Checkpoint along modifying for data trait and analysis

3 files changed, 74 insertions, 47 deletions

diff --git a/wqflask/base/templatePage.py b/wqflask/base/templatePage.py
index 4dece24a..821c6181 100755
--- a/wqflask/base/templatePage.py
+++ b/wqflask/base/templatePage.py
@@ -70,13 +70,13 @@ class templatePage:
 		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 = ''
@@ -89,11 +89,13 @@ class templatePage:
 
 		self.userName = 'Guest'
 		self.privilege = 'guest'
-		if fd.input_session_data.has_key('user'):
-			self.userName = fd.input_session_data['user']
-		if fd.input_session_data.has_key('privilege'):
-			self.privilege = fd.input_session_data['privilege']
-	
+
+		# 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
@@ -126,20 +128,20 @@ class templatePage:
 	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)	
-		
+		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')
@@ -147,9 +149,9 @@ class templatePage:
 			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)           
+                        shutil.move(path_tmp,path_html)
 		except:
-			pass	
+			pass
 
 	def openMysql(self):
 		try:
@@ -176,12 +178,12 @@ class templatePage:
 					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:
@@ -190,7 +192,7 @@ class templatePage:
 			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:
@@ -198,7 +200,7 @@ class templatePage:
 			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)
@@ -210,13 +212,11 @@ class templatePage:
 		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;		
+		# 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/wqflask/show_trait/DataEditingPage.py b/wqflask/wqflask/show_trait/DataEditingPage.py
index c2e1c37f..1186fa03 100755
--- a/wqflask/wqflask/show_trait/DataEditingPage.py
+++ b/wqflask/wqflask/show_trait/DataEditingPage.py
@@ -52,35 +52,62 @@ class DataEditingPage(templatePage):
 		##      titles, etc.
 		#############################
 
-		titleTop = HT.Div()
-
-		title1 = HT.Paragraph("  Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader")
-		title1Body = HT.Paragraph(Id="sectionbody1")
-
-		if fd.enablevariance and not varianceDataPage:
-			title2 = HT.Paragraph("  Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader")
-		else:
-			title2 = HT.Paragraph("  Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader")
-		title2Body = HT.Paragraph(Id="sectionbody2")
-
-		title3 = HT.Paragraph("  Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader")
-		title3Body = HT.Paragraph(Id="sectionbody3")
-
-		title4 = HT.Paragraph("  Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader")
-		title4Body = HT.Paragraph(Id="sectionbody4")
-
-		title5 = HT.Paragraph("  Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader")
-		title5Body = HT.Paragraph(Id="sectionbody5")
+		#titleTop = HT.Div()
+		#
+		#title1 = HT.Paragraph("  Details and Links", style="border-radius: 5px;", Id="title1", Class="sectionheader")
+		#title1Body = HT.Paragraph(Id="sectionbody1")
+		#
+		#if fd.enablevariance and not varianceDataPage:
+		#	title2 = HT.Paragraph("  Submit Variance", style="border-radius: 5px;", Id="title2", Class="sectionheader")
+		#else:
+		#	title2 = HT.Paragraph("  Basic Statistics", style="border-radius: 5px;", Id="title2", Class="sectionheader")
+		#title2Body = HT.Paragraph(Id="sectionbody2")
+		#
+		#title3 = HT.Paragraph("  Calculate Correlations", style="border-radius: 5px;", Id="title3", Class="sectionheader")
+		#title3Body = HT.Paragraph(Id="sectionbody3")
+		#
+		#title4 = HT.Paragraph("  Mapping Tools", style="border-radius: 5px;", Id="title4", Class="sectionheader")
+		#title4Body = HT.Paragraph(Id="sectionbody4")
+		#
+		#title5 = HT.Paragraph("  Review and Edit Data", style="border-radius: 5px;", Id="title5", Class="sectionheader")
+		#title5Body = HT.Paragraph(Id="sectionbody5")
 
 		#############################
 		##     Hidden field
 		#############################
 
 		# Some fields, like method, are defaulted to None; otherwise in IE the field can't be changed using jquery
-		hddn = {'FormID':fmID, 'RISet':fd.RISet, 'submitID':'', 'scale':'physic', 'additiveCheck':'ON', 'showSNP':'ON', 'showGenes':'ON', 'method':None,\
-		'parentsf14regression':'OFF', 'stats_method':'1', 'chromosomes':'-1', 'topten':'', 'viewLegend':'ON', 'intervalAnalystCheck':'ON', 'valsHidden':'OFF',\
- 		'database':'', 'criteria':None, 'MDPChoice':None, 'bootCheck':None, 'permCheck':None, 'applyVarianceSE':None, 'strainNames':'_', 'strainVals':'_',\
-		'strainVars':'_', 'otherStrainNames':'_', 'otherStrainVals':'_', 'otherStrainVars':'_', 'extra_attributes':'_', 'other_extra_attributes':'_'}
+		hddn = {
+			'FormID':fmID,
+			'RISet':fd.RISet,
+			'submitID':'',
+			'scale':'physic',
+			'additiveCheck':'ON',
+			'showSNP':'ON',
+			'showGenes':'ON',
+			'method':None,
+			'parentsf14regression':'OFF',
+			'stats_method':'1',
+			'chromosomes':'-1',
+			'topten':'',
+			'viewLegend':'ON',
+			'intervalAnalystCheck':'ON',
+			'valsHidden':'OFF',
+			'database':'',
+			'criteria':None,
+			'MDPChoice':None,
+			'bootCheck':None,
+			'permCheck':None,
+			'applyVarianceSE':None,
+			'strainNames':'_',
+			'strainVals':'_',
+			'strainVars':'_',
+			'otherStrainNames':'_',
+			'otherStrainVals':'_',
+			'otherStrainVars':'_',
+			'extra_attributes':'_',
+			'other_extra_attributes':'_'
+			}
 
 		if fd.enablevariance:
 			hddn['enablevariance']='ON'
diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py
index d4019fd5..a63071c3 100644
--- a/wqflask/wqflask/show_trait/show_trait_page.py
+++ b/wqflask/wqflask/show_trait/show_trait_page.py
@@ -182,6 +182,6 @@ class ShowTraitPage(DataEditingPage):
 			fd.varianceDispName = 'SE'
 			fd.formID = 'varianceChoice'
 
-		self.dict['body']= thisTrait
+		#self.dict['body']= thisTrait
 		DataEditingPage.__init__(self, fd, thisTrait)
-		self.dict['title'] = '%s: Display Trait' % fd.identification
+		#self.dict['title'] = '%s: Display Trait' % fd.identification