Removed several unused files from the base folder and their references in other files

28 files changed, 0 insertions, 1318 deletions

diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
deleted file mode 100755
index 53d1357b..00000000
--- a/wqflask/base/GeneralObject.py
+++ /dev/null
@@ -1,68 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-class GeneralObject:
-    """
-    Base class to define an Object.
-    a = [Spam(1, 4), Spam(9, 3), Spam(4,6)]
-    a.sort(lambda x, y: cmp(x.eggs, y.eggs))
-    """
-
-    def __init__(self, *args, **kw):
-        self.contents = list(args)
-        for name, value in kw.items():
-            setattr(self, name, value)
-
-    def __setitem__(self, key, value):
-        setattr(self, key, value)
-
-    def __getitem__(self, key):
-        return getattr(self, key)
-
-    def __getattr__(self, key):
-        if key in self.__dict__.keys():
-            return self.__dict__[key]
-        else:
-            return eval("self.__dict__.%s" % key)
-
-    def __len__(self):
-        return len(self.__dict__) - 1
-
-    def __str__(self):
-        s = ''
-        for key in 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():
-            s += '%s = %s\n' % (key,self.__dict__[key])
-        return s
-
-    def __cmp__(self,other):
-        return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys()))
diff --git a/wqflask/base/JinjaPage.py b/wqflask/base/JinjaPage.py
deleted file mode 100755
index 07e485b1..00000000
--- a/wqflask/base/JinjaPage.py
+++ /dev/null
@@ -1,28 +0,0 @@
-import logging
-logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
-_log = logging.getLogger("search")
-
-from pprint import pformat as pf
-
-import templatePage
-
-from utility import formatting
-
-import jinja2
-JinjaEnv = jinja2.Environment(loader=jinja2.FileSystemLoader('/gnshare/gn/web/webqtl/templates'))
-JinjaEnv.globals['numify'] = formatting.numify
-
-
-class JinjaPage(templatePage.templatePage):
-    """Class derived from our regular templatePage, but uses Jinja2 instead.
-
-    When converting pages from Python generated templates, change the base class from templatePage
-    to JinjaPage
-
-    """
-
-
-    def write(self):
-        """We override the base template write so we can use Jinja2."""
-        _log.info(pf(self.__dict__))
-        return self.jtemplate.render(**self.__dict__)
diff --git a/wqflask/base/admin.py b/wqflask/base/admin.py
deleted file mode 100755
index 1ba75117..00000000
--- a/wqflask/base/admin.py
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-
-
-
-
-#XZ, 04/02/2009: we should put this into database.
-
-
-###LIST of databases used into gene name query
-
-
-ADMIN_search_dbs = {
-                    'rat': {'PERITONEAL FAT': ['FT_2A_0605_Rz'],
-                            'KIDNEY': ['KI_2A_0405_Rz'],
-                            'ADRENAL GLAND': ['HXB_Adrenal_1208'],
-                            'HEART': ['HXB_Heart_1208']
-                           },
-                    'mouse': {'CEREBELLUM': ['CB_M_0305_R'],
-                              'STRIATUM': ['SA_M2_0905_R', 'SA_M2_0405_RC', 'UTHSC_1107_RankInv', 'Striatum_Exon_0209'],
-                              'HIPPOCAMPUS': ['HC_M2_0606_R', 'UMUTAffyExon_0209_RMA'],
-                              'WHOLE BRAIN': ['BR_M2_1106_R', 'IBR_M_0106_R', 'BRF2_M_0805_R', 'UCLA_BHF2_BRAIN_0605'],
-                              'LIVER': ['LV_G_0106_B', 'UCLA_BHF2_LIVER_0605'],
-                              'EYE': ['Eye_M2_0908_R'],
-                              'HEMATOPOIETIC STEM CELLS': ['HC_U_0304_R'],
-                              'KIDNEY': ['MA_M2_0806_R'],
-                              'MAMMARY TUMORS': ['MA_M_0704_R', 'NCI_Agil_Mam_Tum_RMA_0409'],
-                              'PREFRONTAL CORTEX': ['VCUSal_1206_R'],
-                              'SPLEEN': ['IoP_SPL_RMA_0509'],
-                              'NUCLEUS ACCUMBENS': ['VCUSalo_1007_R'],
-                              'NEOCORTEX': ['HQFNeoc_0208_RankInv'],
-                              'ADIPOSE': ['UCLA_BHF2_ADIPOSE_0605'],
-                              'RETINA': ['Illum_Retina_BXD_RankInv0410']
-                             },
-                    'human': {
-                              'LYMPHOBLAST B CELL': ['Human_1008', 'UT_CEPH_RankInv0909'],
-                              'WHOLE BRAIN': ['GSE5281_F_RMA0709', 'GSE15222_F_RI_0409']
-                             }
-                   }
-
-
-###LIST of tissue alias
-
-ADMIN_tissue_alias = {'CEREBELLUM': ['Cb'],
-                      'STRIATUM': ['Str'],
-                      'HIPPOCAMPUS': ['Hip'],
-                      'WHOLE BRAIN': ['Brn'],
-                      'LIVER': ['Liv'],
-                      'EYE': ['Eye'],
-                      'PERITONEAL FAT': ['Fat'],
-                      'HEMATOPOIETIC STEM CELLS': ['Hsc'],
-                      'KIDNEY': ['Kid'],
-                      'ADRENAL GLAND': ['Adr'],
-                      'HEART': ['Hea'],
-                      'MAMMARY TUMORS': ['Mam'],
-                      'PREFRONTAL CORTEX': ['Pfc'],
-                      'SPLEEN': ['Spl'],
-                      'NUCLEUS ACCUMBENS': ['Nac'],
-                      'NEOCORTEX': ['Ctx'],
-                      'ADIPOSE': ['Wfat'],
-                      'RETINA': ['Ret']
-                     }
diff --git a/wqflask/base/cgiData.py b/wqflask/base/cgiData.py
deleted file mode 100755
index 155b3ec3..00000000
--- a/wqflask/base/cgiData.py
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#########################################
-#convert Field storage object to Dict object
-#in order to be able to saved into a session file
-#########################################
-
-class cgiData(dict):
-    '''convert Field storage object to Dict object
-       Filed storage object cannot be properly dumped
-    '''
-
-    def __init__(self, field_storage=None):
-
-        if not field_storage:
-            field_storage={}
-
-        for key in field_storage.keys():
-            temp = field_storage.getlist(key)
-            if len(temp) > 1:
-                temp = map(self.toValue, temp)
-            elif len(temp) == 1:
-                temp = self.toValue(temp[0])
-            else:
-                temp = None
-            self[key]= temp
-
-    def toValue(self, obj):
-        '''fieldstorge returns different type of objects, \
-                need to convert to string or None'''
-        try:
-            return obj.value
-        except:
-            return ""
-
-    def getvalue(self, k, default= None):
-        try:
-            return self[k]
-        except:
-            return default
-
-    getfirst = getvalue
diff --git a/wqflask/base/cookieData.py b/wqflask/base/cookieData.py
deleted file mode 100755
index eeb7c0cf..00000000
--- a/wqflask/base/cookieData.py
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#########################################
-#convert mod_python object to Dict object
-#in order to be able to be pickled
-#########################################
-
-class cookieData(dict):
-    'convert mod python Cookie object to Dict object'
-
-    def __init__(self, cookies=None):
-
-        if not cookies:
-            cookies={}
-
-        for key in cookies.keys():
-            self[key.lower()]= cookies[key].value
-
-    def getvalue(self, k, default= None):
-        try:
-            return self[k.lower()]
-        except:
-            return default
-
-    getfirst = getvalue
diff --git a/wqflask/base/footer.py b/wqflask/base/footer.py
deleted file mode 100755
index 6f92fdf8..00000000
--- a/wqflask/base/footer.py
+++ /dev/null
@@ -1,6 +0,0 @@
-import webqtlConfig
-
-footer_html = open(webqtlConfig.HTMLPATH + 'footer.html', 'r').read()
-footer = footer_html.replace('%"','%%"')
-
-footer_string = footer.replace('<!-- %s -->', '%s')
diff --git a/wqflask/base/generate_probesetfreeze_file.py b/wqflask/base/generate_probesetfreeze_file.py
deleted file mode 100755
index a0ff804b..00000000
--- a/wqflask/base/generate_probesetfreeze_file.py
+++ /dev/null
@@ -1,31 +0,0 @@
-from __future__ import absolute_import, print_function, division
-import os
-import math
-
-import json
-import itertools
-
-from flask import Flask, g
-
-from base import webqtlConfig
-from dbFunction import webqtlDatabaseFunction
-from utility import webqtlUtil
-
-from MySQLdb import escape_string as escape
-from pprint import pformat as pf
-
-
-query = """ select ProbeSet.Name
-            from ProbeSetXRef,
-                 ProbeSetFreeze,
-                 ProbeSet
-            where ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
-                  ProbeSetFreeze.Name = "EPFLMouseMuscleCDRMA1211" and
-                  ProbeSetXRef.ProbeSetId = ProbeSet.Id;
-        """
-
-markers = g.db.execute(query).fetchall()
-print("markers: ", pf(markers))
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file
diff --git a/wqflask/base/header.py b/wqflask/base/header.py
deleted file mode 100755
index ec15e174..00000000
--- a/wqflask/base/header.py
+++ /dev/null
@@ -1,6 +0,0 @@
-import webqtlConfig
-
-header_string = open(webqtlConfig.HTMLPATH + 'header.html', 'r').read()
-header_string = header_string.replace("\\'", "'")
-header_string = header_string.replace('%"','%%"')
-header_string = header_string.replace('<!-- %s -->', '%s')
diff --git a/wqflask/base/indexBody.py b/wqflask/base/indexBody.py
deleted file mode 100755
index a5bc4c17..00000000
--- a/wqflask/base/indexBody.py
+++ /dev/null
@@ -1,290 +0,0 @@
-index_body_string = """
-<TD vAlign=top width="40%" align="left" height=10 bgColor=#eeeeee>
-                                                        <p style="font-size:18px;font-family:verdana;color:black"><B> Select and Search</B>
-                                                        <Form METHOD="POST" ACTION="/webqtl/main.py" ENCTYPE="multipart/form-data" NAME="SEARCHFORM">
-
-                                                                <TABLE width="100%">
-
-                                        <!--  SPECIES  SELECTION -->
-                                                                        <TR>
-                                                                                <TD align=right height="35" style="font-size:14px;font-family:verdana;color:black" width="16%">
-                                                                                        <B>Species:</B>
-                                                                                </TD>
-
-                                                                                <TD width="3%">
-                                                                                </TD>
-
-                                                                                <TD NOWRAP width="85%" align="left">
-                                                                                        <DIV Id="menu0">
-                                                                                                <Select NAME="species" size=1 id="species" onchange="fillOptions('species');">
-                                                                                                </Select>
-                                                                                        </DIV>
-                                                                                </TD>
-                                                                        </TR>
-
-                                        <!--  GROUP  SELECTION -->
-
-                                                                        <TR>
-
-                                                                                <TD align="right" height="35" style="font-size:14px;font-family:verdana;color:black">
-                                                                                        <B>Group:</B>
-                                                                                </TD>
-
-                                                                                <TD width="3%">
-                                                                                </TD>
-
-                                                                                <TD NOWRAP width="85%" align="left">
-                                                                                        <DIV Id="menu1">
-
-                                                                                                <Select NAME="cross" size=1 id="cross" onchange="fillOptions('cross');">
-                                                                                                </Select>
-                                                                                        <input type="button" class="button" value=" Info " onCLick="javascript:crossinfo();">
-                                                                                        </DIV>
-                                                                                </TD>
-                                                                        </TR>
-
-
-                                        <!--  TYPE  SELECTION -->
-
-                                                                        <TR>
-
-                                                                                <TD align=right height=35 style="font-size:14px;font-family:verdana;color:black">
-                                                                                        <B>Type:</B>
-                                                                                </TD>
-
-                                                                                <TD width="3%">
-                                                                                </TD>
-                                                                                <TD NOWRAP width="85%" align="left">
-                                                                                        <DIV Id="menu2">
-                                                                                                <Select NAME="tissue" size=1 id="tissue" onchange="fillOptions('tissue');">
-
-                                                                                                </Select>
-                                                                                        </DIV>
-                                                                                </TD>
-                                                                        </TR>
-
-
-                                        <!--  DATABASE  SELECTION -->
-                                                                        <TR>
-                                                                                <TD align=right height=35 style="font-size:14px;font-family:verdana;color:black">
-                                                                                        <B>Database:</B>
-                                                                                </TD>
-
-                                                                                <TD width="3%">
-                                                                                </TD>
-
-                                                                                <TD NOWRAP width="85%" align="left">
-                                                                                        <DIV Id="menu3">
-                                                                                                <Select NAME="database" size=1 id="database">
-                                                                                                </Select>
-                                                                                                <input type="button" class="button" value=" Info " onCLick="javascript:databaseinfo();">
-                                                                                        </DIV>
-
-                                                                                </TD>
-                                                                        </TR>
-
-                                        <!--  USER HELP   -->
-                                                                        <TR>
-                                                                                <TD align=right height=20 width="10%">
-                                                                                </TD>
-                                                                                <TD width="3%">
-                                                                                </TD>
-
-                                                                                <TD align="left" width="85%">
-                                                                                        <P class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Databases marked with <B>**</B> suffix are not public yet.
-                                                                                        <BR>&nbsp;&nbsp;&nbsp;&nbsp;Access requires <A HREF="/account.html" target="_blank" class="fs14"><small>user login</small></A>.</P>
-                                                                                </TD>
-                                                                        </TR>
-
-
-<!--  GET ANY  SEARCH -->
-                                                                        <TR>
-                                                                                <TD align=right height=35 NOWRAP="on" style="font-size:14px;font-family:verdana;color:black" width="10%">
-                                                                                        <B>Get Any:</B>
-                                                                                </TD>
-
-                                                                                <TD width="3%">
-                                                                                </TD>
-
-                                                                                <TD NOWRAP width="85%" align="left">
-
-                                                                                        <input id="tfor" name="ORkeyword" style="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500">
-                                                                                </TD>
-                                                                        </TR>
-
-
-
-<!--  GET ANY HELP   -->
-                                                                        <TR>
-                                                                                <TD align=right height=20 width="10%">
-                                                                                </TD>
-                                                                                <TD width="3%">
-
-                                                                                </TD>
-                                                                                <TD width="85%" align="left">
-                                                                                        <P class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Enter terms, genes, ID numbers in the <B>Get Any</B> field.
-                                                                                        <BR>&nbsp;&nbsp;&nbsp;&nbsp;Use <B>*</B> or <B>?</B> wildcards (Cyp*a?, synap*).
-                                                                                        <BR>&nbsp;&nbsp;&nbsp;&nbsp;Use <B>Combined</B> for terms such as <I>tyrosine kinase</I>.</P>
-
-                                                                                </TD>
-                                                                        </TR>
-
-
-
-<!--  COMBINED SEARCH  -->
-
-                                                                        <TR>
-                                                                                <TD align=right height=35 NOWRAP="on" STYLE="font-size:14px;font-family:verdana;color:black" width="10%">
-                                                                                        <B>Combined:</B>
-                                                                                </TD>
-
-                                                                                <TD width="3%">
-                                                                                </TD>
-
-                                                                                <TD NOWRAP width="85%" align="left">
-                                                                                        <input id="tfand" NAME="ANDkeyword"  STYLE="width:420px; background-color:white; font-family:verdana; font-size:14px" type="text" maxlength="500">
-                                                                                        <input name="matchwhole" type="hidden" value="ON">
-                                                                                </TD>
-                                                                        </TR>
-
-
-
-<!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-
-                                                                        <TR ALIGN="center">
-                                                                                <TD width="3%">
-                                                                                </TD>
-                                                                                <TD width="3%">
-                                                                                </TD>
-                                                                                <TD ALIGN="left" HEIGHT="40" COLSPAN=3>
-                                                                                        <INPUT id="btsearch" TYPE="Submit" CLASS="button" STYLE="font-size:12px" VALUE="  Search  ">&nbsp;&nbsp;&nbsp;&nbsp;
-                                                                                       <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE="  Make Default  " onClick = "setDefault(this.form);">&nbsp;&nbsp;&nbsp;&nbsp;
-                                                                                        <INPUT TYPE="button" CLASS="button" STYLE="font-size:12px" VALUE="  Advanced Search  " onClick="javascript:window.open('/index3.html', '_self');">
-
-                                                                                </TD>
-                                                                        </TR>
-                                                                </TABLE>
-                                                                <INPUT TYPE="hidden" NAME="FormID" VALUE="searchResult">
-                                                                <INPUT TYPE="hidden" NAME="RISet" VALUE="BXD">
-                                                                <SCRIPT SRC="/javascript/selectDatasetMenu.js"></SCRIPT>
-                                                        </FORM>
-                                                        </CENTER>
-
-
-
-
-
-<!--  QUICK HELP  -->
-
-<P><LEFT>&nbsp;______________________________________________________
-
-<P STYLE="font-size:13px;font-family:verdana;color:black"><B>&nbsp;
-
-Quick HELP Examples and </B>
-<A HREF="http://www.genenetwork.org/index4.html" target="_blank"  class="fs14"><B>
- User's Guide</B></A></P>
-
-</CENTER style="font-size:12px;font-family:verdana;color:black">
-&nbsp;&nbsp;You can also use advanced commands. Copy these simple examples
-<BR>&nbsp;&nbsp;into the <B>Get Any</B> or <B>Combined</B> search fields:
-<UL style="font-size:12px;font-family:verdana;color:black">
-
-<LI><B><I>POSITION=(chr1 25 30)</I></B> finds genes, markers, or transcripts on chromosome 1 between 25 and 30 Mb.
-
-<LI><B><I>MEAN=(15 16) LRS=(23 46)</I></B> in the <B>Combined</B> field finds highly expressed genes (15 to 16 log2 units) AND with peak <A HREF="http://www.genenetwork.org/glossary.html#L" target="_blank"  class="fs14"><small>LRS</small></A> linkage between 23 and 46.
-
-
-<LI><B><I>RIF=mitochondrial</I></B> searches RNA databases for <A HREF="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank"  class="fs14"><small>GeneRIF</small></A> links.
-
-<LI><B><I>WIKI=nicotine</I></B> searches <A HREF="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank"  class="fs14"><small>GeneWiki</small></A> for genes that you or other users have annotated with the word <I>nicotine</I>.
-
-<LI><B><I>GO:0045202</I></B> searches for synapse-associated genes listed in the <A HREF="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank"  class="fs14"><small>Gene Ontology</small></A>.
-
-
-<LI><B><I>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds synapse-associated genes with <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank"  class="fs14"><small>cis eQTL</small></A> on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.
-
-<LI><B><I>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</I> </B><BR> in <B>Combined</B> finds diabetes-associated transcripts with peak <A HREF="http://www.genenetwork.org/glossary.html#E" target="_blank"  class="fs14"><small>trans eQTLs</small></A> on Chr 2 between 100 and 105 Mb with LRS scores between 9 and 999.
-
-
-</UL>
-</DIR>
-                                        </TD>
-<!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE)  -->
-
-<!-- START OF TOP RIGHT PANEL  -->
-
-<TD vAlign=top width="40%" bgColor=#FFFFFF>
-                                                        <p style="font-size:15px;font-family:verdana;color:black"><B>Websites Affiliated with GeneNetwork</B></p>
-                <p style="font-size:12px;font-family:verdana;color:black">
-                        <ul>
-                                <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome Browser</a> at UTHSC</li>
-                                <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at UTHSC</li>
-                                <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon Cloud (EC2)</a></li>
-                                <li>GeneNetwork Source Codes at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
-                        </ul>
-                </p>
-                                                        <P>____________________________
-
-                                                        <p style="font-size:15px;font-family:verdana;color:black"><B>Getting Started</B> &nbsp;&nbsp; </p>
-                                                        <OL style="font-size:12px;font-family:verdana;color:black">
-                                                                <LI>Select <B>Species</B> (or select All)
-                                                                <LI>Select <B>Group</B> (a specific sample)
-                                                                <LI>Select <B>Type</B> of data:
-                                                                <UL>
-                                                                        <LI>Phenotype (traits)
-                                                                        <LI>Genotype (markers)
-                                                                        <LI>Expression (mRNAs)
-                                                                </UL>
-                                                                <LI>Select a <B>Database</B>
-                                                                <LI>Enter search terms in the <B>Get Any</B> or <B>Combined</B> field: words, genes, ID numbers, probes, advanced search commands
-                                                                <LI>Click on the <B>Search</B> button
-                                                                <LI>Optional: Use the <B>Make Default</B> button to save your preferences
-                                                        </OL>
-
-                                                        <P>____________________________
-
-<p style="font-size:14px;font-family:verdana;color:black"><B>How to Use GeneNetwork</B>
-
-                                                        <BLOCKQUOTE>
-                                                                <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute GeneNetwork <A HREF="http://www.genenetwork.org/tutorial/WebQTLTour/" target="_blank" class="fs14"><small>Tour</small></A> that includes screen shots and typical steps in the analysis.</P>
-                                                        </BLOCKQUOTE>
-                                                        <BLOCKQUOTE>
-                                                                <p style="font-size:12px;font-family:verdana;color:black">For information about resources and methods, select the <img src="http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border= 0 valign="middle"> buttons.</P>
-
-
-
-<p style="font-size:12px;font-family:verdana;color:black">Try the <A HREF="http://alexandria.uthsc.edu/" target="_blank" class="fs14"><small>Workstation</small></A> site to explore data and features that are being implemented.</P>
-
-
-<p style="font-size:12px;font-family:verdana;color:black">Review the <A HREF="/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></A> and <A HREF="/statusandContact.html" target="_blank" class="fs14"><small>Contacts</small></A> pages for information on the status of data sets and advice on their use and citation.</P>
-
-
-                                                        </BLOCKQUOTE>
-
-
-
-                                                        <p style="font-size:14px;font-family:verdana;color:black"><B>Mirror and Development Sites</B></P>
-
-                                                        <UL>
-                                                                <LI><A HREF="http://www.genenetwork.org/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</A> (main site)
-                                                                <LI><A HREF="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Australia at the UWA</A>
-                                                                <LI><A HREF="http://gn.genetics.ucla.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">California at UCLA</A>
-                                                                <LI><A HREF="http://genenetwork.helmholtz-hzi.de/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Germany at the HZI</A>
-                                                                <LI><A HREF="https://genenetwork.hubrecht.eu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</A> (Development)
-                                                                <LI><A HREF="http://xzhou3.memphis.edu/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</A>
-                                                                <LI><A HREF="http://webqtl.bic.nus.edu.sg/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</A>
-                                                                <LI><A HREF="http://genenetwork.epfl.ch/" target="_blank" style="font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</A>
-                                                        </UL>
-
-
-                                                        <p style="font-size:14px;font-family:verdana;color:black"><B>History and Archive</B>
-
-                                                        <BLOCKQUOTE>
-                                                                <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <A HREF="http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time Machine</small></A> links to earlier versions that correspond to specific publication dates.</P>
-
-                                                        </BLOCKQUOTE>
-
-
-</P>
-                                                </TD>
-"""
diff --git a/wqflask/base/myCookie.py b/wqflask/base/myCookie.py
deleted file mode 100755
index add7e6ea..00000000
--- a/wqflask/base/myCookie.py
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#########################################
-## python cookie and mod python cookie are
-## not compatible
-#########################################
-
-class myCookie(dict):
-    'define my own cookie'
-
-    def __init__(self, name="", value="", expire = None, path="/"):
-        self['name']= name
-        self['value']= value
-        self['expire']= expire
-        self['path']= path
-
-    def __getattr__(self, key):
-        if key in self.keys():
-            return self[key]
-        else:
-            return None
-
-    def __nonzero__ (self):
-        if self['name']:
-            return 1
-        else:
-            return 0
diff --git a/wqflask/base/sessionData.py b/wqflask/base/sessionData.py
deleted file mode 100755
index 4b23060f..00000000
--- a/wqflask/base/sessionData.py
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#########################################
-#convert mod_python object to Dict object
-#in order to be able to be pickled
-#########################################
-
-class sessionData(dict):
-    'convert mod python Session object to Dict object'
-
-    def __init__(self, mod_python_session=None):
-
-        if not mod_python_session:
-            mod_python_session = {}
-
-        for key in mod_python_session.keys():
-            self[key]= mod_python_session[key]
-
-
-    def getvalue(self, k, default= None):
-        try:
-            return self[k]
-        except:
-            return default
-
-    getfirst = getvalue
diff --git a/wqflask/base/templatePage.py b/wqflask/base/templatePage.py
deleted file mode 100755
index a94d5153..00000000
--- a/wqflask/base/templatePage.py
+++ /dev/null
@@ -1,222 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#templatePage.py
-#
-#--Genenetwork generates a lot of pages; this file is the generic version of them, defining routines they all use.
-#
-#Classes:
-#templatePage
-#
-#Functions (of templatePage):
-#__init__(...) -- class constructor, allows a more specific template to be used in addition to templatePage
-#__str__(self) -- returns the object's elements as a tuple
-#__del__(self) -- closes the current connection to MySQL, if there is one
-#write -- explained below
-#writefile -- explained below
-#openMysql(self) -- opens a MySQL connection and stores the resulting cursor in the object's cursor variable
-#updMysql(self) -- same as openMysql
-#error -- explained below
-#session -- explained below
-
-
-import socket
-import time
-import shutil
-import MySQLdb
-import os
-
-from htmlgen import HTMLgen2 as HT
-
-import template
-import webqtlConfig
-import header
-import footer
-from utility import webqtlUtil
-
-
-
-class templatePage:
-
-    contents = ['title','basehref','js1','js2', 'layer', 'header', 'body', 'footer']
-
-    # you can pass in another template here if you want
-    def __init__(self, fd=None, template=template.template):
-
-        # initiate dictionary
-        self.starttime = time.time()
-        self.dict = {}
-        self.template = template
-
-        for item in self.contents:
-            self.dict[item] = ""
-
-        self.dict['basehref'] = "" #webqtlConfig.BASEHREF
-        self.cursor = None
-
-        self.cookie = [] #XZ: list to hold cookies (myCookie object) being changed
-        self.content_type = 'text/html'
-        self.content_disposition = ''
-        self.redirection = ''
-        self.debug = ''
-        self.attachment = ''
-
-        #XZ: Holding data (new data or existing data being changed) that should be saved to session. The data must be picklable!!!
-        self.session_data_changed = {}
-
-        self.userName = 'Guest'
-        self.privilege = 'guest'
-
-        # Commenting this out for flask - we'll have to reimplement later - Sam
-        #if fd.input_session_data.has_key('user'):
-        #       self.userName = fd.input_session_data['user']
-        #if fd.input_session_data.has_key('privilege'):
-        #       self.privilege = fd.input_session_data['privilege']
-
-    def __str__(self):
-
-        #XZ: default setting
-        thisUserName = self.userName
-        thisPrivilege = self.privilege
-        #XZ: user may just go through login or logoff page
-        if self.session_data_changed.has_key('user'):
-            thisUserName = self.session_data_changed['user']
-        if self.session_data_changed.has_key('privilege'):
-            thisPrivilege = self.session_data_changed['privilege']
-
-        if thisUserName == 'Guest':
-            userInfo = 'Welcome! <a href=/account.html><U>Login</U></a>'
-        else:
-            userInfo = 'Hi, %s! <a href=/webqtl/main.py?FormID=userLogoff><U>Logout</U></a>' % thisUserName
-
-        reload(header)
-        self.dict['header'] = header.header_string % userInfo
-
-        serverInfo = "It took %2.3f second(s) for %s to generate this page" % (time.time()-self.starttime, socket.getfqdn())
-        reload(footer)
-        self.dict['footer'] = footer.footer_string % serverInfo
-
-        slist = []
-        for item in self.contents:
-            slist.append(self.dict[item])
-        return self.template % tuple(slist)
-
-
-    def __del__(self):
-        if self.cursor:
-            self.cursor.close()
-
-    def write(self):
-        'return string representation of this object'
-
-        if self.cursor:
-            self.cursor.close()
-
-        return str(self)
-
-    def writeFile(self, filename):
-        'save string representation of this object into a file'
-        if self.cursor:
-            self.cursor.close()
-
-        try:
-            'it could take a long time to generate the file, save to .tmp first'
-            fp = open(os.path.join(webqtlConfig.TMPDIR, filename+'.tmp'), 'wb')
-            fp.write(str(self))
-            fp.close()
-            path_tmp = os.path.join(webqtlConfig.TMPDIR, filename+'.tmp')
-            path_html = os.path.join(webqtlConfig.TMPDIR, filename)
-            shutil.move(path_tmp,path_html)
-        except:
-            pass
-
-    def openMysql(self):
-        try:
-            self.db_conn = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \
-                                    user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-            self.cursor = self.db_conn.cursor()
-            return True
-        except Exception:
-            heading = "Connect MySQL Server"
-            detail = ["Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_SERVER+"':100061. \
-                            The server may be down at this time"]
-            self.error(heading=heading,detail=detail,error="Error 2003")
-            return False
-
-    def updMysql(self):
-        try:
-            self.db_conn = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \
-                                    user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD)
-            self.cursor = self.db_conn.cursor()
-            return True
-        except Exception:
-            heading = "Connect MySQL Server"
-            detail = ["update: Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_UPDSERVER+"':100061. \
-                            The server may be down at this time "]
-            self.error(heading=heading,detail=detail,error="Error 2003")
-            return False
-
-    def error(self,heading="",intro=[],detail=[],title="Error",error="Error"):
-        'generating a WebQTL style error page'
-        Heading = HT.Paragraph(heading)
-        Heading.__setattr__("class","title")
-
-        Intro = HT.Blockquote()
-        if intro:
-            for item in intro:
-                Intro.append(item)
-        else:
-            Intro.append(HT.Strong('Sorry!'),' Error occurred while processing\
-                    your request.', HT.P(),'The nature of the error generated is as\
-                    follows:')
-
-        Detail = HT.Blockquote()
-        Detail.append(HT.Span("%s : " % error,Class="fwb cr"))
-        if detail:
-            Detail2 = HT.Blockquote()
-            for item in detail:
-                Detail2.append(item)
-            Detail.append(HT.Italic(Detail2))
-
-        #Detail.__setattr__("class","subtitle")
-        TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="top")
-        TD_LR.append(Heading,Intro,Detail)
-        self.dict['body'] = str(TD_LR)
-        self.dict['title'] = title
-
-    def session(self,mytitle="",myHeading=""):
-        'generate a auto-refreshing temporary html file(waiting page)'
-        self.filename = webqtlUtil.generate_session()
-        self.dict['title'] = mytitle
-        self.dict['basehref'] = webqtlConfig.REFRESHSTR % (webqtlConfig.CGIDIR, self.filename) + "" #webqtlConfig.BASEHREF
-
-        TD_LR = HT.TD(align="center", valign="middle", height=200,width="100%", bgColor='#eeeeee')
-        Heading = HT.Paragraph(myHeading, Class="fwb fs16 cr")
-        # NL, 07/27/2010. variable 'PROGRESSBAR' has been moved from templatePage.py to webqtlUtil.py;
-        TD_LR.append(Heading, HT.BR(), webqtlUtil.PROGRESSBAR)
-        self.dict['body'] = TD_LR
-        self.writeFile(self.filename + '.html')
-        return self.filename
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index a3537c87..44fdcc3f 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -35,15 +35,9 @@ import os
 import reaper
 
 import webqtlConfig
-import cookieData
-import sessionData
-from cgiData import cgiData
 from webqtlCaseData import webqtlCaseData
 from utility import webqtlUtil
 
-
-
-
 class webqtlFormData(object):
     'Represents data from a WebQTL form page, needed to generate the next page'
 
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index a2958108..df1edb13 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -37,8 +37,6 @@ from dbFunction import webqtlDatabaseFunction
 
 from utility import formatting
 
-#from base.JinjaPage import JinjaEnv, JinjaPage
-
 #class QuickSearchResult(object):
     #def __init__(self, key, result_fields):
     #    self.key = key
diff --git a/wqflask/wqflask/static/new/javascript/css/bar_chart.css b/wqflask/wqflask/static/new/javascript/css/bar_chart.css
deleted file mode 100755
index 78d31eee..00000000
--- a/wqflask/wqflask/static/new/javascript/css/bar_chart.css
+++ /dev/null
@@ -1,15 +0,0 @@
-.barchart .axis path,

-.barchart .axis line {

-  fill: none;

-  stroke: #000;

-  shape-rendering: crispEdges;

-}

-

-.bar {

-  fill: steelblue;

-  shape-rendering: crispEdges;

-}

-/*

-.x.axis path {

-  display: none;

-}*/
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/box_plot.css b/wqflask/wqflask/static/new/javascript/css/box_plot.css
deleted file mode 100755
index 4c743b33..00000000
--- a/wqflask/wqflask/static/new/javascript/css/box_plot.css
+++ /dev/null
@@ -1,20 +0,0 @@
-.box {

-  font: 10px sans-serif;

-}

-

-.box line,

-.box rect,

-.box circle {

-  fill: #fff;

-  stroke: #000;

-  stroke-width: 1.5px;

-}

-

-.box .center {

-  stroke-dasharray: 3,3;

-}

-

-.box .outlier {

-  fill: none;

-  stroke: #ccc;

-}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/charts.css b/wqflask/wqflask/static/new/javascript/css/charts.css
deleted file mode 100644
index 5f2d4d23..00000000
--- a/wqflask/wqflask/static/new/javascript/css/charts.css
+++ /dev/null
@@ -1,28 +0,0 @@
-body {

-  font-family: sans-serif;

-}

-

-svg {

-  margin-top:  10px;

-  margin-left: 50px;

-}

-

-.line {

-  stroke-width: 1;

-  fill: none;

-}

-

-text {

- font-family: sans-serif;

- font-size: 11pt;

-}

-

-p {

- font-family: sans-serif;

- font-size: 12pt;

-}

-

-p#caption {

-  margin-left: 100px;

-  width: 500px;

-}

diff --git a/wqflask/wqflask/static/new/javascript/css/corr_matrix.css b/wqflask/wqflask/static/new/javascript/css/corr_matrix.css
deleted file mode 100755
index f4838f77..00000000
--- a/wqflask/wqflask/static/new/javascript/css/corr_matrix.css
+++ /dev/null
@@ -1,12 +0,0 @@
-.vertical_label {
-    -webkit-transform: rotate(-90deg);
-       -moz-transform: rotate(-90deg);
-        -ms-transform: rotate(-90deg);
-         -o-transform: rotate(-90deg);
-            trasnform: rotate(-90deg);
-              color: #000
-              font-size: 22px;
-              height: 50px;
-              width: 100px;
-    float: left; 
-}
diff --git a/wqflask/wqflask/static/new/javascript/css/corr_scatter_plot.css b/wqflask/wqflask/static/new/javascript/css/corr_scatter_plot.css
deleted file mode 100755
index c62d4c9a..00000000
--- a/wqflask/wqflask/static/new/javascript/css/corr_scatter_plot.css
+++ /dev/null
@@ -1,13 +0,0 @@
-.chart {
-
-}
-
-.main text {
-    font: 10px sans-serif;	
-}
-
-.axis line, .axis path {
-    shape-rendering: crispEdges;
-    stroke: black;
-    fill: none;
-}
diff --git a/wqflask/wqflask/static/new/javascript/css/d3-tip.min.css b/wqflask/wqflask/static/new/javascript/css/d3-tip.min.css
deleted file mode 100644
index 3d253caf..00000000
--- a/wqflask/wqflask/static/new/javascript/css/d3-tip.min.css
+++ /dev/null
@@ -1 +0,0 @@
-.d3-tip{line-height:1;font-weight:bold;padding:12px;background:rgba(0,0,0,0.8);color:#fff;border-radius:2px;pointer-events:none}.d3-tip:after{box-sizing:border-box;display:inline;font-size:10px;width:100%;line-height:1;color:rgba(0,0,0,0.8);position:absolute;pointer-events:none}.d3-tip.n:after{content:"\25BC";margin:-1px 0 0 0;top:100%;left:0;text-align:center}.d3-tip.e:after{content:"\25C0";margin:-4px 0 0 0;top:50%;left:-8px}.d3-tip.s:after{content:"\25B2";margin:0 0 1px 0;top:-8px;left:0;text-align:center}.d3-tip.w:after{content:"\25B6";margin:-4px 0 0 -1px;top:50%;left:100%}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/interval_mapping.css b/wqflask/wqflask/static/new/javascript/css/interval_mapping.css
deleted file mode 100755
index 4a55d2e3..00000000
--- a/wqflask/wqflask/static/new/javascript/css/interval_mapping.css
+++ /dev/null
@@ -1,32 +0,0 @@
-.chr_interval_map .y_axis path,

-.chr_interval_map .y_axis line {

-    fill: none;

-    stroke: black;

-    shape-rendering: crispEdges;

-}

-.chr_interval_map .y_axis text {

-    font-family: sans-serif;

-    font-size: 14px;

-}

-

-.chr_interval_map .x_axis path,

-.chr_interval_map .x_axis line {

-    fill: none;

-    stroke: black;

-    shape-rendering: crispEdges;

-}

-.chr_interval_map .x_axis text {

-    text-anchor: end;

-    font-family: sans-serif;

-    font-size: 8px;

-}

-/*

-interval_map rect {

-    stroke: WhiteSmoke;

-    fill: white;

-}

-

-interval_map path {

-    stroke: steelblue;

-    stroke-width: 1;

-}*/
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/main.css b/wqflask/wqflask/static/new/javascript/css/main.css
deleted file mode 100755
index 017bbdb8..00000000
--- a/wqflask/wqflask/static/new/javascript/css/main.css
+++ /dev/null
@@ -1,4 +0,0 @@
-.security_box {
-    padding-left: 30px;
-    padding-right: 30px;
-}
diff --git a/wqflask/wqflask/static/new/javascript/css/marker_regression.css b/wqflask/wqflask/static/new/javascript/css/marker_regression.css
deleted file mode 100755
index d81b5021..00000000
--- a/wqflask/wqflask/static/new/javascript/css/marker_regression.css
+++ /dev/null
@@ -1,38 +0,0 @@
-.chr_manhattan_plot .y_axis path,
-.chr_manhattan_plot .y_axis line {
-    fill: none;
-    stroke: black;
-    shape-rendering: crispEdges;
-}
-.chr_manhattan_plot .y_axis text {
-    font-family: sans-serif;
-    font-size: 14px;
-}
-
-.chr_manhattan_plot .x_axis path,
-.chr_manhattan_plot .x_axis line {
-    fill: none;
-    stroke: black;
-    shape-rendering: crispEdges;
-}
-
-.chr_manhattan_plot .x_axis text {
-    text-anchor: end;
-    font-family: sans-serif;
-    font-size: 10px;
-}
-
-rect.pane {
-  cursor: move;
-  fill: none;
-  pointer-events: all;
-}
-
-/*rect {
-    stroke: WhiteSmoke;
-    fill: lightgrey;
-}*/
-/*rect {
-    stroke: WhiteSmoke;
-    fill: Azure;
-}*/
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/panelutil.css b/wqflask/wqflask/static/new/javascript/css/panelutil.css
deleted file mode 100644
index ccd7eb01..00000000
--- a/wqflask/wqflask/static/new/javascript/css/panelutil.css
+++ /dev/null
@@ -1,91 +0,0 @@
-

-/* figures will always be within a div with class="qtlcharts" */

-div.qtlcharts {

-  font-family: sans-serif;

-  font-size: 11pt;

-}

-

-div.qtlcharts .title text {

-  dominant-baseline: middle;

-  fill: blue;

-  text-anchor: middle;

-}

-

-div.qtlcharts .y.axis text {

-  dominant-baseline: middle;

-  text-anchor: end;

-}

-

-div.qtlcharts .y.axis text.title {

-  text-anchor: middle;

-  fill: slateblue;

-}

-

-div.qtlcharts .x.axis text {

-  dominant-baseline: hanging;

-  text-anchor: middle;

-}

-

-div.qtlcharts .x.axis text.title {

-  fill: slateblue;

-}

-

-/*div.qtlcharts line.axis.grid {

-  fill: none;

-  stroke-width: 1;

-  pointer-events: none;

-}

-

-div.qtlcharts line.x.axis.grid {

-  stroke: rgb(200, 200, 200);

-  stroke-width: 3;

-}

-

-div.qtlcharts line.y.axis.grid {

-  stroke: white;

-}*/

-

-div.qtlcharts .extent {

-  fill: #cac;

-  opacity: 0.3;

-}

-

-div.qtlcharts circle.selected {

-  fill: hotpink;

-  opacity: 1;

-}

-

-div.qtlcharts a {

-  color: #08c;

-  text-decoration: none;

-}

-

-div.qtlcharts a:hover {

-  color: #333;

-  text-decoration: underline;

-}

-

-

-/* figure captions */

-.caption {

-  font-family: Sans-serif;

-  font-size: 11pt;

-  margin-left: 60px;

-  width: 600px;

-}

-

-

-/* d3 tip for tool tips */

-.d3-tip {

-  background: darkslateblue;

-  color: #fff;

-  stroke: none;

-  font-weight: bold;

-  font-size: 16px;

-  font-family: sans-serif;

-  padding: 5px;

-}

-

-.d3-tip.e:after {

-  color: darkslateblue;

-}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/parsley.css b/wqflask/wqflask/static/new/javascript/css/parsley.css
deleted file mode 100755
index 7d244579..00000000
--- a/wqflask/wqflask/static/new/javascript/css/parsley.css
+++ /dev/null
@@ -1,20 +0,0 @@
-/* Adapted from parsleyjs.org/documentation.html#parsleyclasses */
-
-input.parsley-success, textarea.parsley-success {
-  color: #468847 !important;
-  background-color: #DFF0D8 !important;
-  border: 1px solid #D6E9C6 !important;
-}
-input.parsley-error, textarea.parsley-error {
-  color: #B94A48 !important;
-  background-color: #F2DEDE !important;
-  border: 1px solid #EED3D7 !important;
-}
-ul.parsley-error-list {
-    font-size: 11px;
-    margin: 2px;
-    list-style-type:none;
-}
-ul.parsley-error-list li {
-    line-height: 11px;
-}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/scatter-matrix.css b/wqflask/wqflask/static/new/javascript/css/scatter-matrix.css
deleted file mode 100644
index 147903be..00000000
--- a/wqflask/wqflask/static/new/javascript/css/scatter-matrix.css
+++ /dev/null
@@ -1,40 +0,0 @@
-#scatter-matrix { font-size: 14px; }
-
-.axis { shape-rendering: crispEdges; }
-.axis line { stroke: #ddd; stroke-width: 1px; }
-.axis path { display: none; }
-.axis text { font-size: 0.8em; }
-
-rect.extent { fill: #000; fill-opacity: .125; stroke: #fff; }
-rect.frame { fill: #fff; fill-opacity: .7; stroke: #aaa; }
-
-circle { fill: #ccc; fill-opacity: .5; }
-
-.legend circle { fill-opacity: 1; }
-.legend text { font-size: 18px; font-style: oblique; }
-
-.cell text { pointer-events: none; }
-
-.color-0  { fill: #800; }
-.color-1  { fill: #080; }
-.color-2  { fill: #008; }
-.color-3  { fill: #440; }
-.color-4  { fill: #044; }
-.color-5  { fill: #404; }
-.color-6  { fill: #400; }
-.color-7  { fill: #040; }
-.color-8  { fill: #004; }
-.color-9  { fill: #cc0; }
-.color-10 { fill: #0cc; }
-.color-11 { fill: #c0c; }
-.color-12 { fill: #880; }
-.color-13 { fill: #088; }
-.color-14 { fill: #808; }
-.color-15 { fill: #c00; }
-.color-16 { fill: #0c0; }
-.color-17 { fill: #00c; }
-
-.scatter-matrix-filter-control ul { list-style: none; padding-left: 10px; }
-.scatter-matrix-variable-control ul { list-style: none; padding-left: 10px; }
-.scatter-matrix-drill-control ul { list-style: none; padding-left: 10px; }
-
diff --git a/wqflask/wqflask/static/new/javascript/css/show_trait.css b/wqflask/wqflask/static/new/javascript/css/show_trait.css
deleted file mode 100644
index 9fc82a85..00000000
--- a/wqflask/wqflask/static/new/javascript/css/show_trait.css
+++ /dev/null
@@ -1,7 +0,0 @@
-tr .outlier {
-    background-color: #ffff99;
-}
-
-#bar_chart_container {
-    overflow-x:scroll;
-}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/css/table.css b/wqflask/wqflask/static/new/javascript/css/table.css
deleted file mode 100755
index 1910ef88..00000000
--- a/wqflask/wqflask/static/new/javascript/css/table.css
+++ /dev/null
@@ -1,36 +0,0 @@
-/* Adapted from http://coding.smashingmagazine.com/2008/08/13/top-10-css-table-designs/ */
-
-.one-column-emphasis
-{
-    font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;
-    font-size: 12px;
-    line-height: 1.6em;
-    margin: 45px;
-    width: 480px;
-    text-align: left;
-    border-collapse: collapse;
-}
-.one-column-emphasis th
-{
-    font-size: 14px;
-    font-weight: normal;
-    padding: 12px 15px;
-    color: #039;
-}
-.one-column-emphasis td
-{
-    padding: 10px 15px;
-    color: #669;
-    border-top: 1px solid #e8edff;
-}
-.oce-first
-{
-    background: #d0dafd;
-    border-right: 10px solid transparent;
-    border-left: 10px solid transparent;
-}
-.one-column-emphasis tr:hover td
-{
-    color: #339;
-    background: #eff2ff;
-}