From 69c04531e0168ed9cb9da27f532e150f45cb80b3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 29 Jul 2021 20:49:18 +0000
Subject: Fixed some issues with the Pair Scan options and JS

---
 .../new/javascript/show_trait_mapping_tools.js     | 29 +++++++++++++---------
 .../templates/show_trait_mapping_tools.html        | 20 +++++++--------
 2 files changed, 27 insertions(+), 22 deletions(-)

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 e457fa4a..2650b809 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -156,6 +156,8 @@ $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) {
       $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
       $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
       $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
+      $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_geno').val());
+      $('input[name=mapmethod_rqtl]').val($('#mapmethod_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());
@@ -178,11 +180,13 @@ $(".rqtl-pair-tab, #rqtl_pair_compute").on("click", (function(_this) {
       url = "/loading";
       $('input[name=method]').val("rqtl_geno");
       $('input[name=pair_scan]').val("");
-      $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
-      $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
+      $('input[name=genofile]').val($('#genofile_rqtl_pair').val());
+      $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_pair').val());
+      $('input[name=mapmethod_rqtl]').val($('#mapmethod_rqtl_pair').val());
+      $('input[name=num_perm]').val($('input[name=num_perm_rqtl_pair]').val());
       $('input[name=categorical_vars]').val(js_data.categorical_vars)
-      $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
-      $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
+      $('input[name=control_marker]').val($('input[name=control_rqtl_pair]').val());
+      $('input[name=do_control]').val($('input[name=do_control_rqtl_pair]:checked').val());
       $('input[name=tool_used]').val("Mapping");
       $('input[name=form_url]').val("/run_mapping");
       $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
@@ -259,25 +263,26 @@ $("#use_composite_choice").change(composite_mapping_fields);
 
 $("#mapping_method_choice").change(mapping_method_fields);
 
-$("#mapmodel_rqtl_geno").change(function() {
+$("#mapmodel_rqtl_geno,#mapmodel_rqtl_pair").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');
+    $("#missing_geno,#missing_geno_pair").attr('disabled', 'disabled');
+    $("#missing_geno,#missing_geno_pair").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');
+    $("#missing_geno,#missing_geno_pair").removeAttr('disabled');
+    $("#missing_geno,#missing_geno_pair").css('background-color', '#FFF');
   }
 });
 
-$("#mapmethod_rqtl_geno").change(function() {
+$("#mapmethod_rqtl_geno,#mapmethod_rqtl_pair").change(function() {
+  console.log("IN IT")
   if ($(this).val() == "mr"){
-    $("#missing_geno_div").css('display', 'block');
+    $("#missing_geno_div,#missing_geno_pair_div").css('display', 'block');
   } else {
-    $("#missing_geno_div").css('display', 'none');
+    $("#missing_geno_div,#missing_geno_pair_div").css('display', 'none');
   }
 });
 
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 28aff876..d1078620 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -358,7 +358,7 @@
                         <div class="mapping_method_fields form-group">
                             <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                             <div class="col-xs-6 controls">
-                                <select id="genofile_rqtl_geno" class="form-control">
+                                <select id="genofile_rqtl_pair" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                     {% endfor %}
@@ -369,7 +369,7 @@
                         <div class="mapping_method_fields form-group">
                             <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div class="col-xs-4 controls">
-                                <input name="num_perm_rqtl_geno" value="200" type="text" class="form-control">
+                                <input name="num_perm_rqtl_pair" value="200" type="text" class="form-control">
                             </div>
                         </div>
                         {% if sample_groups[0].attributes|length > 0 %}
@@ -390,7 +390,7 @@
                         <div class="mapping_method_fields form-group">
                             <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
                             <div class="col-xs-6 controls">
-                              <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
+                              <input name="control_rqtl_pair" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
                               <label class="radio-inline">
                                   <input type="radio" name="do_control_rqtl" value="true">
                                   Yes
@@ -402,9 +402,9 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
+                            <label for="mapmodel_rqtl_pair" class="col-xs-3 control-label">Model</label>
                             <div class="col-xs-4 controls">
-                              <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control">
+                              <select id="mapmodel_rqtl_pair" name="mapmodel_rqtl_pair" class="form-control">
                                 <option value="normal">Normal</option>
                                 {% if binary == "true" %}<option value="binary">Binary</option>{% endif %}
                                 <!--<option value="2part">2-part</option>-->
@@ -413,9 +413,9 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
+                            <label for="mapmethod_rqtl_pair" class="col-xs-3 control-label">Method</label>
                             <div class="col-xs-6 controls">
-                              <select id="mapmethod_rqtl_geno" name="mapmethod_rqtl_geno" class="form-control">
+                              <select id="mapmethod_rqtl_pair" name="mapmethod_rqtl_pair" class="form-control">
                                 <option value="hk" selected>Haley-Knott</option>
                                 <option value="ehk">Extended Haley-Knott</option>
                                 <option value="mr">Marker Regression</option>
@@ -424,10 +424,10 @@
                               </select>
                             </div>
                         </div>
-                        <div id="missing_geno_div" class="mapping_method_fields form-group" style="display: none;">
-                            <label for="missing_genotypes" class="col-xs-3 control-label"></label>
+                        <div id="missing_geno_pair_div" class="mapping_method_fields form-group" style="display: none;">
+                            <label for="missing_genotypes_pair" class="col-xs-3 control-label"></label>
                             <div class="col-xs-6 controls">
-                              <select id="missing_genotype" name="missing_genotypes" class="form-control">
+                              <select id="missing_genotype_pair" name="missing_genotypes" class="form-control">
                                 <option value="mr">Remove Samples w/o Genotypes</option>
                                 <option value="mr-imp">Single Imputation</option>
                                 <option value="mr-argmax">Imputation w/ Viterbi Algorithm</option>
-- 
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