From a1d6d81ceddd757370cd093aae6feeafa30d3858 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 2 Oct 2020 15:23:14 -0500
Subject: There were two copies of the "submit_special" function in both
 show_trait.js and show_trait_mapping_tools.js. The latter now just calls the
 function from the former

* wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js - Everything in this file was previously inside its own function, which made its functions unable to access the functions from show_trait.js (and necessitated it having its own "copy" of the submit_special function
---
 .../new/javascript/show_trait_mapping_tools.js     | 545 ++++++++++-----------
 1 file changed, 268 insertions(+), 277 deletions(-)

(limited to 'wqflask')

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 4dce0705..c0f36eaa 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,307 +1,298 @@
-// Generated by CoffeeScript 1.8.0
-(function() {
-  var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
+var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
 
-  submit_special = function(url) {
-    $("#trait_data_form").attr("action", url);
-    $("#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");
-      }
+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;
+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
   };
-
-  block_outliers = function() {
-    return $('.outlier').each((function(_this) {
-      return function(_index, element) {
-        return $(element).find('.trait_value_input').val('x');
+  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));
-  };
-
-  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');
-          $('#static_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');
-          $('#static_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%",
-      onComplete: (function(_this) {
-        return function() {
-          var filename, getSvgXml;
-          root.create_lod_chart();
-          filename = "lod_chart_" + js_data.this_trait;
-          getSvgXml = function() {
-            var svg;
-            svg = $("#topchart").find("svg")[0];
-            return (new XMLSerializer).serializeToString(svg);
-          };
-          $("#exportform > #export").click(function() {
-            var form, svg_xml;
-            svg_xml = getSvgXml();
-            form = $("#exportform");
-            form.find("#data").val(svg_xml);
-            form.find("#filename").val(filename);
-            return form.submit();
-          });
-          return $("#exportpdfform > #export_pdf").click(function() {
-            var form, svg_xml;
-            svg_xml = getSvgXml();
-            form = $("#exportpdfform");
-            form.find("#data").val(svg_xml);
-            form.find("#filename").val(filename);
-            return form.submit();
-          });
-        };
-      })(this)
-    });
-  };
-
-  outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
-  showalert = function(message, alerttype) {
-    return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
-  };
-
-  $('#suggestive').hide();
+    })(this)
+  });
+  return false;
+};
 
-  $('input[name=display_all]').change((function(_this) {
-    return function() {
-      console.log("check");
-      if ($('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));
+};
 
-  //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-  var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
-                            'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
-                            'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
-                            'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
-                            'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
-
-  $(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
-    return function() {
-      if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
-        var form_data, url;
-        url = "/loading";
-        $('input[name=method]').val("rqtl_geno");
-        $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
-        $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
-        $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
-        $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
-        $('input[name=categorical_vars]').val(js_data.categorical_vars)
-        $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
-        $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
-        $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
-        $('input[name=tool_used]').val("Mapping");
-        $('input[name=form_url]').val("/run_mapping");
-        $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
-        return submit_special(url);
-      } else {
-        return true
-      }
-    };
-  })(this));
-  
-  $(".gemma_tab, #gemma_compute").on("click", (function(_this) {
-    return function() {
-      if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){
-        var form_data, url;
-        console.log("RUNNING GEMMA");
-        url = "/loading";
-        $('input[name=method]').val("gemma");
-        $('input[name=selected_chr]').val($('#chr_gemma').val());
-        $('input[name=num_perm]').val(0);
-        $('input[name=genofile]').val($('#genofile_gemma').val());
-        $('input[name=maf]').val($('input[name=maf_gemma]').val());
-        $('input[name=tool_used]').val("Mapping");
-        $('input[name=form_url]').val("/run_mapping");
-        $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
-        return submit_special(url);
-      } else {
-        return true
-      }
-    };
-  })(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');
+        $('#static_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');
+        $('#static_progress_bar_container').modal('hide');
+        return open_mapping_results(data);
+      };
+    })(this)
+  });
+  console.log("settingInterval");
+  this.my_timer = setInterval(get_progress, 1000);
+  return false;
+};
 
-  $(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) {
-    return function() {
-      if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){
-        var form_data, url;
-        console.log("In interval mapping");
-        url = "/loading";
-        $('input[name=method]').val("reaper");
-        $('input[name=selected_chr]').val($('#chr_reaper').val());
-        $('input[name=mapping_scale]').val($('#scale_reaper').val());
-        $('input[name=genofile]').val($('#genofile_reaper').val());
-        $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
-        $('input[name=control_marker]').val($('input[name=control_reaper]').val());
-        $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
-        $('input[name=manhattan_plot]').val($('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]'));
-        $('input[name=tool_used]').val("Mapping");
-        $('input[name=form_url]').val("/run_mapping");
-        $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
-        return submit_special(url);
-      } else {
-        return true
-      }
-    };
-  })(this));
+open_mapping_results = function(data) {
+  return $.colorbox({
+    html: data,
+    href: "#mapping_results_holder",
+    height: "90%",
+    width: "90%",
+    onComplete: (function(_this) {
+      return function() {
+        var filename, getSvgXml;
+        root.create_lod_chart();
+        filename = "lod_chart_" + js_data.this_trait;
+        getSvgXml = function() {
+          var svg;
+          svg = $("#topchart").find("svg")[0];
+          return (new XMLSerializer).serializeToString(svg);
+        };
+        $("#exportform > #export").click(function() {
+          var form, svg_xml;
+          svg_xml = getSvgXml();
+          form = $("#exportform");
+          form.find("#data").val(svg_xml);
+          form.find("#filename").val(filename);
+          return form.submit();
+        });
+        return $("#exportpdfform > #export_pdf").click(function() {
+          var form, svg_xml;
+          svg_xml = getSvgXml();
+          form = $("#exportpdfform");
+          form.find("#data").val(svg_xml);
+          form.find("#filename").val(filename);
+          return form.submit();
+        });
+      };
+    })(this)
+  });
+};
 
-  $("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
-    return function() {
-      if ($(".outlier").length && $(".outlier-alert").length < 1) {
-        return showalert(outlier_text, "alert-success outlier-alert");
-      }
-    };
-  })(this));
+outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
+showalert = function(message, alerttype) {
+  return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
+};
 
-  composite_mapping_fields = function() {
-    return $(".composite_fields").toggle();
-  };
+$('#suggestive').hide();
 
-  mapping_method_fields = function() {
-    return $(".mapping_method_fields").toggle();
+$('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));
 
-  $("#use_composite_choice").change(composite_mapping_fields);
-
-  $("#mapping_method_choice").change(mapping_method_fields);
+//ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+                          'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
+                          'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
+                          'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
+                          'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples']
 
-  $("#mapmodel_rqtl_geno").change(function() {
-    if ($(this).val() == "np"){
-      $("#mapmethod_rqtl_geno").attr('disabled', 'disabled');
-      $("#mapmethod_rqtl_geno").css('background-color', '#CCC');
-      $("#missing_geno").attr('disabled', 'disabled');
-      $("#missing_geno").css('background-color', '#CCC');
+$(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) {
+  return function() {
+    if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){
+      var form_data, url;
+      url = "/loading";
+      $('input[name=method]').val("rqtl_geno");
+      $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
+      $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
+      $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
+      $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+      $('input[name=categorical_vars]').val(js_data.categorical_vars)
+      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
+      $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+      $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+      return submit_special(url);
     } else {
-      $("#mapmethod_rqtl_geno").removeAttr('disabled');
-      $("#mapmethod_rqtl_geno").css('background-color', '#FFF');
-      $("#missing_geno").removeAttr('disabled');
-      $("#missing_geno").css('background-color', '#FFF');
+      return true
     }
-  });
+  };
+})(this));
 
-  $("#mapmethod_rqtl_geno").change(function() {
-    if ($(this).val() == "mr"){
-      $("#missing_geno_div").css('display', 'block');
+$(".gemma_tab, #gemma_compute").on("click", (function(_this) {
+  return function() {
+    if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){
+      var form_data, url;
+      console.log("RUNNING GEMMA");
+      url = "/loading";
+      $('input[name=method]').val("gemma");
+      $('input[name=selected_chr]').val($('#chr_gemma').val());
+      $('input[name=num_perm]').val(0);
+      $('input[name=genofile]').val($('#genofile_gemma').val());
+      $('input[name=maf]').val($('input[name=maf_gemma]').val());
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+      return submit_special(url);
     } else {
-      $("#missing_geno_div").css('display', 'none');
+      return true
     }
-  });
+  };
+})(this));
 
-  $("li.mapping_tab").click(function() {
-    if ($(this).hasClass("rqtl")){
-      $(".rqtl_description").css("display", "block");
+$(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) {
+  return function() {
+    if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){
+      var form_data, url;
+      console.log("In interval mapping");
+      url = "/loading";
+      $('input[name=method]').val("reaper");
+      $('input[name=selected_chr]').val($('#chr_reaper').val());
+      $('input[name=mapping_scale]').val($('#scale_reaper').val());
+      $('input[name=genofile]').val($('#genofile_reaper').val());
+      $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
+      $('input[name=control_marker]').val($('input[name=control_reaper]').val());
+      $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
+      $('input[name=manhattan_plot]').val($('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]'));
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+      return submit_special(url);
     } else {
-      $(".rqtl_description").css("display", "none");
+      return true
     }
-  });
+  };
+})(this));
 
-  toggle_enable_disable = function(elem) {
-    return $(elem).prop("disabled", !$(elem).prop("disabled"));
+$("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
+  return function() {
+    if ($(".outlier").length && $(".outlier-alert").length < 1) {
+      return showalert(outlier_text, "alert-success outlier-alert");
+    }
   };
+})(this));
 
-  $("#choose_closet_control").change(function() {
-    return toggle_enable_disable("#control_locus");
-  });
+composite_mapping_fields = function() {
+  return $(".composite_fields").toggle();
+};
 
-  $("#display_all_lrs").change(function() {
-    return toggle_enable_disable("#suggestive_lrs");
-  });
+mapping_method_fields = function() {
+  return $(".mapping_method_fields").toggle();
+};
 
-  $('#genofile_rqtl_geno').change(function() {
-    geno_location = $(this).children("option:selected").val().split(":")[0]
-    $('#scale_rqtl_geno').empty()
-    the_scales = js_data.scales_in_geno[geno_location]
-    for (var i = 0; i < the_scales.length; i++){
-      $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
-    }
-  });
-  $('#genofile_reaper').change(function() {
-    geno_location = $(this).children("option:selected").val().split(":")[0]
-    $('#scale_reaper').empty()
-    the_scales = js_data.scales_in_geno[geno_location]
-    for (var i = 0; i < the_scales.length; i++){
-      $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
-    }
-  });
+$("#use_composite_choice").change(composite_mapping_fields);
+
+$("#mapping_method_choice").change(mapping_method_fields);
+
+$("#mapmodel_rqtl_geno").change(function() {
+  if ($(this).val() == "np"){
+    $("#mapmethod_rqtl_geno").attr('disabled', 'disabled');
+    $("#mapmethod_rqtl_geno").css('background-color', '#CCC');
+    $("#missing_geno").attr('disabled', 'disabled');
+    $("#missing_geno").css('background-color', '#CCC');
+  } else {
+    $("#mapmethod_rqtl_geno").removeAttr('disabled');
+    $("#mapmethod_rqtl_geno").css('background-color', '#FFF');
+    $("#missing_geno").removeAttr('disabled');
+    $("#missing_geno").css('background-color', '#FFF');
+  }
+});
+
+$("#mapmethod_rqtl_geno").change(function() {
+  if ($(this).val() == "mr"){
+    $("#missing_geno_div").css('display', 'block');
+  } else {
+    $("#missing_geno_div").css('display', 'none');
+  }
+});
+
+$("li.mapping_tab").click(function() {
+  if ($(this).hasClass("rqtl")){
+    $(".rqtl_description").css("display", "block");
+  } else {
+    $(".rqtl_description").css("display", "none");
+  }
+});
+
+toggle_enable_disable = function(elem) {
+  return $(elem).prop("disabled", !$(elem).prop("disabled"));
+};
+
+$("#choose_closet_control").change(function() {
+  return toggle_enable_disable("#control_locus");
+});
+
+$("#display_all_lrs").change(function() {
+  return toggle_enable_disable("#suggestive_lrs");
+});
 
-}).call(this);
+$('#genofile_rqtl_geno').change(function() {
+  geno_location = $(this).children("option:selected").val().split(":")[0]
+  $('#scale_rqtl_geno').empty()
+  the_scales = js_data.scales_in_geno[geno_location]
+  for (var i = 0; i < the_scales.length; i++){
+    $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+  }
+});
+$('#genofile_reaper').change(function() {
+  geno_location = $(this).children("option:selected").val().split(":")[0]
+  $('#scale_reaper').empty()
+  the_scales = js_data.scales_in_geno[geno_location]
+  for (var i = 0; i < the_scales.length; i++){
+    $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+  }
+});
-- 
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