Add all the source codes into the github.

1 files changed, 222 insertions, 0 deletions

diff --git a/web/webqtl/base/templatePage.py b/web/webqtl/base/templatePage.py
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+# 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
+		
+