Merge branch 'development' of github.com:genenetwork/genenetwork2

8 files changed, 163 insertions, 69 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 6cabadb1..e37a838f 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -54,7 +54,7 @@ from pprint import pformat as pf
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, dataset_type = None):
+def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
         #dataset_type = get_dataset_type_from_json(dataset_name)
@@ -71,7 +71,7 @@ def create_dataset(dataset_name, dataset_type = None):
 
     dataset_ob = DS_NAME_MAP[dataset_type]
     dataset_class = globals()[dataset_ob]
-    return dataset_class(dataset_name)
+    return dataset_class(dataset_name, get_samplelist)
 
 
 #def get_dataset_type_from_json(dataset_name):
@@ -501,7 +501,7 @@ class DataSet(object):
 
     """
 
-    def __init__(self, name):
+    def __init__(self, name, get_samplelist = True):
 
         assert name, "Need a name"
         self.name = name
@@ -517,7 +517,8 @@ class DataSet(object):
         self.retrieve_other_names()
         
         self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
-        self.group.get_samplelist()
+        if get_samplelist == True:
+             self.group.get_samplelist()
         self.species = species.TheSpecies(self)
 
 
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index ff149ba3..acff38d9 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -67,7 +67,7 @@ class GeneralTrait(object):
         # Todo: These two lines are necessary most of the time, but perhaps not all of the time
         # So we could add a simple if statement to short-circuit this if necessary
         self.retrieve_info(get_qtl_info=get_qtl_info)
-        if kw.get('get_sample_info') != False:
+        if get_sample_info != False:
             self.retrieve_sample_data()
         
         
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index a6efb47f..4179dc48 100755
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -46,7 +46,7 @@ class GSearch(object):
 			self.trait_list = []
 			with Bench("Creating trait objects"):
 				for line in re:
-					dataset = create_dataset(line[3], "ProbeSet")
+					dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
 					trait_id = line[4]
 					#with Bench("Building trait object"):
 					this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 56286ee6..e9052290 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -295,10 +295,13 @@ class MarkerRegression(object):
         self.SNPChecked  = False
         self.draw2X = False
         self.lrsMax = 0
-        if 'mb_range' in start_vars:
-            self.startMb, self.endMb = [float(x) for x in start_vars['mb_range'].split(',')]
+        if 'startMb' in start_vars:
+            self.startMb = start_vars['startMb']
         else:
             self.startMb = -1
+        if 'endMb' in start_vars:
+            self.endMb = start_vars['endMb']
+        else:
             self.endMb = -1
 
         #self.additiveChecked = fd.formdata.getvalue('additiveCheck')
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
index 472ec12d..88003f4e 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
@@ -46,9 +46,5 @@ create_lod_chart = ->
                       .transition().duration(500).attr("r", r)
 
 $ ->
-    #window.setTimeout ( ->
-    #    console.log(js_data)
-    #), 1000
-    #window.setTimeout(create_lod_chart(), 1000)
     root.create_lod_chart = create_lod_chart
 
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js
index c756d842..778eed3a 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.js
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js
@@ -1,45 +1,50 @@
-// Generated by CoffeeScript 1.9.2
-(function() {
-  var create_lod_chart;
+//var create_lod_chart;
 
-  create_lod_chart = function() {
-    var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
-    h = 500;
-    w = 1200;
-    margin = {
-      left: 60,
-      top: 40,
-      right: 40,
-      bottom: 40,
-      inner: 5
-    };
-    halfh = h + margin.top + margin.bottom;
-    totalh = halfh * 2;
-    totalw = w + margin.left + margin.right;
-    console.log("js_data:", js_data);
-    mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").mappingScale(js_data.mapping_scale).manhattanPlot(js_data.manhattan_plot);
-    data = js_data.json_data;
-    d3.select("div#topchart").datum(data).call(mychart);
-    chrrect = mychart.chrSelect();
-    chrrect.on("mouseover", function() {
-      return d3.select(this).attr("fill", "#E9CFEC");
-    }).on("mouseout", function(d, i) {
-      return d3.select(this).attr("fill", function() {
-        if (i % 2) {
-          return "#F1F1F9";
-        }
-        return "#FBFBFF";
-      });
-    });
-    return mychart.markerSelect().on("click", function(d) {
-      var r;
-      r = d3.select(this).attr("r");
-      return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
-    });
+create_lod_chart = function() {
+  var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
+  h = 500;
+  w = 1200;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
   };
-
-  $(function() {
-    return root.create_lod_chart = create_lod_chart;
+  halfh = h + margin.top + margin.bottom;
+  totalh = halfh * 2;
+  totalw = w + margin.left + margin.right;
+  if ('additive' in js_data) {
+    additive = js_data.additive;
+  } else {
+    additive = false;
+  }
+  console.log("js_data:", js_data);
+  mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot);
+  data = js_data.json_data;
+  d3.select("div#topchart").datum(data).call(mychart);
+  chrrect = mychart.chrSelect();
+  chrrect.on("mouseover", function() {
+    return d3.select(this).attr("fill", "#E9CFEC");
+  }).on("mouseout", function(d, i) {
+    return d3.select(this).attr("fill", function() {
+      if (i % 2) {
+        return "#F1F1F9";
+      }
+      return "#FBFBFF";
+    });
+  });
+  return mychart.markerSelect().on("click", function(d) {
+    var r;
+    r = d3.select(this).attr("r");
+    return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
   });
+};
+
+create_lod_chart()
 
-}).call(this);
+/*
+$(function() {
+  return root.create_lod_chart = create_lod_chart;
+});
+*/
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index dd8ae236..4eb5862a 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -3,22 +3,23 @@
 {% block 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/new/css/marker_regression.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 {% from "base_macro.html" import header %}
 {% block content %}
-    {{ header("Whole Genome Mapping Results",
-        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
-
     <div class="container">
         <form method="post" target="_blank" action="/marker_regression" name="marker_regression" id="marker_regression_form">
         <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
+        <input type="hidden" name="method" value="{{ mapping_method }}">
+        {% if mapping_method != "gemma" %}
         {% for sample in dataset.group.samplelist %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
         <input type="hidden" name="maf">
-        <input type="hidden" name="method" value="{{ mapping_method }}">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
         <input type="hidden" name="mb_range" value="{{ startMb|string + "," + endMb|string }}">
         <input type="hidden" name="manhattan_plot">
@@ -28,13 +29,80 @@
         <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}">
         <input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}">
         <input type="hidden" name="pair_scan" value="{{ pair_scan }}">
-        <div id="chart_container">
-            <div class="qtlcharts" id="topchart">
-                {{ gifmap|safe }}
-                <img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+        {% endif %}
+        
+        <div class="container">
+          <div class="col-xs-5">
+              <h2>Map Viewer: Whole Genome</h2><br>
+              <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br>
+              <b>Database:</b> {{ dataset.fullname }}<br>
+              {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.name }}</a><br>
+              {% if dataset.type == "ProbeSet" %}
+              <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br>
+              <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb
+              {% endif %}
+          </div>
+          {% if mapping_method != "gemma" %}
+          <div id="gn1_map_options" class="col-xs-5" style="border:2px solid black; padding: 10px; margin: 10px;">
+            <div class="col-xs-7" style="padding-left: 0px;">
+              <table>
+                <tr>
+                  <td><b>Chr:&nbsp;</b></td>
+                  <td>
+                    <select name="chromosomes" size="1">
+                        {% for chr in ChrList %}
+                        <option value="{{ chr[1] }}">{{ chr[0] }}</option>
+                        {% endfor %}
+                    </select>&nbsp;
+                    <button type="button" class="btn btn-primary">Remap</button>
+                  </td>
+                </tr>
+                <tr>
+                  <td><b>View:&nbsp;</b></td>
+                  <td>
+                    <input type="text" name="startMb"
+                  </td>
+                </tr>
+              </table>
+              </div>
+              <div class="col-xs-3">
+              </div>
+          </div>
+        </div>
+        {% endif %}
+        
+ 
+        <div class="tabbable" style="margin: 10px;">
+          <ul class="nav nav-tabs">
+            {% if mapping_method != "gemma" %}
+            <li id="gn1_map_tab">
+              <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a>
+            </li>
+            {% endif %}
+            <li id="vector_map_tab">
+              <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
+            </li>
+          </ul>
+          <div class="tab-content">
+            {% if mapping_method != "gemma" %}
+            <div class="tab-pane active" id="gn1_map">
+              <div class="qtlcharts">
+                  {{ gifmap|safe }}
+                  <img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+              </div>
             </div>
+            {% endif %}
+            <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
+              <div id="chart_container">
+                <div class="qtlcharts" id="topchart"></div>
+              </div>
+            </div>
+          </div>
         </div>
+
         </form>
+        
+        {% if mapping_method != "gemma" %} 
         <div style="width:48%;">
             <h2>
                 Results
@@ -87,6 +155,7 @@
                 </tbody>
             </table>
         </div>
+        {% endif %}
     </div>
 
     <!-- End of body -->
@@ -95,8 +164,10 @@
 
 {% block js %}  
 
+    <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
@@ -111,6 +182,11 @@
         js_data = {{ js_data | safe }}
     </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/lod_chart.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
+    
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
             console.time("Creating table");
@@ -137,7 +213,15 @@
             } );
             console.timeEnd("Creating table");
 
-        });
+            $('#vector_map_tab').click(function(){
+                $('div#gn1_map_options').hide();
+            });
+
+            $('#gn1_map_tab').click(function(){
+                $('div#gn1_map_options').show();
+            });
+
+            });
 
         chrView = function(this_chr, chr_mb_list) {
             $('input[name=selected_chr]').val(this_chr + 1)
@@ -148,10 +232,10 @@
 
         rangeView = function(this_chr, start_mb, end_mb) {
             $('input[name=selected_chr]').val(this_chr)
-            $('input[name=mb_range]').val(start_mb + "," + end_mb)
-            
-            console.log("mb_range:", $('input[name=mb_range]').val())
-            
+            $('input[name=startMb]').val(start_mb)
+            $('input[name=endMb]').val(end_mb)
+            //$('input[name=mb_range]').val(start_mb + "," + end_mb)
+
             return $('#marker_regression_form').submit();
         };
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 65b6dae4..17845826 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -352,7 +352,8 @@ def marker_regression_page():
         'control_marker_db',
         'do_control',
         'pair_scan',
-        'mb_range',
+        'startMb',
+        'endMb',
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno'
     )
@@ -391,7 +392,8 @@ def marker_regression_page():
         #for item in template_vars.__dict__.keys():
         #    print("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
         
-        gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
+        if start_vars['method'] != "gemma":
+            gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
 
         #qtl_length = len(result['js_data']['qtl_results'])
         #print("qtl_length:", qtl_length)
@@ -414,7 +416,10 @@ def marker_regression_page():
             rendered_template = render_template("pair_scan_results.html", **result)
         else:
             #rendered_template = render_template("marker_regression.html", **result)
-            rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
+            if start_vars['method'] != "gemma":
+                rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
+            else:
+                rendered_template = render_template("marker_regression_gn1.html", **result)
 
     return rendered_template