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-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee26
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js399
-rwxr-xr-xwqflask/wqflask/templates/base.html6
-rwxr-xr-xwqflask/wqflask/templates/interval_mapping.html2
-rwxr-xr-xwqflask/wqflask/templates/marker_regression.html11
-rwxr-xr-xwqflask/wqflask/templates/show_trait.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_progress_bar.html15
-rwxr-xr-xwqflask/wqflask/views.py2
9 files changed, 218 insertions, 247 deletions
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 881ea74d..9e070c97 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -76,18 +76,20 @@ do_ajax_post = (url, form_data) ->
         return false
 
 open_mapping_results = (data) ->
-    $.colorbox(
-        html: data
-        href: "#mapping_results_holder"
-        height: "90%"
-        width: "90%"
-    )
+    results_window = window.open()
+    $(results_window.document.body).html(data)
+    #$.colorbox(
+    #    html: data
+    #    href: "#mapping_results_holder"
+    #    height: "90%"
+    #    width: "90%"
+    #)
 
 showalert = (message,alerttype) ->
     $('#alert_placeholder').append('<div id="alertdiv" class="alert ' +  alerttype + '"><a class="close" data-dismiss="alert">×</a><span>'+message+'</span></div>')
     
 
-$("#interval_mapping_compute").click(() =>
+$("#interval_mapping_compute").on("click", =>
         showalert("One or more outliers exist in this data set. Please review values before mapping. \
                   Including outliers when mapping may lead to misleading results. \
                   We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers \
@@ -116,8 +118,8 @@ $('input[name=display_all]').change(() =>
             $('#suggestive').hide()
 )
 
-$("#pylmm_compute").click(() =>
-        $("#progress_bar_container").modal({show:true})
+$("#pylmm_compute").on("click", =>
+        #$("#progress_bar_container").modal()
         url = "/marker_regression"
         $('input[name=method]').val("pylmm")
         $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val())
@@ -133,7 +135,7 @@ $("#pylmm_compute").click(() =>
     
     
     
-$("#rqtl_geno_compute").click(() =>
+$("#rqtl_geno_compute").on("click", =>
         $("#progress_bar_container").modal()
         url = "/marker_regression"
         $('input[name=method]').val("rqtl_geno")
@@ -150,7 +152,7 @@ $("#rqtl_geno_compute").click(() =>
 )
 
 
-$("#plink_compute").click(() =>
+$("#plink_compute").on("click", =>
         $("#static_progress_bar_container").modal()
         url = "/marker_regression"
         $('input[name=method]').val("plink")
@@ -163,7 +165,7 @@ $("#plink_compute").click(() =>
         do_ajax_post(url, form_data)
 )
 
-$("#gemma_compute").click(() =>
+$("#gemma_compute").on("click", =>
         console.log("RUNNING GEMMA")
         $("#static_progress_bar_container").modal()
         url = "/marker_regression"
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 1779df4b..cc1ddf37 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,223 +1,218 @@
 // Generated by CoffeeScript 1.8.0
-var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, showalert, submit_special, toggle_enable_disable, update_time_remaining;
-
-submit_special = function() {
-  var url;
-  console.log("In submit_special");
-  console.log("this is:", this);
-  console.log("$(this) is:", $(this));
-  url = $(this).data("url");
-  console.log("url is:", url);
-  $("#trait_data_form").attr("action", url);
-  return $("#trait_data_form").submit();
-};
-
-update_time_remaining = function(percent_complete) {
-  var minutes_remaining, now, period, total_seconds_remaining;
-  now = new Date();
-  period = now.getTime() - root.start_time;
-  console.log("period is:", period);
-  if (period > 8000) {
-    total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
-    minutes_remaining = Math.round(total_seconds_remaining / 60);
-    if (minutes_remaining < 3) {
-      return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
-    } else {
-      return $('#time_remaining').text(minutes_remaining + " minutes remaining");
+(function() {
+  var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, showalert, submit_special, toggle_enable_disable, update_time_remaining;
+
+  submit_special = function() {
+    var url;
+    console.log("In submit_special");
+    console.log("this is:", this);
+    console.log("$(this) is:", $(this));
+    url = $(this).data("url");
+    console.log("url is:", url);
+    $("#trait_data_form").attr("action", url);
+    return $("#trait_data_form").submit();
+  };
+
+  update_time_remaining = function(percent_complete) {
+    var minutes_remaining, now, period, total_seconds_remaining;
+    now = new Date();
+    period = now.getTime() - root.start_time;
+    console.log("period is:", period);
+    if (period > 8000) {
+      total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
+      minutes_remaining = Math.round(total_seconds_remaining / 60);
+      if (minutes_remaining < 3) {
+        return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
+      } else {
+        return $('#time_remaining').text(minutes_remaining + " minutes remaining");
+      }
     }
-  }
-};
-
-get_progress = function() {
-  var params, params_str, temp_uuid, url;
-  console.log("temp_uuid:", $("#temp_uuid").val());
-  temp_uuid = $("#temp_uuid").val();
-  params = {
-    key: temp_uuid
   };
-  params_str = $.param(params);
-  url = "/get_temp_data?" + params_str;
-  console.log("url:", url);
-  $.ajax({
-    type: "GET",
-    url: url,
-    success: (function(_this) {
-      return function(progress_data) {
-        var percent_complete;
-        percent_complete = progress_data['percent_complete'];
-        console.log("in get_progress data:", progress_data);
-        $('#marker_regression_progress').css("width", percent_complete + "%");
-        if (root.start_time) {
-          if (!isNaN(percent_complete)) {
-            return update_time_remaining(percent_complete);
-          }
-        } else {
-          return root.start_time = new Date().getTime();
-        }
-      };
-    })(this)
-  });
-  return false;
-};
 
-block_outliers = function() {
-  return $('.outlier').each((function(_this) {
-    return function(_index, element) {
-      return $(element).find('.trait_value_input').val('x');
+  get_progress = function() {
+    var params, params_str, temp_uuid, url;
+    console.log("temp_uuid:", $("#temp_uuid").val());
+    temp_uuid = $("#temp_uuid").val();
+    params = {
+      key: temp_uuid
     };
-  })(this));
-};
-
-do_ajax_post = function(url, form_data) {
-  $.ajax({
-    type: "POST",
-    url: url,
-    data: form_data,
-    error: (function(_this) {
-      return function(xhr, ajaxOptions, thrownError) {
-        alert("Sorry, an error occurred");
-        console.log(xhr);
-        clearInterval(_this.my_timer);
-        $('#progress_bar_container').modal('hide');
-        return $("body").html("We got an error.");
-      };
-    })(this),
-    success: (function(_this) {
-      return function(data) {
-        clearInterval(_this.my_timer);
-        $('#progress_bar_container').modal('hide');
-        return open_mapping_results(data);
-      };
-    })(this)
-  });
-  console.log("settingInterval");
-  this.my_timer = setInterval(get_progress, 1000);
-  return false;
-};
-
-open_mapping_results = function(data) {
-  return $.colorbox({
-    html: data,
-    href: "#mapping_results_holder",
-    height: "90%",
-    width: "90%"
-  });
-};
-
-showalert = function(message, alerttype) {
-  return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
-};
-
-$("#interval_mapping_compute").click((function(_this) {
-  return function() {
-    var form_data, url;
-    showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success");
-    console.log("In interval mapping");
-    $("#progress_bar_container").modal();
-    url = "/interval_mapping";
-    $('input[name=method]').val("reaper");
-    $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
-    $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
-    $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+    params_str = $.param(params);
+    url = "/get_temp_data?" + params_str;
+    console.log("url:", url);
+    $.ajax({
+      type: "GET",
+      url: url,
+      success: (function(_this) {
+        return function(progress_data) {
+          var percent_complete;
+          percent_complete = progress_data['percent_complete'];
+          console.log("in get_progress data:", progress_data);
+          $('#marker_regression_progress').css("width", percent_complete + "%");
+          if (root.start_time) {
+            if (!isNaN(percent_complete)) {
+              return update_time_remaining(percent_complete);
+            }
+          } else {
+            return root.start_time = new Date().getTime();
+          }
+        };
+      })(this)
+    });
+    return false;
   };
-})(this));
-
-$('#suggestive').hide();
 
-$('input[name=display_all]').change((function(_this) {
-  return function() {
-    console.log("check");
-    if ($('input[name=display_all]:checked').val() === "False") {
-      return $('#suggestive').show();
-    } else {
-      return $('#suggestive').hide();
-    }
+  block_outliers = function() {
+    return $('.outlier').each((function(_this) {
+      return function(_index, element) {
+        return $(element).find('.trait_value_input').val('x');
+      };
+    })(this));
   };
-})(this));
 
-$("#pylmm_compute").click((function(_this) {
-  return function() {
-    var form_data, url;
-    $("#progress_bar_container").modal({
-      show: true
+  do_ajax_post = function(url, form_data) {
+    $.ajax({
+      type: "POST",
+      url: url,
+      data: form_data,
+      error: (function(_this) {
+        return function(xhr, ajaxOptions, thrownError) {
+          alert("Sorry, an error occurred");
+          console.log(xhr);
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          return $("body").html("We got an error.");
+        };
+      })(this),
+      success: (function(_this) {
+        return function(data) {
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          return open_mapping_results(data);
+        };
+      })(this)
     });
-    url = "/marker_regression";
-    $('input[name=method]').val("pylmm");
-    $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
-    $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+    console.log("settingInterval");
+    this.my_timer = setInterval(get_progress, 1000);
+    return false;
   };
-})(this));
-
-$("#rqtl_geno_compute").click((function(_this) {
-  return function() {
-    var form_data, url;
-    $("#progress_bar_container").modal();
-    url = "/marker_regression";
-    $('input[name=method]').val("rqtl_geno");
-    $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
-    $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
-    $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  open_mapping_results = function(data) {
+    var results_window;
+    results_window = window.open();
+    return $(results_window.document.body).html(data);
   };
-})(this));
-
-$("#plink_compute").click((function(_this) {
-  return function() {
-    var form_data, url;
-    $("#static_progress_bar_container").modal();
-    url = "/marker_regression";
-    $('input[name=method]').val("plink");
-    $('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val());
-    $('input[name=suggestive]').val($('input[name=suggestive_plink]').val());
-    $('input[name=maf]').val($('input[name=maf_plink]').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  showalert = function(message, alerttype) {
+    return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
   };
-})(this));
-
-$("#gemma_compute").click((function(_this) {
-  return function() {
-    var form_data, url;
-    console.log("RUNNING GEMMA");
-    $("#static_progress_bar_container").modal();
-    url = "/marker_regression";
-    $('input[name=method]').val("gemma");
-    $('input[name=maf]').val($('input[name=maf_gemma]').val());
-    form_data = $('#trait_data_form').serialize();
-    console.log("form_data is:", form_data);
-    return do_ajax_post(url, form_data);
+
+  $("#interval_mapping_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      showalert("One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.", "alert-success");
+      console.log("In interval mapping");
+      $("#progress_bar_container").modal();
+      url = "/interval_mapping";
+      $('input[name=method]').val("reaper");
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
+      $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $('#suggestive').hide();
+
+  $('input[name=display_all]').change((function(_this) {
+    return function() {
+      console.log("check");
+      if ($('input[name=display_all]:checked').val() === "False") {
+        return $('#suggestive').show();
+      } else {
+        return $('#suggestive').hide();
+      }
+    };
+  })(this));
+
+  $("#pylmm_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      url = "/marker_regression";
+      $('input[name=method]').val("pylmm");
+      $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $("#rqtl_geno_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      $("#progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("rqtl_geno");
+      $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
+      $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $("#plink_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      $("#static_progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("plink");
+      $('input[name=maf]').val($('input[name=maf_plink]').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  $("#gemma_compute").on("click", (function(_this) {
+    return function() {
+      var form_data, url;
+      console.log("RUNNING GEMMA");
+      $("#static_progress_bar_container").modal();
+      url = "/marker_regression";
+      $('input[name=method]').val("gemma");
+      $('input[name=maf]').val($('input[name=maf_gemma]').val());
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      return do_ajax_post(url, form_data);
+    };
+  })(this));
+
+  composite_mapping_fields = function() {
+    return $(".composite_fields").toggle();
   };
-})(this));
 
-composite_mapping_fields = function() {
-  return $(".composite_fields").toggle();
-};
+  mapping_method_fields = function() {
+    return $(".mapping_method_fields").toggle();
+  };
 
-mapping_method_fields = function() {
-  return $(".mapping_method_fields").toggle();
-};
+  $("#use_composite_choice").change(composite_mapping_fields);
 
-$("#use_composite_choice").change(composite_mapping_fields);
+  $("#mapping_method_choice").change(mapping_method_fields);
 
-$("#mapping_method_choice").change(mapping_method_fields);
+  toggle_enable_disable = function(elem) {
+    return $(elem).prop("disabled", !$(elem).prop("disabled"));
+  };
 
-toggle_enable_disable = function(elem) {
-  return $(elem).prop("disabled", !$(elem).prop("disabled"));
-};
+  $("#choose_closet_control").change(function() {
+    return toggle_enable_disable("#control_locus");
+  });
 
-$("#choose_closet_control").change(function() {
-  return toggle_enable_disable("#control_locus");
-});
+  $("#display_all_lrs").change(function() {
+    return toggle_enable_disable("#suggestive_lrs");
+  });
 
-$("#display_all_lrs").change(function() {
-  return toggle_enable_disable("#suggestive_lrs");
-});
+}).call(this);
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 462a59a2..30519e24 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -10,12 +10,6 @@
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" />
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
-
-    <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
-    <!--[if lt IE 9]>
-        <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-    <![endif]-->
-
     <link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css"  />
     <link rel="stylesheet" type="text/css" href="/static/new/css/main.css"  />
     <link rel="stylesheet" type="text/css" href="/static/new/css/parsley.css"  />
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
index 82a96ba1..4d99d2e7 100755
--- a/wqflask/wqflask/templates/interval_mapping.html
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -80,7 +80,7 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_interval_map.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+    <!--<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>-->
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 6aed69d5..62146662 100755
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -1,7 +1,8 @@
 {% extends "base.html" %}
 {% block title %}Interval Mapping{% endblock %}
 {% block css %}
-<!--    <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />-->
+    <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
@@ -75,22 +76,16 @@
         js_data = {{ js_data | safe }}
     </script>
 
-    <!--[if lt IE 9]>
-<!--        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
-    <![endif]-->
     <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
-<!--    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>-->
+    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
-<!--    <script language="javascript" type="text/javascript" src="/static/new/javascript/manhattan_plot.js"></script>-->
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 1f53e089..ca530162 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -134,12 +134,10 @@
     <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
     <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
     
-    <script language="javascript" type="text/javascript" src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
-"></script>
     <script type="text/javascript" charset="utf-8">
             
            function getValue(x) {
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index bd1e6f1e..1550647a 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -66,7 +66,7 @@
                         </div>
                         <div class="form-group">
                             <div style="padding-left:15px;" class="controls">
-                                <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+                                <button id="pylmm_compute" class="btn submit_special btn-primary" title="Compute Marker Regression">
                                     <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
                                 </button>
                             </div>
diff --git a/wqflask/wqflask/templates/show_trait_progress_bar.html b/wqflask/wqflask/templates/show_trait_progress_bar.html
index 99906338..f9a34070 100755
--- a/wqflask/wqflask/templates/show_trait_progress_bar.html
+++ b/wqflask/wqflask/templates/show_trait_progress_bar.html
@@ -32,17 +32,4 @@
       </div>
     </div>
   </div>
-</div>
-
-<!--<div id="static_progress_bar_container" class="modal hide fade" tabindex="-1" role="dialog" aria-labelledby="progress_bar" aria-hidden="true">
-  <div class="modal-header">
-    <h3 id="progress_bar">Loading... (Estimated time ~10-15m)</h3>
-  </div>
-    <div class="modal-body">
-        <div class="progress progress-striped active">
-            <div id="marker_regression_progress" class="bar" style="width: 100%"></div>
-        </div>
-        <div id="time_remaining">
-        </div>
-    </div>
-</div>-->
\ No newline at end of file
+</div>
\ No newline at end of file
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 79c1c967..c16c22df 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -312,7 +312,7 @@ def marker_regression_page():
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
 
-    version = "v4"
+    version = "v3"
     key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
     print("key is:", pf(key))
     with Bench("Loading cache"):
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-07 11:20:49 +0000