From 3d6be932e5185e4dd7170b3ea740591de01341a0 Mon Sep 17 00:00:00 2001
From: Sam Ockman
Date: Sun, 3 Jun 2012 05:47:07 -0400
Subject: Before changing fd for trait analysis into a webQTLFormData object

---
 wqflask/base/webqtlTrait.py                   | 17 +++++++++--------
 wqflask/wqflask/show_trait/show_trait_page.py | 21 +++++++++++++++------
 2 files changed, 24 insertions(+), 14 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/webqtlTrait.py b/wqflask/base/webqtlTrait.py
index c3c0cded..88226894 100755
--- a/wqflask/base/webqtlTrait.py
+++ b/wqflask/base/webqtlTrait.py
@@ -92,12 +92,13 @@ class webqtlTrait:
 					WHERE
 						ProbeSet.Id=ProbeSetXRef.ProbeSetId and
 						ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
-						ProbeSet.Name = "%s" and
-						ProbeSetFreeze.Name = "%s"
-				''' % (self.name, self.db.name)
+						ProbeSet.Name = %s and
+						ProbeSetFreeze.Name = %s
+				''', (self.name, self.db.name)
 				print("query is:", query)
-				self.cursor.execute(query)
+				self.cursor.execute(*query)
 				self.sequence = self.cursor.fetchone()[0]
+				print("self.sequence is:", self.sequence)
 
 
 	def getName(self):
@@ -124,7 +125,7 @@ class webqtlTrait:
 		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)
+				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()
@@ -206,7 +207,7 @@ class webqtlTrait:
 	def getSequence(self):
 		assert self.cursor
 		if self.db.type == 'ProbeSet':
-			query = '''
+			self.cursor.execute('''
 					SELECT
 						ProbeSet.BlatSeq
 					FROM
@@ -216,8 +217,8 @@ class webqtlTrait:
 						ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
 						ProbeSet.Name = %s
 						ProbeSetFreeze.Name = %s
-				''' , (self.name, self.db.name)
-			self.cursor.execute(query)
+				''', self.name, self.db.name)
+			#self.cursor.execute(query)
 			results = self.fetchone()
 
 			return results[0]
diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py
index c7d6618e..a34c20cf 100644
--- a/wqflask/wqflask/show_trait/show_trait_page.py
+++ b/wqflask/wqflask/show_trait/show_trait_page.py
@@ -24,6 +24,10 @@
 #
 # Last updated by GeneNetwork Core Team 2010/10/20
 
+from __future__ import division, print_function
+
+from flask import request
+
 from htmlgen import HTMLgen2 as HT
 
 from base import webqtlConfig
@@ -96,8 +100,12 @@ class ShowTraitPage(DataEditingPage):
 					at this time, please go back and select other database." % indFullName]
 					self.error(heading=heading,detail=detail,error="Confidential Database")
 					return
+		print("environ:", request.environ)
 
-		user_ip = fd.remote_ip
+		# Becuase of proxying remote_addr is probably localhost, so we first try for
+		# HTTP_X_FORWARDED_FOR
+		user_ip = request.environ.get('HTTP_X_FORWARDED_FOR') or request.remote_addr   # in old app was fd.remote_ip
+		print("user_ip is:", user_ip)
 		query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \
 				UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"
 		self.cursor.execute(query,user_ip)
@@ -143,9 +151,9 @@ class ShowTraitPage(DataEditingPage):
 		"""
 
 		##identification, etc.
-		fd.identification = '%s : %s'%(thisTrait.db.shortname,ProbeSetID)
+		fd.identification = '%s : %s' % (thisTrait.db.shortname,ProbeSetID)
 		thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
-			&ProbeSetID=%s&RISet=%s&parentsf1=on' %(database,ProbeSetID,fd.RISet)
+			&ProbeSetID=%s&RISet=%s&parentsf1=on' %(database, ProbeSetID, fd['RISet'])
 
 		if CellID:
 			fd.identification = '%s/%s'%(fd.identification, CellID)
@@ -156,12 +164,13 @@ class ShowTraitPage(DataEditingPage):
 			thisTrait.retrieveInfo()
 			thisTrait.retrieveData()
 			self.updMysql()
-			self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)" ,user_ip)
+			self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip)
 			self.openMysql()
-		except:
+		except Exception as why:
+			print("Got an exception:", why)
 			heading = "Retrieve Data"
 			detail = ["The information you requested is not avaiable at this time."]
-			self.error(heading=heading,detail=detail)
+			self.error(heading=heading, detail=detail)
 			return
 
 		##read genotype file
-- 
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