From af330a2aa7b36fd0cf8505eb20fa06d2ed58b86b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 17 Aug 2020 17:41:58 +0300
Subject: Wrap print statements in parentheses

---
 wqflask/utility/svg.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index db13b9d1..6285ea63 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -102,7 +102,7 @@ if use_dom_implementation<>0:
         from xml.dom import implementation
         from xml.dom.ext import PrettyPrint
     except:
-        raise exceptions.ImportError, "PyXML is required for using the dom implementation"
+        raise exceptions.ImportError("PyXML is required for using the dom implementation")
 #The implementation is used for the creating the XML document.
 #The prettyprint module is used for converting the xml document object to a xml file
 
@@ -1018,12 +1018,12 @@ class drawing:
                         PrettyPrint(root,f)
                         f.close()
                 except:
-                    print "Cannot write SVG file: " + filename
+                    print(("Cannot write SVG file: " + filename))
     def validate(self):
         try:
             import xml.parsers.xmlproc.xmlval
         except:
-            raise exceptions.ImportError,'PyXml is required for validating SVG'
+            raise exceptions.ImportError('PyXml is required for validating SVG')
         svg=self.toXml()
         xv=xml.parsers.xmlproc.xmlval.XMLValidator()
         try:
@@ -1031,7 +1031,7 @@ class drawing:
         except:
             raise Exception("SVG is not well formed, see messages above")
         else:
-            print "SVG well formed"
+            print("SVG well formed")
 if __name__=='__main__':
 
 
@@ -1065,4 +1065,4 @@ if __name__=='__main__':
             s.addElement(c)
     d.setSVG(s)
 
-    print d.toXml()
+    print((d.toXml()))
-- 
cgit v1.2.3


From acdc611247c8eaccbba3dec00ad640e10a4c99b1 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 17 Aug 2020 21:45:04 +0300
Subject: Replace "<>" with "!="

* wqflask/utility/svg.py: Use "!=". The operator, "<>" is removed in Python3
---
 wqflask/utility/svg.py | 196 ++++++++++++++++++++++++-------------------------
 1 file changed, 98 insertions(+), 98 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 6285ea63..f737d2f2 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -97,7 +97,7 @@ use_dom_implementation=0
 
 
 import exceptions
-if use_dom_implementation<>0:
+if use_dom_implementation!=0:
     try:
         from xml.dom import implementation
         from xml.dom.ext import PrettyPrint
@@ -398,22 +398,22 @@ class rect(SVGelement):
     """
     def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args):
         if width==None or height==None:
-            if width<>None:
                 raise ValueError, 'height is required'
-            if height<>None:
                 raise ValueError, 'width is required'
+            if width!=None:
+            if height!=None:
             else:
                 raise ValueError, 'both height and width are required'
         SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
-        if x<>None:
+        if x!=None:
             self.attributes['x']=x
-        if y<>None:
+        if y!=None:
             self.attributes['y']=y
-        if fill<>None:
+        if fill!=None:
             self.attributes['fill']=fill
-        if stroke<>None:
+        if stroke!=None:
             self.attributes['stroke']=stroke
-        if stroke_width<>None:
+        if stroke_width!=None:
             self.attributes['stroke-width']=stroke_width
 
 class ellipse(SVGelement):
@@ -423,22 +423,22 @@ class ellipse(SVGelement):
     """
     def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args):
         if rx==None or ry== None:
-            if rx<>None:
                 raise ValueError, 'rx is required'
-            if ry<>None:
                 raise ValueError, 'ry is required'
+            if rx!=None:
+            if ry!=None:
             else:
                 raise ValueError, 'both rx and ry are required'
         SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
-        if cx<>None:
+        if cx!=None:
             self.attributes['cx']=cx
-        if cy<>None:
+        if cy!=None:
             self.attributes['cy']=cy
-        if fill<>None:
+        if fill!=None:
             self.attributes['fill']=fill
-        if stroke<>None:
+        if stroke!=None:
             self.attributes['stroke']=stroke
-        if stroke_width<>None:
+        if stroke_width!=None:
             self.attributes['stroke-width']=stroke_width
 
 
@@ -451,15 +451,15 @@ class circle(SVGelement):
         if r==None:
             raise ValueError, 'r is required'
         SVGelement.__init__(self,'circle',{'r':r},**args)
-        if cx<>None:
+        if cx!=None:
             self.attributes['cx']=cx
-        if cy<>None:
+        if cy!=None:
             self.attributes['cy']=cy
-        if fill<>None:
+        if fill!=None:
             self.attributes['fill']=fill
-        if stroke<>None:
+        if stroke!=None:
             self.attributes['stroke']=stroke
-        if stroke_width<>None:
+        if stroke_width!=None:
             self.attributes['stroke-width']=stroke_width
 
 class point(circle):
@@ -478,17 +478,17 @@ class line(SVGelement):
     """
     def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args):
         SVGelement.__init__(self,'line',**args)
-        if x1<>None:
+        if x1!=None:
             self.attributes['x1']=x1
-        if y1<>None:
+        if y1!=None:
             self.attributes['y1']=y1
-        if x2<>None:
+        if x2!=None:
             self.attributes['x2']=x2
-        if y2<>None:
+        if y2!=None:
             self.attributes['y2']=y2
-        if stroke_width<>None:
+        if stroke_width!=None:
             self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
+        if stroke!=None:
             self.attributes['stroke']=stroke
 
 class polyline(SVGelement):
@@ -498,11 +498,11 @@ class polyline(SVGelement):
     """
     def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
         SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args)
-        if fill<>None:
+        if fill!=None:
             self.attributes['fill']=fill
-        if stroke_width<>None:
+        if stroke_width!=None:
             self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
+        if stroke!=None:
             self.attributes['stroke']=stroke
 
 class polygon(SVGelement):
@@ -512,11 +512,11 @@ class polygon(SVGelement):
     """
     def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
         SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args)
-        if fill<>None:
+        if fill!=None:
             self.attributes['fill']=fill
-        if stroke_width<>None:
+        if stroke_width!=None:
             self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
+        if stroke!=None:
             self.attributes['stroke']=stroke
 
 class path(SVGelement):
@@ -526,13 +526,13 @@ class path(SVGelement):
     """
     def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args):
         SVGelement.__init__(self,'path',{'d':str(pathdata)},**args)
-        if stroke<>None:
+        if stroke!=None:
             self.attributes['stroke']=stroke
-        if fill<>None:
+        if fill!=None:
             self.attributes['fill']=fill
-        if stroke_width<>None:
+        if stroke_width!=None:
             self.attributes['stroke-width']=stroke_width
-        if id<>None:
+        if id!=None:
             self.attributes['id']=id
 
 
@@ -543,17 +543,17 @@ class text(SVGelement):
     """
     def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args):
         SVGelement.__init__(self,'text',**args)
-        if x<>None:
+        if x!=None:
             self.attributes['x']=x
-        if y<>None:
+        if y!=None:
             self.attributes['y']=y
-        if font_size<>None:
+        if font_size!=None:
             self.attributes['font-size']=font_size
-        if font_family<>None:
+        if font_family!=None:
             self.attributes['font-family']=font_family
-        if text<>None:
+        if text!=None:
             self.text=text
-        if text_anchor<>None:
+        if text_anchor!=None:
             self.attributes['text-anchor']=text_anchor
 
 
@@ -564,7 +564,7 @@ class textpath(SVGelement):
     """
     def __init__(self,link,text=None,**args):
         SVGelement.__init__(self,'textPath',{'xlink:href':link},**args)
-        if text<>None:
+        if text!=None:
             self.text=text
 
 class pattern(SVGelement):
@@ -576,15 +576,15 @@ class pattern(SVGelement):
     """
     def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args):
         SVGelement.__init__(self,'pattern',**args)
-        if x<>None:
+        if x!=None:
             self.attributes['x']=x
-        if y<>None:
+        if y!=None:
             self.attributes['y']=y
-        if width<>None:
+        if width!=None:
             self.attributes['width']=width
-        if height<>None:
+        if height!=None:
             self.attributes['height']=height
-        if patternUnits<>None:
+        if patternUnits!=None:
             self.attributes['patternUnits']=patternUnits
 
 class title(SVGelement):
@@ -595,7 +595,7 @@ class title(SVGelement):
     """
     def __init__(self,text=None,**args):
         SVGelement.__init__(self,'title',**args)
-        if text<>None:
+        if text!=None:
             self.text=text
 
 class description(SVGelement):
@@ -606,7 +606,7 @@ class description(SVGelement):
     """
     def __init__(self,text=None,**args):
         SVGelement.__init__(self,'desc',**args)
-        if text<>None:
+        if text!=None:
             self.text=text
 
 class lineargradient(SVGelement):
@@ -617,15 +617,15 @@ class lineargradient(SVGelement):
     """
     def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args):
         SVGelement.__init__(self,'linearGradient',**args)
-        if x1<>None:
+        if x1!=None:
             self.attributes['x1']=x1
-        if y1<>None:
+        if y1!=None:
             self.attributes['y1']=y1
-        if x2<>None:
+        if x2!=None:
             self.attributes['x2']=x2
-        if y2<>None:
+        if y2!=None:
             self.attributes['y2']=y2
-        if id<>None:
+        if id!=None:
             self.attributes['id']=id
 
 class radialgradient(SVGelement):
@@ -636,17 +636,17 @@ class radialgradient(SVGelement):
     """
     def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args):
         SVGelement.__init__(self,'radialGradient',**args)
-        if cx<>None:
+        if cx!=None:
             self.attributes['cx']=cx
-        if cy<>None:
+        if cy!=None:
             self.attributes['cy']=cy
-        if r<>None:
+        if r!=None:
             self.attributes['r']=r
-        if fx<>None:
+        if fx!=None:
             self.attributes['fx']=fx
-        if fy<>None:
+        if fy!=None:
             self.attributes['fy']=fy
-        if id<>None:
+        if id!=None:
             self.attributes['id']=id
 
 class stop(SVGelement):
@@ -656,7 +656,7 @@ class stop(SVGelement):
     """
     def __init__(self,offset,stop_color=None,**args):
         SVGelement.__init__(self,'stop',{'offset':offset},**args)
-        if stop_color<>None:
+        if stop_color!=None:
             self.attributes['stop-color']=stop_color
 
 class style(SVGelement):
@@ -675,16 +675,16 @@ class image(SVGelement):
     """
     def __init__(self,url,x=None,y=None,width=None,height=None,**args):
         if width==None or height==None:
-            if width<>None:
                 raise ValueError, 'height is required'
-            if height<>None:
                 raise ValueError, 'width is required'
+            if width!=None:
+            if height!=None:
             else:
                 raise ValueError, 'both height and width are required'
         SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
-        if x<>None:
+        if x!=None:
             self.attributes['x']=x
-        if y<>None:
+        if y!=None:
             self.attributes['y']=y
 
 class cursor(SVGelement):
@@ -704,17 +704,17 @@ class marker(SVGelement):
     """
     def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args):
         SVGelement.__init__(self,'marker',**args)
-        if id<>None:
+        if id!=None:
             self.attributes['id']=id
-        if viewBox<>None:
+        if viewBox!=None:
             self.attributes['viewBox']=_viewboxlist(viewBox)
-        if refx<>None:
+        if refx!=None:
             self.attributes['refX']=refx
-        if refy<>None:
+        if refy!=None:
             self.attributes['refY']=refy
-        if markerWidth<>None:
+        if markerWidth!=None:
             self.attributes['markerWidth']=markerWidth
-        if markerHeight<>None:
+        if markerHeight!=None:
             self.attributes['markerHeight']=markerHeight
 
 class group(SVGelement):
@@ -725,7 +725,7 @@ class group(SVGelement):
     """
     def __init__(self,id=None,**args):
         SVGelement.__init__(self,'g',**args)
-        if id<>None:
+        if id!=None:
             self.attributes['id']=id
 
 class symbol(SVGelement):
@@ -739,9 +739,9 @@ class symbol(SVGelement):
 
     def __init__(self,id=None,viewBox=None,**args):
         SVGelement.__init__(self,'symbol',**args)
-        if id<>None:
+        if id!=None:
             self.attributes['id']=id
-        if viewBox<>None:
+        if viewBox!=None:
             self.attributes['viewBox']=_viewboxlist(viewBox)
 
 class defs(SVGelement):
@@ -770,14 +770,14 @@ class use(SVGelement):
     """
     def __init__(self,link,x=None,y=None,width=None,height=None,**args):
         SVGelement.__init__(self,'use',{'xlink:href':link},**args)
-        if x<>None:
+        if x!=None:
             self.attributes['x']=x
-        if y<>None:
+        if y!=None:
             self.attributes['y']=y
 
-        if width<>None:
+        if width!=None:
             self.attributes['width']=width
-        if height<>None:
+        if height!=None:
             self.attributes['height']=height
 
 
@@ -796,7 +796,7 @@ class view(SVGelement):
     a view can be used to create a view with different attributes"""
     def __init__(self,id=None,**args):
         SVGelement.__init__(self,'view',**args)
-        if id<>None:
+        if id!=None:
             self.attributes['id']=id
 
 class script(SVGelement):
@@ -815,11 +815,11 @@ class animate(SVGelement):
     """
     def __init__(self,attribute,fr=None,to=None,dur=None,**args):
         SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
-        if fr<>None:
+        if fr!=None:
             self.attributes['from']=fr
-        if to<>None:
+        if to!=None:
             self.attributes['to']=to
-        if dur<>None:
+        if dur!=None:
             self.attributes['dur']=dur
 
 class animateMotion(SVGelement):
@@ -829,9 +829,9 @@ class animateMotion(SVGelement):
     """
     def __init__(self,pathdata,dur,**args):
         SVGelement.__init__(self,'animateMotion',**args)
-        if pathdata<>None:
+        if pathdata!=None:
             self.attributes['path']=str(pathdata)
-        if dur<>None:
+        if dur!=None:
             self.attributes['dur']=dur
 
 class animateTransform(SVGelement):
@@ -842,13 +842,13 @@ class animateTransform(SVGelement):
     def __init__(self,type=None,fr=None,to=None,dur=None,**args):
         SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args)
         #As far as I know the attributeName is always transform
-        if type<>None:
+        if type!=None:
             self.attributes['type']=type
-        if fr<>None:
+        if fr!=None:
             self.attributes['from']=fr
-        if to<>None:
+        if to!=None:
             self.attributes['to']=to
-        if dur<>None:
+        if dur!=None:
             self.attributes['dur']=dur
 class animateColor(SVGelement):
     """ac=animateColor(attribute,type,from,to,dur,**args)
@@ -857,13 +857,13 @@ class animateColor(SVGelement):
     """
     def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args):
         SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args)
-        if type<>None:
+        if type!=None:
             self.attributes['type']=type
-        if fr<>None:
+        if fr!=None:
             self.attributes['from']=fr
-        if to<>None:
+        if to!=None:
             self.attributes['to']=to
-        if dur<>None:
+        if dur!=None:
             self.attributes['dur']=dur
 class set(SVGelement):
     """st=set(attribute,to,during,**args)
@@ -872,9 +872,9 @@ class set(SVGelement):
     """
     def __init__(self,attribute,to=None,dur=None,**args):
         SVGelement.__init__(self,'set',{'attributeName':attribute},**args)
-        if to<>None:
+        if to!=None:
             self.attributes['to']=to
-        if dur<>None:
+        if dur!=None:
             self.attributes['dur']=dur
 
 
@@ -896,11 +896,11 @@ class svg(SVGelement):
     """
     def __init__(self,viewBox=None, width=None, height=None,**args):
         SVGelement.__init__(self,'svg',**args)
-        if viewBox<>None:
+        if viewBox!=None:
             self.attributes['viewBox']=_viewboxlist(viewBox)
-        if width<>None:
+        if width!=None:
             self.attributes['width']=width
-        if height<>None:
+        if height!=None:
             self.attributes['height']=height
         self.namespace="http://www.w3.org/2000/svg"
 
-- 
cgit v1.2.3


From 4e10f4bd8fb902810ee033abb8d509ab641308e1 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 18 Aug 2020 17:09:51 +0300
Subject: Apply pep8

* wqflask/utility/svg.py: Apply pep8 to fix indentation error when running
`2to3-3.8 -w .`:
````
RefactoringTool: Can't parse ./wqflask/utility/svg.py: IndentationError: unindent does not match any outer indentation level (<tokenize>, line 403)
````
---
 wqflask/utility/svg.py | 321 ++++++++++++++++++++++++++++---------------------
 1 file changed, 184 insertions(+), 137 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index f737d2f2..c850feb8 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -25,54 +25,56 @@
 # Last updated by GeneNetwork Core Team 2010/10/20
 
 #!/usr/bin/env python
-##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen)
-##All rights reserved.
+# Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen)
+# All rights reserved.
 ##
-##Redistribution and use in source and binary forms, with or without modification,
-##are permitted provided that the following conditions are met:
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
 ##
-##Redistributions of source code must retain the above copyright notice, this
-##list of conditions and the following disclaimer.
+# Redistributions of source code must retain the above copyright notice, this
+# list of conditions and the following disclaimer.
 ##
-##Redistributions in binary form must reproduce the above copyright notice,
-##this list of conditions and the following disclaimer in the documentation and/or
-##other materials provided with the distribution.
+# Redistributions in binary form must reproduce the above copyright notice,
+# this list of conditions and the following disclaimer in the documentation and/or
+# other materials provided with the distribution.
 ##
-##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of
-##its contributors may be used to endorse or promote products derived from this
-##software without specific prior written permission.
+# Neither the name of the Stichting Farmaceutische Kengetallen nor the names of
+# its contributors may be used to endorse or promote products derived from this
+# software without specific prior written permission.
 ##
-##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
-##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# Thanks to Gerald Rosennfellner for his help and useful comments.
 
-##Thanks to Gerald Rosennfellner for his help and useful comments.
-
-__doc__="""Use SVGdraw to generate your SVGdrawings.
+import sys
+import exceptions
+__doc__ = """Use SVGdraw to generate your SVGdrawings.
 
 SVGdraw uses an object model drawing and a method toXML to create SVG graphics
 by using easy to use classes and methods usualy you start by creating a drawing eg
 
     d=drawing()
-    #then you create a SVG root element
+    # then you create a SVG root element
     s=svg()
-    #then you add some elements eg a circle and add it to the svg root element
+    # then you add some elements eg a circle and add it to the svg root element
     c=circle()
-    #you can supply attributes by using named arguments.
+    # you can supply attributes by using named arguments.
     c=circle(fill='red',stroke='blue')
-    #or by updating the attributes attribute:
+    # or by updating the attributes attribute:
     c.attributes['stroke-width']=1
     s.addElement(c)
-    #then you add the svg root element to the drawing
+    # then you add the svg root element to the drawing
     d.setSVG(s)
-    #and finaly you xmlify the drawing
+    # and finaly you xmlify the drawing
     d.toXml()
 
 
@@ -82,7 +84,7 @@ This module was created using the SVG specification of www.w3c.org and the
 O'Reilly (www.oreilly.com) python books as information sources. A svg viewer
 is available from www.adobe.com"""
 
-__version__="1.0"
+__version__ = "1.0"
 
 # there are two possibilities to generate svg:
 # via a dom implementation and directly using <element>text</element> strings
@@ -93,33 +95,34 @@ __version__="1.0"
 # Note that PyXML is required for using the dom implementation.
 # It is also possible to use the standard minidom. But I didn't try that one.
 # Anyway the text based approach is about 60 times faster than using the full dom implementation.
-use_dom_implementation=0
+use_dom_implementation = 0
 
 
-import exceptions
-if use_dom_implementation!=0:
+if use_dom_implementation != 0:
     try:
         from xml.dom import implementation
         from xml.dom.ext import PrettyPrint
     except:
-        raise exceptions.ImportError("PyXML is required for using the dom implementation")
-#The implementation is used for the creating the XML document.
-#The prettyprint module is used for converting the xml document object to a xml file
+        raise exceptions.ImportError(
+            "PyXML is required for using the dom implementation")
+# The implementation is used for the creating the XML document.
+# The prettyprint module is used for converting the xml document object to a xml file
+
+assert sys.version_info[0] >= 2
+if sys.version_info[1] < 2:
+    True = 1
+    False = 0
+    file = open
+
+sys.setrecursionlimit = 50
+# The recursion limit is set conservative so mistakes like s=svg() s.addElement(s)
+# won't eat up too much processor time.
+
+# the following code is pasted form xml.sax.saxutils
+# it makes it possible to run the code without the xml sax package installed
+# To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts
+
 
-import sys
-assert sys.version_info[0]>=2
-if sys.version_info[1]<2:
-    True=1
-    False=0
-    file=open
-
-sys.setrecursionlimit=50
-#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s)
-#won't eat up too much processor time.
-
-#the following code is pasted form xml.sax.saxutils
-#it makes it possible to run the code without the xml sax package installed
-#To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts
 def _escape(data, entities={}):
     """Escape &, <, and > in a string of data.
 
@@ -127,13 +130,14 @@ def _escape(data, entities={}):
     the optional entities parameter.  The keys and values must all be
     strings; each key will be replaced with its corresponding value.
     """
-    #data = data.replace("&", "&amp;")
+    # data = data.replace("&", "&amp;")
     data = data.replace("<", "&lt;")
     data = data.replace(">", "&gt;")
     for chars, entity in entities.items():
         data = data.replace(chars, entity)
     return data
 
+
 def _quoteattr(data, entities={}):
     """Escape and quote an attribute value.
 
@@ -156,96 +160,121 @@ def _quoteattr(data, entities={}):
     return data
 
 
-
 def _xypointlist(a):
     """formats a list of xy pairs"""
-    s=''
-    for e in a: #this could be done more elegant
-        s+=str(e)[1:-1] +'  '
+    s = ''
+    for e in a:  # this could be done more elegant
+        s += str(e)[1:-1] + '  '
     return s
 
+
 def _viewboxlist(a):
     """formats a tuple"""
-    s=''
+    s = ''
     for e in a:
-        s+=str(e)+' '
+        s += str(e)+' '
     return s
 
+
 def _pointlist(a):
     """formats a list of numbers"""
     return str(a)[1:-1]
 
+
 class pathdata:
     """class used to create a pathdata object which can be used for a path.
     although most methods are pretty straightforward it might be useful to look at the SVG specification."""
-    #I didn't test the methods below.
-    def __init__(self,x=None,y=None):
-        self.path=[]
+    # I didn't test the methods below.
+
+    def __init__(self, x=None, y=None):
+        self.path = []
         if x is not None and y is not None:
             self.path.append('M '+str(x)+' '+str(y))
+
     def closepath(self):
         """ends the path"""
         self.path.append('z')
-    def move(self,x,y):
+
+    def move(self, x, y):
         """move to absolute"""
         self.path.append('M '+str(x)+' '+str(y))
-    def relmove(self,x,y):
+
+    def relmove(self, x, y):
         """move to relative"""
         self.path.append('m '+str(x)+' '+str(y))
-    def line(self,x,y):
+
+    def line(self, x, y):
         """line to absolute"""
         self.path.append('L '+str(x)+' '+str(y))
-    def relline(self,x,y):
+
+    def relline(self, x, y):
         """line to relative"""
         self.path.append('l '+str(x)+' '+str(y))
-    def hline(self,x):
+
+    def hline(self, x):
         """horizontal line to absolute"""
         self.path.append('H'+str(x))
-    def relhline(self,x):
+
+    def relhline(self, x):
         """horizontal line to relative"""
         self.path.append('h'+str(x))
-    def vline(self,y):
+
+    def vline(self, y):
         """verical line to absolute"""
         self.path.append('V'+str(y))
-    def relvline(self,y):
+
+    def relvline(self, y):
         """vertical line to relative"""
         self.path.append('v'+str(y))
-    def bezier(self,x1,y1,x2,y2,x,y):
+
+    def bezier(self, x1, y1, x2, y2, x, y):
         """bezier with xy1 and xy2 to xy absolut"""
-        self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def relbezier(self,x1,y1,x2,y2,x,y):
+        self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2) +
+                         ','+str(y2)+' '+str(x)+','+str(y))
+
+    def relbezier(self, x1, y1, x2, y2, x, y):
         """bezier with xy1 and xy2 to xy relative"""
-        self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def smbezier(self,x2,y2,x,y):
+        self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2) +
+                         ','+str(y2)+' '+str(x)+','+str(y))
+
+    def smbezier(self, x2, y2, x, y):
         """smooth bezier with xy2 to xy absolut"""
         self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def relsmbezier(self,x2,y2,x,y):
+
+    def relsmbezier(self, x2, y2, x, y):
         """smooth bezier with xy2 to xy relative"""
         self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def qbezier(self,x1,y1,x,y):
+
+    def qbezier(self, x1, y1, x, y):
         """quadratic bezier with xy1 to xy absolut"""
         self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
-    def relqbezier(self,x1,y1,x,y):
+
+    def relqbezier(self, x1, y1, x, y):
         """quadratic bezier with xy1 to xy relative"""
         self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
-    def smqbezier(self,x,y):
+
+    def smqbezier(self, x, y):
         """smooth quadratic bezier to xy absolut"""
         self.path.append('T'+str(x)+','+str(y))
-    def relsmqbezier(self,x,y):
+
+    def relsmqbezier(self, x, y):
         """smooth quadratic bezier to xy relative"""
         self.path.append('t'+str(x)+','+str(y))
-    def ellarc(self,rx,ry,xrot,laf,sf,x,y):
+
+    def ellarc(self, rx, ry, xrot, laf, sf, x, y):
         """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy absolut"""
-        self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
-    def relellarc(self,rx,ry,xrot,laf,sf,x,y):
+        self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot) +
+                         ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
+
+    def relellarc(self, rx, ry, xrot, laf, sf, x, y):
         """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy relative"""
-        self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
+        self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot) +
+                         ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
+
     def __repr__(self):
         return ' '.join(self.path)
 
 
-
-
 class SVGelement:
     """SVGelement(type,attributes,elements,text,namespace,**args)
     Creates a arbitrary svg element and is intended to be subclassed not used on its own.
@@ -256,52 +285,56 @@ class SVGelement:
     namespace. Note the elements==None, if elements = None:self.elements=[] construction.
     This is done because if you default to elements=[] every object has a reference
     to the same empty list."""
-    def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args):
-        self.type=type
-        if attributes==None:
-            self.attributes={}
+
+    def __init__(self, type='', attributes=None, elements=None, text='', namespace='', cdata=None, **args):
+        self.type = type
+        if attributes == None:
+            self.attributes = {}
         else:
-            self.attributes=attributes
-        if elements==None:
-            self.elements=[]
+            self.attributes = attributes
+        if elements == None:
+            self.elements = []
         else:
-            self.elements=elements
-        self.text=text
-        self.namespace=namespace
-        self.cdata=cdata
+            self.elements = elements
+        self.text = text
+        self.namespace = namespace
+        self.cdata = cdata
         for arg in args.keys():
             arg2 = arg.replace("__", ":")
             arg2 = arg2.replace("_", "-")
-            self.attributes[arg2]=args[arg]
-    def addElement(self,SVGelement):
+            self.attributes[arg2] = args[arg]
+
+    def addElement(self, SVGelement):
         """adds an element to a SVGelement
 
         SVGelement.addElement(SVGelement)
         """
         self.elements.append(SVGelement)
 
-    def toXml(self,level,f):
+    def toXml(self, level, f):
         f.write('\t'*level)
         f.write('<'+self.type)
         for attkey in self.attributes.keys():
-            f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey])))
+            f.write(' '+_escape(str(attkey))+'=' +
+                    _quoteattr(str(self.attributes[attkey])))
         if self.namespace:
-            f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"')
+            f.write(' xmlns="' + _escape(str(self.namespace)) +
+                    '" xmlns:xlink="http://www.w3.org/1999/xlink"')
         if self.elements or self.text or self.cdata:
             f.write('>')
         if self.elements:
             f.write('\n')
         for element in self.elements:
-            element.toXml(level+1,f)
+            element.toXml(level+1, f)
         if self.cdata:
             f.write('\n'+'\t'*(level+1)+'<![CDATA[')
             for line in self.cdata.splitlines():
                 f.write('\n'+'\t'*(level+2)+line)
             f.write('\n'+'\t'*(level+1)+']]>\n')
         if self.text:
-            if type(self.text)==type(''): #If the text is only text
+            if type(self.text) == type(''):  # If the text is only text
                 f.write(_escape(str(self.text)))
-            else:                         #If the text is a spannedtext class
+            else:  # If the text is a spannedtext class
                 f.write(str(self.text))
         if self.elements:
             f.write('\t'*level+'</'+self.type+'>\n')
@@ -312,6 +345,7 @@ class SVGelement:
         else:
             f.write('/>\n')
 
+
 class tspan(SVGelement):
     """ts=tspan(text='',**args)
 
@@ -323,19 +357,22 @@ class tspan(SVGelement):
     st.addtspan(ts)
     t=text(3,5,st)
     """
-    def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'tspan',**args)
-        if self.text<>None:
-            self.text=text
+
+    def __init__(self, text=None, **args):
+        SVGelement.__init__(self, 'tspan', **args)
+        if self.text <> None:
+            self.text = text
+
     def __repr__(self):
-        s="<tspan"
-        for key,value in self.attributes.items():
-            s+= ' %s="%s"' % (key,value)
-        s+='>'
-        s+=self.text
-        s+='</tspan>'
+        s = "<tspan"
+        for key, value in self.attributes.items():
+            s += ' %s="%s"' % (key, value)
+        s += '>'
+        s += self.text
+        s += '</tspan>'
         return s
 
+
 class tref(SVGelement):
     """tr=tref(link='',**args)
 
@@ -346,16 +383,19 @@ class tref(SVGelement):
     st.addtref(tr)
     t=text(3,5,st)
     """
-    def __init__(self,link,**args):
-        SVGelement.__init__(self,'tref',{'xlink:href':link},**args)
+
+    def __init__(self, link, **args):
+        SVGelement.__init__(self, 'tref', {'xlink:href': link}, **args)
+
     def __repr__(self):
-        s="<tref"
+        s = "<tref"
 
-        for key,value in self.attributes.items():
-            s+= ' %s="%s"' % (key,value)
-        s+='/>'
+        for key, value in self.attributes.items():
+            s += ' %s="%s"' % (key, value)
+        s += '/>'
         return s
 
+
 class spannedtext:
     """st=spannedtext(textlist=[])
 
@@ -374,30 +414,37 @@ class spannedtext:
     st.addtext('This text is not bold')
     t=text(3,5,st)
     """
-    def __init__(self,textlist=None):
-        if textlist==None:
-            self.textlist=[]
+
+    def __init__(self, textlist=None):
+        if textlist == None:
+            self.textlist = []
         else:
-            self.textlist=textlist
-    def addtext(self,text=''):
+            self.textlist = textlist
+
+    def addtext(self, text=''):
         self.textlist.append(text)
-    def addtspan(self,tspan):
+
+    def addtspan(self, tspan):
         self.textlist.append(tspan)
-    def addtref(self,tref):
+
+    def addtref(self, tref):
         self.textlist.append(tref)
+
     def __repr__(self):
-        s=""
+        s = ""
         for element in self.textlist:
-            s+=str(element)
+            s += str(element)
         return s
 
+
 class rect(SVGelement):
     """r=rect(width,height,x,y,fill,stroke,stroke_width,**args)
 
     a rectangle is defined by a width and height and a xy pair
     """
-    def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args):
-        if width==None or height==None:
+
+    def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args):
+        if width == None or height == None:
                 raise ValueError, 'height is required'
                 raise ValueError, 'width is required'
             if width!=None:
@@ -841,7 +888,7 @@ class animateTransform(SVGelement):
     """
     def __init__(self,type=None,fr=None,to=None,dur=None,**args):
         SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args)
-        #As far as I know the attributeName is always transform
+        # As far as I know the attributeName is always transform
         if type!=None:
             self.attributes['type']=type
         if fr!=None:
@@ -920,7 +967,7 @@ class drawing:
         self.entity = entity
     def setSVG(self,svg):
         self.svg=svg
-        #Voeg een element toe aan de grafiek toe.
+        # Voeg een element toe aan de grafiek toe.
     if use_dom_implementation==0:
         def toXml(self, filename='',compress=False):
             import cStringIO
@@ -966,10 +1013,10 @@ class drawing:
             doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
 
             global root
-            #root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
-            #that is a bit messy.
+            # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
+            # that is a bit messy.
             root=implementation.createDocument(None,None,doctype)
-            #Create the xml document.
+            # Create the xml document.
             global appender
             def appender(element,elementroot):
                 """This recursive function appends elements to an element and sets the attributes
-- 
cgit v1.2.3


From bafbb5b7a4b7db2ca230f292eb45be7e67985259 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 02:05:05 +0300
Subject: Remove erroneous `if .. else` branch

* wqflask/utility/svg.py [roct, ellipse, SVGelement]: Raise only a single value error
if either height or width is not defined. Fixes parsing error when running
`2to3-3.8 -f apply -w .`
---
 wqflask/utility/svg.py | 23 +++++------------------
 1 file changed, 5 insertions(+), 18 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index c850feb8..d66c954e 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -445,12 +445,8 @@ class rect(SVGelement):
 
     def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args):
         if width == None or height == None:
-                raise ValueError, 'height is required'
-                raise ValueError, 'width is required'
-            if width!=None:
-            if height!=None:
-            else:
-                raise ValueError, 'both height and width are required'
+            raise ValueError, 'both height and width are required'
+
         SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
         if x!=None:
             self.attributes['x']=x
@@ -470,12 +466,8 @@ class ellipse(SVGelement):
     """
     def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args):
         if rx==None or ry== None:
-                raise ValueError, 'rx is required'
-                raise ValueError, 'ry is required'
-            if rx!=None:
-            if ry!=None:
-            else:
-                raise ValueError, 'both rx and ry are required'
+            raise ValueError, 'both rx and ry are required'
+
         SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
         if cx!=None:
             self.attributes['cx']=cx
@@ -722,12 +714,7 @@ class image(SVGelement):
     """
     def __init__(self,url,x=None,y=None,width=None,height=None,**args):
         if width==None or height==None:
-                raise ValueError, 'height is required'
-                raise ValueError, 'width is required'
-            if width!=None:
-            if height!=None:
-            else:
-                raise ValueError, 'both height and width are required'
+            raise ValueError, 'both height and width are required'
         SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
         if x!=None:
             self.attributes['x']=x
-- 
cgit v1.2.3


From ba123e1e0fe693f9778993c3f8e5a70a28658a4c Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 02:31:31 +0300
Subject: Fix dictionary iteration methods

Run `2to3-3.8 -f dict -w .`

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-dict> and
<https://stackoverflow.com/questions/17695456/why-does-python-3-need-dict-items-to-be-wrapped-with-list>
---
 scripts/maintenance/load_genotypes.py              |  4 +--
 wqflask/base/GeneralObject.py                      |  8 ++---
 wqflask/base/trait.py                              |  4 +--
 wqflask/maintenance/gen_select_dataset.py          |  6 ++--
 .../maintenance/generate_probesetfreeze_file.py    |  2 +-
 wqflask/utility/__init__.py                        |  4 +--
 wqflask/utility/benchmark.py                       |  4 +--
 wqflask/utility/gen_geno_ob.py                     |  2 +-
 wqflask/utility/helper_functions.py                |  2 +-
 wqflask/utility/svg.py                             | 14 ++++----
 wqflask/utility/temp_data.py                       |  2 +-
 wqflask/utility/tools.py                           |  2 +-
 wqflask/wqflask/api/correlation.py                 | 16 ++++-----
 wqflask/wqflask/api/gen_menu.py                    |  6 ++--
 wqflask/wqflask/correlation/corr_scatter_plot.py   |  6 ++--
 wqflask/wqflask/correlation/show_corr_results.py   | 30 ++++++++---------
 wqflask/wqflask/ctl/ctl_analysis.py                |  2 +-
 wqflask/wqflask/export_traits.py                   |  4 +--
 wqflask/wqflask/heatmap/heatmap.py                 |  4 +--
 wqflask/wqflask/interval_analyst/GeneUtil.py       |  2 +-
 .../marker_regression/display_mapping_results.py   | 38 +++++++++++-----------
 wqflask/wqflask/marker_regression/run_mapping.py   | 24 +++++++-------
 wqflask/wqflask/resource_manager.py                |  2 +-
 wqflask/wqflask/show_trait/export_trait_data.py    |  2 +-
 wqflask/wqflask/show_trait/show_trait.py           |  8 ++---
 wqflask/wqflask/views.py                           |  6 ++--
 26 files changed, 102 insertions(+), 102 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/scripts/maintenance/load_genotypes.py b/scripts/maintenance/load_genotypes.py
index c235a31f..51278d48 100755
--- a/scripts/maintenance/load_genotypes.py
+++ b/scripts/maintenance/load_genotypes.py
@@ -19,7 +19,7 @@ def fetch_parameters(config):
     config_dic['dataid'] = datastructure.get_nextdataid_genotype()
     config_dic['genofile'] = config.get('config', 'genofile')
     print("config dictionary:")
-    for k, v in config_dic.items():
+    for k, v in list(config_dic.items()):
         print(("\t%s: %s" % (k, v)))
     return config_dic
 
@@ -42,7 +42,7 @@ def parse_genofile(config, config_dic):
         if line.lower().startswith("chr"):
             #
             print("geno file meta dictionary:")
-            for k, v in meta_dic.items():
+            for k, v in list(meta_dic.items()):
                 print(("\t%s: %s" % (k, v)))
             #
             print(("geno file head:\n\t%s" % line))
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 0fccaab3..707569db 100644
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -33,7 +33,7 @@ class GeneralObject:
 
     def __init__(self, *args, **kw):
         self.contents = list(args)
-        for name, value in kw.items():
+        for name, value in list(kw.items()):
             setattr(self, name, value)
 
     def __setitem__(self, key, value):
@@ -50,16 +50,16 @@ class GeneralObject:
 
     def __str__(self):
         s = ''
-        for key in self.__dict__.keys():
+        for key in list(self.__dict__.keys()):
             if key != 'contents':
                 s += '%s = %s\n' % (key, self.__dict__[key])
         return s
 
     def __repr__(self):
         s = ''
-        for key in self.__dict__.keys():
+        for key in list(self.__dict__.keys()):
             s += '%s = %s\n' % (key, self.__dict__[key])
         return s
 
     def __cmp__(self, other):
-        return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys()))
+        return len(list(self.__dict__.keys())).__cmp__(len(list(other.__dict__.keys())))
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7666348e..e82df226 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -118,7 +118,7 @@ class GeneralTrait(object):
         vals = []
         the_vars = []
         sample_aliases = []
-        for sample_name, sample_data in self.data.items():
+        for sample_name, sample_data in list(self.data.items()):
             if sample_data.value != None:
                 if not include_variance or sample_data.variance != None:
                     samples.append(sample_name)
@@ -260,7 +260,7 @@ def get_sample_data():
                 trait_dict['pubmed_link'] = trait_ob.pubmed_link
             trait_dict['pubmed_text'] = trait_ob.pubmed_text
 
-        return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
+        return json.dumps([trait_dict, {key: value.value for key, value in list(trait_ob.data.items()) }])
     else:
         return None
     
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 647e58a2..78217587 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -108,7 +108,7 @@ def get_types(groups):
     """Build types list"""
     types = {}
     #print("Groups: ", pf(groups))
-    for species, group_dict in groups.iteritems():
+    for species, group_dict in list(groups.items()):
         types[species] = {}
         for group_name, _group_full_name in group_dict:
             # make group an alias to shorten the code
@@ -195,9 +195,9 @@ def build_types(species, group):
 def get_datasets(types):
     """Build datasets list"""
     datasets = {}
-    for species, group_dict in types.iteritems():
+    for species, group_dict in list(types.items()):
         datasets[species] = {}
-        for group, type_list in group_dict.iteritems():
+        for group, type_list in list(group_dict.items()):
             datasets[species][group] = {}
             for type_name in type_list:
                 these_datasets = build_datasets(species, group, type_name[0])
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index b7b2dc8e..4231cc7c 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -82,7 +82,7 @@ def get_probeset_vals(cursor, dataset_name):
 def trim_strains(strains, probeset_vals):
     trimmed_strains = []
     #print("probeset_vals is:", pf(probeset_vals))
-    first_probeset = list(probeset_vals.itervalues())[0]
+    first_probeset = list(probeset_vals.values())[0]
     print("\n**** first_probeset is:", pf(first_probeset))
     for strain in strains:
         print("\n**** strain is:", pf(strain))
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index d9856eed..204ff59a 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -19,7 +19,7 @@ class Struct(object):
     '''
 
     def __init__(self, obj):
-        for k, v in obj.iteritems():
+        for k, v in list(obj.items()):
             if isinstance(v, dict):
                 setattr(self, k, Struct(v))
             else:
@@ -30,6 +30,6 @@ class Struct(object):
 
     def __repr__(self):
         return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for
-            (k, v) in self.__dict__.iteritems()))
+            (k, v) in list(self.__dict__.items())))
 
 
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 8f1c916b..221e5151 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -38,9 +38,9 @@ class Bench(object):
 
     @classmethod
     def report(cls):
-        total_time = sum((time_taken for time_taken in cls.entries.itervalues()))
+        total_time = sum((time_taken for time_taken in list(cls.entries.values())))
         print("\nTiming report\n")
-        for name, time_taken in cls.entries.iteritems():
+        for name, time_taken in list(cls.entries.items()):
             percent = int(round((time_taken/total_time) * 100))
             print("[{}%] {}: {}".format(percent, name, time_taken))
         print()
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 23b0b650..ae42f834 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -175,7 +175,7 @@ class Locus(object):
                 start_pos = 3
 
             for allele in marker_row[start_pos:]:
-                if allele in geno_table.keys():
+                if allele in list(geno_table.keys()):
                     self.genotype.append(geno_table[allele])
                 else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
                     self.genotype.append("U")
\ No newline at end of file
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 9ce809b6..9a4a235a 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -13,7 +13,7 @@ logger = logging.getLogger(__name__ )
 
 def get_species_dataset_trait(self, start_vars):
     #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
-    if "temp_trait" in start_vars.keys():
+    if "temp_trait" in list(start_vars.keys()):
       if start_vars['temp_trait'] == "True":
         self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group'])
       else:
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index d66c954e..c6a5c260 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -133,7 +133,7 @@ def _escape(data, entities={}):
     # data = data.replace("&", "&amp;")
     data = data.replace("<", "&lt;")
     data = data.replace(">", "&gt;")
-    for chars, entity in entities.items():
+    for chars, entity in list(entities.items()):
         data = data.replace(chars, entity)
     return data
 
@@ -299,7 +299,7 @@ class SVGelement:
         self.text = text
         self.namespace = namespace
         self.cdata = cdata
-        for arg in args.keys():
+        for arg in list(args.keys()):
             arg2 = arg.replace("__", ":")
             arg2 = arg2.replace("_", "-")
             self.attributes[arg2] = args[arg]
@@ -314,7 +314,7 @@ class SVGelement:
     def toXml(self, level, f):
         f.write('\t'*level)
         f.write('<'+self.type)
-        for attkey in self.attributes.keys():
+        for attkey in list(self.attributes.keys()):
             f.write(' '+_escape(str(attkey))+'=' +
                     _quoteattr(str(self.attributes[attkey])))
         if self.namespace:
@@ -365,7 +365,7 @@ class tspan(SVGelement):
 
     def __repr__(self):
         s = "<tspan"
-        for key, value in self.attributes.items():
+        for key, value in list(self.attributes.items()):
             s += ' %s="%s"' % (key, value)
         s += '>'
         s += self.text
@@ -390,7 +390,7 @@ class tref(SVGelement):
     def __repr__(self):
         s = "<tref"
 
-        for key, value in self.attributes.items():
+        for key, value in list(self.attributes.items()):
             s += ' %s="%s"' % (key, value)
         s += '/>'
         return s
@@ -963,7 +963,7 @@ class drawing:
             xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"")
             if self.entity:
                 xml.write(" [\n")
-                for item in self.entity.keys():
+                for item in list(self.entity.keys()):
                     xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
                 xml.write("]")
             xml.write(">\n")
@@ -1015,7 +1015,7 @@ class drawing:
                 if element.text:
                     textnode=root.createTextNode(element.text)
                     e.appendChild(textnode)
-                for attribute in element.attributes.keys():   #in element.attributes is supported from python 2.2
+                for attribute in list(element.attributes.keys()):   #in element.attributes is supported from python 2.2
                     e.setAttribute(attribute,str(element.attributes[attribute]))
                 if element.elements:
                     for el in element.elements:
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 5bf700c9..2f2726c6 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -20,6 +20,6 @@ class TempData(object):
 
 if __name__ == "__main__":
     redis = Redis()
-    for key in redis.keys():
+    for key in list(redis.keys()):
         for field in redis.hkeys(key):
             print("{}.{}={}".format(key, field, redis.hget(key, field)))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index f790d424..51a87fe1 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -220,7 +220,7 @@ def show_settings():
 
     logger.info(OVERRIDES)
     logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
-    keylist = app.config.keys()
+    keylist = list(app.config.keys())
     print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******")
     keylist.sort()
     for k in keylist:
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index 7f5312c1..eb05645e 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -36,7 +36,7 @@ def do_correlation(start_vars):
     #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
 
     final_results = []
-    for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]):
+    for _trait_counter, trait in enumerate(list(corr_results.keys())[:corr_params['return_count']]):
         if corr_params['type'] == "tissue":
             [sample_r, num_overlap, sample_p, symbol] = corr_results[trait]
             result_dict = {
@@ -76,20 +76,20 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
     if corr_params['type'] == "tissue":
         trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
         corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params)
-        sorted_results = collections.OrderedDict(sorted(corr_results.items(),
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
                                                         key=lambda t: -abs(t[1][1])))
     elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature"
         trait_geneid_dict = this_dataset.retrieve_genes("GeneId")
         corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params)
-        sorted_results = collections.OrderedDict(sorted(corr_results.items(),
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
                                                  key=lambda t: -abs(t[1][1])))
     else:
-        for target_trait, target_vals in target_dataset.trait_data.iteritems():
+        for target_trait, target_vals in list(target_dataset.trait_data.items()):
             result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type'])
             if result is not None:
                 corr_results[target_trait] = result
 
-        sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0])))
 
     return sorted_results
 
@@ -100,10 +100,10 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par
     if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
         primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()]
 
-        corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values())
+        corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values()))
 
         tissue_corr_data = {}
-        for trait, symbol in trait_symbol_dict.iteritems():
+        for trait, symbol in list(trait_symbol_dict.items()):
             if symbol and symbol.lower() in corr_result_tissue_vals_dict:
                 this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
 
@@ -119,7 +119,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g
     input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
 
     lit_corr_data = {}
-    for trait, gene_id in trait_geneid_dict.iteritems():
+    for trait, gene_id in list(trait_geneid_dict.items()):
         mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id)
 
         if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index cc11e14b..71d9ee03 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -61,7 +61,7 @@ def get_types(groups):
     """Build types list"""
     types = {}
 
-    for species, group_dict in groups.iteritems():
+    for species, group_dict in list(groups.items()):
         types[species] = {}
         for group_name, _group_full_name, _family_name in group_dict:
             if phenotypes_exist(group_name):
@@ -136,9 +136,9 @@ def build_types(species, group):
 def get_datasets(types):
     """Build datasets list"""
     datasets = {}
-    for species, group_dict in types.iteritems():
+    for species, group_dict in list(types.items()):
         datasets[species] = {}
-        for group, type_list in group_dict.iteritems():
+        for group, type_list in list(group_dict.items()):
             datasets[species][group] = {}
             for type_name in type_list:
                 these_datasets = build_datasets(species, group, type_name[0])
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 819836b1..57a8d85f 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -36,13 +36,13 @@ class CorrScatterPlot(object):
         samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
 
         self.data = []
-        self.indIDs = samples_1.keys()
+        self.indIDs = list(samples_1.keys())
         vals_1 = []
-        for sample in samples_1.keys():
+        for sample in list(samples_1.keys()):
             vals_1.append(samples_1[sample].value)
         self.data.append(vals_1)
         vals_2 = []
-        for sample in samples_2.keys():
+        for sample in list(samples_2.keys()):
             vals_2.append(samples_2[sample].value)
         self.data.append(vals_2)
 
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index de7a1c0c..15a21ee6 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -145,10 +145,10 @@ class CorrelationResults(object):
                 if corr_samples_group == 'samples_other':
                     primary_samples = [x for x in primary_samples if x not in (
                                     self.dataset.group.parlist + self.dataset.group.f1list)]
-                self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples)
+                self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples)
 
             self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
-            self.target_dataset.get_trait_data(self.sample_data.keys())
+            self.target_dataset.get_trait_data(list(self.sample_data.keys()))
 
             self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method)
 
@@ -168,41 +168,41 @@ class CorrelationResults(object):
 
                 tissue_corr_data = self.do_tissue_correlation_for_all_traits()
                 if tissue_corr_data != None:
-                    for trait in tissue_corr_data.keys()[:self.return_number]:
+                    for trait in list(tissue_corr_data.keys())[:self.return_number]:
                         self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
                 else:
-                    for trait, values in self.target_dataset.trait_data.iteritems():
+                    for trait, values in list(self.target_dataset.trait_data.items()):
                         self.get_sample_r_and_p_values(trait, values)
 
             elif self.corr_type == "lit":
                 self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId")
                 lit_corr_data = self.do_lit_correlation_for_all_traits()
 
-                for trait in lit_corr_data.keys()[:self.return_number]:
+                for trait in list(lit_corr_data.keys())[:self.return_number]:
                     self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
 
             elif self.corr_type == "sample":
-                for trait, values in self.target_dataset.trait_data.iteritems():
+                for trait, values in list(self.target_dataset.trait_data.items()):
                     self.get_sample_r_and_p_values(trait, values)
 
-            self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(),
+            self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
                                                                    key=lambda t: -abs(t[1][0])))
 
             if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
                 #ZS: Convert min/max chromosome to an int for the location range option
                 range_chr_as_int = None
-                for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
                     if 'loc_chr' in start_vars:
                         if chr_info.name == self.location_chr:
                             range_chr_as_int = order_id
 
-            for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
+            for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
                 trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
 
                 if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
                     #ZS: Convert trait chromosome to an int for the location range option
                     chr_as_int = 0
-                    for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                    for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
                         if chr_info.name == trait_object.chr:
                             chr_as_int = order_id
 
@@ -297,14 +297,14 @@ class CorrelationResults(object):
 
             #print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
             corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
-                                                    symbol_list=self.trait_symbol_dict.values())
+                                                    symbol_list=list(self.trait_symbol_dict.values()))
 
             #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
 
             #print("trait_gene_symbols: ", pf(trait_gene_symbols))
 
             tissue_corr_data = {}
-            for trait, symbol in self.trait_symbol_dict.iteritems():
+            for trait, symbol in list(self.trait_symbol_dict.items()):
                 if symbol and symbol.lower() in corr_result_tissue_vals_dict:
                     this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
 
@@ -314,7 +314,7 @@ class CorrelationResults(object):
 
                     tissue_corr_data[trait] = [symbol, result[0], result[2]]
 
-            tissue_corr_data = collections.OrderedDict(sorted(tissue_corr_data.items(),
+            tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()),
                                                            key=lambda t: -abs(t[1][1])))
 
             return tissue_corr_data
@@ -359,7 +359,7 @@ class CorrelationResults(object):
         input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
 
         lit_corr_data = {}
-        for trait, gene_id in self.trait_geneid_dict.iteritems():
+        for trait, gene_id in list(self.trait_geneid_dict.items()):
             mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id)
 
             if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
@@ -387,7 +387,7 @@ class CorrelationResults(object):
             else:
                 lit_corr_data[trait] = [gene_id, 0]
 
-        lit_corr_data = collections.OrderedDict(sorted(lit_corr_data.items(),
+        lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()),
                                                            key=lambda t: -abs(t[1][1])))
 
         return lit_corr_data
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 35067036..f0be7a98 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -125,7 +125,7 @@ class CTL(object):
             gt = create_trait(name = ts[0], dataset_name = ts[1])
             gt = retrieve_sample_data(gt, dataset, individuals)
             for ind in individuals:
-              if ind in gt.data.keys():
+              if ind in list(gt.data.keys()):
                 traits.append(gt.data[ind].value)
               else:
                 traits.append("-999")
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 6646cc36..28c6593d 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -61,7 +61,7 @@ def export_search_results_csv(targs):
     traits_by_group = sort_traits_by_group(trait_list)
 
     file_list = []
-    for group in traits_by_group.keys():
+    for group in list(traits_by_group.keys()):
         group_traits = traits_by_group[group]
         buff = StringIO.StringIO()
         writer = csv.writer(buff)
@@ -135,7 +135,7 @@ def export_search_results_csv(targs):
 def sort_traits_by_group(trait_list=[]):
     traits_by_group = {}
     for trait in trait_list:
-        if trait.dataset.group.name not in traits_by_group.keys():
+        if trait.dataset.group.name not in list(traits_by_group.keys()):
             traits_by_group[trait.dataset.group.name] = []
 
         traits_by_group[trait.dataset.group.name].append(trait)
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 5098a184..577426b0 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -60,7 +60,7 @@ class Heatmap(object):
 
         chrnames = []
         self.species = species.TheSpecies(dataset=self.trait_list[0][1])
-        for key in self.species.chromosomes.chromosomes.keys():
+        for key in list(self.species.chromosomes.chromosomes.keys()):
             chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
 
         for trait_db in self.trait_list:
@@ -93,7 +93,7 @@ class Heatmap(object):
         pos = []
         markernames = []
 
-        for trait in self.trait_results.keys():
+        for trait in list(self.trait_results.keys()):
             lodnames.append(trait)
 
         self.dataset.group.get_markers()
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 273168a8..a39e5d0f 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -24,7 +24,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
 	
 	##List current Species and other Species
 	speciesId = speciesDict[species]
-	otherSpecies = [[X, speciesDict[X]] for X in speciesDict.keys()]
+	otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
 	otherSpecies.remove([species, speciesId])
 
 	results = g.db.execute("""
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 7b6e70d2..0328ce85 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -229,7 +229,7 @@ class DisplayMappingResults(object):
 
         self.manhattan_plot = start_vars['manhattan_plot']
 
-        if 'permCheck' in start_vars.keys():
+        if 'permCheck' in list(start_vars.keys()):
             self.permChecked = start_vars['permCheck']
         else:
             self.permChecked = False
@@ -242,46 +242,46 @@ class DisplayMappingResults(object):
         else:
             self.nperm = 0
 
-        if 'bootCheck' in start_vars.keys():
+        if 'bootCheck' in list(start_vars.keys()):
             self.bootChecked = start_vars['bootCheck']
         else:
             self.bootChecked = False
-        if 'num_bootstrap' in start_vars.keys():
+        if 'num_bootstrap' in list(start_vars.keys()):
             self.nboot = int(start_vars['num_bootstrap'])
         else:
             self.nboot = 0
-        if 'bootstrap_results' in start_vars.keys():
+        if 'bootstrap_results' in list(start_vars.keys()):
             self.bootResult = start_vars['bootstrap_results']
         else:
             self.bootResult = []
 
-        if 'do_control' in start_vars.keys():
+        if 'do_control' in list(start_vars.keys()):
             self.doControl = start_vars['do_control']
         else:
             self.doControl = "false"
-        if 'control_marker' in start_vars.keys():
+        if 'control_marker' in list(start_vars.keys()):
             self.controlLocus = start_vars['control_marker']
         else:
             self.controlLocus = ""
-        if 'covariates' in start_vars.keys():
+        if 'covariates' in list(start_vars.keys()):
             self.covariates = start_vars['covariates']
-        if 'maf' in start_vars.keys():
+        if 'maf' in list(start_vars.keys()):
             self.maf = start_vars['maf']
         else:
             self.maf = ""
-        if 'output_files' in start_vars.keys():
+        if 'output_files' in list(start_vars.keys()):
             self.output_files = start_vars['output_files']
-        if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma":
+        if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma":
             self.use_loco = start_vars['use_loco']
 
-        if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper":
+        if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper":
             self.reaper_version = start_vars['reaper_version']
             if 'output_files' in start_vars:
                 self.output_files = ",".join(start_vars['output_files'])
 
         self.categorical_vars = ""
         self.perm_strata = ""
-        if 'perm_strata' in start_vars.keys() and 'categorical_vars' in start_vars.keys():
+        if 'perm_strata' in list(start_vars.keys()) and 'categorical_vars' in list(start_vars.keys()):
             self.categorical_vars = start_vars['categorical_vars']
             self.perm_strata = start_vars['perm_strata']
 
@@ -323,7 +323,7 @@ class DisplayMappingResults(object):
                self.graphWidth  = self.MULT_GRAPH_DEFAULT_WIDTH
 
 ## BEGIN HaplotypeAnalyst
-        if 'haplotypeAnalystCheck' in start_vars.keys():
+        if 'haplotypeAnalystCheck' in list(start_vars.keys()):
             self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck']
         else:
             self.haplotypeAnalystChecked = False
@@ -331,25 +331,25 @@ class DisplayMappingResults(object):
 
         self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
         self.dominanceChecked = False
-        if 'LRSCheck' in start_vars.keys():
+        if 'LRSCheck' in list(start_vars.keys()):
             self.LRS_LOD = start_vars['LRSCheck']
         else:
             self.LRS_LOD = start_vars['score_type']
         self.intervalAnalystChecked = True
         self.draw2X = False
-        if 'additiveCheck' in start_vars.keys():
+        if 'additiveCheck' in list(start_vars.keys()):
             self.additiveChecked = start_vars['additiveCheck']
         else:
             self.additiveChecked = False
-        if 'viewLegend' in start_vars.keys():
+        if 'viewLegend' in list(start_vars.keys()):
             self.legendChecked = start_vars['viewLegend']
         else:
             self.legendChecked = False
-        if 'showSNP' in start_vars.keys():
+        if 'showSNP' in list(start_vars.keys()):
             self.SNPChecked = start_vars['showSNP']
         else:
             self.SNPChecked = False
-        if 'showGenes' in start_vars.keys():
+        if 'showGenes' in list(start_vars.keys()):
             self.geneChecked = start_vars['showGenes']
         else:
             self.geneChecked = False
@@ -530,7 +530,7 @@ class DisplayMappingResults(object):
             showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data',
                 name=showLocusForm, submit=HT.Input(type='hidden'))
             hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
-            for key in hddn.keys():
+            for key in list(hddn.keys()):
                 showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
             showLocusForm.append(intImg)
         else:
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index c9d10f7c..145dbc77 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -347,7 +347,7 @@ class RunMapping(object):
                   if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
                       if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
                           highest_chr = marker['chr1']
-                      if 'lod_score' in marker.keys():
+                      if 'lod_score' in list(marker.keys()):
                           self.qtl_results.append(marker)
 
               self.trimmed_markers = results
@@ -411,7 +411,7 @@ class RunMapping(object):
                   if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
                       if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
                           highest_chr = marker['chr']
-                      if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+                      if ('lod_score' in list(marker.keys())) or ('lrs_value' in list(marker.keys())):
                           self.qtl_results.append(marker)
 
               with Bench("Exporting Results"):
@@ -538,28 +538,28 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
             output_file.write("Mb," + score_type)
         else:
             output_file.write("Cm," + score_type)
-        if "additive" in markers[0].keys():
+        if "additive" in list(markers[0].keys()):
             output_file.write(",Additive")
-        if "dominance" in markers[0].keys():
+        if "dominance" in list(markers[0].keys()):
             output_file.write(",Dominance")
         output_file.write("\n")
         for i, marker in enumerate(markers):
             output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",")
-            if "lod_score" in marker.keys():
+            if "lod_score" in list(marker.keys()):
                 output_file.write(str(marker['lod_score']))
             else:
                 output_file.write(str(marker['lrs_value']))
-            if "additive" in marker.keys():
+            if "additive" in list(marker.keys()):
                 output_file.write("," + str(marker['additive']))
-            if "dominance" in marker.keys():
+            if "dominance" in list(marker.keys()):
                 output_file.write("," + str(marker['dominance']))
             if i < (len(markers) - 1):
                 output_file.write("\n")
 
 def trim_markers_for_figure(markers):
-    if 'p_wald' in markers[0].keys():
+    if 'p_wald' in list(markers[0].keys()):
         score_type = 'p_wald'
-    elif 'lod_score' in markers[0].keys():
+    elif 'lod_score' in list(markers[0].keys()):
         score_type = 'lod_score'
     else:
         score_type = 'lrs_value'
@@ -617,7 +617,7 @@ def trim_markers_for_figure(markers):
     return filtered_markers
 
 def trim_markers_for_table(markers):
-    if 'lod_score' in markers[0].keys():
+    if 'lod_score' in list(markers[0].keys()):
         sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
     else:
         sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True)
@@ -695,10 +695,10 @@ def get_genofile_samplelist(dataset):
 def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
     perm_strata_strings = []
     for sample in used_samples:
-        if sample in sample_list.sample_attribute_values.keys():
+        if sample in list(sample_list.sample_attribute_values.keys()):
             combined_string = ""
             for var in categorical_vars:
-                if var in sample_list.sample_attribute_values[sample].keys():
+                if var in list(sample_list.sample_attribute_values[sample].keys()):
                     combined_string += str(sample_list.sample_attribute_values[sample][var])
                 else:
                     combined_string += "NA"
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 39a07310..6b3e00fb 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -125,7 +125,7 @@ def add_group_to_resource():
 
 def get_group_names(group_masks):
     group_masks_with_names = {}
-    for group_id, group_mask in group_masks.iteritems():
+    for group_id, group_mask in list(group_masks.items()):
         this_mask = group_mask
         group_name = get_group_info(group_id)['name']
         this_mask['name'] = group_name
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 253c887b..68c3ad7d 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -47,7 +47,7 @@ def get_export_metadata(trait_id, dataset_name):
 
 
 def dict_to_sorted_list(dictionary):
-    sorted_list = [item for item in dictionary.iteritems()]
+    sorted_list = [item for item in list(dictionary.items())]
     sorted_list = sorted(sorted_list, cmp=cmp_samples)
     sorted_values = [item[1] for item in sorted_list]
     return sorted_values
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f188fd9d..c156e61b 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -261,7 +261,7 @@ class ShowTrait(object):
         hddn['export_data'] = ""
         hddn['export_format'] = "excel"
         if len(self.scales_in_geno) < 2:
-            hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0][0]
+            hddn['mapping_scale'] = self.scales_in_geno[list(self.scales_in_geno.keys())[0]][0][0]
 
         # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
         self.hddn = hddn
@@ -405,7 +405,7 @@ class ShowTrait(object):
 
         if not self.temp_trait:
             other_sample_names = []
-            for sample in self.this_trait.data.keys():
+            for sample in list(self.this_trait.data.keys()):
                 if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
                     primary_sample_names.append(self.this_trait.data[sample].name)
                     primary_sample_names.remove(self.this_trait.data[sample].name2)
@@ -558,7 +558,7 @@ def get_table_widths(sample_groups, has_num_cases=False):
 def has_num_cases(this_trait):
     has_n = False
     if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno":
-        for name, sample in this_trait.data.iteritems():
+        for name, sample in list(this_trait.data.items()):
             if sample.num_cases:
                 has_n = True
                 break
@@ -611,7 +611,7 @@ def get_categorical_variables(this_trait, sample_list):
     if len(sample_list.attributes) > 0:
         for attribute in sample_list.attributes:
             attribute_vals = []
-            for sample_name in this_trait.data.keys():
+            for sample_name in list(this_trait.data.keys()):
                 if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes:
                     attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name])
                 else:
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index d67f1a2e..394a9e28 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -533,7 +533,7 @@ def heatmap_page():
 
             result = template_vars.__dict__
 
-            for item in template_vars.__dict__.keys():
+            for item in list(template_vars.__dict__.keys()):
                 logger.info("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
 
             pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
@@ -637,7 +637,7 @@ def loading_page():
     if 'wanted_inputs' in initial_start_vars:
         wanted = initial_start_vars['wanted_inputs'].split(",")
         start_vars = {}
-        for key, value in initial_start_vars.iteritems():
+        for key, value in list(initial_start_vars.items()):
             if key in wanted or key.startswith(('value:')):
                 start_vars[key] = value
 
@@ -737,7 +737,7 @@ def mapping_results_page():
         'transform'
     )
     start_vars = {}
-    for key, value in initial_start_vars.iteritems():
+    for key, value in list(initial_start_vars.items()):
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
     #logger.debug("Mapping called with start_vars:", start_vars)
-- 
cgit v1.2.3


From caec08fa1e738fa9bc1b0b6bf626d8325f798712 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:08:08 +0300
Subject: Convert the old not-equal syntax, <>, to !=

Run `2to3-3.8 -f ne -w .`

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-ne>
---
 wqflask/utility/svg.py                             | 2 +-
 wqflask/wqflask/marker_regression/plink_mapping.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index c6a5c260..c7356e57 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -360,7 +360,7 @@ class tspan(SVGelement):
 
     def __init__(self, text=None, **args):
         SVGelement.__init__(self, 'tspan', **args)
-        if self.text <> None:
+        if self.text != None:
             self.text = text
 
     def __repr__(self):
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 38ef7190..d4ee6fe6 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -156,7 +156,7 @@ def parse_plink_output(output_filename, species):
 #######################################################
 def build_line_list(line=None):
     line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
-    line_list = [item for item in line_list if item <>'']
+    line_list = [item for item in line_list if item !='']
     line_list = list(map(string.strip, line_list))
 
     return line_list
\ No newline at end of file
-- 
cgit v1.2.3


From 7e60647223017220747d248ed1c986cc8374435e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:13:53 +0300
Subject: Wrap `raise` statements in parenthesis

Run `2to3-3.8 -f raise -w .`

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-raise>
---
 wqflask/base/trait.py  | 2 +-
 wqflask/utility/svg.py | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index e82df226..c2d260e3 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -605,6 +605,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 if trait.lrs != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
     else:
-        raise KeyError, `trait.name`+' information is not found in the database.'
+        raise KeyError(`trait.name`+' information is not found in the database.')
         
     return trait
\ No newline at end of file
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index c7356e57..872f22fe 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -445,7 +445,7 @@ class rect(SVGelement):
 
     def __init__(self, x=None, y=None, width=None, height=None, fill=None, stroke=None, stroke_width=None, **args):
         if width == None or height == None:
-            raise ValueError, 'both height and width are required'
+            raise ValueError('both height and width are required')
 
         SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
         if x!=None:
@@ -466,7 +466,7 @@ class ellipse(SVGelement):
     """
     def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args):
         if rx==None or ry== None:
-            raise ValueError, 'both rx and ry are required'
+            raise ValueError('both rx and ry are required')
 
         SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
         if cx!=None:
@@ -488,7 +488,7 @@ class circle(SVGelement):
     """
     def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args):
         if r==None:
-            raise ValueError, 'r is required'
+            raise ValueError('r is required')
         SVGelement.__init__(self,'circle',{'r':r},**args)
         if cx!=None:
             self.attributes['cx']=cx
@@ -714,7 +714,7 @@ class image(SVGelement):
     """
     def __init__(self,url,x=None,y=None,width=None,height=None,**args):
         if width==None or height==None:
-            raise ValueError, 'both height and width are required'
+            raise ValueError('both height and width are required')
         SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
         if x!=None:
             self.attributes['x']=x
-- 
cgit v1.2.3


From 3aaa28ea762c496eeb84e09e45194e3fd2a51673 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:45:49 +0300
Subject: Make Python more idiomatic

Run `2to3-3.8 -f idioms -w .`

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
---
 scripts/maintenance/readProbeSetMean_v7.py | 6 ++----
 scripts/maintenance/readProbeSetSE_v7.py   | 6 ++----
 wqflask/base/data_set.py                   | 4 ++--
 wqflask/utility/authentication_tools.py    | 2 +-
 wqflask/utility/svg.py                     | 2 +-
 wqflask/wqflask/ctl/ctl_analysis.py        | 2 +-
 wqflask/wqflask/show_trait/SampleList.py   | 2 +-
 wqflask/wqflask/show_trait/show_trait.py   | 2 +-
 wqflask/wqflask/user_login.py              | 2 +-
 9 files changed, 12 insertions(+), 16 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index 97767715..864b4e08 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -80,8 +80,7 @@ while line:
 	if kj%100000 == 0:
 		print(('checked ',kj,' lines'))
 
-GeneList = list(map(string.lower, GeneList))
-GeneList.sort()
+GeneList = sorted(map(string.lower, GeneList))
 	
 if isCont==0:
 	sys.exit(0)
@@ -148,9 +147,8 @@ for item in results:
 	
 print(Names)
 
-Names = list(map(string.lower, Names))
+Names = sorted(map(string.lower, Names))
 
-Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at  doesn't exist --#
 
 
 ##---- compare genelist with names ----##
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 833c3f5f..20a846a4 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -91,8 +91,7 @@ while line:
     if kj % 100000 == 0:
         print(('checked ', kj, ' lines'))
 
-GeneList = list(map(string.lower, GeneList))
-GeneList.sort()
+GeneList = sorted(map(string.lower, GeneList))
 
 if isCont == 0:
     sys.exit(0)
@@ -158,8 +157,7 @@ results = db.fetchall()
 Names = []
 for item in results:
     Names.append(item[0])
-    Names = list(map(string.lower, Names))
-    Names.sort()  # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at  doesn't exist --#
+    Names = sorted(map(string.lower, Names))
 
 ##---- compare genelist with names ----##
 x = y = 0
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b0119b58..06e1c551 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -254,7 +254,7 @@ class Markers(object):
         logger.debug("length of self.markers:", len(self.markers))
         logger.debug("length of p_values:", len(p_values))
 
-        if type(p_values) is list:
+        if isinstance(p_values, list):
             # THIS IS only needed for the case when we are limiting the number of p-values calculated
             # if len(self.markers) > len(p_values):
             #    self.markers = self.markers[:len(p_values)]
@@ -270,7 +270,7 @@ class Markers(object):
                     marker['lod_score'] = -math.log10(marker['p_value'])
                     # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
                     marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-        elif type(p_values) is dict:
+        elif isinstance(p_values, dict):
             filtered_markers = []
             for marker in self.markers:
                 #logger.debug("marker[name]", marker['name'])
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index ece7022c..bc03eb55 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -17,7 +17,7 @@ logger = logging.getLogger(__name__ )
 def check_resource_availability(dataset, trait_id=None):
 
     #At least for now assume temporary entered traits are accessible
-    if type(dataset) == str:
+    if isinstance(dataset, str):
         return webqtlConfig.DEFAULT_PRIVILEGES
     if dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 872f22fe..874ada9d 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -332,7 +332,7 @@ class SVGelement:
                 f.write('\n'+'\t'*(level+2)+line)
             f.write('\n'+'\t'*(level+1)+']]>\n')
         if self.text:
-            if type(self.text) == type(''):  # If the text is only text
+            if isinstance(self.text, type('')):  # If the text is only text
                 f.write(_escape(str(self.text)))
             else:  # If the text is a spannedtext class
                 f.write(str(self.text))
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index f0be7a98..e58a7b87 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -175,7 +175,7 @@ class CTL(object):
         sys.stdout.flush()
 
         # Create the interactive graph for cytoscape visualization (Nodes and Edges)
-        if not type(significant) == ri.RNULLType:
+        if not isinstance(significant, ri.RNULLType):
           for x in range(len(significant[0])):
             logger.debug(significant[0][x], significant[1][x], significant[2][x])     # Debug to console
             tsS = significant[0][x].split(':')                                        # Source
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index ad78ebcc..21ba7f63 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -43,7 +43,7 @@ class SampleList(object):
         for counter, sample_name in enumerate(sample_names, 1):
             sample_name = sample_name.replace("_2nd_", "")
 
-            if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
+            if isinstance(self.this_trait, list): #ZS: self.this_trait will be a list if it is a Temp trait
                 if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X':
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
                 else:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c156e61b..65899ab2 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -625,7 +625,7 @@ def get_categorical_variables(this_trait, sample_list):
 
 def get_genotype_scales(genofiles):
     geno_scales = {}
-    if type(genofiles) is list:
+    if isinstance(genofiles, list):
         for the_file in genofiles:
             file_location = the_file['location']
             geno_scales[file_location] = get_scales_from_genofile(file_location)
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index cfee0079..04672b45 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -193,7 +193,7 @@ def login():
             if user_details:
                 submitted_password = params['password']
                 pwfields = user_details['password']
-                if type(pwfields) is str:
+                if isinstance(pwfields, str):
                     pwfields = json.loads(pwfields)
                 encrypted_pass_fields = encode_password(pwfields, submitted_password)
                 password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password'])
-- 
cgit v1.2.3


From db41cd49b6d8ccd2c3318209118ffe098bc9293e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:57:05 +0300
Subject: Remove extra whitespace(or add it) from comma separated items

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
---
 etc/default_settings.py                            |   2 +-
 scripts/maintenance/QTL_Reaper_v6.py               |   4 +-
 scripts/maintenance/readProbeSetMean_v7.py         |  28 ++--
 setup.py                                           |   2 +-
 wqflask/base/trait.py                              |   6 +-
 wqflask/db/call.py                                 |  10 +-
 wqflask/db/webqtlDatabaseFunction.py               |   8 +-
 wqflask/maintenance/gen_select_dataset.py          |   2 +-
 wqflask/maintenance/quantile_normalize.py          |   2 +-
 wqflask/maintenance/set_resource_defaults.py       |   2 +-
 wqflask/utility/Plot.py                            |  48 +++---
 wqflask/utility/elasticsearch_tools.py             |   2 +-
 wqflask/utility/logger.py                          |  26 +--
 wqflask/utility/pillow_utils.py                    |   4 +-
 wqflask/utility/startup_config.py                  |   2 +-
 wqflask/utility/svg.py                             | 130 +++++++-------
 wqflask/utility/tools.py                           |  32 ++--
 wqflask/utility/webqtlUtil.py                      |  16 +-
 wqflask/wqflask/api/router.py                      |   8 +-
 wqflask/wqflask/correlation/show_corr_results.py   |  12 +-
 .../wqflask/correlation_matrix/show_corr_matrix.py |   8 +-
 wqflask/wqflask/do_search.py                       |   4 +-
 .../wqflask/external_tools/send_to_geneweaver.py   |   8 +-
 .../marker_regression/display_mapping_results.py   | 186 ++++++++++-----------
 wqflask/wqflask/marker_regression/plink_mapping.py |   6 +-
 wqflask/wqflask/marker_regression/run_mapping.py   |   2 +-
 wqflask/wqflask/search_results.py                  |   2 +-
 wqflask/wqflask/show_trait/SampleList.py           |   2 +-
 wqflask/wqflask/user_manager.py                    |   2 +-
 wqflask/wqflask/views.py                           |   8 +-
 30 files changed, 287 insertions(+), 287 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/etc/default_settings.py b/etc/default_settings.py
index f368237b..82c605da 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -24,7 +24,7 @@
 import os
 import sys
 
-GN_VERSION = open("../etc/VERSION","r").read()
+GN_VERSION = open("../etc/VERSION", "r").read()
 GN_SERVER_URL = "http://localhost:8880/" # REST API server
 
 # ---- MySQL
diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py
index 2fbeb53b..35f2d1a1 100755
--- a/scripts/maintenance/QTL_Reaper_v6.py
+++ b/scripts/maintenance/QTL_Reaper_v6.py
@@ -7,7 +7,7 @@ import reaper
 import MySQLdb
 import time
 
-con = MySQLdb.Connect(db='db_webqtl',user='username',passwd='', host="localhost")
+con = MySQLdb.Connect(db='db_webqtl', user='username', passwd='', host="localhost")
 cursor = con.cursor()
 
 genotypeDir = '/gnshare/gn/web/genotypes/'
@@ -102,7 +102,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds:
 
 		kj += 1
 		if kj%1000==0:
-			print((ProbeSetFreezeId, InbredSets[InbredSetId],kj))
+			print((ProbeSetFreezeId, InbredSets[InbredSetId], kj))
 
 
 	print(ProbeSetFreezeIds)
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index 864b4e08..59a51cf9 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -39,7 +39,7 @@ fp = open("%s" % input_file_name, 'rb')
 
 try:
         passwd = getpass.getpass('Please enter mysql password here : ') 
-        con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd)
+        con = MySQLdb.Connect(db='db_webqtl', host='localhost', user='username', passwd=passwd)
 
         db = con.cursor()
         print("You have successfully connected to mysql.\n")
@@ -60,14 +60,14 @@ print('Checking if each line have same number of members')
 GeneList = []
 isCont = 1
 header = fp.readline()
-header = string.split(string.strip(header),'\t')
+header = string.split(string.strip(header), '\t')
 header = list(map(string.strip, header))
 nfield = len(header)
 line = fp.readline()
 
 kj=0
 while line:
-	line2 = string.split(string.strip(line),'\t')
+	line2 = string.split(string.strip(line), '\t')
 	line2 = list(map(string.strip, line2))
 	if len(line2) != nfield:
 		print(("Error : " + line))
@@ -78,7 +78,7 @@ while line:
 
 	kj+=1
 	if kj%100000 == 0:
-		print(('checked ',kj,' lines'))
+		print(('checked ', kj, ' lines'))
 
 GeneList = sorted(map(string.lower, GeneList))
 	
@@ -86,7 +86,7 @@ if isCont==0:
 	sys.exit(0)
 
 
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 #########################################################################
 #
 #  Check if each strain exist in database
@@ -98,7 +98,7 @@ print('Checking if each strain exist in database')
 isCont = 1
 fp.seek(0)
 header = fp.readline()
-header = string.split(string.strip(header),'\t')
+header = string.split(string.strip(header), '\t')
 header = list(map(string.strip, header))
 header = list(map(translateAlias, header))
 header = header[dataStart:]
@@ -108,14 +108,14 @@ for item in header:
 		db.execute('select Id from Strain where Name = "%s"' % item)
 		Ids.append(db.fetchall()[0][0])
 	except:
-		print((item,'does not exist, check the if the strain name is correct'))
+		print((item, 'does not exist, check the if the strain name is correct'))
 		isCont=0
 
 if isCont==0:
 	sys.exit(0)
 
 
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 ########################################################################
 #
 # Check if each ProbeSet exist in database
@@ -126,7 +126,7 @@ print('Check if each ProbeSet exist in database')
 ##---- find PID is name or target ----##
 line = fp.readline()
 line = fp.readline()
-line2 = string.split(string.strip(line),'\t')
+line2 = string.split(string.strip(line), '\t')
 line2 = list(map(string.strip, line2))
 PId = line2[0]
 
@@ -185,7 +185,7 @@ if isCont==0:
 	sys.exit(0)
 
 
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 #########################################################################
 #
 # Insert data into database
@@ -200,7 +200,7 @@ results = db.fetchall()
 NameIds = {}
 for item in results:
 	NameIds[item[0]] = item[1]
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 
 
 print('inserting data')
@@ -220,7 +220,7 @@ kj = 0
 values1 = []
 values2 = []
 while line:
-	line2 = string.split(string.strip(line),'\t')
+	line2 = string.split(string.strip(line), '\t')
 	line2 = list(map(string.strip, line2))
 	PId = line2[0]
 	recordId = NameIds[PId]
@@ -253,8 +253,8 @@ while line:
 
 		values1=[]
 		values2=[]
-		print(('Inserted ', kj,' lines'))
-		print(('used ',time.time()-time0,' seconds'))
+		print(('Inserted ', kj, ' lines'))
+		print(('used ', time.time()-time0, ' seconds'))
 	
 	line = fp.readline()
 
diff --git a/setup.py b/setup.py
index a9b71fab..8436dcd3 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@ setup(name='genenetwork2',
       url = "https://github.com/genenetwork/genenetwork2/blob/master/README.md",
       description = 'Website and tools for genetics.',
       include_package_data=True,
-      packages=['wqflask','etc'],
+      packages=['wqflask', 'etc'],
       scripts=['bin/genenetwork2'],
       # package_data = {
       #   'etc': ['*.py']
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2b8f2e72..05b272c3 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -193,7 +193,7 @@ class GeneralTrait(object):
         '''
 
         if self.chr and self.mb:
-            self.location = 'Chr %s @ %s Mb'  % (self.chr,self.mb)
+            self.location = 'Chr %s @ %s Mb'  % (self.chr, self.mb)
         elif self.chr:
             self.location = 'Chr %s @ Unknown position' % (self.chr)
         else:
@@ -440,7 +440,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
         #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
         # to avoid the problem of same marker name from different species.
         elif dataset.type == 'Geno':
-            display_fields_string = string.join(dataset.display_fields,',Geno.')
+            display_fields_string = string.join(dataset.display_fields, ',Geno.')
             display_fields_string = 'Geno.' + display_fields_string
             query = """
                     SELECT %s
@@ -459,7 +459,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             query = """SELECT %s FROM %s WHERE Name = %s"""
             logger.sql(query)
             trait_info = g.db.execute(query,
-                                    (string.join(dataset.display_fields,','),
+                                    (string.join(dataset.display_fields, ','),
                                                 dataset.type, trait.name)).fetchone()
 
     if trait_info:
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 82cfebb4..3b8f782e 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -26,8 +26,8 @@ GN_SERVER result when set (which should return a Tuple)
         else:
             res2 = result,
         if LOG_SQL:
-            logger.debug("Replaced SQL call",query)
-        logger.debug(path,res2)
+            logger.debug("Replaced SQL call", query)
+        logger.debug(path, res2)
         return res2
     else:
         return fetchone(query)
@@ -37,7 +37,7 @@ def fetchone(query):
 original fetchone, but with logging)
 
     """
-    with Bench("SQL",LOG_SQL):
+    with Bench("SQL", LOG_SQL):
         def helper(query):
             res = g.db.execute(query)
             return res.fetchone()
@@ -48,7 +48,7 @@ def fetchall(query):
 original fetchall, but with logging)
 
     """
-    with Bench("SQL",LOG_SQL):
+    with Bench("SQL", LOG_SQL):
         def helper(query):
             res = g.db.execute(query)
             return res.fetchall()
@@ -58,7 +58,7 @@ def gn_server(path):
     """Return JSON record by calling GN_SERVER
 
     """
-    with Bench("GN_SERVER",LOG_SQL):
+    with Bench("GN_SERVER", LOG_SQL):
         res = urllib.request.urlopen(GN_SERVER_URL+path)
         rest = res.read()
         res2 = json.loads(rest)
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 8a9dc79d..2805febd 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -35,13 +35,13 @@ def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
 
     """
-    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0]
-    logger.debug("retrieve_species result:",result)
+    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0]
+    logger.debug("retrieve_species result:", result)
     return result
 
 
 def retrieve_species_id(group):
 
-    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0]
-    logger.debug("retrieve_species_id result:",result)
+    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0]
+    logger.debug("retrieve_species_id result:", result)
     return result
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 78217587..d12b328f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -41,7 +41,7 @@ from __future__ import print_function, division
 import sys
 
 # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
 # NEW: import app to avoid a circular dependency on utility.tools
 from wqflask import app
 
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 82b695f4..43edfd13 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -1,7 +1,7 @@
 from __future__ import absolute_import, print_function, division
 
 import sys
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
 
 
 
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 54fd8e7e..d53a255b 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -22,7 +22,7 @@ import sys
 import json
 
 # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
 
 # NEW: import app to avoid a circular dependency on utility.tools
 from wqflask import app
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index c9053dde..4f6e694e 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -58,7 +58,7 @@ def cformat(d, rank=0):
     strD = "%2.6f" % d
 
     if rank == 0:
-        while strD[-1] in ('0','.'):
+        while strD[-1] in ('0', '.'):
             if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
                 break
             elif strD[-1] == '.':
@@ -162,7 +162,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
        j = int((item-xLow)/step)
        Count[j] += 1
 
-    yLow, yTop, stepY=detScale(0,max(Count))
+    yLow, yTop, stepY=detScale(0, max(Count))
 
     #draw data
     xScale = plotWidth/(xTop-xLow)
@@ -174,7 +174,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
            xc = (dataXY[i]-xLow)*xScale+xLeftOffset
            yc =-(count-yLow)*yScale+yTopOffset+plotHeight
            im_drawer.rectangle(
-               xy=((xc+2,yc),(xc+barWidth-2,yTopOffset+plotHeight)),
+               xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)),
                outline=barColor, fill=barColor)
 
     #draw drawing region
@@ -183,81 +183,81 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     )
 
     #draw scale
-    scaleFont=ImageFont.truetype(font=COUR_FILE,size=11)
+    scaleFont=ImageFont.truetype(font=COUR_FILE, size=11)
     x=xLow
     for i in range(int(stepX)+1):
        xc=xLeftOffset+(x-xLow)*xScale
        im_drawer.line(
-           xy=((xc,yTopOffset+plotHeight),(xc,yTopOffset+plotHeight+5)),
+           xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)),
            fill=axesColor)
        strX = cformat(d=x, rank=0)
        im_drawer.text(
            text=strX,
-           xy=(xc-im_drawer.textsize(strX,font=scaleFont)[0]/2,
-               yTopOffset+plotHeight+14),font=scaleFont)
+           xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2,
+               yTopOffset+plotHeight+14), font=scaleFont)
        x+= (xTop - xLow)/stepX
 
     y=yLow
     for i in range(int(stepY)+1):
        yc=yTopOffset+plotHeight-(y-yLow)*yScale
-       im_drawer.line(xy=((xLeftOffset,yc),(xLeftOffset-5,yc)), fill=axesColor)
+       im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor)
        strY = "%d" %y
        im_drawer.text(
            text=strY,
-           xy=(xLeftOffset-im_drawer.textsize(strY,font=scaleFont)[0]-6,yc+5),
+           xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5),
            font=scaleFont)
        y+= (yTop - yLow)/stepY
 
     #draw label
-    labelFont=ImageFont.truetype(font=TAHOMA_FILE,size=17)
+    labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17)
     if XLabel:
        im_drawer.text(
            text=XLabel,
            xy=(xLeftOffset+(
-               plotWidth-im_drawer.textsize(XLabel,font=labelFont)[0])/2.0,
+               plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0,
                yTopOffset+plotHeight+yBottomOffset-10),
-           font=labelFont,fill=labelColor)
+           font=labelFont, fill=labelColor)
 
     if YLabel:
         draw_rotated_text(canvas, text=YLabel,
                           xy=(19,
                               yTopOffset+plotHeight-(
                                   plotHeight-im_drawer.textsize(
-                                      YLabel,font=labelFont)[0])/2.0),
+                                      YLabel, font=labelFont)[0])/2.0),
                           font=labelFont, fill=labelColor, angle=90)
 
-    labelFont=ImageFont.truetype(font=VERDANA_FILE,size=16)
+    labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16)
     if title:
        im_drawer.text(
            text=title,
            xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
-               title,font=labelFont)[0])/2.0,
+               title, font=labelFont)[0])/2.0,
                20),
-           font=labelFont,fill=labelColor)
+           font=labelFont, fill=labelColor)
 
 # This function determines the scale of the plot
-def detScaleOld(min,max):
+def detScaleOld(min, max):
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         if a < c*5.0:
             c/=2.0
         #print a,b,c
         low=c*floor(min/c)
         high=c*ceil(max/c)
-        return [low,high,round((high-low)/c)]
+        return [low, high, round((high-low)/c)]
 
 def detScale(min=0,max=0):
 
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         if max != 0:
@@ -269,7 +269,7 @@ def detScale(min=0,max=0):
                 min -= 0.1*a
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         low=c*floor(min/c)
         high=c*ceil(max/c)
         n = round((high-low)/c)
@@ -287,7 +287,7 @@ def detScale(min=0,max=0):
             high=c*ceil(max/c)
             n = round((high-low)/c)
 
-        return [low,high,n]
+        return [low, high, n]
 
 def bluefunc(x):
     return 1.0 / (1.0 + exp(-10*(x-0.6)))
@@ -296,7 +296,7 @@ def redfunc(x):
     return 1.0 / (1.0 + exp(10*(x-0.5)))
 
 def greenfunc(x):
-    return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3)
+    return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3)
 
 def colorSpectrum(n=100):
     multiple = 10
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 15cdd0bc..a5580811 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -59,7 +59,7 @@ def get_elasticsearch_connection(for_user=True):
     try:
         assert(ELASTICSEARCH_HOST)
         assert(ELASTICSEARCH_PORT)
-        logger.info("ES HOST",ELASTICSEARCH_HOST)
+        logger.info("ES HOST", ELASTICSEARCH_HOST)
 
         es = Elasticsearch([{
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 510b1041..e904eb94 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -42,10 +42,10 @@ class GNLogger:
 
     """
 
-    def __init__(self,name):
+    def __init__(self, name):
         self.logger = logging.getLogger(name)
 
-    def setLevel(self,value):
+    def setLevel(self, value):
         """Set the undelying log level"""
         self.logger.setLevel(value)
 
@@ -54,7 +54,7 @@ class GNLogger:
 level=num to filter on LOG_LEVEL_DEBUG.
 
         """
-        self.collect(self.logger.debug,*args)
+        self.collect(self.logger.debug, *args)
 
     def debug20(self,*args):
         """Call logging.debug for multiple args. Use level=num to filter on
@@ -63,15 +63,15 @@ LOG_LEVEL_DEBUG (NYI).
         """
         if level <= LOG_LEVEL_DEBUG:
             if self.logger.getEffectiveLevel() < 20:
-                self.collect(self.logger.debug,*args)
+                self.collect(self.logger.debug, *args)
 
     def info(self,*args):
         """Call logging.info for multiple args"""
-        self.collect(self.logger.info,*args)
+        self.collect(self.logger.info, *args)
 
     def warning(self,*args):
         """Call logging.warning for multiple args"""
-        self.collect(self.logger.warning,*args)
+        self.collect(self.logger.warning, *args)
         # self.logger.warning(self.collect(*args))
 
     def error(self,*args):
@@ -79,13 +79,13 @@ LOG_LEVEL_DEBUG (NYI).
         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)
+        self.collect(self.logger.error, *l)
 
     def infof(self,*args):
         """Call logging.info for multiple args lazily"""
         # only evaluate function when logging
         if self.logger.getEffectiveLevel() < 30:
-            self.collectf(self.logger.debug,*args)
+            self.collectf(self.logger.debug, *args)
 
     def debugf(self,level=0,*args):
         """Call logging.debug for multiple args lazily and handle
@@ -95,15 +95,15 @@ LOG_LEVEL_DEBUG (NYI).
         # only evaluate function when logging
         if level <= LOG_LEVEL_DEBUG:
             if self.logger.getEffectiveLevel() < 20:
-                self.collectf(self.logger.debug,*args)
+                self.collectf(self.logger.debug, *args)
 
     def sql(self, sqlcommand, fun = None):
         """Log SQL command, optionally invoking a timed fun"""
         if LOG_SQL:
             caller = stack()[1][3]
-            if caller in ['fetchone','fetch1','fetchall']:
+            if caller in ['fetchone', 'fetch1', 'fetchall']:
                 caller = stack()[2][3]
-            self.info(caller,sqlcommand)
+            self.info(caller, sqlcommand)
         if fun:
             result = fun(sqlcommand)
             if LOG_SQL:
@@ -119,7 +119,7 @@ LOG_LEVEL_DEBUG (NYI).
             if isinstance(a, str):
                 out = out + a
             else:
-                out = out + pf(a,width=160)
+                out = out + pf(a, width=160)
         fun(out)
 
     def collectf(self,fun,*args):
@@ -134,7 +134,7 @@ LOG_LEVEL_DEBUG (NYI).
                     if isinstance(a, str):
                         out = out + a
                     else:
-                        out = out + pf(a,width=160)
+                        out = out + pf(a, width=160)
         fun(out)
 
 # Get the module logger. You can override log levels at the
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index dfbf3e19..1e2ed075 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -10,9 +10,9 @@ WHITE = ImageColor.getrgb("white")
 def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
     # type: (Image, str, ImageFont, tuple, ImageColor, int)
     """Utility function draw rotated text"""
-    tmp_img = Image.new("RGBA", font.getsize(text), color=(0,0,0,0))
+    tmp_img = Image.new("RGBA", font.getsize(text), color=(0, 0, 0, 0))
     draw_text = ImageDraw.Draw(tmp_img)
-    draw_text.text(text=text, xy=(0,0), font=font, fill=fill)
+    draw_text.text(text=text, xy=(0, 0), font=font, fill=fill)
     tmp_img2 = tmp_img.rotate(angle, expand=1)
     tmp_img2.save("/tmp/{}.png".format(text), format="png")
     canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy]))
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 42ead709..f1aaebb6 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -36,4 +36,4 @@ def app_config():
     # import utility.elasticsearch_tools as es
     # es.test_elasticsearch_connection()
 
-    print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))))
+    print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL"))))
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 874ada9d..19eda0ce 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -447,7 +447,7 @@ class rect(SVGelement):
         if width == None or height == None:
             raise ValueError('both height and width are required')
 
-        SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
+        SVGelement.__init__(self, 'rect', {'width':width,'height':height}, **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -468,7 +468,7 @@ class ellipse(SVGelement):
         if rx==None or ry== None:
             raise ValueError('both rx and ry are required')
 
-        SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
+        SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args)
         if cx!=None:
             self.attributes['cx']=cx
         if cy!=None:
@@ -489,7 +489,7 @@ class circle(SVGelement):
     def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args):
         if r==None:
             raise ValueError('r is required')
-        SVGelement.__init__(self,'circle',{'r':r},**args)
+        SVGelement.__init__(self, 'circle', {'r':r}, **args)
         if cx!=None:
             self.attributes['cx']=cx
         if cy!=None:
@@ -508,7 +508,7 @@ class point(circle):
     very small rectangle if you use many points because a circle is difficult to render.
     """
     def __init__(self,x,y,fill='black',**args):
-        circle.__init__(self,x,y,1,fill,**args)
+        circle.__init__(self, x, y, 1, fill, **args)
 
 class line(SVGelement):
     """l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
@@ -516,7 +516,7 @@ class line(SVGelement):
     A line is defined by a begin x,y pair and an end x,y pair
     """
     def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'line',**args)
+        SVGelement.__init__(self, 'line', **args)
         if x1!=None:
             self.attributes['x1']=x1
         if y1!=None:
@@ -536,7 +536,7 @@ class polyline(SVGelement):
     a polyline is defined by a list of xy pairs
     """
     def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args)
+        SVGelement.__init__(self, 'polyline', {'points':_xypointlist(points)}, **args)
         if fill!=None:
             self.attributes['fill']=fill
         if stroke_width!=None:
@@ -550,7 +550,7 @@ class polygon(SVGelement):
     a polygon is defined by a list of xy pairs
     """
     def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args)
+        SVGelement.__init__(self, 'polygon', {'points':_xypointlist(points)}, **args)
         if fill!=None:
             self.attributes['fill']=fill
         if stroke_width!=None:
@@ -564,7 +564,7 @@ class path(SVGelement):
     a path is defined by a path object and optional width, stroke and fillcolor
     """
     def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args):
-        SVGelement.__init__(self,'path',{'d':str(pathdata)},**args)
+        SVGelement.__init__(self, 'path', {'d':str(pathdata)}, **args)
         if stroke!=None:
             self.attributes['stroke']=stroke
         if fill!=None:
@@ -581,7 +581,7 @@ class text(SVGelement):
     a text element can bge used for displaying text on the screen
     """
     def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args):
-        SVGelement.__init__(self,'text',**args)
+        SVGelement.__init__(self, 'text', **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -602,7 +602,7 @@ class textpath(SVGelement):
     a textpath places a text on a path which is referenced by a link.
     """
     def __init__(self,link,text=None,**args):
-        SVGelement.__init__(self,'textPath',{'xlink:href':link},**args)
+        SVGelement.__init__(self, 'textPath', {'xlink:href':link}, **args)
         if text!=None:
             self.text=text
 
@@ -614,7 +614,7 @@ class pattern(SVGelement):
     in x and y to cover the areas to be painted.
     """
     def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args):
-        SVGelement.__init__(self,'pattern',**args)
+        SVGelement.__init__(self, 'pattern', **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -633,7 +633,7 @@ class title(SVGelement):
     add at least one to the root svg element
     """
     def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'title',**args)
+        SVGelement.__init__(self, 'title', **args)
         if text!=None:
             self.text=text
 
@@ -644,7 +644,7 @@ class description(SVGelement):
     Add this element before adding other elements.
     """
     def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'desc',**args)
+        SVGelement.__init__(self, 'desc', **args)
         if text!=None:
             self.text=text
 
@@ -655,7 +655,7 @@ class lineargradient(SVGelement):
     stop elements van be added to define the gradient colors.
     """
     def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args):
-        SVGelement.__init__(self,'linearGradient',**args)
+        SVGelement.__init__(self, 'linearGradient', **args)
         if x1!=None:
             self.attributes['x1']=x1
         if y1!=None:
@@ -674,7 +674,7 @@ class radialgradient(SVGelement):
     stop elements van be added to define the gradient colors.
     """
     def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args):
-        SVGelement.__init__(self,'radialGradient',**args)
+        SVGelement.__init__(self, 'radialGradient', **args)
         if cx!=None:
             self.attributes['cx']=cx
         if cy!=None:
@@ -694,7 +694,7 @@ class stop(SVGelement):
     Puts a stop color at the specified radius
     """
     def __init__(self,offset,stop_color=None,**args):
-        SVGelement.__init__(self,'stop',{'offset':offset},**args)
+        SVGelement.__init__(self, 'stop', {'offset':offset}, **args)
         if stop_color!=None:
             self.attributes['stop-color']=stop_color
 
@@ -704,7 +704,7 @@ class style(SVGelement):
     Add a CDATA element to this element for defing in line stylesheets etc..
     """
     def __init__(self,type,cdata=None,**args):
-        SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args)
+        SVGelement.__init__(self, 'style', {'type':type}, cdata=cdata, **args)
 
 
 class image(SVGelement):
@@ -715,7 +715,7 @@ class image(SVGelement):
     def __init__(self,url,x=None,y=None,width=None,height=None,**args):
         if width==None or height==None:
             raise ValueError('both height and width are required')
-        SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
+        SVGelement.__init__(self, 'image', {'xlink:href':url,'width':width,'height':height}, **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -727,7 +727,7 @@ class cursor(SVGelement):
     defines a custom cursor for a element or a drawing
     """
     def __init__(self,url,**args):
-        SVGelement.__init__(self,'cursor',{'xlink:href':url},**args)
+        SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args)
 
 
 class marker(SVGelement):
@@ -737,7 +737,7 @@ class marker(SVGelement):
     add an element to it which should be used as a marker.
     """
     def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args):
-        SVGelement.__init__(self,'marker',**args)
+        SVGelement.__init__(self, 'marker', **args)
         if id!=None:
             self.attributes['id']=id
         if viewBox!=None:
@@ -758,7 +758,7 @@ class group(SVGelement):
     g.addElement(SVGelement)
     """
     def __init__(self,id=None,**args):
-        SVGelement.__init__(self,'g',**args)
+        SVGelement.__init__(self, 'g', **args)
         if id!=None:
             self.attributes['id']=id
 
@@ -772,7 +772,7 @@ class symbol(SVGelement):
     """
 
     def __init__(self,id=None,viewBox=None,**args):
-        SVGelement.__init__(self,'symbol',**args)
+        SVGelement.__init__(self, 'symbol', **args)
         if id!=None:
             self.attributes['id']=id
         if viewBox!=None:
@@ -784,7 +784,7 @@ class defs(SVGelement):
     container for defining elements
     """
     def __init__(self,**args):
-        SVGelement.__init__(self,'defs',**args)
+        SVGelement.__init__(self, 'defs', **args)
 
 class switch(SVGelement):
     """sw=switch(**args)
@@ -794,7 +794,7 @@ class switch(SVGelement):
     Refer to the SVG specification for details.
     """
     def __init__(self,**args):
-        SVGelement.__init__(self,'switch',**args)
+        SVGelement.__init__(self, 'switch', **args)
 
 
 class use(SVGelement):
@@ -803,7 +803,7 @@ class use(SVGelement):
     references a symbol by linking to its id and its position, height and width
     """
     def __init__(self,link,x=None,y=None,width=None,height=None,**args):
-        SVGelement.__init__(self,'use',{'xlink:href':link},**args)
+        SVGelement.__init__(self, 'use', {'xlink:href':link}, **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -822,14 +822,14 @@ class link(SVGelement):
     a.addElement(SVGelement)
     """
     def __init__(self,link='',**args):
-        SVGelement.__init__(self,'a',{'xlink:href':link},**args)
+        SVGelement.__init__(self, 'a', {'xlink:href':link}, **args)
 
 class view(SVGelement):
     """v=view(id,**args)
 
     a view can be used to create a view with different attributes"""
     def __init__(self,id=None,**args):
-        SVGelement.__init__(self,'view',**args)
+        SVGelement.__init__(self, 'view', **args)
         if id!=None:
             self.attributes['id']=id
 
@@ -840,7 +840,7 @@ class script(SVGelement):
 
     """
     def __init__(self,type,cdata=None,**args):
-        SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args)
+        SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args)
 
 class animate(SVGelement):
     """an=animate(attribute,from,to,during,**args)
@@ -848,7 +848,7 @@ class animate(SVGelement):
     animates an attribute.
     """
     def __init__(self,attribute,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
+        SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args)
         if fr!=None:
             self.attributes['from']=fr
         if to!=None:
@@ -862,7 +862,7 @@ class animateMotion(SVGelement):
     animates a SVGelement over the given path in dur seconds
     """
     def __init__(self,pathdata,dur,**args):
-        SVGelement.__init__(self,'animateMotion',**args)
+        SVGelement.__init__(self, 'animateMotion', **args)
         if pathdata!=None:
             self.attributes['path']=str(pathdata)
         if dur!=None:
@@ -874,7 +874,7 @@ class animateTransform(SVGelement):
     transform an element from and to a value.
     """
     def __init__(self,type=None,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args)
+        SVGelement.__init__(self, 'animateTransform', {'attributeName':'transform'}, **args)
         # As far as I know the attributeName is always transform
         if type!=None:
             self.attributes['type']=type
@@ -890,7 +890,7 @@ class animateColor(SVGelement):
     Animates the color of a element
     """
     def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args)
+        SVGelement.__init__(self, 'animateColor', {'attributeName':attribute}, **args)
         if type!=None:
             self.attributes['type']=type
         if fr!=None:
@@ -905,7 +905,7 @@ class set(SVGelement):
     sets an attribute to a value for a
     """
     def __init__(self,attribute,to=None,dur=None,**args):
-        SVGelement.__init__(self,'set',{'attributeName':attribute},**args)
+        SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args)
         if to!=None:
             self.attributes['to']=to
         if dur!=None:
@@ -929,7 +929,7 @@ class svg(SVGelement):
     d.toXml()
     """
     def __init__(self,viewBox=None, width=None, height=None,**args):
-        SVGelement.__init__(self,'svg',**args)
+        SVGelement.__init__(self, 'svg', **args)
         if viewBox!=None:
             self.attributes['viewBox']=_viewboxlist(viewBox)
         if width!=None:
@@ -952,7 +952,7 @@ class drawing:
     def __init__(self, entity={}):
         self.svg=None
         self.entity = entity
-    def setSVG(self,svg):
+    def setSVG(self, svg):
         self.svg=svg
         # Voeg een element toe aan de grafiek toe.
     if use_dom_implementation==0:
@@ -967,12 +967,12 @@ class drawing:
                     xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
                 xml.write("]")
             xml.write(">\n")
-            self.svg.toXml(0,xml)
+            self.svg.toXml(0, xml)
             if not filename:
                 if compress:
                     import gzip
                     f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
+                    zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
                     f.seek(0)
@@ -982,11 +982,11 @@ class drawing:
             else:
                 if filename[-4:]=='svgz':
                     import gzip
-                    f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9)
+                    f=gzip.GzipFile(filename=filename, mode="wb", compresslevel=9)
                     f.write(xml.getvalue())
                     f.close()
                 else:
-                    f=file(filename,'w')
+                    f=file(filename, 'w')
                     f.write(xml.getvalue())
                     f.close()
 
@@ -997,40 +997,40 @@ class drawing:
             writes a svg drawing to the screen or to a file
             compresses if filename ends with svgz or if compress is true
             """
-            doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
+            doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
 
             global root
             # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
             # that is a bit messy.
-            root=implementation.createDocument(None,None,doctype)
+            root=implementation.createDocument(None, None, doctype)
             # Create the xml document.
             global appender
-            def appender(element,elementroot):
+            def appender(element, elementroot):
                 """This recursive function appends elements to an element and sets the attributes
                 and type. It stops when alle elements have been appended"""
                 if element.namespace:
-                    e=root.createElementNS(element.namespace,element.type)
+                    e=root.createElementNS(element.namespace, element.type)
                 else:
                     e=root.createElement(element.type)
                 if element.text:
                     textnode=root.createTextNode(element.text)
                     e.appendChild(textnode)
                 for attribute in list(element.attributes.keys()):   #in element.attributes is supported from python 2.2
-                    e.setAttribute(attribute,str(element.attributes[attribute]))
+                    e.setAttribute(attribute, str(element.attributes[attribute]))
                 if element.elements:
                     for el in element.elements:
-                        e=appender(el,e)
+                        e=appender(el, e)
                 elementroot.appendChild(e)
                 return elementroot
-            root=appender(self.svg,root)
+            root=appender(self.svg, root)
             if not filename:
                 import cStringIO
                 xml=cStringIO.StringIO()
-                PrettyPrint(root,xml)
+                PrettyPrint(root, xml)
                 if compress:
                     import gzip
                     f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
+                    zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
                     f.seek(0)
@@ -1043,13 +1043,13 @@ class drawing:
                         import gzip
                         import cStringIO
                         xml=cStringIO.StringIO()
-                        PrettyPrint(root,xml)
-                        f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9)
+                        PrettyPrint(root, xml)
+                        f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
                         f.write(xml.getvalue())
                         f.close()
                     else:
-                        f=open(filename,'w')
-                        PrettyPrint(root,f)
+                        f=open(filename, 'w')
+                        PrettyPrint(root, f)
                         f.close()
                 except:
                     print(("Cannot write SVG file: " + filename))
@@ -1070,32 +1070,32 @@ if __name__=='__main__':
 
 
     d=drawing()
-    s=svg((0,0,100,100))
-    r=rect(-100,-100,300,300,'cyan')
+    s=svg((0, 0, 100, 100))
+    r=rect(-100, -100, 300, 300, 'cyan')
     s.addElement(r)
 
     t=title('SVGdraw Demo')
     s.addElement(t)
     g=group('animations')
-    e=ellipse(0,0,5,2)
+    e=ellipse(0, 0, 5, 2)
     g.addElement(e)
-    c=circle(0,0,1,'red')
+    c=circle(0, 0, 1, 'red')
     g.addElement(c)
-    pd=pathdata(0,-10)
+    pd=pathdata(0, -10)
     for i in range(6):
-        pd.relsmbezier(10,5,0,10)
-        pd.relsmbezier(-10,5,0,10)
-    an=animateMotion(pd,10)
+        pd.relsmbezier(10, 5, 0, 10)
+        pd.relsmbezier(-10, 5, 0, 10)
+    an=animateMotion(pd, 10)
     an.attributes['rotate']='auto-reverse'
     an.attributes['repeatCount']="indefinite"
     g.addElement(an)
     s.addElement(g)
-    for i in range(20,120,20):
-        u=use('#animations',i,0)
+    for i in range(20, 120, 20):
+        u=use('#animations', i, 0)
         s.addElement(u)
-    for i in range(0,120,20):
-        for j in range(5,105,10):
-            c=circle(i,j,1,'red','black',.5)
+    for i in range(0, 120, 20):
+        for j in range(5, 105, 10):
+            c=circle(i, j, 1, 'red', 'black', .5)
             s.addElement(c)
     d.setSVG(s)
 
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 51a87fe1..68ef0f04 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -15,7 +15,7 @@ OVERRIDES = {}
 
 def app_set(command_id, value):
     """Set application wide value"""
-    app.config.setdefault(command_id,value)
+    app.config.setdefault(command_id, value)
     return value
 
 def get_setting(command_id,guess=None):
@@ -45,7 +45,7 @@ def get_setting(command_id,guess=None):
     def value(command):
         if command:
             # sys.stderr.write("Found "+command+"\n")
-            app_set(command_id,command)
+            app_set(command_id, command)
             return command
         else:
             return None
@@ -68,7 +68,7 @@ def get_setting(command_id,guess=None):
 
 def get_setting_bool(id):
     v = get_setting(id)
-    if v not in [0,False,'False','FALSE',None]:
+    if v not in [0, False, 'False', 'FALSE', None]:
       return True
     return False
 
@@ -108,16 +108,16 @@ def js_path(module=None):
     raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
 
 def reaper_command(guess=None):
-    return get_setting("REAPER_COMMAND",guess)
+    return get_setting("REAPER_COMMAND", guess)
 
 def gemma_command(guess=None):
-    return assert_bin(get_setting("GEMMA_COMMAND",guess))
+    return assert_bin(get_setting("GEMMA_COMMAND", guess))
 
 def gemma_wrapper_command(guess=None):
-    return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess))
+    return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess))
 
 def plink_command(guess=None):
-    return assert_bin(get_setting("PLINK_COMMAND",guess))
+    return assert_bin(get_setting("PLINK_COMMAND", guess))
 
 def flat_file_exists(subdir):
     base = get_setting("GENENETWORK_FILES")
@@ -180,7 +180,7 @@ def locate(name, subdir=None):
     raise Exception("Can not locate "+name+" in "+base)
 
 def locate_phewas(name, subdir=None):
-    return locate(name,'/phewas/'+subdir)
+    return locate(name, '/phewas/'+subdir)
 
 def locate_ignore_error(name, subdir=None):
     """
@@ -204,7 +204,7 @@ def tempdir():
     """
     Get UNIX TMPDIR by default
     """
-    return valid_path(get_setting("TMPDIR","/tmp"))
+    return valid_path(get_setting("TMPDIR", "/tmp"))
 
 BLUE  = '\033[94m'
 GREEN = '\033[92m'
@@ -225,9 +225,9 @@ def show_settings():
     keylist.sort()
     for k in keylist:
         try:
-            print(("%s: %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)))
+            print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC)))
         except:
-            print(("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)))
+            print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC)))
 
 
 # Cached values
@@ -279,10 +279,10 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT')
 SMTP_USERNAME = get_setting('SMTP_USERNAME')
 SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
 
-REAPER_COMMAND     = app_set("REAPER_COMMAND",reaper_command())
-GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
+REAPER_COMMAND     = app_set("REAPER_COMMAND", reaper_command())
+GEMMA_COMMAND      = app_set("GEMMA_COMMAND", gemma_command())
 assert(GEMMA_COMMAND is not None)
-PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
+PLINK_COMMAND      = app_set("PLINK_COMMAND", plink_command())
 GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 assert_dir(TEMPDIR)
@@ -295,11 +295,11 @@ assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
 CSS_PATH = JS_GUIX_PATH  # The CSS is bundled together with the JS
 # assert_dir(JS_PATH)
 
-JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher"))
 assert_dir(JS_TWITTER_POST_FETCHER_PATH)
 assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
 
-JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape"))
+JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape"))
 assert_dir(JS_CYTOSCAPE_PATH)
 assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')
 
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 79991149..77cc3416 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -41,22 +41,22 @@ ParInfo ={
 'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
 'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
 'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
-'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
-'BHF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
+'BHHBF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
+'BHF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
 'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
 'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
 'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'CTB6F2':['CTB6F2','B6CTF2','C57BL/6J','Castaneous'],
+'CTB6F2':['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
 'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
 'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
 'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
 'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
 'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'],
 'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
-'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'],
-'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'],
-'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'],
-'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'],
+'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
+'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
+'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
+'SXM':['SMF1', 'MSF1', 'Steptoe', 'Morex'],
 'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
 }
 
@@ -91,7 +91,7 @@ def readLineCSV(line): ### dcrowell July 2008
     returnList[0]=returnList[0][1:]
     return returnList
 
-def cmpEigenValue(A,B):
+def cmpEigenValue(A, B):
     try:
         if A[0] > B[0]:
             return -1
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 3fa1d5ba..b81da0dc 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -558,10 +558,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
         sample_list = []
         for sample in sample_data:
             sample_dict = {
-              "sample_name"   : sample[0],
-              "sample_name_2" : sample[1],
-              "value"         : sample[2],
-              "data_id"       : sample[3],
+              "sample_name": sample[0],
+              "sample_name_2": sample[1],
+              "value": sample[2],
+              "data_id": sample[3],
             }
             if sample[4]:
                 sample_dict["se"] = sample[4]
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 15a21ee6..4116e2df 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -108,17 +108,17 @@ class CorrelationResults(object):
             self.sample_data = {}
             self.corr_type = start_vars['corr_type']
             self.corr_method = start_vars['corr_sample_method']
-            self.min_expr = get_float(start_vars,'min_expr')
-            self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0)
-            self.p_range_upper = get_float(start_vars,'p_range_upper',1.0)
+            self.min_expr = get_float(start_vars, 'min_expr')
+            self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
+            self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
 
             if ('loc_chr' in start_vars and
                 'min_loc_mb' in start_vars and
                 'max_loc_mb' in start_vars):
 
-                self.location_chr = get_string(start_vars,'loc_chr')
-                self.min_location_mb = get_int(start_vars,'min_loc_mb')
-                self.max_location_mb = get_int(start_vars,'max_loc_mb')
+                self.location_chr = get_string(start_vars, 'loc_chr')
+                self.min_location_mb = get_int(start_vars, 'min_loc_mb')
+                self.max_location_mb = get_int(start_vars, 'max_loc_mb')
             else:
                 self.location_chr = self.min_location_mb = self.max_location_mb = None
 
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 832746bb..b582cd23 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -275,8 +275,8 @@ def zScore(trait_data_array):
         i = 0
         for data in trait_data_array:
             N = len(data)
-            S = reduce(lambda x,y: x+y, data, 0.)
-            SS = reduce(lambda x,y: x+y*y, data, 0.)
+            S = reduce(lambda x, y: x+y, data, 0.)
+            SS = reduce(lambda x, y: x+y*y, data, 0.)
             mean = S/N
             var = SS - S*S/N
             stdev = math.sqrt(var/(N-1))
@@ -294,7 +294,7 @@ def sortEigenVectors(vector):
         combines = []
         i = 0
         for item in eigenValues:
-            combines.append([eigenValues[i],eigenVectors[i]])
+            combines.append([eigenValues[i], eigenVectors[i]])
             i += 1
         combines.sort(webqtlUtil.cmpEigenValue)
         A = []
@@ -302,7 +302,7 @@ def sortEigenVectors(vector):
         for item in combines:
             A.append(item[0])
             B.append(item[1])
-        sum = reduce(lambda x,y: x+y, A, 0.0)
+        sum = reduce(lambda x, y: x+y, A, 0.0)
         A = [x*100.0/sum for x in A] 
         return [A, B]
     except:
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1e15d28f..cc9c1860 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -46,8 +46,8 @@ class DoSearch(object):
 
     def handle_wildcard(self, str):
         keyword = str.strip()
-        keyword = keyword.replace("*",".*")
-        keyword = keyword.replace("?",".")
+        keyword = keyword.replace("*", ".*")
+        keyword = keyword.replace("?", ".")
 
         return keyword
 
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 7a5dba73..9844bab4 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -54,10 +54,10 @@ class SendToGeneWeaver(object):
             trait_name_list = get_trait_name_list(self.trait_list)
 
             self.hidden_vars = {
-                                 'client'                     : "genenetwork",
-                                 'species'                    : species_name,
-                                 'idtype'                     : self.chip_name,
-                                 'list'                       : string.join(trait_name_list, ","),
+                                 'client': "genenetwork",
+                                 'species': species_name,
+                                 'idtype': self.chip_name,
+                                 'list': string.join(trait_name_list, ","),
                                }
 
 def get_trait_name_list(trait_list):
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index c8b9c405..f282b010 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -27,8 +27,8 @@
 import datetime
 import string
 from math import *
-from PIL import (Image,ImageDraw,ImageFont,ImageColor)
-import sys,os
+from PIL import (Image, ImageDraw, ImageFont, ImageColor)
+import sys, os
 import cPickle
 import httplib
 import json
@@ -426,7 +426,7 @@ class DisplayMappingResults(object):
                 else:
                     continue
             samplelist = list(self.genotype.prgy)
-            for j,_geno in enumerate (self.genotype[0][1].genotype):
+            for j, _geno in enumerate (self.genotype[0][1].genotype):
                 for item in smd:
                     if item.name == samplelist[j]:
                         self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
@@ -518,7 +518,7 @@ class DisplayMappingResults(object):
 
         #Scales plot differently for high resolution
         if self.draw2X:
-            intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2,self.graphHeight*2))
+            intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2))
             gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
             intCanvasX2.save(
                 "{}.png".format(
@@ -745,17 +745,17 @@ class DisplayMappingResults(object):
         bootScale = bootScale[:-1] + [highestPercent]
 
         bootOffset = 50*fontZoom
-        bootScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=13*fontZoom)
+        bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom)
         im_drawer.rectangle(
             xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh),
-                (canvas.size[0]-bootOffset-15*zoom,yZero)),
+                (canvas.size[0]-bootOffset-15*zoom, yZero)),
             fill = YELLOW, outline=BLACK)
         im_drawer.line(
             xy=((canvas.size[0]-bootOffset+4, yZero),
                 (canvas.size[0]-bootOffset, yZero)),
             fill=BLACK)
         TEXT_Y_DISPLACEMENT = -8
-        im_drawer.text(xy=(canvas.size[0]-bootOffset+10,yZero+TEXT_Y_DISPLACEMENT), text='0%',
+        im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
                        font=bootScaleFont, fill=BLACK)
 
         for item in bootScale:
@@ -763,10 +763,10 @@ class DisplayMappingResults(object):
                 continue
             bootY = yZero-bootHeightThresh*item/highestPercent
             im_drawer.line(
-                xy=((canvas.size[0]-bootOffset+4,bootY),
-                 (canvas.size[0]-bootOffset,bootY)),
+                xy=((canvas.size[0]-bootOffset+4, bootY),
+                 (canvas.size[0]-bootOffset, bootY)),
                 fill=BLACK)
-            im_drawer.text(xy=(canvas.size[0]-bootOffset+10,bootY+TEXT_Y_DISPLACEMENT),
+            im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT),
                            text='%2.1f'%item, font=bootScaleFont, fill=BLACK)
 
         if self.legendChecked:
@@ -775,7 +775,7 @@ class DisplayMappingResults(object):
             smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
             leftOffset = xLeftOffset+(nCol-1)*200
             im_drawer.rectangle(
-                xy=((leftOffset,startPosY-6), (leftOffset+12,startPosY+6)),
+                xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)),
                 fill=YELLOW, outline=BLACK)
             im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT),
                            text='Frequency of the Peak LRS',
@@ -872,7 +872,7 @@ class DisplayMappingResults(object):
             TEXT_Y_DISPLACEMENT = -8
             im_drawer.text(
                 text="Sequence Site",
-                xy=(leftOffset+15,startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
+                xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
                 fill=self.TOP_RIGHT_INFO_COLOR)
 
     def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -922,7 +922,7 @@ class DisplayMappingResults(object):
     def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1):
         nameWidths = []
         yPaddingTop = 10
-        colorFont=ImageFont.truetype(font=TREBUC_FILE,size=12)
+        colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12)
         if len(self.qtlresults) >20 and self.selectedChr > -1:
             rightShift = 20
             rightShiftStep = 60
@@ -941,20 +941,20 @@ class DisplayMappingResults(object):
                 rightShift += rightShiftStep
 
             name = thisTrait.displayName()
-            nameWidth, nameHeight = im_drawer.textsize(name,font=colorFont)
+            nameWidth, nameHeight = im_drawer.textsize(name, font=colorFont)
             nameWidths.append(nameWidth)
 
             im_drawer.rectangle(
-                xy=((rightShift,yPaddingTop+kstep*15),
-                    (rectWidth+rightShift,yPaddingTop+10+kstep*15)),
+                xy=((rightShift, yPaddingTop+kstep*15),
+                    (rectWidth+rightShift, yPaddingTop+10+kstep*15)),
                 fill=thisLRSColor, outline=BLACK)
             im_drawer.text(
-                text=name,xy=(rectWidth+2+rightShift,yPaddingTop+10+kstep*15),
-                font=colorFont,fill=BLACK)
+                text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15),
+                font=colorFont, fill=BLACK)
             if thisTrait.db:
-                COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
+                COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,)
                 HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
-                Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
+                Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
                 gifmap.areas.append(Areas)
 
     def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
@@ -968,80 +968,80 @@ class DisplayMappingResults(object):
         if zoom == 2:
             fontZoom = 1.5
 
-        labelFont=ImageFont.truetype(font=TREBUC_FILE,size=12*fontZoom)
+        labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
         startPosY = 15
         stepPosY = 12*fontZoom
         if self.manhattan_plot != True:
             im_drawer.line(
-                xy=((xLeftOffset,startPosY),(xLeftOffset+32,startPosY)),
+                xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)),
                 fill=self.LRS_COLOR, width=2)
             im_drawer.text(
-                text=self.LRS_LOD, xy=(xLeftOffset+40,startPosY+TEXT_Y_DISPLACEMENT),
-                font=labelFont,fill=BLACK)
+                text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT),
+                font=labelFont, fill=BLACK)
             startPosY += stepPosY
 
         if self.additiveChecked:
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+32,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+32, startPosY)),
                 fill=self.ADDITIVE_COLOR_NEGATIVE, width=2)
             im_drawer.text(
-                text='Additive Effect',xy=(startPosX+40,startPosY+TEXT_Y_DISPLACEMENT),
-                font=labelFont,fill=BLACK)
+                text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
+                font=labelFont, fill=BLACK)
 
         if self.genotype.type == 'intercross' and self.dominanceChecked:
             startPosX = xLeftOffset
             startPosY += stepPosY
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
                 fill=self.DOMINANCE_COLOR_NEGATIVE, width=4)
             im_drawer.text(
-                text='Dominance Effect', xy=(startPosX+42,startPosY+5),
-                font=labelFont,fill=BLACK)
+                text='Dominance Effect', xy=(startPosX+42, startPosY+5),
+                font=labelFont, fill=BLACK)
 
         if self.haplotypeAnalystChecked:
             startPosY += stepPosY
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.HAPLOTYPE_POSITIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
                 fill=self.HAPLOTYPE_NEGATIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+36,startPosY),(startPosX+53,startPosY)),
+                xy=((startPosX+36, startPosY), (startPosX+53, startPosY)),
                 fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
             im_drawer.line(
-                xy=((startPosX+54,startPosY),(startPosX+67,startPosY)),
+                xy=((startPosX+54, startPosY), (startPosX+67, startPosY)),
                 fill=self.HAPLOTYPE_RECOMBINATION, width=4)
             im_drawer.text(
                 text='Haplotypes (Pat, Mat, Het, Unk)',
-                xy=(startPosX+76,startPosY+5),font=labelFont,fill=BLACK)
+                xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK)
 
         if self.permChecked and self.nperm > 0:
             startPosY += stepPosY
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX, startPosY),( startPosX + 32, startPosY)),
+                xy=((startPosX, startPosY), ( startPosX + 32, startPosY)),
                 fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
             im_drawer.line(
-                xy=((startPosX, startPosY + stepPosY),( startPosX + 32, startPosY + stepPosY)),
+                xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
                 fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
             im_drawer.text(
-                text='Significant %s = %2.2f' % (self.LRS_LOD,self.significant),
-                xy=(xLeftOffset+42,startPosY+TEXT_Y_DISPLACEMENT),font=labelFont,fill=BLACK)
+                text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
+                xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
             im_drawer.text(
                 text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
-                xy=(xLeftOffset+42,startPosY + TEXT_Y_DISPLACEMENT +stepPosY),font=labelFont,
+                xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
                 fill=BLACK)
 
-        labelFont = ImageFont.truetype(font=VERDANA_FILE,size=12*fontZoom)
+        labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
         labelColor = BLACK
         if self.dataset.type == "Publish" or self.dataset.type == "Geno":
             dataset_label = self.dataset.fullname
@@ -1109,22 +1109,22 @@ class DisplayMappingResults(object):
                 im_drawer.textsize(string2, font=labelFont)[0])
             im_drawer.text(
                 text=identification,
-                xy=(canvas.size[0] - xRightOffset-d,20*fontZoom),font=labelFont,
+                xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont,
                 fill=labelColor)
         else:
             d = 4+ max(
                 im_drawer.textsize(string1, font=labelFont)[0],
                 im_drawer.textsize(string2, font=labelFont)[0])
         im_drawer.text(
-            text=string1,xy=(canvas.size[0] - xRightOffset-d,35*fontZoom),
-            font=labelFont,fill=labelColor)
+            text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom),
+            font=labelFont, fill=labelColor)
         im_drawer.text(
-            text=string2,xy=(canvas.size[0] - xRightOffset-d,50*fontZoom),
-            font=labelFont,fill=labelColor)
+            text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom),
+            font=labelFont, fill=labelColor)
         if string3 != '':
             im_drawer.text(
-                text=string3,xy=(canvas.size[0] - xRightOffset-d,65*fontZoom),
-                font=labelFont,fill=labelColor)
+                text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom),
+                font=labelFont, fill=labelColor)
 
 
     def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1345,7 +1345,7 @@ class DisplayMappingResults(object):
                             labelText = "3'"
                             im_drawer.text(
                                 text=labelText,
-                                xy=(utrEndPix+2,geneYLocation+self.EACH_GENE_HEIGHT),
+                                xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT),
                                 font=ImageFont.truetype(font=ARIAL_FILE, size=2))
 
             #draw the genes as rectangles
@@ -1357,7 +1357,7 @@ class DisplayMappingResults(object):
 
             COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
             # NL: 06-02-2011 Rob required to display NCBI info in a new window
-            gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
+            gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE, target="_blank"))
 
 ## BEGIN HaplotypeAnalyst
     def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1490,7 +1490,7 @@ class DisplayMappingResults(object):
                                         counter = counter + 1
                                         if item.name == samplelist[k]:
                                             ind = counter
-                                    maxind=max(ind,maxind)
+                                    maxind=max(ind, maxind)
 
                                     # lines
                                     if (oldgeno[k] == -1 and _geno == -1):
@@ -1523,7 +1523,7 @@ class DisplayMappingResults(object):
                                     COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
                                     TITLE = "Strain: %s, marker (%s) \n Position  %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
                                     HREF = ''
-                                    gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
+                                    gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE))
 
                                     # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
                                     # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
@@ -1642,14 +1642,14 @@ class DisplayMappingResults(object):
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
 
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
-                gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
+                gifmap.areas.append(HT.Area(shape='rect', coords=WEBQTL_COORDS, href=WEBQTL_HREF, title=WEBQTL_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, paddingTop),
                         (xBrowse2, (paddingTop + self.BAND_HEIGHT))),
                     outline=self.CLICKABLE_WEBQTL_REGION_COLOR,
                     fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
                 im_drawer.line(
-                    xy=((xBrowse1, paddingTop),( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
+                    xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
                     fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
 
                 if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
@@ -1659,14 +1659,14 @@ class DisplayMappingResults(object):
                     else:
                         PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                     PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
-                    gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+                    gifmap.areas.append(HT.Area(shape='rect', coords=PHENOGEN_COORDS, href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
                     im_drawer.rectangle(
                         xy=((xBrowse1, phenogenPaddingTop),
                             (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))),
                         outline=self.CLICKABLE_PHENOGEN_REGION_COLOR,
                         fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
                     im_drawer.line(
-                        xy=((xBrowse1, phenogenPaddingTop),( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
+                        xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
                         fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
 
                 UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
@@ -1675,7 +1675,7 @@ class DisplayMappingResults(object):
                 else:
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
-                gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
+                gifmap.areas.append(HT.Area(shape='rect', coords=UCSC_COORDS, href=UCSC_HREF, title=UCSC_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, ucscPaddingTop),
                         (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))),
@@ -1692,7 +1692,7 @@ class DisplayMappingResults(object):
                 else:
                     ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
-                gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+                gifmap.areas.append(HT.Area(shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, ensemblPaddingTop),
                         (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))),
@@ -1789,8 +1789,8 @@ class DisplayMappingResults(object):
                         continue
                     Xc = xLeftOffset + plotXScale*(_Mb - startMb)
                     if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
-                        im_drawer.line(xy=((Xc,yZero),
-                                           (Xc,yZero+xMajorTickHeight)),
+                        im_drawer.line(xy=((Xc, yZero),
+                                           (Xc, yZero+xMajorTickHeight)),
                                        fill=xAxisTickMarkColor,
                                        width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
                         labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
@@ -1800,8 +1800,8 @@ class DisplayMappingResults(object):
                                        text=labelStr, font=MBLabelFont,
                                        fill=xAxisLabelColor)
                     else:
-                        im_drawer.line(xy=((Xc,yZero),
-                                          (Xc,yZero+xMinorTickHeight)),
+                        im_drawer.line(xy=((Xc, yZero),
+                                          (Xc, yZero+xMinorTickHeight)),
                                        fill=xAxisTickMarkColor,
                                        width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
 
@@ -1834,7 +1834,7 @@ class DisplayMappingResults(object):
                 text="Megabases",
                 xy=(
                     xLeftOffset+(plotWidth-im_drawer.textsize(
-                        "Megabases",font=megabaseLabelFont)[0])/2,
+                        "Megabases", font=megabaseLabelFont)[0])/2,
                     strYLoc+MBLabelFont.font.height+10*(zoom%2)),
                 font=megabaseLabelFont, fill=BLACK)
             pass
@@ -1889,7 +1889,7 @@ class DisplayMappingResults(object):
             for j, ChrInfo in enumerate(ChrAInfo):
                 preLpos = -1
                 for i, item in enumerate(ChrInfo):
-                    Lname,Lpos = item
+                    Lname, Lpos = item
                     if Lpos != preLpos:
                         offsetA += stepA
                         differ = 1
@@ -1903,17 +1903,17 @@ class DisplayMappingResults(object):
                         Zorder = 0
                     if differ:
                         im_drawer.line(
-                            xy=((startPosX+Lpos,yZero),(xLeftOffset+offsetA,\
+                            xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\
                         yZero+25)),
                             fill=lineColor)
                         im_drawer.line(
-                            xy=((xLeftOffset+offsetA,yZero+25),(xLeftOffset+offsetA,\
+                            xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\
                         yZero+40+Zorder*(LRectWidth+3))),
                             fill=lineColor)
                         rectColor = ORANGE
                     else:
                         im_drawer.line(
-                            xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3),(\
+                            xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\
                         xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))),
                             fill=lineColor)
                         rectColor = DEEPPINK
@@ -1921,9 +1921,9 @@ class DisplayMappingResults(object):
                         xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)),
                             (xLeftOffset+offsetA-LRectHeight,
                              yZero+40+Zorder*(LRectWidth+3)+LRectWidth)),
-                        outline=rectColor,fill=rectColor,width = 0)
+                        outline=rectColor, fill=rectColor, width = 0)
                     COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
-                            xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
+                            xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
                     HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
                     #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
                     Areas=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
@@ -1931,7 +1931,7 @@ class DisplayMappingResults(object):
                 ##piddle bug
                 if j == 0:
                     im_drawer.line(
-                        xy=((startPosX,yZero),(startPosX,yZero+40)),
+                        xy=((startPosX, yZero), (startPosX, yZero+40)),
                         fill=lineColor)
                 startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
 
@@ -1943,7 +1943,7 @@ class DisplayMappingResults(object):
                     strYLoc + MBLabelFont.font.height+ 10*(zoom%2)),
                 font=centimorganLabelFont, fill=BLACK)
 
-        im_drawer.line(xy=((xLeftOffset,yZero), (xLeftOffset+plotWidth,yZero)),
+        im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)),
                        fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
 
 
@@ -2079,7 +2079,7 @@ class DisplayMappingResults(object):
                 LRS_LOD_Max = 0.000001
             yTopOffset + 30*(zoom - 1)
             yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh
-            im_drawer.line(xy=((xLeftOffset,yLRS), (xLeftOffset-4,yLRS)),
+            im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)),
                            fill=self.LRS_COLOR, width=1*zoom)
             if all_int:
                 scaleStr = "%d" % item
@@ -2127,8 +2127,8 @@ class DisplayMappingResults(object):
                 else:
                     sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
                     sig_title = "Significant LOD = %0.2f" % (self.significant/4.61)
-                Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
-                Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
+                Areas1 = HT.Area(shape='rect', coords=sugg_coords, title=sugg_title)
+                Areas2 = HT.Area(shape='rect', coords=sig_coords, title=sig_title)
                 gifmap.areas.append(Areas1)
                 gifmap.areas.append(Areas2)
 
@@ -2316,7 +2316,7 @@ class DisplayMappingResults(object):
                     im_drawer.text(
                         text="5",
                         xy=(
-                            Xc-im_drawer.textsize("5",font=symbolFont)[0]/2+1,
+                            Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1,
                             Yc-4),
                         fill=point_color, font=symbolFont)
                 else:
@@ -2383,8 +2383,8 @@ class DisplayMappingResults(object):
                             )
                         else:
                             im_drawer.line(
-                                xy=((Xc0,yZero-(Yc0-yZero)),
-                                    (Xc,yZero-(Yc-yZero))),
+                                xy=((Xc0, yZero-(Yc0-yZero)),
+                                    (Xc, yZero-(Yc-yZero))),
                                 fill=minusColor, width=lineWidth
                                 #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
                             )
@@ -2471,8 +2471,8 @@ class DisplayMappingResults(object):
 
         ###draw additive scale
         if not self.multipleInterval and self.additiveChecked:
-            additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=16*zoom)
-            additiveScale = Plot.detScaleOld(0,additiveMax)
+            additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
+            additiveScale = Plot.detScaleOld(0, additiveMax)
             additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
             additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
             addPlotScale = AdditiveHeightThresh/additiveMax
@@ -2482,18 +2482,18 @@ class DisplayMappingResults(object):
             for item in additiveAxisList:
                 additiveY = yZero - item*addPlotScale
                 im_drawer.line(
-                    xy=((xLeftOffset + plotWidth,additiveY),
-                        (xLeftOffset+4+ plotWidth,additiveY)),
+                    xy=((xLeftOffset + plotWidth, additiveY),
+                        (xLeftOffset+4+ plotWidth, additiveY)),
                     fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
                 scaleStr = "%2.3f" % item
                 im_drawer.text(
                     text=scaleStr,
-                    xy=(xLeftOffset + plotWidth +6,additiveY+TEXT_Y_DISPLACEMENT),
-                    font=additiveScaleFont,fill=self.ADDITIVE_COLOR_POSITIVE)
+                    xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT),
+                    font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
 
             im_drawer.line(
-                xy=((xLeftOffset+plotWidth,additiveY),
-                    (xLeftOffset+plotWidth,yZero)),
+                xy=((xLeftOffset+plotWidth, additiveY),
+                    (xLeftOffset+plotWidth, yZero)),
                 fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
 
         im_drawer.line(
@@ -2553,7 +2553,7 @@ class DisplayMappingResults(object):
                 chrFontZoom = 2
             else:
                 chrFontZoom = 1
-            chrLabelFont=ImageFont.truetype(font=VERDANA_FILE,size=24*chrFontZoom)
+            chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom)
 
             for i, _chr in enumerate(self.genotype):
                 if (i % 2 == 0):
@@ -2575,10 +2575,10 @@ class DisplayMappingResults(object):
                 TEXT_Y_DISPLACEMENT = 0
                 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT),
                                text=_chr.name, font=chrLabelFont, fill=BLACK)
-                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
+                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20)
 
                 #add by NL 09-03-2010
-                HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList)
+                HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList)
                 #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
                 Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
                 gifmap.areas.append(Areas)
@@ -2720,7 +2720,7 @@ class DisplayMappingResults(object):
                     else:
                         chr_as_int = int(theGO["Chromosome"]) - 1
                     if refGene:
-                        literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
+                        literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A")
 
                         this_row = [selectCheck.__str__(),
                                     str(tableIterationsCnt),
@@ -2820,8 +2820,8 @@ class DisplayMappingResults(object):
         lCorr = None
         try:
             query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
-            for x,y in [(geneId1,geneId2),(geneId2,geneId1)]:
-                cursor.execute(query,(x,y))
+            for x, y in [(geneId1, geneId2), (geneId2, geneId1)]:
+                cursor.execute(query, (x, y))
                 lCorr =  cursor.fetchone()
                 if lCorr:
                     lCorr = lCorr[0]
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index d4ee6fe6..2f282adc 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -54,7 +54,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
     for i, sample in enumerate(ped_sample_list):
         try:
             value = vals[i]
-            value = str(value).replace('value=','')
+            value = str(value).replace('value=', '')
             value = value.strip()
         except:
             value = -9999
@@ -78,7 +78,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
 
 # get strain name from ped file in order
 def get_samples_from_ped_file(dataset):
-    ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r")
+    ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r")
     line = ped_file.readline()
     sample_list=[]
 
@@ -155,7 +155,7 @@ def parse_plink_output(output_filename, species):
 # output: lineList list
 #######################################################
 def build_line_list(line=None):
-    line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
+    line_list = string.split(string.strip(line), ' ')# irregular number of whitespaces between columns
     line_list = [item for item in line_list if item !='']
     line_list = list(map(string.strip, line_list))
 
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 145dbc77..1e6dff57 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -707,7 +707,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
 
         perm_strata_strings.append(combined_string)
 
-    d = dict([(y,x+1) for x,y in enumerate(sorted(set(perm_strata_strings)))])
+    d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))])
     list_to_numbers = [d[x] for x in perm_strata_strings]
     perm_strata = list_to_numbers
 
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 5b3946e3..c07a7670 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -53,7 +53,7 @@ views.py).
         search = self.search_terms
         self.original_search_string = self.search_terms
         # check for dodgy search terms
-        rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE)
+        rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
         if rx.match(search):
             logger.info("Regex failed search")
             self.search_term_exists = False
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 21ba7f63..f17e825e 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -57,7 +57,7 @@ class SampleList(object):
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
 
             sample.extra_info = {}
-            if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'):
+            if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17'):
                 sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
                 sample.extra_info['css_class'] = "fs12"
 
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index a871e91a..232cb8da 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -867,7 +867,7 @@ def forgot_password_submit():
     email_address = params['email_address']
     next_page = None
     if email_address != "":
-        logger.debug("Wants to send password E-mail to ",email_address)
+        logger.debug("Wants to send password E-mail to ", email_address)
         user_details = get_user_by_unique_column("email_address", email_address)
         if user_details:
             ForgotPasswordEmail(user_details["email_address"])
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 394a9e28..92c20fc7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -55,7 +55,7 @@ from wqflask.ctl import ctl_analysis
 from wqflask.snp_browser import snp_browser
 
 from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
+from utility.tools import SQL_URI, TEMPDIR, USE_REDIS, USE_GN_SERVER, GN_SERVER_URL, GN_VERSION, JS_TWITTER_POST_FETCHER_PATH, JS_GUIX_PATH, CSS_PATH
 from utility.helper_functions import get_species_groups
 from utility.authentication_tools import check_resource_availability
 from utility.redis_tools import get_redis_conn
@@ -133,10 +133,10 @@ def handle_bad_request(e):
         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,version=GN_VERSION))
+    resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION))
 
     # logger.error("Set cookie %s with %s" % (err_msg, animation))
-    resp.set_cookie(err_msg[:32],animation)
+    resp.set_cookie(err_msg[:32], animation)
     return resp
 
 @app.route("/authentication_needed")
@@ -257,7 +257,7 @@ def docedit():
 @app.route('/generated/<filename>')
 def generated_file(filename):
     logger.info(request.url)
-    return send_from_directory(GENERATED_IMAGE_DIR,filename)
+    return send_from_directory(GENERATED_IMAGE_DIR, filename)
 
 @app.route("/help")
 def help():
-- 
cgit v1.2.3


From 1f4fb6b24f3508d80be1f07cd62e38ac9385ef41 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 20 Aug 2020 16:35:17 +0300
Subject: Handle module renames in the standard library

Run:
```
2to3-3.8 -f imports -w . && \
2to3-3.8 -f imports2 -w .
```

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-imports> and
<https://docs.python.org/2/library/2to3.html#2to3fixer-imports2>
---
 wqflask/base/data_set.py                                 |  2 +-
 wqflask/maintenance/gen_select_dataset.py                |  4 ++--
 wqflask/maintenance/quantile_normalize.py                |  4 ++--
 wqflask/maintenance/set_resource_defaults.py             |  4 ++--
 wqflask/utility/svg.py                                   | 16 ++++++++--------
 wqflask/wqflask/api/router.py                            | 14 +++++++-------
 wqflask/wqflask/collect.py                               |  2 +-
 .../wqflask/comparison_bar_chart/comparison_bar_chart.py |  2 +-
 wqflask/wqflask/correlation/show_corr_results.py         |  2 +-
 wqflask/wqflask/correlation_matrix/show_corr_matrix.py   |  2 +-
 wqflask/wqflask/export_traits.py                         |  4 ++--
 wqflask/wqflask/heatmap/heatmap.py                       |  4 ++--
 .../wqflask/marker_regression/display_mapping_results.py |  4 ++--
 wqflask/wqflask/marker_regression/run_mapping.py         |  2 +-
 wqflask/wqflask/network_graph/network_graph.py           |  2 +-
 wqflask/wqflask/show_trait/show_trait.py                 |  2 +-
 wqflask/wqflask/user_manager.py                          |  2 +-
 wqflask/wqflask/views.py                                 | 12 ++++++------
 18 files changed, 42 insertions(+), 42 deletions(-)

(limited to 'wqflask/utility/svg.py')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 43beec26..8151a29d 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -44,7 +44,7 @@ import codecs
 import json
 import requests
 import gzip
-import cPickle as pickle
+import pickle as pickle
 import itertools
 
 from redis import Redis
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index d12b328f..fd65a52a 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -50,7 +50,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
 import MySQLdb
 
 import simplejson as json
-import urlparse
+import urllib.parse
 
 
 #import sqlalchemy as sa
@@ -66,7 +66,7 @@ from pprint import pformat as pf
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
-    parsed_uri = urlparse.urlparse(SQL_URI)
+    parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
                         db = parsed_uri.path[1:],
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 43edfd13..4d6e03bf 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -6,7 +6,7 @@ sys.path.insert(0, './')
 
 
 import MySQLdb
-import urlparse
+import urllib.parse
 
 import numpy as np
 import pandas as pd
@@ -22,7 +22,7 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
-    parsed_uri = urlparse.urlparse(SQL_URI)
+    parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
                         db = parsed_uri.path[1:],
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index d53a255b..abd5416c 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -34,7 +34,7 @@ Redis = get_redis_conn()
 
 import MySQLdb
 
-import urlparse
+import urllib.parse
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
@@ -42,7 +42,7 @@ logger = getLogger(__name__)
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
-    parsed_uri = urlparse.urlparse(SQL_URI)
+    parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
                         db = parsed_uri.path[1:],
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 19eda0ce..b92cc2d1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -957,8 +957,8 @@ class drawing:
         # Voeg een element toe aan de grafiek toe.
     if use_dom_implementation==0:
         def toXml(self, filename='',compress=False):
-            import cStringIO
-            xml=cStringIO.StringIO()
+            import io
+            xml=io.StringIO()
             xml.write("<?xml version='1.0' encoding='UTF-8'?>\n")
             xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"")
             if self.entity:
@@ -971,7 +971,7 @@ class drawing:
             if not filename:
                 if compress:
                     import gzip
-                    f=cStringIO.StringIO()
+                    f=io.StringIO()
                     zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
@@ -1024,12 +1024,12 @@ class drawing:
                 return elementroot
             root=appender(self.svg, root)
             if not filename:
-                import cStringIO
-                xml=cStringIO.StringIO()
+                import io
+                xml=io.StringIO()
                 PrettyPrint(root, xml)
                 if compress:
                     import gzip
-                    f=cStringIO.StringIO()
+                    f=io.StringIO()
                     zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
@@ -1041,8 +1041,8 @@ class drawing:
                 try:
                     if filename[-4:]=='svgz':
                         import gzip
-                        import cStringIO
-                        xml=cStringIO.StringIO()
+                        import io
+                        xml=io.StringIO()
                         PrettyPrint(root, xml)
                         f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
                         f.write(xml.getvalue())
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index b81da0dc..5f9b81b8 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -6,7 +6,7 @@ import os, io, csv, json, datetime, requests, yaml
 import zlib
 from zipfile import ZipFile, ZIP_DEFLATED
 
-import StringIO
+import io
 
 import flask
 from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, send_file
@@ -308,7 +308,7 @@ def fetch_traits(dataset_name, file_format = "json"):
         else:
             filename = dataset_name + "_trait_ids.csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows([[trait_id] for trait_id in trait_ids])
             output = make_response(si.getvalue())
@@ -322,7 +322,7 @@ def fetch_traits(dataset_name, file_format = "json"):
         else:
             filename = dataset_name + "_trait_names.csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows([[trait_name] for trait_name in trait_names])
             output = make_response(si.getvalue())
@@ -413,7 +413,7 @@ def fetch_traits(dataset_name, file_format = "json"):
                 for result in g.db.execute(final_query).fetchall():
                     results_list.append(result)
 
-                si = StringIO.StringIO()
+                si = io.StringIO()
                 csv_writer = csv.writer(si)
                 csv_writer.writerows(results_list)
                 output = make_response(si.getvalue())
@@ -519,7 +519,7 @@ def all_sample_data(dataset_name, file_format = "csv"):
 
             results_list = list(map(list, zip(*results_list)))
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows(results_list)
             output = make_response(si.getvalue())
@@ -706,7 +706,7 @@ def get_mapping_results():
         if format == "csv":
             filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows(results)
             output = make_response(si.getvalue())
@@ -732,7 +732,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
         if request.args['limit_to'].isdigit():
             limit_num = int(request.args['limit_to'])
 
-    si = StringIO.StringIO()
+    si = io.StringIO()
     if file_format == "csv" or file_format == "geno":
         filename = group_name + ".geno"
 
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 4c6e38e6..d77567f8 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -10,7 +10,7 @@ import uuid
 import hashlib
 import base64
 
-import urlparse
+import urllib.parse
 
 import simplejson as json
 
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 09d6b9cc..3e5daa50 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -24,7 +24,7 @@ import sys
 # sys.path.append(".")   Never do this in a webserver!
 
 import string
-import cPickle
+import pickle
 import os
 import time
 import pp
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 4116e2df..65360040 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -23,7 +23,7 @@ from __future__ import absolute_import, print_function, division
 import sys
 
 import string
-import cPickle
+import pickle
 import os
 import time
 import pp
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index b582cd23..ea786289 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -24,7 +24,7 @@ import sys
 # sys.path.append(".")   Never do this in a webserver!
 
 import string
-import cPickle
+import pickle
 import os
 import datetime
 import time
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index a8b49829..2f4e9aac 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -2,7 +2,7 @@ from __future__ import print_function, division
 
 import csv
 import xlsxwriter
-import StringIO 
+import io 
 import datetime
 import itertools
 
@@ -63,7 +63,7 @@ def export_search_results_csv(targs):
     file_list = []
     for group in list(traits_by_group.keys()):
         group_traits = traits_by_group[group]
-        buff = StringIO.StringIO()
+        buff = io.StringIO()
         writer = csv.writer(buff)
         csv_rows = []
 
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 577426b0..4fdc1f13 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -4,7 +4,7 @@ import sys
 # sys.path.append(".") Never in a running webserver
 
 import string
-import cPickle
+import pickle
 import os
 import datetime
 import time
@@ -30,7 +30,7 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 
 from MySQLdb import escape_string as escape
 
-import cPickle as pickle
+import pickle as pickle
 import simplejson as json
 
 from pprint import pformat as pf
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f282b010..f06db5d5 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -29,8 +29,8 @@ import string
 from math import *
 from PIL import (Image, ImageDraw, ImageFont, ImageColor)
 import sys, os
-import cPickle
-import httplib
+import pickle
+import http.client
 import json
 
 from flask import Flask, g
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 1e6dff57..67512bc6 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -18,7 +18,7 @@ import uuid
 import rpy2.robjects as ro
 import numpy as np
 
-import cPickle as pickle
+import pickle as pickle
 import itertools
 
 import simplejson as json
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index ac2ff017..7916651f 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -23,7 +23,7 @@ from __future__ import absolute_import, print_function, division
 import sys
 
 import string
-import cPickle
+import pickle
 import os
 import time
 import pp
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 65899ab2..738aa28a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -3,7 +3,7 @@ from __future__ import absolute_import, print_function, division
 import string
 import os
 import datetime
-import cPickle
+import pickle
 import uuid
 import requests
 import json as json
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 232cb8da..56d1c084 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -9,7 +9,7 @@ import uuid
 import hashlib
 import hmac
 import base64
-import urlparse
+import urllib.parse
 
 import simplejson as json
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 92c20fc7..83d5202e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -14,13 +14,13 @@ import csv
 import simplejson as json
 import yaml
 import xlsxwriter
-import StringIO  # Todo: Use cStringIO?
+import io  # Todo: Use cStringIO?
 
 from zipfile import ZipFile, ZIP_DEFLATED
 
 import gc
 import numpy as np
-import cPickle as pickle
+import pickle as pickle
 import uuid
 
 import flask
@@ -373,7 +373,7 @@ def export_trait_excel():
 
     logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     workbook = xlsxwriter.Workbook(buff, {'in_memory': True})
     worksheet = workbook.add_worksheet()
     for i, row in enumerate(sample_data):
@@ -397,7 +397,7 @@ def export_trait_csv():
 
     logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     writer = csv.writer(buff)
     for row in sample_data:
         writer.writerow(row)
@@ -417,7 +417,7 @@ def export_traits_csv():
     file_list = export_traits.export_search_results_csv(request.form)
 
     if len(file_list) > 1:
-        memory_file = StringIO.StringIO()
+        memory_file = io.StringIO()
         with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf:
             for the_file in file_list:
                 zf.writestr(the_file[0], the_file[1])
@@ -460,7 +460,7 @@ def export_perm_data():
         ["#Comment: Results sorted from low to high peak linkage"]
     ]
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     writer = csv.writer(buff)
     writer.writerows(the_rows)
     for item in perm_info['perm_data']:
-- 
cgit v1.2.3