);
+      var dataTypeOpts = solGS.cluster.getDataTypeOpts(selectedPop);
 
-    if (selectedPopType.match(/selection_index/) && dataType.match(/Genotype/i)) {
-      jQuery("#cluster_div #cluster_options #selection_proportion_div").show();
-    } else {
-      jQuery("#cluster_div #cluster_options #selection_proportion_div").hide();
+      dataTypeOpts = solGS.cluster.createDataTypeSelect(dataTypeOpts, selectedPopId);
+      jQuery("#cluster_div #cluster_options #cluster_data_type_opts").html(dataTypeOpts);
+
+      if (selectedPopType.match(/selection_index/) && dataType.match(/Genotype/i)) {
+        jQuery("#cluster_div #cluster_options #selection_proportion_div").show();
+      } else {
+        jQuery("#cluster_div #cluster_options #selection_proportion_div").hide();
+      }
     }
   });
 });

From 88c7caabb07d57b8b3e18a79a1e60d95e9859d34 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 21 Jun 2023 15:32:27 +0200
Subject: [PATCH 55/61] respond with cached clustering data, instead of T or F

---
 lib/SGN/Controller/solGS/CachedResult.pm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/SGN/Controller/solGS/CachedResult.pm b/lib/SGN/Controller/solGS/CachedResult.pm
index 19c430ce89..f18865d02a 100644
--- a/lib/SGN/Controller/solGS/CachedResult.pm
+++ b/lib/SGN/Controller/solGS/CachedResult.pm
@@ -346,7 +346,7 @@ sub _check_pca_output {
 sub _check_cluster_output {
     my ( $self, $c, $file_id ) = @_;
     my $cached = $self->check_cluster_output( $c, $file_id );
-    $c->stash->{rest}{cached} = $self->check_cluster_output( $c, $file_id );
+    $c->stash->{rest} = $self->check_cluster_output( $c, $file_id );
 }
 
 sub check_single_trial_training_data {
@@ -579,10 +579,11 @@ sub check_cluster_output {
             $cached_file = $c->stash->{"${cluster_type}_result_newick_file"};
         }
         if ( -s $cached_file ) {
-            return 1;
+            my $res = $c->controller('solGS::Cluster')->prepare_response($c);
+            return $res;
         }
         else {
-            return 0;
+            return { cached => 0 };
         }
     }
 

From 19632293c30f07fe6f7368ed9b255e42af627e57 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 21 Jun 2023 15:33:48 +0200
Subject: [PATCH 56/61] update selection pop object name

---
 js/source/legacy/solGS/selectionIndex.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/source/legacy/solGS/selectionIndex.js b/js/source/legacy/solGS/selectionIndex.js
index 2a9a0d8f53..4120db60f9 100644
--- a/js/source/legacy/solGS/selectionIndex.js
+++ b/js/source/legacy/solGS/selectionIndex.js
@@ -29,7 +29,7 @@ solGS.sIndex = {
 
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
+      var listTypeSelPops = solGS.listTypeSelectionPopulation.getListTypeSelPopulations();
       if (listTypeSelPops) {
         sIndexPops.push(listTypeSelPops);
       }

From 98fca5ee7885afd950bc1201562f133b25d6959e Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 21 Jun 2023 15:36:41 +0200
Subject: [PATCH 57/61] update getListTypeSelPopulations func name

---
 js/source/entries/heritability.js             |  2 +-
 js/source/legacy/heritability/heritability.js |  2 +-
 .../legacy/qualityControl/qualityControl.js   |  2 +-
 js/source/legacy/solGS/correlation.js         |  2 +-
 js/source/legacy/solGS/geneticGain.js         |  2 +-
 .../solGS/listTypeSelectionPopulation.js      | 30 ++++++++++---------
 6 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/js/source/entries/heritability.js b/js/source/entries/heritability.js
index cae7a3145e..a9bbcb5d2d 100644
--- a/js/source/entries/heritability.js
+++ b/js/source/entries/heritability.js
@@ -91,7 +91,7 @@ function listGenCorPopulations ()  {
     var listTypeSelPops = jQuery("#list_type_selection_pops_table").length;
    
     if (listTypeSelPops) {
-        var selPopsList = solGS.listTypeSelPopulations.getListTypeSelPops();
+        var selPopsList = solGS.listTypeSelectionPopulation.getListTypeSelPopulations();
 
         if (selPopsList) {
             jQuery("#h2_select_a_population_div ul").append(selPopsList);  
diff --git a/js/source/legacy/heritability/heritability.js b/js/source/legacy/heritability/heritability.js
index cae7a3145e..a9bbcb5d2d 100644
--- a/js/source/legacy/heritability/heritability.js
+++ b/js/source/legacy/heritability/heritability.js
@@ -91,7 +91,7 @@ function listGenCorPopulations ()  {
     var listTypeSelPops = jQuery("#list_type_selection_pops_table").length;
    
     if (listTypeSelPops) {
-        var selPopsList = solGS.listTypeSelPopulations.getListTypeSelPops();
+        var selPopsList = solGS.listTypeSelectionPopulation.getListTypeSelPopulations();
 
         if (selPopsList) {
             jQuery("#h2_select_a_population_div ul").append(selPopsList);  
diff --git a/js/source/legacy/qualityControl/qualityControl.js b/js/source/legacy/qualityControl/qualityControl.js
index a3bd579125..fd985109f9 100644
--- a/js/source/legacy/qualityControl/qualityControl.js
+++ b/js/source/legacy/qualityControl/qualityControl.js
@@ -91,7 +91,7 @@ function listGenCorPopulations ()  {
     var listTypeSelPops = jQuery("#list_type_selection_pops_table").length;
    
     if (listTypeSelPops) {
-        var selPopsList = solGS.listTypeSelPopulations.getListTypeSelPops();
+        var selPopsList = solGS.listTypeSelectionPopulation.getListTypeSelPopulations();
 
         if (selPopsList) {
             jQuery("#qc_select_a_population_div ul").append(selPopsList);  
diff --git a/js/source/legacy/solGS/correlation.js b/js/source/legacy/solGS/correlation.js
index 092807008b..e99e2107a1 100644
--- a/js/source/legacy/solGS/correlation.js
+++ b/js/source/legacy/solGS/correlation.js
@@ -216,7 +216,7 @@ solGS.correlation = {
 
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
+      var listTypeSelPops = solGS.listTypeSelectionPopulation.getListTypeSelPopulations();
       if (listTypeSelPops) {
         corrPops.push(listTypeSelPops);
       }
diff --git a/js/source/legacy/solGS/geneticGain.js b/js/source/legacy/solGS/geneticGain.js
index fbc0c8519c..d43aca9ec4 100644
--- a/js/source/legacy/solGS/geneticGain.js
+++ b/js/source/legacy/solGS/geneticGain.js
@@ -226,7 +226,7 @@ solGS.geneticGain = {
 
     var listTypeSelPopsTable = jQuery("#list_type_selection_pops_table").length;
     if (listTypeSelPopsTable) {
-      var listTypeSelPops = solGS.listTypeSelPopulations.getListTypeSelPops();
+      var listTypeSelPops = solGS.listTypeSelectionPopulation.getListTypeSelPopulations();
       if (listTypeSelPops) {
         ggPops.push(listTypeSelPops);
       }
diff --git a/js/source/legacy/solGS/listTypeSelectionPopulation.js b/js/source/legacy/solGS/listTypeSelectionPopulation.js
index 91ae6a7f06..9a2d0166b3 100644
--- a/js/source/legacy/solGS/listTypeSelectionPopulation.js
+++ b/js/source/legacy/solGS/listTypeSelectionPopulation.js
@@ -103,7 +103,6 @@ solGS.listTypeSelectionPopulation = {
 
       jQuery(`#${tableId} tr:last`).after(row);
     }
-
   },
 
   populateSelectionPopsMenu: function () {
@@ -140,13 +139,21 @@ solGS.listTypeSelectionPopulation = {
     var popsList = [];
     for (var i = 1; i < listTypeSelPopsRows.length; i++) {
       var row = listTypeSelPopsRows[i];
-      var popRow = row.innerHTML;
+      var notPredicted = row.innerHTML.match(/predict/gi);
+      if (!notPredicted) {
+        var selectedPop = row.dataset.listSelectionPop;
+        selectedPop = JSON.parse(selectedPop);
+
+        if (selectedPop.id.match(/\w+_/)) {
+          if (selectedPop.id.match(/list/)) {
+            selectedPop.data_str = "list";
+          } else {
+            selectedPop.data_str = "dataset";
+          }
+          selectedPop.id = selectedPop.id.replace(/\w+_/, "");
+        }
 
-      var predict = popRow.match(/predict/gi);
-      if (!predict) {
-        var selPopsInput = row.getElementsByTagName("input")[0];
-        var sIndexPopData = selPopsInput.value;
-        popsList.push(JSON.parse(sIndexPopData));
+        popsList.push(selectedPop);
       }
     }
     return popsList;
@@ -165,14 +172,10 @@ jQuery(document).ready(function () {
   var menuId = solGS.listTypeSelectionPopulation.selectionPopsSelectMenuId;
   jQuery(`${menuId}`).change(function () {
     var selectedPop = jQuery("option:selected", this).data("pop");
-   
+
     if (selectedPop.id) {
       jQuery(" #list_type_selection_pop_go_btn").click(function () {
-
-        if (
-          typeof selectedPop.data_str === "undefined" ||
-          selectedPop.data_str.match(/list/i)
-        ) {
+        if (typeof selectedPop.data_str === "undefined" || selectedPop.data_str.match(/list/i)) {
           const listObj = new solGSList(selectedPop.id);
           var listDetail = listObj.getListDetail();
 
@@ -205,7 +208,6 @@ jQuery(document).ready(function () {
             //	loadTrialListTypeSelectionPop(trialsNames);
           }
         } else {
-        
           solGS.dataset.checkPredictedDatasetSelection(selectedPop.id, selectedPop.name);
         }
       });

From 21f21efe550921e0d06bed0cf313e5ba58b7b4e8 Mon Sep 17 00:00:00 2001
From: Isaak <iyt2@cornell.edu>
Date: Wed, 21 Jun 2023 15:38:26 +0200
Subject: [PATCH 58/61] update elem ids, xpaths and pass test

---
 t/selenium2/solgs/cluster.t  |  62 +++++++++----------
 t/selenium2/solgs/hcluster.t |  38 ++++++------
 t/selenium2/solgs/kcluster.t | 111 +++++++++++++++++++----------------
 3 files changed, 112 insertions(+), 99 deletions(-)

diff --git a/t/selenium2/solgs/cluster.t b/t/selenium2/solgs/cluster.t
index 8d72c008b1..5f20abfc8e 100644
--- a/t/selenium2/solgs/cluster.t
+++ b/t/selenium2/solgs/cluster.t
@@ -85,7 +85,7 @@ $d->while_logged_in_as(
         $d->get_ok( '/cluster/analysis', 'cluster home page' );
         sleep(5);
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select clones list'
@@ -134,7 +134,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select clones list'
@@ -177,7 +177,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $plots_list_name . '"]',
             'xpath',
             'select plots list'
@@ -222,7 +222,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $plots_list_name . '"]',
             'xpath',
             'select plots list'
@@ -261,7 +261,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -310,7 +310,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -354,7 +354,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -400,7 +400,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -440,7 +440,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -480,7 +480,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_dt_name . '"]',
             'xpath',
             'select trials dataset'
@@ -519,7 +519,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -565,7 +565,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_dt_name . '"]',
             'xpath',
             'select trials dataset'
@@ -612,7 +612,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_dt_name . '"]',
             'xpath',
             'select trials dataset'
@@ -1001,7 +1001,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
@@ -1076,7 +1076,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(2);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -1152,7 +1152,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select accessions dataset sel pop'
@@ -1221,7 +1221,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -1286,7 +1286,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -1549,11 +1549,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial type tr pop'
         )->click();
@@ -1619,11 +1619,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial type tr pop'
         )->click();
@@ -2032,11 +2032,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial type tr pop'
         )->click();
@@ -2105,11 +2105,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial type tr pop'
         )->click();
@@ -2762,11 +2762,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Training population 2804608595"]',
+'//select[@id="si_pops_select"]/option[text()="Training population 2804608595"]',
             'xpath',
             'select combo pop'
         )->click();
@@ -2837,7 +2837,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2906,7 +2906,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2976,7 +2976,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+'//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
diff --git a/t/selenium2/solgs/hcluster.t b/t/selenium2/solgs/hcluster.t
index cdbc12aa9c..45e06f8ba0 100644
--- a/t/selenium2/solgs/hcluster.t
+++ b/t/selenium2/solgs/hcluster.t
@@ -67,7 +67,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(1);
     $d->get_ok('/cluster/analysis', 'cluster home page');
     sleep(1);
-    $d->find_element_ok('//select[@id="cluster_pops_list_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select clones list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -89,7 +89,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(3);
 
-    $d->find_element_ok('//select[@id="cluster_pops_list_select"]/option[text()="' . $plots_list_name . '"]', 'xpath', 'select plots list')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $plots_list_name . '"]', 'xpath', 'select plots list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -111,7 +111,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(3);
 
-    $d->find_element_ok('//select[@id="cluster_pops_list_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -134,7 +134,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(3);
 
-    $d->find_element_ok('//select[@id="cluster_pops_list_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $trials_list_name . '"]', 'xpath', 'select trials list')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -155,7 +155,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(3);
 
-    $d->find_element_ok('//select[@id="cluster_pops_list_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'select trials dataset')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'select trials dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -176,7 +176,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->driver->refresh();
     sleep(3);
 
-    $d->find_element_ok('//select[@id="cluster_pops_list_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'select trials dataset')->click();
+    $d->find_element_ok('//select[@id="cluster_pops_select"]/option[text()="' . $trials_dt_name . '"]', 'xpath', 'select trials dataset')->click();
     sleep(5);
     $d->find_element_ok('//input[@value="View"]', 'xpath', 'go btn')->click();
     sleep(5);
@@ -354,7 +354,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $list = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
+    my $list = $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
     $list->click();
     sleep(5);
 
@@ -390,7 +390,7 @@ $d->while_logged_in_as("submitter", sub {
     $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
 
-    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
+    my $dataset = $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
     $dataset->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'GO select dataset sel popp')->click();
@@ -425,7 +425,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
+    my $dataset = $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
     $dataset->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
@@ -517,9 +517,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $cor);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
@@ -696,9 +696,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $cor);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
@@ -737,9 +737,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $cor);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]', 'xpath', 'select trial type tr pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
@@ -1031,9 +1031,9 @@ $d->while_logged_in_as("submitter", sub {
     my $cor = $d->find_element('Genetic correlation', 'partial_link_text', 'scroll up');
     $d->driver->execute_script( "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);", $cor);
     sleep(5);
-    $d->find_element_ok('si_select_pops', 'id', 'select list sl pop')->click();
+    $d->find_element_ok('si_pops_select', 'id', 'select list sl pop')->click();
     sleep(3);
-    $d->find_element_ok('//select[@id="si_select_pops"]/option[text()="Training population 2804608595"]', 'xpath', 'select combo pop')->click();
+    $d->find_element_ok('//select[@id="si_pops_select"]/option[text()="Training population 2804608595"]', 'xpath', 'select combo pop')->click();
     sleep(3);
     $d->find_element_ok('DMCP', 'id', 'rel wt 1st')->send_keys(3);
     sleep(5);
@@ -1070,7 +1070,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $dataset = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
+    my $dataset = $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_dt_name . '"]', 'xpath', 'select dataset sel pop');
     $dataset->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
@@ -1105,7 +1105,7 @@ $d->while_logged_in_as("submitter", sub {
     sleep(5);
     $d->find_element_ok('list_type_selection_pops_select', 'id', 'select clones list menu')->click();
     sleep(5);
-    my $list = $d->find_element_ok('//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
+    my $list = $d->find_element_ok('//select[@id="list_type_selection_pops_select"]/option[text()="' . $accessions_list_name . '"]', 'xpath', 'select list sel pop');
     $list->click();
     sleep(5);
     $d->find_element_ok('//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]', 'xpath', 'select list sel pop')->click();
diff --git a/t/selenium2/solgs/kcluster.t b/t/selenium2/solgs/kcluster.t
index 25910fdfa4..326e1647fc 100644
--- a/t/selenium2/solgs/kcluster.t
+++ b/t/selenium2/solgs/kcluster.t
@@ -20,10 +20,10 @@ my $solgs_data = SGN::Test::solGSData->new(
     }
 );
 
-my $cache_dir = $solgs_data->site_cluster_shared_dir();
+my $cache_dir    = $solgs_data->site_cluster_shared_dir();
 my $protocol_dir = $solgs_data->default_protocol_dir();
-my $cluster_dir =  catdir($protocol_dir, 'cluster');
-my $log_dir = catdir($protocol_dir, 'log');
+my $cluster_dir  = catdir( $protocol_dir, 'cluster' );
+my $log_dir      = catdir( $protocol_dir, 'log' );
 
 my $accessions_list = $solgs_data->load_accessions_list();
 
@@ -75,7 +75,6 @@ print STDERR
 print STDERR "\nplots list: $plots_list_name -- $plots_list_id\n";
 
 `rm -r $cache_dir`;
-# `rm -r /tmp/localhost/GBSApeKIgenotypingv4/log/`;
 
 $d->while_logged_in_as(
     "submitter",
@@ -84,7 +83,7 @@ $d->while_logged_in_as(
         $d->get_ok( '/cluster/analysis', 'cluster home page' );
         sleep(5);
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select clones list'
@@ -133,7 +132,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $plots_list_name . '"]',
             'xpath',
             'select plots list'
@@ -178,7 +177,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -227,7 +226,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -274,7 +273,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -314,7 +313,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_list_name . '"]',
             'xpath',
             'select trials list'
@@ -360,7 +359,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_dt_name . '"]',
             'xpath',
             'select trials dataset'
@@ -407,7 +406,7 @@ $d->while_logged_in_as(
         sleep(3);
 
         $d->find_element_ok(
-            '//select[@id="cluster_pops_list_select"]/option[text()="'
+            '//select[@id="cluster_pops_select"]/option[text()="'
               . $trials_dt_name . '"]',
             'xpath',
             'select trials dataset'
@@ -646,7 +645,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'accessions list sl pop'
@@ -676,7 +675,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'accession select list sl pop'
@@ -713,13 +712,15 @@ $d->while_logged_in_as(
 
         $d->find_element_ok(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
-            'xpath', 'select list sel pop' )->click();
+            'xpath',
+            'select list sel pop'
+        )->click();
         sleep(5);
         $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
@@ -734,7 +735,9 @@ $d->while_logged_in_as(
             $sel_pops );
         $d->find_element_ok(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
-            'xpath', 'select list sel pop' )->click();
+            'xpath',
+            'select list sel pop'
+        )->click();
         sleep(3);
 
         my $clustering =
@@ -792,7 +795,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(2);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -801,7 +804,9 @@ $d->while_logged_in_as(
         sleep(2);
         $d->find_element_ok(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
-            'xpath', 'select list sel pop' )->click();
+            'xpath',
+            'select list sel pop'
+        )->click();
         sleep(5);
         my $clustering =
           $d->find_element( 'Clustering', 'partial_link_text', 'scroll up' );
@@ -866,7 +871,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select accessions dataset sel pop'
@@ -875,7 +880,9 @@ $d->while_logged_in_as(
         sleep(5);
         $d->find_element_ok(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
-            'xpath', 'select list sel pop' )->click();
+            'xpath',
+            'select list sel pop'
+        )->click();
         sleep(15);
 
         my $clustering =
@@ -1052,11 +1059,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial type tr pop'
         )->click();
@@ -1203,10 +1210,10 @@ $d->while_logged_in_as(
         $d->driver->refresh();
         sleep(3);
 
-    `rm -r $cluster_dir`;
-    sleep(3);
-    `rm -r $log_dir`;
-    sleep(5);
+        `rm -r $cluster_dir`;
+        sleep(3);
+        `rm -r $log_dir`;
+        sleep(5);
 
 # # $d->get_ok('solgs/traits/all/population/139/traits/1971973596/gp/1', 'models page');
 # # sleep(15);
@@ -1396,11 +1403,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial type tr pop'
         )->click();
@@ -1469,11 +1476,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Kasese solgs trial"]',
+'//select[@id="si_pops_select"]/option[text()="Kasese solgs trial"]',
             'xpath',
             'select trial type tr pop'
         )->click();
@@ -1531,10 +1538,10 @@ $d->while_logged_in_as(
         sleep(3);
 
 #########################
-   `rm -r $cluster_dir`;
-    sleep(3);
-    `rm -r $log_dir`;
-    sleep(5);
+        `rm -r $cluster_dir`;
+        sleep(3);
+        `rm -r $log_dir`;
+        sleep(5);
 ########################################
 
         my $clustering =
@@ -1581,10 +1588,10 @@ $d->while_logged_in_as(
         $d->driver->refresh();
         sleep(3);
 
-# #    #  #######    #
-# #    #  $d->get_ok('/solgs/trait/70666/population/139/gp/1', 'open model page');
-# #    #  sleep(5);
-# #    #
+ # #    #  #######    #
+ #  # # $d->get_ok('/solgs/trait/70666/population/139/gp/1', 'open model page');
+ # ## sleep(5);
+ # #    #
 
         my $clustering =
           $d->find_element( 'Models summary', 'partial_link_text',
@@ -1793,7 +1800,7 @@ $d->while_logged_in_as(
         sleep(15);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'list sl pop'
@@ -1825,7 +1832,7 @@ $d->while_logged_in_as(
         sleep(5);
 
         $d->find_element_ok(
-'//select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select list sl pop'
@@ -1986,11 +1993,11 @@ $d->while_logged_in_as(
             "arguments[0].scrollIntoView(true);window.scrollBy(0,-100);",
             $cor );
         sleep(5);
-        $d->find_element_ok( 'si_select_pops', 'id', 'select list sl pop' )
+        $d->find_element_ok( 'si_pops_select', 'id', 'select list sl pop' )
           ->click();
         sleep(3);
         $d->find_element_ok(
-'//select[@id="si_select_pops"]/option[text()="Training population 2804608595"]',
+'//select[@id="si_pops_select"]/option[text()="Training population 2804608595"]',
             'xpath',
             'select combo pop'
         )->click();
@@ -2048,7 +2055,7 @@ $d->while_logged_in_as(
         $d->driver->refresh();
         sleep(5);
 
-        # #$d->get_ok('/solgs/models/combined/trials/2804608595/traits/1971973596/gp/1', 'combined trials models summary page');
+# #$d->get_ok('/solgs/models/combined/trials/2804608595/traits/1971973596/gp/1', 'combined trials models summary page');
         ## sleep(5);
 
         my $sel_pops =
@@ -2061,7 +2068,7 @@ $d->while_logged_in_as(
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $dataset = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_dt_name . '"]',
             'xpath',
             'select dataset sel pop'
@@ -2070,7 +2077,9 @@ $d->while_logged_in_as(
         sleep(5);
         $d->find_element_ok(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
-            'xpath', 'select list sel pop' )->click();
+            'xpath',
+            'select list sel pop'
+        )->click();
         sleep(15);
 
         my $clustering =
@@ -2126,13 +2135,15 @@ $d->while_logged_in_as(
 
         $d->find_element_ok(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
-            'xpath', 'select list type sel pop' )->click();
+            'xpath',
+            'select list type sel pop'
+        )->click();
         sleep(5);
         $d->find_element_ok( 'list_type_selection_pops_select',
             'id', 'select clones list menu' )->click();
         sleep(5);
         my $list = $d->find_element_ok(
-'//div[@id="list_type_selection_pops_list"]/select[@id="list_type_selection_pops_select"]/option[text()="'
+            '//select[@id="list_type_selection_pops_select"]/option[text()="'
               . $accessions_list_name . '"]',
             'xpath',
             'select list sel pop'
@@ -2141,7 +2152,9 @@ $d->while_logged_in_as(
         sleep(5);
         $d->find_element_ok(
             '//div[ @id="list_type_selection_pop_go_btn"]/input[@value="View"]',
-            'xpath', 'select list sel pop' )->click();
+            'xpath',
+            'select list sel pop'
+        )->click();
         sleep(15);
 
         my $clustering =

From 51bd51e01d38a6b86647888b551f132c7e6a67f4 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Fri, 14 Jul 2023 11:05:38 -0400
Subject: [PATCH 59/61] Accession Upload: verify accessions file character
 encoding Prevent the JSON serializer from re-encoding text that is already
 utf-8 encoded

---
 lib/SGN/Controller/AJAX/Accessions.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/SGN/Controller/AJAX/Accessions.pm b/lib/SGN/Controller/AJAX/Accessions.pm
index 116c2c354a..3c72433eb4 100644
--- a/lib/SGN/Controller/AJAX/Accessions.pm
+++ b/lib/SGN/Controller/AJAX/Accessions.pm
@@ -41,6 +41,7 @@ __PACKAGE__->config(
     default   => 'application/json',
     stash_key => 'rest',
     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON'  },
+    json_options_encode => { 'utf8' => 0 }
    );
 
 sub verify_accession_list : Path('/ajax/accession_list/verify') : ActionClass('REST') { }

From 1288cf17ca3175a3c49da7bac37aa58e06451a63 Mon Sep 17 00:00:00 2001
From: David Waring <djw64@cornell.edu>
Date: Sun, 16 Jul 2023 12:04:11 -0400
Subject: [PATCH 60/61] Accession Upload: remove encoding of text/html response
 restore encoding of json response

---
 js/source/legacy/CXGN/BreedersToolbox/Accessions.js | 2 +-
 lib/SGN/Controller/AJAX/Accessions.pm               | 9 ++++-----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/js/source/legacy/CXGN/BreedersToolbox/Accessions.js b/js/source/legacy/CXGN/BreedersToolbox/Accessions.js
index c0c879e4b2..0739b1ed5f 100644
--- a/js/source/legacy/CXGN/BreedersToolbox/Accessions.js
+++ b/js/source/legacy/CXGN/BreedersToolbox/Accessions.js
@@ -381,7 +381,7 @@ jQuery(document).ready(function ($) {
         },
         complete: function (r) {
 	    //alert("DONE WITH UPLOAD "+r);
-	    var clean_r = r.replace('<pre>', '');
+	    var clean_r = r.replace(/^<pre[^>]*>/, '');
 	    clean_r = clean_r.replace('</pre>', '');
 	    response = JSON.parse(clean_r); //decodeURIComponent(clean_r));
             console.log(response);
diff --git a/lib/SGN/Controller/AJAX/Accessions.pm b/lib/SGN/Controller/AJAX/Accessions.pm
index 3c72433eb4..e443407067 100644
--- a/lib/SGN/Controller/AJAX/Accessions.pm
+++ b/lib/SGN/Controller/AJAX/Accessions.pm
@@ -40,9 +40,8 @@ BEGIN { extends 'Catalyst::Controller::REST' }
 __PACKAGE__->config(
     default   => 'application/json',
     stash_key => 'rest',
-    map       => { 'application/json' => 'JSON', 'text/html' => 'JSON'  },
-    json_options_encode => { 'utf8' => 0 }
-   );
+    map       => { 'application/json' => 'JSON' },
+);
 
 sub verify_accession_list : Path('/ajax/accession_list/verify') : ActionClass('REST') { }
 
@@ -63,7 +62,7 @@ sub verify_accession_list_POST : Args(0) {
         my $dbh = $c->dbc->dbh;
         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
         if (!$user_info[0]){
-            $c->stash->{rest} = {error=>'You must be logged in to upload this seedlot info!'};
+            $c->stash->{rest} = {error=>'You must be logged in to upload this info!'};
             $c->detach();
         }
         $user_id = $user_info[0];
@@ -72,7 +71,7 @@ sub verify_accession_list_POST : Args(0) {
         $user_name = $p->get_username;
     } else {
         if (!$c->user){
-            $c->stash->{rest} = {error=>'You must be logged in to upload this seedlot info!'};
+            $c->stash->{rest} = {error=>'You must be logged in to upload this info!'};
             $c->detach();
         }
         $user_id = $c->user()->get_object()->get_sp_person_id();

From 758d336501e25a367f801905a806c8f5329becd8 Mon Sep 17 00:00:00 2001
From: Clay Birkett <clb343@cornell.edu>
Date: Tue, 18 Jul 2023 10:00:49 -0400
Subject: [PATCH 61/61] remove duplicate file

---
 Search.pm | 2249 -----------------------------------------------------
 1 file changed, 2249 deletions(-)
 delete mode 100644 Search.pm

diff --git a/Search.pm b/Search.pm
deleted file mode 100644
index a761b270aa..0000000000
--- a/Search.pm
+++ /dev/null
@@ -1,2249 +0,0 @@
-package CXGN::Genotype::Search;
-
-=head1 NAME
-
-CXGN::Genotype::Search - an object to handle searching genotypes for stocks
-
-=head1 USAGE
-
-PLEASE BE AWARE THAT THE DEFAULT OPTIONS FOR genotypeprop_hash_select, protocolprop_top_key_select, protocolprop_marker_hash_select ARE PRONE TO EXCEEDING THE MEMORY LIMITS OF VM. CHECK THE MOOSE ATTRIBUTES BELOW TO SEE THE DEFAULTS, AND ADJUST YOUR MOOSE INSTANTIATION ACCORDINGLY
-
-my $genotypes_search = CXGN::Genotype::Search->new({
-    bcs_schema=>$schema,
-    people_schema=>$people_schema,
-    accession_list=>$accession_list,
-    tissue_sample_list=>$tissue_sample_list,
-    trial_list=>$trial_list,
-    protocol_id_list=>$protocol_id_list,
-    markerprofile_id_list=>$markerprofile_id_list,
-    genotype_data_project_list=>$genotype_data_project_list,
-    chromosome_list=>\@chromosome_numbers,
-    start_position=>$start_position,
-    end_position=>$end_position,
-    marker_name_list=>['S80_265728', 'S80_265723'],
-    genotypeprop_hash_select=>['DS', 'GT', 'DP'], #THESE ARE THE KEYS IN THE GENOTYPEPROP OBJECT
-    protocolprop_top_key_select=>['reference_genome_name', 'header_information_lines', 'marker_names', 'markers'], #THESE ARE THE KEYS AT THE TOP LEVEL OF THE PROTOCOLPROP OBJECT
-    protocolprop_marker_hash_select=>['name', 'chrom', 'pos', 'alt', 'ref'], #THESE ARE THE KEYS IN THE MARKERS OBJECT IN THE PROTOCOLPROP OBJECT
-    return_only_first_genotypeprop_for_stock=>0, #THIS IS TO CONSERVE MEMORY USAGE
-    limit=>$limit,
-    offset=>$offset,
-    forbid_cache=>$forbid_cache
-    # marker_search_hash_list=>[{'S80_265728' => {'pos' => '265728', 'chrom' => '1'}}], NOT IMPLEMENTED
-    # marker_score_search_hash_list=>[{'S80_265728' => {'GT' => '0/0', 'GQ' => '99'}}], NOT IMPLEMENTED
-});
-# my ($total_count, $genotypes) = $genotypes_search->get_genotype_info();
-
-# RECOMMENDED
-If you just want to get a file with the genotype result in a dosage matrix or VCF file, use get_cached_file_dosage_matrix or get_cached_file_VCF functions instead.
-If you want results in json format use get_cached_file_search_json
-If you want results in json format for only the metadata (no genotype call data), use get_cached_file_search_json()
-
-=head1 DESCRIPTION
-
-
-=head1 AUTHORS
-
- Nicolas Morales <nm529@cornell.edu>
- With code moved from CXGN::BreederSearch
- Lukas Mueller <lam87@cornell.edu>
- Aimin Yan <ay247@cornell.edu>
-
-=cut
-
-use strict;
-use warnings;
-use Moose;
-use Try::Tiny;
-use Data::Dumper;
-use SGN::Model::Cvterm;
-use CXGN::Trial;
-use JSON;
-use CXGN::Stock::Accession;
-use CXGN::Genotype::Protocol;
-use CXGN::Genotype::ComputeHybridGenotype;
-use Cache::File;
-use Digest::MD5 qw | md5_hex |;
-use File::Slurp qw | write_file |;
-use File::Temp qw | tempfile |;
-use File::Copy;
-use POSIX;
-
-has 'bcs_schema' => (
-    isa => 'Bio::Chado::Schema',
-    is => 'rw',
-    required => 1
-);
-
-has 'people_schema' => (
-    isa => 'CXGN::People::Schema',
-    is => 'rw',
-    required => 1
-);
-
-has 'protocol_id_list' => (
-    isa => 'ArrayRef[Int]|Undef',
-    is => 'rw',
-);
-
-has 'markerprofile_id_list' => (
-    isa => 'ArrayRef[Int]|Undef',
-    is => 'ro',
-);
-
-has 'accession_list' => (
-    isa => 'ArrayRef[Int]|Undef',
-    is => 'ro',
-);
-
-has 'tissue_sample_list' => (
-    isa => 'ArrayRef[Int]|Undef',
-    is => 'ro',
-);
-
-has 'trial_list' => (
-    isa => 'ArrayRef[Int]|Undef',
-    is => 'ro',
-);
-
-has 'genotype_data_project_list' => (
-    isa => 'ArrayRef[Int]|Undef',
-    is => 'ro',
-);
-
-has 'chromosome_list' => (
-    isa => 'ArrayRef[Int]|ArrayRef[Str]|Undef',
-    is => 'ro',
-);
-
-has 'start_position' => (
-    isa => 'Int|Undef',
-    is => 'ro',
-);
-
-has 'end_position' => (
-    isa => 'Int|Undef',
-    is => 'ro',
-);
-
-has 'marker_name_list' => (
-    isa => 'ArrayRef[Str]|Undef',
-    is => 'ro',
-);
-
-has 'genotypeprop_hash_select' => (
-    isa => 'ArrayRef[Str]',
-    is => 'ro',
-    default => sub {['GT', 'AD', 'DP', 'GQ', 'DS', 'PL', 'NT']} #THESE ARE THE GENERIC AND EXPECTED VCF ATRRIBUTES
-);
-
-has 'protocolprop_top_key_select' => (
-    isa => 'ArrayRef[Str]',
-    is => 'ro',
-    default => sub {['reference_genome_name', 'species_name', 'header_information_lines', 'sample_observation_unit_type_name', 'marker_names', 'markers', 'markers_array']} #THESE ARE ALL POSSIBLE TOP LEVEL KEYS IN PROTOCOLPROP BASED ON VCF LOADING
-);
-
-has 'protocolprop_marker_hash_select' => (
-    isa => 'ArrayRef[Str]',
-    is => 'ro',
-    default => sub {['name', 'chrom', 'pos', 'alt', 'ref', 'qual', 'filter', 'info', 'format']} #THESE ARE ALL POSSIBLE PROTOCOLPROP MARKER HASH KEYS BASED ON VCF LOADING
-);
-
-has 'return_only_first_genotypeprop_for_stock' => (
-    isa => 'Bool',
-    is => 'ro',
-    default => 0
-);
-
-# When using the get_cached_file_dosage_matrix or get_cached_file_VCF functions, need the following three keys.
-has 'cache_root' => (
-    isa => 'Str',
-    is => 'rw',
-);
-
-has 'cache' => (
-    isa => 'Cache::File',
-    is => 'rw',
-);
-
-has 'cache_expiry' => (
-    isa => 'Int',
-    is => 'rw',
-    default => 0, # never expires?
-);
-
-has 'forbid_cache' => (
-    isa => 'Bool',
-    is => 'ro',
-    default => 0
-);
-
-has 'prevent_transpose' => (
-    isa => 'Bool',
-    is => 'ro',
-    default => 0
-);
-
-has '_iterator_query_handle' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_iterator_genotypeprop_query_handle' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_filtered_markers' => (
-    isa => 'HashRef',
-    is => 'rw',
-    default => sub {{}}
-);
-
-has '_snp_genotyping_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_vcf_snp_genotyping_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_vcf_map_details_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_vcf_map_details_markers_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_vcf_map_details_markers_array_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_igd_genotypeprop_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_accession_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_tissue_sample_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_plot_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_plant_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_tissue_sample_of_cvterm_id' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_protocolprop_markers_h' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_protocolprop_top_key_h' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_protocolprop_top_key_markers_h' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_protocolprop_top_key_markers_array_h' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_genotypeprop_h' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_protocolprop_marker_hash_select_arr' => (
-    isa => 'ArrayRef',
-    is => 'rw'
-);
-
-has '_protocolprop_top_key_select_arr' => (
-    isa => 'ArrayRef',
-    is => 'rw'
-);
-
-has '_selected_protocol_marker_info' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_selected_protocol_top_key_info' => (
-    isa => 'Ref',
-    is => 'rw'
-);
-
-has '_genotypeprop_infos' => (
-    isa => 'ArrayRef',
-    is => 'rw'
-);
-
-has '_genotypeprop_infos_counter' => (
-    isa => 'Int',
-    is => 'rw'
-);
-
-has '_genotypeprop_hash_select_arr' => (
-    isa => 'ArrayRef',
-    is => 'rw'
-);
-
-#NOT IMPLEMENTED
-has 'marker_search_hash_list' => (
-    isa => 'ArrayRef[HashRef]|Undef',
-    is => 'ro',
-);
-
-#NOT IMPLEMENTED
-has 'marker_score_search_hash_list' => (
-    isa => 'ArrayRef[HashRef]|Undef',
-    is => 'ro',
-);
-
-has 'limit' => (
-    isa => 'Int|Undef',
-    is => 'rw',
-);
-
-has 'offset' => (
-    isa => 'Int|Undef',
-    is => 'rw',
-);
-
-=head2 get_genotype_info
-
-returns: an array with genotype information
-
-=cut
-
-=head2 get_genotype_info()
-
-Function for getting genotype data iteratively.
-Should be used like:
-
-my $genotype_search = CXGN::Genotype::Search->new({
-    bcs_schema=>$schema,
-    etc...
-});
-my ($count, $genotype_data) = $genotype_search->get_genotype_info();
-
-If you want to get results iteratively, use the init and iterator function defined below instead. Iterative retrieval minimizes memory load.
-
-If you just want to get a file with the genotype result in a dosage matrix or VCF file, use get_cached_file_dosage_matrix or get_cached_file_VCF functions instead.
-If you want results in json format use get_cached_file_search_json
-If you want results in json format for only the metadata (no genotype call data), use get_cached_file_search_json()
-
-=cut
-
-sub get_genotype_info {
-    my $self = shift;
-    my $schema = $self->bcs_schema;
-    my $trial_list = $self->trial_list;
-    my $genotype_data_project_list = $self->genotype_data_project_list;
-    my $protocol_id_list = $self->protocol_id_list;
-    my $markerprofile_id_list = $self->markerprofile_id_list;
-    my $accession_list = $self->accession_list;
-    my $tissue_sample_list = $self->tissue_sample_list;
-    my $marker_name_list = $self->marker_name_list;
-    my $chromosome_list = $self->chromosome_list;
-    my $start_position = $self->start_position;
-    my $end_position = $self->end_position;
-    my $genotypeprop_hash_select = $self->genotypeprop_hash_select;
-    my $protocolprop_top_key_select = $self->protocolprop_top_key_select;
-    my $protocolprop_marker_hash_select = $self->protocolprop_marker_hash_select;
-    my $marker_search_hash_list = $self->marker_search_hash_list;
-    my $marker_score_search_hash_list = $self->marker_score_search_hash_list;
-    my $return_only_first_genotypeprop_for_stock = $self->return_only_first_genotypeprop_for_stock;
-    my $limit = $self->limit;
-    my $offset = $self->offset;
-    my @data;
-    my %search_params;
-    my @where_clause;
-
-    my $snp_genotyping_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'snp genotyping', 'genotype_property')->cvterm_id();
-    my $vcf_snp_genotyping_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_snp_genotyping', 'genotype_property')->cvterm_id();
-    my $vcf_map_details_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details', 'protocol_property')->cvterm_id();
-    my $vcf_map_details_markers_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details_markers', 'protocol_property')->cvterm_id();
-    my $vcf_map_details_markers_array_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details_markers_array', 'protocol_property')->cvterm_id();
-    my $igd_genotypeprop_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'igd number', 'genotype_property')->cvterm_id();
-    my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'accession', 'stock_type')->cvterm_id();
-    my $tissue_sample_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'tissue_sample', 'stock_type')->cvterm_id();
-    my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'plot', 'stock_type')->cvterm_id();
-    my $plant_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'plant', 'stock_type')->cvterm_id();
-    my $tissue_sample_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id();
-
-    my @trials_accessions;
-    foreach (@$trial_list){
-        my $trial = CXGN::Trial->new({bcs_schema=>$schema, trial_id=>$_});
-        my $accessions = $trial->get_accessions();
-        foreach (@$accessions){
-            push @trials_accessions, $_->{stock_id};
-        }
-    }
-
-    #If accessions are explicitly given, then accessions found from trials will not be added to the search.
-    if (!$accession_list || scalar(@$accession_list)==0) {
-        push @$accession_list, @trials_accessions;
-    }
-
-    #For projects inserted into database during the addition of genotypes and genotypeprops
-    if (scalar(@trials_accessions)==0){
-        if ($trial_list && scalar(@$trial_list)>0) {
-            my $trial_sql = join ("," , @$trial_list);
-            push @where_clause, "project.project_id in ($trial_sql)";
-        }
-    }
-
-    #For genotyping_data_project
-    if ($genotype_data_project_list && scalar($genotype_data_project_list)>0) {
-        my $sql = join ("," , @$genotype_data_project_list);
-        push @where_clause, "project.project_id in ($sql)";
-    }
-    if ($protocol_id_list && scalar(@$protocol_id_list)>0) {
-        my $protocol_sql = join ("," , @$protocol_id_list);
-        push @where_clause, "nd_protocol.nd_protocol_id in ($protocol_sql)";
-    }
-    if ($accession_list && scalar(@$accession_list)>0) {
-        my $accession_sql = join ("," , @$accession_list);
-        push @where_clause, " ( stock.stock_id in ($accession_sql) OR (accession_of_tissue_sample.stock_id in ($accession_sql) AND accession_of_tissue_sample.type_id = $accession_cvterm_id) ) ";
-        push @where_clause, "stock.type_id in ($accession_cvterm_id, $tissue_sample_cvterm_id)";
-    }
-    if ($tissue_sample_list && scalar(@$tissue_sample_list)>0) {
-        my $stock_sql = join ("," , @$tissue_sample_list);
-        push @where_clause, "stock.stock_id in ($stock_sql)";
-        push @where_clause, "stock.type_id = $tissue_sample_cvterm_id";
-    }
-    if ($markerprofile_id_list && scalar(@$markerprofile_id_list)>0) {
-        my $markerprofile_sql = join ("," , @$markerprofile_id_list);
-        push @where_clause, "genotype.genotype_id in ($markerprofile_sql)";
-    }
-    if ($marker_name_list && scalar(@$marker_name_list)>0) {
-        my $search_vals_sql = "'".join ("','" , @$marker_name_list)."'";
-        push @where_clause, "nd_protocolprop.value->'marker_names' \\?& array[$search_vals_sql]";
-    }
-    if ($marker_search_hash_list && scalar(@$marker_search_hash_list)>0) {
-        foreach (@$marker_search_hash_list){
-            my $json_val = encode_json $_;
-            push @where_clause, "nd_protocolprop.value->'markers' \\@> $json_val"."::jsonb";
-        }
-    }
-    if ($marker_score_search_hash_list && scalar(@$marker_score_search_hash_list)>0) {
-        foreach (@$marker_score_search_hash_list){
-            my $json_val = encode_json $_;
-            push @where_clause, "genotype_values.value \\@> $json_val"."::jsonb";
-        }
-    }
-
-    my $where_clause = scalar(@where_clause)>0 ? " WHERE " . (join (" AND " , @where_clause)) : '';
-
-    my $offset_clause = '';
-    my $limit_clause = '';
-    if ($limit){
-        $limit_clause = " LIMIT $limit ";
-    }
-    if ($offset){
-        $offset_clause = " OFFSET $offset ";
-    }
-
-    my $stock_select = '';
-    if ($return_only_first_genotypeprop_for_stock) {
-        $stock_select = 'distinct on (stock.stock_id) stock.stock_id';
-    } else {
-        $stock_select = 'stock.stock_id';
-    }
-
-    my $q = "SELECT $stock_select, igd_number_genotypeprop.value, nd_protocol.nd_protocol_id, nd_protocol.name, stock.uniquename, stock.type_id, stock_cvterm.name, genotype.genotype_id, genotype.uniquename, genotype.description, project.project_id, project.name, project.description, accession_of_tissue_sample.stock_id, accession_of_tissue_sample.uniquename, count(genotype.genotype_id) OVER() AS full_count
-        FROM stock
-        JOIN cvterm AS stock_cvterm ON(stock.type_id = stock_cvterm.cvterm_id)
-        LEFT JOIN stock_relationship ON(stock_relationship.subject_id=stock.stock_id AND stock_relationship.type_id = $tissue_sample_of_cvterm_id)
-        LEFT JOIN stock AS accession_of_tissue_sample ON(stock_relationship.object_id=accession_of_tissue_sample.stock_id)
-        JOIN nd_experiment_stock ON(stock.stock_id=nd_experiment_stock.stock_id)
-        JOIN nd_experiment USING(nd_experiment_id)
-        JOIN nd_experiment_protocol USING(nd_experiment_id)
-        JOIN nd_experiment_project USING(nd_experiment_id)
-        JOIN nd_experiment_genotype USING(nd_experiment_id)
-        JOIN nd_protocol USING(nd_protocol_id)
-        LEFT JOIN nd_protocolprop ON(nd_protocolprop.nd_protocol_id = nd_protocol.nd_protocol_id AND nd_protocolprop.type_id = $vcf_map_details_cvterm_id)
-        JOIN genotype USING(genotype_id)
-        LEFT JOIN genotypeprop AS igd_number_genotypeprop ON(igd_number_genotypeprop.genotype_id = genotype.genotype_id AND igd_number_genotypeprop.type_id = $igd_genotypeprop_cvterm_id)
-        JOIN project USING(project_id)
-        $where_clause
-        ORDER BY stock.stock_id, genotype.genotype_id ASC
-        $limit_clause
-        $offset_clause;";
-
-    #print STDERR Dumper $q;
-    my $h = $schema->storage->dbh()->prepare($q);
-    $h->execute();
-
-    my $total_count = 0;
-    my @genotype_id_array;
-    my @genotypeprop_array;
-    my %genotype_hash;
-    my %genotypeprop_hash;
-    my %protocolprop_hash;
-    while (my ($stock_id, $igd_number_json, $protocol_id, $protocol_name, $stock_name, $stock_type_id, $stock_type_name, $genotype_id, $genotype_uniquename, $genotype_description, $project_id, $project_name, $project_description, $accession_id, $accession_uniquename, $full_count) = $h->fetchrow_array()) {
-        my $igd_number_hash = $igd_number_json ? decode_json $igd_number_json : undef;
-        my $igd_number = $igd_number_hash ? $igd_number_hash->{'igd number'} : undef;
-        $igd_number = !$igd_number && $igd_number_hash ? $igd_number_hash->{'igd_number'} : undef;
-
-        my $germplasmName = '';
-        my $germplasmDbId = '';
-        if ($stock_type_name eq 'accession'){
-            $germplasmName = $stock_name;
-            $germplasmDbId = $stock_id;
-        }
-        if ($stock_type_name eq 'tissue_sample'){
-            $germplasmName = $accession_uniquename;
-            $germplasmDbId = $accession_id;
-        }
-
-        my $stock_object = CXGN::Stock::Accession->new({schema=>$self->bcs_schema, stock_id=>$germplasmDbId});
-
-        push @genotype_id_array, $genotype_id;
-
-        $genotype_hash{$genotype_id} = {
-            markerProfileDbId => $genotype_id,
-            germplasmDbId => $germplasmDbId,
-            germplasmName => $germplasmName,
-            synonyms => $stock_object->synonyms,
-            stock_id => $stock_id,
-            stock_name => $stock_name,
-            stock_type_id => $stock_type_id,
-            stock_type_name => $stock_type_name,
-            genotypeDbId => $genotype_id,
-            genotypeUniquename => $genotype_uniquename,
-            genotypeDescription => $genotype_description,
-            analysisMethodDbId => $protocol_id,
-            analysisMethod => $protocol_name,
-            genotypingDataProjectDbId => $project_id,
-            genotypingDataProjectName => $project_name,
-            genotypingDataProjectDescription => $project_description,
-            igd_number => $igd_number,
-        };
-        $protocolprop_hash{$protocol_id}++;
-        $total_count = $full_count;
-    }
-    print STDERR "CXGN::Genotype::Search has genotype_ids $total_count\n";
-
-    my @found_protocolprop_ids = keys %protocolprop_hash;
-    my @protocolprop_marker_hash_select_arr;
-    foreach (@$protocolprop_marker_hash_select){
-        push @protocolprop_marker_hash_select_arr, "s.value->>'$_'";
-    }
-    my @protocolprop_top_key_select_arr;
-    my %protocolprop_top_key_select_hash;
-    foreach (@$protocolprop_top_key_select){
-        if ($_ ne 'markers' && $_ ne 'markers_array') {
-            push @protocolprop_top_key_select_arr, "value->>'$_'";
-        }
-        $protocolprop_top_key_select_hash{$_}++;
-    }
-    my %selected_protocol_marker_info;
-    my %selected_protocol_top_key_info;
-    my %filtered_markers;
-    my $genotypeprop_chromosome_rank_string = '';
-    if (scalar(@found_protocolprop_ids)>0){
-        my $protocolprop_id_sql = join ("," , @found_protocolprop_ids);
-        my $protocolprop_where_sql = "nd_protocol_id in ($protocolprop_id_sql) and type_id = $vcf_map_details_cvterm_id";
-        my $protocolprop_where_markers_sql = "nd_protocol_id in ($protocolprop_id_sql) and type_id = $vcf_map_details_markers_cvterm_id";
-        my $protocolprop_where_markers_array_sql = "nd_protocol_id in ($protocolprop_id_sql) and type_id = $vcf_map_details_markers_array_cvterm_id";
-        my $protocolprop_hash_select_sql = scalar(@protocolprop_marker_hash_select_arr) > 0 ? ', '.join ',', @protocolprop_marker_hash_select_arr : '';
-
-        my $chromosome_where = '';
-        if ($chromosome_list && scalar(@$chromosome_list)>0) {
-            my $chromosome_list_sql = '\'' . join('\', \'', @$chromosome_list) . '\'';
-            $chromosome_where = " AND (s.value->>'chrom')::text IN ($chromosome_list_sql)";
-            #$genotypeprop_chromosome_rank_string = " AND value->>'CHROM' IN ($chromosome_list_sql) ";
-        }
-        my $start_position_where = '';
-        if (defined($start_position)) {
-            $start_position_where = " AND (s.value->>'pos')::int >= $start_position";
-        }
-        my $end_position_where = '';
-        if (defined($end_position)) {
-            $end_position_where = " AND (s.value->>'pos')::int <= $end_position";
-        }
-
-        my $protocolprop_q = "SELECT nd_protocol_id, s.key $protocolprop_hash_select_sql
-            FROM nd_protocolprop, jsonb_each(nd_protocolprop.value) as s
-            WHERE $protocolprop_where_markers_sql $chromosome_where $start_position_where $end_position_where;";
-
-        my $protocolprop_h = $schema->storage->dbh()->prepare($protocolprop_q);
-        $protocolprop_h->execute();
-        while (my ($protocol_id, $marker_name, @protocolprop_info_return) = $protocolprop_h->fetchrow_array()) {
-            for my $s (0 .. scalar(@protocolprop_marker_hash_select_arr)-1){
-                $selected_protocol_marker_info{$protocol_id}->{$marker_name}->{$protocolprop_marker_hash_select->[$s]} = $protocolprop_info_return[$s];
-            }
-            $filtered_markers{$marker_name}++;
-        }
-        my $protocolprop_top_key_select_sql = scalar(@protocolprop_top_key_select_arr) > 0 ? ', '.join ',', @protocolprop_top_key_select_arr : '';
-        my $protocolprop_top_key_q = "SELECT nd_protocol_id $protocolprop_top_key_select_sql from nd_protocolprop WHERE $protocolprop_where_sql;";
-        my $protocolprop_top_key_h = $schema->storage->dbh()->prepare($protocolprop_top_key_q);
-        $protocolprop_top_key_h->execute();
-        while (my ($protocol_id, @protocolprop_top_key_return) = $protocolprop_top_key_h->fetchrow_array()) {
-            for my $s (0 .. scalar(@protocolprop_top_key_select_arr)-1){
-                my $protocolprop_i = $protocolprop_top_key_select->[$s];
-                my $val;
-                if ($protocolprop_i eq 'header_information_lines' || $protocolprop_i eq 'marker_names') {
-                    $val = decode_json $protocolprop_top_key_return[$s];
-                } else {
-                    $val = $protocolprop_top_key_return[$s];
-                }
-                $selected_protocol_top_key_info{$protocol_id}->{$protocolprop_i} = $val;
-            }
-        }
-        if (exists($protocolprop_top_key_select_hash{'markers'})) {
-            my $protocolprop_top_key_q = "SELECT nd_protocol_id, value from nd_protocolprop WHERE $protocolprop_where_markers_sql;";
-            my $protocolprop_top_key_h = $schema->storage->dbh()->prepare($protocolprop_top_key_q);
-            $protocolprop_top_key_h->execute();
-            while (my ($protocol_id, $markers_value) = $protocolprop_top_key_h->fetchrow_array()) {
-                $selected_protocol_top_key_info{$protocol_id}->{'markers'} = decode_json $markers_value;
-            }
-        }
-        if (exists($protocolprop_top_key_select_hash{'markers_array'})) {
-            my $protocolprop_top_key_q = "SELECT nd_protocol_id, value from nd_protocolprop WHERE $protocolprop_where_markers_array_sql;";
-            my $protocolprop_top_key_h = $schema->storage->dbh()->prepare($protocolprop_top_key_q);
-            $protocolprop_top_key_h->execute();
-            while (my ($protocol_id, $markers_value) = $protocolprop_top_key_h->fetchrow_array()) {
-                $selected_protocol_top_key_info{$protocol_id}->{'markers_array'} = decode_json $markers_value;
-            }
-        }
-    }
-
-    my @genotypeprop_hash_select_arr;
-    foreach (@$genotypeprop_hash_select){
-        push @genotypeprop_hash_select_arr, "s.value->>'$_'";
-    }
-    if (scalar(@genotype_id_array)>0) {
-        my $genotypeprop_id_sql = join ("," , @genotype_id_array);
-        my $genotypeprop_hash_select_sql = scalar(@genotypeprop_hash_select_arr) > 0 ? ', '.join ',', @genotypeprop_hash_select_arr : '';
-
-        my $filtered_markers_sql = '';
-        if (scalar(keys %filtered_markers) >0 && scalar(keys %filtered_markers) < 10000) {
-            $filtered_markers_sql = " AND s.key IN ('". join ("','", keys %filtered_markers) ."')";
-        }
-
-        my $q2 = "SELECT genotypeprop_id
-            FROM genotypeprop WHERE genotype_id = ? AND type_id=$vcf_snp_genotyping_cvterm_id $genotypeprop_chromosome_rank_string;";
-        my $h2 = $schema->storage->dbh()->prepare($q2);
-
-        my $genotypeprop_q = "SELECT s.key $genotypeprop_hash_select_sql
-            FROM genotypeprop, jsonb_each(genotypeprop.value) as s
-            WHERE genotypeprop_id = ? AND s.key != 'CHROM' AND type_id = $vcf_snp_genotyping_cvterm_id $filtered_markers_sql;";
-        my $genotypeprop_h = $schema->storage->dbh()->prepare($genotypeprop_q);
-
-        foreach my $genotype_id (@genotype_id_array){
-            $h2->execute($genotype_id);
-            while (my ($genotypeprop_id) = $h2->fetchrow_array()) {
-                $genotypeprop_h->execute($genotypeprop_id);
-                while (my ($marker_name, @genotypeprop_info_return) = $genotypeprop_h->fetchrow_array()) {
-                    for my $s (0 .. scalar(@genotypeprop_hash_select_arr)-1){
-                        $genotype_hash{$genotype_id}->{selected_genotype_hash}->{$marker_name}->{$genotypeprop_hash_select->[$s]} = $genotypeprop_info_return[$s];
-                    }
-                }
-            }
-        }
-    }
-
-    foreach (@genotype_id_array) {
-        my $info = $genotype_hash{$_};
-        my $selected_marker_info = $selected_protocol_marker_info{$info->{analysisMethodDbId}} ? $selected_protocol_marker_info{$info->{analysisMethodDbId}} : {};
-        my $selected_protocol_info = $selected_protocol_top_key_info{$info->{analysisMethodDbId}} ? $selected_protocol_top_key_info{$info->{analysisMethodDbId}} : {};
-        my @all_protocol_marker_names = keys %$selected_marker_info;
-        $selected_protocol_info->{markers} = $selected_marker_info;
-        $info->{resultCount} = scalar(keys %{$info->{selected_genotype_hash}});
-        $info->{all_protocol_marker_names} = \@all_protocol_marker_names;
-        $info->{selected_protocol_hash} = $selected_protocol_info;
-        push @data, $info;
-    }
-
-    #print STDERR Dumper \@data;
-    return ($total_count, \@data);
-}
-
-=head2 init_genotype_iterator()
-
-Function for initiating genotype search query and then used to get genotype data iteratively. Iterative search retrieval minimizes memory usage.
-Should be used like:
-
-my $genotype_search = CXGN::Genotype::Search->new({
-    bcs_schema=>$schema,
-    etc...
-});
-$genotype_search->init_genotype_iterator();
-while (my ($count, $genotype_data) = $genotype_search->get_next_genotype_info) {
-    #Do something with genotype data
-}
-
-If you just want to get a file with the genotype result in a dosage matrix or VCF file, use get_cached_file_dosage_matrix or get_cached_file_VCF functions instead.
-If you want results in json format use get_cached_file_search_json
-If you want results in json format for only the metadata (no genotype call data), use get_cached_file_search_json()
-
-=cut
-
-sub init_genotype_iterator {
-    my $self = shift;
-    my $schema = $self->bcs_schema;
-    my $trial_list = $self->trial_list;
-    my $genotype_data_project_list = $self->genotype_data_project_list;
-    my $protocol_id_list = $self->protocol_id_list;
-    my $markerprofile_id_list = $self->markerprofile_id_list;
-    my $accession_list = $self->accession_list;
-    my $tissue_sample_list = $self->tissue_sample_list;
-    my $marker_name_list = $self->marker_name_list;
-    my $chromosome_list = $self->chromosome_list;
-    my $start_position = $self->start_position;
-    my $end_position = $self->end_position;
-    my $genotypeprop_hash_select = $self->genotypeprop_hash_select;
-    my $protocolprop_top_key_select = $self->protocolprop_top_key_select;
-    my $protocolprop_marker_hash_select = $self->protocolprop_marker_hash_select;
-    my $marker_search_hash_list = $self->marker_search_hash_list;
-    my $marker_score_search_hash_list = $self->marker_score_search_hash_list;
-    my $return_only_first_genotypeprop_for_stock = $self->return_only_first_genotypeprop_for_stock;
-    my $limit = $self->limit;
-    my $offset = $self->offset;
-    my @data;
-    my %search_params;
-    my @where_clause;
-
-    my $snp_genotyping_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'snp genotyping', 'genotype_property')->cvterm_id();
-    $self->_snp_genotyping_cvterm_id($snp_genotyping_cvterm_id);
-    my $vcf_snp_genotyping_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_snp_genotyping', 'genotype_property')->cvterm_id();
-    $self->_vcf_snp_genotyping_cvterm_id($vcf_snp_genotyping_cvterm_id);
-    my $vcf_map_details_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details', 'protocol_property')->cvterm_id();
-    $self->_vcf_map_details_cvterm_id($vcf_map_details_cvterm_id);
-    my $vcf_map_details_markers_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details_markers', 'protocol_property')->cvterm_id();
-    $self->_vcf_map_details_markers_cvterm_id($vcf_map_details_markers_cvterm_id);
-    my $vcf_map_details_markers_array_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'vcf_map_details_markers_array', 'protocol_property')->cvterm_id();
-    $self->_vcf_map_details_markers_array_cvterm_id($vcf_map_details_markers_array_cvterm_id);
-    my $igd_genotypeprop_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'igd number', 'genotype_property')->cvterm_id();
-    $self->_igd_genotypeprop_cvterm_id($igd_genotypeprop_cvterm_id);
-    my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'accession', 'stock_type')->cvterm_id();
-    $self->_accession_cvterm_id($accession_cvterm_id);
-    my $tissue_sample_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'tissue_sample', 'stock_type')->cvterm_id();
-    $self->_tissue_sample_cvterm_id($tissue_sample_cvterm_id);
-    my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'plot', 'stock_type')->cvterm_id();
-    $self->_plot_cvterm_id($plot_cvterm_id);
-    my $plant_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'plant', 'stock_type')->cvterm_id();
-    $self->_plant_cvterm_id($plant_cvterm_id);
-    my $tissue_sample_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id();
-    $self->_tissue_sample_of_cvterm_id($tissue_sample_of_cvterm_id);
-
-    my @trials_accessions;
-    foreach (@$trial_list){
-        my $trial = CXGN::Trial->new({bcs_schema=>$schema, trial_id=>$_});
-        my $accessions = $trial->get_accessions();
-        foreach (@$accessions){
-            push @trials_accessions, $_->{stock_id};
-        }
-    }
-
-    #If accessions are explicitly given, then accessions found from trials will not be added to the search.
-    if (!$accession_list || scalar(@$accession_list)==0) {
-        push @$accession_list, @trials_accessions;
-    }
-
-    #For projects inserted into database during the addition of genotypes and genotypeprops
-    if (scalar(@trials_accessions)==0){
-        if ($trial_list && scalar(@$trial_list)>0) {
-            my $trial_sql = join ("," , @$trial_list);
-            push @where_clause, "project.project_id in ($trial_sql)";
-        }
-    }
-
-    #For genotyping_data_project
-    if ($genotype_data_project_list && scalar($genotype_data_project_list)>0) {
-        my $sql = join ("," , @$genotype_data_project_list);
-        push @where_clause, "project.project_id in ($sql)";
-    }
-    if ($protocol_id_list && scalar(@$protocol_id_list)>0) {
-        my $protocol_sql = join ("," , @$protocol_id_list);
-        push @where_clause, "nd_protocol.nd_protocol_id in ($protocol_sql)";
-    }
-    if ($accession_list && scalar(@$accession_list)>0) {
-        my $accession_sql = join ("," , @$accession_list);
-        push @where_clause, " ( stock.stock_id in ($accession_sql) OR (accession_of_tissue_sample.stock_id in ($accession_sql) AND accession_of_tissue_sample.type_id = $accession_cvterm_id) ) ";
-        push @where_clause, "stock.type_id in ($accession_cvterm_id, $tissue_sample_cvterm_id)";
-    }
-    if ($tissue_sample_list && scalar(@$tissue_sample_list)>0) {
-        my $stock_sql = join ("," , @$tissue_sample_list);
-        push @where_clause, "stock.stock_id in ($stock_sql)";
-        push @where_clause, "stock.type_id = $tissue_sample_cvterm_id";
-    }
-    if ($markerprofile_id_list && scalar(@$markerprofile_id_list)>0) {
-        my $markerprofile_sql = join ("," , @$markerprofile_id_list);
-        push @where_clause, "genotype.genotype_id in ($markerprofile_sql)";
-    }
-    my %filtered_markers;
-    if ($marker_name_list && scalar(@$marker_name_list)>0) {
-        my $search_vals_sql = "'".join ("','" , @$marker_name_list)."'";
-        push @where_clause, "nd_protocolprop.value->'marker_names' \\?& array[$search_vals_sql]";
-
-        foreach (@$marker_name_list) {
-            $filtered_markers{$_}++;
-        }
-    }
-    if ($marker_search_hash_list && scalar(@$marker_search_hash_list)>0) {
-        foreach (@$marker_search_hash_list){
-            my $json_val = encode_json $_;
-            push @where_clause, "nd_protocolprop.value->'markers' \\@> $json_val"."::jsonb";
-        }
-    }
-    if ($marker_score_search_hash_list && scalar(@$marker_score_search_hash_list)>0) {
-        foreach (@$marker_score_search_hash_list){
-            my $json_val = encode_json $_;
-            push @where_clause, "genotype_values.value \\@> $json_val"."::jsonb";
-        }
-    }
-
-    my $where_clause = scalar(@where_clause)>0 ? " WHERE " . (join (" AND " , @where_clause)) : '';
-
-    my $offset_clause = '';
-    my $limit_clause = '';
-    if ($limit){
-        $limit_clause = " LIMIT $limit ";
-    }
-    if ($offset){
-        $offset_clause = " OFFSET $offset ";
-    }
-
-    my $stock_select = '';
-    if ($return_only_first_genotypeprop_for_stock) {
-        $stock_select = 'distinct on (stock.stock_id) stock.stock_id';
-    } else {
-        $stock_select = 'stock.stock_id';
-    }
-
-    # Setup protocolprop query handles
-    my @protocolprop_marker_hash_select_arr;
-    foreach (@$protocolprop_marker_hash_select){
-        push @protocolprop_marker_hash_select_arr, "s.value->>'$_'";
-    }
-    $self->_protocolprop_marker_hash_select_arr(\@protocolprop_marker_hash_select_arr);
-
-    my @protocolprop_top_key_select_arr;
-    foreach (@$protocolprop_top_key_select){
-        if ($_ ne 'markers' && $_ ne 'markers_array') {
-            push @protocolprop_top_key_select_arr, "value->>'$_'";
-        }
-    }
-    $self->_protocolprop_top_key_select_arr(\@protocolprop_top_key_select_arr);
-
-    my $protocolprop_hash_select_sql = scalar(@protocolprop_marker_hash_select_arr) > 0 ? ', '.join ',', @protocolprop_marker_hash_select_arr : '';
-
-    my $chromosome_where = '';
-    my $genotypeprop_chromosome_rank_string = '';
-    if ($chromosome_list && scalar(@$chromosome_list)>0) {
-        my $chromosome_list_sql = '\'' . join('\', \'', @$chromosome_list) . '\'';
-        $chromosome_where = " AND (s.value->>'chrom')::text IN ($chromosome_list_sql)";
-        #$genotypeprop_chromosome_rank_string = " AND value->>'CHROM' IN ($chromosome_list_sql) ";
-    }
-    my $start_position_where = '';
-    if (defined($start_position)) {
-        $start_position_where = " AND (s.value->>'pos')::int >= $start_position";
-    }
-    my $end_position_where = '';
-    if (defined($end_position)) {
-        $end_position_where = " AND (s.value->>'pos')::int <= $end_position";
-    }
-    my $marker_name_list_where = '';
-    if ($marker_name_list && scalar(@$marker_name_list)>0) {
-        my $search_vals_sql = '\''.join ('\', \'' , @$marker_name_list).'\'';
-        $marker_name_list_where = "AND (s.value->>'name')::text IN ($search_vals_sql)";
-    }
-
-    my $protocolprop_q = "SELECT nd_protocol_id, s.key $protocolprop_hash_select_sql
-        FROM nd_protocolprop, jsonb_each(nd_protocolprop.value) as s
-        WHERE nd_protocol_id = ? AND type_id = $vcf_map_details_markers_cvterm_id $chromosome_where $start_position_where $end_position_where $marker_name_list_where;";
-    #print STDERR Dumper $protocolprop_q;
-    my $protocolprop_h = $schema->storage->dbh()->prepare($protocolprop_q);
-    $self->_protocolprop_markers_h($protocolprop_h);
-
-    my $protocolprop_top_key_select_sql = scalar(@protocolprop_top_key_select_arr) > 0 ? ', '.join ',', @protocolprop_top_key_select_arr : '';
-    my $protocolprop_top_key_q = "SELECT nd_protocol_id $protocolprop_top_key_select_sql from nd_protocolprop WHERE nd_protocol_id = ? AND type_id = $vcf_map_details_cvterm_id;";
-    my $protocolprop_top_key_h = $schema->storage->dbh()->prepare($protocolprop_top_key_q);
-    $self->_protocolprop_top_key_h($protocolprop_top_key_h);
-
-    my $protocolprop_top_key_markers_q = "SELECT nd_protocol_id, value from nd_protocolprop WHERE nd_protocol_id = ? AND type_id = $vcf_map_details_markers_cvterm_id;";
-    my $protocolprop_top_key_markers_h = $schema->storage->dbh()->prepare($protocolprop_top_key_markers_q);
-    $self->_protocolprop_top_key_markers_h($protocolprop_top_key_markers_h);
-
-    my $protocolprop_top_key_markers_array_q = "SELECT nd_protocol_id, value from nd_protocolprop WHERE nd_protocol_id = ? AND type_id = $vcf_map_details_markers_array_cvterm_id;";
-    my $protocolprop_top_key_markers_array_h = $schema->storage->dbh()->prepare($protocolprop_top_key_markers_array_q);
-    $self->_protocolprop_top_key_markers_array_h($protocolprop_top_key_markers_array_h);
-
-    my $q = "SELECT $stock_select, igd_number_genotypeprop.value, nd_protocol.nd_protocol_id, nd_protocol.name, stock.uniquename, stock.type_id, stock_cvterm.name, genotype.genotype_id, genotype.uniquename, genotype.description, project.project_id, project.name, project.description, accession_of_tissue_sample.stock_id, accession_of_tissue_sample.uniquename, count(genotype.genotype_id) OVER() AS full_count
-        FROM stock
-        JOIN cvterm AS stock_cvterm ON(stock.type_id = stock_cvterm.cvterm_id)
-        LEFT JOIN stock_relationship ON(stock_relationship.subject_id=stock.stock_id AND stock_relationship.type_id = $tissue_sample_of_cvterm_id)
-        LEFT JOIN stock AS accession_of_tissue_sample ON(stock_relationship.object_id=accession_of_tissue_sample.stock_id)
-        JOIN nd_experiment_stock ON(stock.stock_id=nd_experiment_stock.stock_id)
-        JOIN nd_experiment USING(nd_experiment_id)
-        JOIN nd_experiment_protocol USING(nd_experiment_id)
-        JOIN nd_experiment_project USING(nd_experiment_id)
-        JOIN nd_experiment_genotype USING(nd_experiment_id)
-        JOIN nd_protocol USING(nd_protocol_id)
-        LEFT JOIN nd_protocolprop ON(nd_protocolprop.nd_protocol_id = nd_protocol.nd_protocol_id AND nd_protocolprop.type_id = $vcf_map_details_cvterm_id)
-        JOIN genotype USING(genotype_id)
-        LEFT JOIN genotypeprop AS igd_number_genotypeprop ON(igd_number_genotypeprop.genotype_id = genotype.genotype_id AND igd_number_genotypeprop.type_id = $igd_genotypeprop_cvterm_id)
-        JOIN project USING(project_id)
-        $where_clause
-        ORDER BY stock.stock_id, genotype.genotype_id ASC
-        $limit_clause
-        $offset_clause;";
-
-    #print STDERR Dumper $q;
-    my $h = $schema->storage->dbh()->prepare($q);
-    $h->execute();
-    my @genotypeprop_infos;
-    my %seen_protocol_ids;
-    while (my ($stock_id, $igd_number_json, $protocol_id, $protocol_name, $stock_name, $stock_type_id, $stock_type_name, $genotype_id, $genotype_uniquename, $genotype_description, $project_id, $project_name, $project_description, $accession_id, $accession_uniquename, $full_count) = $h->fetchrow_array()) {
-
-        my $germplasmName = '';
-        my $germplasmDbId = '';
-
-        my $igd_number_hash = $igd_number_json ? decode_json $igd_number_json : undef;
-        my $igd_number = $igd_number_hash ? $igd_number_hash->{'igd number'} : undef;
-        $igd_number = !$igd_number && $igd_number_hash ? $igd_number_hash->{'igd_number'} : undef;
-
-        if ($stock_type_name eq 'accession'){
-            $germplasmName = $stock_name;
-            $germplasmDbId = $stock_id;
-        }
-        if ($stock_type_name eq 'tissue_sample'){
-            $germplasmName = $accession_uniquename;
-            $germplasmDbId = $accession_id;
-        }
-
-        my $stock_object = CXGN::Stock::Accession->new({schema=>$self->bcs_schema, stock_id=>$germplasmDbId});
-
-        my %genotypeprop_info = (
-            markerProfileDbId => $genotype_id,
-            germplasmDbId => $germplasmDbId,
-            germplasmName => $germplasmName,
-            synonyms => $stock_object->synonyms,
-            stock_id => $stock_id,
-            stock_name => $stock_name,
-            stock_type_id => $stock_type_id,
-            stock_type_name => $stock_type_name,
-            genotypeDbId => $genotype_id,
-            genotypeUniquename => $genotype_uniquename,
-            genotypeDescription => $genotype_description,
-            analysisMethodDbId => $protocol_id,
-            analysisMethod => $protocol_name,
-            genotypingDataProjectDbId => $project_id,
-            genotypingDataProjectName => $project_name,
-            genotypingDataProjectDescription => $project_description,
-            igd_number => $igd_number,
-            full_count => $full_count
-        );
-        $seen_protocol_ids{$protocol_id}++;
-        push @genotypeprop_infos, \%genotypeprop_info;
-    }
-    $self->_genotypeprop_infos(\@genotypeprop_infos);
-    $self->_genotypeprop_infos_counter(0);
-
-    my @seen_protocol_ids = keys %seen_protocol_ids;
-    my %protocolprop_top_key_select_hash = map {$_ => 1} @protocolprop_top_key_select_arr;
-    my %selected_protocol_marker_info;
-    my %selected_protocol_top_key_info;
-    my $val;
-
-    foreach my $protocol_id (@seen_protocol_ids){
-        $protocolprop_h->execute($protocol_id);
-        while (my ($protocol_id, $marker_name, @protocolprop_info_return) = $protocolprop_h->fetchrow_array()) {
-            for my $s (0 .. scalar(@protocolprop_marker_hash_select_arr)-1){
-                $selected_protocol_marker_info{$protocol_id}->{$marker_name}->{$protocolprop_marker_hash_select->[$s]} = $protocolprop_info_return[$s];
-            }
-            $filtered_markers{$marker_name}++;
-        }
-
-        $protocolprop_top_key_h->execute($protocol_id);
-        while (my ($protocol_id, @protocolprop_top_key_return) = $protocolprop_top_key_h->fetchrow_array()) {
-            for my $s (0 .. scalar(@protocolprop_top_key_select_arr)-1){
-                my $protocolprop_i = $protocolprop_top_key_select->[$s];
-                if ($protocolprop_i eq 'header_information_lines' || $protocolprop_i eq 'marker_names') {
-                    $val = decode_json $protocolprop_top_key_return[$s];
-                } else {
-                    $val = $protocolprop_top_key_return[$s];
-                }
-                $selected_protocol_top_key_info{$protocol_id}->{$protocolprop_i} = $val;
-            }
-        }
-        if (exists($protocolprop_top_key_select_hash{'markers'})) {
-            $protocolprop_top_key_markers_h->execute($protocol_id);
-            while (my ($protocol_id, $markers_value) = $protocolprop_top_key_markers_h->fetchrow_array()) {
-                $selected_protocol_top_key_info{$protocol_id}->{'markers'} = decode_json $markers_value;
-            }
-        }
-        if (exists($protocolprop_top_key_select_hash{'markers_array'})) {
-            $protocolprop_top_key_markers_array_h->execute($protocol_id);
-            while (my ($protocol_id, $markers_value) = $protocolprop_top_key_markers_array_h->fetchrow_array()) {
-                $selected_protocol_top_key_info{$protocol_id}->{'markers_array'} = decode_json $markers_value;
-            }
-        }
-    }
-    $self->_selected_protocol_marker_info(\%selected_protocol_marker_info);
-    $self->_selected_protocol_top_key_info(\%selected_protocol_top_key_info);
-    $self->_filtered_markers(\%filtered_markers);
-
-    # Setup genotypeprop query handle
-    my @genotypeprop_hash_select_arr;
-    foreach (@$genotypeprop_hash_select){
-        push @genotypeprop_hash_select_arr, "s.value->>'$_'";
-    }
-    $self->_genotypeprop_hash_select_arr(\@genotypeprop_hash_select_arr);
-    my $genotypeprop_hash_select_sql = scalar(@genotypeprop_hash_select_arr) > 0 ? ', '.join ',', @genotypeprop_hash_select_arr : '';
-
-    my $filtered_markers_sql = '';
-    # If filtered markers by providing a location range or chromosome these markers will be in %filered_markers, but we dont want to use this SQL if there are too many markers (>10000) )
-    if (scalar(keys %filtered_markers) >0 && scalar(keys %filtered_markers) < 10000) {
-        $filtered_markers_sql = " AND s.key IN ('". join ("','", keys %filtered_markers) ."')";
-    }
-
-    my $genotypeprop_q = "SELECT s.key $genotypeprop_hash_select_sql
-        FROM genotypeprop, jsonb_each(genotypeprop.value) as s
-        WHERE genotypeprop_id = ? AND s.key != 'CHROM' AND type_id = $vcf_snp_genotyping_cvterm_id $filtered_markers_sql;";
-    my $genotypeprop_h = $schema->storage->dbh()->prepare($genotypeprop_q);
-    $self->_genotypeprop_h($genotypeprop_h);
-
-    my $q2 = "SELECT genotypeprop_id
-        FROM genotypeprop WHERE genotype_id = ? AND type_id=$vcf_snp_genotyping_cvterm_id $genotypeprop_chromosome_rank_string;";
-    my $h2 = $schema->storage->dbh()->prepare($q2);
-    $self->_iterator_genotypeprop_query_handle($h2);
-
-    return;
-}
-
-=head2 get_next_genotype_info()
-
-Function for getting genotype data iteratively. Iterative search retrieval minimizes memory usage.
-Should be used like:
-
-my $genotype_search = CXGN::Genotype::Search->new({
-    bcs_schema=>$schema,
-    ...etc
-});
-$genotype_search->init_genotype_iterator();
-while (my ($count, $genotype_data) = $genotype_search->get_next_genotype_info) {
-    #Do something with genotype data
-}
-
-If you just want to get a file with the genotype result in a dosage matrix or VCF file, use get_cached_file_dosage_matrix or get_cached_file_VCF instead.
-If you want results in json format use get_cached_file_search_json
-If you want results in json format for only the metadata (no genotype call data), use get_cached_file_search_json()
-
-=cut
-
-sub get_next_genotype_info {
-    my $self = shift;
-    my $schema = $self->bcs_schema;
-    my $trial_list = $self->trial_list;
-    my $genotype_data_project_list = $self->genotype_data_project_list;
-    my $protocol_id_list = $self->protocol_id_list;
-    my $markerprofile_id_list = $self->markerprofile_id_list;
-    my $accession_list = $self->accession_list;
-    my $tissue_sample_list = $self->tissue_sample_list;
-    my $marker_name_list = $self->marker_name_list;
-    my $chromosome_list = $self->chromosome_list;
-    my $start_position = $self->start_position;
-    my $end_position = $self->end_position;
-    my $genotypeprop_hash_select = $self->genotypeprop_hash_select;
-    my $protocolprop_top_key_select = $self->protocolprop_top_key_select;
-    my $protocolprop_marker_hash_select = $self->protocolprop_marker_hash_select;
-    my $marker_search_hash_list = $self->marker_search_hash_list;
-    my $marker_score_search_hash_list = $self->marker_score_search_hash_list;
-    my $return_only_first_genotypeprop_for_stock = $self->return_only_first_genotypeprop_for_stock;
-    my $h = $self->_iterator_query_handle();
-    my $h_genotypeprop = $self->_iterator_genotypeprop_query_handle();
-    my $protocolprop_markers_h = $self->_protocolprop_markers_h();
-    my $protocolprop_top_key_h = $self->_protocolprop_top_key_h();
-    my $protocolprop_top_key_markers_h = $self->_protocolprop_top_key_markers_h();
-    my $genotypeprop_h = $self->_genotypeprop_h();
-    my $protocolprop_top_key_markers_array_h = $self->_protocolprop_top_key_markers_array_h();
-    my $protocolprop_marker_hash_select_arr = $self->_protocolprop_marker_hash_select_arr();
-    my $protocolprop_top_key_select_arr = $self->_protocolprop_top_key_select_arr();
-    my $genotypeprop_hash_select_arr = $self->_genotypeprop_hash_select_arr();
-    my $snp_genotyping_cvterm_id = $self->_snp_genotyping_cvterm_id();
-    my $vcf_snp_genotyping_cvterm_id = $self->_vcf_snp_genotyping_cvterm_id();
-    my $vcf_map_details_cvterm_id = $self->_vcf_map_details_cvterm_id();
-    my $vcf_map_details_markers_cvterm_id = $self->_vcf_map_details_markers_cvterm_id();
-    my $vcf_map_details_markers_array_cvterm_id = $self->_vcf_map_details_markers_array_cvterm_id();
-    my $igd_genotypeprop_cvterm_id = $self->_igd_genotypeprop_cvterm_id();
-    my $accession_cvterm_id = $self->_accession_cvterm_id();
-    my $tissue_sample_cvterm_id = $self->_tissue_sample_cvterm_id();
-    my $tissue_sample_of_cvterm_id = $self->_tissue_sample_of_cvterm_id();
-
-
-    my $total_count = 0;
-    my @genotypeprop_array;
-    my %protocolprop_hash;
-
-    my %selected_protocol_marker_info = %{$self->_selected_protocol_marker_info};
-    my %selected_protocol_top_key_info = %{$self->_selected_protocol_top_key_info};
-    my %filtered_markers = %{$self->_filtered_markers};
-    my $genotypeprop_infos = $self->_genotypeprop_infos;
-    my $genotypeprop_infos_counter = $self->_genotypeprop_infos_counter;
-
-    if ($genotypeprop_infos->[$genotypeprop_infos_counter]) {
-        my %genotypeprop_info = %{$genotypeprop_infos->[$genotypeprop_infos_counter]};
-        my $genotype_id = $genotypeprop_info{markerProfileDbId};
-        my $protocol_id = $genotypeprop_info{analysisMethodDbId};
-        my $full_count = $genotypeprop_info{full_count};
-
-        $h_genotypeprop->execute($genotype_id);
-        while (my ($genotypeprop_id) = $h_genotypeprop->fetchrow_array) {
-            $genotypeprop_h->execute($genotypeprop_id);
-            while (my ($marker_name, @genotypeprop_info_return) = $genotypeprop_h->fetchrow_array()) {
-                for my $s (0 .. scalar(@$genotypeprop_hash_select_arr)-1){
-		    $genotypeprop_info{selected_genotype_hash}->{$marker_name}->{$genotypeprop_hash_select->[$s]} = $genotypeprop_info_return[$s];
-                }
-            }
-
-        }
-        my $selected_marker_info = $selected_protocol_marker_info{$protocol_id} ? $selected_protocol_marker_info{$protocol_id} : {};
-        my $selected_protocol_info = $selected_protocol_top_key_info{$protocol_id} ? $selected_protocol_top_key_info{$protocol_id} : {};
-        my @all_protocol_marker_names = keys %$selected_marker_info;
-        $selected_protocol_info->{markers} = $selected_marker_info;
-        $genotypeprop_info{resultCount} = scalar(keys %{$genotypeprop_info{selected_genotype_hash}});
-        $genotypeprop_info{all_protocol_marker_names} = \@all_protocol_marker_names;
-        $genotypeprop_info{selected_protocol_hash} = $selected_protocol_info;
-
-        $self->_genotypeprop_infos_counter($self->_genotypeprop_infos_counter + 1);
-
-        return ($full_count, \%genotypeprop_info);
-    }
-
-    return;
-}
-
-sub key {
-    my $self = shift;
-    my $datatype = shift;
-
-    my $json = JSON->new();
-    #preserve order of hash keys to get same text
-    $json = $json->canonical();
-    my $accessions = $json->encode( $self->accession_list() || [] );
-    my $tissues = $json->encode( $self->tissue_sample_list() || [] );
-    my $trials = $json->encode( $self->trial_list() || [] );
-    my $protocols = $json->encode( $self->protocol_id_list() || [] );
-    my $markerprofiles = $json->encode( $self->markerprofile_id_list() || [] );
-    my $genotypedataprojects = $json->encode( $self->genotype_data_project_list() || [] );
-    my $markernames = $json->encode( $self->marker_name_list() || [] );
-    my $genotypeprophash = $json->encode( $self->genotypeprop_hash_select() || [] );
-    my $protocolprophash = $json->encode( $self->protocolprop_top_key_select() || [] );
-    my $protocolpropmarkerhash = $json->encode( $self->protocolprop_marker_hash_select() || [] );
-    my $chromosomes = $json->encode( $self->chromosome_list() || [] );
-    my $start = $self->start_position() || '' ;
-    my $end = $self->end_position() || '';
-    my $prevent_transpose = $self->prevent_transpose() || '';
-    my $key = md5_hex($accessions.$tissues.$trials.$protocols.$markerprofiles.$genotypedataprojects.$markernames.$genotypeprophash.$protocolprophash.$protocolpropmarkerhash.$chromosomes.$start.$end.$self->return_only_first_genotypeprop_for_stock().$prevent_transpose.$self->limit().$self->offset()."_$datatype");
-    #print STDERR Dumper($genotypeprophash);
-    return $key;
-}
-
-=head2 get_cached_file_search_json()
-
-Function for getting the file handle for the genotype search result from cache. Will write the cached file if it does not exist.
-Returns the genotype result in a line-by-line json format.
-Uses the file iterator to write the cached file, so that it uses little memory.
-
-First line in file has all marker objects, while subsequent lines have markerprofiles for each sample
-If you want results in json format for only the metadata (no genotype call data), pass 1 for metadata_only
-
-=cut
-
-sub get_cached_file_search_json {
-    my $self = shift;
-    my $shared_cluster_dir_config = shift;
-    my $metadata_only = shift;
-    my $protocol_ids = $self->protocol_id_list;
-
-    my $metadata_only_string = $metadata_only ? "metadata_only" : "all_data";
-    my $key = $self->key("get_cached_file_search_json_v03_".$metadata_only_string);
-    $self->cache( Cache::File->new( cache_root => $self->cache_root() ));
-
-    my $file_handle;
-    if ($self->cache()->exists($key) && !$self->forbid_cache()) {
-        $file_handle = $self->cache()->handle($key);
-    } else {
-        # Set the temp dir and temp output file
-        my $tmp_output_dir = $shared_cluster_dir_config."/tmp_genotype_download_json";
-	print STDERR "creating cached json file in $tmp_output_dir\n";
-        mkdir $tmp_output_dir if ! -d $tmp_output_dir;
-        my ($tmp_fh, $tempfile) = tempfile(
-            "wizard_download_XXXXX",
-            DIR=> $tmp_output_dir,
-        );
-
-        my @all_marker_objects;
-        foreach (@$protocol_ids) {
-            my $protocol = CXGN::Genotype::Protocol->new({
-                bcs_schema => $self->bcs_schema,
-                nd_protocol_id => $_,
-                chromosome_list=>$self->chromosome_list,
-                start_position=>$self->start_position,
-                end_position=>$self->end_position,
-                marker_name_list=>$self->marker_name_list
-            });
-            my $markers = $protocol->markers;
-            push @all_marker_objects, values %$markers;
-        }
-
-        foreach (@all_marker_objects) {
-            $self->_filtered_markers()->{$_->{name}}++;
-        }
-
-        $self->init_genotype_iterator();
-
-        #VCF should be sorted by chromosome and position
-        no warnings 'uninitialized';
-        @all_marker_objects = sort { $a->{chrom} cmp $b->{chrom} || $a->{pos} <=> $b->{pos} || $a->{name} cmp $b->{name} } @all_marker_objects;
-        @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-
-        my $counter = 0;
-        while (my $geno = $self->get_next_genotype_info) {
-
-            # OLD GENOTYPING PROTCOLS DID NOT HAVE ND_PROTOCOLPROP INFO...
-            if (scalar(@all_marker_objects) == 0) {
-                foreach my $o (sort genosort keys %{$geno->{selected_genotype_hash}}) {
-                    push @all_marker_objects, {name => $o};
-                }
-                @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-            }
-
-            if ($metadata_only) {
-                @all_marker_objects = [];
-                delete $geno->{selected_genotype_hash};
-                delete $geno->{selected_protocol_hash};
-                delete $geno->{all_protocol_marker_names};
-            }
-
-            my $genotype_string = encode_json $geno;
-            $genotype_string .= "\n";
-            if ($counter == 0) {
-                my $marker_string = encode_json \@all_marker_objects;
-                $marker_string .= "\n";
-                write_file($tempfile, {append => 1}, $marker_string);
-            }
-            write_file($tempfile, {append => 1}, $genotype_string);
-            $counter++;
-        }
-        close $tempfile;
-
-        open my $out_copy, '<', $tempfile or die "Can't open output file: $!";
-
-        $self->cache()->set($key, '');
-        $file_handle = $self->cache()->handle($key);
-        copy($out_copy, $file_handle);
-
-        close $out_copy;
-        $file_handle = $self->cache()->handle($key);
-    }
-    return $file_handle;
-}
-
-=head2 get_cached_file_dosage_matrix()
-
-Function for getting the file handle for the genotype search result from cache. Will write the cached file if it does not exist.
-Returns the genotype result as a dosage matrix format.
-Uses the file iterator to write the cached file, so that it uses little memory.
-
-=cut
-
-sub get_cached_file_dosage_matrix {
-    my $self = shift;
-    my $shared_cluster_dir_config = shift;
-    my $backend_config = shift;
-    my $cluster_host_config = shift;
-    my $web_cluster_queue_config = shift;
-    my $basepath_config = shift;
-    my $protocol_ids = $self->protocol_id_list;
-
-    my $key = $self->key("get_cached_file_dosage_matrix_v03");
-    $self->cache( Cache::File->new( cache_root => $self->cache_root() ));
-
-    my $file_handle;
-    if ($self->cache()->exists($key) && !$self->forbid_cache()) {
-        $file_handle = $self->cache()->handle($key);
-    }
-    else {
-        # Set the temp dir and temp output file
-        my $tmp_output_dir = $shared_cluster_dir_config."/tmp_genotype_download_dosage_matrix";
-        mkdir $tmp_output_dir if ! -d $tmp_output_dir;
-        my ($tmp_fh, $tempfile) = tempfile(
-            "wizard_download_XXXXX",
-            DIR=> $tmp_output_dir,
-        );
-
-        my @all_marker_objects;
-        foreach (@$protocol_ids) {
-            my $protocol = CXGN::Genotype::Protocol->new({
-                bcs_schema => $self->bcs_schema,
-                nd_protocol_id => $_,
-                chromosome_list=>$self->chromosome_list,
-                start_position=>$self->start_position,
-                end_position=>$self->end_position,
-                marker_name_list=>$self->marker_name_list
-            });
-            my $markers = $protocol->markers;
-            push @all_marker_objects, values %$markers;
-        }
-
-        foreach (@all_marker_objects) {
-            $self->_filtered_markers()->{$_->{name}}++;
-        }
-        $self->init_genotype_iterator();
-
-        #VCF should be sorted by chromosome and position
-        no warnings 'uninitialized';
-        @all_marker_objects = sort { $a->{chrom} cmp $b->{chrom} || $a->{pos} <=> $b->{pos} || $a->{name} cmp $b->{name} } @all_marker_objects;
-        @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-
-        my $counter = 0;
-        while (my $geno = $self->get_next_genotype_info) {
-
-            # OLD GENOTYPING PROTCOLS DID NOT HAVE ND_PROTOCOLPROP INFO...
-            if (scalar(@all_marker_objects) == 0) {
-                foreach my $o (sort genosort keys %{$geno->{selected_genotype_hash}}) {
-                    push @all_marker_objects, {name => $o};
-                }
-                @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-            }
-
-            my $genotype_string = "";
-            if ($counter == 0) {
-                $genotype_string .= "Marker\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $m->{name} . "\t";
-                }
-                $genotype_string .= "\n";
-            }
-            my $genotype_id = $geno->{germplasmName};
-            if (!$self->return_only_first_genotypeprop_for_stock) {
-                $genotype_id = $geno->{germplasmName}."|".$geno->{markerProfileDbId};
-            }
-            my $genotype_data_string = "";
-            foreach my $m (@all_marker_objects) {
-                my $current_genotype = $geno->{selected_genotype_hash}->{$m->{name}}->{DS};
-                $genotype_data_string .= $current_genotype."\t";
-            }
-
-            $genotype_string .= $genotype_id."\t".$genotype_data_string."\n";
-
-            write_file($tempfile, {append => 1}, $genotype_string);
-            $counter++;
-        }
-
-        my $transpose_tempfile = $tempfile . "_transpose";
-
-        my $cmd = CXGN::Tools::Run->new(
-            {
-                backend => $backend_config,
-                submit_host => $cluster_host_config,
-                temp_base => $tmp_output_dir,
-                queue => $web_cluster_queue_config,
-                do_cleanup => 0,
-                out_file => $transpose_tempfile,
-    #            out_file => $transpose_tempfile,
-                # don't block and wait if the cluster looks full
-                max_cluster_jobs => 1_000_000_000,
-            }
-        );
-
-        my $out_copy;
-        if ($self->prevent_transpose()) {
-            open $out_copy, '<', $tempfile or die "Can't open output file: $!";
-        }
-        else {
-            # Do the transposition job on the cluster
-            $cmd->run_cluster(
-                    "perl ",
-                    $basepath_config."/bin/transpose_matrix.pl",
-                    $tempfile,
-            );
-            $cmd->is_cluster(1);
-            $cmd->wait;
-
-            open $out_copy, '<', $transpose_tempfile or die "Can't open output file: $!";
-        }
-
-        $self->cache()->set($key, '');
-        $file_handle = $self->cache()->handle($key);
-        copy($out_copy, $file_handle);
-
-        close $out_copy;
-        $file_handle = $self->cache()->handle($key);
-    }
-    return $file_handle;
-}
-
-=head2 get_cached_file_dosage_matrix_compute_from_parents()
-Computes the genotypes for the queried accessions computed from the parental dosages. Parents are known from pedigrees of accessions.
-Function for getting the file handle for the genotype search result from cache. Will write the cached file if it does not exist.
-Returns the genotype result as a dosage matrix format.
-Uses the file iterator to write the cached file, so that it uses little memory.
-=cut
-
-sub get_cached_file_dosage_matrix_compute_from_parents {
-    my $self = shift;
-    my $shared_cluster_dir_config = shift;
-    my $backend_config = shift;
-    my $cluster_host_config = shift;
-    my $web_cluster_queue_config = shift;
-    my $basepath_config = shift;
-    my $schema = $self->bcs_schema;
-    my $protocol_ids = $self->protocol_id_list;
-    my $marker_name_list = $self->marker_name_list;
-    my $accession_ids = $self->accession_list;
-    my $cache_root_dir = $self->cache_root();
-
-    if (scalar(@$protocol_ids)>1) {
-        die "Only one protocol at a time can be done when computing genotypes from parents\n";
-    }
-    my $protocol_id = $protocol_ids->[0];
-
-    my $key = $self->key("get_cached_file_dosage_matrix_compute_from_parents_v03");
-    $self->cache( Cache::File->new( cache_root => $cache_root_dir ));
-
-    my $file_handle;
-    if ($self->cache()->exists($key) && !$self->forbid_cache()) {
-        $file_handle = $self->cache()->handle($key);
-    }
-    else {
-        # Set the temp dir and temp output file
-        my $tmp_output_dir = $shared_cluster_dir_config."/tmp_genotype_download_dosage_matrix_compute_from_parents";
-        mkdir $tmp_output_dir if ! -d $tmp_output_dir;
-        my ($tmp_fh, $tempfile) = tempfile(
-            "wizard_download_XXXXX",
-            DIR=> $tmp_output_dir,
-        );
-
-        my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
-        my $female_parent_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'female_parent', 'stock_relationship')->cvterm_id();
-        my $male_parent_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'male_parent', 'stock_relationship')->cvterm_id();
-
-        my $accession_list_string = join ',', @$accession_ids;
-        my $q = "SELECT accession.stock_id, female_parent.stock_id, male_parent.stock_id
-            FROM stock AS accession
-            JOIN stock_relationship AS female_parent_rel ON(accession.stock_id=female_parent_rel.object_id AND female_parent_rel.type_id=$female_parent_cvterm_id)
-            JOIN stock AS female_parent ON(female_parent_rel.subject_id = female_parent.stock_id AND female_parent.type_id=$accession_cvterm_id)
-            JOIN stock_relationship AS male_parent_rel ON(accession.stock_id=male_parent_rel.object_id AND male_parent_rel.type_id=$male_parent_cvterm_id)
-            JOIN stock AS male_parent ON(male_parent_rel.subject_id = male_parent.stock_id AND male_parent.type_id=$accession_cvterm_id)
-            WHERE accession.stock_id IN ($accession_list_string) AND accession.type_id=$accession_cvterm_id ORDER BY accession.stock_id;";
-        my $h = $schema->storage->dbh()->prepare($q);
-        $h->execute();
-        my @accession_stock_ids_found = ();
-        my @female_stock_ids_found = ();
-        my @male_stock_ids_found = ();
-        while (my ($accession_stock_id, $female_parent_stock_id, $male_parent_stock_id) = $h->fetchrow_array()) {
-            push @accession_stock_ids_found, $accession_stock_id;
-            push @female_stock_ids_found, $female_parent_stock_id;
-            push @male_stock_ids_found, $male_parent_stock_id;
-        }
-
-        # print STDERR Dumper \@accession_stock_ids_found;
-        # print STDERR Dumper \@female_stock_ids_found;
-        # print STDERR Dumper \@male_stock_ids_found;
-
-        my %unique_germplasm;
-        my $protocol = CXGN::Genotype::Protocol->new({
-            bcs_schema => $schema,
-            nd_protocol_id => $protocol_id,
-            chromosome_list=>$self->chromosome_list,
-            start_position=>$self->start_position,
-            end_position=>$self->end_position,
-            marker_name_list=>$self->marker_name_list
-        });
-        my $markers = $protocol->markers;
-        my @all_marker_objects = values %$markers;
-
-        foreach (@all_marker_objects) {
-            $self->_filtered_markers()->{$_->{name}}++;
-        }
-
-        no warnings 'uninitialized';
-        @all_marker_objects = sort { $a->{chrom} cmp $b->{chrom} || $a->{pos} <=> $b->{pos} || $a->{name} cmp $b->{name} } @all_marker_objects;
-        @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-
-        my $counter = 0;
-        for my $i (0..scalar(@accession_stock_ids_found)-1) {
-            my $female_stock_id = $female_stock_ids_found[$i];
-            my $male_stock_id = $male_stock_ids_found[$i];
-            my $accession_stock_id = $accession_stock_ids_found[$i];
-
-            my $dataset = CXGN::Dataset::Cache->new({
-                people_schema=>$self->people_schema,
-                schema=>$schema,
-                cache_root=>$cache_root_dir,
-                accessions=>[$female_stock_id, $male_stock_id]
-            });
-            my $genotypes = $dataset->retrieve_genotypes($protocol_id, ['DS'], ['markers'], ['name'], 1, $self->chromosome_list, $self->start_position, $self->end_position, $self->marker_name_list);
-
-            # For old protocols with no protocolprop info...
-            if (scalar(@all_marker_objects) == 0) {
-                foreach my $o (sort genosort keys %{$genotypes->[0]->{selected_genotype_hash}}) {
-                    push @all_marker_objects, {name => $o};
-                }
-                @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-            }
-
-            my $genotype_string = "";
-            if ($counter == 0) {
-                $genotype_string .= "Marker\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $m->{name} . "\t";
-                }
-                $genotype_string .= "\n";
-            }
-
-            my $geno = CXGN::Genotype::ComputeHybridGenotype->new({
-                parental_genotypes=>$genotypes,
-                marker_objects=>\@all_marker_objects
-            });
-            my $progeny_genotype = $geno->get_hybrid_genotype();
-            my $genotype_string_scores = join "\t", @$progeny_genotype;
-
-            my $genotype_id = $accession_stock_id;
-            if (!$self->return_only_first_genotypeprop_for_stock) {
-                $genotype_id = $accession_stock_id."|".$geno->{markerProfileDbId};
-            }
-
-            $genotype_string .= $genotype_id."\t".$genotype_string_scores."\n";
-            write_file($tempfile, {append => 1}, $genotype_string);
-            $counter++;
-        }
-
-        my $transpose_tempfile = $tempfile . "_transpose";
-
-        my $cmd = CXGN::Tools::Run->new(
-            {
-                backend => $backend_config,
-                submit_host => $cluster_host_config,
-                temp_base => $tmp_output_dir,
-                queue => $web_cluster_queue_config,
-                do_cleanup => 0,
-                out_file => $transpose_tempfile,
-    #            out_file => $transpose_tempfile,
-                # don't block and wait if the cluster looks full
-                max_cluster_jobs => 1_000_000_000,
-            }
-        );
-
-        my $out_copy;
-        if ($self->prevent_transpose()) {
-            open $out_copy, '<', $tempfile or die "Can't open output file: $!";
-        }
-        else {
-            # Do the transposition job on the cluster
-            $cmd->run_cluster(
-                    "perl ",
-                    $basepath_config."/bin/transpose_matrix.pl",
-                    $tempfile,
-            );
-            $cmd->is_cluster(1);
-            $cmd->wait;
-
-            open $out_copy, '<', $transpose_tempfile or die "Can't open output file: $!";
-        }
-
-        $self->cache()->set($key, '');
-        $file_handle = $self->cache()->handle($key);
-        copy($out_copy, $file_handle);
-
-        close $out_copy;
-        $file_handle = $self->cache()->handle($key);
-    }
-    return $file_handle;
-}
-
-sub get_cached_file_VCF {
-    my $self = shift;
-    my $shared_cluster_dir_config = shift;
-    my $backend_config = shift;
-    my $cluster_host_config = shift;
-    my $web_cluster_queue_config = shift;
-    my $basepath_config = shift;
-
-    my $key = $self->key("get_cached_file_VCF_v04");
-    $self->cache( Cache::File->new( cache_root => $self->cache_root() ));
-    my $protocol_ids = $self->protocol_id_list;
-
-    my $file_handle;
-    if ($self->cache()->exists($key) && !$self->forbid_cache()) {
-        $file_handle = $self->cache()->handle($key);
-    } else {
-        # Set the temp dir and temp output file
-        my $tmp_output_dir = $shared_cluster_dir_config."/tmp_genotype_download_VCF";
-	print STDERR "creating cached VCF file in $tmp_output_dir\n";
-        mkdir $tmp_output_dir if ! -d $tmp_output_dir;
-        my ($tmp_fh, $tempfile) = tempfile(
-            "wizard_download_XXXXX",
-            DIR=> $tmp_output_dir,
-        );
-
-        my $time = DateTime->now();
-        my $timestamp = $time->ymd()."_".$time->hms();
-
-        my @all_protocol_info_lines;
-
-        #Get all marker information for the protocol(s) requested. this is important if they are requesting subsets of markers or if they are querying more than one protocol at once. Also important for ordering VCF output. Old genotypes did not have protocolprop marker info so markers are taken from first genotypeprop return below.
-        my @all_marker_objects;
-        my %unique_germplasm;
-        foreach (@$protocol_ids) {
-            my $protocol = CXGN::Genotype::Protocol->new({
-                bcs_schema => $self->bcs_schema,
-                nd_protocol_id => $_,
-                chromosome_list=>$self->chromosome_list,
-                start_position=>$self->start_position,
-                end_position=>$self->end_position,
-                marker_name_list=>$self->marker_name_list
-            });
-            my $markers = $protocol->markers;
-            push @all_protocol_info_lines, @{$protocol->header_information_lines};
-            push @all_marker_objects, values %$markers;
-        }
-	push @all_protocol_info_lines, "##source=FILE GENERATED BY BREEDBASE";
-	push @all_protocol_info_lines, "##fileDate=$timestamp";
-
-        foreach (@all_marker_objects) {
-            $self->_filtered_markers()->{$_->{name}}++;
-        }
-
-        $self->init_genotype_iterator();
-
-        #VCF should be sorted by chromosome and position
-        no warnings 'uninitialized';
-	@all_marker_objects = sort { $a->{chrom} cmp $b->{chrom} || $a->{pos} <=> $b->{pos} || $a->{name} cmp $b->{name} } @all_marker_objects;
-        @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-
-        my $counter = 0;
-        while (my $geno = $self->get_next_genotype_info) {
-
-            # OLD GENOTYPING PROTCOLS DID NOT HAVE ND_PROTOCOLPROP INFO...
-            if (scalar(@all_marker_objects) == 0) {
-                foreach my $o (sort genosort keys %{$geno->{selected_genotype_hash}}) {
-                    push @all_marker_objects, {name => $o};
-                }
-                @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-            }
-
-            $unique_germplasm{$geno->{germplasmDbId}}++;
-
-	    #print STDERR "GENO = ".Dumper($geno);
-	    
-            my $genotype_string = "";
-            if ($counter == 0) {
-                $genotype_string .= "#CHROM\t";
-                foreach my $m (@all_marker_objects) {
-		    my $chrom = $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{chrom};
-
-		    if (! $chrom) {
-			($chrom) = split /\_/, $m->{name};
-			#print STDERR "Warning! No chrom data, using $chrom extracted from $m->{name}\n";
-		    }		    
-                    #$genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{chrom} . "\t";
-		    $genotype_string .= $chrom ."\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "POS\t";
-                foreach my $m (@all_marker_objects) {
-		    my $pos = $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{pos};
-		    if (! $pos) {
-			(undef, $pos) = split /\_/, $m->{name};
-			#print STDERR "Warning! No position data, using $pos extracted from $m->{name}\n";
-		    }
-                    #$genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{pos} . "\t";
-		    $genotype_string .= $pos ."\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "ID\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $m->{name} . "\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "REF\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{ref} . "\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "ALT\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{alt} . "\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "QUAL\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{qual} . "\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "FILTER\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{filter} . "\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "INFO\t";
-                foreach my $m (@all_marker_objects) {
-                    $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{info} . "\t";
-                }
-                $genotype_string .= "\n";
-                $genotype_string .= "FORMAT\t";
-                foreach my $m (@all_marker_objects) {
-                    my $format = $m->{format};
-                    my @format_array;
-                    #In case of old genotyping protocols where there was no protocolprop marker info
-                    if (!$format) {
-                        my $first_g = $geno->{selected_genotype_hash}->{$m->{name}};
-			if (defined($first_g->{'GT'})) {
-			    push @format_array, 'GT';
-			}
-                        foreach my $k (sort keys %$first_g) {
-		            if ($k eq 'GT') {
-			    } elsif (defined($first_g->{$k})) {
-                                push @format_array, $k;
-                            }
-                        }
-                    } else {
-                        @format_array = split ':', $format;
-                    }
-
-                    if (scalar(@format_array) > 1) { #ONLY ADD NT FOR NOT OLD GENOTYPING PROTOCOLS
-                        my %format_check = map {$_ => 1} @format_array;
-                        if (!exists($format_check{'NT'})) {
-                            push @format_array, 'NT';
-                        }
-                        if (!exists($format_check{'DS'})) {
-                            push @format_array, 'DS';
-                        }
-                    }
-                    $format = join ':', @format_array;
-                    $genotype_string .= $format . "\t";
-                    $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{format} = $format;
-                    $m->{format} = $format;
-                }
-                $genotype_string .= "\n";
-            }
-            my $genotype_id = $geno->{germplasmName};
-            if (!$self->return_only_first_genotypeprop_for_stock) {
-                $genotype_id = $geno->{germplasmName}."|".$geno->{markerProfileDbId};
-            }
-            my $genotype_data_string = "";
-            foreach my $m (@all_marker_objects) {
-                my @current_geno = ();
-                my $name = $m->{name};
-                my $format = $m->{format};
-                my @format;
-		my $gt;
-
-                #In case of old genotyping protocols where there was no protocolprop marker info
-                if (!$format) {
-                    my $first_g = $geno->{selected_genotype_hash}->{$name};
-                    foreach my $k (sort keys %$first_g) {
-                        if (defined($first_g->{$k})) {
-                            push @format, $k;
-                        }
-                    }
-                } else {
-                    @format = split ':', $format;
-                }
-
-		#VCF requires the GT field to be first
-		if (defined($geno->{selected_genotype_hash}->{$m->{name}}->{'GT'})) {
-		    my $val = $geno->{selected_genotype_hash}->{$m->{name}}->{'GT'};
-		    if ($val eq '') {
-                        $val = './.';
-                    }
-		    push @current_geno, $val;
-		} else {
-		    push @current_geno, './.';
-		}
-                foreach my $format_key (@format) {
-                    my $val = $geno->{selected_genotype_hash}->{$m->{name}}->{$format_key};
-                    if ($format_key eq 'GT') {
-                    } else {
-                        push @current_geno, $val;
-		    }
-                }
-                my $current_g = join ':', @current_geno;
-                $genotype_data_string .= $current_g."\t";
-            }
-            $genotype_string .= $genotype_id."\t".$genotype_data_string."\n";
-
-            write_file($tempfile, {append => 1}, $genotype_string);
-            $counter++;
-        }
-
-        my $transpose_tempfile = $tempfile . "_transpose";
-
-        my $cmd = CXGN::Tools::Run->new(
-            {
-                backend => $backend_config,
-                submit_host => $cluster_host_config,
-                temp_base => $tmp_output_dir,
-                queue => $web_cluster_queue_config,
-                do_cleanup => 0,
-                out_file => $transpose_tempfile,
-    #            out_file => $transpose_tempfile,
-                # don't block and wait if the cluster looks full
-                max_cluster_jobs => 1_000_000_000,
-            }
-        );
-
-        # Do the transposition job on the cluster
-        $cmd->run_cluster(
-                "perl ",
-                $basepath_config."/bin/transpose_matrix.pl",
-                $tempfile,
-        );
-        $cmd->is_cluster(1);
-        $cmd->wait;
-
-        my $transpose_tempfile_hdr = $tempfile . "_transpose_hdr";
-
-        open my $in,  '<',  $transpose_tempfile or die "Can't read input file: $!";
-        open my $out, '>', $transpose_tempfile_hdr or die "Can't write output file: $!";
-
-        #Get synonyms of the accessions
-        my $stocklookup = CXGN::Stock::StockLookup->new({schema => $self->bcs_schema});
-        my @accession_ids = keys %unique_germplasm;
-        my $synonym_hash = $stocklookup->get_stock_synonyms('stock_id', 'accession', \@accession_ids);
-        my $synonym_string = "##SynonymsOfAccessions=\"";
-        while( my( $uniquename, $synonym_list ) = each %{$synonym_hash}){
-            if(scalar(@{$synonym_list})>0){
-                if(not length($synonym_string)<1){
-                    $synonym_string.=" ";
-                }
-                $synonym_string.=$uniquename."=(";
-                $synonym_string.= (join ", ", @{$synonym_list}).")";
-            }
-        }
-        $synonym_string .= "\"";
-        push @all_protocol_info_lines, $synonym_string;
-
-        my $vcf_header = join "\n", @all_protocol_info_lines;
-        $vcf_header .= "\n";
-
-        print $out $vcf_header;
-
-        while( <$in> )
-            {
-            print $out $_;
-            }
-        close $in;
-        close $out;
-
-        open my $out_copy, '<', $transpose_tempfile_hdr or die "Can't open output file: $!";
-
-        $self->cache()->set($key, '');
-        $file_handle = $self->cache()->handle($key);
-        copy($out_copy, $file_handle);
-
-        close $out_copy;
-        $file_handle = $self->cache()->handle($key);
-    }
-    return $file_handle;
-}
-
-=head2 get_cached_file_VCF_compute_from_parents()
-Computes the genotypes for the queried accessions computed from the parental dosages. Parents are known from pedigrees of accessions.
-Function for getting the file handle for the genotype search result from cache. Will write the cached file if it does not exist.
-Returns the genotype result as a dosage matrix format.
-Uses the file iterator to write the cached file, so that it uses little memory.
-=cut
-
-sub get_cached_file_VCF_compute_from_parents {
-    my $self = shift;
-    my $shared_cluster_dir_config = shift;
-    my $backend_config = shift;
-    my $cluster_host_config = shift;
-    my $web_cluster_queue_config = shift;
-    my $basepath_config = shift;
-    my $schema = $self->bcs_schema;
-    my $protocol_ids = $self->protocol_id_list;
-    my $accession_ids = $self->accession_list;
-    my $cache_root_dir = $self->cache_root();
-    my $marker_name_list = $self->marker_name_list;
-
-    if (scalar(@$protocol_ids)>1) {
-        die "Only one protocol at a time can be done when computing genotypes from parents\n";
-    }
-    my $protocol_id = $protocol_ids->[0];
-
-    my $key = $self->key("get_cached_file_VCF_compute_from_parents_v04");
-    $self->cache( Cache::File->new( cache_root => $cache_root_dir ));
-
-    my $file_handle;
-    if ($self->cache()->exists($key) && !$self->forbid_cache()) {
-        $file_handle = $self->cache()->handle($key);
-    }
-    else {
-        # Set the temp dir and temp output file
-        my $tmp_output_dir = $shared_cluster_dir_config."/tmp_genotype_download_VCF_compute_from_parents";
-        mkdir $tmp_output_dir if ! -d $tmp_output_dir;
-        my ($tmp_fh, $tempfile) = tempfile(
-            "wizard_download_XXXXX",
-            DIR=> $tmp_output_dir,
-        );
-
-        my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
-        my $female_parent_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'female_parent', 'stock_relationship')->cvterm_id();
-        my $male_parent_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'male_parent', 'stock_relationship')->cvterm_id();
-
-        my $accession_list_string = join ',', @$accession_ids;
-        my $q = "SELECT accession.stock_id, female_parent.stock_id, male_parent.stock_id
-            FROM stock AS accession
-            JOIN stock_relationship AS female_parent_rel ON(accession.stock_id=female_parent_rel.object_id AND female_parent_rel.type_id=$female_parent_cvterm_id)
-            JOIN stock AS female_parent ON(female_parent_rel.subject_id = female_parent.stock_id AND female_parent.type_id=$accession_cvterm_id)
-            JOIN stock_relationship AS male_parent_rel ON(accession.stock_id=male_parent_rel.object_id AND male_parent_rel.type_id=$male_parent_cvterm_id)
-            JOIN stock AS male_parent ON(male_parent_rel.subject_id = male_parent.stock_id AND male_parent.type_id=$accession_cvterm_id)
-            WHERE accession.stock_id IN ($accession_list_string) AND accession.type_id=$accession_cvterm_id ORDER BY accession.stock_id;";
-        my $h = $schema->storage->dbh()->prepare($q);
-        $h->execute();
-        my @accession_stock_ids_found = ();
-        my @female_stock_ids_found = ();
-        my @male_stock_ids_found = ();
-        while (my ($accession_stock_id, $female_parent_stock_id, $male_parent_stock_id) = $h->fetchrow_array()) {
-            push @accession_stock_ids_found, $accession_stock_id;
-            push @female_stock_ids_found, $female_parent_stock_id;
-            push @male_stock_ids_found, $male_parent_stock_id;
-        }
-
-        # print STDERR Dumper \@accession_stock_ids_found;
-        # print STDERR Dumper \@female_stock_ids_found;
-        # print STDERR Dumper \@male_stock_ids_found;
-
-        my $time = DateTime->now();
-        my $timestamp = $time->ymd()."_".$time->hms();
-
-        my @all_protocol_info_lines;
-
-        my %unique_germplasm;
-        my $protocol = CXGN::Genotype::Protocol->new({
-            bcs_schema => $schema,
-            nd_protocol_id => $protocol_id,
-            chromosome_list=>$self->chromosome_list,
-            start_position=>$self->start_position,
-            end_position=>$self->end_position,
-            marker_name_list=>$self->marker_name_list
-        });
-        my $markers = $protocol->markers;
-        my @all_marker_objects = values %$markers;
-        push @all_protocol_info_lines, @{$protocol->header_information_lines};
-	push @all_protocol_info_lines, "##source=FILE GENERATED BY BREEDBASE";
-        push @all_protocol_info_lines, "##fileDate=$timestamp";
-
-        foreach (@all_marker_objects) {
-            $self->_filtered_markers()->{$_->{name}}++;
-        }
-
-        no warnings 'uninitialized';
-        @all_marker_objects = sort { $a->{chrom} cmp $b->{chrom} || $a->{pos} <=> $b->{pos} || $a->{name} cmp $b->{name} } @all_marker_objects;
-        @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-
-        my $counter = 0;
-        for my $i (0..scalar(@accession_stock_ids_found)-1) {
-            my $female_stock_id = $female_stock_ids_found[$i];
-            my $male_stock_id = $male_stock_ids_found[$i];
-            my $accession_stock_id = $accession_stock_ids_found[$i];
-
-            my $dataset = CXGN::Dataset::Cache->new({
-                people_schema=>$self->people_schema,
-                schema=>$schema,
-                cache_root=>$cache_root_dir,
-                accessions=>[$female_stock_id, $male_stock_id]
-            });
-            my $genotypes = $dataset->retrieve_genotypes($protocol_id, ['DS'], ['markers'], ['name', 'chrom', 'pos', 'alt', 'ref'], 1, $self->chromosome_list, $self->start_position, $self->end_position, $self->marker_name_list);
-
-            # For old protocols with no protocolprop info...
-            if (scalar(@all_marker_objects) == 0) {
-                foreach my $o (sort genosort keys %{$genotypes->[0]->{selected_genotype_hash}}) {
-                    push @all_marker_objects, {name => $o};
-                }
-                @all_marker_objects = $self->_check_filtered_markers(\@all_marker_objects);
-            }
-
-            if (scalar(@$genotypes)>0) {
-                my $geno = $genotypes->[0];
-                $unique_germplasm{$accession_stock_id}++;
-
-                my $genotype_string = "";
-                if ($counter == 0) {
-                    $genotype_string .= "#CHROM\t";
-                    foreach my $m (@all_marker_objects) {
-			my $chrom = $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{chrom};
-			if (! $chrom) {
-			    ($chrom) = split /\_/, $m->{name};
-			}
-                        $genotype_string .=  $chrom . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "POS\t";
-                    foreach my $m (@all_marker_objects) {
-			my $pos = $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{pos};
-			if (! $pos) {
-			    (undef, $pos) = split /\_/, $m->{name};
-			}
-                        $genotype_string .= $pos . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "ID\t";
-                    foreach my $m (@all_marker_objects) {
-                        $genotype_string .= $m->{name} . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "REF\t";
-                    foreach my $m (@all_marker_objects) {
-                        $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{ref} . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "ALT\t";
-                    foreach my $m (@all_marker_objects) {
-                        $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{alt} . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "QUAL\t";
-                    foreach my $m (@all_marker_objects) {
-                        $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{qual} . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "FILTER\t";
-                    foreach my $m (@all_marker_objects) {
-                        $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{filter} . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "INFO\t";
-                    foreach my $m (@all_marker_objects) {
-                        $genotype_string .= $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{info} . "\t";
-                    }
-                    $genotype_string .= "\n";
-                    $genotype_string .= "FORMAT\t";
-                    foreach my $m (@all_marker_objects) {
-                        my $format = 'DS'; #When calculating genotypes from parents, only will return dosages atleast for now
-                        $genotype_string .= $format . "\t";
-                        $geno->{selected_protocol_hash}->{markers}->{$m->{name}}->{format} = $format;
-                        $m->{format} = $format;
-                    }
-                    $genotype_string .= "\n";
-                }
-                my $genotype_id = $geno->{germplasmName};
-                if (!$self->return_only_first_genotypeprop_for_stock) {
-                    $genotype_id = $geno->{germplasmName}."|".$geno->{markerProfileDbId};
-                }
-
-                my $geno_h = CXGN::Genotype::ComputeHybridGenotype->new({
-                    parental_genotypes=>$genotypes,
-                    marker_objects=>\@all_marker_objects
-                });
-                my $progeny_genotype = $geno_h->get_hybrid_genotype();
-                my $genotype_string_scores = join "\t", @$progeny_genotype;
-
-                $genotype_string .= $genotype_id."\t".$genotype_string_scores."\n";
-
-                write_file($tempfile, {append => 1}, $genotype_string);
-                $counter++;
-            }
-        }
-
-        my $transpose_tempfile = $tempfile . "_transpose";
-
-        my $cmd = CXGN::Tools::Run->new(
-            {
-                backend => $backend_config,
-                submit_host => $cluster_host_config,
-                temp_base => $tmp_output_dir,
-                queue => $web_cluster_queue_config,
-                do_cleanup => 0,
-                out_file => $transpose_tempfile,
-    #            out_file => $transpose_tempfile,
-                # don't block and wait if the cluster looks full
-                max_cluster_jobs => 1_000_000_000,
-            }
-        );
-
-        # Do the transposition job on the cluster
-        $cmd->run_cluster(
-                "perl ",
-                $basepath_config."/bin/transpose_matrix.pl",
-                $tempfile,
-        );
-        $cmd->is_cluster(1);
-        $cmd->wait;
-
-        my $transpose_tempfile_hdr = $tempfile . "_transpose_hdr";
-
-        open my $in,  '<',  $transpose_tempfile or die "Can't read input file: $!";
-        open my $out, '>', $transpose_tempfile_hdr or die "Can't write output file: $!";
-
-        #Get synonyms of the accessions
-        my $stocklookup = CXGN::Stock::StockLookup->new({schema => $self->bcs_schema});
-        my @accession_ids = keys %unique_germplasm;
-        my $synonym_hash = $stocklookup->get_stock_synonyms('stock_id', 'accession', \@accession_ids);
-        my $synonym_string = "##SynonymsOfAccessions=\"";
-        while( my( $uniquename, $synonym_list ) = each %{$synonym_hash}){
-            if(scalar(@{$synonym_list})>0){
-                if(not length($synonym_string)<1){
-                    $synonym_string.=" ";
-                }
-                $synonym_string.=$uniquename."=(";
-                $synonym_string.= (join ", ", @{$synonym_list}).")";
-            }
-        }
-        $synonym_string .= "\"";
-        push @all_protocol_info_lines, $synonym_string;
-
-        my $vcf_header = join "\n", @all_protocol_info_lines;
-        $vcf_header .= "\n";
-
-        print $out $vcf_header;
-
-        while( <$in> )
-            {
-            print $out $_;
-            }
-        close $in;
-        close $out;
-
-        open my $out_copy, '<', $transpose_tempfile_hdr or die "Can't open output file: $!";
-
-        $self->cache()->set($key, '');
-        $file_handle = $self->cache()->handle($key);
-        copy($out_copy, $file_handle);
-
-        close $out_copy;
-        $file_handle = $self->cache()->handle($key);
-    }
-    return $file_handle;
-}
-
-sub genosort {
-    my ($a_chr, $a_pos, $b_chr, $b_pos);
-    if ($a =~ m/S(\d+)\_(.*)/) {
-        $a_chr = $1;
-        $a_pos = $2;
-    }
-    if ($b =~ m/S(\d+)\_(.*)/) {
-        $b_chr = $1;
-        $b_pos = $2;
-    }
-
-    if ($a_chr && $b_chr) {
-        if ($a_chr == $b_chr) {
-            return $a_pos <=> $b_pos;
-        }
-        return $a_chr <=> $b_chr;
-    } else {
-        return -1;
-    }
-}
-
-sub _check_filtered_markers {
-    my $self = shift;
-    my $all_marker_objs = shift;
-    my @all_marker_objects = @$all_marker_objs;
-    my @filtered_marker_objects;
-    if ($self->_filtered_markers && scalar(keys %{$self->_filtered_markers}) > 0) {
-        my $filtered_markers = $self->_filtered_markers;
-        foreach (@all_marker_objects) {
-            if (exists($filtered_markers->{$_->{name}})) {
-                push @filtered_marker_objects, $_;
-            }
-        }
-        @all_marker_objects = @filtered_marker_objects;
-    }
-    return @all_marker_objects;
-}
-
-
-sub get_pcr_genotype_info {
-    my $self = shift;
-    my $schema = $self->bcs_schema;
-    my $genotype_data_project_list = $self->genotype_data_project_list;
-    my $protocol_id_list = $self->protocol_id_list;
-    my $genotype_id_list = $self->markerprofile_id_list;
-    my $protocol_id = $protocol_id_list->[0];
-    my @where_clause = ();
-#    print STDERR "GENOTYPE ID =".Dumper($genotype_id_list)."\n";
-#    print STDERR "PROTOCOL ID =".Dumper($protocol_id_list)."\n";
-
-    if ($protocol_id_list && scalar(@$protocol_id_list)>0) {
-        my $query = join ("," , @$protocol_id_list);
-        push @where_clause, "nd_protocol.nd_protocol_id in ($query)";
-    }
-
-    if ($genotype_id_list && scalar(@$genotype_id_list)>0) {
-        my $query = join ("," , @$genotype_id_list);
-        push @where_clause, "genotype.genotype_id in ($query)";
-    }
-#    print STDERR "WHERE CLAUSE =".Dumper(\@where_clause)."\n";
-    my $where_clause = scalar(@where_clause)>0 ? " WHERE " . (join (" AND " , @where_clause)) : '';
-
-    my $pcr_genotyping_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'pcr_marker_genotyping', 'genotype_property')->cvterm_id();
-    my $pcr_protocolprop_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'pcr_marker_details', 'protocol_property')->cvterm_id();
-    my $pcr_protocol_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'pcr_marker_protocol', 'protocol_type')->cvterm_id();
-    my $ploidy_level_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, "ploidy_level", "stock_property")->cvterm_id();
-
-    my $q1 = "SELECT nd_protocolprop.value->>'marker_names' FROM nd_protocolprop WHERE nd_protocol_id = ? AND nd_protocolprop.type_id = ?";
-    my $h1 = $schema->storage->dbh()->prepare($q1);
-    $h1->execute($protocol_id, $pcr_protocolprop_cvterm_id);
-    my $marker_names = $h1->fetchrow_array();
-
-    my $q = "SELECT stock.stock_id, stock.uniquename, stockprop.value, cvterm.name, genotype.genotype_id, genotype.description, genotypeprop.value
-        FROM nd_protocol
-        JOIN nd_experiment_protocol ON (nd_protocol.nd_protocol_id = nd_experiment_protocol.nd_protocol_id)
-        JOIN nd_experiment_genotype ON (nd_experiment_protocol.nd_experiment_id = nd_experiment_genotype.nd_experiment_id)
-        JOIN genotype ON (nd_experiment_genotype.genotype_id = genotype.genotype_id)
-        JOIN genotypeprop ON (genotype.genotype_id = genotypeprop.genotype_id) AND genotypeprop.type_id = ?
-        JOIN nd_experiment_stock ON (nd_experiment_genotype.nd_experiment_id = nd_experiment_stock.nd_experiment_id)
-        JOIN stock ON (nd_experiment_stock.stock_id = stock.stock_id)
-        LEFT JOIN stockprop ON (stockprop.stock_id = stock.stock_id) AND stockprop.type_id = ?
-        JOIN cvterm ON (stock.type_id = cvterm.cvterm_id)
-        $where_clause ORDER BY stock.uniquename ASC";
-
-    my $h = $schema->storage->dbh()->prepare($q);
-    $h->execute($pcr_genotyping_cvterm_id, $ploidy_level_cvterm_id);
-
-    my @pcr_genotype_data = ();
-    while (my ($stock_id, $stock_name, $ploidy_level, $stock_type, $genotype_id, $genotype_description, $genotype_data, $protocol_id) = $h->fetchrow_array()){
-        push @pcr_genotype_data, [$stock_id, $stock_name, $stock_type, $ploidy_level, $genotype_description, $genotype_id, $genotype_data]
-    }
-
-    my %protocol_genotype_data = (
-        marker_names => $marker_names,
-        protocol_genotype_data => \@pcr_genotype_data
-    );
-
-#    print STDERR "PCR GENOTYPE INFO =".Dumper(\%protocol_genotype_data)."\n";
-
-    return \%protocol_genotype_data;
-
-}
-
-1;