Changed loading page to work for any feature, instead of having to make a separate one like I did for correlation previously

Fixed some wrong text on heatmap page

11 files changed, 64 insertions, 145 deletions

diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index ebb1651d..86e7d63e 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -228,48 +228,54 @@ $(function() {
           return $(this).val();
       }).get();
       $("#trait_list").val(traits)
-      url = $(this).data("url")
-      return submit_special(url)
+      $("input[name=tool_used]").val("Correlation Matrix")
+      $("input[name=form_url]").val($(this).data("url"))
+      return submit_special("/loading")
   });
   $("#network_graph").on("click", function() {
       traits = $("#trait_table input:checked").map(function() {
          return $(this).val();
       }).get();
       $("#trait_list").val(traits)
-      url = $(this).data("url")
-      return submit_special(url)
+      $("input[name=tool_used]").val("Network Graph")
+      $("input[name=form_url]").val($(this).data("url"))
+      return submit_special("/loading")
   });
   $("#wgcna_setup").on("click", function() {
       traits = $("#trait_table input:checked").map(function() {
           return $(this).val();
       }).get();
       $("#trait_list").val(traits)
-      url = $(this).data("url")
-      return submit_special(url)
+      $("input[name=tool_used]").val("WGCNA Setup")
+      $("input[name=form_url]").val($(this).data("url"))
+      return submit_special("/loading")
   });
   $("#ctl_setup").on("click", function() {
       traits = $("#trait_table input:checked").map(function() {
           return $(this).val();
       }).get();
       $("#trait_list").val(traits)
-      url = $(this).data("url")
-      return submit_special(url)
+      $("input[name=tool_used]").val("CTL Setup")
+      $("input[name=form_url]").val($(this).data("url"))
+      return submit_special("/loading")
   });
   $("#heatmap").on("click", function() {
       traits = $("#trait_table input:checked").map(function() {
           return $(this).val();
       }).get();
       $("#trait_list").val(traits)
-      url = $(this).data("url")
-      return submit_special(url)
+      $("input[name=tool_used]").val("Heatmap")
+      $("input[name=form_url]").val($(this).data("url"))
+      return submit_special("/loading")
   });
   $("#comp_bar_chart").on("click", function() {
       traits = $("#trait_table input:checked").map(function() {
           return $(this).val();
       }).get();
       $("#trait_list").val(traits)
-      url = $(this).data("url")
-      return submit_special(url)
+      $("input[name=tool_used]").val("Comparison Bar Chart")
+      $("input[name=form_url]").val($(this).data("url"))
+      return submit_special("/loading")
   });
 
   $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver").on("click", function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index f278b840..e985078b 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -445,16 +445,15 @@ submit_special = function(url) {
   return $("#trait_data_form").submit();
 };
 
-submit_corr = function(){
-    var url;
-    url = "/corr_loading";
-    return submit_special(url);
-};
+var corr_input_list = ['corr_type', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+                        'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
 
 $(".corr_compute").on("click", (function(_this) {
   return function() {
-    var url;
-    url = "/corr_loading";
+    $('input[name=tool_used]').val("Correlation");
+    $('input[name=form_url]').val("/corr_compute");
+    $('input[name=wanted_inputs]').val(corr_input_list.join(","));
+    url = "/loading";
     return submit_special(url);
   };
 })(this));
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 4e82fff2..d9cf50e2 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -4,9 +4,6 @@
 
   submit_special = function(url) {
     console.log("In submit_special");
-    console.log("this is:", this);
-    console.log("$(this) is:", $(this));
-    console.log("url is:", url);
     $("#trait_data_form").attr("action", url);
     return $("#trait_data_form").submit();
   };
@@ -154,6 +151,13 @@
     };
   })(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', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+                            'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', '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']
+
   $("#rqtl_geno_compute").on("click", (function(_this) {
     return function() {
       var form_data, url;
@@ -165,10 +169,10 @@
       $('input[name=manhattan_plot]').val($('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());
-      form_data = $('#trait_data_form').serialize();
-      console.log("form_data is:", form_data);
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=form_url]').val("/run_mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
       if ($('input[name=pair_scan]:checked').val() == "true") {
-        console.log("PAIR SCAN:", $('input[name=pair_scan]:checked').val())
         run_pair_scan = confirm(runtime_warning_text)
         if (run_pair_scan == true) {
           submit_special(url);
@@ -193,8 +197,8 @@
       $('input[name=num_perm]').val(0);
       $('input[name=genofile]').val($('#genofile_gemma').val());
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
-      form_data = $('#trait_data_form').serialize();
-      console.log("form_data is:", form_data);
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
       return submit_special(url);
     };
   })(this));
@@ -203,7 +207,6 @@
     return function() {
       var form_data, url;
       console.log("In interval mapping");
-      //$("#progress_bar_container").modal();
       url = "/loading";
       $('input[name=method]').val("reaper");
       $('input[name=selected_chr]').val($('#chr_reaper').val());
@@ -214,10 +217,9 @@
       $('input[name=manhattan_plot]').val($('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);
+      $('input[name=tool_used]').val("Mapping");
+      $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
       return submit_special(url);
-      //return do_ajax_post(url, form_data);
     };
   })(this));
 
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 75b65b5a..a000b07d 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -24,6 +24,8 @@
             <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
             {% endif %}
             <input type="hidden" name="collection_name" id="collection_name" value="{{ collection_name }}" />
+            <input type="hidden" name="tool_used" value="" />
+            <input type="hidden" name="form_url" value="" />
             <input type="hidden" name="trait_list" id="trait_list" value= "
             {% for this_trait in trait_obs %}
                 {{ this_trait.name }}:{{ this_trait.dataset.name }},
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 2b5a7f33..427dacc9 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -21,6 +21,8 @@
 
         <div>
           <form id="correlation_form" target="_blank" action="/corr_matrix" method="post">
+            <input type="hidden" name="tool_used" value="" />
+            <input type="hidden" name="form_url" value="" />
             <input type="hidden" name="trait_list" id="trait_list" value= "
             {% for this_trait in trait_list %}
                 {{ this_trait.name }}:{{ this_trait.dataset }},
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index 68880829..3abac194 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -12,8 +12,8 @@
         <div>
             <h3>
                 The following heatmap is a work in progress. The heatmap for each trait runs horizontally (as opposed to vertically in GeneNetwork 1),
-                and hovering over a given trait's heatmap track will display its corresponding QTL chart below. Black on the heatmap corresponds with a 
-                low positive or negative z-score (darker when closer to 0), while light blue and yellow correspond to high negative and positive z-scores respectively. 
+                and hovering over a given trait's heatmap track will display its corresponding QTL chart below. White on the heatmap corresponds with a
+                low positive or negative z-score (darker when closer to 0), while light blue and red correspond to high negative and positive z-scores respectively.
             </h3>
         </div>
         <div id="chart_container">
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 99fa4a89..25560249 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -1,6 +1,6 @@
-<title>Loading Mapping Results</title>
+<title>Loading {{ start_vars.tool_used }} Results</title>
 <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
-<form method="post" action="/run_mapping" name="loading_form" id="loading_form" class="form-horizontal">
+<form method="post" action="" name="loading_form" id="loading_form" class="form-horizontal">
   {% for key, value in start_vars.iteritems() %}
   <input type="hidden" name="{{ key }}" value="{{ value }}">
   {% endfor %}
@@ -8,7 +8,7 @@
     <div>
       <div style="min-height: 80vh; display: flex; align-items: center;">
         <div style="margin-bottom: 10px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;">
-        <h1>Loading&nbsp;Mapping&nbsp;Results...</h1>
+        <h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
         </div>
         <div class="progress center-block" style="margin-top: 5px; margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
           <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
@@ -20,5 +20,7 @@
 <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
 <script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
 <script  type="text/javascript">
+
+$("#loading_form").attr("action", "{{ start_vars.form_url }}");
 $("#loading_form").submit();
 </script>
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/loading_correlation.html b/wqflask/wqflask/templates/loading_correlation.html
deleted file mode 100644
index 2017c3de..00000000
--- a/wqflask/wqflask/templates/loading_correlation.html
+++ /dev/null
@@ -1,24 +0,0 @@
-<title>Loading Correlation Results</title>
-<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
-<form method="post" action="/corr_compute" name="loading_form" id="loading_form" class="form-horizontal">
-  {% for key, value in start_vars.iteritems() %}
-  <input type="hidden" name="{{ key }}" value="{{ value }}">
-  {% endfor %}
-  <div class="container">
-    <div>
-      <div style="min-height: 80vh; display: flex; align-items: center;">
-        <div style="margin-bottom: 10px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;">
-        <h1>Loading&nbsp;Correlation&nbsp;Results...</h1>
-        </div>
-        <div class="progress center-block" style="margin-top: 5px; margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
-          <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
-        </div>
-      </div>
-    </div>
-  </div>
-</form>
-<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
-<script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
-<script  type="text/javascript">
-$("#loading_form").submit();
-</script>
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 5f529edb..a0ef4ab4 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -51,6 +51,8 @@
 
         <div>
           <form id="trait_submission_form" target="_blank" action="/corr_matrix" method="post">
+            <input type="hidden" name="tool_used" value="" />
+            <input type="hidden" name="form_url" value="" />
             <input type="hidden" name="trait_list" id="trait_list" value= "
             {% for this_trait in trait_list %}
                 {{ this_trait.name }}:{{ this_trait.dataset }},
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index d7d85741..3bd57f89 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -32,6 +32,9 @@
         </div>
 
         <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}">
+        <input type="hidden" name="tool_used" value="">
+        <input type="hidden" name="form_url" value="">
+        <input type="hidden" name="wanted_inputs" value="">
         <input type="hidden" name="genofile" value="">
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3aea2541..67e83366 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -550,58 +550,17 @@ def mapping_results_container_page():
 def loading_page():
     logger.info(request.url)
     initial_start_vars = request.form
-    logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
-    #temp_uuid = initial_start_vars['temp_uuid']
-    wanted = (
-        'temp_uuid',
-        'trait_id',
-        'dataset',
-        'method',
-        'trimmed_markers',
-        'selected_chr',
-        'chromosomes',
-        'mapping_scale',
-        'score_type',
-        'suggestive',
-        'significant',
-        'num_perm',
-        'permCheck',
-        'perm_output',
-        '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'
-    )
     start_vars_container = {}
-    start_vars = {}
-    for key, value in initial_start_vars.iteritems():
-        if key in wanted or key.startswith(('value:')):
-            start_vars[key] = value
-
-    start_vars_container['start_vars'] = start_vars
+    if 'wanted_inputs' in initial_start_vars:
+        wanted = initial_start_vars['wanted_inputs'].split(",")
+        start_vars = {}
+        for key, value in initial_start_vars.iteritems():
+            if key in wanted or key.startswith(('value:')):
+                start_vars[key] = value
+
+        start_vars_container['start_vars'] = start_vars
+    else:
+        start_vars_container['start_vars'] = initial_start_vars
     rendered_template = render_template("loading.html", **start_vars_container)
 
     return rendered_template
@@ -773,40 +732,6 @@ def network_graph_page():
     else:
         return render_template("empty_collection.html", **{'tool':'Network Graph'})
 
-@app.route("/corr_loading", methods=('POST',))
-def corr_loading_page():
-    logger.info(request.url)
-    initial_start_vars = request.form
-    logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
-    #temp_uuid = initial_start_vars['temp_uuid']
-    wanted = (
-        'corr_type',
-        'trait_id',
-        'dataset',
-        'group',
-        'corr_sample_method',
-        'corr_samples_group',
-        'corr_dataset',
-        'min_expr',
-        'corr_return_results',
-        'loc_chr',
-        'min_loc_mb',
-        'max_loc_mb',
-        'p_range_lower',
-        'p_range_upper'
-    )
-    start_vars_container = {}
-    start_vars = {}
-    for key, value in initial_start_vars.iteritems():
-        if key in wanted or key.startswith(('value:')):
-            start_vars[key] = value
-
-    start_vars_container['start_vars'] = start_vars
-    rendered_template = render_template("loading_correlation.html", **start_vars_container)
-
-    return rendered_template
-
-
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
     logger.info("In corr_compute, request.form is:", pf(request.form))