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

47 files changed, 119 insertions, 13 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 900e050c..32032ba7 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -363,7 +363,7 @@ class GeneralTrait(object):
                             FROM
                                     Homologene, Species, InbredSet
                             WHERE
-                                    Homologene.GeneId =%s AND
+                                    Homologene.GeneId ='%s' AND
                                     InbredSet.Name = '%s' AND
                                     InbredSet.SpeciesId = Species.Id AND
                                     Species.TaxonomyId = Homologene.TaxonomyId
diff --git a/wqflask/maintenance/__init__.py b/wqflask/maintenance/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/maintenance/__init__.py
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index ddc0ea82..b873e16f 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -31,6 +31,7 @@ import string
 from inspect import isfunction
 from pprint import pformat as pf
 from inspect import stack
+import datetime
 
 from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT
 
@@ -66,7 +67,10 @@ LOG_LEVEL_DEBUG (NYI).
 
     def error(self,*args):
         """Call logging.error for multiple args"""
-        self.collect(self.logger.error,*args)
+        now = datetime.datetime.utcnow()
+        time_str = now.strftime('%H:%M:%S UTC %Y%m%d')
+        l = [time_str]+list(args)
+        self.collect(self.logger.error,*l)
 
     def infof(self,*args):
         """Call logging.info for multiple args lazily"""
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index f2a2eb8c..f28407b3 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -41,6 +41,9 @@ from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMM
 from utility.external import shell
 from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
 class MarkerRegression(object):
 
     def __init__(self, start_vars, temp_uuid):
@@ -197,6 +200,7 @@ class MarkerRegression(object):
 
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
+            logger.info("Running qtlreaper")
             results = self.gen_reaper_results()
         elif self.mapping_method == "plink":
             results = self.run_plink()
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9cef3cec..bc147f75 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -44,6 +44,9 @@ from utility import Plot
 from wqflask.interval_analyst import GeneUtil
 from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
 
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
 #########################################
 #      Inteval Mapping Plot Page
 #########################################
@@ -159,6 +162,7 @@ class MarkerRegression(object):
 
         #if not self.openMysql():
         #    return
+        logger.info("Running qtlreaper")
 
         #helper_functions.get_species_dataset_trait(self, start_vars)
 
@@ -211,7 +215,7 @@ class MarkerRegression(object):
             self.plotScale = start_vars['mapping_scale']
         else:
             self.plotScale = "physic"
-            
+
         self.manhattan_plot = start_vars['manhattan_plot']
 
         if 'permCheck' in start_vars.keys():
@@ -514,13 +518,13 @@ class MarkerRegression(object):
 
             if self.dataset.group.species == "mouse":
                 if self.selectedChr == 20:
-                    chrName = "X" 
+                    chrName = "X"
                 else:
                     chrName = self.selectedChr
                 self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
             elif self.dataset.group.species == "rat":
                 if self.selectedChr == 21:
-                    chrName = "X" 
+                    chrName = "X"
                 else:
                     chrName = self.selectedChr
                 self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
@@ -860,7 +864,7 @@ class MarkerRegression(object):
         BootCoord = []
         i = 0
         startX = xLeftOffset
-     
+
         if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
             for j, _chr in enumerate(self.genotype):
                 BootCoord.append( [])
@@ -883,8 +887,8 @@ class MarkerRegression(object):
                         else:
                             Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
                         BootCoord[-1].append([Xc, self.bootResult[i]])
-                    i += 1   
-                    
+                    i += 1
+
         #reduce bootResult
         if self.selectedChr > -1:
             maxBootBar = 80.0
@@ -1851,7 +1855,7 @@ class MarkerRegression(object):
                 if j == 0:
                     canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor)
                 startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
-                
+
             centimorganLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0)
             canvas.drawString("Centimorgans", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=centimorganLabelFont))/2,
                     strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=pid.black)
@@ -2963,7 +2967,7 @@ class MarkerRegression(object):
                     chr_as_int = 20
                 else:
                     chr_as_int = int(theGO["Chromosome"]) - 1
-                    
+
                 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
                 #geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
                 geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
diff --git a/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif b/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif
new file mode 100644
index 00000000..2c68b5ee
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/Wild-Type-Mouse.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif b/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif
new file mode 100644
index 00000000..e9d38277
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-aliens-29.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif b/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif
new file mode 100644
index 00000000..94e11847
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-angels-04.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif
new file mode 100644
index 00000000..7e6ec9a3
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-cats-016.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif
new file mode 100644
index 00000000..af7ef655
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-cats-031.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif
new file mode 100644
index 00000000..89c79ddf
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-03.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif b/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif
new file mode 100644
index 00000000..7530d180
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-cell-phones-16.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif
new file mode 100644
index 00000000..afb05c62
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-13.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif
new file mode 100644
index 00000000..f5b4a563
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-28.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif
new file mode 100644
index 00000000..7258e594
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-32.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif
new file mode 100644
index 00000000..ed1f8722
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-42.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif
new file mode 100644
index 00000000..f58d69f1
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-60.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif
new file mode 100644
index 00000000..5d5b4fdf
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-64.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif
new file mode 100644
index 00000000..b4b10845
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-65.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-72.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-72.gif
new file mode 100644
index 00000000..e60cb4fe
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-72.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-74.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-74.gif
new file mode 100644
index 00000000..bd7b72f3
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-74.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-computers-75.gif b/wqflask/wqflask/static/gif/error/animated-gifs-computers-75.gif
new file mode 100644
index 00000000..916d6b33
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-computers-75.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-construction-sites-038.gif b/wqflask/wqflask/static/gif/error/animated-gifs-construction-sites-038.gif
new file mode 100644
index 00000000..0ec782c4
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-construction-sites-038.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif
new file mode 100644
index 00000000..9515c18a
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-04.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-14.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-14.gif
new file mode 100644
index 00000000..f1e2e1f5
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-14.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-18.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-18.gif
new file mode 100644
index 00000000..572849d5
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-18.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-47.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-47.gif
new file mode 100644
index 00000000..d808c9ee
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-47.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-dogs-50.gif b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-50.gif
new file mode 100644
index 00000000..9865ee45
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-dogs-50.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif b/wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif
new file mode 100644
index 00000000..ee9c113d
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-lava-lamps-01.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif b/wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif
new file mode 100644
index 00000000..5ca2ee5c
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-mice-02.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif b/wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif
new file mode 100644
index 00000000..7cb361e4
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-mice-09.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-mice-24.gif b/wqflask/wqflask/static/gif/error/animated-gifs-mice-24.gif
new file mode 100644
index 00000000..96a26450
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-mice-24.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif
new file mode 100644
index 00000000..62de166c
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-063.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-068.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-068.gif
new file mode 100644
index 00000000..3550e978
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-068.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-134.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-134.gif
new file mode 100644
index 00000000..954ab614
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-134.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-211.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-211.gif
new file mode 100644
index 00000000..596174d7
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-211.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-smileys-234.gif b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-234.gif
new file mode 100644
index 00000000..5aba636b
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-smileys-234.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-001.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-001.gif
new file mode 100644
index 00000000..7896ff1f
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-001.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-002.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-002.gif
new file mode 100644
index 00000000..89da6441
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-002.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-005.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-005.gif
new file mode 100644
index 00000000..b7887630
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-005.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-012.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-012.gif
new file mode 100644
index 00000000..f6697d02
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-012.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-056.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-056.gif
new file mode 100644
index 00000000..2b2496a4
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-056.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-059.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-059.gif
new file mode 100644
index 00000000..f2188656
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-059.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-060.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-060.gif
new file mode 100644
index 00000000..aa8f7bd3
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-060.gif
diff --git a/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif
new file mode 100644
index 00000000..473212e4
--- /dev/null
+++ b/wqflask/wqflask/static/gif/error/animated-gifs-stickmen-069.gif
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
new file mode 100644
index 00000000..7ab2bf2f
--- /dev/null
+++ b/wqflask/wqflask/templates/error.html
@@ -0,0 +1,61 @@
+{% extends "base.html" %}
+{% block title %}Error: {{message}}{% endblock %}
+{% block content %}
+<!-- Start of body -->
+
+<div class="col-md-8">
+<div class="form-group has-error">
+  <div class="control-label" for="inputError1">
+
+    <img src="/static/gif/error/{{ error_image }}">
+
+    <h1>ERROR</h1>
+
+    <p>
+      This error is not what we wanted to see. Unfortunately errors
+      are part of all software systems and we need to resolve this
+      together.
+    </p>
+    <p>
+      <b>It is important to report this ERROR so we can fix it for everyone</b>.
+    </p>
+
+    <p>
+      Report to the GeneNetwork team by recording the steps you take
+      to reproduce this ERROR. Next to those steps, copy-paste below
+      stack trace, either as
+      a <a href="https://github.com/genenetwork/genenetwork2/issues/new">new
+      issue</a> or E-mail this full page to one of the developers
+      directly.
+    </p>
+  </div>
+
+  <p>
+  (GeneNetwork error: {{message[:128]}})
+  </p>
+
+  <pre>
+    {{ stack[0] }}
+    {{ message }} (error)
+    {{ stack[-3] }}
+    {{ stack[-2] }}
+  </pre>
+
+  <p>
+    To check if this already a known issue, search the
+    <a href="https://github.com/genenetwork/genenetwork2/issues">issue
+      tracker</a>.
+  </p>
+
+  <a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
+  <div id="Stack" class="collapse">
+    <pre>
+      {% for line in stack %} {{ line }}
+      {% endfor %}
+    </pre>
+  </div>
+</div>
+</div>
+
+
+{% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 41e2c7be..cf316bee 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -4,6 +4,11 @@
 
 from __future__ import absolute_import, division, print_function
 
+import traceback # for error page
+import os        # for error gifs
+import random    # for random error gif
+import datetime  # for errors
+import time      # for errors
 import sys
 import csv
 import xlsxwriter
@@ -26,7 +31,7 @@ import base64
 import array
 import sqlalchemy
 from wqflask import app
-from flask import g, Response, request, render_template, send_from_directory, jsonify, redirect
+from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect
 from wqflask import search_results
 from wqflask import gsearch
 from wqflask import update_search_results
@@ -58,6 +63,8 @@ from wqflask import user_manager
 from wqflask import collect
 from wqflask.database import db_session
 
+import werkzeug
+
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
@@ -82,6 +89,31 @@ def shutdown_session(exception=None):
 #    from wqflask import tracer
 #    tracer.turn_on()
 
+@app.errorhandler(Exception)
+def handle_bad_request(e):
+    err_msg = str(e)
+    logger.error(err_msg)
+    logger.error(request.url)
+    # get the stack trace and send it to the logger
+    exc_type, exc_value, exc_traceback = sys.exc_info()
+    logger.error(traceback.format_exc())
+    now = datetime.datetime.utcnow()
+    time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
+    formatted_lines = [request.url + " ("+time_str+")"]+traceback.format_exc().splitlines()
+
+    # Handle random animations
+    # Use a cookie to have one animation on refresh
+    animation = request.cookies.get(err_msg[:64])
+    if not animation:
+        list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
+        animation = random.choice(list)
+
+    resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation))
+
+    # logger.error("Set cookie %s with %s" % (err_msg, animation))
+    resp.set_cookie(err_msg[:64],animation)
+    return resp
+
 @app.route("/")
 def index_page():
     logger.info("Sending index_page")
@@ -395,6 +427,7 @@ def mapping_results_container_page():
 @app.route("/marker_regression", methods=('POST',))
 def marker_regression_page():
     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 = (
         'trait_id',
@@ -432,11 +465,11 @@ def marker_regression_page():
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno'
     )
-    logger.info("Marker regression called with initial_start_vars:", initial_start_vars)
     start_vars = {}
     for key, value in initial_start_vars.iteritems():
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
+    logger.debug("Marker regression called with start_vars:", start_vars)
 
     version = "v3"
     key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
@@ -546,7 +579,7 @@ def network_graph_page():
         return render_template("network_graph.html", **template_vars.__dict__)
     else:
         return render_template("empty_collection.html", **{'tool':'Network Graph'})
-    
+
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
     logger.info("In corr_compute, request.form is:", pf(request.form))