Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

author: zsloan 2015-03-27 20:28:51 +0000
committer: zsloan 2015-03-27 20:28:51 +0000
commit: d0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree: 3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/base
parent: a840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
download: genenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
18 files changed, 0 insertions, 2220 deletions
diff --git a/web/webqtl/base/GeneralObject.py b/web/webqtl/base/GeneralObject.py
deleted file mode 100755
index 311c9e22..00000000
--- a/web/webqtl/base/GeneralObject.py
+++ /dev/null
@@ -1,71 +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/web/webqtl/base/__init__.py b/web/webqtl/base/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/base/__init__.py
+++ /dev/null
diff --git a/web/webqtl/base/admin.py b/web/webqtl/base/admin.py
deleted file mode 100755
index a04df2da..00000000
--- a/web/webqtl/base/admin.py
+++ /dev/null
@@ -1,88 +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/web/webqtl/base/cgiData.py b/web/webqtl/base/cgiData.py
deleted file mode 100755
index 57416060..00000000
--- a/web/webqtl/base/cgiData.py
+++ /dev/null
@@ -1,70 +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/web/webqtl/base/cookieData.py b/web/webqtl/base/cookieData.py
deleted file mode 100755
index 4b7c9046..00000000
--- a/web/webqtl/base/cookieData.py
+++ /dev/null
@@ -1,52 +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/web/webqtl/base/footer.py b/web/webqtl/base/footer.py
deleted file mode 100755
index 6f92fdf8..00000000
--- a/web/webqtl/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/web/webqtl/base/header.py b/web/webqtl/base/header.py
deleted file mode 100755
index b6136b51..00000000
--- a/web/webqtl/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')
-\ No newline at end of file
diff --git a/web/webqtl/base/indexBody.py b/web/webqtl/base/indexBody.py
deleted file mode 100755
index e73409a5..00000000
--- a/web/webqtl/base/indexBody.py
+++ /dev/null
@@ -1,291 +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>Data Set:</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>
-				<li>GeneNetwork Source Codes at <a href="https://github.com/genenetwork/genenetwork" target="_blank">GitHub</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://genenetwork.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/web/webqtl/base/myCookie.py b/web/webqtl/base/myCookie.py
deleted file mode 100755
index db5320df..00000000
--- a/web/webqtl/base/myCookie.py
+++ /dev/null
@@ -1,55 +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/web/webqtl/base/sessionData.py b/web/webqtl/base/sessionData.py
deleted file mode 100755
index 01555f87..00000000
--- a/web/webqtl/base/sessionData.py
+++ /dev/null
@@ -1,53 +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/web/webqtl/base/template.py b/web/webqtl/base/template.py
deleted file mode 100755
index 85bd86df..00000000
--- a/web/webqtl/base/template.py
+++ /dev/null
@@ -1,123 +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
-
-template = """
-<?XML VERSION="1.0" ENCODING="UTF-8">
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<HTML>
-<HEAD>
-<TITLE>%s</TITLE>
-
-<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
-<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine">
-<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." >
-<META NAME="author" CONTENT ="GeneNetwork developers" >
-<META NAME="geo.placename" CONTENT ="Memphis, TN" >
-<META NAME="geo.region" CONTENT="US-TN">
-%s
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'>
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'>
-<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" />
-<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" />
-<link type="text/css" href='/css/custom-theme/jquery-ui-1.8.12.custom.css' rel='Stylesheet' />
-<link type="text/css" href='/css/tab_style.css' rel='Stylesheet' />
-
-<script type="text/javascript" src="/javascript/jquery-1.5.2.min.js"></script>
-<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>
-<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT>
-<SCRIPT SRC="/javascript/tablesorter.js"></SCRIPT>
-<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT>
-<script src="/javascript/tabbed_pages.js" type="text/javascript"></script>
-<script src="/javascript/jquery-ui-1.8.12.custom.min.js" type="text/javascript"></script>
-%s
-
-<script type="text/javascript">
-  var _gaq = _gaq || [];
-  _gaq.push(['_setAccount', 'UA-3782271-1']);
-  _gaq.push(['_trackPageview']);
-  (function() {
-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
-    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
-  })();
-</script>
-</HEAD>
-<BODY  bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff %s>
-%s
-<TABLE cellSpacing=5 cellPadding=4 width="100%%" border=0>
-	<TBODY>
-	<!-- Start of header -->
-	<TR>
-		%s
-	</TR>
-	<!-- End of header -->
-
-	<!-- Start of body -->
-	<TR>
-		<TD  bgColor=#eeeeee class="solidBorder">
-		<Table width= "100%%" cellSpacing=0 cellPadding=5>
-		<TR>
-		%s
-		</TR>
-		</TABLE>
-		</TD>
-	</TR>
-	<!-- End of body -->
-
-        <!-- Start of footer -->
-	<TR>
-		<TD align=center bgColor=#ddddff class="solidBorder">
-			<TABLE width="90%%">%s</table>
-		</td>
-	</TR>
-	<!-- End of footer -->
-</TABLE>
-
-<!-- menu script itself. you should not modify this file -->
-<script language="JavaScript" src="/javascript/menu_new.js"></script>
-<!-- items structure. menu hierarchy and links are stored there -->
-<script language="JavaScript" src="/javascript/menu_items.js"></script>
-<!-- files with geometry and styles structures -->
-<script language="JavaScript" src="/javascript/menu_tpl.js"></script>
-<script language="JavaScript">
-	<!--//
-	// Note where menu initialization block is located in HTML document.
-	// Don't try to position menu locating menu initialization block in
-	// some table cell or other HTML element. Always put it before </body>
-	// each menu gets two parameters (see demo files)
-	// 1. items structure
-	// 2. geometry structure
-	new menu (MENU_ITEMS, MENU_POS);
-	// make sure files containing definitions for these variables are linked to the document
-	// if you got some javascript error like "MENU_POS is not defined", then you've made syntax
-	// error in menu_tpl.js file or that file isn't linked properly.
-	
-	// also take a look at stylesheets loaded in header in order to set styles
-	//-->
-</script>
-</BODY>
-</HTML>
-"""
diff --git a/web/webqtl/base/templatePage.py b/web/webqtl/base/templatePage.py
deleted file mode 100755
index 4dece24a..00000000
--- a/web/webqtl/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'
-		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.con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \
-						user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-			self.cursor = self.con.cursor()
-			return 1
-		except:
-			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 0
-
-	def updMysql(self):
-		try:
-			self.con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \
-						user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD)
-			self.cursor = self.con.cursor()
-			return 1
-		except:
-			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 0
-	
-	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/web/webqtl/base/webqtlCaseData.py b/web/webqtl/base/webqtlCaseData.py
deleted file mode 100755
index 4df32ca4..00000000
--- a/web/webqtl/base/webqtlCaseData.py
+++ /dev/null
@@ -1,54 +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 webqtlCaseData:
-	"""
-	one case data in one trait
-	"""
-
-	val = None		#Trait Value
-	var = None		#Trait Variance
-	N   = None		#Number of individuals
-
-	def __init__(self, val=val, var=var, N=N):
-		self.val = val
-		self.var = var
-		self.N = N
-	
-	def __str__(self):
-		str = ""
-		if self.val != None:
-			str += "value=%2.3f" % self.val
-		if self.var != None:
-			str += " variance=%2.3f" % self.var
-		if self.N != None:
-			str += " ndata=%d" % self.N
-		return str
-	
-	__repr__ = __str__
-
-
-
diff --git a/web/webqtl/base/webqtlConfig.py b/web/webqtl/base/webqtlConfig.py
deleted file mode 100755
index 87e2f3d0..00000000
--- a/web/webqtl/base/webqtlConfig.py
+++ /dev/null
@@ -1,73 +0,0 @@
-from webqtlConfigLocal import *
-#########################################'
-#      Environment Variables - public
-#########################################
-
-#Debug Level
-#1 for debug, mod python will reload import each time
-DEBUG = 1
-
-#USER privilege
-USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4} 
-
-#minimum number of informative strains
-KMININFORMATIVE = 5
-
-#maximum number of traits for interval mapping
-MULTIPLEMAPPINGLIMIT = 11
-
-#maximum number of traits for correlation
-MAXCORR = 100
-
-#Daily download limit from one IP
-DAILYMAXIMUM = 1000
-
-#maximum LRS value
-MAXLRS = 460.0
-
-#temporary data life span
-MAXLIFE = 86400 
-
-#MINIMUM Database public value
-PUBLICTHRESH = 0
-
-#NBCI address
-NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s"
-UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
-GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
-OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
-UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"
-HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s"
-PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
-UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
-UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s"
-ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s'
-DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
-UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s"
-GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
-ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
-
-SECUREDIR = GNROOT + 'secure/'
-COMMON_LIB = GNROOT + 'support/admin'
-HTMLPATH = GNROOT + 'web/'
-IMGDIR = HTMLPATH +'image/'
-IMAGESPATH = HTMLPATH + 'images/'
-UPLOADPATH = IMAGESPATH + 'upload/' 
-TMPDIR = HTMLPATH +'tmp/'
-GENODIR = HTMLPATH + 'genotypes/'
-GENO_ARCHIVE_DIR = GENODIR + 'archive/'
-TEXTDIR = HTMLPATH + 'ProbeSetFreeze_DataMatrix/'
-CMDLINEDIR = HTMLPATH + 'webqtl/cmdLine/'
-ChangableHtmlPath = GNROOT + 'web/'
-
-SITENAME = 'GN'
-PORTADDR = "http://132.192.47.32"
-BASEHREF = '<base href="http://132.192.47.32/">'
-INFOPAGEHREF = '/dbdoc/%s.html'
-GLOSSARYFILE = "/glossary.html"
-CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
-SCRIPTFILE = 'main.py'
-REFRESHSTR = '<meta http-equiv="refresh" content="5;url=%s' + SCRIPTFILE +'?sid=%s">'
-REFRESHDIR = '%s' + SCRIPTFILE +'?sid=%s'
diff --git a/web/webqtl/base/webqtlConfigLocal.py b/web/webqtl/base/webqtlConfigLocal.py
deleted file mode 100755
index 1f986aa7..00000000
--- a/web/webqtl/base/webqtlConfigLocal.py
+++ /dev/null
@@ -1,17 +0,0 @@
-#########################################'
-#      Environment Variables - private
-#########################################
-
-MYSQL_SERVER = 'localhost'
-DB_NAME = 'db_webqtl_zas1024'
-DB_USER = 'webqtlupd'
-DB_PASSWD = 'webqtl'
-
-MYSQL_UPDSERVER = 'localhost'
-DB_UPDNAME = 'db_webqtl_zas1024'
-DB_UPDUSER = 'webqtlupd'
-DB_UPDPASSWD = 'webqtl'
-
-GNROOT = '/home/zas1024/gn/'
-PythonPath = '/usr/bin/python'
-PIDDLE_FONT_PATH = '/usr/lib/python2.4/site-packages/piddle/truetypefonts/'
diff --git a/web/webqtl/base/webqtlDataset.py b/web/webqtl/base/webqtlDataset.py
deleted file mode 100755
index da1b8601..00000000
--- a/web/webqtl/base/webqtlDataset.py
+++ /dev/null
@@ -1,160 +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
-
-from htmlgen import HTMLgen2 as HT
-
-import webqtlConfig
-
-
-
-class webqtlDataset:
-	"""
-	Database class defines a database in webqtl, can be either Microarray, 	
-	Published phenotype, genotype, or user input database(temp)
-	"""
-
-	def __init__(self, dbName, cursor=None):
-
-		assert dbName
-		self.id = 0
-		self.name = ''
-		self.type = ''
-		self.riset = ''
-		self.cursor = cursor
-
-                #temporary storage
-		if dbName.find('Temp') >= 0:
-			self.searchfield = ['name','description']
-			self.disfield = ['name','description']
-			self.type = 'Temp'
-			self.id = 1
-			self.fullname = 'Temporary Storage'
-			self.shortname = 'Temp'
-		elif dbName.find('Publish') >= 0:
-			self.searchfield = ['name','post_publication_description','abstract','title','authors']
-			self.disfield = ['name','pubmed_id', 
-					'pre_publication_description', 'post_publication_description', 'original_description', 
-					'pre_publication_abbreviation', 'post_publication_abbreviation',
-					'lab_code', 'submitter', 'owner', 'authorized_users',
-					'authors','title','abstract', 'journal','volume','pages','month',
-					'year','sequence', 'units', 'comments']
-			self.type = 'Publish'
-		elif dbName.find('Geno') >= 0:
-			self.searchfield = ['name','chr']
-			self.disfield = ['name','chr','mb', 'source2', 'sequence']
-			self.type = 'Geno'
-		else: #ProbeSet
-			self.searchfield = ['name','description','probe_target_description',
-				'symbol','alias','genbankid','unigeneid','omim',
-				'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score']
-			self.disfield = ['name','symbol','description','probe_target_description',
-				'chr','mb','alias','geneid','genbankid', 'unigeneid', 'omim',
-				'refseq_transcriptid','blatseq','targetseq','chipid', 'comments',
-				'strand_probe','strand_gene','probe_set_target_region', 
-				'probe_set_specificity', 'probe_set_blat_score','probe_set_blat_mb_start',
-				'probe_set_blat_mb_end', 'probe_set_strand', 
-				'probe_set_note_by_rw', 'flag']
-			self.type = 'ProbeSet'
-		self.name = dbName
-		if self.cursor and self.id == 0:
-			self.retrieveName()
-	
-	def __str__(self):
-		return self.name
-	
-	__repr__ = __str__
-
-
-	def getRISet(self):
-		assert self.cursor
-		if self.type == 'Publish':
-			query = '''
-					SELECT 
-						InbredSet.Name, InbredSet.Id
-					FROM 
-						InbredSet, PublishFreeze 
-					WHERE 
-						PublishFreeze.InbredSetId = InbredSet.Id AND 
-						PublishFreeze.Name = "%s"
-				''' % self.name
-		elif self.type == 'Geno':
-			query = '''
-					SELECT 
-						InbredSet.Name, InbredSet.Id
-					FROM 
-						InbredSet, GenoFreeze 
-					WHERE 
-						GenoFreeze.InbredSetId = InbredSet.Id AND 
-						GenoFreeze.Name = "%s"
-				''' % self.name
-		elif self.type == 'ProbeSet':
-			query = '''
-					SELECT 
-						InbredSet.Name, InbredSet.Id
-					FROM 
-						InbredSet, ProbeSetFreeze, ProbeFreeze 
-					WHERE 
-						ProbeFreeze.InbredSetId = InbredSet.Id AND 
-						ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND 
-						ProbeSetFreeze.Name = "%s"
-				''' % self.name
-		else:
-			return ""
-		self.cursor.execute(query)
-		RISet, RIID = self.cursor.fetchone()
-		if RISet == 'BXD300':
-			RISet = "BXD"
-		self.riset = RISet
-		self.risetid = RIID
-		return RISet
-
-		
-	def retrieveName(self):
-		assert self.id == 0 and self.cursor
-		query = '''
-			SELECT 
-				Id, Name, FullName, ShortName 
-			FROM 
-				%sFreeze 
-			WHERE 
-				public > %d AND 
-				(Name = "%s" OR FullName = "%s" OR ShortName = "%s")
-		  '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name)
-		try:
-			self.cursor.execute(query)
-			self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone()
-		except:
-			raise KeyError, `self.name`+' doesn\'t exist.'
-
-	
-	def genHTML(self, Class='c0dd'):
-		return  HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class), 
-			url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank")
-
-
-
-
-	
diff --git a/web/webqtl/base/webqtlFormData.py b/web/webqtl/base/webqtlFormData.py
deleted file mode 100755
index 84e41cae..00000000
--- a/web/webqtl/base/webqtlFormData.py
+++ /dev/null
@@ -1,289 +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
-
-from mod_python import Cookie
-import string
-import os
-
-import reaper
-
-import webqtlConfig
-import cookieData
-import sessionData
-from cgiData import cgiData
-from webqtlCaseData import webqtlCaseData
-from utility import webqtlUtil
-
-
-
-class webqtlFormData:
-	'Represents data from a WebQTL form page, needed to generate the next page'
-	attrs = ('formID','RISet','genotype','strainlist','allstrainlist',
-	'suggestive','significance','submitID','identification', 'enablevariance',
-	'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
-
-	#XZ: Attention! All attribute values must be picklable!
-
-	def __init__(self, req = None, mod_python_session=None, FieldStorage_formdata=None):
-
-		for item in self.attrs:
-			setattr(self,item, None)
-
-		try:
-			self.remote_ip = req.connection.remote_ip
-		except:
-			self.remote_ip = '1.2.3.4'
-
-		if req and req.headers_in.has_key('referer'):
-			self.refURL = req.headers_in['referer']
-		else:
-			self.refURL = None
-
-
-		self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie.
-
-		#XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable.
-		self.input_session_data = sessionData.sessionData( mod_python_session )
-
-		#XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data.
-		self.formdata = cgiData( FieldStorage_formdata )
-
-		#get Form ID
-		self.formID = self.formdata.getfirst('FormID')
-
-		#get rest of the attributes
-		if self.formID:
-			for item in self.attrs:
-				value = self.formdata.getfirst(item)
-				if value != None:
-					setattr(self,item,string.strip(value))
-		
-		self.ppolar = ""
-		self.mpolar	= ""
-		if self.RISet:
-			try:
-				# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; 
-				f1, f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.RISet]
-			except:
-				f1 = f12 = self.mpolar = self.ppolar = None
-		
-		try:
-			self.nperm = int(self.nperm)
-			self.nboot = int(self.nboot)
-		except:
-			self.nperm = 2000 #XZ: Rob asked to change the default value to 2000
-			self.nboot = 2000 #XZ: Rob asked to change the default value to 2000
-
-		if self.allstrainlist:
-			self.allstrainlist = map(string.strip, string.split(self.allstrainlist))
-		#self.readGenotype()
-		#self.readData()
-		
-		if self.RISet == 'BXD300':
-			self.RISet = 'BXD'
-		else:
-			pass
-	
-	def __str__(self):
-		rstr = ''
-		for item in self.attrs:
-			if item != 'genotype':
-				rstr += '%s:%s\n' % (item,str(getattr(self,item)))
-		return rstr
-
-		
-	def readGenotype(self):
-		'read genotype from .geno file'
-		if self.RISet == 'BXD300':
-			self.RISet = 'BXD'
-		else:
-			pass
-		assert  self.RISet
-		#genotype_1 is Dataset Object without parents and f1
-		#genotype_2 is Dataset Object with parents and f1 (not for intercross)
-		self.genotype_1 = reaper.Dataset()
-		self.genotype_1.read(os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno'))
-		try:
-			# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; 
-			_f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet]
-		except:
-			_f1 = _f12 = _mat = _pat = None
-		
-		self.genotype_2 =self.genotype_1
-		if self.genotype_1.type == "riset" and _mat and _pat:
-			self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat)	#, F1=_f1)
-			
-		#determine default genotype object
-		if self.incparentsf1 and self.genotype_1.type != "intercross":
-			self.genotype = self.genotype_2
-		else:
-			self.incparentsf1 = 0
-			self.genotype = self.genotype_1
-		self.strainlist = list(self.genotype.prgy)
-		self.f1list = self.parlist = []
-		if _f1 and _f12:
-			self.f1list = [_f1, _f12]
-		if _mat and _pat:
-			self.parlist = [_mat, _pat]
-		
-	def readData(self, strainlst=[], incf1=[]):
-		'read user input data or from trait data and analysis form'
-
-		if not self.genotype:
-			self.readGenotype()
-		if not strainlst:
-			if incf1:
-				strainlst = self.f1list + self.strainlist
-			else:
-				strainlst = self.strainlist	
-	
-	
-		traitfiledata = self.formdata.getfirst('traitfile')
-		traitpastedata = self.formdata.getfirst('traitpaste')
-		variancefiledata = self.formdata.getfirst('variancefile')
-		variancepastedata = self.formdata.getfirst('variancepaste')
-		Nfiledata = self.formdata.getfirst('Nfile')
-
-	
-		if traitfiledata:
-			tt = string.split(traitfiledata)
-			vals = map(webqtlUtil.StringAsFloat, tt)
-		elif traitpastedata:
-			tt = string.split(traitpastedata)
-			vals = map(webqtlUtil.StringAsFloat, tt)
-		else:
-			vals = map(self.FormDataAsFloat, strainlst)
-
-		if len(vals) < len(strainlst):
-				vals += [None]*(len(strainlst) - len(vals))
-		elif len(vals) > len(strainlst):
-				vals = vals[:len(strainlst)]
-		else:
-			pass
-		
-	
-		if variancefiledata:
-			tt = string.split(variancefiledata)
-			vars = map(webqtlUtil.StringAsFloat, tt)
-		elif variancepastedata:
-			tt = string.split(variancepastedata)
-			vars = map(webqtlUtil.StringAsFloat, tt)
-		else:
-			vars = map(self.FormVarianceAsFloat, strainlst)
-
-		if len(vars) < len(strainlst):
-				vars += [None]*(len(strainlst) - len(vars))
-		elif len(vars) > len(strainlst):
-				vars = vars[:len(strainlst)]
-		else:
-			pass
-		
-		if Nfiledata:
-			tt = string.split(Nfiledata)
-			nstrains = map(webqtlUtil.IntAsFloat, tt)
-			if len(nstrains) < len(strainlst):
-				nstrains += [None]*(len(strainlst) - len(nstrains))
-		else:
-			nstrains = map(self.FormNAsFloat, strainlst)
-		
-		##vals, vars, nstrains is obsolete
-		self.allTraitData = {}
-		for i, _strain in enumerate(strainlst):
-			if vals[i] != None:
-				self.allTraitData[_strain] = webqtlCaseData(vals[i], vars[i], nstrains[i])
-
-	
-
-	def informativeStrains(self, strainlst=[], incVars = 0):
-		'''if readData was called, use this to output the informative strains
-		   (strain with values)'''
-		if not strainlst:
-			strainlst = self.strainlist
-		strains = []
-		vals = []
-		vars = []
-		for _strain in strainlst:
-			if self.allTraitData.has_key(_strain):
-				_val, _var = self.allTraitData[_strain].val, self.allTraitData[_strain].var
-				if _val != None:
-					if incVars:
-						if _var != None:
-							strains.append(_strain)
-							vals.append(_val)
-							vars.append(_var)
-					else:
-						strains.append(_strain)
-						vals.append(_val)
-						vars.append(None)
-		return strains, vals, vars, len(strains)
-
-
-				
-	def FormDataAsFloat(self, key):
-		try:
-			return float(self.formdata.getfirst(key))
-		except:
-			return None
-
-	
-	def FormVarianceAsFloat(self, key):
-		try:
-			return float(self.formdata.getfirst('V' + key))
-		except:
-			return None
-	
-	def FormNAsFloat(self, key):
-		try:
-			return int(self.formdata.getfirst('N' + key))
-		except:
-			return None
-		
-	def Sample(self):
-		'Create some dummy data for testing'
-		self.RISet = 'BXD'
-		self.incparentsf1 = 'on'
-		#self.display = 9.2
-		#self.significance = 16.1
-		self.readGenotype()
-		self.identification = 'BXD : Coat color example by Lu Lu, et al'
-		#self.readGenotype()
-		#self.genotype.ReadMM('AXBXAforQTL')
-		#self.strainlist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
-		#self.strainlist.sort()
-		self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2), 
-		'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2), 
-		'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4), 
-		'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2), 
-		'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3), 
-		'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3), 
-		'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2), 
-		'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4), 
-		'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4), 
-		'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1), 
-		'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4), 
-		'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4), 
-		'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)}
-
diff --git a/web/webqtl/base/webqtlTrait.py b/web/webqtl/base/webqtlTrait.py
deleted file mode 100644
index 2469504f..00000000
--- a/web/webqtl/base/webqtlTrait.py
+++ /dev/null
@@ -1,590 +0,0 @@
-import string
-
-from htmlgen import HTMLgen2 as HT
-
-import webqtlConfig
-from webqtlCaseData import webqtlCaseData
-from webqtlDataset import webqtlDataset
-from dbFunction import webqtlDatabaseFunction
-from utility import webqtlUtil
-
-
-from __future__ import print_function, division
-
-from pprint import pformat as pf
-
-class webqtlTrait:
-	"""
-	Trait class defines a trait in webqtl, can be either Microarray, 	
-	Published phenotype, genotype, or user input trait
-	"""
-
-	def __init__(self, cursor = None, **kw):
-		self.cursor = cursor
-		self.db = None			# database object
-		self.name = ''			# Trait ID, ProbeSet ID, Published ID, etc.
-		self.cellid = ''
-		self.identification = 'un-named trait'
-		self.riset = ''
-		self.haveinfo = 0
-		self.sequence = ''		# Blat sequence, available for ProbeSet
-		self.data = {}
-		for name, value in kw.items():
-			if self.__dict__.has_key(name):
-				setattr(self, name, value)
-			elif name == 'fullname':
-				name2 = value.split("::")
-				if len(name2) == 2:
-					self.db, self.name = name2
-				elif len(name2) == 3:
-					self.db, self.name, self.cellid = name2
-				else:
-					raise KeyError, `value` + ' parameter format error.'
-			else:
-				raise KeyError, `name`+' not a valid parameter for this class.'
-		
-		if self.db and type(self.db) == type("1"):
-			assert self.cursor
-			self.db = webqtlDataset(self.db, self.cursor)
-
-		#if self.db == None, not from a database
-		if self.db:
-			if self.db.type == "Temp":
-				self.cursor.execute('''
-					SELECT 
-						InbredSet.Name 
-					FROM 
-						InbredSet, Temp 
-					WHERE 
-						Temp.InbredSetId = InbredSet.Id AND 
-						Temp.Name = "%s"
-				''' % self.name)
-				self.riset = self.cursor.fetchone()[0]
-			else:	
-				self.riset = self.db.getRISet()
-
-		#
-		# In ProbeSet, there are maybe several annotations match one sequence
-		# so we need use sequence(BlatSeq) as the identification, when we update
-		# one annotation, we update the others who match the sequence also.
-		#
-		# Hongqiang Li, 3/3/2008
-		#
-
-                #XZ, 05/08/2009: This block is not neccessary. We can add 'BlatSeq' into disfield.
-                # The variable self.sequence should be changed to self.BlatSeq
-                # It also should be changed in other places where it are used.
-
-		if self.db:
-			if self.db.type == 'ProbeSet':
-				query = '''
-					SELECT 
-						ProbeSet.BlatSeq
-					FROM
-						ProbeSet, ProbeSetFreeze, ProbeSetXRef
-					WHERE
-						ProbeSet.Id=ProbeSetXRef.ProbeSetId and
-						ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
-						ProbeSet.Name = "%s" and
-						ProbeSetFreeze.Name = "%s"
-				''' % (self.name, self.db.name)
-				self.cursor.execute(query)
-				self.sequence = self.cursor.fetchone()[0]
-
-	
-	def getName(self):
-		str = ""
-		if self.db and self.name:
-			str = "%s::%s" % (self.db, self.name)
-			if self.cellid:
-				str += "::" + self.cellid
-		else:
-			str = self.description
-		return str
-
-	# 
-	# when user enter a trait or GN generate a trait, user want show the name
-	# not the name that generated by GN randomly, the two follow function are
-	# used to give the real name and the database. displayName() will show the 
-	# database also, getGivenName() just show the name. 
-	# For other trait, displayName() as same as getName(), getGivenName() as 
-	# same as self.name
-	#
-	# Hongqiang 11/29/07
-	#
-	def getGivenName(self):
-		str = self.name
-		if self.db and self.name:
-			if self.db.type=='Temp':
-				self.cursor.execute('SELECT description FROM Temp WHERE Name=%s',self.name)
-				desc = self.cursor.fetchone()[0]
-				if desc.__contains__('PCA'):
-					desc = desc[desc.rindex(':')+1:].strip()
-				else:
-					desc = desc[:desc.index('entered')].strip()
-				str = desc
-		return str
-
-	def displayName(self):
-		str = ""
-		if self.db and self.name:
-			if self.db.type=='Temp':
-				desc = self.description
-				if desc.__contains__('PCA'):
-					desc = desc[desc.rindex(':')+1:].strip()
-				else:
-					desc = desc[:desc.index('entered')].strip()
-				str = "%s::%s" % (self.db, desc)
-			else:
-				str = "%s::%s" % (self.db, self.name)
-				if self.cellid:
-					str += "::" + self.cellid
-		else:
-			str = self.description
-	
-		return str
-
-	
-	#def __str__(self):
-	#	#return "%s %s" % (self.getName(), self.riset)
-	#	return self.getName()
-	__str__ = getName
-	__repr__ = __str__
-
-	def exportData(self, strainlist, type="val"):
-		"""
-			export data according to strainlist
-			mostly used in calculating correlation
-		"""
-		result = []
-		for strain in strainlist:
-			if self.data.has_key(strain):
-				if type=='val':
-					result.append(self.data[strain].val)
-				elif type=='var':
-					result.append(self.data[strain].var)
-				elif type=='N':
-					result.append(self.data[strain].N)
-				else:
-					raise KeyError, `type`+' type is incorrect.'
-			else:
-				result.append(None)
-		return result
-		
-	def exportInformative(self, incVar=0):
-		"""
-			export informative strain
-			mostly used in qtl regression
-		"""
-		strains = []
-		vals = []
-		vars = []
-		for strain, value in self.data.items():
-			if value.val != None:
-				if not incVar or value.var != None:
-					strains.append(strain)
-					vals.append(value.val)
-					vars.append(value.var)
-		return 	strains, vals, vars
-
-
-	#
-	# In ProbeSet, there are maybe several annotations match one sequence
-	# so we need use sequence(BlatSeq) as the identification, when we update
-	# one annotation, we update the others who match the sequence also.
-	#
-	# Hongqiang Li, 3/3/2008
-	#
-	def getSequence(self):
-		assert self.cursor
-		if self.db.type == 'ProbeSet':
-			query = '''
-					SELECT 
-						ProbeSet.BlatSeq
-					FROM
-						ProbeSet, ProbeSetFreeze, ProbeSetXRef
-					WHERE
-						ProbeSet.Id=ProbeSetXRef.ProbeSetId and
-						ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
-						ProbeSet.Name = %s
-						ProbeSetFreeze.Name = %s
-				''' , (self.name, self.db.name)
-			self.cursor.execute(query)
-			results = self.fetchone()
-
-			return results[0]
-			
-			
-		
-	def retrieveData(self, strainlist=[]):
-		assert self.db and self.cursor
-
-		debug_file = open("/home/zas1024/gn/web/traitlist_debug.txt", "w")
-		debug_file.write("strianlist is:" + strainlist + "\n")
-
-		if self.db.type == 'Temp':
-			query = '''
-				SELECT 
-					Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id 
-				FROM 
-					TempData, Temp, Strain 
-				WHERE 
-					TempData.StrainId = Strain.Id AND 
-					TempData.Id = Temp.DataId AND 
-					Temp.name = '%s'
-				Order BY
-					Strain.Name
-				''' % self.name
-		#XZ, 03/02/2009: Xiaodong changed Data to PublishData, SE to PublishSE
-		elif self.db.type == 'Publish': 
-			query = '''
-				SELECT 
-					Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id 
-				FROM 
-					(PublishData, Strain, PublishXRef, PublishFreeze)
-				left join PublishSE on 
-					(PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
-				left join NStrain on 
-					(NStrain.DataId = PublishData.Id AND 
-					NStrain.StrainId = PublishData.StrainId) 
-				WHERE 
-					PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND 
-					PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND 
-					PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
-				Order BY
-					Strain.Name
-				''' % (self.name, self.db.id)
-
-                #XZ, 03/02/2009: Xiaodong changed Data to ProbeData, SE to ProbeSE
-		elif self.cellid:
-			#Probe Data
-			query = '''
-				SELECT 
-					Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id 
-				FROM 
-					(ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef, 
-					Strain, Probe, ProbeSet)
-				left join ProbeSE on 
-					(ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId)
-				WHERE 
-					Probe.Name = '%s' AND ProbeSet.Name = '%s' AND 
-					Probe.ProbeSetId = ProbeSet.Id AND 
-					ProbeXRef.ProbeId = Probe.Id AND 
-					ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND 
-					ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND 
-					ProbeSetFreeze.Name = '%s' AND 
-					ProbeXRef.DataId = ProbeData.Id AND 
-					ProbeData.StrainId = Strain.Id
-				Order BY
-					Strain.Name
-				''' % (self.cellid, self.name, self.db.name)
-                #XZ, 03/02/2009: Xiaodong added this block for ProbeSetData and ProbeSetSE
-		elif self.db.type == 'ProbeSet':
-			#ProbeSet Data
-                        query = '''
-                                SELECT
-                                        Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
-                                FROM
-                                        (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
-                                left join ProbeSetSE on
-                                        (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
-                                WHERE
-                                        ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                                        ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-                                        ProbeSetFreeze.Name = '%s' AND
-                                        ProbeSetXRef.DataId = ProbeSetData.Id AND
-                                        ProbeSetData.StrainId = Strain.Id
-                                Order BY
-                                        Strain.Name
-                                ''' % (self.name, self.db.name)
-                #XZ, 03/02/2009: Xiaodong changeded Data to GenoData, SE to GenoSE
-		else:
-			#Geno Data
-			#XZ: The SpeciesId is not necessary, but it's nice to keep it to speed up database search.
-			query = '''
-				SELECT 
-					Strain.Name, GenoData.value, GenoSE.error, GenoData.Id 
-				FROM 
-					(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
-				left join GenoSE on
-					(GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
-				WHERE 
-					Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
-					GenoXRef.GenoFreezeId = GenoFreeze.Id AND 
-					GenoFreeze.Name = '%s' AND 
-					GenoXRef.DataId = GenoData.Id AND 
-					GenoData.StrainId = Strain.Id
-				Order BY
-					Strain.Name
-				''' % (webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.db.riset), self.name, self.db.name)
-
-		
-		self.cursor.execute(query)
-		results = self.cursor.fetchall()
-		self.data.clear()
-		if results:
-			self.mysqlid = results[0][-1]
-			if strainlist:
-				for item in results:
-					if item[0] in strainlist:
-						val = item[1]
-						if val != None:
-							var = item[2]
-							ndata = None
-							if self.db.type in ('Publish', 'Temp'):
-								ndata = item[3]
-							self.data[item[0]] = webqtlCaseData(val, var, ndata)
-				#end for
-			else:	
-				for item in results:
-					val = item[1]
-					if val != None:
-						var = item[2]
-						ndata = None
-						if self.db.type in ('Publish', 'Temp'):
-							ndata = item[3]
-						self.data[item[0]] = webqtlCaseData(val, var, ndata)
-				#end for
-			#end if
-		else:
-			pass
-
-		debug_file.write("self.data is:", pf(self.data) + "\n")
-			
-	def keys(self):
-		return self.__dict__.keys()
-	
-	def has_key(self, key):
-		return self.__dict__.has_key(key)
-	
-	def items(self):
-		return self.__dict__.items()
-	
-	def retrieveInfo(self, QTL = None):
-		assert self.db and self.cursor
-		if self.db.type == 'Publish':
-			#self.db.DisField = ['Name','PubMed_ID','Phenotype','Abbreviation','Authors','Title',\
-			#	'Abstract', 'Journal','Volume','Pages','Month','Year','Sequence',\
-			#	'Units', 'comments']
-			query = '''
-				SELECT 
-					PublishXRef.Id, Publication.PubMed_ID, 
-					Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, 
-					Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, 
-					Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
-					Publication.Authors, Publication.Title, Publication.Abstract, 
-					Publication.Journal, Publication.Volume, Publication.Pages, 
-					Publication.Month, Publication.Year, PublishXRef.Sequence, 
-					Phenotype.Units, PublishXRef.comments 
-				FROM 
-					PublishXRef, Publication, Phenotype, PublishFreeze 
-				WHERE 
-					PublishXRef.Id = %s AND 
-					Phenotype.Id = PublishXRef.PhenotypeId AND 
-					Publication.Id = PublishXRef.PublicationId AND 
-					PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND 
-					PublishFreeze.Id =%s
-				''' % (self.name, self.db.id)
-		#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
-		#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
-		elif self.db.type == 'ProbeSet':
-			disfieldString = string.join(self.db.disfield,',ProbeSet.')
-			disfieldString = 'ProbeSet.' + disfieldString
-			query = """
-				SELECT %s 
-				FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
-				WHERE
-					ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-					ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-					ProbeSetFreeze.Name = '%s' AND
-					ProbeSet.Name = '%s'
-				""" % (disfieldString, self.db.name, self.name)
-		#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 self.db.type == 'Geno':
-			disfieldString = string.join(self.db.disfield,',Geno.')
-			disfieldString = 'Geno.' + disfieldString
-			query = """
-				SELECT %s 
-				FROM Geno, GenoFreeze, GenoXRef
-				WHERE
-					GenoXRef.GenoFreezeId = GenoFreeze.Id AND
-					GenoXRef.GenoId = Geno.Id AND
-					GenoFreeze.Name = '%s' AND
-					Geno.Name = '%s'
-				""" % (disfieldString, self.db.name, self.name)
-		else: #Temp type
-			query = 'SELECT %s FROM %s WHERE Name = "%s"' % \
-				(string.join(self.db.disfield,','), self.db.type, self.name)
-
-		
-		self.cursor.execute(query)
-		traitInfo = self.cursor.fetchone()
-		if traitInfo:
-			self.haveinfo = 1
-
-			#XZ: assign SQL query result to trait attributes.
-			for i, field in enumerate(self.db.disfield):
-				setattr(self, field, traitInfo[i])
-
-			if self.db.type == 'Publish':
-				self.confidential = 0
-				if self.pre_publication_description and not self.pubmed_id:
-					self.confidential = 1
-
-			self.homologeneid = None
-			if self.db.type == 'ProbeSet' and self.riset and self.geneid:
-				#XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
-				#XZ: So I have to test if geneid is number before execute the query.
-				#XZ: The geneid values in database should be cleaned up.
-				try:
-					junk = float(self.geneid)
-					geneidIsNumber = 1
-				except:
-					geneidIsNumber = 0
-
-				if geneidIsNumber:
-					query = """
-						SELECT
-							HomologeneId
-						FROM
-							Homologene, Species, InbredSet
-						WHERE
-							Homologene.GeneId =%s AND
-							InbredSet.Name = '%s' AND
-							InbredSet.SpeciesId = Species.Id AND
-							Species.TaxonomyId = Homologene.TaxonomyId
-						""" % (self.geneid, self.riset)
-					self.cursor.execute(query)
-					result = self.cursor.fetchone()
-				else:
-					result = None
-
-				if result:
-					self.homologeneid = result[0]
-
-			if QTL:
-				if self.db.type == 'ProbeSet' and not self.cellid:
-					query = '''
-						SELECT 
-							ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean 
-						FROM 
-							ProbeSetXRef, ProbeSet
-						WHERE 
-							ProbeSetXRef.ProbeSetId = ProbeSet.Id AND 
-							ProbeSet.Name = "%s" AND
-							ProbeSetXRef.ProbeSetFreezeId =%s
-						''' % (self.name, self.db.id)
-					self.cursor.execute(query)
-					traitQTL = self.cursor.fetchone()
-					if traitQTL:
-						self.locus, self.lrs, self.pvalue, self.mean = traitQTL
-					else:
-						self.locus = self.lrs = self.pvalue = self.mean = ""
-				if self.db.type == 'Publish':
-					query = '''
-						SELECT
-							PublishXRef.Locus, PublishXRef.LRS
-						FROM
-							PublishXRef, PublishFreeze
-						WHERE
-							PublishXRef.Id = %s AND
-							PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-							PublishFreeze.Id =%s
-						''' % (self.name, self.db.id)
-					self.cursor.execute(query)
-					traitQTL = self.cursor.fetchone()
-					if traitQTL:
-						self.locus, self.lrs = traitQTL
-					else:
-						self.locus = self.lrs = ""
-		else:
-			raise KeyError, `self.name`+' information is not found in the database.'
-	
-	def genHTML(self, formName = "", dispFromDatabase=0, privilege="guest", userName="Guest", authorized_users=""):
-		if not self.haveinfo:
-			self.retrieveInfo()
-		
-		if self.db.type == 'Publish':
-			PubMedLink = ""
-	 		if self.pubmed_id:
-	 			PubMedLink = HT.Href(text="PubMed %d : " % self.pubmed_id,
-	 			target = "_blank", url = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id)
-			else:
-				PubMedLink = HT.Span("Unpublished : ", Class="fs15")
-			
-			if formName:
-				setDescription2 = HT.Href(url="javascript:showDatabase3('%s','%s','%s','')" % 
-				(formName, self.db.name, self.name), Class = "fs14")
-			else:
-				setDescription2 = HT.Href(url="javascript:showDatabase2('%s','%s','')" % 
-				(self.db.name,self.name), Class = "fs14")
-	
-			if self.confidential and not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=privilege, userName=userName, authorized_users=authorized_users):
-					setDescription2.append('RecordID/%s - %s' % (self.name, self.pre_publication_description))
-			else:
-				setDescription2.append('RecordID/%s - %s' % (self.name, self.post_publication_description))
-
-			#XZ 03/26/2011: Xiaodong comment out the following two lins as Rob asked. Need to check with Rob why in PublishXRef table, there are few row whose Sequence > 1.
-			#if self.sequence > 1:
-			#	setDescription2.append(' btach %d' % self.sequence)
-			if self.authors:
-				a1 = string.split(self.authors,',')[0]
-				while a1[0] == '"' or a1[0] == "'" :
-					a1 = a1[1:]
-				setDescription2.append(' by ')
-				setDescription2.append(HT.Italic('%s, and colleagues' % a1))
-			setDescription = HT.Span(PubMedLink, setDescription2)
-			
-		elif self.db.type == 'Temp':
-			setDescription = HT.Href(text="%s" % (self.description),url="javascript:showDatabase2\
-			('%s','%s','')" % (self.db.name,self.name), Class = "fs14")
-			setDescription = HT.Span(setDescription)
-			
-		elif self.db.type == 'Geno': # Genome DB only available for single search
-			if formName:
-				setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\
-			'%2.3f' % self.mb),url="javascript:showDatabase3('%s','%s','%s','')" % \
-			(formName, self.db.name, self.name), Class = "fs14")
-			else:
-				setDescription = HT.Href(text="Locus %s [Chr %s @ %s Mb]" % (self.name,self.chr,\
-			'%2.3f' % self.mb),url="javascript:showDatabase2('%s','%s','')" % \
-			(self.db.name,self.name), Class = "fs14")
-				
-			setDescription = HT.Span(setDescription)
-			
-		else:
-			if self.cellid:
-				if formName:	
-					setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name, self.cellid),url=\
-				"javascript:showDatabase3('%s','%s','%s','%s')" % (formName, self.db.name,self.name,self.cellid), \
-				Class = "fs14")
-				else:	
-					setDescription = HT.Href(text="ProbeSet/%s/%s" % (self.name,self.cellid),url=\
-				"javascript:showDatabase2('%s','%s','%s')" % (self.db.name,self.name,self.cellid), \
-				Class = "fs14")
-			else:
-				if formName:
-					setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\
-				"javascript:showDatabase3('%s','%s','%s','')" % (formName, self.db.name,self.name), \
-				Class = "fs14")
-				else:
-					setDescription = HT.Href(text="ProbeSet/%s" % self.name, url=\
-				"javascript:showDatabase2('%s','%s','')" % (self.db.name,self.name), \
-				Class = "fs14")
-			if self.symbol and self.chr and self.mb:
-				setDescription.append(' [')
-				setDescription.append(HT.Italic('%s' % self.symbol,Class="cdg fwb"))
-				setDescription.append(' on Chr %s @ %s Mb]' % (self.chr,self.mb))
-			if self.description:
-				setDescription.append(': %s' % self.description)
-			if self.probe_target_description:
-				setDescription.append('; %s' % self.probe_target_description)
-			setDescription = HT.Span(setDescription)
-			
-		if self.db.type != 'Temp' and dispFromDatabase:
-			setDescription.append( ' --- FROM : ')
-			setDescription.append(self.db.genHTML(Class='cori'))
-		return setDescription
-	
-
author	zsloan	2015-03-27 20:28:51 +0000
committer	zsloan	2015-03-27 20:28:51 +0000
commit	d0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree	3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/base
parent	a840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
download	genenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz