Added change to remove qtlreaper use from correlation and prevent the inconsistent error

Added change to change maf depending upon number of sample values

Committing in-process changes to how sample table is built on trait page (to make it look better and more compact)
:

6 files changed, 43 insertions, 16 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 9f3f7982..0b2875cc 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -99,7 +99,7 @@ class CorrelationResults(object):
             else:
                 helper_functions.get_species_dataset_trait(self, start_vars)
 
-            self.dataset.group.read_genotype_file()
+            #self.dataset.group.read_genotype_file()
 
             corr_samples_group = start_vars['corr_samples_group']
 
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f75302f6..34447853 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -188,13 +188,23 @@ class ShowTrait(object):
 
         self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, self.has_num_cases)
 
-        #ZS: Needed to know whether to display bar chart
+        #ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width
         self.num_values = 0
+        max_samplename_width = 1
         for group in self.sample_groups:
             for sample in group.sample_list:
+                if len(sample.name) > max_samplename_width:
+                    max_samplename_width = len(sample.name)
                 if sample.display_value != "x":
                     self.num_values += 1
 
+        sample_column_width = max_samplename_width * 8
+
+        if self.num_values >= 500:
+            self.maf = 0.01
+        else:
+            self.maf = 0.05
+
         trait_symbol = None
         if not self.temp_trait:
             if self.this_trait.symbol:
@@ -208,6 +218,7 @@ class ShowTrait(object):
                        sample_lists = sample_lists,
                        attribute_names = self.sample_groups[0].attributes,
                        num_values = self.num_values,
+                       sample_column_width = sample_column_width,
                        temp_uuid = self.temp_uuid)
         self.js_data = js_data
 
@@ -368,15 +379,14 @@ def get_table_widths(sample_groups, has_num_cases=False):
     if len(sample_groups) > 1:
         stats_table_width = 450
 
-    trait_table_width = 25
+    trait_table_width = 380
     if sample_groups[0].se_exists():
-        trait_table_width += 15
+        trait_table_width += 70
     if has_num_cases:
-        trait_table_width += 5
-    if (trait_table_width + len(sample_groups[0].attributes)*10) > 100:
-        trait_table_width = 100
-    else:
-        trait_table_width += len(sample_groups[0].attributes)*10
+        trait_table_width += 30
+    trait_table_width += len(sample_groups[0].attributes)*40
+
+    trait_table_width = str(trait_table_width) + "px"
 
     return stats_table_width, trait_table_width
 
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 135a7643..69c4418a 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -12,4 +12,21 @@ div.sample_group {
 
 .js-plotly-plot .plotly .modebar {
   left: 100px;
+}
+
+table.dataTable thead th{
+  border-right: 1px solid white;
+  color: white;
+  background-color: #369;
+}
+
+table.dataTable thead .sorting_asc {
+  background-image: url("../packages/DataTables/images/sort_asc_disabled.png");
+}
+table.dataTable thead .sorting_desc {
+  background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
+}
+
+table.dataTable tbody td {
+  padding: 3px 20px 1px 10px;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index ef05e321..8726226c 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -1,7 +1,6 @@
 {% extends "base.html" %}
 {% block title %}Trait Data and Analysis{% endblock %}
 {% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/bar_chart.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
@@ -12,6 +11,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.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/show_trait.css" />
 
 {% endblock %}
 {% block content %} <!-- Start of body -->
@@ -192,7 +192,7 @@
                     "columns": [
                         { "bSortable": false },
                         { "type": "natural" },
-                        { "type": "natural", "width": "25%" },
+                        { "type": "natural", "width": js_data.sample_column_width},
                         { "type": "cust-txt" },
                         { "bSortable": false },
                         { "type": "cust-txt" }{% if has_num_cases %},
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index bd40946d..7ac4b2c0 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -86,11 +86,11 @@
     <!--<div id="edit_sample_lists">-->
     {% for sample_type in sample_groups %}
         {% set outer_loop = loop %}
-        <div class="sample_group" style="width:{{ trait_table_width }}%;">
+        <div class="sample_group" style="width:{{ trait_table_width }};">
             <h3>{{ sample_type.header }}</h3>
             <hr>
             <div id="table_container">
-            <table class="table-hover table-striped" id="samples_{{ sample_type.sample_group_type }}" style="float: left; width:100%;">
+            <table class="table-hover table-striped cell-border" id="samples_{{ sample_type.sample_group_type }}" style="float: left; width:100%;">
                 <thead>
                     <tr>
                         <th></th>
@@ -98,7 +98,7 @@
                         <th>Sample</th>
                         <th style="text-align: right;">Value</th>
                         {% if sample_type.se_exists() %}
-                        <th>&nbsp;</th>
+                        <th style="padding-left: 3px; padding-right: 3px;">&nbsp;</th>
                         <th style="text-align: right;">SE</th>
                         {% endif %}
                         {% if has_num_cases %}
@@ -134,7 +134,7 @@
                         </td>
         
                         {% if sample_type.se_exists() %}
-                        <td>
+                        <td align="center" style="padding-left: 2px; padding-right: 2px;">
                           ±
                         </td>
         
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 72b3b00b..8e003897 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -54,7 +54,7 @@
                         <div class="mapping_method_fields form-group">
                             <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
-                                <input name="maf_gemma" value="0.05" type="text" class="form-control">
+                                <input name="maf_gemma" value="{{ maf }}" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">