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

8 files changed, 21 insertions, 6 deletions

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index cd4c6fdc..9227d641 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -15,7 +15,7 @@ import urlparse
 
 import simplejson as json
 
-from sqlalchemy import orm
+#from sqlalchemy import orm
 
 #from redis import StrictRedis
 import redis
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 5ea32e1f..5ea32e1f 100755..100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index 3eb6295f..1eeb6e73 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -46,7 +46,7 @@
         chart.pointRange([50, 50]);
         chart.legend.updateState(false);
         chart.xAxis.axisLabel("Theoretical quantiles").tickFormat(d3.format('.02f'));
-        chart.yAxis.axisLabel("Sample quantiles").tickFormat(d3.format('.02f'));
+        //chart.yAxis.axisLabel("Sample quantiles").tickFormat(d3.format('.02f'));
         chart.tooltipContent(function(obj) {
           return '<b style="font-size: 20px">' + obj.point.name + '</b>';
         });
@@ -66,15 +66,20 @@
         sorted_names = names.sort(function(x, y) {
           return all_samples[x].value - all_samples[y].value;
         });
+        max_decimals = 0
         sorted_values = (function() {
           var j, len, results;
           results = [];
           for (j = 0, len = sorted_names.length; j < len; j++) {
             x = sorted_names[j];
             results.push(all_samples[x].value);
+            if (all_samples[x].value.countDecimals() > max_decimals) {
+                max_decimals = all_samples[x].value.countDecimals()-1
+            }
           }
           return results;
         })();
+        chart.yAxis.axisLabel("Sample quantiles").tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
         sw_result = ShapiroWilkW(sorted_values);
         W = sw_result.w.toFixed(3);
         pvalue = sw_result.p.toFixed(3);
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 34d1a139..589b1074 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -521,5 +521,10 @@
     $('#reset').click(edit_data_change);
     return console.log("end");
   });
+  
+  Number.prototype.countDecimals = function () {
+    if(Math.floor(this.valueOf()) === this.valueOf()) return 0;
+      return this.toString().split(".")[1].length || 0; 
+  }
 
 }).call(this);
diff --git a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
index 726f76c3..694b9218 100644
--- a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
+++ b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.css
@@ -16,7 +16,7 @@
 }

 

 .nvd3 .nv-axis.nv-x path.domain {

-    stroke-opacity: 0;

+    stroke-opacity: 1;

 }

 

 .nvd3 .nv-axis line {

diff --git a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.js b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.js
index b11ce58f..4d8b9d65 100644
--- a/wqflask/wqflask/static/new/packages/nvd3/nv.d3.js
+++ b/wqflask/wqflask/static/new/packages/nvd3/nv.d3.js
@@ -1556,7 +1556,7 @@ nv.models.axis = function() {
         , width = 75 //only used for tickLabel currently
         , height = 60 //only used for tickLabel currently
         , axisLabelText = null
-        , showMaxMin = true //TODO: showMaxMin should be disabled on all ordinal scaled axes
+        , showMaxMin = false //TODO: showMaxMin should be disabled on all ordinal scaled axes
         , rotateLabels = 0
         , rotateYLabel = true
         , staggerLabels = false
@@ -7894,7 +7894,8 @@ nv.models.multiBar = function() {
 
                 bars.select('polyline')
                     .attr('fill', 'none')
-                    .attr('stroke', function(d, i, j) { return errorBarColor(d, j, i); })
+                    .attr('stroke', 'black')
+                    //.attr('stroke', function(d, i, j) { return errorBarColor(d, j, i); })
                     .attr('points', function(d,i) {
                         var yerr = getYerr(d,i)
                             , mid = 0.8 * x.rangeBand() / ((stacked ? 1 : data.length) * 2);
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 5e2dc6fa..1890cf3f 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -7,7 +7,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <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" />
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index e16a397d..e334a9aa 100755
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -12,6 +12,7 @@ import os
 import hashlib
 import datetime
 import time
+import logging
 
 import uuid
 import hashlib
@@ -141,6 +142,9 @@ class UserSession(object):
         """Actual sqlalchemy record"""
         # Only look it up once if needed, then store it
         try:
+            logging.basicConfig()
+            logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
+
             # Already did this before
             return self.db_object
         except AttributeError: