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

1 files changed, 0 insertions, 222 deletions

diff --git a/web/webqtl/base/templatePage.py b/web/webqtl/base/templatePage.py
deleted file mode 100755
index 4dece24a..00000000
--- a/web/webqtl/base/templatePage.py
+++ /dev/null
@@ -1,222 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#templatePage.py
-#
-#--Genenetwork generates a lot of pages; this file is the generic version of them, defining routines they all use.
-#
-#Classes:
-#templatePage
-#
-#Functions (of templatePage):
-#__init__(...) -- class constructor, allows a more specific template to be used in addition to templatePage
-#__str__(self) -- returns the object's elements as a tuple
-#__del__(self) -- closes the current connection to MySQL, if there is one
-#write -- explained below
-#writefile -- explained below
-#openMysql(self) -- opens a MySQL connection and stores the resulting cursor in the object's cursor variable
-#updMysql(self) -- same as openMysql
-#error -- explained below
-#session -- explained below
-
-
-import socket
-import time
-import shutil
-import MySQLdb
-import os
-
-from htmlgen import HTMLgen2 as HT
-
-import template
-import webqtlConfig
-import header
-import footer
-from utility import webqtlUtil
-
-
-
-class templatePage:
-
-	contents = ['title','basehref','js1','js2', 'layer', 'header', 'body', 'footer']
-
-	# you can pass in another template here if you want
-	def __init__(self, fd=None, template=template.template):
-
-		# initiate dictionary
-		self.starttime = time.time()
-		self.dict = {}
-		self.template = template
-		
-		for item in self.contents:
-			self.dict[item] = ""
-		
-		self.dict['basehref'] = "" #webqtlConfig.BASEHREF
-		self.cursor = None
-		
-		self.cookie = [] #XZ: list to hold cookies (myCookie object) being changed
-		self.content_type = 'text/html'
-		self.content_disposition = ''
-		self.redirection = ''
-		self.debug = ''
-		self.attachment = ''
-
-		#XZ: Holding data (new data or existing data being changed) that should be saved to session. The data must be picklable!!!
-		self.session_data_changed = {}
-
-		self.userName = 'Guest'
-		self.privilege = 'guest'
-		if fd.input_session_data.has_key('user'):
-			self.userName = fd.input_session_data['user']
-		if fd.input_session_data.has_key('privilege'):
-			self.privilege = fd.input_session_data['privilege']
-	
-	def __str__(self):
-
-		#XZ: default setting
-		thisUserName = self.userName
-		thisPrivilege = self.privilege
-		#XZ: user may just go through login or logoff page
-		if self.session_data_changed.has_key('user'):
-			thisUserName = self.session_data_changed['user']
-		if self.session_data_changed.has_key('privilege'):
-			thisPrivilege = self.session_data_changed['privilege']
-
-		if thisUserName == 'Guest':
-			userInfo = 'Welcome! <a href=/account.html><U>Login</U></a>'
-		else:
-			userInfo = 'Hi, %s! <a href=/webqtl/main.py?FormID=userLogoff><U>Logout</U></a>' % thisUserName
-
-		reload(header)
-		self.dict['header'] = header.header_string % userInfo
-
-		serverInfo = "It took %2.3f second(s) for %s to generate this page" % (time.time()-self.starttime, socket.getfqdn())
-		reload(footer)
-		self.dict['footer'] = footer.footer_string % serverInfo
-
-		slist = []
-		for item in self.contents:
-			slist.append(self.dict[item])
-		return self.template % tuple(slist)
-
-
-	def __del__(self):
-		if self.cursor:
-			self.cursor.close()
-			
-	def write(self):
-		'return string representation of this object'
-
-		if self.cursor:
-			self.cursor.close()
-
-		return str(self)	
-		
-	def writeFile(self, filename):
-		'save string representation of this object into a file'
-		if self.cursor:
-			self.cursor.close()
-			
-		try:
-			'it could take a long time to generate the file, save to .tmp first'
-			fp = open(os.path.join(webqtlConfig.TMPDIR, filename+'.tmp'), 'wb')
-			fp.write(str(self))
-			fp.close()
-                        path_tmp = os.path.join(webqtlConfig.TMPDIR, filename+'.tmp')
-                        path_html = os.path.join(webqtlConfig.TMPDIR, filename)
-                        shutil.move(path_tmp,path_html)           
-		except:
-			pass	
-
-	def openMysql(self):
-		try:
-			self.con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, \
-						user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-			self.cursor = self.con.cursor()
-			return 1
-		except:
-			heading = "Connect MySQL Server"
-			detail = ["Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_SERVER+"':100061. \
-					The server may be down at this time"]
-			self.error(heading=heading,detail=detail,error="Error 2003")
-			return 0
-
-	def updMysql(self):
-		try:
-			self.con = MySQLdb.Connect(db=webqtlConfig.DB_UPDNAME,host=webqtlConfig.MYSQL_UPDSERVER, \
-						user=webqtlConfig.DB_UPDUSER,passwd=webqtlConfig.DB_UPDPASSWD)
-			self.cursor = self.con.cursor()
-			return 1
-		except:
-			heading = "Connect MySQL Server"
-			detail = ["update: Can't connect to MySQL server on '"+ webqtlConfig.MYSQL_UPDSERVER+"':100061. \
-					The server may be down at this time "]
-			self.error(heading=heading,detail=detail,error="Error 2003")
-			return 0
-	
-	def error(self,heading="",intro=[],detail=[],title="Error",error="Error"):
-		'generating a WebQTL style error page'
-		Heading = HT.Paragraph(heading)
-		Heading.__setattr__("class","title")
-		
-		Intro = HT.Blockquote()
-		if intro:
-			for item in intro:
-				Intro.append(item)
-		else:
-			Intro.append(HT.Strong('Sorry!'),' Error occurred while processing\
-				your request.', HT.P(),'The nature of the error generated is as\
-				follows:')
-		
-		Detail = HT.Blockquote()
-		Detail.append(HT.Span("%s : " % error,Class="fwb cr"))
-		if detail:
-			Detail2 = HT.Blockquote()
-			for item in detail:
-				Detail2.append(item)
-			Detail.append(HT.Italic(Detail2))
-			
-		#Detail.__setattr__("class","subtitle")
-		TD_LR = HT.TD(height=200,width="100%",bgColor='#eeeeee',valign="top")
-		TD_LR.append(Heading,Intro,Detail)
-		self.dict['body'] = str(TD_LR)
-		self.dict['title'] = title
-
-	def session(self,mytitle="",myHeading=""):
-		'generate a auto-refreshing temporary html file(waiting page)'
-		self.filename = webqtlUtil.generate_session()
-		self.dict['title'] = mytitle
-		self.dict['basehref'] = webqtlConfig.REFRESHSTR % (webqtlConfig.CGIDIR, self.filename) + "" #webqtlConfig.BASEHREF
-		
-		TD_LR = HT.TD(align="center", valign="middle", height=200,width="100%", bgColor='#eeeeee')
-		Heading = HT.Paragraph(myHeading, Class="fwb fs16 cr")
-		# NL, 07/27/2010. variable 'PROGRESSBAR' has been moved from templatePage.py to webqtlUtil.py;		
-		TD_LR.append(Heading, HT.BR(), webqtlUtil.PROGRESSBAR)
-		self.dict['body'] = TD_LR
-		self.writeFile(self.filename + '.html')
-		return self.filename
-		
-