Ran reindent.py recursively on wqflask directory

14 files changed, 1501 insertions, 1528 deletions

diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 311c9e22..53d1357b 100755
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -25,47 +25,44 @@
 # 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))
-	"""
+    """
+    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()))
+    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/admin.py b/wqflask/base/admin.py
index a04df2da..1ba75117 100755
--- a/wqflask/base/admin.py
+++ b/wqflask/base/admin.py
@@ -35,18 +35,18 @@
 
 
 ADMIN_search_dbs = {
-                    'rat': {'PERITONEAL FAT': ['FT_2A_0605_Rz'], 
+                    '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'], 
+                    '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'], 
+                              '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'],
@@ -65,14 +65,14 @@ ADMIN_search_dbs = {
 
 ###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'], 
+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'],
@@ -84,5 +84,3 @@ ADMIN_tissue_alias = {'CEREBELLUM': ['Cb'],
                       'ADIPOSE': ['Wfat'],
                       'RETINA': ['Ret']
                      }
-
-
diff --git a/wqflask/base/cgiData.py b/wqflask/base/cgiData.py
index 57416060..155b3ec3 100755
--- a/wqflask/base/cgiData.py
+++ b/wqflask/base/cgiData.py
@@ -30,41 +30,37 @@
 #########################################
 
 class cgiData(dict):
-	'''convert Field storage object to Dict object
-	   Filed storage object cannot be properly dumped	
-	'''
+    '''convert Field storage object to Dict object
+       Filed storage object cannot be properly dumped
+    '''
 
-	def __init__(self, field_storage=None):
+    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
+        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
index 4b7c9046..eeb7c0cf 100755
--- a/wqflask/base/cookieData.py
+++ b/wqflask/base/cookieData.py
@@ -30,23 +30,20 @@
 #########################################
 
 class cookieData(dict):
-	'convert mod python Cookie object to Dict object'
+    'convert mod python Cookie object to Dict object'
 
-	def __init__(self, cookies=None):
+    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
+        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/header.py b/wqflask/base/header.py
index b6136b51..ec15e174 100755
--- a/wqflask/base/header.py
+++ b/wqflask/base/header.py
@@ -3,4 +3,4 @@ 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
+header_string = header_string.replace('<!-- %s -->', '%s')
diff --git a/wqflask/base/indexBody.py b/wqflask/base/indexBody.py
index aa67dffa..a5bc4c17 100755
--- a/wqflask/base/indexBody.py
+++ b/wqflask/base/indexBody.py
@@ -1,174 +1,174 @@
 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>
+                                                        <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%">
+                                                                        <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>
+                                                                                <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>
+                                                                                </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>
+                                                                        <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 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>
+                                                                                <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');">
+                                                                        <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>
+                                                                                </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>
 
 
 
@@ -185,7 +185,7 @@ Quick HELP Examples and </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 
+&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">
 
@@ -206,85 +206,85 @@ Quick HELP Examples and </B>
 <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> 
+</UL>
 </DIR>
-					</TD>				
+                                        </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: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>
+                                                        <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> 
+<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>
 
-							</BLOCKQUOTE>
 
-							
 
-							<p style="font-size:14px;font-family:verdana;color:black"><B>Mirror and Development Sites</B></P>
+                                                        <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>
+                                                        <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>
+                                                        <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 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> 
+                                                        </BLOCKQUOTE>
 
 
 </P>
-						</TD>
+                                                </TD>
 """
diff --git a/wqflask/base/myCookie.py b/wqflask/base/myCookie.py
index db5320df..add7e6ea 100755
--- a/wqflask/base/myCookie.py
+++ b/wqflask/base/myCookie.py
@@ -25,31 +25,27 @@
 # Last updated by GeneNetwork Core Team 2010/10/20
 
 #########################################
-## python cookie and mod python cookie are 
+## 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	
-
+    '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
index 01555f87..4b23060f 100755
--- a/wqflask/base/sessionData.py
+++ b/wqflask/base/sessionData.py
@@ -30,24 +30,21 @@
 #########################################
 
 class sessionData(dict):
-	'convert mod python Session object to Dict object'
+    'convert mod python Session object to Dict object'
 
-	def __init__(self, mod_python_session=None):
-	
-		if not mod_python_session:
-			mod_python_session = {}
+    def __init__(self, mod_python_session=None):
 
-		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
+        if not mod_python_session:
+            mod_python_session = {}
 
-	getfirst = getvalue
+        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/template.py b/wqflask/base/template.py
index 85bd86df..aa8f90dc 100755
--- a/wqflask/base/template.py
+++ b/wqflask/base/template.py
@@ -68,32 +68,32 @@ template = """
 <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 -->
+        <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 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 -->
+        <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 -->
@@ -103,20 +103,20 @@ template = """
 <!-- 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
-	//-->
+        <!--//
+        // 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/wqflask/base/templatePage.py b/wqflask/base/templatePage.py
index 821c6181..7ef58a72 100755
--- a/wqflask/base/templatePage.py
+++ b/wqflask/base/templatePage.py
@@ -61,162 +61,162 @@ 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.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
+    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.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/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 4df32ca4..f68354be 100755
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -25,30 +25,27 @@
 # Last updated by GeneNetwork Core Team 2010/10/20
 
 class webqtlCaseData:
-	"""
-	one case data in one trait
-	"""
+    """
+    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__
+    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/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py
index da1b8601..f8491bb1 100755
--- a/wqflask/base/webqtlDataset.py
+++ b/wqflask/base/webqtlDataset.py
@@ -31,130 +31,125 @@ 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")
-
-
-
-
-	
+    """
+    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/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index c94dbe53..06faacc0 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -40,261 +40,261 @@ 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, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=None):
-
-		self.__dict__.update(start_vars)
-
-		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
-
-		# For now let's just comment all this out - Sam
-
-		#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 __getitem__(self, key):
-		return self.__dict__[key]
-
-	def get(self, key, default=None):
-		if key in self.__dict__:
-			return self.__dict__[key]
-		else:
-			return default
-
-	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)}
+    '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, start_vars = None, req = None, mod_python_session=None, FieldStorage_formdata=None):
+
+        self.__dict__.update(start_vars)
+
+        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
+
+        # For now let's just comment all this out - Sam
+
+        #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 __getitem__(self, key):
+        return self.__dict__[key]
+
+    def get(self, key, default=None):
+        if key in self.__dict__:
+            return self.__dict__[key]
+        else:
+            return default
+
+    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/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index 88226894..812d112a 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -14,579 +14,579 @@ 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):
-		print("in webqtlTrait")
-		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 = {}
-		print("foo")
-		print("kw in webqtlTrait are:", pf(kw))
-		print("printed\n\n")
-		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, repr(value) + ' parameter format error.'
-			else:
-				raise KeyError, repr(name) + ' not a valid parameter for this class.'
-
-		if self.db and isinstance(self.db, basestring):
-			assert self.cursor, "Don't have a cursor"
-			self.db = webqtlDataset(self.db, self.cursor)
-
-		#if self.db == None, not from a database
-		print("self.db is:", self.db, type(self.db))
-		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':
-				print("Doing ProbeSet Query")
-				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)
-				print("query is:", query)
-				self.cursor.execute(*query)
-				self.sequence = self.cursor.fetchone()[0]
-				print("self.sequence is:", self.sequence)
-
-
-	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':
-			self.cursor.execute('''
-					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
-
-		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
-
-	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
+    """
+    Trait class defines a trait in webqtl, can be either Microarray,
+    Published phenotype, genotype, or user input trait
+
+    """
+
+    def __init__(self, cursor = None, **kw):
+        print("in webqtlTrait")
+        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 = {}
+        print("foo")
+        print("kw in webqtlTrait are:", pf(kw))
+        print("printed\n\n")
+        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, repr(value) + ' parameter format error.'
+            else:
+                raise KeyError, repr(name) + ' not a valid parameter for this class.'
+
+        if self.db and isinstance(self.db, basestring):
+            assert self.cursor, "Don't have a cursor"
+            self.db = webqtlDataset(self.db, self.cursor)
+
+        #if self.db == None, not from a database
+        print("self.db is:", self.db, type(self.db))
+        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':
+                print("Doing ProbeSet Query")
+                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)
+                print("query is:", query)
+                self.cursor.execute(*query)
+                self.sequence = self.cursor.fetchone()[0]
+                print("self.sequence is:", self.sequence)
+
+
+    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':
+            self.cursor.execute('''
+                            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
+
+        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
+
+    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